gebhart/patrepeval huggingface dataset:
Molecular dissection of membrane-transport proteins: mass spectrometry and sequence determination of the galactose‒H+ symport protein, GalP, of Escherichia coli and quantitative assay of the incorporation of [ring-2-13C]histidine and 15NH3 (2002)

The molecular mass of the galactose—H+ symport protein GalP, as its histidine-tagged derivative GalP(His)6, has been determined by electrospray MS (ESI-MS) with an error of <0.02%. One methionine residue, predicted to be present from the DNA sequence, was deduced to be absent. This is a significant advance on the estimation of the molecular masses of membrane-transport proteins by SDS/PAGE, where there is a consistent under-estimation of the true molecular mass due to anomalous electrophoretic migration. Addition of a size-exclusion chromatography step after Ni2+-nitrilotriacetate affinity purification was essential to obtain GalP(His)6 suitable for ESI-MS. Controlled trypsin, trypsin+chymotrypsin and CNBr digestion of the protein yielded peptide fragments suitable for ESI-MS and tandem MS analysis, and accurate mass determination of the derived fragments resulted in identification of 82% of the GalP(His)6 protein. Tandem MS analysis of selected peptides then afforded 49% of the actual amino acid sequence of the protein; the absence of the N-terminal methionine was confirmed. Matrix-assisted laser-desorption ionization MS allowed identification of one peptide that was not detected by ESI-MS. All the protein/peptide mass and sequence determinations were in accord with the predictions of amino acid sequence deduced from the DNA sequence of the galP gene. [ring-2-13C]Histidine was incorporated into GalP(His)6in vivo, and ESI-MS analysis enabled the measurement of a high (80%) and specific incorporation of label into the histidine residues in the protein. MS could also be used to confirm the labelling of the protein by 15NH3 (93% enrichment) and [19F]tryptophan (83% enrichment). Such MS measurements will serve in the future analysis of the structures of membrane-transport proteins by NMR, and of their topology by indirect techniques.
Gain characteristics of a frequency nondegenerate phase-sensitive fiber-optic parametric amplifier with phase self-stabilized input (2005)

We experimentally demonstrate, for the first time to our knowledge, a phase-sensitive amplifier based on frequency nondegenerate parametric amplification in optical fiber, where the input signal-idler pair is prepared all-optically. Using two fiber-optic parametric amplifier sections separated by a fiber-based wavelength-dependent phase shifter, we observe and investigate phase-sensitive gain profile in the 1550 nm region both experimentally and theoretically. The realized scheme automatically generates gain-defining phase that is environmentally stable, making it advantageous for building phase-sensitive transmission links.
Molecular screening of patients with long standing extensive ulcerative colitis: detection of p53 and Ki- <i>ras</i> mutations by single strand conformation polymorphism analysis and differential hybridisation in colonic lavage fluid (1999)

Mutations were more frequent in patients with long standing ulcerative colitis (19%) than in control patients (3%, p = 0.07). The technique may be useful for screening for early malignancy in ulcerative colitis.
Peptostreptococcus micros coaggregates with Fusobacterium nucleatum and non-encapsulated Porphyromonas gingivalis (2000)

Coaggregation is one of the potential colonization strategies of oral microorganisms, often involving fimbrial structures in the interactions. In this study, the coaggregation characteristics of the rough and smooth genotypes of the periodontal pathogen Peptostreptococcus micros were compared to investigate the role of the fibril-like structures of the rough genotype in coaggregation. Of the 11 oral species tested, only Fusobacterium nucleatum strains and non-encapsulated Porphyromonas gingivalis strains coaggregated with P. micros. No differences in coaggregation between the smooth type (Sm), the rough type (Rg) and the smooth variant of the Rg type (RgSm) of P. micros were observed. Heat-stable, periodate-sensitive structures on P. micros appeared to interact with heat- and protease-sensitive structures on F. nucleatum and P. gingivalis. These data indicate that these unimodal coaggregations are not mediated by the proteinaceous fibril-like structures of the Rg genotype, but by carbohydrates present on both genotypes of P. micros.
Nanometer-level path-length control scheme for nulling interferometry (1999)

A method of stabilizing a dual-output rotational shearing inteferometer to the nanometer-level accuracy required for deep starlight nulling in planet searches is presented. In this approach one of the nulling beam combiner s two balanced outputs is used to control the other through a combination of external and internal path-length offsets. The path-length offsets sum to zero for the nulling output and to lambda/4 for the control, or the quadrature, output. In the quadrature output a 1-nm path-length error corresponds to a 1% output-power variation, thus allowing subnanometer control.
Expression of antral somatostatin mRNA in duodenal ulcer disease complicated with antral gastritis associated with<i>Helicobacter pylori</i> (1998)

Expression of antral somatostatin mRNA in duodenal ulcer disease complicated with antral gastritis associated with Helicobacter pylori
Local Amplification of Glucocorticoids by 11β‐Hydroxysteroid Dehydrogenase Type 1 and Its Role in the Inflammatory Response (2006)

Glucocorticoids are widely used to treat chronic inflammatory conditions including rheumatoid arthritis. They promote mechanisms important for normal resolution of inflammation, notably macrophage phagocytosis of leukocytes undergoing apoptosis. Prereceptor metabolism of glucocorticoids by 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1) amplifies intracellular levels of glucocorticoids by oxoreduction of intrinsically inert cortisone (in humans, 11-dehydrocorticosterone in mice) into active cortisol (corticosterone in mice) within cells expressing the enzyme. Recently, we have shown in a mouse model of acute inflammation, high expression of 11beta-HSD oxoreductase but not dehydrogenase activity in cells elicited rapidly in the peritoneum by a single thioglycollate injection. 11beta-HSD oxoreductase activity remained high in peritoneal cells until the inflammation resolved. In vitro, the 11beta-HSD1 substrate, 11-dehydrocorticosterone, increased macrophage phagocytosis of apoptotic neutrophils to the same extent as corticosterone. This effect was dependent upon 11beta-HSD1: these cells solely expressed the type 1 11beta-HSD isozyme (not 11beta-HSD2), and carbenoxolone, an 11beta-HSD inhibitor, prevented the increase in phagocytosis elicited by 11-dehydrocorticosterone. Macrophages from 11beta-HSD1-deficient mice failed to respond to 11-dehydrocorticosterone. In vivo, 11beta-HSD1-deficient mice showed a delay in acquisition of macrophage phagocytic competence and had an increased number of free apoptotic neutrophils during sterile peritonitis. Importantly, in preliminary experiments, 11beta-HSD1-deficient mice exhibited delayed resolution of inflammation in experimental arthritis. These findings suggest 11beta-HSD1 may be a component of mechanisms engaged early during the inflammatory response that promote its subsequent resolution.
Human sex hormones stimulate the growth and maturation of Coccidioides immitis (1981)

Because men and pregnant women show increased susceptibility to extrapulmonary dissemination of coccidioidomycosis, studies were conducted to determine the direct effect of human sex hormones and related compounds on the growth and maturation of Coccidioides immitis in vitro. 17 beta-Estradiol, progesterone, and testosterone were highly stimulatory for the parasitic phase of C. immitis growth whereas cholesterol, ergosterol, and 17 alpha-estradiol (a physiologically inactive stereoisomer of 17 beta-estradiol) lacked such effects. Rates of spherule maturation and endospore release were accelerated, in a dose-dependent fashion, by concentrations of 17 beta-estradiol occurring in normal women, with the most striking effects seen at levels encountered in advanced pregnancy. A stimulatory effect of 17 beta-estradiol on the saprobic phase of fungal growth was also detected. The nonsteroidal "antiestrogens" tamoxifen and nafoxidine had either stimulatory or inhibitory effects, depending on fungal strain and experimental conditions. Diverse strains of Cryptococcus neoformans, Candida sp, and Petriellidium boydii were unaffected by hormones that had distinct effects on C. immitis. These studies suggest that direct stimulation of C. immitis by human sex hormones may help to account for sex- and pregnancy-related predisposition to dissemination of coccidioidomycosis.
UISketch: A Large-Scale Dataset of UI Element Sketches (2021)

This paper contributes the first large-scale dataset of 17,979 hand-drawn sketches of 21 UI element categories collected from 967 participants, including UI/UX designers, front-end developers, HCI, and CS grad students, from 10 different countries. We performed a perceptual study with this dataset and found out that UI/UX designers can recognize the UI element sketches with ~96% accuracy. To compare human performance against computational recognition methods, we trained the state-of-the-art DNN-based image classification models to recognize the UI elements sketches. This study revealed that the ResNet-152 model outperforms other classification networks and detects unknown UI element sketches with 91.77% accuracy (chance is 4.76%). We have open-sourced the entire dataset of UI element sketches to the community intending to pave the way for further research in utilizing AI to assist the conversion of lo-fi UI sketches to higher fidelities.
Antibiofilm Activity of the Marine Bacterium <i>Pseudoalteromonas</i> sp. Strain 3J6 (2010)

Biofilm formation results in medical threats or economic losses and is therefore a major concern in a variety of domains. In two-species biofilms of marine bacteria grown under dynamic conditions, Pseudoalteromonas sp. strain 3J6 formed mixed biofilms with Bacillus sp. strain 4J6 but was largely predominant over Paracoccus sp. strain 4M6 and Vibrio sp. strain D01. The supernatant of Pseudoalteromonas sp. 3J6 liquid culture (SN(3J6)) was devoid of antibacterial activity against free-living Paracoccus sp. 4M6 and Vibrio sp. D01 cells, but it impaired their ability to grow as single-species biofilms and led to higher percentages of nonviable cells in 48-h biofilms. Antibiofilm molecules of SN(3J6) were able to coat the glass surfaces used to grow biofilms and reduced bacterial attachment about 2-fold, which might partly explain the biofilm formation defect but not the loss of cell viability. SN(3J6) had a wide spectrum of activity since it affected all Gram-negative marine strains tested except other Pseudoalteromonas strains. Biofilm biovolumes of the sensitive strains were reduced 3- to 530-fold, and the percentages of nonviable cells were increased 3- to 225-fold. Interestingly, SN(3J6) also impaired biofilm formation by three strains belonging to the human-pathogenic species Pseudomonas aeruginosa, Salmonella enterica, and Escherichia coli. Such an antibiofilm activity is original and opens up a variety of applications for Pseudoalteromonas sp. 3J6 and/or its active exoproducts in biofilm prevention strategies.
Glucopyranosyl Isocyanates as Versatile Glycosylating Reagents for the Preparation of Neoglycoconjugates. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Rapid direct writing of high-aspect ratio trenches in silicon: Process physics (1988)

The processes governing direct-write etching of semiconductors with halogen gases are studied by concentrating on a specific materials system: the etching of silicon using the output from an argon-ion laser and chlorine gas to form high-aspect ratio trenches. Specifically, the effects of laser power, laser polarization, laser scan velocity, Cl2-gas pressure, and the addition of buffer gases on the trench formation process have been studied. A simple model has been developed which relates trench depth and these parameters. Model results are presented and compared with experimental data.
Adhesion Molecules and Inflammatory Cell Migration Pathways in the Skin (2004)

I. Introduction ........................................................................................................................457 II. Immunologic Aspects of Photocarcinogenesis ..................................................................458
Polymorphism, recombination, and linkage disequilibrium within the HLA class II region (1992)

Thirty-nine CEPH (Centre d'Etude du Polymorphisme Humain) families, comprised of 502 individuals, have been typed for the HLA class II genes DRB1, DQA1, DQB1, and DPB1 using nonradioactive sequence-specific oligonucleotide probes to analyze polymerase chain reaction amplified DNA. This population, which consists of 266 independent chromosomes, contains 27 DRB1, 7 DQA1, 12 DQB1, and 17 DPB1 alleles. Analysis of the distribution of allele frequencies using the homozygosity statistic, which gives an indication of past selection pressures, suggests that balancing selection has acted on the DRB1, DQA1, and DQB1 loci. The distribution of DPB1 alleles, however, suggests a different evolutionary past. Family data permits the estimation of recombination rates and the unambiguous assignment of haplotypes. No recombinants were found between DRB1, DQA1, and DQB1; however, recombinants were detected between DQB1 and DPB1, resulting in an estimated recombination fraction of greater than or equal to 0.008 +/- 0.004. Only 33 distinct DRB1-DQA1-DQB1 haplotypes were found in this population which illustrates the extreme nonrandom haplotypic association of alleles at these loci. A few of these haplotypes are unusual (previously unreported) for a Caucasian population and most likely result from past recombination events between the DR and DQ subregions. Examination of disequilibrium across the HLA region using these data and the available serologic HLA-A and HLA-B types of these samples shows that global disequilibrium between these loci declines with the recombination fraction, approaching statistic nonsignificance at the most distant interval, HLA-A to HLA-DP.DR-DQ haplotypes in linkage disequilibrium with DPB1 and B are noted and, finally, the evolutionary origin of certain class II haplotypes is addressed.
Reflection-induced frequency shifts in single-mode laser diodes coupled to optical fibers (1985)

Coherent optical communication systems will require optical sources having narrow linewidths and stable frequencies. It has been reported that reflections can cause frequency pulling of a laser.1,2 In an optical fiber communication system reflections will arise at optical interfaces, such as those occurring in the coupling region between a laser and a fiber or between a fiber and an integrated optic device. Thus it is important to study the effects of reflections on the frequency stability of lasers. We report measurements of frequency shifts due to changes of phase of reflections from the microlens tip of a single-mode fiber. Frequency shifts as large as 6 GHz were measured for phase changes of Π rad in both a C3 laser3 and a GRECC laser.4
A novel coupling structure suitable for cross-coupled filters with folded quarter-wave resonators (2003)

A new class of coupling structure for cross-coupled filters with folded quarter-wave resonators is presented. The cross coupling mechanism is realized by magnetic coupling from the short ends of the resonator. The proposed magnetic coupling solves the problem of response limitation of folded quarter-wave resonator cross-coupled filters that were introduced previously using electrical cross coupling. Several quadruplet and trisection filters are proposed and fabricated. The measured results matched well with the theoretical prediction.
Antibacterial Susceptibility of Intestinal Lactobacilli of Healthy Children (2001)

We investigated the antibacterial susceptibility of intestinal lactobacilli of Estonian and Swedish children aged 1-2 y. Sixty isolates (10 species) of lactobacilli (29 Estonian and 31 Swedish strains) were tested against ampicillin, cefuroxime, cefoxitin, gentamicin, ciprofloxacin, tetracycline, vancomycin, metronidazole and erythromycin. We observed that intestinal lactobacilli do not display uniform susceptibility to antibiotics. None of the tested lactobacilli was resistant to ampicillin, gentamicin and erythromycin. Single strains were resistant to cefuroxime and tetracycline, about half of the strains to cefoxitin and ciprofloxacin and 73% of the strains to vancomycin. All studied strains were resistant to metronidazole. Most of the strains investigated were resistant to two or three antibiotics out of nine. Some differences in susceptibility were noted between strains belonging to different fermentation types. No differences in susceptibility were found between Estonian and Swedish isolates. Metronidazole, cefoxitin, vancomycin and ciprofloxacin seem to be safer for gastrointestinal lactoflora than other tested antibiotics in both countries.
Biomimetic Synthesis of Grossularines‐1 (2005)

Like a sea squirt: An efficient biomimetic synthesis of the antitumor α-carboline marine alkaloids grossularine-1 (1) and N,N-didesmethylgrossularine-1 (2) is based on a novel oxidative dimerization of 2-amino-4-(3-indolyl)imidazole. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z500055_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.
Lightweight Authentication Protocols for Low-Cost RFID Tags (2003)

Providing security in low-cost RFID tags is a challenging task because tags are highly resource constrained and cannot support strong cryptography. Special lightweight algorithms and protocols need to be designed that take into account the limitations of the tags. In this paper, we propose a set of extremely lightweight tag authentication protocols. We also provide an analysis of the proposed protocols.
Marketing's contribution to the implementation of business strategy: an empirical analysis (2001)

Abstract This paper describes a study that assesses the performance implications of matching marketing strategy to business strategy. In order to conduct this study we first reviewed the literature on marketing strategy to identify its key dimensions. We then conducted a survey of 1000 senior marketing executives about the strategic marketing practices adopted in their respective firms or business units, and developed scales to describe 11 strategic marketing activities. We next performed a K‐means cluster analysis using these scales to develop a taxonomy of marketing strategy types consisting of: Aggressive Marketers, Mass Marketers, Marketing Minimizers, and Value Marketers. We then observed that superior performance at the firm or SBU level was achieved when specific marketing strategy types were matched with appropriate Miles and Snow (1978) business strategy types. Copyright © 2001 John Wiley & Sons, Ltd.
The Impact of Chronic Urticaria from the Patient’s Perspective: A Survey in Five European Countries (2015)

This research adds to the existing evidence showing significant burden of CSU.
A plant <i>in vitro</i> system for the nuclear import of proteins (1996)

This paper reports the development of an in vitro system that allows the direct assay of protein import into plant nuclei. In this assay the import of fluorescently labelled karyophilic protein substrates into nuclei isolated from evacuolated tobacco BY-2 suspension cells is monitored. It is demonstrated that import of the fluorescently labelled peptide conjugates is rapid, saturable and nuclear localization signal (NLS)-dependent. Exclusion of high molecular weight (70 kDa) dextran and substrates carrying mutated NLS sequences further underline the specificity of this system. Nuclear translocation of karyophilic import substrates in tobacco, similar to mammalian systems, is inhibited by the non-hydrolysable GTP analogue GTP-gamma-S. In contrast, protein uptake is not blocked by wheat germ agglutinin, N-ethyl-maleinimide and iodoacetic acid. Furthermore, it is shown that nuclear import of proteins is only partially inhibited by low temperature (0-4 degrees C). The in vitro nuclear import assay does not depend on exogenously added ATP or cytosolic factors. However, a block of nuclear import with GTP-gamma-S could be overcome by the addition of cytosolic extract, suggesting the dependence on cytosolic factors or proteins. These data indicate that the characteristics of nuclear protein import in plant and mammalian cells are similar, but may be, at least in some respects, also different from each other.
Hyaline Cartilage Regeneration by Combined Therapy of Microfracture and Long-Term Bone Morphogenetic Protein-2 Delivery (2011)

Microfracture of cartilage induces migration of bone-marrow-derived mesenchymal stem cells. However, this treatment often results in fibrocartilage regeneration. Growth factors such as bone morphogenetic protein (BMP)-2 induce the differentiation of bone-marrow-derived mesenchymal stem cells into chondrocytes, which can be used for hyaline cartilage regeneration. Here, we tested the hypothesis that long-term delivery of BMP-2 to cartilage defects subjected to microfracture results in regeneration of high-quality hyaline-like cartilage, as opposed to short-term delivery of BMP-2 or no BMP-2 delivery. Heparin-conjugated fibrin (HCF) and normal fibrin were used as carriers for the long- and short-term delivery of BMP-2, respectively. Rabbit articular cartilage defects were treated with microfracture combined with one of the following: no treatment, fibrin, short-term delivery of BMP-2, HCF, or long-term delivery of BMP-2. Eight weeks after treatment, histological analysis revealed that the long-term delivery of BMP-2 group (microfracture + HCF + BMP-2) showed the most staining with alcian blue. A biochemical assay, real-time polymerase chain reaction assay and Western blot analysis all revealed that the long-term delivery of BMP-2 group had the highest glucosaminoglycan content as well as the highest expression level of collagen type II. Taken together, the long-term delivery of BMP-2 to cartilage defects subjected to microfracture resulted in regeneration of hyaline-like cartilage, as opposed to short-term delivery or no BMP-2 delivery. Therefore, this method could be more convenient for hyaline cartilage regeneration than autologous chondrocyte implantation due to its less invasive nature and lack of cell implantation.
Production and propagation of cylindrically polarized Laguerre–Gaussian laser beams (1998)

The x-polarized and y-polarized beam modes of simple confining circularly symmetric spherical-mirror laser resonators may be represented with Laguerre–Gaussian functions. The corresponding r- and ϕ-polarized beam-mode profiles are found to be represented by a different Laguerre–Gaussian mode set. Though similar in name, these cylindrically polarized modes are fundamentally different from their rectangularly polarized counterparts. For example, the fundamental x-polarized mode is Gaussian, which has a maximum at the center of the beam, while the fundamental ϕ-polarized mode has a null at the beam center. The complete propagation characteristics of several types of azimuthally polarized Laguerre–Gaussian beams through optical systems representable by complex ABCD matrices are obtained. Cylindrically polarized Laguerre–Gaussian beams may be produced by inserting the appropriate Brewster window into a simple confining circularly symmetric laser resonator.