gebhart/patrepeval huggingface dataset:
Synthetic wavelength based phase unwrapping in spectral domain optical coherence tomography (2009)

Phase sensing implementations of spectral domain optical coherence tomography (SDOCT) have demonstrated the ability to measure nanometer-scale temporal and spatial profiles of samples. However, the phase information suffers from a 2pi ambiguity that limits observations of larger sample displacements to lengths less than half the source center wavelength. We introduce a synthetic wavelength phase unwrapping technique in SDOCT that uses spectral windowing and corrects the 2pi ambiguity, providing accurate measurements of sample motion with information gained from standard SDOCT processing. We demonstrate this technique by using a common path implementation of SDOCT and correctly measure phase profiles from a phantom phase object and human epithelial cheek cells which produce multiple wrapping artifacts. Using a synthetic wavelength for phase unwrapping could prove useful in Doppler or other phase based implementations of OCT.
Crystal Growth of DAST (2008)

We explore the growth of the highly nonlinear optical trans-4′-(dimethylamino)-N-methyl-4-stilbazolium tosylate) (DAST) crystals from methanol solutions. We determined the key thermodynamic quantities of the DAST/methanol system, which allowed us to optimize the conditions of the crystal growth and to manipulate the size and morphology of the obtained crystals. We developed confined spontaneous nucleation (CSN), a new technique to control the nucleation and produce good quality seeds and platelets for nonlinear optical applications such as the generation of THz waves. We propose the total excess of Gibbs free energy per volume of the solution as a new parameter (ΔG/Vsol) that fundamentally affects the growth rate from solution instead of the commonly used supersaturation. This parameter involves also concentration and temperature dependence and is therefore applicable to a large range of growth conditions. A model for the growth dynamics of DAST crystals based on the mass balance equations and the measurements of the growth rate at different experimental conditions allowed us to determine the optimal temperature cooling profile for the growth of large crystals at a constant rate. We also present a numerical analysis of the growth dynamics under various commonly used cooling rates and their effect on the crystalline quality of crystals. It is demonstrated that high quality, record size crystals with dimensions 28 × 28 × 8 mm3 can be grown with our new optimized cooling profile based on the constant excess of Gibbs free energy density in the solution during the growth.
Drosophila transforming growth factor beta superfamily proteins induce endochondral bone formation in mammals. (1993)

Both decapentaplegic (dpp) protein and 60A protein have been implicated in pattern formation during Drosophila melanogaster embryogenesis. Within the C-terminal domain, dpp and 60A are similar to human bone morphogenetic protein 2 (75% identity) and human osteogenic protein 1 (70% identity), respectively. Both recombinant human bone morphogenetic protein 2 and recombinant human osteogenic protein 1 have been shown to induce bone formation in vivo and to restore large diaphyseal segmental defects in various animal models. We examined whether the Drosophila proteins, dpp and 60A, have the capacity to induce bone formation in mammals by using the rat subcutaneous bone induction model. Highly purified recombinant dpp and 60A induced the formation of cartilage, bone, and bone marrow in mammals, as determined by histological observations and by measurements of the specific activity of alkaline phosphatase and calcium content of the implants, thereby demonstrating that related proteins from phylogenetically distant species are capable of inducing bone formation in mammals when placed in sites where progenitor cells are available.
Genomic DNA Released by Dying Cells Induces the Maturation of APCs (2001)

Mature APCs play a key role in the induction of Ag-specific immunity. This work examines whether genomic DNA released by dying cells provides a stimulus for APC maturation. Double-stranded but not single-stranded genomic DNA triggered APC to up-regulate expression of MHC class I/II and various costimulatory molecules. Functionally, dsDNA enhanced APC function in vitro and improved primary cellular and humoral immune responses in vivo. These effects were dependent on the length and concentration of the dsDNA but were independent of nucleotide sequence. The maturation of APC induced by dsDNA may promote host survival by improving immune surveillance at sites of tissue injury/infection.
A Phase I Trial of Imetelstat in Children with Refractory or Recurrent Solid Tumors: A Children's Oncology Group Phase I Consortium Study (ADVL1112) (2013)

The recommended phase II dose of imetelstat given on days 1 and 8 of a 21-day cycle is 285 mg/m(2).
Chromosomal position of a VH gene segment determines its activation and inactivation as a substrate for V(D)J recombination (2007)

Complete IgHC gene rearrangement occurs only in B cells in a stage-specific and ordered manner. We used gene targeting to reposition a distal V(H) gene segment to a region just 5' of the D(H) gene cluster and found its activation to be highly dependent on the chromosomal domain within which it resides. The targeted V(H) gene segment rearranged at a higher frequency than its endogenous counterpart, its rearrangement was no longer ordered, and its ability to be silenced by allelic exclusion was lost. Additionally, the targeted V(H) gene segment lost lineage specificity, as VDJ(H) rearrangement was observed in thymocytes. These data suggest that locus contraction, mimicked by proximal targeting, can override any regulation imposed by DNA sequences immediately surrounding V(H) gene segments.
Photoactive mitochondria: in vivo transfer of a light-driven proton pump into the inner mitochondrial membrane of Schizosaccharomyces pombe. (1994)

The light-driven proton pump bacteriorhodopsin (bR) from Halobacterium salinarium has been genetically transferred into the inner mitochondrial membrane (IM) of the eukaryotic cell Schizosaccharomyces pombe, where the archaebacterial proton pump replaces or increases the proton gradient usually formed by the respiratory chain. For targeting and integration, as well as for the correct orientation of bR in the IM, the bacterioopsin gene (bop) was fused to signal sequences of IM proteins. Northern and Western blot analysis proved that all hybrid gene constructs containing the bop gene and a mitochondrial signal sequence were expressed and processed to mature bR. Fast transient absorption spectroscopy showed photocycle activity of bR integrated in the IM by formation of the M intermediate. Experiments with the pH-sensitive fluorescence dye 2',7'-bis(2-carboxyethyl)-5 (and -6)-carboxyfluorescein revealed bR-mediated proton pumping from the mitochondrial matrix into the intermembrane space. Glucose uptake measurements under anaerobic conditions showed that yeast cells containing photoactive mitochondria need less sugar under illumination. In summary, our experiments demonstrate the functional genetic transfer of a light energy converter to a naturally nonphotoactive eukaryotic organism.
α-Aminoadipate Pathway for the Biosynthesis of Lysine in Lower Eukaryotes (1985)

Bacteria and green plants use the diaminopimelate pathway for the biosynthesis of the essential amino acid, lysine; however, yeast and other higher fungi use the alpha-aminoadipate (AA) pathway. The AA pathway has been investigated in detail biochemically, genetically, and in terms of regulatory mechanisms in the baker's yeast Saccharomyces cerevisiae. The genetic analysis of lysine auxotrophs of S. cerevisiae revealed that there are more than 12 lysine genes for 8 enzyme-catalyzed steps. Lysine genes are not linked to each other and seven of the genes are mapped on six different linkage groups (chromosomes). The gene-enzyme relationships have been determined for ten of the lysine loci which include two unlinked gene functions required for each of AA reductase (LYS2 and LYS5) and Saccharopine reductase (LYS9 and LYS14). Five of the lysine enzymes are localized in mitochondria and three in cytosol. The lysine pathway of S. cerevisiae is regulated by feedback inhibition and end product repression. Two, and possibly three, of the enzymes exhibit general control of amino acid biosynthesis and at least five of the enzymes coded for, by unlinked genes, are simultaneously depressed in a regulatory (repressor) gene-mutant.
Chromosome aberrations in lymphocytes of nurses handling cytostatic agents. (1984)

In an evaluation of the possible chromosome damage caused by cytostatic agents 11 nurses with long-term exposure to such agents were studied. Five laboratory workers and 11 hospital clerks served as referents. The number of chromosomally aberrant lymphocytes was significantly higher in the group of nurses than in the group of laboratory workers or hospital clerks. The number of chromosome-type breaks was increased significantly among the nurses as compared to the reference groups. There was no significant difference in the number of chromatid-type breaks between the groups. The observed increase in chromosome-type aberrations may have been due to long-term occupational exposure to cytostatic agents.
Synthesis of a new carbohydrate mimetics: “carbopeptoid” containing a C-1 carboxylate and C-2 amino group (1996)

Readily access to a new class of carbohydrate mimetics has been demonstrated from a d-glucosamine derivative by the synthesis of a tetrameric carbopeptoid in which the glycosidic bonds are replaced with amido linkages.
Fundamental Investigation on Electrostatic Ink Jet Phenomena in Pin-to-Plate Discharge System (2005)

A fundamental investigation was conducted on electrostatic ink jet phenomena. High voltage was applied between an insulative capillary tube filled with ion conductive water and a metal plate electrode. A large water drop was formed and dropped from the tube at the dark discharge under conditions of appropriate voltage application and water level. The diameter of the drop was about one millimeter. At the beginning of corona discharge, however, a Taylor cone of water was formed at the tip of the tube and the tip of the cone was broken to form a very small droplet that was dispersed like mist at wide angle due to the Coulomb repulsive force of charged mist. When the applied voltage was further increased, water droplet was formed periodically. Application of adjusted pulse voltage can form a droplet of which formation is synchronized with the pulse. The diameter of the droplet depended on the applied voltage and the tube diameter. It was less than a Rayleigh's limit and agreed fairly well with a Vonnegut's limit. Preliminary printing on a paper was also demonstrated. This phenomenon is expected to be utilized for a new ink jet print head.
Characterization of Benzoyl Coenzyme A Biosynthesis Genes in the Enterocin-Producing Bacterium “ Streptomyces maritimus ” (2003)

The novel benzoyl coenzyme A (benzoyl-CoA) biosynthesis pathway in "Streptomyces maritimus" was investigated through a series of target-directed mutations. Genes involved in benzoyl-CoA formation were disrupted through single-crossover homologous recombination, and the resulting mutants were analyzed for their ability to biosynthesize the benzoyl-CoA-primed polyketide antibiotic enterocin. Inactivation of the unique phenylalanine ammonia-lyase-encoding gene encP was previously shown to be absolutely required for benzoyl-CoA formation in "S. maritimus". The fatty acid beta-oxidation-related genes encH, -I, and -J, on the other hand, are necessary but not required. In each case, the yield of benzoyl-CoA-primed enterocin dropped below wild-type levels. We attribute the reduced benzoyl-CoA formation in these specific mutants to functional substitution and cross-talk between the products of genes encH, -I, and -J and the enzyme homologues of primary metabolism. Disruption of the benzoate-CoA ligase encN gene did not perturb enterocin production, however, demonstrating that encN is extraneous and that benzoic acid is not a pathway intermediate. EncN rather serves as a substitute pathway for utilizing exogenous benzoic acid. These experiments provide further support that benzoyl-CoA is formed in a novel bacterial pathway that resembles the eukaryotic assembly of benzoyl-CoA from phenylalanine via a beta-oxidative path.
In vitro cloning of complex mixtures of DNA on microbeads: Physical separation of differentially expressed cDNAs (2000)

We describe a method for cloning nucleic acid molecules onto the surfaces of 5-micrometer microbeads rather than in biological hosts. A unique tag sequence is attached to each molecule, and the tagged library is amplified. Unique tagging of the molecules is achieved by sampling a small fraction (1%) of a very large repertoire of tag sequences. The resulting library is hybridized to microbeads that each carry approximately 10(6) strands complementary to one of the tags. About 10(5) copies of each molecule are collected on each microbead. Because such clones are segregated on microbeads, they can be operated on simultaneously and then assayed separately. To demonstrate the utility of this approach, we show how to label and extract microbeads bearing clones differentially expressed between two libraries by using a fluorescence-activated cell sorter (FACS). Because no prior information about the cloned molecules is required, this process is obviously useful where sequence databases are incomplete or nonexistent. More importantly, the process also permits the isolation of clones that are expressed only in given tissues or that are differentially expressed between normal and diseased states. Such clones then may be spotted on much more cost-effective, tissue- or disease-directed, low-density planar microarrays.
[Construction of recombinant adenoviruses encoding TK suicide gene driven by VEGF promoter using efficient AdEasier-1 system]. (2004)

AdEasier-1 system is an efficient way to construct the recombinant adenoviruses encoding TK gene under control of VEGFP.
The Collingridge dictionary of plant names (1985)

With over 3500 entries, this dictionary contains information about the derivation, meaning and pronunciation of plant names. The book is cross-referenced and includes a glossary of technical terms.
Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest treePopulus trichocarpa (2012)

• Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype-genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination. • We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29,213 single-nucleotide polymorphisms. • Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r(2) dropping below 0.2 within 3-6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N(e) ≈ 4000-6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features. • Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed.
Characterization of cDNA encoding the mouse hepatic triglyceride lipase and expression by in vitro translation (1991)

A cDNA coding for the mouse hepatic triglyceride lipase has been isolated from a mouse liver cDNA library. The nucleotide sequence of the cDNA shows an open reading frame encoding a polypeptide of 510 amino acids that is 91.5% and 86% homologous to rat and human hepatic lipase, respectively. The most drastic protein sequence divergence is found at the carboxyterminal end which was speculated to harbour one heparin-binding site. By in vitro translation of cRNA in the presence of pancreatic membranes the hepatic lipase was shown to be glycosylated and to have an electrophoretic mobility of 53 kDa.
Effect of Cigarette Smoke on the Permeability and IL-1 β and sICAM-1 Release from Cultured Human Bronchial Epithelial Cells of Never-Smokers, Smokers, and Patients with Chronic Obstructive Pulmonary Disease (2000)

Although cigarette smoking is of paramount importance in the development of chronic obstructive pulmonary disease (COPD), only a small proportion of smokers develop the disease. We tested the hypothesis that the response of the bronchial epithelium to cigarette smoke (CS) differs in patients with COPD. Such a difference might explain in part why only some cigarette smokers develop the disease. We established primary explant cultures of human bronchial epithelial cells (HBEC) from biopsy material obtained from never-smokers who had normal pulmonary function, smokers with normal pulmonary function, and smokers with COPD, and exposed these for 20 min to CS or air. Measurements were subsequently made over a period of 24 h of transepithelial permeability and release of interleukin (IL)-1beta and soluble intercellular adhesion molecule-1 (sICAM-1). In addition, intracellular reduced glutathione (GSH) levels were measured after 24 h incubation. Exposure to CS increased the permeability of these cultures in all study groups, but the most marked effect was observed in cultures from patients with COPD (mean increase, 85.5%). The smallest CS-induced increase in the permeability was observed in HBEC cultured from smokers with normal pulmonary function (mean, 25.0%), and this was significantly lower than that of HBEC from never-smokers (mean, 53.4%) (P<0.001). Compared with exposure to air, exposure to CS led to a significantly increased release of these mediators from cultures of the never-smoker group (mean 250.0% increase in IL-1beta and mean 175.3% increase in sICAM-1 24 h after exposure) and COPD group (mean 383.3% increase in IL-1beta and mean 97.4% increase in sICAM-1 24 h after exposure). In contrast, CS exposure did not influence significantly the release of either mediator from the cells of smokers with normal pulmonary function. Levels of intracellular GSH were significantly higher in cultures of HBEC derived from smokers, both those with normal pulmonary function and those with COPD, compared with cultures from healthy never-smokers. Exposure to CS significantly decreased the concentration of intracellular GSH in all cultures. However, the fall in intracellular GSH was significantly greater in cells from patients with COPD (mean 72.9% decrease) than in cells from never-smokers (mean 61.4% decrease; P = 0.048) or smokers with normal pulmonary function (mean 43.9% decrease; P = 0.02). These results suggest that whereas smokers with or without COPD demonstrate increased levels of GSH within bronchial epithelial cell cultures, those with COPD have a greater susceptibility to the effects of CS in reducing GSH levels and causing increased permeability and release of proinflammatory mediators such as IL-1beta and sICAM-1.
Studies on the Formation and Stability of the Roast-Flavor Compound 2-Acetyl-2-thiazoline (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies on the Formation and Stability of the Roast-Flavor Compound 2-Acetyl-2-thiazolineThomas Hofmann and Peter SchieberleCite this: J. Agric. Food Chem. 1995, 43, 11, 2946–2950Publication Date (Print):November 1, 1995Publication History Published online1 May 2002Published inissue 1 November 1995https://pubs.acs.org/doi/10.1021/jf00059a032https://doi.org/10.1021/jf00059a032research-articleACS PublicationsRequest reuse permissionsArticle Views488Altmetric-Citations41LEARN 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
Induction of saccharolytic enzymes by sucrose in Bacillus subtilis: evidence for two partially interchangeable regulatory pathways (1989)

Sucrose induces two saccharolytic enzymes in Bacillus subtilis, an intracellular sucrase and an extracellular levansucrase, encoded by sacA and sacB, respectively. It was previously shown that the sacY gene encodes a positive regulator involved in a sucrose-dependent antitermination upstream from the sacB coding sequence. We show here that the sacY product is not absolutely required for sacB induction: a weak but significant induction can be observed in strains harboring a sacY deletion. The sacY-independent induction was altered by mutations located in the sacP and sacT loci but was observed in both sacU+ and sacU32 genetic backgrounds. These results suggest that B. subtilis has two alternative systems allowing sacB induction by sucrose. Both systems also seem to be involved in sacA induction.
Structure and function of the aromatic amino acid hydroxylases (1995)

Research Article| October 15 1995 Structure and function of the aromatic amino acid hydroxylases S E Hufton; S E Hufton 1Olive Miller Protein Chemistry Laboratory, Murdoch Institute, Royal Children′s Hospital, Parkville, Victoria 3052, Australia Search for other works by this author on: This Site PubMed Google Scholar I G Jennings; I G Jennings 1Olive Miller Protein Chemistry Laboratory, Murdoch Institute, Royal Children′s Hospital, Parkville, Victoria 3052, Australia Search for other works by this author on: This Site PubMed Google Scholar R G H Cotton R G H Cotton 1Olive Miller Protein Chemistry Laboratory, Murdoch Institute, Royal Children′s Hospital, Parkville, Victoria 3052, Australia Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd Online ISSN: 1470-8728 Print ISSN: 0264-6021 © 1995 The Biochemical Society, London1995 Biochem J (1995) 311 (2): 353–366. https://doi.org/10.1042/bj3110353 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation S E Hufton, I G Jennings, R G H Cotton; Structure and function of the aromatic amino acid hydroxylases. Biochem J 15 October 1995; 311 (2): 353–366. doi: https://doi.org/10.1042/bj3110353 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1995 The Biochemical Society, London1995 Article PDF first page preview Close Modal You do not currently have access to this content.