gebhart/patrepeval huggingface dataset:
Decreased neointimal formation in Mac-1–/– mice reveals a role for inflammation in vascular repair after angioplasty (2000)

Inflammation plays an essential role in the initiation and progression of atherosclerosis, but its role in vascular repair after mechanical arterial injury (i.e., percutaneous transluminal coronary angioplasty, PTCA) is unknown. In animal models of vascular injury, leukocytes are recruited as a precursor to intimal thickening. Furthermore, markers of leukocyte activation - in particular, increased expression of the beta2-integrin Mac-1 (alphaMbeta2, or CD11b/CD18), which is responsible for firm leukocyte adhesion to platelets and fibrinogen on denuded vessels - predict restenosis after PTCA. To determine whether Mac-1-mediated leukocyte recruitment is causally related to neointimal formation, we subjected mice lacking Mac-1 to a novel form of mechanical carotid artery dilation and complete endothelial denudation. We now report that the selective absence of Mac-1 impairs transplatelet leukocyte migration into the vessel wall, reducing leukocyte accumulation over time. Diminished medial leukocyte accumulation was accompanied by markedly reduced neointimal thickening after vascular injury. These data establish a role for inflammation in neointimal thickening and suggest that leukocyte recruitment to mechanically injured arteries may prevent restenosis.
Preclinical validation: LV/IL-12 transduction of patient leukemia cells for immunotherapy of AML (2016)

Interleukin-12 (IL-12) is a potent cytokine that may be harnessed to treat cancer. To date, nearly 100 IL-12-based clinical trials have been initiated worldwide. Yet systemic administration of IL-12 is toxic. Different strategies are being developed to reduce such toxicities by restricting IL-12 distribution. Our previous studies employed lentivector-mediated expression of murine IL-12 in tumor cells and demonstrated effective protection in both mouse leukemia and solid tumor challenge models. In this study, we carried out preclinical validation studies using a novel lentivector to engineer expression of human IL-12 in acute myeloid leukemia blast cells isolated from 21 patients. Acute myeloid leukemia cells were transduced with a bicistronic lentivector that encodes the human IL-12 cDNA as a fusion, as well as a LNGFR (ΔLNGFR)/mutant thymidylate kinase cassette as a marking and cell-fate control element. A range of 20-70% functional transduction efficiencies was achieved. Transduced acute myeloid leukemia cells produced bioactive IL-12 protein and displayed dose-dependent sensitivity to the prodrug 3'-azido-3'-deoxythymidine. <i>In vitro</i> immortalization assays using transduced mouse hematopoietic stem cells demonstrated minimal genotoxic risk from our IL-12 vector. Scale-up transduction and cell processing was subsequently validated in a GMP facility to support our (now approved) Clinical Trial Application (CTA).
Polymerase chain reaction for detection of Mycobacterium tuberculosis (1990)

A polymerase chain reaction for the specific detection of mycobacteria belonging to the Mycobacterium tuberculosis complex was developed. Using a single primer pair derived from the nucleotide sequence of protein antigen b of M. tuberculosis, we achieved specific amplification of a 419-base-pair DNA fragment in M. tuberculosis and M. bovis. After DNA was extracted from mycobacteria by using a simple, safe lysis procedure, we detected the 419-base-pair sequence in samples containing few mycobacteria. Preliminary data suggested that this technique could be applied to clinical specimens for early and specific diagnosis of tuberculosis.
Toll-Like Receptors and Viruses: Induction of Innate Antiviral Immune Responses (2008)

Induction of antiviral innate immune responses depends on a family of innate immune receptors, the Toll-like receptors (TLR). TLR mediate the antiviral immune responses by recognizing virus infection, activating signaling pathways and inducing the production of antiviral cytokines and chemokines. ssRNA and dsRNA viruses can be recognized by TLR7/8 and TLR3, respectively. TLR receptors are also involved in the recognition of viruses containing genomes rich in CpG DNA motifs as well as envelope glycoproteins. Cytoplasmic recognition of dsRNA by RNA helicases such as RIG-I and MDA5 provides another means of recognizing viral nucleic acid. In order to counteract the innate host immune system viruses evolved mechanisms that block recognition and signaling through pattern recognition receptors, such as TLRs and RNA helicases. Recently, TLR agonists represent a promising approach for the treatment of infectious diseases. This review will focus on the current knowledge of TLR-mediated immune responses to several viral infections.
Drug Discovery at the Enzyme Level (1987)

This chapter deals with enzymes as targets of drug action. The focus is on inhibition of enzyme activity by drugs, although other actions of drugs on enzymes are possible, such as activation or allosteric modification of enzyme function. This chapter will not deal with enzymes themselves as drugs, e. g., L-asparaginase in the treatment of acute lymphocytic leukemia, papain used for proteolysis in wound debridement, and urokinase used in thrombolytic therapy. Metabolism of drugs by enzymes and inhibition or induction of drug-metabolizing enzymes are other drug-enzyme interactions that can be important considerations in drug development, but our focus will be entirely on drug inhibition of enzymes as a primary mechanism to which drugs owe their efficacy. We will consider how enzyme activity is assayed, how inhibitors are found (or made) and characterized, how enzyme inhibition is demonstrated in vivo, and some specific examples of enzyme inhibitors that are used as drugs.
Larger and more invasive colorectal carcinoma contains larger amounts of plasminogen activator inhibitor type 1 and its relative ratio over urokinase receptor correlates well with tumor size (1999)

Higher expression of uPAR was related to poor prognosis of patients with colorectal carcinoma and excess amounts of PAI-1 over uPAR or uPAR-bound uPA appeared to play an important role in tumor progression.
Crystallization of the receptor binding domain of vascular endothelial growth factor (1996)

Vascular endothelial growth factor (VEGF) is a potent angiogenic factor with a unique specificity for vascular endothelial cells. In addition to its role in vasculogenesis and embryonic angiogenesis, VEGF is implicated in pathologic neovascularization associated with tumors and diabetic retinopathy. Four different constructs of a short variant of VEGF sufficient for receptor binding were overexpressed in Escherichia coli, refolded, purified, and crystallized in five different space groups. In order to facilitate the production of heavy atom derivatives, single cysteine mutants were designed based on the crystal structure of platelet-derived growth factor. A construct consisting of residues 8 to 109 was crystallized in space group P2(1), with cell parameters a = 55.6 A, b = 60.4 A, c = 77.7 A, beta = 90.0 degrees, and four monomers in the asymmetric unit. Native and derivative data were collected for two of the cysteine mutants as well as for wild-type VEGF.
Somatic cell cloning in polyester stacks. (1982)

Single somatic cells, including fibroblasts, myelomas, and hybridomas, proliferate normally when trapped between a plastic dish and a disc of polyester cloth. Contact between the overlay and the plastic for 8-16 days results in identical colony patterns on the cloth and the plate. When several cloth discs are simultaneously stacked over Chinese hamster ovary cells, three or four-high resolution colony copies can be generated from a single master dish. The colonies on the cloth can be analyzed by radiochemical methods [Esko, J. D. & Raetz, C. R. H. (1978) Proc. Natl. Acad. Sci. USA 75, 1190-1193] or by "replica plating" to a new disc. The use of polyester cloth, singly or in stacks, has several major advantages over previous techniques for somatic cell replica plating, including: (i) broad applicability to diverse cell lines such as fragile membrane mutants of Chinese hamster ovary cells and relatively nonadherent myelomas or hybridomas; (ii) the possibility of generating multiple copies of the same colony population, allowing simultaneous analysis for several enzymes or cellular components; and (iii) superior resolution and transfer efficiency in copying colony patterns from one surface to another. The remarkable capacity of animal cell colonies to proliferate upward through "polyester stacks" may reflect chemotropic movement of individual cells and opens new approaches to somatic cell genetics.
The Membrane-spanning Proteoglycan NG2 Binds to Collagens V and VI through the Central Nonglobular Domain of Its Core Protein (1997)

NG2 is a membrane-spanning proteoglycan with a primary structure unique among cell surface or extracellular matrix proteins. To characterize the interaction between NG2 and extracellular matrix proteins, we have used a eukaryotic expression system to produce and purify several recombinant fragments covering not only the entire ectodomain of NG2 but also distinct subdomains of the molecule. Using a solid phase binding assay with various extracellular matrix proteins, we have identified two main ligands for NG2, namely, collagens V and VI. Consistent with previous models of glycosaminoglycan attachment, roughly 50% of the recombinant NG2 fragments containing the central domain have chondroitin sulfate chains attached to the protein core. These glycosaminoglycan chains are not directly involved in collagen binding, since chondroitinase-treated fragments exhibit an unimpaired ability to bind to both collagens. Using more restricted recombinant fragments of NG2, we mapped the binding site for both collagens to the central domain of NG2. Electron microscopy after rotary shadowing of native NG2 molecules indicates that this extended nonglobular domain provides a flexible connection joining the two N- and C-terminal globular regions of NG2. Rotary shadowing of mixtures of NG2 and collagen V or VI confirms a direct interaction between the molecules and indicates that the collagens align with the central region of NG2, giving the appearance of a rod between the N- and C-terminal globules.
Transduction of Human Bone Marrow by Adenoviral Vector (1994)

Recombinant adenoviral vectors have been shown to be potential new tools for a variety of human gene therapy protocols. We examined the effectiveness of an adenovirus vector for gene transfer into human bone marrow (BM). Mononuclear cells from one adenosine deaminase (ADA)-deficient and two normal human BM samples were transduced by an E1-defective adenoviral vector encoding human ADA and kept in myeloid long-term culture. Retroviral gene transfer was also performed with the ADA-deficient bone marrow as a control. The transduced cells were harvested at different times and the expression of the vector-encoded ADa in crude cell extracts of nonadherent cells was analyzed. The expression from Ad-ADA was higher than that from a retroviral vector at 1 week post-transduction. In half of the experiments, the ADA activity decreased with passage. Unexpectedly, sustained expression from Ad-ADA was observed in the other half. At the end of the experiments (2 months), free virus from BM cultures which showed sustained expression of ADA was detected on 293 cells. Several independent virus clones were isolated and analyzed and found to be Ad-ADA. Our results suggest potential use of adenoviral vectors for gene therapy that does not require sustained expression, as with cytokine gene transfer for cancer gene therapy. However, our finding that infectious virus can sometimes persist might raise issues regarding the leakiness of human adenovirus vectors in cells of some human tissues.
Long-Distance Decoy-State Quantum Key Distribution in Optical Fiber (2007)

The theoretical existence of photon-number-splitting attacks creates a security loophole for most quantum key distribution (QKD) demonstrations that use a highly attenuated laser source. Using ultralow-noise, high-efficiency transition-edge sensor photodetectors, we have implemented the first version of a decoy-state protocol that incorporates finite statistics without the use of Gaussian approximations in a one-way QKD system, enabling the creation of secure keys immune to photon-number-splitting attacks and highly resistant to Trojan horse attacks over 107 km of optical fiber.
Protein prenylcysteine analog inhibits agonist-receptor-mediated signal transduction in human platelets. (1993)

Signal transduction components, including the Ras superfamily of low molecular weight GTP-binding proteins and the gamma subunits of heterotrimeric G proteins, are reversibly carboxyl methylated at C-terminal prenylcysteine residues. We have previously shown that the prenylcysteine analog N-acetyl-S-trans,trans-farnesyl-L-cysteine (AFC) inhibits carboxyl methylation of these proteins in human platelets. Here we show that concentrations of AFC that inhibit Ras carboxyl methylation (10-50 microM) also block responses to agonists such as ADP, collagen, arachidonic acid, U46619 (a stable analog of prostaglandin H2), thrombin, and guanosine 5'-[gamma-thio]triphosphate. AFC does not inhibit aggregation induced by effectors such as ionomycin, phorbol 12,13-dibutyrate, and bacterial phospholipase C that bypass G proteins to activate platelets at the level of cytosolic Ca2+ concentration and protein kinase C. These findings indicate that AFC inhibits agonist-receptor-mediated signal transduction in human platelets.
Serum interleukin-10 is an independent prognostic factor in advanced solid tumors. (2000)

Interleukin (IL)-10 is a Th2 type pleiotropic cytokine that has been found to be produced at the tumor site and to be increased in sera of patients suffering from different types of cancer. IL-10 has been shown to hinder a number of immune functions, i.e., T lymphocyte proliferation, Th1 type cytokine production, antigen presentation, and lymphokine-activated killer cell cytotoxicity. To assess its prognostic value, we measured serum levels of IL-10 in 118 patients with advanced solid tumors before treatment, after completion of therapy, and during follow-up. Other prognostic variables, to which IL-10 results were compared, were analyzed as well. IL-10 serum levels were found significantly elevated in cancer patients with respect to healthy controls. Of interest, a significant decrease in IL-10 serum levels was observed in the responder group, whereas a significant increase was recorded in the non-responder group. Using univariate and multivariate analyses, a significant relationship was shown between IL-10 serum levels and both overall survival (OS) and time to treatment failure (TTF). Stepwise regression analysis selected IL-10 serum level, performance status (PS), and stage as the best association of variables with significant impact on OS and TTF. In conclusion, this study shows that IL-10 has an independent prognostic significance in patients with advanced solid tumors and may be useful for monitoring disease progression.
Secretion and Biological Activity of Short Signal Peptide IL-15 Is Chaperoned by IL-15 Receptor Alpha In Vivo (2009)

The two known isoforms of IL-15 contain either a long signal peptide (LSP) or a short signal peptide (SSP), and are produced by alternatively spliced transcripts. It has been proposed that SSP IL-15 remains exclusively intracellular, and its function is unclear. In this study, we show that, similar to LSP IL-15, the SSP IL-15 is stabilized and secreted efficiently upon coexpression of IL-15Ralpha. Coinjection of SSP IL-15- and IL-15Ralpha-expressing plasmids into mice resulted in increased plasma levels of bioactive heterodimeric IL-15 and mobilization and expansion of NK and T cells. Therefore, SSP IL-15 is secreted and bioactive when produced as a heterodimer with IL-15Ralpha in the same cell. The apparent t(1/2) of this heterodimer is lower compared with LSP IL-15/IL-15Ralpha, due to different intracellular processing. Coexpression of both LSP IL-15 and SSP IL-15 in the presence of IL-15Ralpha results in lower levels of bioactive IL-15, indicating that LSP and SSP IL-15 compete for the binding to IL-15Ralpha when expressed in the same cell. Because the SSP IL-15 interaction to IL-15Ralpha leads to a complex with lower apparent stability, SSP IL-15 functions as competitive inhibitor of LSP IL-15. The data suggest that usage of alternative splicing is an additional level of control of IL-15 activity. Expression of both SSP and LSP forms of IL-15 appears to be conserved in many mammals, suggesting that SSP may be important for expressing a form of IL-15 with lower magnitude or duration of biological effects.
Diacylglycerol acyltransferase: A key mediator of plant triacylglycerol synthesis (2006)

Many plants deposit TAG in seeds and fruits as the major form of storage lipid. TAG production is of tremendous socioeconomic value in food, nutraceutical, and industrial applications, and thus numerous conventional and molecular genetic strategies have been explored in attempts to increase TAG content and modify the FA composition of plant seed oils. Much research has focused on the acyl-CoA-dependent reaction catalyzed by diacylglycerol acyltransferase (DGAT), which is an integral endoplasmic reticulum protein and has also been shown to be present in oil bodies and plastids. DGAT enzymes exhibit diverse biochemical properties among different plant species, many of which are summarized here. In addition to catalyzing a critical step in TAG biosynthesis, there is evidence that DGAT has roles in lipid metabolism associated with germination and leaf senescence. TAG can also be formed in plants via two different acyl-CoA-independent pathways, catalyzed by phospholipid: diacylglycerol acyltransferase and diacylglycerol transacylase. The current understanding of the terminal step in TAG formation in plants and the development of molecular genetic approaches aimed at altering TAG yield and FA composition of TAG are discussed.
Development of a Quasi-Dynamic Pharmacophore Model for Anti-Complement Peptide Analogues (2005)

Three quasi-dynamic pharmacophore models have been constructed for the complement inhibitor peptide compstatin, using first principles. Uniform sampling along 5-ns molecular dynamics trajectories provided dynamic conformers that are thought to represent the entire conformational space for nine training set molecules, compstatin, four active analogues, and four inactive analogues. The pharmacophore models were built using mixed physicochemical and structural properties of residues indispensable for structural stability and activity. Owing to the size and flexibility of compstatin, one-dimensional probability distributions of intrapharmacophore point distances, angles, and dihedral angles of different analogues spread over wide and overlapping ranges. More robust two-dimensional distance-angle probability distributions for two pharmacophore models discriminated individual analogues in terms of specific distance-angle pairs, but overall failed to identify the active and the inactive analogues as two distinct groups. Two-dimensional distance-dihedral angle probability distributions in a third pharmacophore model allowed discrimination of the groups of active and inactive analogues more effectively, with the highest-activity analogue having distinct behavior. The present study indicates that more stringent structural constraints should be used for a set of structurally similar but flexible peptides, as opposed to organic molecules, to convert dynamic conformers into pharmacophore models. Flexibility is a general aspect of the structure and function of peptides and should be taken into account in ligand-based pharmacophore design. However, the discrimination of activity using multidimensional probability surfaces depends on the peptide system, the selection of the training set, the molecular dynamics protocol, and the selection of the type and number of pharmacophore points.
Particle Growth by Condensation in a System with Limited Vapor (1998)

ABSTRACT Condensational growth of monodisperse aerosols in a system with limited vapor is studied. The equations for particle size and vapor concentration variation due to condensation are derived for the free molecular and continuum regimes, respectively. The corresponding condensation characteristic times for both size regimes are also developed. The particle size increase and vapor concentration decrease in a system with a limited vapor source are examined for varying surface vapor concentration and particle loading. The differences in the characteristic time expression derived in this work and those developed previously for constant particle size and unlimited vapor source are discussed. The expression of the condensation characteristic time developed is used to study the effect of sample aerosol concentration on the operation of the condensation particle counter, and compared to the characteristic times of other mechanisms such as nucleation, coagulation, and chemical reaction. The characteristic time estimation is shown to be a convenient and effective tool for estimating the relative importance of condensation in comparison to other concurrently occurring mechanisms in the system.
Liquid–Metal Vertical Interconnects for Flip Chip Assembly of GaAs C-Band Power Amplifiers Onto Micro-Rectangular Coaxial Transmission Lines (2012)

Prior work has demonstrated a new process utilizing room-temperature liquid metal, Galinstan, as an interconnect material for flip-chip bonding. This interconnect forms a flexible bond between chips and carriers, and, therefore, a flip-chip assembly using this technology is much less susceptible to thermomechanical stresses. This paper applies this concept to interconnect GaAs MMIC chips to 3-D Polystrata transmission-line structures. Passive assemblies are utilized to model, test, and verify liquid-metal interconnections, giving average losses per liquid-metal transition of about 0.11 dB out to 26.5 GHz, low parasitics per transition, and demonstrated reliability after temperature cycling. A prefabricated GaAs MMIC chip is postprocessed for liquid-metal assembly. Measured results show, over the MMIC's 4.9-8.5-GHz frequency range, the system's overall reduction in gain of the MMIC is 1.4 dB or 0.7 dB per RF transition as compared with direct probing of the MMIC chip.
Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome (2000)

Helicobacter pylori is a gram-negative bacterium, which colonizes the gastric mucosa of humans and is implicated in a wide range of gastroduodenal diseases. The genomic sequences of two H.pylori strains, 26695 and J99, have been published recently. About two dozen potential restriction-modification (R-M) systems have been annotated in both genomes, which is far above the average number of R-M systems in other sequenced genomes. Here we describe a functional analysis of the 16 putative Type II R-M systems in the H. pylori J99 genome. To express potentially toxic endonuclease genes, a unique vector was constructed, which features repression and antisense transcription as dual control elements. To determine the methylation activities of putative DNA methyltransferases, we developed polyclonal antibodies able to detect DNA containing N6-methyladenine or N4-methylcytosine. We found that <30% of the potential Type II R-M systems in H.pylori J99 strain were fully functional, displaying both endonuclease and methyltransferase activities. Helicobacter pylori may maintain a variety of functional R-M systems, which are believed to be a primitive bacterial 'immune' system, by alternatively turning on/off a subset of numerous R-M systems.