gebhart/patrepeval huggingface dataset:
Replication, Integration, and Packaging of Plasmid DNA following Cotransfection with Baculovirus Viral DNA (1999)

Infection-dependent replication assays have been used to identify numerous putative origins of baculovirus replication. However, plasmid DNA, when cotransfected into insect cells with Autographa californica multinucleocapsid nucleopolyhedrovirus (AcMNPV) DNA, replicates independently of any viral sequence in cis (11). Cotransfection of transfer plasmids and baculovirus DNA is a common procedure used in generating recombinant viruses and in measuring the level of gene expression in transient-expression assays. We have examined the fate of a series of vector plasmids in cotransfection experiments. The data reveal that these plasmids replicate following cotransfection and the replication of plasmid DNA is not due to acquisition of viral putative origin sequences. The conformation of plasmid DNA replicating in the cotransfected cells was analyzed and found to exist as high-molecular-weight concatemers. Ten to 25% of the replicated plasmid DNA was integrated into multiple locations on the viral genome and was present in progeny virions following serial passage. Sequence analysis of plasmid-viral DNA junction sites revealed no homologous or conserved sequences in the proximity of the integration sites, suggesting that nonhomologous recombination was involved during the integration process. These data suggest that while a rolling-circle mechanism could be used for baculovirus DNA replication, recombination may also be involved in this process. Plasmid integration may generate large deletions of the viral genome, suggesting that the process of DNA replication in baculovirus may be prone to generation of defective genomes.
l -Serine Deaminase of Escherichia coli (1968)

The native l-serine deaminase (l-serine hydrolyase, deaminating, EC 4.2.1.13) of Escherichia coli K-12, which seems to be a very labile protein, is rather stable in concentrated solution. Dilution rapidly inactivates it, but in the presence of a saturating concentration of l-serine the molecule is protected from inactivation. It is a very specific enzyme; l-serine is the sole substrate with a K(m) value of 6.60 x 10(-3)m. d-Serine and l-cysteine are competitive inhibitors. Substrate saturation curves of the native enzyme show sigmoid shape, whereas the enzyme liberated from the bacteria in the presence of l-serine exhibits normal Michaelis-Menten kinetics.
A new method of colorectal anastomosis in abdominoperineal resection (1961)

Summary and Conclusions A new technic of colorectal anastomosis in abdominoperineal rectosigmoidectomy is presented. Justification of this technic is based on the principle of “adhesion by contact between the muscular surface of the everted rectum and the serosa surface of the pulled colon, and in the suture of the mucosa coat of the rectum to the mucosa coat of the colon.” The anastomosis is performed in two stages. The results obtained on 40 patients with acquired megacolon and on five with cancer of the rectum and rectosigmoid are described. There was a gratifying reduction in the incidence of disruption of the anastomosis.
A influência das questões candentes contemporâneas para a identidade da Igreja Evangélica de Confissão Luterana no Brasil (2010)

In a time of great transformation in the religious scenario, the IECLB has been trying to be faithful about its self-understanding, but without ignoring the signs of its context. Briefly, the present article presents the ethical scope in which the IECLB lines up its position in the conceptual scenario inside and outside the Christian community. The second point is about mission aspects, in which the church takes its prophetic role in a proactive way. The third part brings the issue of sustainability as a concern related to the maintenance of the structure of the church and the means to make possible its growth. The ecumenical commitment and the diakonia appear as two further circles in which the identity of the IECLB is renewed today.
Diffusion Tensor MR Imaging and Fiber Tractography: Theoretic Underpinnings (2008)

In this article, the underlying theory of clinical diffusion MR imaging, including diffusion tensor imaging (DTI) and fiber tractography, is reviewed. First, a brief explanation of the basic physics of diffusion-weighted imaging (DWI) and apparent diffusion coefficient (ADC) mapping is provided. This is followed by an overview of the additional information that can be derived from the diffusion tensor, including diffusion anisotropy, color-encoded fiber orientation maps, and 3D fiber tractography. This article provides the requisite background for the second article in this 2-part review to appear next month, which covers the major technical factors that affect image quality in diffusion MR imaging, including the acquisition sequence, magnet field strength, gradient amplitude and slew rate, and multichannel radio-frequency coils and parallel imaging. The emphasis is on optimizing these factors for state-of-the-art DWI and DTI based on the best available evidence in the literature.
Development of an Expedient Process for the Multi-Kilogram Synthesis of Chk1 Inhibitor GDC-0425 (2015)

A process leading to the multikilogram GMP synthesis of Chk1 inhibitor GDC-0425 (1) was developed. Highlights of the synthesis include protection of the pyrrole ring of a 1,7-diazacarbazole as propyl ethyl ether, an efficient Pd catalyzed cyanation of an aryl chloride, aryl ether formation by SNAr fluoride displacement, and development of a controlled crystallization providing the API with the required polymorphic form. The process delivered high-quality GDC-0425 with low levels of impurities and residual metals in five steps and 31% overall yield.
Terpenoids and Their Biosynthesis in Cyanobacteria (2015)

Terpenoids, or isoprenoids, are a family of compounds with great structural diversity which are essential for all living organisms. In cyanobacteria, they are synthesized from the methylerythritol-phosphate (MEP) pathway, using glyceraldehyde 3-phosphate and pyruvate produced by photosynthesis as substrates. The products of the MEP pathway are the isomeric five-carbon compounds isopentenyl diphosphate and dimethylallyl diphosphate, which in turn form the basic building blocks for formation of all terpenoids. Many terpenoid compounds have useful properties and are of interest in the fields of pharmaceuticals and nutrition, and even potentially as future biofuels. The MEP pathway, its function and regulation, and the subsequent formation of terpenoids have not been fully elucidated in cyanobacteria, despite its relevance for biotechnological applications. In this review, we summarize the present knowledge about cyanobacterial terpenoid biosynthesis, both regarding the native metabolism and regarding metabolic engineering of cyanobacteria for heterologous production of non-native terpenoids.
Strategies for quantum computing molecular energies using the unitary coupled cluster ansatz (2018)

Abstract The variational quantum eigensolver (VQE) algorithm combines the ability of quantum computers to efficiently compute expectation values with a classical optimization routine in order to approximate ground state energies of quantum systems. In this paper, we study the application of VQE to the simulation of molecular energies using the unitary coupled cluster (UCC) ansatz. We introduce new strategies to reduce the circuit depth for the implementation of UCC and improve the optimization of the wavefunction based on efficient classical approximations of the cluster amplitudes. Additionally, we propose an analytical method to compute the energy gradient that reduces the sampling cost for gradient estimation by several orders of magnitude compared to numerical gradients. We illustrate our methodology with numerical simulations for a system of four hydrogen atoms that exhibit strong correlation and show that the circuit depth of VQE using a UCC ansatz can be reduced without introducing significant loss of accuracy in the final wavefunctions and energies.
Tinmith - mobile outdoor augmented reality modelling demonstration (2004)

This paper outlines some of the capabilities of the Tinmith-Metro modeling system, based on mobile outdoor augmented reality technology. This system implements a new user interface based on tracked pinch gloves and a series of techniques named construction at a distance for the capture and creation of 3D geometry. The user controls the modeling process using hand and head motions, with modelling accuracy guided by the requirements of the user. Using Tinmith-Metro, users are able to model outdoor geometry representing buildings and natural features in an intuitive fashion.
Vertical cavity SOAs (2004)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text J. Bowers, "Vertical cavity SOAs," in Optical Amplifiers and Their Applications/Integrated Photonics Research, Technical Digest (CD) (Optica Publishing Group, 2004), paper OMB1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
The Structural Biology of CD2 (1989)

The CD2 molecule is a 50-55KD transmembrane glycoprotein expressed on the vast majority of thymocytes and virtually all peripheral T lymphocytes. Its functions are two-fold: adhesion and activation. CD2 serves to facilitate conjugate formation between the T-lineage cell and its cognate partner via intermolecular interaction of CD2 and LFA-3 on the former and latter cells, respectively. Perturbation of the CD2 extracellular segment by certain combinations of anti-CD2 MAbs or LFA-3 and a single anti-CD2 MAb activate T-lineage function. These CD2-mediated activation events also synergize with signals mediated through the TCR to augment T-cell response. Based on microchemical analysis of immunoaffinity-purified human CD2 and cDNA and genomic cloning of mouse and human molecules, considerable structural information is now available. The mature surface human CD2 molecule consists of 327 amino acids: a 185 aa extracellular segment; a 25 aa hydrophobic transmembrane segment; and a 117 aa cytoplasmic domain rich in prolines and basic residues. The CD2 gene is comprised of five exons which span approximately 12 Kb on chromosome 1. A similar protein structure and gene exon organization is found for the mouse CD2 homologue. The CD2 adhesion domain is approximately 103 aa in length and is encoded by a single exon (exon 2). This domain is resistant to proteolysis, even though it lacks any intrachain disulfides and, like the entire extracellular segment protein expressed in a baculovirus system, binds to its cellular ligand, LFA-3. The latter occurs with a micromolar Kd. This relatively low affinity suggests that multivalent interactions among CD2 monomers on the T cells and individual LFA-3 structures on the cognate partner are important in enhancing the avidity of the T-cell interaction with its target or stimulator cell. The affinity of the CD2 extracellular segment for LFA-3 is not affected by truncations in the CD2 cytoplasmic domain, implying that ligand binding is not regulated by intracellular mechanisms. Given that CD2 mRNA expression and surface CD2 copy number are increased by more than one order of magnitude post-TCR stimulation, it is more likely that adhesion via CD2 is modulated by alteration in surface copy number. Analysis of early transduction events occurring via CD3-Ti (TCR) and CD2 including single channel Ca2+ patch-clamp recordings on living human T lymphocytes indicate a virtual identity of signals.(ABSTRACT TRUNCATED AT 400 WORDS)
Screening for trisomy 13 by fetal nuchal translucency and maternal serum free ?-hCG and PAPP-A at 10-14 weeks of gestation (2000)

In 42 cases of trisomy 13 at 10–14 weeks of gestation, compared with 947 controls, the median multiple of the median (MoM) of maternal serum free β-human chorionic gonadotrophin (β-hCG) and pregnancy associated plasma protein A (PAPP-A) was significantly decreased (0.506 MoM and 0.248 MoM respectively), whilst fetal nuchal translucency was increased (2.872 MoM). In 38% and 71% of cases of trisomy 13 maternal serum free β-hCG and PAPP-A was below the 5th centile of the appropriate normal range for gestation and in 62% of cases the nuchal translucency was above the 95th centile. When combined together in a multivariate algorithm with maternal age, 90% of cases of trisomy 13 could be detected at a 0.5% false positive rate or 84% at a 0.1% false positive rate. We conclude that specific trisomy 13 risks should be part of developing risk algorithms combining maternal serum biochemistry and nuchal translucency for use in first trimester screening alongside those for trisomy 21 and trisomy 18. Copyright © 2000 John Wiley & Sons, Ltd.
Cutting Edge: Tumor Secreted Heat Shock-Fusion Protein Elicits CD8 Cells for Rejection (1999)

The endoplasmic reticulum resident heat shock protein gp96 chaperons peptides, including those derived from tumor Ags, on their way to presentation by MHC class I. Replacement of the endoplasmic reticulum retention signal of gp96 with the Fc portion of murine IgG1 generated a secretory form of gp96, gp96-Ig. Tumor cells secreting gp96-Ig exhibited decreased tumorigenicity and increased immunogenicity in vivo and were rejected after initial growth. Rejection required CD8 T cells during the priming and effector phase. CD4 T cells were not required for rejection in either phase. Carrageenan, a compound known to inactivate macrophages in vivo, did not diminish CD8-mediated tumor rejection. Therefore, immunization with tumors secreting gp96-Ig generates efficient tumor-rejecting CD8 CTL without requirement for CD4 or macrophage help. In contrast, immunization with purified, tumor-derived gp96 or with irradiated tumor cells requires both.
Between-lot variability in chromatographic and biochemical properties of hMG (1990)

Ten lots of dissociated hMG were characterized by reverse-phase gradient high-performance liquid chromatography. Areas of 12 discrete peaks were directly related to dosages of hMG injected. The lots were further analysed for immunoactive-FSH (41.6-106.2 IU/ampule), immunoactive-LH (11.0-20.4 IU/ampule), bioactive-LH (2.7-17.1 IU/ampule) and bioactive-hMG (149-298 pg E2/mIU immunoactive-FSH/ml). Relationships between integrated areas of the HPLC peaks and biochemical properties of the hMG lots were analysed by stepwise multiple linear regression. Between-lot differences in immunoactive-LH and immunoactive-FSH were related to HPLC peak areas (p less than 0.05); differences in bioactive-LH were not. Areas of 8 peaks were related to differences in bioactive-hMG activity, facilitating close approximation of bioactive-hMG from the derived multi-linear model (p less than 0.001). Rapid characterization of hMG by HPLC is of relevance as recent reports have shown that ovarian responses and pregnancy outcomes of patients are related to the immunoactive and bioactive gonadotropin content of hMG preparations used to induce multiple folliculogenesis before oocyte aspiration, in vitro fertilization, and embryo replacement.
Sequence and expression of a membrane-associated C-type lectin that exhibits CD4-independent binding of human immunodeficiency virus envelope glycoprotein gp120. (1992)

The binding of the human immunodeficiency virus (HIV) envelope glycoprotein gp120 to the cell surface receptor CD4 has been considered a primary determinant of viral tropism. A number of cell types, however, can be infected by the virus, or bind gp120, in the absence of CD4 expression. Human placenta was identified as a tissue that binds gp120 in a CD4-independent manner. A placental cDNA library was screened by expression cloning and a cDNA (clone 11) encoding a gp120-binding protein unrelated to CD4 was isolated. The 1.3-kilobase cDNA predicts a protein of 404 amino acids with a calculated M(r) of 45,775 and organized into three domains: an N-terminal cytoplasmic and hydrophobic region, a set of seven complete and one incomplete tandem repeat, and a C-terminal domain with homology to C-type (calcium-dependent) lectins. A type II membrane orientation (N-terminal cytoplasmic) is predicted both by the cDNA sequence and by the reactivity of C-terminal peptide-specific antiserum with the surface of clone 11 transfected cells. Native and recombinant gp120 and whole virus bind transfected cells. gp120 binding is high affinity (kd, 1.3-1.6 nM) and inhibited by mannan, D-mannose, and L-fucose; once bound, gp120 is internalized rapidly. Collectively, these data demonstrate that the gp120-binding protein is a membrane-associated mannose-binding lectin. Proteins of this type may play an important role in the CD4-independent association of HIV with cells.
Deviation of the Allergic IgE to an IgG Response by Gene Immunotherapy (1999)

The Th1/Th2 type immune response to E. coli beta-galactosidase (beta-gal) was compared to that to gene vaccination with plasmid (p) DNA encoding beta-gal. BALB/c mice were immunized with beta-gal in alum or a pDNA construct consisting of a CMV-based promoter and the beta-gal gene (pCMV-LacZ). Beta-gal in alum induced IgG1 and IgE antibodies and the CD4+ T cells from these mice secreted interleukin 4 (IL-4) and IL-5 but no interferon-gamma (IFN-gamma) after in vitro antigen stimulation. In contrast, mice immunized with pCMV-LacZ formed predominantly IgG2a antibodies and their CD4+ T cells secreted IFN-gamma but no IL-4 and IL-5. These data indicate that beta-gal induced a Th2 and the pCMV-LacZ a Th1 response to beta-gal. The pDNA induced Th1 response dominated over the Th2 response. Mice primed with pCMV-LacZ failed to produce IgE antibodies after a booster injection of beta-gal in alum. Boosting of mice primed with beta-gal in alum with pCMV-LacZ resulted in a 75% decrease in the IgE antibody titer within 6 weeks and IgG2a antibody formation and CD4+ T cells that secreted IFN-gamma in amounts similar to T cells from pDNA primed mice. As shown by adoptive cell transfer, both CD4+ and CD8+ T cells from pDNA immunized mice inhibited an IgE response to beta-gal in alum in the recipient mice. pDNA immunization also inhibited the eosinophilic infiltration of the lung of ovalbumin (OVA) immunized mice after OVA inhalation challenge in an animal model of the late phase reaction. The mechanism of the pDNA induced Th1 immune response was shown to be the result of stimulation by distinct non-coding immunostimulatory DNA sequences (ISS) in the backbone of the pDNA. The ISS induced antigen presenting cells to secrete cytokines that cause naive T cells to differentiate into Th1 cells (e.g. IFN-alpha, IL-12). The data indicate that gene vaccination induces a Th1 immune response that is capable of down-regulating a preexisting Th2 response and IgE antibody formation. Thus, immunization with pDNA encoding for allergens may provide a novel type of immunotherapy for allergic diseases.
CD22 and Siglec‐G: B‐cell inhibitory receptors with distinct functions (2009)

Siglecs (sialic acid-binding immunoglobulin-like lectins) are sialic acid-binding proteins, which are expressed on many cell types of the immune system. B cells express two members of the Siglec family, CD22 (Siglec-2) and Siglec-G, both of which have been shown to inhibit B-cell signaling. CD22 recruits the tyrosine phosphatase Src homology 2 domain-containing phosphatase 1 (SHP-1) to immunoreceptor tyrosine-based inhibitory motifs (ITIMs) and inhibits B-cell receptor (BCR)-induced Ca2+ signaling on normal B cells. CD22 interacts specifically with ligands carrying alpha2-6-linked sialic acids. Interaction with these ligands in cis regulates the association of CD22 with the BCR and thereby modulates the inhibitory function of CD22. Interaction of CD22 to ligands in trans can regulate both B-cell migration as well as the BCR signaling threshold. Siglec-G is a recently identified protein with an inhibitory function restricted to a B-cell subset, the B1 cells. Siglec-G inhibits Ca2+ signaling specifically in these cells. In addition, it controls the cellular expansion and antibody secretion of B1 cells. Thus, both Siglecs modulate BCR signaling on different B-cell populations in a mutually exclusive fashion.
A unique three-dimensional SCID-polymeric scaffold (SCID-synth-hu) model for in vivo expansion of human primary multiple myeloma cells (2011)

Multiple myeloma (MM) cells home to the bone marrow (BM) and adhere to extracellular matrix (ECM) proteins and to bone marrow stromal cells (BMSCs). The close cross talk between MM cells and cells of the non-tumor compartment within the BM has a key role in supporting tumor growth, survival and development of drug resistance. This biological scenario has led to a growing interest in novel drugs, targeting MM cells and/or interfering with their human BM milieu (HuBMM).1, 2 Based on this, appropriate in vivo models that recapitulate the complex interactions occurring between MM and its HuBMM are required for preclinical evaluation of new anti-MM agents. To date, the in vivo study of MM pathobiology and the validation of therapeutic anti-MM agents has been carried out using a variety of models of murine MM or human MM xenografts in immunocompromised mice.3 These models, however, do not replicate the HuBMM. The development of the SCID (severe combined immunodeficiency)-hu model has been an important advance, as it was the first model to recapitulate a HuBMM in mice.4, 5, 6 However, although the SCID-hu system remains a highly relevant model for preclinical investigation, it does have important limitations: (i) restricted availability of human fetal bone chips; (ii) the allogeneic nature of the fetal BM milieu versus MM cells; and (iii) the significant heterogeneity of implanted human bone chips, collected from different individuals at different gestational age, that may produce experimental variability.
89Zr immuno-PET: comprehensive procedures for the production of 89Zr-labeled monoclonal antibodies. (2003)

Methods were developed for improved purification of the long-lived positron emitter (89)Zr. Moreover, a novel bifunctional Df chelate was synthesized for the reproducible coupling of (89)Zr to mAbs. The suitability of such conjugates to detect millimeter-sized tumors in xenograft-bearing nude mice was demonstrated.
Ablation of cholesterol biosynthesis in neural stem cells increases their VEGF expression and angiogenesis but causes neuron apoptosis (2009)

Although sufficient cholesterol supply is known to be crucial for neurons in the developing mammalian brain, the cholesterol requirement of neural stem and progenitor cells in the embryonic central nervous system has not been addressed. Here we have conditionally ablated the activity of squalene synthase (SQS), a key enzyme for endogenous cholesterol production, in the neural stem and progenitor cells of the ventricular zone (VZ) of the embryonic mouse brain. Mutant embryos exhibited a reduced brain size due to the atrophy of the neuronal layers, and died at birth. Analyses of the E11.5-E15.5 dorsal telencephalon and diencephalon revealed that this atrophy was due to massive apoptosis of newborn neurons, implying that this progeny of the SQS-ablated neural stem and progenitor cells was dependent on endogenous cholesterol biosynthesis for survival. Interestingly, the neural stem and progenitor cells of the VZ, the primary target of SQS inactivation, did not undergo significant apoptosis. Instead, vascular endothelial growth factor (VEGF) expression in these cells was strongly upregulated via a hypoxia-inducible factor-1-independent pathway, and angiogenesis in the VZ was increased. Consistent with an increased supply of lipoproteins to these cells, the level of lipid droplets containing triacylglycerides with unsaturated fatty acyl chains was found to be elevated. Our study establishes a direct link between intracellular cholesterol levels, VEGF expression, and angiogenesis. Moreover, our data reveal a hitherto unknown compensatory process by which the neural stem and progenitor cells of the developing mammalian brain evade the detrimental consequences of impaired endogenous cholesterol biosynthesis.