gebhart/patrepeval huggingface dataset:
Multiple-locus variable number of tandem repeat analysis (MLVA) of Irish verocytotoxigenic Escherichia coliO157 from feedlot cattle: uncovering strain dissemination routes (2008)

Application of MLVA is a broadly useful and convenient tool when applied to uncover the dissemination of E. coli O157 in the environment and in supporting improved on-farm management of this important pathogen. These data identified diverse strain types based on amplification of VNTR markers in each case.
The facilitative glucose transporter GLUT3: 20 years of distinction (2008)

Glucose metabolism is vital to most mammalian cells, and the passage of glucose across cell membranes is facilitated by a family of integral membrane transporter proteins, the GLUTs. There are currently 14 members of the SLC2 family of GLUTs, several of which have been the focus of this series of reviews. The subject of the present review is GLUT3, which, as implied by its name, was the third glucose transporter to be cloned (Kayano T, Fukumoto H, Eddy RL, Fan YS, Byers MG, Shows TB, Bell GI. J Biol Chem 263: 15245-15248, 1988) and was originally designated as the neuronal GLUT. The overriding question that drove the early work on GLUT3 was why would neurons need a separate glucose transporter isoform? What is it about GLUT3 that specifically suits the needs of the highly metabolic and oxidative neuron with its high glucose demand? More recently, GLUT3 has been studied in other cell types with quite specific requirements for glucose, including sperm, preimplantation embryos, circulating white blood cells, and an array of carcinoma cell lines. The last are sufficiently varied and numerous to warrant a review of their own and will not be discussed here. However, for each of these cases, the same questions apply. Thus, the objective of this review is to discuss the properties and tissue and cellular localization of GLUT3 as well as the features of expression, function, and regulation that distinguish it from the rest of its family and make it uniquely suited as the mediator of glucose delivery to these specific cells.
Delivery of protein to the cytosol of macrophages using Escherichia coli K‐12 (1999)

Listeriolysin O (LLO) is an essential determinant of pathogenicity whose natural biological role is to mediate lysis of Listeria monocytogenes containing phagosomes. In this study, we report that Escherichia coli expressing cytoplasmic recombinant LLO can efficiently deliver co-expressed proteins to the cytosol of macrophages. We propose a model in which subsequent or concomitant to phagocytosis the E. coli are killed and degraded within phagosomes causing the release of LLO and target proteins from the bacteria. LLO acts by forming large pores in the phagosomal membrane, thus releasing the target protein into the cytosol. Delivery was shown to be rapid, within minutes after phagocytosis. Using this method, a large enzymatically active protein was delivered to the cytosol. Furthermore, we demonstrated that the E. coli/LLO system is very efficient for delivery of ovalbumin (OVA) to the major histocompatibility (MHC) class I pathway for antigen processing and presentation, greater than 4 logs compared with E. coli expressing OVA alone. Moreover, the time required for processing and presentation of an OVA-derived peptide was similar to that previously reported when purified OVA was introduced directly into the cytosol by other methods. Using this system, potentially large amounts of any protein that can be expressed in E. coli can be delivered to the cytosol without protein purification. The potential use of this system for the delivery of antigenic protein in vivo and the delivery of DNA are discussed.
Clinical perspectives of TRAIL: insights into central nervous system disorders (2016)

The TNF-related apoptosis inducing ligand TRAIL is a member of the TNF superfamily that has been firstly studied and evaluated for its anti-cancer activity, and the insights into its biology have already led to the identification of several TRAIL-based anticancer strategies with strong clinical therapeutic potentials. Nonetheless, the TRAIL system is far more complex and it can lead to a wider range of biological effects other than the ability of inducing apoptosis in cancer cells. By virtue of the different receptors and the different signalling pathways involved, TRAIL plays indeed a role in the regulation of different processes of the innate and adaptive immune system and this feature makes it an intriguing molecule under consideration in the development/progression/treatment of several immunological disorders. In this context, central nervous system represents a peculiar anatomic site where, despite its "status" of immune-privileged site, both innate and adaptive inflammatory responses occur and are involved in several pathological conditions. A number of studies have evaluated the role of TRAIL and of TRAIL-related pathways as pro-inflammatory or protective stimuli, depending on the specific pathological condition, confirming a twofold nature of this molecule. In this light, the aim of this review is to summarize the main preclinical evidences of the potential/involvement of TRAIL molecule and TRAIL pathways for the treatment of central nervous system disorders and the key suggestions coming from their assessment in preclinical models as proof of concept for future clinical studies.
A region-based fuzzy feature matching approach to content-based image retrieval (2002)

This paper proposes a fuzzy logic approach, UFM (unified feature matching), for region-based image retrieval. In our retrieval system, an image is represented by a set of segmented regions, each of which is characterized by a fuzzy feature (fuzzy set) reflecting color, texture, and shape properties. As a result, an image is associated with a family of fuzzy features corresponding to regions. Fuzzy features naturally characterize the gradual transition between regions (blurry boundaries) within an image and incorporate the segmentation-related uncertainties into the retrieval algorithm. The resemblance of two images is then defined as the overall similarity between two families of fuzzy features and quantified by a similarity measure, UFM measure, which integrates properties of all the regions in the images. Compared with similarity measures based on individual regions and on all regions with crisp-valued feature representations, the UFM measure greatly reduces the influence of inaccurate segmentation and provides a very intuitive quantification. The UFM has been implemented as a part of our experimental SIMPLIcity image retrieval system. The performance of the system is illustrated using examples from an image database of about 60,000 general-purpose images.
Intravesical Chemotherapy in a Controlled Trial with Thio-Tepa Versus Doxorubicin Hydrochloride (1981)

No AccessJournal of Urology1 May 1981Intravesical Chemotherapy in a Controlled Trial with Thio-Tepa Versus Doxorubicin Hydrochloride Yoav Horn, Abraham Eidelman, Natalio Walach, and Mahmoud Ilian Yoav HornYoav Horn More articles by this author , Abraham EidelmanAbraham Eidelman More articles by this author , Natalio WalachNatalio Walach More articles by this author , and Mahmoud IlianMahmoud Ilian More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)55151-4AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail We treated 25 patients with recurrent transitional cell carcinoma of the bladder with intravesical chemotherapy. The 2 drugs used were doxorubicin hydrochloride and thio-tepa introduced at 3-week intervals and checked for efficacy by repeated cystoscopy after every 3 instillations. The clinical data and results of both groups are presented, and the importance of intravesical treatment with minimal toxicity in this relatively benign condition is discussed. © 1981 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetailsCited BySeraphim L, Perrapato S, Slocum H, Rustum Y and Huben R (2018) In Vitro Study of the Interaction of Doxorubicin, Thiotepa, and Mitomycin-C, Agents Used for Intravesical Chemotherapy of Superficial Bladder CancerJournal of Urology, VOL. 145, NO. 3, (613-617), Online publication date: 1-Mar-1991.Okamura T, Ohtani M, Inoue K, Fukushima S, Ohtaguro K and Kakizoe T (2018) Effects of Intravesical Instillation of Antitumor Chemotherapeutic and Immunotherapeutic Agents on Bladder Lesion Development in Rats Pretreated with N-Butyl-N-(4-Hydroxybutyl)NitrosamineJournal of Urology, VOL. 138, NO. 5, (1305-1307), Online publication date: 1-Nov-1987.Crawford E, McKenzie D, Mansson W, Totonchy M, Grossman H, Davis M, Lamm D and Duchek M (2018) Adverse Reactions to the Intravesical Administration of Doxorubicin Hydrochloride: Report of 6 CasesJournal of Urology, VOL. 136, NO. 3, (668-669), Online publication date: 1-Sep-1986.Leissner K and Gustavsson B (2018) Intravesical High Dose 5-Fluorouracil Instillations Combined with Allopurinol—A Therapeutic Alternative in the Treatment of Multiple Bladder TumorsJournal of Urology, VOL. 132, NO. 1, (34-36), Online publication date: 1-Jul-1984.Engelmann U, Bürger R, Rumpelt J and Jacobi G (2018) Adriamycin Permeability of the Rat Bladder under Different ConditionsJournal of Urology, VOL. 129, NO. 4, (862-864), Online publication date: 1-Apr-1983. Volume 125Issue 5May 1981Page: 652-654 Advertisement Copyright & Permissions© 1981 by The American Urological Association Education and Research, Inc.MetricsAuthor Information Yoav Horn More articles by this author Abraham Eidelman More articles by this author Natalio Walach More articles by this author Mahmoud Ilian More articles by this author Expand All Advertisement PDF DownloadLoading ...
ATM-Dependent Downregulation of USP7/HAUSP by PPM1G Activates p53 Response to DNA Damage (2012)

The deubiquitylation enzyme USP7/HAUSP plays a major role in regulating genome stability and cancer prevention by controlling the key proteins involved in the DNA damage response. Despite this important role in controlling other proteins, USP7 itself has not been recognized as a target for regulation. Here, we report that USP7 regulation plays a central role in DNA damage signal transmission. We find that stabilization of Mdm2, and correspondingly p53 downregulation in unstressed cells, is accomplished by a specific isoform of USP7 (USP7S), which is phosphorylated at serine 18 by the protein kinase CK2. Phosphorylation stabilizes USP7S and thus contributes to Mdm2 stabilization and downregulation of p53. After ionizing radiation, dephosphorylation of USP7S by the ATM-dependent protein phosphatase PPM1G leads to USP7S downregulation, followed by Mdm2 downregulation and accumulation of p53. Our findings provide a quantitative transmission mechanism of the DNA damage signal to coordinate a p53-dependent DNA damage response.
Sustained transgene expression in cartilage defects in vivo after transplantation of articular chondrocytes modified by lipid‐mediated gene transfer in a gel suspension delivery system (2003)

These data demonstrate the successful introduction of articular chondrocytes modified by lipid-mediated gene transfer in a gel suspension delivery system into osteochondral defects and the sustained expression of the transgene in vivo. This method may be used to define the effects of genes involved in cartilage repair and may provide alternative treatments for articular cartilage defects.
Evaluation of Quantum Yields for Decomposition of I-Line Sensitive Photoacid Generators. (2003)

Quantum yields for decomposition of a series of i-line sensitive photoacid generators were evaluated in acetonitrile solution or in polystyrene films. Sulfonate ester derivatives of N-hydroxynaphtaleneimide, fluorenone oxime, and thioxanthone oxime were investigated. Photolysis degree of photoacid generators was successfully estimated by UV or in situ FT-IR spectral changes. First-order decomposition profiles were observed for all photoacid generators on i-line irradiation. Quantum yields for decomposition (Φd) were calculated based on the rate of decomposition and molar absorption coefficient of photoacid generators. The Φd values were determined by using fluorenylideneimino p-toluenesulfonate as a standard. The Φd values of photoacid generators derived from fluorenone oxime and thioxanthone oxime were similar to those of conventional photoacid generators. The relationship between thermal stability of photoacid generators and those Φd values was also discussed.
Proton synchrotrons for cancer therapy (2001)

Synchrotrons have long been recognized for their superior capabilities in proton and heavy ion therapy. Their compactness and ease of beam energy control make them ideally suited to this application. The range of available intensities insures safety against high dose accidents such as have occurred with conventional electron accelerators. For heavy ion and heavy ion therapy, synchrotrons have been the exclusive choice among particle accelerators. In this paper, four synchrotrons designed for dedicated therapy facilities are reviewed and performance data are discussed.
Immunohistological Changes in Dilated Cardiomyopathy Induced by Immunoadsorption Therapy and Subsequent Immunoglobulin Substitution (2001)

IA and subsequent IgG substitution mitigate myocardial inflammation in DCM.
Glyphosate‐Resistant Soybean Cultivar Response to Glyphosate (2001)

Glyphosate ( N ‐(phosphonomethyl) glycine)‐resistant (GR) soybean [ Glycine max (L.) Merr.] technology is gaining acceptance in U.S. cropping systems, yet potential yield suppression from either cultivar genetic differentials, the GR gene/gene insertion process, or glyphosate is a concern. Other work shows that the GR gene/gene insertion process may suppress soybean yield. No one has reported the effects of glyphosate on a diverse group of commercially available GR soybean cultivars. In this study we evaluated one of the potential sources of GR yield suppression—the effect of glyphosate on yield, growth, and development of GR cultivars. Field experiments were conducted at four Nebraska locations with12 GR cultivars in 1998 and 13 GR cultivars in 1999. Soybean response to glyphosate, ammonium sulfate (AMS), and water application at 21 and 42 d after soybean emergence was compared with control plots treated with AMS and water in 1998. An additional control, water alone, was added in 1999. Grain yield among cultivars differed as expected with a range of 3.44 to 3.96 Mg ha −1 in the 2‐yr averages. Glyphosate did not affect the majority of the soybean growth and development characteristics measured. Grain yield of GR soybean was not affected by glyphosate at any location or when averaged over locations. Two‐year average grain yield of cultivars treated with glyphosate, AMS, and water was 3.74 Mg ha −1 ; this was not different from 3.79 Mg ha −1 with AMS and water treatment.
Degradation of STAT1 and STAT2 by the V Proteins of Simian Virus 5 and Human Parainfluenza Virus Type 2, Respectively: Consequences for Virus Replication in the Presence of Alpha/Beta and Gamma Interferons (2002)

Human cell lines were isolated that express the V protein of either simian virus 5 (SV5) or human parainfluenza virus type 2 (hPIV2); the cell lines were termed 2f/SV5-V and 2f/PIV2-V, respectively. STAT1 was not detectable in 2f/SV5-V cells, and the cells failed to signal in response to either alpha/beta interferons (IFN-alpha and IFN-beta, or IFN-alpha/beta) or gamma interferon (IFN-gamma). In contrast, STAT2 was absent from 2f/PIV2-V cells, and IFN-alpha/beta but not IFN-gamma signaling was blocked in these cells. Treatment of both 2f/SV5-V and 2f/PIV2-V cells with a proteasome inhibitor allowed the respective STAT levels to accumulate at rates similar to those seen in 2fTGH cells, indicating that the V proteins target the STATs for proteasomal degradation. Infection with SV5 can lead to a complete loss of both phosphorylated and nonphosphorylated forms of STAT1 by 6 h postinfection. Since the turnover of STAT1 in uninfected cells is longer than 24 h, we conclude that degradation of STAT1 is the main mechanism by which SV5 blocks interferon (IFN) signaling. Pretreatment of 2fTGH cells with IFN-alpha severely inhibited both SV5 and hPIV2 protein synthesis. However, and in marked contrast, pretreatment of 2fTGH cells with IFN-gamma had little obvious effect on SV5 protein synthesis but did significantly reduce the replication of hPIV2. Pretreament with IFN-alpha or IFN-gamma did not induce an antiviral state in 2f/SV5-V cells, indicating either that the induction of an antiviral state is completely dependent on STAT signaling or that the V protein interferes with other, STAT-independent cell signaling pathways that may be induced by IFNs. Even though SV5 blocked IFN signaling, the addition of exogenous IFN-alpha to the culture medium of 2fTGH cells 12 h after a low-multiplicity infection with SV5 significantly reduced the subsequent cell-to-cell spread of virus. The significance of the results in terms of the strategy that these viruses have evolved to circumvent the IFN response is discussed.
Deuterioglucose: alteration of biodistribution by an isotope effect. (1986)

Carbon-14 glucose, in which all carbon-hydrogen bonds were replaced by carbon-deuterium bonds (deuterioglucose), was extracted from algae growing in heavy water and exposed to [14C]carbon dioxide. The identity of [14C]deuterioglucose was confirmed by comparison with authentic material on two high performance liquid chromatography and two thin layer chromatography systems. Fermentation to lactate followed by oxidative decarboxylation demonstrated that 35% of the 14C was on carbons 3 and 4 for deuterioglucose isolated from a 24-hr algal incubation, and 61% for a 20-min incubation. Mice were injected intravenously with either (24-hr) deuterioglucose or with 14C-labeled (protio)glucose labeled uniformly. The deuterioglucose cleared more slowly from the blood, while heart and brain accumulated label more slowly. Tissue concentrations peaked at later times for deuterioglucose. Deuteration may be a useful feature of radiopharmaceutical design.
Herpes simplex virus type 1-induced ribonucleotide reductase activity is dispensable for virus growth and DNA synthesis: isolation and characterization of an ICP6 lacZ insertion mutant (1988)

Herpes simplex virus (HSV) encodes a ribonucleotide reductase consisting of two subunits (140 and 38 kilodaltons) whose genes map to coordinates 0.56 to 0.60 on the viral genome. Host cell lines containing the HpaI F fragment which includes the reductase subunit genes of HSV type 1 strain KOS (coordinates 0.535 to 0.620) were generated. Transfection of these cells with a plasmid containing the immediate-early ICP0 gene resulted in the expression of ICP6; interestingly, ICP4 plasmids failed to induce expression, indicating an unusual pattern of ICP6 regulation. One such cell line (D14) was used to isolate a mutant with the structural gene of lacZ inserted into the ICP6 gene such that the lacZ gene is read in frame with the N-terminal region of ICP6. This mutant generated a protein containing 434 amino acids (38%) of the N terminus of ICP6 fused to beta-galactosidase under control of the endogenous ICP6 promoter. Screening for virus recombinants was greatly facilitated by staining virus plaques with 5-bromo-4-chloro-3-indoyl-beta-D-galactoside (X-gal). Enzyme assays of infected BHK cells indicated that the mutant is incapable of inducing viral ribonucleotide reductase activity. Surprisingly, although plaque size was greatly reduced, mutant virus yield was reduced only four- to fivefold compared with that of the wild type grown in exponentially growing Vero cells. Mutant virus plaque size, yields, and ability to synthesize viral DNA were more severely compromised in serum-starved cells as compared with the wild type grown under the same condition. Although our evidence suggests that the HSV type 1 ribonucleotide reductase is not required for virus growth and DNA replication in dividing cells, it may be required for growth in nondividing cells.
Regulation of contact hypersensitivity by interleukin 10. (1994)

Contact hypersensitivity (CHS) responses require the participation of T cells, along with a variety of cytokines and adhesion molecules. In the classical CHS, antigen-specific T cells are recruited to a site of antigenic challenge, where they react with antigen, release cytokines, and attract other inflammatory cells. In the mouse model of CHS, this reaction is elicited in sensitized mice by application of the immunogen 4-7 d after immunization. The reaction peaks at 24 h, is slightly reduced by 48 h, and can return to normal by 72 h. This is in spite of the fact that some antigen is still present at the site of challenge. Here we examined the hypothesis that locally produced interleukin 10 (IL-10) regulates the duration of the response. Our data show that IL-10 protein peaked 10-14 h after antigenic challenge and returned to background by 24 h. The production of IL-10 protein corresponded with, and followed IL-10 mRNA transcription as detected by reverse transcriptase-polymerase chain reaction. During peak IL-10 production after antigenic challenge, it was not possible to transfer CHS with immune lymphoid cells, unless neutralizing antibody to IL-10 was given first. Additionally, when sensitized mice were given neutralizing anti-IL-10 antibody at the time of antigenic challenge, the duration of CHS was prolonged well beyond the natural course of the response. Finally, we demonstrate that rIL-10, when injected into the skin before antigenic challenge, prevented the elicitation of CHS in previously sensitized mice. Taken together, our data show an important role for IL-10 in the natural regulation of CHS responses in vivo.
Adeno-associated virus serotype rh.10 displays strong muscle tropism following intraperitoneal delivery (2017)

Recombinant adeno-associated virus (rAAV) is an attractive tool for basic science and translational medicine including gene therapy, due to the versatility in its cell and organ transduction. Previous work indicates that rAAV transduction patterns are highly dependent on route of administration. Based on this relationship, we hypothesized that intraperitoneal (IP) administration of rAAV produces unique patterns of tissue tropism. To test this hypothesis, we investigated the transduction efficiency of 12 rAAV serotypes carrying an enhanced green fluorescent protein (EGFP) reporter gene in a panel of 12 organs after IP injection. Our data suggest that IP administration emphasizes transduction patterns that are different from previously reported intravascular delivery methods. Using this approach, rAAV efficiently transduces the liver, pancreas, skeletal muscle, heart and diaphragm without causing significant histopathological changes. Of note, rAAVrh.10 showed excellent muscle transduction following IP administration, highlighting its potential as a new muscle-targeting vector.
T helper cell subsets require the expression of distinct costimulatory signals by antigen-presenting cells. (1988)

We examined the ability of macrophages and B cells to function as antigen-presenting cells (APCs) for murine TH1 and TH2 cloned T helper cell lines. Antigen presented by concanavalin A-elicited peritoneal macrophages or resting splenic B cells stimulated antigen-dependent proliferation of both T helper subsets. Paraformaldehyde fixation of the APCs following different conditions of activation indicated differential requirements for costimulatory signals by TH1 and TH2 cells. TH2 proliferative responses were strictly dependent on APC expression of IL-1. TH1 proliferation was dependent on APC expression of a non-IL-1 costimulatory signal present on freshly isolated macrophages and on splenic B cells activated with anti-immunoglobulin plus interferon gamma.