gebhart/patrepeval huggingface dataset:
Promiscuous patching of broken chromosomes in mammalian cells with extrachromosomal DNA (2001)

To study double-strand break (DSB)-induced mutations in mammalian chromosomes, we stably transfected thymidine kinase (tk)-deficient mouse fibroblasts with a DNA substrate containing a recognition site for yeast endonuclease I-SceI embedded within a functional tk gene. Cells were then electroporated with a plasmid expressing endonuclease I-SceI to induce a DSB, and clones that had lost tk function were selected. In a previous study of DSB-induced tk-deficient clones, we found that approximately 8% of recovered tk mutations involved the capture of one or more DNA fragments at the DSB site. Almost half of the DNA capture events involved the I-SceI expression plasmid, and several events involved retrotransposable elements. To learn whether only certain DNA sequences or motifs are efficiently captured, in the current work we electroporated an I-SceI expression plasmid along with HaeIII fragments of &phi;X174 genomic DNA. We report that 18 out of 132 tk-deficient clones recovered had captured DNA fragments, and 14 DNA capture events involved one or more fragments of &phi;X174 DNA. Microhomology existed at most junctions between &phi;X174 DNA and genomic sequences. Our work suggests that virtually any extrachromosomal DNA molecule may be recruited for the patching of DSBs in a mammalian genome.
The frequent Marburg I polymorphism impairs the pro-urokinase activating potency of the factor VII activating protease (FSAP) (2002)

The recently reported plasmatic, Factor Seven Activating Protease (FSAP), has also been found to be a potent activator of pro-urokinase [single-chain plasminogen activator, urinary type (scuPA)]. An initial epidemiological study surprisingly showed that plasmas of 5-10% of healthy blood donors had an impaired potential to activate scuPA. Analysis of the respective genomic DNAs revealed one particular single nucleotide polymorphism of FSAP resulting in an identical amino acid exchange (G511E), which correlates with the reduced activities. The corresponding mutation was named FSAP Marburg I. Thrombelastographies of wild-type and mutant plasmas were performed, facilitating the auto-activation of the intrinsic FSAP pro-enzymes by addition of dextran sulfate (DXS) and accelerated clot lysis by addition of scuPA. On these conditions, tissue-factor-induced coagulation revealed that clot lysis was significantly delayed in the Marburg I mutant plasmas as compared with wild-type plasmas. Furthermore, in the presence of DXS and scuPA, a FSAP-deficient plasma revealed significantly prolonged plasma clot lysis times, whereas the addition of purified FSAP pro-enzyme plus scuPA reversed this effect. These results support the hypothesis that FSAP contributes to the scuPA-dependent plasma fibrinolytic potential, which can be impaired in plasmas containing the FSAP Marburg I polymorphism, for instance.
Molecular Pharmacological approach reveals potential new strategies to suppress androgen receptor signaling in prostate cancer (2011)

Androgen receptor (AR) plays a pivotal role in growth and survival of prostate cancer cells. Currently, androgen deprivation therapy is a standard approach to manage advanced and metastatic prostate cancer. In most patients, however, relapse eventually occurs and so far, only few treatment options are available to manage recurrence. Previous studies have demonstrated that, in hormone-refractory prostate cancer (HRPC), various mechanisms affect AR including overexpresssion, mutations and alternative splicing. These alterations can lead to androgen-independent AR activation or resistance to antiandrogen-mediated AR inhibition. In many cases, HRPC growth is still dependent on AR and therefore, AR inhibition by alternative methods would be a rational strategy to treat HRPC. Our recent work indicated that simultaneous inhibition of multiple forms of AR via small interfering RNA (siRNA)-mediated knockdown or by treatment with nigericin, an antibiotic derived from Streptomyces hygroscopicus , resulted in efficient growth suppression of HRPC. These data indicated that the inhibition of AR expression at the mRNA level could be an effective strategy to block a wide range of AR mutants or variants that are expressed in HRPC. Our chemical screening additionally identified new inhibitors of the AR-mediated signaling, such as SU1498 that is an inhibitor of vascular endothelial growth factor receptor 2 and 5-azacytidine that inhibits DNA methyltransferase. Collectively, these results provide novel potential strategies to suppress androgen receptor signaling in prostate cancer cells.
Marrow stromal cells form guiding strands in the injured spinal cord and promote recovery (2002)

Marrow stromal cells (MSC) can be expanded rapidly in vitro and differentiated into multiple mesodermal cell types. In addition, differentiation into neuron-like cells expressing markers typical for mature neurons has been reported. To analyze whether such cells, exposed to differentiation media, could develop electrophysiological properties characteristic of neurons, we performed whole-cell recordings. Neuron-like MSC, however, lacked voltage-gated ion channels necessary for generation of action potentials. We then delivered MSC into the injured spinal cord to study the fate of transplanted MSC and possible effects on functional outcome in animals rendered paraplegic. MSC given 1 week after injury led to significantly larger numbers of surviving cells than immediate treatment and significant improvements of gait. Histology 5 weeks after spinal cord injury revealed that MSC were tightly associated with longitudinally arranged immature astrocytes and formed bundles bridging the epicenter of the injury. Robust bundles of neurofilament-positive fibers and some 5-hydroxytryptamine-positive fibers were found mainly at the interface between graft and scar tissue. MSC constitute an easily accessible, easily expandable source of cells that may prove useful in the establishment of spinal cord repair protocols.
Mechanism of first-dose cytokine-release syndrome by CAMPATH 1-H: involvement of CD16 (FcgammaRIII) and CD11a/CD18 (LFA-1) on NK cells. (1996)

The administration of the immunosuppressive humanized monoclonal antibody CAMPATH 1-H, which recognizes CD52 on lymphocytes and monocytes, is associated with a first-dose cytokine-release syndrome involving TNFalpha, IFNgamma, and IL-6 clinically. In vitro models have been used to establish the cellular source and mechanism responsible for cytokine release, demonstrating that cytokine release is isotype dependent, with the rat IgG2b and human IgG1 isotype inducing the highest levels of cytokine release, which was inhibited with antibody to CD16, the low affinity Fc-receptor for IgG (FcgammaR). Cross-linking antibody opsonized CD4 T lymphocytes failed to stimulate TNFalpha release, which together with the observation that TNFalpha release by purified natural killer (NK) cells stimulated by fixed autologous CAMPATH 1-H-opsonized targets was inhibited with anti-CD16, indicates that cytokine release results from ligation of CD16 on the NK cells, rather than Fc-receptor (FcR)-dependent cross-linking of CD52 on the targeted cell. Since the hierarchy of isotypes inducing cytokine release in these cultures matches that seen clinically, we conclude that ligation of CD16 on NK cells is also responsible for cytokine release after injection of CAMPATH 1-H in vivo.
Activation of G12/G13 Results in Shape Change and Rho/Rho-Kinase–mediated Myosin Light Chain Phosphorylation in Mouse Platelets (1999)

Platelets respond to various stimuli with rapid changes in shape followed by aggregation and secretion of their granule contents. Platelets lacking the alpha-subunit of the heterotrimeric G protein Gq do not aggregate and degranulate but still undergo shape change after activation through thromboxane-A2 (TXA2) or thrombin receptors. In contrast to thrombin, the TXA2 mimetic U46619 led to the selective activation of G12 and G13 in Galphaq-deficient platelets indicating that these G proteins mediate TXA2 receptor-induced shape change. TXA2 receptor-mediated activation of G12/G13 resulted in tyrosine phosphorylation of pp72(syk) and stimulation of pp60(c-src) as well as in phosphorylation of myosin light chain (MLC) in Galphaq-deficient platelets. Both MLC phosphorylation and shape change induced through G12/G13 in the absence of Galphaq were inhibited by the C3 exoenzyme from Clostridium botulinum, by the Rho-kinase inhibitor Y-27632 and by cAMP-analogue Sp-5,6-DCl-cBIMPS. These data indicate that G12/G13 couple receptors to tyrosine kinases as well as to the Rho/Rho-kinase-mediated regulation of MLC phosphorylation. We provide evidence that G12/G13-mediated Rho/Rho-kinase-dependent regulation of MLC phosphorylation participates in receptor-induced platelet shape change.
Angiopoietin 2 expression in the retina: upregulation during physiologic and pathologic neovascularization (2000)

Vascular development in the embryo requires coordinated signaling through several endothelial cell-specific receptors; however, it is not known whether this is also required later during retinal vascular development or as part of retinal neovascularization in adults. The Tie2 receptor has been implicated in stabilization and maturation of vessels through action of an agonist ligand, angiopoietin 1 (Ang1) and an antagonistic ligand, Ang2. In this study, we have demonstrated that ang2 mRNA levels are increased in the retina during development of the deep retinal capillaries by angiogenesis and during pathologic angiogenesis in a model of ischemic retinopathy. Mice with hemizygous disruption of the ang2 gene by insertion of a promoterless β-galactosidase (βgal) gene behind the ang2 promoter, show constitutive βgal staining primarily in cells along the outer border of the inner nuclear layer identified as horizontal cells by colocalization of calbindin. During development of the deep capillary bed or retinal neovascularization, other cells in the inner nuclear layer and ganglion cell layer, in regions of neovascularization, stain for βgal. Thus, there is temporal and spatial correlation of Ang2 expression with developmental and pathologic angiogenesis in the retina, suggesting that it may play a role. J. Cell. Physiol. 184:275–284, 2000. © 2000 Wiley-Liss, Inc.
BET Bromodomain Inhibitors Block Growth of Pancreatic Cancer Cells in Three-Dimensional Collagen (2014)

Pancreatic ductal adenocarcinoma (PDAC) is associated with pronounced fibrosis that contributes to chemoresistance, in part, through increased histone acetylation. Because bromodomain (BRD) and extra terminal domain (BET) proteins are "readers" of histone acetylation marks, we targeted BET proteins in PDAC cells grown in three-dimensional collagen. We show that treatment with BET inhibitors decreases growth of PDAC cells (AsPC1, CD18, and Panc1) in collagen. Transfection with siRNA against BRD4, which is increased in human PDAC tumors, also decreases growth of PDAC cells. BET inhibitors additionally decrease growth in collagen of PDAC cells that have undergone epithelial-to-mesenchymal transition or have become resistant to chemotherapy. Although BET inhibitors and BRD4 siRNA repress c-MYC only in AsPC1 and CD18 cells, downregulating c-MYC decreases growth of all three PDAC cell lines in collagen. FOSL1, which is also targeted by BET inhibitors and BRD4 siRNA in AsPC1, CD18, and Panc1 cells, additionally regulates growth of all three PDAC cell lines in collagen. BET inhibitors and BRD4 siRNA repress HMGA2, an architectural protein that modulates chromatin state and also contributes to chemoresistance, in PDAC cells grown in collagen. Importantly, we show that there is a statistically significant correlation between BRD4 and HMGA2 in human PDAC tumors. Significantly, overexpression of HMGA2 partially mitigates the effect of BET inhibitors on growth and c-MYC and/or FOSL1 expression in collagen. Overall, these results demonstrate that BET inhibitors block growth of PDAC cells in collagen and that BET proteins may be potential targets for the treatment of pancreatic cancer.
Policy hierarchies for distributed systems management (1993)

Distributed system management, involves monitoring the activity of a system, making management decisions and performing control actions to modify the behavior of the system. Most of the research on management has concentrated on management mechanisms related to network management or operating systems. However, in order to automate the management of very large distributed systems, it is necessary to be able to represent and manipulate management policy within the system. These objectives are typically set out in the form of general policies which require detailed interpretation by the system managers. The paper explores the refinement of general high-level policies into a number of more specific policies to form a policy hierarchy in which each policy in the hierarchy represents, to its maker, his plans to meet his objectives and, to its subject, the objectives which he must plan to meet. Management action policies are introduced, and the distinction between imperatival and authority policies is made. The relationship of hierarchies of imperatival policies to responsibility, and to authority policies, is discussed. An outline approach to the provision of automated support for the analysis of policy hierarchies is provided, by means of a more formal definition of policy hierarchy refinement relationships in Prolog.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
p15, A nuclear‐associated protein of human sperm: Identification of four variants and their occurrence in normal and abnormal seminal cells (1983)

Abstract A basic protein of apparent molecular weight 15,000 d (p15) has been identified as a tissue‐specific species‐unique component of spermatogenic cells of human semen. Cytoimmunochemical study with a monoclonal antibody indicates that p15 resides in a perinuclear space in morphologically normal spermatozoa and differs in distribution and stat in abnormal seminal cell and nonnucleated bodeis. Biochemical analysis indicateds that p15 occurs as four variiants, differentially migratory on acetic acid/urea gel and differnetially extractable by NaCl in reducing solution. By correlation of the cytologic and biochemical data, we propose that variant 1 is the unmodified form of p15; in the normal progression of spermiogenesis p15 is modified to variants 2 and 3 and in the absence of the normal progression is unmodified or aberrantly modified to variant 4. The association of molecular abnormality in p15 with morphologically abnormal sperm suggests that p15 may play a role in sperm‐head shaping.
Receptor-mediated monocytoid differentiation of human promyelocytic cells by tumor necrosis factor: synergistic actions with interferon- gamma and 1,25-dihydroxyvitamin D3 [published erratum appears in Blood 1988 Jan;71(1):272] (1987)

Human myeloid leukemia cells respond to various signals by differentiating to more mature cells. This study was designed to evaluate the effects of a mononuclear phagocyte-derived factor, tumor necrosis factor/cachectin (TNF), on the proliferation and differentiation of the human cell lines HL-60 (promyelocytic) and U937 (monoblastic), and to characterize TNF receptors on these cells. TNF had no effect on HL-60 cell growth or thymidine incorporation, but it markedly inhibited that of U937 cells. HL-60 cells treated with TNF formed osteoclast-like polykaryons and developed nonspecific esterase positivity. In a dose-dependent fashion, TNF enhanced HL-60 cell nonspecific esterase activity, H2O2 production, NBT reduction, and acid phosphatase content. Together, TNF and interferon-gamma (IFN-gamma) additively and synergistically caused increases in these activities as well as the expression of HLA-DR and the monocyte antigens LeuM3 (CDw14) and OKM1 (CD11). TNF also synergistically enhanced the differentiating effects of 1,25-dihydroxyvitamin D3. The potentiating actions of D3 of IFN-gamma on the TNF effect were maximal when the two agents were present together throughout the incubation, and pretreatment with TNF augmented the subsequent response to D3, but not IFN-gamma. HL-60 and U937 cells bound 125I-labeled TNF specifically, rapidly, and reversibly with binding constants of 227 and 333 pmol/L and receptors per cell of 4,435 and 6,806 for HL-60 and U937, respectively. Scatchard plots were linear, which suggested single classes of receptors. HL-60 TNF receptors were not changed by a three-day treatment with IFN-gamma or D3. U937 and HL-60 cells internalized and degraded 125I-labeled TNF to comparable degrees. TNF has differing effects on HL-60 and U937 cells that are apparently mediated through comparable high-affinity TNF receptors. The unique responses of different cell types to TNF may be due to postreceptor factors.
The amino acid sequence of radioimmunoassayable neurotensin from bovine intestine. (1978)

The amino acid sequence of radioimmunoassayable neurotensin, isolated from bovine small intestinal extracts, has been shown to be the same as that of the peptide originally isolated from bovine hypothalamic extracts. This was accomplished by sequence studies on the intact peptide as well as on its chymotryptic and papain-generated fragments. Thus, neurotensin joins the group of biologically active peptides shown to be present in the same molecular form in both brain and intestine.
Geoacoustic inversion via local, global, and hybrid algorithms (1999)

In this paper, local, global, and hybrid inversion algorithms are developed and applied to the problem of determining geoacoustic properties by minimizing the mismatch between measured and modeled acoustic fields. Local inversion methods are sensitive to gradients in the mismatch and move effectively downhill, but generally become trapped in local minima and must be initiated from a large number of starting points. Global inversion methods use a directed random process to search the parameter space for the optimal solution. They include the ability to escape from local minima, but as no gradient information is used, the search can be relatively inefficient. Hybrid inversion methods combine local and global approaches to produce a more efficient and effective algorithm. Here, downhill simplex (local) and simulated annealing (global) methods are developed individually and combined to produce a hybrid simplex simulated annealing algorithm. The hybrid inversion is found to be faster by more than an order of magnitude for a benchmark testcase in which the form of the geoacoustic model is known. The hybrid inversion algorithm is also applied to a testcase consisting of an unknown number of layers representing a general geoacoustic profile. Since the form of the model is not known, an underparameterized approach is employed to determine a minimum-structure solution.
Fimbrial adhesins: similarities and variations in structure and biogenesis (1996)

Fimbriae are wiry (2 to 4 nm diam.) or rod-shaped (6 to 8 nm diam.), fibre-like structures on the surfaces of bacteria which mediate attachment to host cells. Much has been learned in recent years about the biogenesis, structure and regulation of expression of these adhesive organelles in Gram-negative bacteria. Analyses of the genetic determinants encoding the biogenesis of fimbriae has revealed that the adhesive interaction of fimbriae can be mediated by major subunits (CFA/I and CS1 fimbriae) or minor subunits (P, S, and type 1 fimbriae), with the adhesin being located either at the tip of the fimbria or along the length of the fimbrial shaft. Minor subunits can also act as adapters, anchors, initiators or elongators. Post-translational glycosylation of the type 4 pilins of Neisseria gonorrhoeae, Neisseria meningitidis and Pseudomonas aeruginosa has been demonstrated. The structures of the PapD chaperone of Escherichia coli and of N. gonorrhoeae type 4 fimbrin have been resolved at 2.0-2.6 A. Rod-shaped fimbriae should not be thought of as being rigid inflexible structures but rather as dynamic structures which can undergo transition from a helicoidal to a fibrillar conformation to provide a degree of elasticity and plasticity to the fimbriae so that they can resist shear forces, rather like a bungee cord. At least four mechanisms have been identified in the assembly of fimbriae from fimbrin subunits, namely the chaperone-usher pathway (e.g., P-fimbriae of uropathogenic E. coli), the general secretion assembly pathway (e.g., type 4 fimbriae or N-methylphenylalanine fimbriae of P. aeruginosa, the extracellular nucleation-precipitation pathway (e.g., curli of E. coli) and the CFA/I, CS1 and CS2 fimbrial pathway.
A Combinatorial System for Cloning and Expressing the Catalytic Antibody Repertoire in Escherichia coli (1989)

Hybridoma monoclonal antibody technology is one of the fundamental techniques for the study of biological macromolecules (Lerner 1984). Monoclonal antibodies are used for important applications such as clinical diagnosis, immunofluorescence, cell sorting, gene product analysis, and many other techniques. Recently, a new technology involving catalytic monoclonal antibodies has appeared. This quickly evolving field combines the programmable specificity of antibody binding with chemical catalysis (Lerner and Benkovic 1988). Several of the reactions catalyzed with antibodies are listed in Figure 1.
The chemokine SDF1 regulates migration of dentate granule cells (2002)

The dentate gyrus is the primary afferent pathway into the hippocampus, but there is little information concerning the molecular influences that govern its formation. In particular, the control of migration and cell positioning of dentate granule cells is not clear. We have characterized more fully the timing and route of granule cell migration during embryogenesis using in utero retroviral injections. Using this information, we developed an in vitro assay that faithfully recapitulates important events in dentate gyrus morphogenesis. In searching for candidate ligands that may regulate dentate granule cell migration, we found that SDF1, a chemokine that regulates cerebellar and leukocyte migration, and its receptor CXCR4 are expressed in patterns that suggest a role in dentate granule cell migration. Furthermore, CXCR4 mutant mice have a defect in granule cell position. Ectopic expression of SDF1 in our explant assay showed that it directly regulates dentate granule cell migration. Our study shows that a chemokine is necessary for the normal development of the dentate gyrus, a forebrain structure crucial for learning and memory.
Generation of HIV Latency in Humanized BLT Mice (2011)

Here we demonstrate that a combination of tenofovir, emtricitabine, and raltegravir effectively suppresses peripheral and systemic HIV replication in humanized BLT mice. We also demonstrate that antiretroviral therapy (ART)-treated humanized BLT mice harbor latently infected resting human CD4+ T cells that can be induced ex vivo to produce HIV. We observed that the levels of infected resting human CD4+ T cells present in BLT mice are within the range of those observed circulating in patients undergoing suppressive ART. These results demonstrate the potential of humanized BLT mice as an attractive model for testing the in vivo efficacy of novel HIV eradication strategies.