gebhart/patrepeval huggingface dataset:
Author index (2003)

Patients with diabetes mellitus suffer from an increased incidence of complications including cardiovascular disease and cataracts; the mechanisms responsible for this are not fully understood. One characteristic of such complications is an accumulation of advanced glycation end-products formed by the adduction of glucose or species derived from glucose, such as low-molecular mass aldehydes, to proteins. These reactions can be nonoxidative (glycation) or oxidative (glycoxidation) and result in the conversion of low-density lipoproteins (LDL) to a form that is recognized by the scavenger receptors of macrophages. This results in the accumulation of cholesterol and cholesteryl esters within macrophages and the formation of foam cells, a hallmark of atherosclerosis. The nature of the LDL modifications required for cellular recognition and unregulated uptake are poorly understood. We have therefore examined the nature, time course, and extent of LDL modifications induced by glucose and two aldehydes, methylglyoxal and glycolaldehyde. It has been shown that these agents modify Arg, Lys and Trp residues of the apoB protein of LDL, with the extent of modification induced by the two aldehydes being more rapid than with glucose. These processes are rapid and unaffected by low concentrations of copper ions. In contrast, lipid and protein oxidation are slow processes and occur to a limited extent in the absence of added copper ions. No evidence was obtained for the stimulation of lipid or protein oxidation by glucose or methylglyoxal in the presence of copper ions, whereas glycolaldehyde stimulated such reactions to a modest extent. These results suggest that the earliest significant events in this system are metal ion-independent glycation (modification) of the protein component of LDL, whilst oxidative events (glycoxidation or direct oxidation of lipid or proteins) only occur to any significant extent at later time points. This 'carbonyl-stress' may facilitate the formation of foam cells and the vascular complications of diabetes.
A Common Variation in Deiodinase 1 Gene DIO1 Is Associated with the Relative Levels of Free Thyroxine and Triiodothyronine (2008)

This study provides convincing evidence that common genetic variation in DIO1 alters deiodinase function, resulting in an alteration in the balance of circulating free T(3) to free T(4). This should prove a valuable tool to assess the relative effects of circulating free T(3) vs. free T(4) on a wide range of biological parameters.
Selective expansion of a subset of exhausted CD8 T cells by αPD-L1 blockade (2008)

Programmed death-1 (PD-1) regulates T cell exhaustion during chronic infections. Blocking the PD-1:PD-ligand (PD-L) pathway reinvigorates exhausted CD8 T cells. Exactly how blocking PD-1:PD-L interactions improves T cell immunity, however, remains unclear. PD-1:PD-L blockade could reprogram all exhausted T cells to become antiviral effectors. Alternatively, this blockade might selectively expand a subset of exhausted T cells. We have identified two subpopulations of exhausted CD8 T cells during chronic viral infection in mice. One subset of exhausted CD8 T cells is rescued by alphaPD-L1 blockade, whereas the other subset appears more terminally differentiated and responds poorly to PD-1:PD-L blockade. Blocking PD-1:PD-L interactions reduces spontaneous apoptosis and enhances expansion and protective immunity of the rescuable subset, but not the more terminally differentiated subset of exhausted CD8 T cells. These results have implications for predicting clinical responses to PD-1-based therapeutic interventions and for understanding T cell dynamics during persisting infections.
σ 54 -Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111 (2015)

Members of the genus Burkholderia are versatile bacteria capable of colonizing highly diverse environmental niches. In this study, we investigated the global response of the opportunistic pathogen Burkholderia cenocepacia H111 to nitrogen limitation at the transcript and protein expression levels. In addition to a classical response to nitrogen starvation, including the activation of glutamine synthetase, PII proteins, and the two-component regulatory system NtrBC, B. cenocepacia H111 also upregulated polyhydroxybutyrate (PHB) accumulation and exopolysaccharide (EPS) production in response to nitrogen shortage. A search for consensus sequences in promoter regions of nitrogen-responsive genes identified a σ(54) consensus sequence. The mapping of the σ(54) regulon as well as the characterization of a σ(54) mutant suggests an important role of σ(54) not only in control of nitrogen metabolism but also in the virulence of this organism.
Biomimetic aerobic 1,4-oxidation of 1,3-dienes catalyzed by cobalt tetraphenylporphyrin-hydroquinone-palladium(II). An example of triple catalysis (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBiomimetic aerobic 1,4-oxidation of 1,3-dienes catalyzed by cobalt tetraphenylporphyrin-hydroquinone-palladium(II). An example of triple catalysisJ. E. Baeckvall, A. K. Awasthi, and Z. D. RenkoCite this: J. Am. Chem. Soc. 1987, 109, 15, 4750–4752Publication Date (Print):July 1, 1987Publication History Published online1 May 2002Published inissue 1 July 1987https://pubs.acs.org/doi/10.1021/ja00249a065https://doi.org/10.1021/ja00249a065research-articleACS PublicationsRequest reuse permissionsArticle Views916Altmetric-Citations138LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Human leucocyte antigen typing: techniques and technology, a critical appraisal (2011)

Methods for the identification of Human Leukocyte Antigens (HLA) have changed significantly since this group of polymorphic proteins were first characterized by serological reagents in the 1960s and 1970s. The invention and development of the Polymerase Chain Reaction (PCR) has been key in the progress of methods for HLA genotyping. As the complexity of HLA polymorphism has unravelled so it has exposed the weaknesses in techniques such as PCR - Restriction Fragment Length Polymorphism (RFLP) and Reference Strand Mediated Conformation Analysis (RSCA), which are no longer in use today. Methods which have been considered routine laboratory tools in recent years, such as Sequence-Specific Primer - PCR and Sequencing Based Typing (SBT) are now also threatened with extinction, not only because of the depth of HLA variation but also because of the rapid development of Next Generation Sequencing and technologies which will follow this. This review describes the merits and disadvantages of current technologies available to HLA Typing laboratories, future trends and the problems posed by new alleles.
Autophagy Regulates Endoplasmic Reticulum Homeostasis and Calcium Mobilization in T Lymphocytes (2010)

Macroautophagy (hereafter referred to as autophagy) is an evolutionarily conserved intracellular bulk degradation pathway that plays critical roles in eliminating intracellular pathogens, presenting endogenous Ags, and regulating T lymphocyte survival and proliferation. In this study, we have investigated the role of autophagy in regulating the endoplasmic reticulum (ER) compartment in T lymphocytes. We found that ER content is expanded in mature autophagy-related protein (Atg) 7-deficient T lymphocytes. Atg7-deficient T cells stimulated through the TCR display impaired influx, but not efflux, of calcium, and ER calcium stores are increased in Atg7-deficient T cells. Treatment with the ER sarco/ER Ca(2+)-ATPase pump inhibitor thapsigargin rescues the calcium influx defect in Atg7-deficient T lymphocytes, suggesting that this impairment is caused by an intrinsic defect in ER. Furthermore, we found that the stimulation-induced redistribution of stromal interaction molecule-1, a critical event for the store-operated Ca(2+) release-activated Ca(2+) channel opening, is impaired in Atg7-deficient T cells. Together, these findings indicate that the expanded ER compartment in Atg7-deficient T cells contains increased calcium stores, and the inability of these stores to be depleted causes defective calcium influx in these cells. Our results demonstrate that autophagy plays an important role in maintaining ER and calcium homeostasis in T lymphocytes.
The Muscle Protein Dok-7 Is Essential for Neuromuscular Synaptogenesis (2006)

The formation of the neuromuscular synapse requires muscle-specific receptor kinase (MuSK) to orchestrate postsynaptic differentiation, including the clustering of receptors for the neurotransmitter acetylcholine. Upon innervation, neural agrin activates MuSK to establish the postsynaptic apparatus, although agrin-independent formation of neuromuscular synapses can also occur experimentally in the absence of neurotransmission. Dok-7, a MuSK-interacting cytoplasmic protein, is essential for MuSK activation in cultured myotubes; in particular, the Dok-7 phosphotyrosine-binding domain and its target in MuSK are indispensable. Mice lacking Dok-7 formed neither acetylcholine receptor clusters nor neuromuscular synapses. Thus, Dok-7 is essential for neuromuscular synaptogenesis through its interaction with MuSK.
Three agonist antibodies in combination with high-dose IL-2 eradicate orthotopic kidney cancer in mice (2010)

Responses of subcutaneous tumors to immunotherapy do not necessarily reflect how orthotopic tumors respond. The use of combination immunotherapy stimulating multiple facets of immunity and including cytokine support for T cells can induce effective anti-tumor responses against orthotopic and metastatic tumors.
Observation of stimulated Brillouin scattering in low-loss silica fibre at 1.3 μm (1982)

Stimulated Brillouin scattering (SBS) in low-loss single-mode silica fibre is observed at 1.32 μm using a continuous-wave single-frequency Nd:YAG laser. The threshold for SBS is 5 mW and the transmitted power reaches a saturated maximum for launch powers exceeding about 10 mW. A conversion efficiency of 65% is observed. The Stokes frequency shift is 12.7±0.2 GHz.
Mouse hepatitis virus spike and nucleocapsid proteins expressed by adenovirus vectors protect mice against a lethal infection (1993)

Infection with the mouse hepatitis coronavirus (MHV) provides an excellent model for the study of viral diseases of the central nervous system and the gastrointestinal tract. With the ultimate aim of studying mucosal immunity to MHV we have cloned the genes encoding the structural proteins of MHV strain A59 (MHV-A59) into the E3 region of a human adenovirus type 5 vector. Infection of HeLa cells with the resulting recombinant adenoviruses AdMHVS, AdMHVN and AdMHVM revealed the correct expression of the spike (S), nucleocapsid (N) and membrane (M) proteins, respectively. Intraperitoneal inoculation of BALB/c mice with the recombinant viruses elicited serum antibodies which specifically recognized the respective MHV proteins in an immunoprecipitation assay. Only antibodies to the S protein neutralized MHV-A59 in vitro but titres were low. When analysed by ELISA or by immunofluorescence only the antibody response to the N protein was significant; weak responses or no detectable response at all were found for S and M, respectively. Upon intracerebral challenge with a lethal dose of MHV-A59 we found that a significant fraction of animals vaccinated with adenovirus vectors expressing either the S protein or N protein were protected. This protective effect was significantly stronger when the animals were given a booster immunization with the same vector prior to challenge. No protection was induced by AdMHVM. Interestingly, enhanced protection resulted when AdMHVS and AdMHVN were applied in combination as compared to survival after single immunizations. The results indicate that both the N and S proteins generate a protective immune response and suggest that this response is enhanced by combined expression of the two proteins.
Morphology Evolution of SiO2 Films Deposited by Tetraethylorthosilicate/O3 Atmospheric-Pressure Chemical Vapor Deposition on Thermal SiO2 (1999)

To understand the surface dependence of chemical vapor deposition using tetraethylorthosilicate and O 3 , the evolution of the morphology of 5.3-µm-thick oxide films deposited on thermal oxide was observed by scanning electron microscopy. The surface roughness and low etching resistance of the films was caused by different growth rates at different surface sites. Some sites grow much faster that other sites, evolving from island, to tree, and finally to continuous films. Because of this growth sequence, the film has high porosity and is rough. This growth mode might be caused by site-dependent tetraethylorthosilicate absorption rates.
Field Demonstration of the Electrofrac Heatflood Process (1994)

Abstract This paper will present the results of a field demonstration of a less known enhanced oil recovery process named Electrofrac Heatflood process. The process entails the use of down-hole electrodes mounted in the oil sand, a specially configured electric power unit, and facilities for injecting air and fuel into a controlled combustion zone within the area stimulated. One essential feature is creation of electrically conductive paths within the oil sand. This is accomplished in either, or both of two mutually supportive ways: (1) electrocarbonization of a small portion of the oil present between electrodes mounted in the oil sand and (2) injection of electrically conductive pellets with, or in place of the sand normally injected during hydrofracing as part of the original well completion. The process has been field tested successfully for the typical largely heterogeneous oil sands found in predominately fluvial deltaic formations. Field test was initially performed during 1979 and 1980 on a lease named Beachner-1 located in the east-central portion of Neosho County, Kansas and again in 1983 to 1985 expanded to Beachner-1 and Beachner-2. The oil reservoir at the location is shallow and generally unproductive with essentially no natural driving pressure, and natural flow is typically just 1 to 3 gallons per day per well from about twenty feet of pay sand. During the initial field test, an enhancement ratio of 4.5 to 5.4 was achieved relative to natural production, even though the field was only partially stimulated Observed enhancement ratio during the second field test ranged from 4.6 to 10.7. And the enhancement ratio at the other more remote wells ranged from 1.8 to 3.1 giving overall enhancement ratios of 2.4 to 5.5 for all wells then on the lease at that time. Increased production was sustained for more than two years through partial stimulation of the field containing fifty wells. The neighboring leases to the south also benefitted indirectly from the stimulation on the Beachner-1 and Beachner-2 leases. The Electrofrac Heatflood process facilities included a specially outfitted 500 KVA diesel electric generator, electrodes mounted down-hole in the oil sand, air and fuel injection facilities, and proprietary means for distributing electric energy deep into the oil sand to promote heat cycles through controlled combustion within patterns of injection and production wells. The process has been proven to be an effective recovery technique for those reservoirs that because of nature of their heterogeneity the conventional recovery techniques fail.
Identification and characterization of a novel non-infectious herpes simplex virus-related particle (1991)

During gradient purification of herpes simplex virus type 1 (HSV-1) two bands of particles were observed: a sharp lower band and a more diffuse upper band. The lower band contained almost exclusively HSV-1 virions (H particles) whereas the upper band consisted of membrane-enclosed particles (L particles). These L particles resembled the virions in appearance, but lacked the viral nucleocapsid and were not infectious. Many polypeptides of the viral envelope and the tegument were common to both types of particles. The H particles had polypeptide profiles typical of HSV virions. The L particles contained at least three phosphoproteins (175K, 92K and 55K) and a further two phosphorylated polypeptides not normally observed in virion profiles which comigrated with the 134K and 60K glycoproteins. This clearly indicates that the novel L particles were not merely virions which had formed without the inclusion of a nucleocapsid or virions which had subsequently lost their nucleocapsid during preparative handling. Thus these novel L particles are genuine products of the infectious processes occurring when HSV-1 replicates.
Loss of Function in Mlo Orthologs Reduces Susceptibility of Pepper and Tomato to Powdery Mildew Disease Caused by Leveillula taurica (2013)

Powdery mildew disease caused by Leveillula taurica is a serious fungal threat to greenhouse tomato and pepper production. In contrast to most powdery mildew species which are epiphytic, L. taurica is an endophytic fungus colonizing the mesophyll tissues of the leaf. In barley, Arabidopsis, tomato and pea, the correct functioning of specific homologues of the plant Mlo gene family has been found to be required for pathogenesis of epiphytic powdery mildew fungi. The aim of this study was to investigate the involvement of the Mlo genes in susceptibility to the endophytic fungus L. taurica. In tomato (Solanum lycopersicum), a loss-of-function mutation in the SlMlo1 gene results in resistance to powdery mildew disease caused by Oidium neolycopersici. When the tomato Slmlo1 mutant was inoculated with L. taurica in this study, it proved to be less susceptible compared to the control, S. lycopersicum cv. Moneymaker. Further, overexpression of SlMlo1 in the tomato Slmlo1 mutant enhanced susceptibility to L. taurica. In pepper, the CaMlo2 gene was isolated by applying a homology-based cloning approach. Compared to the previously identified CaMlo1 gene, the CaMlo2 gene is more similar to SlMlo1 as shown by phylogenetic analysis, and the expression of CaMlo2 is up-regulated at an earlier time point upon L. taurica infection. However, results of virus-induced gene silencing suggest that both CaMlo1 and CaMlo2 may be involved in the susceptibility of pepper to L. taurica. The fact that overexpression of CaMlo2 restored the susceptibility of the tomato Slmlo1 mutant to O. neolycopersici and increased its susceptibility to L. taurica confirmed the role of CaMlo2 acting as a susceptibility factor to different powdery mildews, though the role of CaMlo1 as a co-factor for susceptibility cannot be excluded.
Only the soluble form of the scavenger receptor CD163 acts inhibitory on phorbol ester‐activated T‐lymphocytes, whereas membrane‐bound protein has no effect (2002)

The extracellular moiety of the hemoglobin/haptoglobin scavenger receptor CD163 (RM3/1 antigen) can be shed from monocytes and is a normal plasma component. We found that in a dose-dependent manner soluble CD163 induces a decrease in CD69 expression, a reduced [(3)H]thymidine uptake and a down-regulated matrix metalloproteinase-9 RNA expression in phorbol myristate acetate-stimulated T-cells. Co-culturing T-cells on transgenic fibroblasts, expressing membrane-bound CD163, yielded no differences compared to culture on non-transfected cells. We conclude that CD163 has at least two distinct functions: the clearance of hemoglobin in its cell-bound form and participation in anti-inflammation as a soluble factor, exhibiting cytokine-like functions.
Oncogenes and onco‐suppressor genes: Their involvement in cancer (1989)

We review the involvement of two groups of genes, oncogenes and onco-suppressor genes, in malignant transformation. Approximately 40 oncogenes have been described mainly through studies on retroviruses and by in vitro functional analyses such as transfection of transforming genes into 'normal' cells. Because they are more difficult to identify, only a handful of onco-suppressor genes have been described so far, but potentially they could number as many as oncogenes. Where these genes have been isolated and sequenced, they have been shown to be highly conserved among species, suggesting that these genes play an essential role in the normal cell. Although some of properties of oncogenes have been identified, we do not know in detail the role these genes play in normal cells or how genetic damage contributes to malignancy. The effect of oncogene expression on a cell depends both on the cell type and on the oncogene, and in some circumstances oncogenes act as onco-suppressor genes and vice versa. The elucidation of the mechanism of action of oncogenes and onco-suppressor genes will not only increase our understanding of these important genes but might also provide the framework for a biological approach to the treatment of cancer.
Reversion of a live porcine reproductive and respiratory syndrome virus vaccine investigated by parallel mutations (2001)

A live attenuated porcine reproductive and respiratory syndrome (PRRS) vaccine virus has been shown to revert to virulence under field conditions. In order to identify genetic virulence determinants, ORF1 from the attenuated vaccine virus and three Danish vaccine-derived field isolates was sequenced and compared with the parental strain of the vaccine virus (VR2332). This revealed five mutations that had occurred independently in all three vaccine-derived field isolates, indicating strong parallel selective pressure on these positions in the vaccine virus when used in swine herds. Two of these parallel mutations were direct reversions to the parental VR2332 sequence and were situated in a papain-like cysteine protease domain and in the helicase domain. The remaining parallel mutations might be seen as second-site compensatory mutations for one or more of the mutations that accumulated in the vaccine virus sequence during cell-culture adaptation. Evaluation of the remaining mutations in the ORF1 sequence revealed stronger selective pressure for amino acid conservation during spread in pigs than during vaccine production. Furthermore, it was found that the selective pressure did not change during the time period studied. The implications of these findings for PRRS vaccine attenuation and reversion are discussed.