gebhart/patrepeval huggingface dataset:
Targeting coagulation factor XII provides protection from pathological thrombosis in cerebral ischemia without interfering with hemostasis (2006)

Formation of fibrin is critical for limiting blood loss at a site of blood vessel injury (hemostasis), but may also contribute to vascular thrombosis. Hereditary deficiency of factor XII (FXII), the protease that triggers the intrinsic pathway of coagulation in vitro, is not associated with spontaneous or excessive injury-related bleeding, indicating FXII is not required for hemostasis. We demonstrate that deficiency or inhibition of FXII protects mice from ischemic brain injury. After transient middle cerebral artery occlusion, the volume of infarcted brain in FXII-deficient and FXII inhibitor-treated mice was substantially less than in wild-type controls, without an increase in infarct-associated hemorrhage. Targeting FXII reduced fibrin formation in ischemic vessels, and reconstitution of FXII-deficient mice with human FXII restored fibrin deposition. Mice deficient in the FXII substrate factor XI were similarly protected from vessel-occluding fibrin formation, suggesting that FXII contributes to pathologic clotting through the intrinsic pathway. These data demonstrate that some processes involved in pathologic thrombus formation are distinct from those required for normal hemostasis. As FXII appears to be instrumental in pathologic fibrin formation but dispensable for hemostasis, FXII inhibition may offer a selective and safe strategy for preventing stroke and other thromboembolic diseases.
Feasibility of molecular-resolution fluorescence near-field microscopy using multi-photon absorption and field enhancement near a sharp tip (1999)

Aperture-based near-field microscopy suffers from fundamental limitations imposed by the electromagnetic skin depth of the aperture material and a rapidly decreasing throughput as the aperture is made smaller. Apertureless approaches without these limitations have been demonstrated for coherent imaging but are not easily applicable to incoherent processes such as fluorescence or Raman scattering and to photochemical surface modification. Using multi-photon processes in conjunction with the field enhancement that occurs at a sharp tip in close apposition to a substrate should permit substantial localization of absorption and excitation to a nm sized volume. The expected enhancement of the optical field at the tip edge is calculated here for various combinations of metallic and nonmetallic tip and substrate materials. It is estimated that when using 100 fs pulses repeating at 100 MHz average laser powers of about 10 mW should be sufficient to reach saturating field strengths for three-photon absorption. Steady state and instantaneous temperature rises at the tip are estimated and found likely not to be a limiting factor. Fluorescence quenching is expected to limit the resolution achievable with metallic tips to about 5 nm, but tips made from highly refracting insulators or semiconductors should allow truly molecular resolution.
Corner detection with covariance propagation (2002)

This paper presents a statistical approach for detecting corners from chain encoded digital arcs. An arc point is declared as a corner if the estimated parameters of the two fitted lines of the two arc segments immediately to the right and left of the are point are statistically significantly different. The corner detection algorithm consists of two steps: corner detection and optimization. While corner detection involves statistically identifying the most likely corner points along an arc sequence, corner optimization deals with improving the locational errors of the detected corners. The major contributions of this research include developing a method for analytically estimating the covariance matrix of the fitted line parameters and developing a hypothesis test statistic to statistically test the difference between the parameters of two fitted lines. Performance evaluation study showed that the algorithm is robust and accurate for complex images. It has an average misdetection rate of 2.5% and false alarm rate of 2.2% for the complex RADIUS images. This paper discusses the theory and performance characterization of the proposed corner detector.
Biochemical and biophysical identification of cystic fibrosis transmembrane conductance regulator chloride channels as components of endocytic clathrin-coated vesicles. (1994)

Cystic fibrosis results from mutations in the gene encoding the CFTR Cl- channel. Although CFTR occurs as an integral component of the plasma membrane, recent studies implicate CFTR in endocytic recycling and suggest that the protein may also exist in intracellular vesicular compartments. To test this, we analyzed CFTR in clathrin-coated vesicles (CCV) purified from cells constitutively expressing CFTR at high levels. CFTR immunoreactivity was detected in CCV by immunoblot and was identified as CFTR based on labeling of immunoprecipitates with protein kinase A and by tryptic phosphopeptide mapping. Fusion of uncoated CCV with planar lipid bilayers resulted in the incorporation of kinase- and ATP-activated Cl- channel activity (7.8 pS at 20 degrees C; 11.9 pS at 37 degrees C), with a linear current-voltage relation under symmetrical conditions. Thus, functional CFTR occurs in CCV. Moreover, CFTR interacts with the plasma membrane specific adaptor complex during endocytosis through clathrin-coated pits. Therefore, the abundance of CFTR in the plasma membrane may be regulated by exocytic insertion and endocytic recycling, and these processes may provide an augmentation to protein kinase A activation as a mechanism for regulating CFTR Cl channels in the plasma membrane.
Purification and Molecular Genetic Characterization of ZPU1, a Pullulanase-Type Starch-Debranching Enzyme from Maize1 (1999)

This study identified and purified specific isoamylase- and pullulanase-type starch-debranching enzymes (DBEs) present in developing maize (Zea mays L.) endosperm. The cDNA clone Zpu1 was isolated based on its homology with a rice (Oryza sativa L.) cDNA coding for a pullulanase-type DBE. Comparison of the protein product, ZPU1, with 18 other DBEs identified motifs common to both isoamylase- and pullulanase-type enzymes, as well as class-specific sequence blocks. Hybridization of Zpu1 to genomic DNA defined a single-copy gene, zpu1, located on chromosome 2. Zpu1 mRNA was abundant in endosperm throughout starch biosynthesis, but was not detected in the leaf or the root. Anti-ZPU1 antiserum specifically recognized the approximately 100-kD ZPU1 protein in developing endosperm, but not in leaves. Pullulanase- and isoamylase-type DBEs were purified from extracts of developing maize kernels. The pullulanase-type activity was identified as ZPU1 and the isoamylase-type activity as SU1. Mutations of the sugary1 (su1) gene are known to cause deficiencies of SU1 isoamylase and a pullulanase-type DBE. ZPU1 activity, protein level, and electrophoretic mobility were altered in su1-mutant kernels, indicating that it is the affected pullulanase-type DBE. The Zpu1 transcript levels were equivalent in nonmutant and su1-mutant kernels, suggesting that coordinated regulation of ZPU1 and SU1 occurs posttranscriptionally.
Myofibroblast Development Is Characterized by Specific Cell-Cell Adherens Junctions (2004)

Myofibroblasts of wound granulation tissue, in contrast to dermal fibroblasts, join stress fibers at sites of cadherin-type intercellular adherens junctions (AJs). However, the function of myofibroblast AJs, their molecular composition, and the mechanisms of their formation are largely unknown. We demonstrate that fibroblasts change cadherin expression from N-cadherin in early wounds to OB-cadherin in contractile wounds, populated with alpha-smooth muscle actin (alpha-SMA)-positive myofibroblasts. A similar shift occurs during myofibroblast differentiation in culture and seems to be responsible for the homotypic segregation of alpha-SMA-positive and -negative fibroblasts in suspension. AJs of plated myofibroblasts are reinforced by alpha-SMA-mediated contractile activity, resulting in high mechanical resistance as demonstrated by subjecting cell pairs to hydrodynamic forces in a flow chamber. A peptide that inhibits alpha-SMA-mediated contractile force causes the reorganization of large stripe-like AJs to belt-like contacts as shown for enhanced green fluorescent protein-alpha-catenin-transfected cells and is associated with a reduced mechanical resistance. Anti-OB-cadherin but not anti-N-cadherin peptides reduce the contraction of myofibroblast-populated collagen gels, suggesting that AJs are instrumental for myofibroblast contractile activity.
The temporal nature of forces acting on metal drops in gas metal arc welding (1996)

At moderate and high welding currents, the most important forces in gas metal arc welding acting on the molten electrode are magnetic forces arising from the interaction between the welding current and its own magnetic field. These forces drive the dy-namic evolution of the drop and also de-pend on the instantaneous shape of the drop. In this paper, experimentally ob-served manifestations of magnetic forces are shown, and a technique for approx-imating the temporal evolution of these forces from experimentally measured drops shapes is reported. The technique provides
22. The Clusters of Orthologous Groups (COGs) Database: Phylogenetic Classification of Proteins from Complete Genomes (2003)

Summary The protein database of Clusters of Orthologous Groups (COGs) is an attempt to phylogenetically classify the complete complement of proteins (both predicted and characterized) encoded by complete genomes. Each COG is a group of three or more proteins that are inferred to be orthologs, i.e., they are direct evolutionary counterparts. The current release of the COGs database consists of 4,873 COGs, which include 136,711 proteins (~71% of all encoded proteins) from 50 bacterial genomes, 13 archaeal genomes, and 3 genomes of unicellular eukaryotes, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, and the microsporidian Encephalitozoon cuniculi. The COG database is updated periodically as new genomes become available. The COGs for complete eukaryotic genomes are in preparation. The COGs can be applied to the task of functional annotation of newly sequenced genomes by using the COGnitor program, which is available on the COGs homepage [http://www.ncbi.nlm.nih.gov/COG/].
Characterization and protective properties of attenuated mutants of Salmonella choleraesuis (1992)

We have constructed crp::Tn10 and cya::Tn10 Salmonella choleraesuis mutants and their fusaric acid-resistant derivatives with deletions (delta) of the Tn10 and adjacent DNA sequences and found them to be avirulent and able to induce protection against a wild-type challenge in 8-week-old BALB/c mice. Mice survived infection with the crp and cya mutants at doses of more than 7 x 10(3) times the oral (p.o.) 50% lethal dose (LD50) and more than 8 x 10(2) times the intraperitoneal LD50 of the wild-type S. choleraesuis parent. Mice vaccinated with attenuated strains were protected against challenge with more than 1.6 x 10(4) times the p.o. LD50 and more than 80 times the intraperitoneal LD50 of the wild-type virulent S. choleraesuis parent. One deletion mutation isolated in the crp region extends to an adjacent gene(s) that was shown to be associated with avirulence. This gene or operon has been designated cdt (colonization of deep tissues). A delta (crp-cdt)19 strain, when complemented with the wild-type crp gene and promoter on a pBR-derived plasmid, had p.o. LD50 values 10(3) times higher than those for the wild type. A delta cya delta (crp-cdt)19 double mutant was less virulent than and afforded more complete protection against a challenge with the wild-type strain than a delta crp-11 delta cya double mutant or the individual cya, crp, or crp+/cdt mutants. The deletion derivatives exhibited reduced invasion of CHO cells in vitro, and the numbers of the mutants recovered from mouse tissues were less than that of the parent strain. These studies suggest that one or more of the genes involved in cell attachment to and/or invasion of S. choleraesuis may be under catabolite repression. In addition, we describe a new deletion of a gene(s) located in the crp region between cysG and argD that is associated with virulence in S. choleraesuis.
Prevention of Silent Aspiration Due to Leaks around Cuffs of Endotracheal Tubes (1986)

Significant aspiration may occur around correctly inflated high volume, low pressure endotracheal tube cuffs. The prevention of silent aspiration due to leaks around cuffs of endotracheal tubes was investigated during general anesthesia for hip replacement in 47 patients. The patients were randomly assigned to one of three groups, in which one of three endotracheal tubes of different designs were used for intubation. The following three tubes were used: the red rubber Rüsch tube with low residual volume cuff, inflated to minimum occluding volume; the Mallinckrodt Hi-Lo tube with high residual volume cuff; the NL tube with high residual volume cuff and automatic cuff pressure regulation. The cuffs on the Mallinckrodt and the NL tubes were inflated to 29-31 cm H2O. One hour before termination of the surgical procedure, 1 ml methylene blue dye was injected into the trachea just above the cuff through a thin channel built into the tubes. At termination of the operation, the trachea below the cuff was inspected with a fiberoptic bronchoscope. Aspiration was found in 12.5% with the Rüsch tube, in 31.2% with the Mallinckrodt tube, and in 0% with the NL tube. Our results show that silent aspiration is still a problem with standard endotracheal tubes, but that it may be minimized by use of appropriate tubes, cuffs, and control of cuff inflation.
Synthesis of 1-(p-isothiocyanatobenzyl) derivatives of DTPA and EDTA. Antibody labeling and tumor-imaging studies (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of 1-(p-isothiocyanatobenzyl) derivatives of DTPA and EDTA. Antibody labeling and tumor-imaging studiesMartin W. Brechbiel, Otto A. Gansow, Robert W. Atcher, Jeffrey Schlom, Jose Esteban, Diane Simpson, and David ColcherCite this: Inorg. Chem. 1986, 25, 16, 2772–2781Publication Date (Print):July 1, 1986Publication History Published online1 May 2002Published inissue 1 July 1986https://pubs.acs.org/doi/10.1021/ic00236a024https://doi.org/10.1021/ic00236a024research-articleACS PublicationsRequest reuse permissionsArticle Views1345Altmetric-Citations218LEARN 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 Get e-Alerts
High expression of the DNA methyltransferase gene characterizes human neoplastic cells and progression stages of colon cancer. (1991)

DNA methylation abnormalities occur consistently in human neoplasia including widespread hypomethylation and more recently recognized local increases in DNA methylation that hold potential for gene inactivation events. To study this imbalance further, we have cloned and localized to chromosome 19 a portion of the human DNA methyltransferase gene that codes for the enzyme catalyzing DNA methylation. Expression of this gene is low in normal human cells, significantly increased (30- to 50-fold by PCR analysis) in virally transformed cells, and strikingly elevated in human cancer cells (several hundredfold). In comparison to colon mucosa from patients without neoplasia, median levels of DNA methyltransferase transcripts are 15-fold increased in histologically normal mucosa from patients with cancers or the benign polyps that can precede cancers, 60-fold increased in the premalignant polyps, and greater than 200-fold increased in the cancers. Thus, increases in DNA methyltransferase gene expression precede development of colonic neoplasia and continue during progression of colonic neoplasms. These increases may play a role in the genetic instability of cancer and mark early events in cell transformation.
Partial Recipe for Brunswick Stew (2012)

Research Article| May 01 2012 Partial Recipe for Brunswick Stew andrea cohen andrea cohen andrea cohen directs the Blacksmith House Poetry Series in Cambridge, Massachusetts. Her most recent poetry collections are Kentucky Derby and Long Division. Search for other works by this author on: This Site PubMed Google Scholar Gastronomica (2012) 12 (2): 9. https://doi.org/10.1525/GFC.2012.12.2.9 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation andrea cohen; Partial Recipe for Brunswick Stew. Gastronomica 1 May 2012; 12 (2): 9. doi: https://doi.org/10.1525/GFC.2012.12.2.9 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 ContentGastronomica Search This content is only available via PDF. © 2012 The Regents of the University of California. All Rights Reserved.2012 Article PDF first page preview Close Modal You do not currently have access to this content.
The Bacillus subtilis and Lactic Acid Bacteria Probiotics Influences Intestinal Mucin Gene Expression, Histomorphology and Growth Performance in Broilers (2012)

The aim of the present study was to evaluate the effect of commercial monostrain and multistrain probiotics in diets on growth performance, intestinal morphology and mucin gene (MUC2) expression in broiler chicks. Three hundred seventy-eight 1-d-old male Arian broiler chicks were allocated in 3 experimental groups for 6 wk. The birds were fed on a corn-soybean based diet and depending on the addition were labeled as follows: control-unsupplemented (C), birds supplemented with Bacillus subtilis (BS) and lactic acid bacteria (LAB) based probiotics. Each treatment had 6 replicates of 21 broilers each. Treatment effects on body weight, feed intake, feed conversion ratio and biomarkers such as intestinal goblet cell density, villus length, villus width, and mucin gene expression were determined. Total feed intake did not differ significantly between control birds and those fed a diet with probiotics (p>0.05). However, significant differences in growth performance were found. Final body weight at 42 d of age was higher in birds fed a diet with probiotics compared to those fed a diet without probiotic (p<0.05). Inclusion of Bacillus subtilis based probiotic in the diets also significantly affected feed conversion rate (FCR) compared with control birds (p<0.05). No differences in growth performance were observed in birds fed different types of probiotic supplemented diets. Inclusion of lactic acid bacteria based probiotic in the diets significantly increased goblet cell number and villus length (p<0.05). Furthermore, diets with Bacillus subtilis based probiotics significantly increased gene expression (p<0.05), with higher intestinal MUC2 mRNA in birds fed diet with probiotics compared to those fed the control diet. In BS and LAB probiotic fed chicks, higher growth performance may be related to higher expression of the MUC2 gene in goblet cells and/or morphological change of small intestinal tract. The higher synthesis of the mucin gene after probiotic administration may positively affect bacterial interactions in the intestinal digestive tract, intestinal mucosal cell proliferation and consequently efficient nutrient absorption.
Model Systems for Investigating Mucin Gene Expression in Airway Diseases (2000)

Overproduction of mucus and of mucin glycoproteins and goblet cell hyperplasia occurs in chronic obstructive airway diseases, including asthma and cystic fibrosis. Mucus overproduction results from alterations in several cellular processes, including altered regulation of airway mucin genes on exposure to environmental and infectious agents and to inflammatory mediators. Seven of the nine identified MUC genes (which encode the protein backbone of mucins) are normally expressed in human respiratory tract tissues. Several inflammatory mediators have now been shown to regulate expression of MUC2, MUC5AC, and MUC5B genes. Importantly, mucin gene expression can be regulated both transcriptionally and posttranscriptionally. Current information on airway mucin gene expression is summarized in this review along with an overview of airway epithelial model systems. In vitro model systems include airway epithelial carcinoma cell lines and primary normal human bronchial epithelial (NHBE) cells. In vivo systems include human respiratory tract tissues and rodent airways. Our laboratory has begun to investigate the role of cytokines on mucin gene expression in vitro and in vivo and on goblet cell metaplasia in vivo. Because cytokines can alter cell proliferation, we characterized the effect of interleukin (IL)-4 and IL-13 on the proliferation of NHBE cells and three human lung carcinoma cell lines--A549, NCI-H292, and Calu-3--that are frequently used for analyses of airway mucin gene expression. Both IL-4 and IL-13 had cell-specific effects. They increased proliferation moderately (1.2-3.0-fold) in NHBE and Calu-3 cells, but markedly inhibited proliferation of A549 cells in a dose-dependent manner. IL-4 increased proliferation of NCI-H292 cells moderately, although IL-13 had no significant effect. We also examined the role of IL-13 and IL-4 on MUC5AC messenger RNA (mRNA) expression in A549, Calu-3, and H292 cell lines and did not observe any significant effect. However, we recently showed an increase in Muc-5ac mRNA and protein expression in a murine model of ovalbumin-induced allergic asthma and in murine airways when IL-13 was delivered intranasally (Alimam, N.Z., et al. Am J. Respir. Cell Mol. Biol. 22:253--260). Thus, we speculate that IL-13 plays a role in the differentiation of murine airway epithelial cells into goblet cells, which then express Muc-5ac mRNA. A detailed analysis of the role of cytokines in airway cell differentiation and mucin gene expression both in vitro and in vivo is required to elucidate the roles of mucins in airway health and diseases. Identification of Muc-5ac as a major gene and gene product in goblet cell metaplasia should facilitate delineation of the molecular mechanisms underlying the induction and reversal of airway goblet cell metaplasia and goblet cell hyperplasia.