gebhart/patrepeval huggingface dataset:
Lentivirus Vectors Encoding Both Central Polypurine Tract and Posttranscriptional Regulatory Element Provide Enhanced Transduction and Transgene Expression (2001)

Incorporation of a central polypurine tract (cPPT) and a posttranscriptional regulatory element (PRE) into lentivirus vectors provides increased transduction efficiency and transgene expression. We compared the effects of these elements individually and together on transduction efficiency and gene expression, using lentivirus vectors pseudotyped with vesicular stomatitis virus G protein (VSV-G) and encoding enhanced green fluorescent protein (GFP) and rat erythropoietin (EPO). The transduction efficiency was greater than 2-fold higher in the vector containing the PRE element, 3-fold higher in vector encoding the cPPT element, and 5-fold increased in the GFP virus containing both cPPT and PRE elements relative to the parent virus. In comparison with parent vector the mean fluorescence intensity (MFI) of GFP expression was 7-fold higher in cells transduced with virus containing PRE, 6-fold increased in cells transduced with virus containing cPPT, and 42-fold increased in GFP-virus containing both cPPT and PRE elements. EPO-virus containing a PRE element showed a nearly 5-fold increase in EPO secretion over the parent vector, and the vector encoding both PRE and cPPT showed a 65-fold increase. Thus, lentivirus vectors incorporating both PRE and cPPT showed expression levels significantly increased over the sum of the components alone, suggesting a synergistic effect.
Dislocation reduction of InAs nanofins prepared on Si substrate using metal-organic vapor-phase epitaxy (2012)

InAs nanofins were prepared on a nanopatterned Si (001) substrate by metal-organic vapor-phase epitaxy. The threading dislocations, stacked on the lowest-energy-facet plane {111}, move along the SiO2 walls, resulting in a dislocation reduction, as confirmed by transmission electron microscopy. The dislocations were trapped within a thin InAs epilayer. The obtained 90-nm-wide InAs nanofins with an almost etching-pit-free surface do not require complex intermediate-layer epitaxial growth processes and large thickness typically required for conventional epitaxial growth.
Sensitization to epithelial antigens in chronic mucosal inflammatory disease. Characterization of human intestinal mucosa-derived mononuclear cells reactive with purified epithelial cell-associated components in vitro. (1985)

To explore the auto-reactive potential of cells infiltrating the gut mucosa in idiopathic chronic inflammatory bowel disease, intestinal lamina propria mononuclear cells (LPMC) were isolated, characterized morphologically and phenotypically, and evaluated for antigen-specific reactivity. The last was assessed by quantitating LPMC cytotoxic capabilities against purified, aqueous-soluble, organ-specific epithelial cell-associated components (ECAC) characterized previously. Enzyme-isolated inflammatory bowel disease LPMC were constituted primarily by T lymphocytes (57 +/- 12% OKT 3-positive), B lymphocytes (18 +/- 9% surface immunoglobulin-positive), and macrophages (11 +/- 6% esterase-positive), and were responsive to phytohemagglutinin (mean uptake 86,933 cpm/5 X 10(5) cells). LPMC present in abnormal segments from 71% of patients with chronic inflammatory bowel disease were cytotoxic for ECAC isolated from colon (12.5 +/- 8.9% specific lysis) and small bowel (7.1 +/- 6.5%), but not for kidney control antigen (0.8 +/- 1.1%) isolated in a manner analogous to that used for ECAC (P less than 0.02). In contrast, despite comparable responses to phytohemagglutinin (mean uptake 59,200 cpm/5 X 10(5) cells), LPMC from histologically normal mucosa of patients with benign (adult megacolon, Hirshsprung's disease, diverticulosis) or malignant disease failed to lyse indicator cells labeled with colon-derived ECAC (0.3 +/- 0.08%), small bowel-derived ECAC (0.4 +/- 1.11%), or kidney antigen (0.29 +/- 0.79%). LPMC reactivity for individual gel-purified macromolecules of small bowel-derived ECAC (designated as the "P" series of components) was greatest against component P1 (by 2-3-fold), but was detectable against three other purified components as well. The addition of patient's serum did not enhance cytotoxicity to ECAC. Characterization of the cytotoxic cell showed that it was nonadherent to plastic surfaces, bore T lymphocyte-specific markers detectable by OKT 11 and OKT 3 monoclonal antibodies, and could be depleted by removal of cells with receptors for sheep erythrocytes. ECAC-specific reactivity was markedly reduced (greater than 93%) in most experiments when LPMC were preincubated for 1 h with ECAC. These data support the concept that autosensitization to several epithelial cell-associated components has occurred in patients with chronic inflammatory bowel disease, and provide initial evidence that antigen-specific, cell-mediated mechanisms may play a role in the pathogenesis of these disorders.
Transduction of nondividing cells using pseudotyped defective high-titer HIV type 1 particles (1996)

The use of Moloney murine leukemia virus (Mo-MLV)-based vectors to deliver therapeutic genes into target cells is limited by their inability to transduce nondividing cells. To test the capacity of HIV-based vectors to deliver genes into nondividing cells, we have generated replication-defective HIV type 1 (HIV-1) reporter vectors carrying neomycin phosphotransferase or mouse heat stable antigen, replacing the HIV-1 sequences encoding gp160. These vectors also harbor inactive vpr, vpu, and nef coding regions. Pseudotyped HIV-1 particles carrying either the ecotropic or the amphotropic Mo-MLV envelope proteins or the vesicular stomatitis virus G protein were released after single or double transfections of either human 293T or monkey COS-7 cells with titers of up to 10(7) colony-forming units per milliliter. A simple ultrafiltration procedure resulted in an additional 10- to 20-fold concentration of the pseudotyped particles. These vectors along with Mo-MLV-based vectors were used to transduce primary human skin fibroblasts and human peripheral blood CD34+ cells. The HIV-1 vector system was significantly more efficient than its Mo-MLV-based counterpart in transducing human skin fibroblasts arrested at the G0/G1 stage of the cell cycle by density-dependent inhibition of growth. Human CD34+ cells were transduced efficiently using HIV-1 pseudotype particles without prior stimulation with cytokines.
The role of hepcidin in iron sequestration during infections and in the pathogenesis of anemia of chronic disease. (2002)

Systemic infection or inflammation causes a decrease in intestinal iron absorption and impairs the release of recycled iron from macrophages. Decreased availability of iron may deny this essential element to invading pathogens and may inhibit their multiplication and other metabolic processes but also results in anemia of chronic disease. This article reviews recent discoveries that shed light on the regulation of iron metabolism during infection and iron overload, and point to the central role of a newly discovered peptide, hepcidin. Evidence to date indicates that hepcidin is a negative regulator of intestinal iron absorption, placental iron transport, and the release of iron from macrophages that recycle iron from senescent red cells. It may also be the central mediator of iron sequestration during infections and inflammatory states and the mediator of anemia of chronic disease. Rapid progress in this area is a good example of the beneficial effects of improvements in peptide analysis and chemistry, advances in genomics, and the increasing use of transgenic mice to determine the function of newly discovered genes and proteins.
Transport Layer Security (TLS) Extensions: Extension Definitions (2011)

This document provides specifications for existing TLS extensions. It
is a companion document for the TLS 1.2 specification [RFC5246]. The
extensions specified are server_name, max_fragment_length,
client_certificate_url, trusted_ca_keys, truncated_hmac, and
status_request. INTERNET-DRAFT TLS Extension Definitions
ChemInform Abstract: RUTHENIUM(0)‐ UND RUTHENIUM(II)‐KOMPLEXE MIT 1,1,1‐TRIS‐(DIPHENYLPHOSPHINOMETHYL)‐AETHAN (1973)

Abstract Dodekacarbonyltriruthenium reagiert mit dem tripodähnlichen Titelliganden in Toluol bei 130°C zu dem luftempfindlichen Dicarbonyl‐Ru(O)‐Komplex (I), der in situ mit Sauerstoff oxidiert den Carbonato‐Ru(II)‐Komplex (II) bildet.
PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families (2005)

PROtein Domain Organization and Comparison (PRODOC) comprises several programs that enable convenient comparison of proteins as a sequence of domains. The in-built dataset currently consists of approximately 698 000 proteins from 192 organisms with complete genomic data, and all the SWISSPROT proteins obtained from the Pfam database. All the entries in PRODOC are represented as a sequence of functional domains, assigned using hidden Markov models, instead of as a sequence of amino acids. On average 69% of the proteins in the proteomes and 49% of the residues are covered by functional domain assignments. Software tools allow the user to query the dataset with a sequence of domains and identify proteins with the same or a jumbled or circularly permuted arrangement of domains. As it is proposed that proteins with jumbled or the same domain sequences have similar functions, this search tool is useful in assigning the overall function of a multi-domain protein. Unique features of PRODOC include the generation of alignments between multi-domain proteins on the basis of the sequence of domains and in-built information on distantly related domain families forming superfamilies. It is also possible using PRODOC to identify domain sharing and gene fusion events across organisms. An exhaustive genome-genome comparison tool in PRODOC also enables the detection of successive domain sharing and domain fusion events across two organisms. The tool permits the identification of gene clusters involved in similar biological processes in two closely related organisms. The URL for PRODOC is http://hodgkin.mbu.iisc.ernet.in/~prodoc.
Phenotype of arylsulfatase A-deficient mice: Relationship to human metachromatic leukodystrophy (1996)

Metachromatic leukodystrophy is a lysosomal sphingolipid storage disorder caused by the deficiency of arylsulfatase A. The disease is characterized by progressive demyelination, causing various neurologic symptoms. Since no naturally occurring animal model of the disease is available, we have generated arylsulfatase A-deficient mice. Deficient animals store the sphingolipid cerebroside-3-sulfate in various neuronal and nonneuronal tissues. The storage pattern is comparable to that of affected humans, but gross defects of white matter were not observed up to the age of 2 years. A reduction of axonal cross-sectional area and an astrogliosis were observed in 1-year-old mice; activation of microglia started at 1 year and was generalized at 2 years. Purkinje cell dendrites show an altered morphology. In the acoustic ganglion numbers of neurons and myelinated fibers are severely decreased, which is accompanied by a loss of brainstem auditory-evoked potentials. Neurologic examination reveals significant impairment of neuromotor coordination.
The Pore-Forming Toxin Listeriolysin O Mediates a Novel Entry Pathway of L. monocytogenes into Human Hepatocytes (2011)

Intracellular pathogens have evolved diverse strategies to invade and survive within host cells. Among the most studied facultative intracellular pathogens, Listeria monocytogenes is known to express two invasins-InlA and InlB-that induce bacterial internalization into nonphagocytic cells. The pore-forming toxin listeriolysin O (LLO) facilitates bacterial escape from the internalization vesicle into the cytoplasm, where bacteria divide and undergo cell-to-cell spreading via actin-based motility. In the present study we demonstrate that in addition to InlA and InlB, LLO is required for efficient internalization of L. monocytogenes into human hepatocytes (HepG2). Surprisingly, LLO is an invasion factor sufficient to induce the internalization of noninvasive Listeria innocua or polystyrene beads into host cells in a dose-dependent fashion and at the concentrations produced by L. monocytogenes. To elucidate the mechanisms underlying LLO-induced bacterial entry, we constructed novel LLO derivatives locked at different stages of the toxin assembly on host membranes. We found that LLO-induced bacterial or bead entry only occurs upon LLO pore formation. Scanning electron and fluorescence microscopy studies show that LLO-coated beads stimulate the formation of membrane extensions that ingest the beads into an early endosomal compartment. This LLO-induced internalization pathway is dynamin-and F-actin-dependent, and clathrin-independent. Interestingly, further linking pore formation to bacteria/bead uptake, LLO induces F-actin polymerization in a tyrosine kinase-and pore-dependent fashion. In conclusion, we demonstrate for the first time that a bacterial pathogen perforates the host cell plasma membrane as a strategy to activate the endocytic machinery and gain entry into the host cell.
One‐step, zero‐background ligation‐independent cloning intron‐containing hairpin RNA constructs for RNAi in plants (2010)

*The hairpin-based RNA interference (RNAi) technique plays an important role in exploring gene function in plants. Although there are several methods for making hairpin RNA (hpRNA) constructs, these methods usually need multiple relatively laborious, time-consuming or high-cost cloning steps. Here we describe a one-step, zero-background ligation-independent cloning (OZ-LIC) method for making intron-containing hpRNA (ihpRNA) constructs by our vector pRNAi-LIC. *To generate the ihpRNA constructs with zero-background, this method only requires treating two PCR products of target gene flanked with different LIC sequences and SmaI-linearized pRNAi-LIC vector by T4 DNA polymerase respectively, and then transforming these treated DNA mixture into Escherichia coli. *The ihpRNA constructs generated with our OZ-LIC RNAi vector can efficiently induce not only transient silencing of the exogenous marker genes and the endogenous resistance-related Nicotiana benthamiana SGT1 gene, but also stable transgenic suppression of Arabidopsis SGT1b gene. *Our new OZ-LIC method and RNAi vector will represent a powerful tool for gene knockdown in plants and may facilitate high-throughput determination of plant gene function.
Cell Transformation: A Study of Regulation with Types 5 and 12 Adenovirus Temperature-sensitive Mutants (1974)

Since the initial isolations of adenoviruses from man (Rowe et al. 1953; Hilleman and Werner 1954), these viruses have served as models for studies of productive (Green 1966; Ginsberg 1969; Schlesinger 1969) and latent infections (Rowe et al. 1953; Strohl and Schlesinger 1965), as well as for the investigation of viral oncogenesis (Trentin et al. 1962) and cell transformation (Pope and Rowe 1964). Extensive biological and biochemical data have been obtained describing this wide array of cellular responses induced by adenoviruses. Yet these studies gave only limited information for a complete understanding of the molecular reactions that regulate viral replication and the pathological consequences of the virus-host cell encounter. It became apparent that viral, and probably host cell, mutants would be needed for further investigation of the precise mechanisms regulating the biochemical events in viral synthesis and cell alterations. Accordingly, several laboratories have isolated a valuable variety of conditionally lethal...
An integration of network communication with workstation architecture (1991)

A workstation may be thought of as a group of cooperatively connected subsystems. Point--to--point channels may be used to create a small--scale Gigabit LAN to which these subsystems are attached as nodes. The architectural focus of such a workstation shifts towards its internal LAN. An attractive attribute of this LAN is that its aggregate capacity scales linearly with the number of nodes attached to it.If the link--layer of the internal LAN is made equivalent to the link--layer of the external LAN, interior nodes become directly accessible externally. Except for latency the distinction between whether a node is inside a workstation versus outside it need not be significant. This property is particularly attractive for distributed communication--intensive applications.
Treatment of a large segmental bone defect with allograft and autogenous bone marrow graft. (1997)

Management of segmental bone defects is a challenge to orthopedic surgeons. We report a 23-year-old man who sustained segmental bone loss of 9 cm in length in his left femur due to an open fracture. Open reduction and internal fixation with a 95 degrees angle blade plate and screws, supplemented with a composite of two femoral head allografts and a graft of 100 mL of autogenous bone marrow, was performed 3 weeks after the injury, when the soft tissues had healed. The postoperative rehabilitation program included delayed weight bearing (crutches for 3 months), a limited early range of motion of the left knee, and quadriceps muscle exercise. Callus bridging was noted on x-ray films 3 months postoperatively. Clinical and radiographic union were noted 6 months after the surgery. We suggest that this new and simple method can be applied to successfully treat segmental bone loss of more than 6 cm in length.
The evolving role of lipid rafts and caveolae in G protein‐coupled receptor signaling: implications for molecular pharmacology (2004)

The many components of G-protein-coupled receptor (GPCR) signal transduction provide cells with numerous combinations with which to customize their responses to hormones, neurotransmitters, and pharmacologic agonists. GPCRs function as guanine nucleotide exchange factors for heterotrimeric (alpha, beta, gamma) G proteins, thereby promoting exchange of GTP for GDP and, in turn, the activation of 'downstream' signaling components. Recent data indicate that individual cells express mRNA for perhaps over 100 different GPCRs (out of a total of nearly a thousand GPCR genes), several different combinations of G-protein subunits, multiple regulators of G-protein signaling proteins (which function as GTPase activating proteins), and various isoforms of downstream effector molecules. The differential expression of such protein combinations allows for modulation of signals that are customized for a specific cell type, perhaps at different states of maturation or differentiation. In addition, in the linear arrangement of molecular interactions involved in a given GPCR-G-protein-effector pathway, one needs to consider the localization of receptors and post-receptor components in subcellular compartments, microdomains, and molecular complexes, and to understand the movement of proteins between these compartments. Co-localization of signaling components, many of which are expressed at low overall concentrations, allows cells to tailor their responses by arranging, or spatially organizing in unique and kinetically favorable ways, the molecules involved in GPCR signal transduction. This review focuses on the role of lipid rafts and a subpopulation of such rafts, caveolae, as a key spatial compartment enriched in components of GPCR signal transduction. Recent data suggest cell-specific patterns for expression of those components in lipid rafts and caveolae. Such domains likely define functionally important, cell-specific regions of signaling by GPCRs and drugs active at those GPCRs.
Prevalence of genotypic and phenotypic resistance to anti-retroviral drugs in a cohort of therapy-naïve HIV-1 infected US military personnel (2000)

Objective While transmission of drug-resistant HIV-1 has been reported, estimates of prevalence of resistance in drug-naïve populations are incomplete. We investigated the prevalence of genotypic mutations and phenotypic antiretroviral resistance in a cohort of HIV-1 infected U.S. military personnel prior to the institution of antiretroviral therapy. Design Cross-sectional cohort study. Methods Plasma was obtained from 114 recently HIV-1 infected subjects enrolled in an epidemiological study. Genotypic resistance was determined by consensus sequencing of a PCR product from the HIV-1 pol gene. Sequences were interpreted by a phenotypic–genotypic correlative database. Resistance phenotypes were determined by a recombinant virus cell culture assay. Results Genotypic mutations and phenotypic resistance were found at a higher than expected frequency. Resistance to non-nucleoside reverse transcriptase inhibitors was most common, with a prevalence of 15% of 95 subjects by genotype and 26% of 91 subjects by phenotype. Genotypic and phenotypic resistance respectively were found in 4% and 8% of subjects for nucleoside reverse transcriptase inhibitors and in 10% and 1% for protease inhibitors. One subject harbored virus with resistance to all three drug classes. Conclusions A substantial frequency of resistance to antiretroviral drugs was identified in a therapy-naïve U.S. cohort. In most cases, the genotypic and phenotypic assays yielded similar results, although the genotypic assay could detect some protease inhibitor resistance-associated mutations in the absence of phenotypic resistance. These data suggest the need for optimization of treatment guidelines based on current estimates of the prevalence of drug resistance in HIV-1 seroconverters.
Learning and generalization in a linear perceptron stochastically trained with noisy data (1993)

A linear perceptron is stochastically trained on a corrupted training data set; this enables the effect of noise on the data to be studied. The average properties of the network are calculated using the Gardner method following Seung et al. A weight decay term is added to the training energy and the effect on generalization studied and compared with previously known results. A prescription for setting the optimal weight decay parameter at finite temperature is presented. The results also suggest an initial temperature for an annealing schedule.
Nitroglycerin reduces myocardial oxygen consumption during exercise despite vascular tolerance (2005)

The long-term benefits of nitroglycerin (NTG) therapy are limited by the development of vascular tolerance and endothelial dysfunction in conductance coronary arteries. We have determined whether nitrate tolerance extends to NTG effects on myocardial O2 consumption (MV(O2)) and the ability of endogenous nitric oxide (NO) to modulate MV(O2) during exercise. In chronically instrumented dogs (n = 8), hemodynamic and MV(O2) responses to treadmill exercise were measured before, during tolerance (3 and 7 days of NTG delivery), and 7 days after NTG withdrawal. Acute NTG delivery caused a parallel downward shift of the MV(O2)-triple product (TP) relations and reversed the disproportionate increases in MV(O2) caused by the blockade of NO formation. After 7 days of continuous transdermal NTG delivery, vascular tolerance was displayed as a >75% reduction of coronary blood flow (CBF) responses to NTG boluses. Despite vascular nitrate tolerance, MV(O2)-TP relations were shifted downward compared with pre-NTG exercise. Seven days after NTG withdrawal, vascular responses to boluses of NTG had recovered from tolerance, and MV(O2)-TP relations during exercise were back to pre-NTG level. At that time, blockade of NO formation failed to alter MV(O2)-TP relations. Thus NTG caused a sustained reduction of cardiac MV(O2), independent of metabolic demand during exercise, despite tolerance of the coronary microcirculation. NTG-induced vascular tolerance and MV(O2) reductions were reversible by NTG withdrawal, but endogenous NO-dependent modulation of O2 consumption was severely impaired.