gebhart/patrepeval huggingface dataset:
Structure and repertoire usage of rat TCR alpha-chain genes in T cells infiltrating heart allografts. (1995)

We have studied the structure and diversity of TCR alpha-chain genes used by graft-infiltrating lymphocytes (GIL) in the ACI-to-LEW rat cardiac allograft model. We previously reported the structure of 16 different V alpha and 17 different J alpha genes isolated in two different cDNA libraries established from LEW thymocytes and GIL. In this report, we obtained new sequence information for 17 additional V alpha and J alpha genes from the GIL cDNA library. This study completes our characterization of 33 different V alpha and 23 different J alpha genes in rats. The V alpha genes are classified into 14 different families. Nucleotide sequence comparison with mouse alpha genes revealed the existence of mouse homologues for all the J alpha and 32 of the 33 V alpha genes. One of the rat V alpha genes seemed to have no known mouse counterpart and is classified here as a V alpha 24 gene family. The definition of rat TCR alpha-chain genes derived from these studies should facilitate a better understanding of the T cell role in pathologic conditions including autoimmune diseases and graft rejection. As for the TCR alpha-chain repertoire usage in allograft rejection, we completed the characterization of 36 productively rearranged TCR alpha-chain cDNA clones from the GIL cDNA library and found 31 different V alpha and 23 different J alpha genes among these clones. Unlike the TCR beta-chain that uses a limited repertoire, the alpha-chain repertoire usage seems to be relatively more diverse in this allograft model. These results suggest that the interaction of beta-chain with allogeneic MHC-encoded determinants may dictate the T cell reaction to the heart allograft in this model.
Generation of Herpesvirus Entry Mediator (HVEM)-Restricted Herpes Simplex Virus Type 1 Mutant Viruses: Resistance of HVEM-Expressing Cells and Identification of Mutations That Rescue Nectin-1 Recognition (2009)

Both initial infection and cell-to-cell spread by herpes simplex virus type 1 (HSV-1) require the interaction of the viral glycoprotein D (gD) with an entry receptor on the cell surface. The two major HSV entry receptors, herpesvirus entry mediator (HVEM) and nectin-1, mediate infection independently but are coexpressed on a variety of cells. To determine if both receptors are active in these instances, we have established mutant viruses that are selectively impaired for recognition of one or the other receptor. In plaque assays, these viruses showed approximately 1,000-fold selectivity for the matched receptor over the mismatched receptor. Separate assays showed that each virus is impaired for both infection and spread through the mismatched receptor. We tested several human tumor cell lines for susceptibility to these viruses and observed that HT29 colon carcinoma cells are susceptible to infection by nectin-1-restricted virus but are highly resistant to HVEM-restricted virus infection, despite readily detectable HVEM expression on the cell surface. HVEM cDNA isolated from HT29 cells rendered HSV-resistant cells permissive for infection by the HVEM-restricted virus, suggesting that HT29 cells lack a cofactor for HVEM-mediated infection or express an HVEM-specific inhibitory factor. Passaging of HVEM-restricted virus on nectin-1-expressing cells yielded a set of gD missense mutations that each restored functional recognition of nectin-1. These mutations identify residues that likely play a role in shaping the nectin-1 binding site of gD. Our findings illustrate the utility of these receptor-restricted viruses in studying the early events in HSV infection.
Modulation of cyclic-nucleotide-gated channels and regulation of vertebrate phototransduction (2001)

Cyclic-nucleotide-gated (CNG) channels are crucial for sensory transduction in the photoreceptors (rods and cones) of the vertebrate retina. Light triggers a decrease in the cytoplasmic concentration of cyclic GMP in the outer segments of these cells, leading to closure of CNG channels and hyperpolarization of the membrane potential. Hence, CNG channels translate a chemical change in cyclic nucleotide concentration into an electrical signal that can spread through the photoreceptor cell and be transmitted to the rest of the visual system. The sensitivity of phototransduction can be altered by exposing the cells to light, through adaptation processes intrinsic to photoreceptors. Intracellular Ca(2+) is a major signal in light adaptation and, in conjunction with Ca(2+)-binding proteins, one of its targets for modulation is the CNG channel itself. However, other intracellular signals may be involved in the fine-tuning of light sensitivity in response to cues internal to organisms. Several intracellular signals are candidates for mediating changes in cyclic GMP sensitivity including transition metals, such as Ni(2+) and Zn(2+), and lipid metabolites, such as diacylglycerol. Moreover, CNG channels are associated with protein kinases and phosphatases that catalyze changes in phosphorylation state and allosterically modulate channel activity. Recent studies suggest that the effects of circadian rhythms and retinal transmitters on CNG channels may be mediated by such changes in phosphorylation. The goal of this paper is to review the molecular mechanisms underlying modulation of CNG channels and to relate these forms of modulation to the regulation of light sensitivity.
Failure of thermoregulation in the cold during hypoglycaemia induced by exercise and ethanol (1973)

1. After young men had exercised for approximately 2 hr at 70% maximum O 2 uptake, and taken 28 ml. ethanol by mouth, their mean blood glucose fell to 2·17 m M . It fell further to 1·77 m M during a 30 min exposure to air at 14·5° C. Plasma lactate, glycerol, β‐hydroxybutyrate and free fatty acid concentrations increased. 2. Rectal temperature fell to reach a mean level of 34·49° C by the end of the cold exposure; oesophageal temperature fell to as low as 33·00° C in one case. 3. Virtually no increase in metabolic rate and no visible shivering occurred during the cold exposure. 4. Administration of glucose (mean 60·4 g) prevented the falls in temperature, and restored metabolic response to the cold to the size found in control experiments without exercise or ethanol. 5. Neither exercise without ethanol or ethanol without exercise significantly lowered the blood glucose or impaired the maintenance of body temperature in the cold. 6. One obese subject showed almost as great a fall in blood glucose and depression of metabolic response to cold as the thinner men, but no fall in body temperature.
Current Status of Zika Virus Vaccines: Successes and Challenges (2020)

The recently emerged Zika virus (ZIKV) spread to the Americas, causing a spectrum of congenital diseases including microcephaly in newborn and Guillain-Barré syndrome (GBS) in adults. The unprecedented nature of the epidemic and serious diseases associated with the viral infections prompted the global research community to understand the immunopathogenic mechanisms of the virus and rapidly develop safe and efficacious vaccines. This has led to a number of ZIKV vaccine candidates that have shown significant promise in human clinical trials. These candidates include nucleic acid vaccines, inactivated vaccines, viral-vectored vaccines, and attenuated vaccines. Additionally, a number of vaccine candidates have been shown to protect animals in preclinical studies. However, as the epidemic has waned in the last three years, further development of the most promising vaccine candidates faces challenges in clinical efficacy trials, which is needed before a vaccine is brought to licensure. It is important that a coalition of government funding agencies and private sector companies is established to move forward with a safe and effective vaccine ready for deployment when the next ZIKV epidemic occurs.
Evidence that the inositol phospholipids are necessary for exocytosis. Loss of inositol phospholipids and inhibition of secretion in permeabilized cells caused by a bacterial phospholipase C and removal of ATP (1990)

We directly manipulated the levels of PtdIns, PtdInsP and PtdInsP2 in digitonin-treated adrenal chromaffin cells with a bacterial phospholipase C (PLC) from Bacillus thuringiensis and by removal of ATP. The PtdIns-PLC acted intracellularly to cause a large decrease in [3H]inositol- or [32P]phosphate-labelled PtdIns, but did not directly hydrolyse PtdInsP or PtdInsP2. [3H]PtdInsP and [3H]PtdInsP2 levels declined markedly, probably because of the action of phosphatases in the absence of synthesis. Removal of ATP also caused marked decreases in [3H]PtdInsP and [3H]PtdInsP2. The decrease in polyphosphoinositide levels by PtdIns-PLC treatment or ATP removal was reflected by the inhibition of the production of inositol phosphates upon subsequent activation of the endogenous PLC by Ca2(+)-dependent catecholamine secretion from permeabilized cells was strongly inhibited by PtdIns-PLC treatment and by ATP removal. Ca2(+)-dependent secretion was similarly correlated with the sum of PtdInsP and PtdInsP2 when the level of these lipids was changed by either manipulation. PtdIns-PLC inhibited only the ATP-dependent component of secretion and did not affect ATP-dependent secretion. Both PtdIns-PLC and ATP removal inhibited the late slow phase of secretion, but had little effect on the initial rapid phase. Although we found a tight correlation between polyphosphoinositide levels and secretion, endogenous phospholipase C activity (stimulated by Ca2+, guanine nucleotides and related agents) was not correlated with secretion. Additional experiments indicated that neither the products of the PtdIns-PLC reaction (diacylglycerol and InsP1) nor the inability to generate products by subsequent activation of the endogenous PLC is likely to account for the inhibition of secretion. Incubation of permeabilized cells with neomycin in the absence of ATP maintained the level of polyphosphoinositides and more than doubled subsequent Ca2(+)-dependent secretion. The data suggest that: (1) Ca2(+)-dependent secretion has a requirement for the presence of inositol phospholipids; (2) the enhancement of secretion by ATP results in part from increased polyphosphoinositide levels; and (3) the role for inositol phospholipids in secretion revealed in these experiments is independent of their being substrates for the generation of diacylglycerol and InsP3.
Liquefaction of lignocellulose at high‐solids concentrations (2006)

To improve process economics of the lignocellulose to ethanol process a reactor system for enzymatic liquefaction and saccharification at high-solids concentrations was developed. The technology is based on free fall mixing employing a horizontally placed drum with a horizontal rotating shaft mounted with paddlers for mixing. Enzymatic liquefaction and saccharification of pretreated wheat straw was tested with up to 40% (w/w) initial DM. In less than 10 h, the structure of the material was changed from intact straw particles (length 1-5 cm) into a paste/liquid that could be pumped. Tests revealed no significant effect of mixing speed in the range 3.3-11.5 rpm on the glucose conversion after 24 h and ethanol yield after subsequent fermentation for 48 h. Low-power inputs for mixing are therefore possible. Liquefaction and saccharification for 96 h using an enzyme loading of 7 FPU/g.DM and 40% DM resulted in a glucose concentration of 86 g/kg. Experiments conducted at 2%-40% (w/w) initial DM revealed that cellulose and hemicellulose conversion decreased almost linearly with increasing DM. Performing the experiments as simultaneous saccharification and fermentation also revealed a decrease in ethanol yield at increasing initial DM. Saccharomyces cerevisiae was capable of fermenting hydrolysates up to 40% DM. The highest ethanol concentration, 48 g/kg, was obtained using 35% (w/w) DM. Liquefaction of biomass with this reactor system unlocks the possibility of 10% (w/w) ethanol in the fermentation broth in future lignocellulose to ethanol plants.
Energy level line-up in polymer light-emitting diodes via electroabsorption spectroscopy (2001)

The influence of carrier-injecting layers on the built-in potential of polymer light-emitting diodes (PLEDs) is analysed by means of electroabsorption spectroscopy. Two promising materials on which research has recently focused are: first, poly(ethylene-dioxythiophene)/poly(styrene sulphonic acid) (PEDOT:PSS), a doped conducting polymer employed as hole injector; and secondly, lithium fluoride (LiF), which has been shown to enhance electron injection of Al-based cathodes. In the first samples LEDs with an indium tin oxide (ITO) anode were compared to those incorporating a PEDOT:PSS layer (in an ITO/PEDOT:PSS bilayer anode). In the second set of samples the comparison was between LEDs with an aluminium cathode and those incorporating a LiF layer (in an Al/LiF bilayer cathode) as a function of LiF thickness. Electroabsorption spectroscopy results supported by work function measurements clearly prove that both PEDOT:PSS and LiF introduce a large reduction in the barrier height at the anode and cathode interfaces, respectively. The ensuing enhancement in carrier injection is considered to be responsible for the marked improvement in device performance (lower operating voltages, higher luminous efficiencies and longer lifetimes).
Capillary electrophoresis with laser-induced fluorescence detection of PCR fragments using thiazole orange (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCapillary electrophoresis with laser-induced fluorescence detection of PCR fragments using thiazole orangeHerbert E. Schwartz and Kathi J. UlfelderCite this: Anal. Chem. 1992, 64, 15, 1737–1740Publication Date (Print):August 1, 1992Publication History Published online1 May 2002Published inissue 1 August 1992https://pubs.acs.org/doi/10.1021/ac00039a019https://doi.org/10.1021/ac00039a019research-articleACS PublicationsRequest reuse permissionsArticle Views290Altmetric-Citations91LEARN 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
Measuring Markers of Liver Function Using a Micropatterned Paper Device Designed for Blood from a Fingerstick (2012)

This paper describes a paper-based microfluidic device that measures two enzymatic markers of liver function (alkaline phosphatase, ALP, and aspartate aminotransferase, AST) and total serum protein. A device consists of four components: (i) a top plastic sheet, (ii) a filter membrane, (iii) a patterned paper chip containing the reagents necessary for analysis, and (iv) a bottom plastic sheet. The device performs both the sample preparation (separating blood plasma from erythrocytes) and the assays; it also enables both qualitative and quantitative analysis of data. The data obtained from the paper-microfluidic devices show standard deviations in calibration runs and "spiked" standards that are acceptable for routine clinical use. This device illustrates a type of test useable for a range of assays in resource-poor settings.
Mechanism of Selective Inhibition of Respiratory Syncytial Virus by a Benzodithiin Compound (RD3–0028) (2001)

RD3-0028, a compound with a benzodithiin structure, was found to be a potent inhibitor of respiratory syncytial virus (RSV) replication. Its action is specific; no activity is seen against influenza A virus, measles virus, herpes simplex virus type 1 or 2, or human cytomegalovirus. A time-dependent drug addition experiment indicated that the antiviral activity occurs in the late stage of the RSV replication cycle, since this compound completely inhibited syncytium formation even when added up to 16 hr after the infection of cell monolayers at an MOI of 3. RD3-0028 had no direct virucidal effect on RSV. Western blotting analysis showed that RD3-0028 significantly decreased the amount of RSV proteins released into the cell culture medium. Moreover, five independent isolates of the RSV long strain were selected for growth in RD3-0028 (5-20 microg/ml). These resistant viruses were more than 80-fold less sensitive to RD3-0028 than the long strain. The F gene segment of each of these viruses was sequenced and in each case the mutant RNA segment contained at least one sequence alteration, converting asparagine 276 to tyrosine (F1 protein). These results suggest that RD3-0028 inhibits RSV replication by interfering with intracellular processing of the RSV fusion protein, or a step immediately thereafter, leading to loss of infectivity.
Increased plaque burden in brains of APP mutant MnSOD heterozygous knockout mice (2004)

Abstract A growing body of evidence suggests a relationship between oxidative stress and β‐amyloid (Aβ) peptide accumulation, a hallmark in the pathogenesis of Alzheimer's disease (AD). However, a direct causal relationship between oxidative stress and Aβ pathology has not been established in vivo . Therefore, we crossed mice with a knockout of one allele of manganese superoxide dismutase (MnSOD), a critical antioxidant enzyme, with Tg19959 mice, which overexpress a doubly mutated human β‐amyloid precursor protein (APP). Partial deficiency of MnSOD, which is well established to cause elevated oxidative stress, significantly increased brain Aβ levels and Aβ plaque burden in Tg19959 mice. These results indicate that oxidative stress can promote the pathogenesis of AD and further support the feasibility of antioxidant approaches for AD therapy.
Selective cancer cell apoptosis induced by FTY720; evidence for a Bcl-dependent pathway and impairment in ERK activity. (2003)

FTY720 may be a promising candidate for a new anticancer therapy, which potentially induces selective apoptosis in cancer cells.
Percutaneous implantation of the corevalve aortic valve prosthesis for patients presenting high risk for surgical valve replacement. (2006)

Introduction Today’s standard practice of care for heart valve replacement requires open-heart surgery. Nevertheless current population with aortic valve disease is both older and has a higher incidence of associated cardiovascular or non-cardiovascular disease increasing the risk of conventionnal surgery. Percutaneous endovascular therapies widely used in the treatment of coronary artery disease is still at a very early stage in the treatment of valve disease with few patients having recently experienced percutaneous or mini-invasive aortic valve replacement1,3. Corevalve has developed a system called “CoreValve ReValvingTM System” (CRS). This system is intended for Percutaneous Aortic Valve Replacement (PAVR) on a beating heart, avoiding open-heart surgery in patients presenting high risk or recused for surgical valve replacement. The present report describes a last generation device, pre-clinical data, anatomic requirements and technique of implantation of the CoreValve Aortic Valve Prosthesis.
Anti-My-28, an antigranulocyte mouse monoclonal antibody, binds to a sugar sequence in lacto-N-neotetraose (1985)

Anti-My-28 is an IgM kappa monoclonal antibody produced by a hybridoma prepared from spleen cells of a mouse immunized with normal human granulocytes. By immunofluorescence it binds to human granulocytes but not to monocytes and lymphocytes. However, after treating cells with neuraminidase, the antibody also binds to lymphocytes and monocytes and to many leukemic cell lines and patient leukemic blast cells. Anti-My- 28 binds to several neutral glycolipids and desialylated gangliosides of leukocytes and erythrocytes as detected by radioimmunoassay and immunostaining of thin-layer chromatograms. It recognizes a sugar sequence in lacto-N-neotetraose, Gal beta 1–4GlcNAc beta 1–3Gal beta 1–4Glc. This tetrasaccharide occurs in the glycolipids paragloboside and sialosylparagloboside, and its distal trisaccharide sequence is found in higher glycolipids and in glycoproteins.
Systematic Evolution of a DNA Aptamer Binding to Rat Brain Tumor Microvessels (2001)

Tumor microvessels differ in structure and metabolic function from normal vasculature, and neoangiogenesis is associated with quantitative and qualitative changes in expression of endothelial proteins. Such molecules could serve as molecular addresses differentiating the tumor vasculature from those of the normal brain. We have applied Systematic Evolution of Ligands by EXponential enrichment (SELEX) against transformed endothelial cells as a complex target to select single-stranded DNA-ligands (aptamers) that function as histological markers to detect microvessels of rat experimental glioma, a fatal brain tumor that is highly vascularized. Both the SELEX selection procedure as well as subsequent deconvolution-SELEX were analyzed by fluorescence based methods (flow cytometry and fluorescence microscopy). Of 25 aptamers analyzed, one aptamer was selected that selectively bound microvessels of rat brain glioblastoma but not the vasculature of the normal rat brain including peritumoral areas. The molecular target protein of aptamer III.1 was isolated from endothelial cells by ligand-mediated magnetic DNA affinity purification. This protein was identified by mass spectrometry as rat homologue of mouse pigpen, a not widely known endothelial protein the expression of which parallels the transition from quiescent to angiogenic phenotypes in vitro. Because neoangiogenesis, the formation of new blood vessels, is a key feature of tumor development, the presented aptamer can be used as a probe to analyze pathological angiogenesis of glioblastoma. The presented data show that pigpen is highly expressed in tumor microvessels of experimental rat brain glioblastoma and may play an important role in warranting blood supply, thus growth of brain tumors.
NUCLEAR RECEPTORS IN MACROPHAGE BIOLOGY: At the Crossroads of Lipid Metabolism and Inflammation (2004)

Macrophages are essential modulators of lipid metabolism and the innate immune system. Lipid and inflammatory pathways induced in activated macrophages are central to the pathogenesis of human diseases including atherosclerosis. Recent work has shown that expression of genes involved in lipid uptake and cholesterol efflux in macrophages is controlled by peroxisome proliferator-activated receptors (PPARs) and liver X receptors (LXRs). Other studies have implicated these same receptors in the modulation of macrophage inflammatory gene expression. Together, these observations position PPARs and LXRs at the crossroads of lipid metabolism and inflammation and suggest that these receptors may serve to integrate these pathways in the control of macrophage gene expression. In this review, we summarize recent work that has advanced our understanding of the roles of PPARs and LXRs in macrophage biology and discuss the implication of these results for cardiovascular physiology and disease.