gebhart/patrepeval huggingface dataset:
Ubiquitin Protein Ligase Activity of IAPs and Their Degradation in Proteasomes in Response to Apoptotic Stimuli (2000)

To determine why proteasome inhibitors prevent thymocyte death, we examined whether proteasomes degrade anti-apoptotic molecules in cells induced to undergo apoptosis. The c-IAP1 and XIAP inhibitors of apoptosis were selectively lost in glucocorticoid- or etoposide-treated thymocytes in a proteasome-dependent manner before death. IAPs catalyzed their own ubiquitination in vitro, an activity requiring the RING domain. Overexpressed wild-type c-IAP1, but not a RING domain mutant, was spontaneously ubiquitinated and degraded, and stably expressed XIAP lacking the RING domain was relatively resistant to apoptosis-induced degradation and, correspondingly, more effective at preventing apoptosis than wild-type XIAP. Autoubiquitination and degradation of IAPs may be a key event in the apoptotic program.
Perspectives on main‐chain hydrogen bonded supramolecular polymers (2007)

Abstract Supramolecular polymers are assembled from monomeric units held together by reversible non‐covalent interactions. These supramolecular materials display polymeric properties and may soon have important industrial applications. This mini review focuses on the advances in main‐chain supramolecular polymers whose assembly is guided primarily by hydrogen bonding interactions. The design constraints of these new systems discussed include assembly motifs, the strength and directionality of the non‐covalent interactions, association versus reversibility, and environmental effects on the degree of polymerization. Selected literature examples including Meijer's ureidopyrimidinone system are used to highlight the challenges and potential of these supramolecular polymeric materials. Copyright © 2007 Society of Chemical Industry
Replacement of softwood kraft pulp with ECF-bleached bamboo kraft pulp in fine paper (2010)

Non-wood fibers such as bamboo and wheat straw have been playing important roles in the pulp and paper industry in China. In this study an ECF-bleached bamboo kraft pulp was compared with a bleached softwood kraft pulp (NBSK) as the reinforcement pulp in fine paper production. Areas that were examined include the refining of pure fibers, influence of bamboo on dewatering, retention, and sizing. The influence of bamboo kraft pulp as a part of a furnish replacing NBSK was compared as well. Results show that fiber shortening was more prominent with bamboo when refined. This resulted in a higher amount of fines, and addition wet-end chemicals may be required to compensate. Handsheets with bamboo as a reinforcement fiber showed similar mechanical and optical properties to handsheets containing NBSK.
A human retinal pigment epithelial cell line that retains epithelial characteristics after prolonged culture. (1995)

This cell line retains many of the metabolic and morphologic characteristics of RPE cells in vivo although there are some differences, particularly the loss of some enzymatic activities and cytoskeletal polarization. These cells should be useful in further studies of RPE cell metabolism and other functions.
KEGG: Kyoto Encyclopedia of Genes and Genomes (2000)

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/).
Diminishing Surgical Site Infections After Colorectal Surgery With Surgical Care Improvement Project: Is It Time to Move on? (2011)

A 5-year multidisciplinary program of targeted initiatives and interventions failed to improve compliance with Surgical Care Improvement Project measures or to decrease surgical site infection at our institution where colon resections are performed almost exclusively by high-volume specialists. These efforts consumed considerable resources and expenditures, but were of little or no value in our setting.
Approaches to the design of anti-fibrotic drugs (1991)

Conference Article| November 01 1991 Approaches to the design of anti-fibrotic drugs Trevor J. Franklin; Trevor J. Franklin 1Research I, ICI Pharmaceuticals, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K. Search for other works by this author on: This Site PubMed Google Scholar Neil J. Hales; Neil J. Hales 1Research I, ICI Pharmaceuticals, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K. Search for other works by this author on: This Site PubMed Google Scholar Donna Johnstone; Donna Johnstone 1Research I, ICI Pharmaceuticals, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K. Search for other works by this author on: This Site PubMed Google Scholar William B. Morris; William B. Morris 1Research I, ICI Pharmaceuticals, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K. Search for other works by this author on: This Site PubMed Google Scholar C. Jane Cunliffe; C. Jane Cunliffe 1Research I, ICI Pharmaceuticals, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K. Search for other works by this author on: This Site PubMed Google Scholar Andrew J. Millest; Andrew J. Millest 1Research I, ICI Pharmaceuticals, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K. Search for other works by this author on: This Site PubMed Google Scholar George B. Hill George B. Hill 1Research I, ICI Pharmaceuticals, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1991) 19 (4): 812–815. https://doi.org/10.1042/bst0190812 Article history Received: July 25 1991 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation Trevor J. Franklin, Neil J. Hales, Donna Johnstone, William B. Morris, C. Jane Cunliffe, Andrew J. Millest, George B. Hill; Approaches to the design of anti-fibrotic drugs. Biochem Soc Trans 1 November 1991; 19 (4): 812–815. doi: https://doi.org/10.1042/bst0190812 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 Society Transactions Search Advanced Search Keywords: FPD, fibro-proliferative disease, ECM, extracellular matrix This content is only available as a PDF. © 1991 Biochemical Society1991 Article PDF first page preview Close Modal You do not currently have access to this content.
Multi-Gbit/sec Low Density Parity Check Decoders with Reduced Interconnect Complexity (2005)

A 3.2-Gbit/sec 2048-bit parallel LDPC decoder is implemented in a 0.18 /spl mu/m CMOS process. We employ two new techniques to address the interconnect problem: A broadcasting technique reduces the total amount of check-to-variable interconnect wires by more than 40%. A hierarchical placement algorithm places the variable and check nodes in the top-level hierarchy of the design and reduces the maximum wire length by up to 50%.
The HtrA family of serine proteases (1997)

HtrA, also known as DegP and probably identical to the Do protease, is a heat shock-induced serine protease that is active in the periplasm of Escherichia coli. Homologues of HtrA have been described in a wide range of bacteria and in eukaryotes. Its chief role is to degrade misfolded proteins in the periplasm. Substrate recognition probably involves the recently described PDZ domains in the C-terminal half of HtrA and, we suspect, has much in common with the substrate recognition system of the tail-specific protease, Prc (which also possesses a PDZ domain). The expression of htrA is regulated by a complex set of signal transduction pathways, which includes an alternative sigma factor, RpoE, an anti-sigma factor, RseA, a two-component regulatory system, CpxRA, and two phosphoprotein phosphatases, PrpA and PrpB. Mutations in the htrA genes of Salmonella, Brucella and Yersinia cause decreased survival in mice and/or macrophages, and htrA mutants can act as vaccines, as cloning hosts and as carriers of heterologous antigens.
ADP-Ribosylation Factor 6 Regulates a Novel Plasma Membrane Recycling Pathway (1997)

ADP-ribosylation factor (ARF) 6 localizes to the plasma membrane (PM) in its GTP state and to a tubulovesicular compartment in its GDP state in HeLa cells that express wild-type or mutant forms of this GTPase. Aluminum fluoride (AlF) treatment of ARF6-transfected cells redistributes ARF6 to the PM and stimulates the formation of actin-rich surface protrusions. Here we show that cytochalasin D (CD) treatment inhibited formation of the AlF-induced protrusions and shifted the distribution of ARF6 to a tubular membrane compartment emanating from the juxtanuclear region of cells, which resembled the compartment where the GTP-binding defective mutant of ARF6 localized. This membrane compartment was distinct from transferrin-positive endosomes, could be detected in the absence of ARF6 overexpression or CD treatment, and was accessible to loading by PM proteins lacking clathrin/AP-2 cytoplasmic targeting sequences, such as the IL-2 receptor alpha subunit Tac. ARF6 and surface Tac moved into this compartment and back out to the PM in the absence of pharmacologic treatment. Whereas AlF treatment blocked internalization, CD treatment blocked the recycling of wild-type ARF6 and Tac back to the PM; these blocks were mimicked by expression of ARF6 mutants Q67L and T27N, which were predicted to be in either the GTP- or GDP-bound state, respectively. Thus, the ARF6 GTP cycle regulates this membrane traffic pathway. The delivery of ARF6 and membrane to defined sites along the PM may provide components necessary for remodeling the cell surface and the underlying actin cytoskeleton.
Bone sialoprotein stimulates in vitro bone resorption (1996)

Bone sialoprotein (BSP) is a protein highly specific for bone, which contains an arginine-glycine-aspartic acid (RGD) cell attachment sequence involved in osteoclast adhesion to bone matrix via the vitronectin receptor. We have investigated its role in in vitro bone resorption using the well described isolated osteoclast resorption pit assay. BSP significantly stimulates bone resorption in a dose-dependent manner, increasing the overall resorbed area on ivory slices and the number of lacunae at concentrations as low as 50 nM. Neither recombinant osteopontin nor intact vitronectin has any effect on bone resorption, suggesting a specific effect of BSP. The stimulation of bone resorption induced by BSP could be partially explained by an increase in osteoclast adhesion to bone via its RGD sequence, and our results suggest another mechanism of action of BSP that might involve another region of the molecule, such as its acidic sequences. Although BSP stimulates bone resorption in a coculture system of bone marrow cells and osteoblastic cells, it dose dependently inhibits the formation of osteoclast-like cells at equivalent concentrations in this culture model. In conclusion, we provide evidence that BSP plays an important role in the bone resorption process and may regulate bone resorption as well as osteoclast formation.
Transfer function method of measuring in-duct acoustic properties. I. Theory (1980)

The theory of a transfer function method of measuring normal incident in-duct acoustic properties is presented. In this method, a broadband stationary random acoustic wave in a tube is mathematically decomposed into its incident and reflected components using a simple transfer-function relation between the acoustic pressure at two locations on the tube wall. The wave decomposition leads to the determination of the complex reflection coefficient from which the complex acoustic impedance and the sound absorption coefficient of a material and the transmission loss of a silencer element can be determined. Also presented are the theories of two techniques for improving transfer function estimates: a sensor-switching technique for automatic system calibration and a coherence function technique for signal enhancement.
Soluble triggering receptor expressed on myeloid cells-1 in acute respiratory infections (2006)

Levels of the soluble form of the triggering receptor expressed on myeloid cells (sTREM)-1 are elevated in severe sepsis. However, it is not known whether sTREM-1 measurements can distinguish milder bacterial infections from noninfectious inflammation. The present authors studied whether serum sTREM-1 levels differ in community-acquired pneumonia, exacerbations of chronic obstructive pulmonary disease (COPD), asthma and controls, and whether sTREM-1 may be used as a surrogate marker for the need for antibiotics. Serum sTREM-1 levels in 150 patients with pneumonia, COPD and asthma exacerbations and 62 healthy controls were measured. Serum sTREM-1 levels were significantly elevated in pneumonia (median 295.2 ng x mL(-1)), COPD (280.3 ng x mL(-1)) and asthma exacerbations (184.0 ng x mL(-1)) compared with controls (83.1 ng x mL(-1)). Levels were higher in pneumonia and Anthonisen type 1 COPD exacerbations than in type 2 and 3 COPD and asthma exacerbations. The area under the receiver operating characteristics curve for sTREM-1 as a surrogate marker for the need for antibiotics was 0.77. Serum levels of the soluble form of the triggering receptor expressed on myeloid cells-1 were elevated predominantly in pneumonia and Anthonisen type 1 COPD exacerbations versus type 2 and 3 chronic obstructive pulmonary disease exacerbations, asthma and controls. Serum levels of the soluble form of the triggering receptor expressed on myeloid cells-1 has moderate but insufficient accuracy as a surrogate marker for the need for antibiotics in lower respiratory tract infections.
An Analysis of Pragmatic Failure in Cross-cultural Communication and the Countermeasures (2009)

Communication may break down due to pragmatic failures in cross-cultural communication. This paper not only analyzes the categories and causes of pragmatic failures but also concludes with suggestions on the effective ways of overcoming pragmatic failures and developing students' pragmatic competence.
Thermoadaptation of α-Galactosidase AgaB1 in Thermus thermophilus (2002)

The evolutionary potential of a thermostable alpha-galactosidase, with regard to improved catalytic activity at high temperatures, was investigated by employing an in vivo selection system based on thermophilic bacteria. For this purpose, hybrid alpha-galactosidase genes of agaA and agaB from Bacillus stearothermophilus KVE39, designated agaA1 and agaB1, were cloned into an autonomously replicating Thermus vector and introduced into Thermus thermophilus OF1053GD (DeltaagaT) by transformation. This selector strain is unable to metabolize melibiose (alpha-galactoside) without recombinant alpha-galactosidases, because the native alpha-galactosidase gene, agaT, has been deleted. Growth conditions were established under which the strain was able to utilize melibiose as a single carbohydrate source when harboring a plasmid-encoded agaA1 gene but unable when harboring a plasmid-encoded agaB1 gene. With incubation of the agaB1 plasmid-harboring strain under selective pressure at a restrictive temperature (67 degrees C) in a minimal melibiose medium, spontaneous mutants as well as N-methyl-N'-nitro-N-nitrosoguanidine-induced mutants able to grow on the selective medium were isolated. The mutant alpha-galactosidase genes were amplified by PCR, cloned in Escherichia coli, and sequenced. A single-base substitution that replaces glutamic acid residue 355 with glycine or valine was found in the mutant agaB1 genes. The mutant enzymes displayed the optimum hydrolyzing activity at higher temperatures together with improved catalytic capacity compared to the wild-type enzyme and furthermore showed an enhanced thermal stability. To our knowledge, this is the first report of an in vivo evolution of glycoside-hydrolyzing enzyme and selection within a thermophilic host cell.
Transfer of the inducible lac repressor/operator system from Escherichia coli to a vaccinia virus expression vector. (1989)

Cis- and trans-acting elements of the Escherichia coli lac operon were transferred to vaccinia virus and used to regulate gene expression. A recombinant virus that constitutively expresses a modified lac repressor gene (lacI) was constructed. We calculated that each infected cell contained approximately 2 x 10(7) active repressor molecules (and 1-2 x 10(4) copies of the vaccinia virus genome). A strong vaccinia-virus late promoter was modified by insertion of the lac operator (lacO) at various positions. The ability of each modified promoter to regulate expression of beta-galactosidase was tested by transient assays in cells infected with wild-type or lacI-containing vaccinia virus. Placement of the lacO just downstream of the conserved TAAAT sequence of a late promoter was consistent with a minimal effect on basal expression and good repressibility, whereas basal expression was severely inhibited when lacO overlapped or preceded the TAAAT motif. A single recombinant vaccinia virus containing lacI and the beta-galactosidase gene under control of the optimal lacO promoter was constructed. In the absence of inducer, cells infected with this double recombinant virus synthesized little or no detectable beta-galactosidase. Addition of isopropyl beta-D-thiogalactoside restored expression to greater than 20% of the unrepressed level. This inducible vector system has potential applications for expression of heterologous and homologous genes.
Fast image search for learned metrics (2008)

We introduce a method that enables scalable image search for learned metrics. Given pairwise similarity and dissimilarity constraints between some images, we learn a Mahalanobis distance function that captures the imagespsila underlying relationships well. To allow sub-linear time similarity search under the learned metric, we show how to encode the learned metric parameterization into randomized locality-sensitive hash functions. We further formulate an indirect solution that enables metric learning and hashing for vector spaces whose high dimensionality make it infeasible to learn an explicit weighting over the feature dimensions. We demonstrate the approach applied to a variety of image datasets. Our learned metrics improve accuracy relative to commonly-used metric baselines, while our hashing construction enables efficient indexing with learned distances and very large databases.
Chemical investigation of ceylonese plants. Part XVI. Extractives of Calophyllum cordato-oblongum Thw. (Guttiferae) (1975)

From the bark of Calophyllum cordato-oblongum Thw. the new resin acid, cordato-oblongic acid (Ia) was isolated and identified as 3-(6,7-dihydro-5-hydroxy-2,2,trans-7,8-tetramethyl-6-oxo-2H,8H-benzo[1,2-b:5,4-b′]-dipyran-10-yl)butyric acid. The timber extract contained the known xanthones 2-hydroxyxanthone (VIII), scriblitifolic acid (X), 1,5,6-trihydroxyxanthone (VIIb), 1,6-dihydroxy-5-methoxyxanthone (VIIa), and jacareubin (XV), and the two new xanthones 3-hydroxy-4-methoxyxanthone (IXa) and cordato-oblonguxanthone (XIII){identified as 1,2-dihydro-6-hydroxy-3,3-dimethylpyrano[2,3-a]xanthen-12(3H)-one}. Friedelin and β-sitosterol were isolated from both extracts.
Low Density Lipoprotein Receptor-related Protein (LRP) Is Required for Lactoferrin-enhanced Collagen Gel Contractile Activity of Human Fibroblasts (2003)

Fibroblasts plated on a type I collagen gel can reduce the size of the gel in a way that mimics the reorganization of the collagen matrix that accompanies the wound healing process. We demonstrated previously that lactoferrin (Lf) specifically binds to WI-38 human fibroblasts and enhances their collagen gel contractile activity. The effect of Lf correlated with the phosphorylation of myosin light chain (MLC), suggesting that Lf promotes fibroblast contractile activity by regulating MLC phosphorylation. We found here that the binding of Lf to WI-38 cells was inhibited by recombinant receptor-associated protein (RAP), a universal competitor for ligand binding to LRP (LDL receptor-related protein), and RAP can also promote the collagen gel contractile activity. These observations suggest that LRP is a receptor that mediates the Lf-induced enhancement of collagen gel contractile activity in WI-38 fibroblasts. To confirm the hypothesis, we utilized LRP antisense oligonucleotide, which was modified by morpholino linkage. Suppression of LRP expression abrogated the Lf-induced enhancement the contractile activity in fibroblasts. Treatment of fibroblasts with Lf enhanced the phosphorylation of ERK1/2 and the activation of MLC kinase (MLCK). These effects were attenuated by suppression of LRP expression. These findings suggest that LRP is involved in the Lf-enhanced collagen gel contractile activity of WI-38 fibroblasts by converting the Lf binding signal into the activation of ERK1/2 and MLCK.
Imaging multiple endogenous and exogenous fluorescent species in cells and tissues (2006)

Hyperspectral imaging provides complex image data with spectral information from many fluorescent species contained within the sample such as the fluorescent labels and cellular or pigment autofluorescence. To maximize the utility of this spectral imaging technique it is necessary to couple hyperspectral imaging with sophisticated multivariate analysis methods to extract meaningful relationships from the overlapped spectra. Many commonly employed multivariate analysis techniques require the identity of the emission spectra of each component to be known or pure component pixels within the image, a condition rarely met in biological samples. Multivariate curve resolution (MCR) has proven extremely useful for analyzing hyperspectral and multispectral images of biological specimens because it can operate with little or no a priori information about the emitting species, making it appropriate for interrogating samples containing autofluorescence and unanticipated contaminating fluorescence. To demonstrate the unique ability of our hyperspectral imaging system coupled with MCR analysis techniques we will analyze hyperspectral images of four-color in-situ hybridized rat brain tissue containing 455 spectral pixels from 550 - 850 nm. Even though there were only four colors imparted onto the tissue in this case, analysis revealed seven fluorescent species, including contributions from cellular autofluorescence and the tissue mounting media. Spectral image analysis will be presented along with a detailed discussion of the origin of the fluorescence and specific illustrations of the adverse effects of ignoring these additional fluorescent species in a traditional microscopy experiment and a hyperspectral imaging system.