gebhart/patrepeval huggingface dataset:
Cloning by Metabolic Interference in Yeast and Enzymatic Characterization of Arabidopsis thaliana Sterol Δ7-Reductase (1996)

Reduction of the delta 7 double bond of sterols, a key biosynthetic step in higher eukaryotes, is lacking in lower eukaryotes like the yeast Saccharomyces cerevisiae, leading to terminal sterols with a delta 5,7-conjugated diene structure. Genes encoding two sterol reductases involved, respectively, in the reduction of sterol delta 14 and delta 24(28) double bonds have been cloned to date, but no sequence information was available on the enzyme responsible for delta 7-bond reduction. This study presents the cloning of the NADPH-sterol delta 7-reductase (delta 7-red) from Arabidopsis thaliana, based on a metabolic interference approach in yeast. The principle is the functional expression of a plant cDNA library in the yeast strain FY1679-28C tolerant to sterol modifications and the selection of clones resistant to the polyene fungicide nystatin. The toxicity of this compound is dependent on the presence of delta 5,7-unsaturated sterols in the yeast plasma membrane. One clone out of 10(5) transformants exhibits a cDNA-dependent alteration of cell sterol composition. The 1290-base pair cDNA open reading frame was isolated and sequenced. The corresponding protein presents a significant sequence similarity with yeast delta 14- and delta 24(28)-reductases and with human lamin B receptor. The coding sequence was extracted by polymerase chain reaction and inserted into a galactose-inducible yeast expression vector to optimize expression. Analysis using transformed wild type yeast or sterol altered mutants, indicated that delta 5,7-ergosta- and cholesta-sterols are efficiently reduced in vivo, regardless of the structural variations on the side chain. No reductase activity was observed toward the delta 14 or the delta 5 positions of sterols. In vivo extensive delta 7-reduction of the free and esterified pools of sterols was observed upon induction of the enzyme. Ergosterol present before induction was reduced into ergosta-5,22-dieneol, whereas ergosta-5-eneol is the new end product of sterol neosynthesis, indicating that the yeast delta 22 desaturase may be no longer active on C-7-saturated sterols. In vitro tests indicated that delta 7-reductase activity is preferentially associated with the endoplasmic reticulum membrane and confirmed the previous finding that NADPH is the reducing agent.
Fabrication of Net‐Shape Functionally Graded Composites by Electrophoretic Deposition and Sintering: Modeling and Experimentation (2007)

It is shown that electrophoretic deposition (EPD) sintering is a technological sequence that is capable of producing net‐shape bulk functionally graded materials (FGM). By controlling the shape of the deposition electrode, components of complex shapes can be obtained. To enable sintering net‐shape capabilities, a novel optimization algorithm and procedure for the fabrication of net‐shape functionally graded composites by EPD and sintering has been developed. The initial shape of the green specimen produced by EPD is designed in such a way that the required final shape is achieved after sintering‐imposed distortions. The optimization is based on a special innovative iteration procedure that is derived from the solution of the inverse sintering problem: the sintering process is modeled in the “backward movie” regime using the continuum theory of sintering incorporated into a finite‐element code. The experiments verifying the modeling approach include the synthesis by EPD of Al 2 O 3 /ZrO 2 3‐D (FGM) structures. In order to consolidate green parts shaped by EPD, post‐EPD sintering is used. The fabricated deposits are characterized by optical and scanning electron microscopy. The experimentally observed shape change of the FGM specimen obtained by EPD and sintering is compared with theoretical predictions.
Conditionally Amplifiable BACs: Switching From Single-Copy to High-Copy Vectors and Genomic Clones (2002)

The widely used, very-low-copy BAC (bacterial artificial chromosome) vectors are the mainstay of present genomic research. The principal advantage of BACs is the high stability of inserted clones, but an important disadvantage is the low yield of DNA, both for vectors alone and when carrying genomic inserts. We describe here a novel class of single-copy/high-copy (SC/HC) pBAC/oriV vectors that retain all the advantages of low-copy BAC vectors, but are endowed with a conditional and tightly controlled oriV /TrfA amplification system that allows: (1) a yield of ∼100 copies of the vector per host cell when conditionally induced with l -arabinose, and (2) analogous DNA amplification (only upon induction and with copy number depending on the insert size) of pBAC/oriV clones carrying &gt;100-kb inserts. Amplifiable clones and libraries facilitate high-throughput DNA sequencing and other applications requiring HC plasmid DNA. To turn on DNA amplification, which is driven by the oriV origin of replication, we used copy-up mutations in the gene trfA whose expression was very tightly controlled by the araC–P ara BAD promoter/regulator system. This system is inducible by l -arabinose, and could be further regulated by glucose and fucose. Amplification of DNA upon induction with l -arabinose and its modulation by glucose are robust and reliable. Furthermore, we discovered that addition of 0.2% d -glucose to the growth medium helped toward the objective of obtaining a real SC state for all BAC systems, thus enhancing the stability of their maintenance, which became equivalent to cloning into the host chromosome. [The following individuals kindly provided reagents, samples or unpublished information as indicated in the paper: F.R. Blattner D. Helinski, S. Valla, F. Schomburg, C. Small, R. Bogden, C. Gaskins, M.P. Mayer, D.C. Schwartz, and O. Azzam.]
Synthesis and Gas Separation Performance of Triblock Copolymer Ion Gels with a Polymerized Ionic Liquid Mid-Block (2011)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTSynthesis and Gas Separation Performance of Triblock Copolymer Ion Gels with a Polymerized Ionic Liquid Mid-BlockYuanyan Gu† and Timothy P. Lodge*†‡View Author Information† Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States‡ Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, United States*E-mail: [email protected]Cite this: Macromolecules 2011, 44, 7, 1732–1736Publication Date (Web):March 14, 2011Publication History Received26 January 2011Revised3 March 2011Published online14 March 2011Published inissue 12 April 2011https://pubs.acs.org/doi/10.1021/ma2001838https://doi.org/10.1021/ma2001838rapid-communicationACS PublicationsCopyright © 2011 American Chemical SocietyRequest reuse permissionsArticle Views5067Altmetric-Citations200LEARN 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 SUBJECTS:Ions,Membranes,Salts,Selectivity,Solvents Get e-Alerts
Genomic organization of the glycoprotein D gene: Duffy blood group Fya/Fyb alloantigen system is associated with a polymorphism at the 44- amino acid residue (1995)

The Duffy blood group antigen has been characterized by its roles on red blood cells: as a receptor for the malarial parasites and as a promiscuous receptor for chemokine superfamily. Recently, the Duffy blood group associated glycoprotein D (gpFy) cDNA has been cloned (Chaudhuri et al: Proc Natl Acad Sci USA 90:10793, 1993). In this report we describe the organization of genomic DNA coding for the gpFy and elucidate the molecular nature of Fya/b polymorphisms. By a Southern blotting analysis probed with gpFy cDNA, gpFy gene was shown to be composed of three DNA fragments; 1.1-kb Sac I, 1.9-kb EcoRI, and their intervening 47-bp fragments. We cloned the 1.1-kb Sac I and 1.9-kb EcoRI fragments by inverted polymerase chain reaction (IPCR) procedure. The promoter region of the gpFy gene was cloned by IPCR of 1.1-kb Sac I fragment and the 3' flanking sequence was cloned by IPCR of 1.9 kb EcoRI fragment. The both IPCR products contained on both side the known gpFy cDNA sequence without introns, as expected. Although no TATA or CCAAT boxes are present in the promoter sequence, several transcription factor binding site motifs are contained, including AP-1, HNF-5, TCF-1, ApoE B2, W-element, H-APF-1, and Sp-1. The 3' flanking region has two additional polyadenylation signals, other than that used in the cDNA, and also has an indirect and a direct repeat sequence clustered with the 5' flanking region. These facts indicate a possibility that the gpFy gene has been evolved by multiple retrotransposition events. By comparing the coding area of the gpFy gene in 28 Duffy-positive individuals, we elucidated that one base change that results in an amino acid substitution [GA-T(Asp44)-->GGT(Gly)] is in accordance with the Fya/Fyb polymorphism. This fact proves that the gpFy cDNA and its gene described in this report encode the Duffy blood group system.
Fluorescent Indicators for Intracellular pH (2009)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTFluorescent Indicators for Intracellular pHJunyan Han and Kevin Burgess*View Author Information Department of Chemistry, Texas A&M University, Box 30012, College Station, Texas 77841* To whom correspondence should be addressed. Phone: 979-845-4345. Fax: 979-845-8839. E-mail: [email protected]Cite this: Chem. Rev. 2010, 110, 5, 2709–2728Publication Date (Web):October 16, 2009Publication History Received14 July 2009Published online16 October 2009Published inissue 12 May 2010https://pubs.acs.org/doi/10.1021/cr900249zhttps://doi.org/10.1021/cr900249zreview-articleACS PublicationsCopyright © 2009 American Chemical SocietyRequest reuse permissionsArticle Views33064Altmetric-Citations1410LEARN 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 SUBJECTS:Absorption,Dyes and pigments,Fluorescence,pH,Probes Get e-Alerts
The classification of ductal carcinoma in situ and its association with biological markers. (1994)

One hundred five cases of pure ductal carcinoma in situ (DCIS) seen in the Guys Hospital breast unit between 1975 and 1991 were reviewed and reclassified using a modified histologic classification based on cytological features as well as histological architecture. The expression of p53 protein, cerbB2 protein, progesterone receptor, and a proliferation antigen KiS1, all factors reported to be of prognostic significance in invasive ductal carcinoma, was also evaluated using immunohistochemical methods. The mode of presentation of these cases was noted, and its relationship to biological markers and histologic type was also assessed. Good interobserver agreement was achieved by two independent observers using the modified histologic classification. Strong correlation was seen between histologic pattern and biological markers as well as between the individual markers. Poorly differentiated DCIS was associated with a high proliferation rate, the presence of cerbB2 and p53 protein and the absence of progesterone receptors. Well-differentiated DCIS showed the reverse, and the intermediate group showed an intermediate pattern. Paget's disease of the nipple was only seen in association with poorly differentiated DCIS, but no other significant association was noted between mode of presentation and DCIS type.
An efficient method for compressing test data (2002)

The overall throughput of automatic test equipment (ATE) is sensitive to the download time of test data. An effective approach to the reduction of the download time is to compress test data before the download. A compression algorithm for test data should meet two requirements: lossless and simple decompression. In this paper we propose a new test data compression method that aims to fully utilize the unique characteristics of test data compression. The key idea of the proposed method is to perform the Burrows-Wheeler transformation on the sequence of test patterns, and then to apply run-length coding. The experimental results show that our compression method performs better than six other methods for compressing test data. The average compression ratio of the proposed method performed on five test data sets is 315, while that for the next best one, the LZW method, is 21.
Inhibition of Tumor-Necrosis-Factor-αDELETEInduced Endothelial Cell Activation by a New Class of PPAR-γ Agonists (2005)

Proinflammatory cytokines and adhesion molecules expressed by endothelial cells (ECs) play a critical role in initiating and promoting atherosclerosis. Agents that oppose these inflammatory effects in vascular cells include peroxisome proliferator-activated receptor-gamma (PPAR-gamma) ligands, including 15-deoxy-delta(12,14)-prostaglandin J2 (15d-PGJ2) and synthetic thiazolidinediones. Recently, a new structural class of potent PPAR-gamma agonists, 1,1-bis(3'-indolyl)-1-(p-substituted phenyl) methanes, has been characterized. The purpose of this study was to evaluate the anti-inflammatory effects of two PPAR-gamma-active members of this class, 1,1-bis(3'-indolyl)-1-(p-t-butylphenyl)methane (DIM-C-pPhtBu) and 1,1-bis(3'-indolyl)-1-(p-biphenyl)methane (DIM-C-pPhC(6)H(5)), in ECs in vitro. Pretreatment of ECs with DIM-C-pPhC(6)H(5), DIM-C- pPhtBu, or 15d-PGJ2 decreased tumor necrosis factor-alpha (TNF-alpha)-induced intercellular adhesion molecule (ICAM)-1 expression in a concentration-dependent manner. At a concentration of 10 microM, DIM-C-pPhtBu and DIM-C-pPhC(6)H(5) decreased ICAM-1 expression by 77.5 and 71.3%, respectively, and comparable inhibition (84.4%) was observed for 10 microM 15d-PGJ2 (p < 0.05). In contrast, 10 microM ciglitazone and DIM-C-pPhCH(3), which exhibits low PPAR-gamma agonist activity, were inactive. The two new PPAR-gamma agonists and 15d-PGJ2 also inhibited TNF-alpha-induced interleukin-6 (IL-6) and monocyte chemoattractant protein-1 (MCP-1) production in supernatants of TNF-alpha-stimulated ECs, whereas ciglitazone and DIM-C-pPhCH(3) did not decrease TNF-alpha-induced expression of these two proteins. This new structural class of PPAR-gamma agonists inhibited the expression of ICAM-1 and the production of IL-6 and MCP-1 in TNF-alpha-activated ECs at lower concentrations than other synthetic PPAR-gamma agonists, suggesting the potential clinical utility of 1,1-bis(3'-indolyl)-1-(p-substituted phenyl) methanes for decreasing endothelial inflammation.
Continuous state feedback guaranteeing uniform ultimate boundedness for uncertain dynamic systems (1981)

We consider a dynamic system containing uncertain elements. Only the set of possible values of these uncertainties is known. Based on this information a class of state feedback controls is proposed in order to guarantee uniform ultimate boundedness of every system response within an arbitrarily small neighborhood of the zero state. These feedback controls are continuous functions of the state.
Dysregulated Sonic hedgehog signaling and medulloblastoma consequent to IFN-α–stimulated STAT2-independent production of IFN-γ in the brain (2003)

The type I IFNs (IFN- and IFN-), which are crucial in antiviral defense and immune regulation, signal via the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway with activation of STAT1 and STAT2. Here, the function of STAT2 was studied in transgenic mice (termed GIFN/STAT2 -/-) with CNS production of IFN-. Surprisingly, GIFN/STAT2 -/-, but not GIFN/STAT1null, transgenic mice, with CNS production of IFN-, died prematurely with medulloblastoma. An immune response also induced in the brain of the GIFN/STAT2 -/-mice was associated with IFN- gene expression by CD3 + T cells and the activation of the STAT1, STAT3, STAT4, and STAT5 molecules. Expression of the Sonic hedgehog (Shh) and the downstream transcriptional factor Gli-1 genes, implicated in the pathogenesis of medulloblastoma, was found to be significantly increased and cotranscribed in cerebellar granule neurons of the GIFN/STAT2 -/-mice. IFN-, but not IFN-, induced STAT1-dependent expression of the Shh gene in cultured cerebellar granule neurons. Thus, there is an unexpected and extraordinarily adverse biological potency of IFN- in the CNS when the primary signal transduction molecule STAT2 is absent. Moreover, a hitherto unknown role is indicated for the immune system in the pathogenesis of developmental disorders and tumorigenesis of the CNS via dysregulated Shh signaling mediated by IFN-.
[ 64 Cu-NOTA-8-Aoc-BBN(7-14)NH 2 ] targeting vector for positron-emission tomography imaging of gastrin-releasing peptide receptor-expressing tissues (2007)

Radiolabeled peptides hold promise as diagnostic/therapeutic targeting vectors for specific human cancers. We report the design and development of a targeting vector, [(64)Cu-NOTA-8-Aoc-BBN(7-14)NH(2)] (NOTA = 1,4,7-triazacyclononane-1,4,7-triacetic acid, 8-Aoc = 8-aminooctanoic acid, and BBN = bombesin), having very high selectivity and affinity for the gastrin-releasing peptide receptor (GRPr). GRPrs are expressed on a variety of human cancers, including breast, lung, pancreatic, and prostate, making this a viable approach toward site-directed localization or therapy of these human diseases. In this study, [NOTA-X-BBN(7-14)NH(2)] conjugates were synthesized, where X = a specific pharmacokinetic modifier. The IC(50) of [NOTA-8-Aoc-BBN(7-14)NH(2)] was determined by a competitive displacement cell-binding assay in PC-3 human prostate cancer cells using (125)I-[Tyr(4)]-BBN as the displacement ligand. An IC(50) of 3.1 +/- 0.5 nM was obtained, demonstrating high binding affinity of [NOTA-8-Aoc-BBN] for the GRPr. [(64)Cu-NOTA-X-BBN] conjugates were prepared by the reaction of (64)CuCl(2) with peptides in buffered aqueous solution. In vivo studies of [(64)Cu-NOTA-8-Aoc-BBN(7-14)NH(2)] in tumor-bearing PC-3 mouse models indicated very high affinity of conjugate for the GRPr. Uptake of conjugate in tumor was 3.58 +/- 0.70% injected dose (ID) per g at 1 h postintravenous injection (p.i.). Minimal accumulation of radioactivity in liver tissue (1.58 +/- 0.40% ID per g, 1 h p.i.) is indicative of rapid renal-urinary excretion and suggests very high in vivo kinetic stability of [(64)Cu-NOTA-8-Aoc-BBN(7-14)NH(2)] with little or no in vivo dissociation of (64)Cu(2+) from the NOTA chelator. Kidney accumulation at 1 h p.i. was 3.79 +/- 1.09% ID per g. Molecular imaging studies in GRPr-expressing tumor models produced high-contrast, high-quality micro-positron-emission tomography images.
Crystallization of proteins from polyethylene glycol. (1976)

Twenty-two proteins available to this laboratory were examined for their ability to crystallize from polyethylene glycol (PEG). Of the 22, 8 had been crystallized previously by conventional means and the remainder had yielded no crystals by other methods. Using a single broad screen with four different concentrations of five different molecular weight sizes of polyethylene glycol, 13 of these proteins were crystallized. Of the 13, 6 proteins were crystallized for the first time, one yielded crystals readily where only infrequent and irreproducible results were obtained before, and one other produced excellent quality crystals where only very disordered or twinned crystals were previously grown. In only one case did polyethylene glycol fail to yield crystals where other agents had succeeded. It is concluded that polyethylene glycol may be the best initial trial reagent for crystallization of proteins for x-ray diffraction analyses.
Endoscopic Procedures of the Upper-Thoracic Sympathetic Chain (1993)

The upsurge of endoscopic surgical procedures now includes procedures of the thoracic sympathetic chain. The number of articles on this issue is rapidly increasing. This article reviews the indications for as well as the technique, complications, side effects, and results of endoscopic upper-thoracic sympathetic ablation. Since 1977, nearly 900 cases have been described in the literature. The main indication is usually hyperhidrosis. The described techniques vary in detail, but the common denominators are simplicity, expedience, minimal surgical trauma, few complications, and low cost compared with standard methods of open surgery. The results are excellent, durable, and stand well compared with results of previous open techniques. Due to the overwhelming advantages of endoscopic methods, we can foresee an increasing adoption of these techniques and a subsequent relegation of the various open surgical procedures of the upper-thoracic sympathetic chain.
Evidence that Non-Fibrillar Tau Causes Pathology Linked to Neurodegeneration and Behavioral Impairments (2008)

The discovery that mutations within the tau gene lead to frontotemporal dementia with Parkinsonism linked to chromosome 17 (FTDP-17) provided direct evidence that tau alterations can lead to neurodegenerative disease. While the presence of tau fibrils and tangles is a common feature of all tauopathies, including Alzheimer's disease (AD), data are emerging from biochemical, cell-based and transgenic mouse studies which suggest that a pre-fibrillar form of pathological tau may play a key role in eliciting central nervous system neurodegeneration and behavioral impairments. Herein we review recent findings that implicate diffusible tau pathology in the onset of neurodegeneration, and discuss the implications of these findings as they relate to tau tangles and possible therapeutic strategies for the treatment of AD and related tauopathies.