gebhart/patrepeval huggingface dataset:
Cloning and Characterization of a Novel Human Alkaline Ceramidase (2001)

Ceramidases are enzymes involved in regulating cellular levels of ceramides, sphingoid bases, and their phosphates. Based on sequence homology to the yeast alkaline ceramidases YPC1p (Mao, C., Xu, R., Bielawska, A., and Obeid, L. M. (2000) J. Biol. Chem. 275, 6876--6884) and YDC1p (Mao, C., Xu, R., Bielawska, A., Szulc, Z. M., and Obeid, L. M. (2000) J. Biol Chem. 275, 31369--31378), we report the identification and cloning of a cDNA encoding for a novel human alkaline ceramidase (aPHC) that hydrolyzes phytoceramide selectively. Northern blot analysis showed that aPHC was ubiquitously expressed, with the highest expression in placenta. Green fluorescent protein tagging showed that it was localized in both the Golgi apparatus and endoplasmic reticulum. Overexpression of aPHC in mammalian cells elevated in vitro ceramidase activity toward N-4-nitrobenz-2-oxa-1,3-diazole-C(12)-phytoceramide. Its expression in a yeast mutant strain devoid of any ceramidase activity restored the ceramidase activity and caused an increase in the hydrolysis of phytoceramide in yeast cells, thus leading to the decreased biosynthesis of sphingolipids. These data collectively suggest that, similar to the yeast phytoceramidase YPC1p, aPHC has phytoceramidase activity both in vitro and in cells; hence, it is a functional homolog of the yeast phytoceramidase YPC1p. However, in contrast to YPC1p, aPHC exhibited no reverse activity of ceramidase either in vitro or in cells. Biochemical characterization showed that aPHC had a pH optimum of 9.5, was activated by Ca(2+), but was inhibited by Zn(2+) and sphingosine. Substrate specificity showed that aPHC hydrolyzed phytoceramide preferentially. Together, these data demonstrate that aPHC is a novel human alkaline phytoceramidase, the first mammalian alkaline ceramidase to be identified as being specific for the hydrolysis of phytoceramide.
Copolymer 1 reduces relapse rate and improves disability in relapsing‐remitting multiple sclerosis (1995)

We studied copolymer 1 (Copaxone) in a multicenter (11-university) phase III trial of patients with relapsing-remitting multiple sclerosis (MS). Two hundred fifty-one patients were randomized to receive copolymer 1 (n = 125) or placebo (n = 126) at a dosage of 20 mg by daily subcutaneous injection for 2 years. The primary end point was a difference in the MS relapse rate. The final 2-year relapse rate was 1.19 +/- 0.13 for patients receiving copolymer 1 and 1.68 +/- 0.13 for those receiving placebo, a 29% reduction in favor of copolymer 1 (p = 0.007) (annualized rates = 0.59 for copolymer 1 and 0.84 for placebo). Trends in the proportion of relapse-free patients and median time to first relapse favored copolymer 1. Disability was measured by the Expanded Disability Status Scale (EDSS), using a two-neurologist (examining and treating) protocol. When the proportion of patients who improved, were unchanged, or worsened by > or = 1 EDSS step from baseline to conclusion (2 years) was evaluated, significantly more patients receiving copolymer 1 were found to have improved and more receiving placebo worsened (p = 0.037). Patient withdrawals were 19 (15.2%) from the copolymer 1 group and 17 (13.5%) from the placebo group at approximately the same intervals. The treatment was well tolerated. The most common adverse experience was an injection-site reaction. Rarely, a transient self-limited systemic reaction followed the injection in 15.2% of those receiving copolymer 1 and 3.2% of those receiving placebo.(ABSTRACT TRUNCATED AT 250 WORDS)
Sequence typing of adenovirus from samples from hematological stem cell transplant recipients (2011)

Adenovirus infections are usually mild or even asymptomatic, but infections with the virus are being recognized increasingly as a major cause of mortality and morbidity in the immunocompromised, particularly hematological stem cell transplant patients where infections can be life threatening and mortality may reach 60%. Typing by sequencing the HVR7 region of the hexon was established and validated using 60 isolates of different serotypes from the six of the seven species which had been typed previously by serum neutralization. Analysis of nucleotide sequences was used to type 227 samples from 41 hematological stem cell transplant recipients. Types from six species were detected but species C types were detected in 51.4% and species A in 34.3% of patients. Seven patients were infected with different adenovirus types sequentially and a further six patients had evidence of simultaneous multiple infections. Many of the sequences had several differences from the prototype strains which will allow tracing of outbreaks and provide evidence for cross-infection in a hospital setting. In this study, the phylogenetic analysis of adenovirus sequences from hematological stem cell transplant patients' samples showed evidence of two possible cross-infection incidents involving three and five patients, respectively.
Mesenchymal Stem Cells Inhibit the Differentiation of Dendritic Cells Through an Interleukin-6-Dependent Mechanism (2007)

Mesenchymal stem cells (MSC) are of particular interest for their potential clinical use in tissue engineering as well as for their capacity to reduce the incidence and severity of graft-versus-host disease in allogeneic transplantation. We have previously shown that MSC-mediated immune suppression acts via the secretion of soluble factor(s) induced upon stimulation. The aim of this study was to identify the molecule(s) involved and the underlying mechanism(s). We show that murine MSC secrete high levels of interleukin (IL)-6 and vascular endothelial growth factor, which are directly correlated to the inhibition of T-cell proliferation. The T-cell activation is partially restored upon addition of a neutralizing anti-IL-6 antibody or the prostaglandin E2 inhibitor indomethacin. Interestingly, no indoleamine 2,3-dioxygenase activity was detected in our conditions. Instead, we show that MSC reduce the expression of major histocompatibility complex class II, CD40, and CD86 costimulatory molecules on mature dendritic cells (DC), which was responsible for a decrease in T-cell proliferation. Moreover, we show that the differentiation of bone marrow progenitors into DC cultured with conditioned supernatants from MSC was partly inhibited through the secretion of IL-6. Altogether, these data suggest that IL-6 is involved in the immunoregulatory mechanism mediated by MSC through a partial inhibition of DC differentiation but is probably not the main mechanism. Disclosure of potential conflicts of interest is found at the end of this article.
Cover Picture: Macromol. Rapid Commun. 7/2005 (2005)

Cover: The combination of atom transfer radical polymerization (ATRP) and “click” chemistry was found to be a very efficient and versatile method for preparing well‐defined end‐functional polymers. Polystyrene prepared by ATRP was first transformed into an azide‐functional polymer, which was subsequently involved in 1,3‐dipolar cycloadditions with various functional alkynes. In all cases, the chain‐end transformation reactions were found to be quantitative. Further details can be found in the Communication by J.‐F. Lutz, * H. G. Börner, and K. Weichenhan on page 514.
Cloning and Functional Characterization of a β-Pinene Synthase from Artemisia annua That Shows a Circadian Pattern of Expression (2002)

Artemisia annua plants produce a broad range of volatile compounds, including monoterpenes, which contribute to the characteristic fragrance of this medicinal species. A cDNA clone, QH6, contained an open reading frame encoding a 582-amino acid protein that showed high sequence identity to plant monoterpene synthases. The prokaryotically expressed QH6 fusion protein converted geranyl diphosphate to (-)-beta-pinene and (-)-alpha-pinene in a 94:6 ratio. QH6 was predominantly expressed in juvenile leaves 2 weeks postsprouting. QH6 transcript levels were transiently reduced following mechanical wounding or fungal elicitor treatment, suggesting that this gene is not directly involved in defense reaction induced by either of these treatments. Under a photoperiod of 12 h/12 h (light/dark), the abundance of QH6 transcripts fluctuated in a diurnal pattern that ebbed around 3 h before daybreak (9th h in the dark phase) and peaked after 9 h in light (9th h in the light phase). The contents of (-)-beta-pinene in juvenile leaves and in emitted volatiles also varied in a diurnal rhythm, correlating strongly with mRNA accumulation. When A. annua was entrained by constant light or constant dark conditions, QH6 transcript accumulation continued to fluctuate with circadian rhythms. Under constant light, advanced cycles of fluctuation of QH6 transcript levels were observed, and under constant dark, the cycle was delayed. However, the original diurnal pattern could be regained when the plants were returned to the normal light/dark (12 h/12 h) photoperiod. This is the first report that monoterpene biosynthesis is transcriptionally regulated in a circadian pattern.
A new aspect of mechanical stress effects in scaled MOS devices (1991)

Deviation in device characteristics due to mechanical stress is investigated experimentally and analytically from the viewpoints of scaling and hot-carrier effects. A stress analysis program, SIMUS (stress analysis program for multilayer structure) 2D/F, which can analyze the stress state of thin multilayer structures such as LSI devices throughout their manufacturing process, was used. In scaled MOS devices, the effect of uniaxial stress is reduced. However, the effect of vertical stress, such as mold stress, becomes a serious problem when the vertical stress causes compressive surface stress. Compressive stress has a serious effect on electron trapping, in SiO/sub 2./ These results provide important guidelines for the manufacture and package design of deep submicrometer devices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
IL-13 Is a Key Regulatory Cytokine for Th2 Cell-Mediated Pulmonary Granuloma Formation and IgE Responses Induced by Schistosoma mansoni Eggs (1999)

Schistosoma mansoni egg-induced pulmonary granuloma formation is a cell-mediated inflammatory response associated with dominant Th2-type cytokine expression, tissue eosinophilia, and high levels of serum IgE. In the present study, we show that in vivo blockade of the Th2 cytokine IL-13, using soluble IL-13R alpha2-Fc fusion protein, significantly reduced the size of pulmonary granulomas in unsensitized as well as egg-sensitized mice. Blocking IL-13 also significantly reduced total serum IgE levels. Interestingly, however, IL-13 blockade did not affect the evolving egg-induced Th2-type cytokine response. IL-4, IL-5, as well as IL-13 responses were indistinguishable in control-Fc- and soluble IL-13R alpha2-Fc fusion protein-treated animals. The smaller granulomas were also phenotypically like the control Fc-treated mice, displaying a similar eosinophil content. Additional studies in IL-4-deficient mice demonstrated that IL-13 was produced, but at much lower levels than in wild-type mice, while IL-4 expression was completely independent of IL-13. Moreover, while granuloma formation was partially reduced in IL-4-deficient mice, blocking IL-13 in these animals almost completely abrogated granuloma development and the pulmonary eosinophilia, while it simultaneously increased IFN-gamma production. Together, these data demonstrate that IL-13 serves as an important mediator of Th2-mediated inflammation and plays a role in eliciting IgE responses triggered by schistosome eggs.
Correlation of tumor growth suppression and methionine aminopetidase-2 activity blockade using an orally active inhibitor (2008)

This laboratory and others have shown that agents that inhibit the in vitro catalytic activity of methionine aminopeptidase-2 (MetAP2) are effective in blocking angiogenesis and tumor growth in preclinical models. However, these prototype MetAP2 inhibitors are clearly not optimized for therapeutic use in the clinic. We have discovered an orally active class of MetAP2 inhibitors, the anthranilic acid sulfonamides exemplified by A-800141, which is highly specific for MetAP2. This orally bioavailable inhibitor exhibits an antiangiogenesis effect and a broad anticancer activity in a variety of tumor xenografts including B cell lymphoma, neuroblastoma, and prostate and colon carcinomas, either as a single agent or in combination with cytotoxic agents. We also have developed a biomarker assay to evaluate in vivo MetAP2 inhibition in circulating mononuclear cells and in tumors. This biomarker assay is based on the N-terminal methionine status of the MetAP2-specific substrate GAPDH in these cells. In cell cultures in vitro, the sulfonamide MetAP2 inhibitor A-800141 caused the formation of GAPDH variants with an unprocessed N-terminal methionine. A-800141 blocked tumor growth and MetAP2 activity in a similar dose-response in mouse models, demonstrating the antitumor effects seen for A-800141 are causally connected to MetAP2 inhibition in vivo. The sulfonamide MetAP2 inhibitor and GAPDH biomarker in circulating leukocytes may be used for the development of a cancer treatment.
Follow-up study of HER-2/neu amplification in primary breast cancer. (1991)

Amplification of the HER-2/neu oncogene was determined in 362 tumors from patients with primary breast cancer (185 node-positive patients and 177 node-negative patients). The overall amplification rate was 33% (30% for node-negative patients; 31% for patients with 1-3 positive nodes; 40% for patients with greater than 3 positive nodes). Gene copy number was not associated with axillary lymph node status, steroid receptor status, or patient age but was weakly correlated with the size of the primary tumor. Amplification of the HER-2/neu gene did not correlate with either disease-free or overall survival in univariate or multivariate analyses. The results were unambiguously negative for patients with node-negative disease. Although the univariate results for node-positive patients were marginally significant (P = 0.07), the significance was not retained in multivariate analyses. Thus, while HER-2/neu amplification may be biologically important in primary breast cancer, it will only be of marginal utility as a prognostic factor for predicting clinical outcome.
Immunofluorescence and Herpes-Type Virus Particles in the P3HR-1 Burkitt Lymphoma Cell Line (1967)

A subline of the P3 (Jijoye) Burkitt lymphoma cell line, designated P3HR-1, initially contained 1 to 5% of cells which were positive by indirect immunofluorescence with selected human sera. After 4 months of propagation, this cell line regularly showed 15 to 40% reactive cells. Antigen(s) in the cell line which was reactive by immunofluorescence was similar or identical to that found in several other Burkitt tumor cell lines in previous studies. When the cells were incubated at 35 or 32 C for 9 to 15 days without refeeding, more than 50% of the cells became immunofluorescence-positive. Thirteen different cultures of P3HR-1 cells, which contained up to 75% immunofluorescence-positive cells, were thin-sectioned and examined by electron microscopy. The percentage of cells containing herpes-type virus particles in the cultures varied from <3 to 78%. There was generally a good correlation between the number of immunofluorescent cells and the number of cells containing virus particles. The number of virus particles per cell section ranged from 1 to more than 100. These results strongly support the hypothesis that the immunofluorescent antigen is related to the presence of the herpes-type virus particle in the cells.
In line with our ancestors: Oct-4 and the mammalian germ (1998)

The transcription factor Oct-4 is expressed specifically in the totipotent germline cycle of mice. Cells that lose Oct-4 differentiate along different paths to form embryonic and extraembryonic somatic tissue. Oct-4 may maintain the potency of stem and germline cells by preventing all other differentiation pathways. Oct-4 may also regulate the molecular differentiation of cells in the germ lineage as it progresses from the fertilized egg, through cleavage stage/morula blastomeres, blastocyst, inner cell mass, epiblast, germ cells, and gametes. The factors that regulate, and are regulated by, Oct-4 are reviewed with respect to the phenomena of cell potency and germ/soma segregation and differentiation. BioEssays 20:722–732, 1998. © 1998 John Wiley & Sons, Inc.
FADS2 Function Loss at the Cancer Hotspot 11q13 Locus Diverts Lipid Signaling Precursor Synthesis to Unusual Eicosanoid Fatty Acids (2011)

The loss of FADS2-encoded activities in cancer cells shuts down normal PUFA biosynthesis, deleting the endogenous supply of eicosanoid and downstream docosanoid precursors, and replacing them with unusual butylene-interrupted fatty acids. If recapitulated in vivo, the normal eicosanoid and docosanoid cell signaling milieu would be depleted and altered due to reduction and substitution of normal substrates with unusual substrates, with unpredictable consequences for cellular communication.
Nanobody-Based Cancer Therapy of Solid Tumors (2015)

The development of tumor-targeted therapies using monoclonal antibodies has been successful during the last 30 years. Nevertheless, the efficacy of antibody-based therapy is still limited and further improvements are eagerly awaited. One of the promising novel developments that may overcome the drawbacks of monoclonal antibody-based therapies is the employment of nanobodies. Current nanobody-based therapeutics can be divided into three different platforms with nanobodies functioning as: receptor antagonists; targeting moieties of effector domains; or targeting molecules on the surface of nanoparticles. In this article, we describe factors that affect their performance at three different stages: their systemic circulation upon intravenous injection; their extravasation and tumor penetration; and, finally, their interaction with target molecules.
The therapeutic potential of antisense-mediated exon skipping. (2008)

Antisense-mediated exon skipping is an approach that uses antisense oligonucleotides (AONs) to modulate splicing by hiding specific sites essential for exon inclusion from the splicing machinery. AONs that block aberrant splice sites can restore normal splicing, whereas AONs targeting alternative splice sites can switch splicing patterns from detrimental to beneficial isoforms or produce non-functional mRNAs that lead to gene knockdown. Furthermore, AONs have also been used to restore a disrupted reading frame, thereby generating semi-functional proteins instead of non-functional proteins. Proof-of-concept has been obtained for each of the above AON applications in vitro and for some applications in vivo. Antisense-mediated reading frame restoration is the most promising therapy for Duchenne muscular dystrophy. Data from a first clinical trial are encouraging and additional trials are ongoing or are expected to be initiated soon.
Isolation and characterization of deletion mutants of herpes simplex virus type 1 in the gene encoding immediate-early regulatory protein ICP4 (1985)

Using Vero cells transformed with the wild-type gene for ICP4 as the permissive host cell, we isolated herpes simplex virus type 1 (HSV-1) mutants containing deletions in both copies of the ICP4 gene. The mutants, d120 and d202, contained deletions of 4.1 and 0.5 kilobases, respectively, in each copy of ICP4. ICP4 mRNA synthesized in d202-infected Vero cells was 0.5 kilobases smaller than that synthesized in cells infected with the wild-type virus. No ICP4 mRNA was detected in d120-infected Vero cells. d120 and d202 specified polypeptides that reacted with ICP4 antiserum and were smaller than the wild-type ICP4 polypeptide by 130 and 30 kilodaltons, respectively. The only other HSV-1 gene products detectable on infection of Vero cells with d120 and d202 were ICP6 (of the early kinetic class of HSV-1 polypeptides), ICP0 (immediate early), ICP22 (immediate early), and ICP27 (immediate early). Immediate-early polypeptides ICP0 and ICP27 were expressed to a higher level in Vero cells infected with an ICP4 temperature-sensitive (ts) mutant (tsB32) at 39 degrees C, indicating immediate-early stimulatory activity associated with the ts ICP4 polypeptide. In addition, the patterns of complementation of d120, d202, and tsB32 in ICP4-transformed cells also demonstrated inhibitory activity associated with the ts form of the ICP4 polypeptide.
Deviations from Expected Frequencies of CpG Dinucleotides in Herpesvirus DNAs May Be Diagnostic of Differences in the States of Their Latent Genomes (1989)

The DNA sequences of genomes from G + C-rich and A + T-rich lymphotropic herpesviruses [i.e. gammaherpesviruses; Epstein-Barr virus and herpesvirus saimiri (HVS)] are deficient in CpG dinucleotides and contain an excess of TpG and CpA dinucleotides relative to frequencies predicted from their mononucleotide compositions. In contrast, for sequences from genomes of G + C-rich and A + T-rich neurotropic herpesviruses (i.e. alphaherpesviruses; herpes simplex virus and varicellazoster virus) and human cytomegalovirus (HCMV; a betaherpesvirus) the mean observed frequencies of these dinucleotides are close to those expected from their mononucleotide compositions. Comparisons between DNA sequences that encode proteins conserved in all these viruses also show that sequences of these lymphotropic viruses are CpG-deficient whereas the homologous genes from the neurotropic viruses and the HCMV are not. Analyses of local variations in dinucleotide frequencies reveal some occurrences of clustered CpG dinucleotides in generally deficient genomes (e.g. upstream of the thymidylate synthase gene of HVS) and locally CpG-deficient regions within some generally non-deficient genomes (e.g. the major immediate early genes of human, simian and murine CMVs). A relative deficiency in CpG and an excess of TpG and CpA dinucleotides is a diagnostic feature of higher eukaryotic DNA sequences that have been subjected to methylation of cytosine residues in CpG doublets with the resulting increase in mutations to give TpG (and thereby its complement, CpA). The available evidence implicates the latent genome as the site of methylation of these herpesviruses. We conclude that in the neurotropic herpesviruses the normal latent precursors to infectious progeny are not methylated whereas there is local methylation of the immediate early locus in the latent genomes of CMVs, and the latent genomes of these lymphotropic herpesviruses are extensively methylated.
Induction of cataract-like changes in rat lens epithelial explants by transforming growth factor beta. (1994)

First, these results suggest a role for TGF beta in regulating normal processes in lens cells such as the production of extracellular matrix and capsule formation. Second, because many of the changes induced by TGF beta resembled changes reported to occur during the formation of various kinds of subcapsular cataracts, the results suggest that detailed studies of factors that influence the ability of lens cells to respond to TGF beta and the bioavailability of TGF beta in the ocular media may provide important insights into the etiology of some forms of cataract.