gebhart/patrepeval huggingface dataset:
Replication-defective recombinant adenovirus expressing the Epstein--Barr virus (EBV) envelope glycoprotein gp340/220 induces protective immunity against EBV-induced lymphomas in the cottontop tamarin (1993)

A replication-defective recombinant adenovirus (Ad) expressing the full length Epstein-Barr virus (EBV) major envelope glycoprotein gp340/220 was tested for its ability to protect against EBV-induced lymphoma in the cottontop tamarin. Antibody responses against Ad capsid proteins and EBV gp340/220 were observed but these antibodies did not neutralize EBV in vitro. However, all immunized animals were protected against challenge following three intramuscular doses of the recombinant Ad. These data indicate that the recombinant Ad is potentially a useful vector for vaccination.
Two short autoepitopes on the nuclear dot antigen are similar to epitopes encoded by the Epstein-Barr virus. (1995)

To understand the relationship between antibodies present in patients with anti-nuclear dot (ND) autoimmune disease and the proteins they recognize, epitopes that react with the autoantibodies were mapped. A panel of fusion proteins containing different portions of the ND protein were overproduced in Escherichia coli. Immunoblot analysis with anti-ND antibodies revealed that most (10 of 12) sera recognize two major autoepitopes that are each a maximum of 8 amino acids long. The other two sera recognize one of the two epitopes. In addition to the short linear autoepitopes, a conformational epitope appears to be present on the ND antigen. Each of the two linear epitope sequences shares sequence similarities with those of several viral proteins found in the databases. Furthermore, two fusion proteins containing short Epstein-Barr virus (EBV) protein sequences that are similar to the ND epitopes were recognized by the human autoimmune sera, indicating that the autoepitopes are present in EBV protein sequences. Our results are consistent with the hypothesis that ND autoimmune disease might be associated with EBV infections.
N‐linked oligosaccharide changes with oncogenic transformation require sialylation of multiantennae (1989)

Glycopeptides derived from NIH 3T3 fibroblasts and these cells transformed by transfection with human DNA containing oncogene H-ras were analyzed by 500-MHz 1H-NMR spectroscopy and binding to immobilized lectins. The cells were metabolically labeled with D-[3H]glucosamine or L-[3H]fucose and the glycopeptides included in Bio-Gel P-10 (Mr 5000-3500) were separated into neutral and charged fractions on DEAE-cellulose. The major portion (80%) of these [3H]fucose glycopeptides from the non-transformed NIH 3T3 fibroblasts were neutral or contained one or two charged residues, whereas 90% of the glycopeptides from the transformed cells contained two or more charged residues. The structure of the predominant neutral glycopeptide from the non-transformed NIH 3T3 cells was determined by 1H-NMR spectroscopy to be tetraantennary containing terminal Gal alpha 1----3. (formula; see text) This structure was verified by binding to the immobilized alpha-Gal-specific lectin, Griffonia simplicifolia I and leukoagglutinating phytohemagglutinin from Phaseolus vulgaris (L-PHA), which binds certain tri- or tetraantennary glycopeptides. In contrast, the structure derived by NMR spectroscopy of one of the predominant charged glycopeptides from the transformed cells was triantennary containing terminal NeuNAc alpha 2----3 in addition to Gal alpha 1----3. (formula; see text) In attempting to verify this structure by lectin-binding properties it was found that removal of NeuNAc alpha 2----3 reduced the affinity to L-PHA - agarose. The other major glycopeptides of the transformed cells which were more charged also cotained NeuNAc alpha 2----3 but no NeuNAc alpha 2----6 or Gal alpha 1----3. A tentative structure was proposed for the major glycopeptide of the first charged class from NIH 3T3 cells on the basis of lectin-binding properties and the NMR spectrum which showed, in addition to NeuNAc alpha 2----3, the presence of NeuNAc alpha 2----6 and Gal alpha 1----3. On the basis of the NMR spectrum and other results, it is concluded that the presence of tetraantennary oligosaccharides are not sufficient for the transformed oligosaccharide phenotype. Rather, the tri- or tetraantennae must be sialylated in alpha 2----3 linkage, on more than one antennae, when properties of transformation are expressed in NIH 3T3 cells. Prior to transformation the tetraantennary oligosaccharides of these cells are terminated in alpha-Gal residues, whereas after transformation alpha-Gal residues appear to be replaced by NeuNAc alpha 2----3.(ABSTRACT TRUNCATED AT 400 WORDS)
Biosynthesis of iso-fatty acids in myxobacteria (2005)

The fatty acid (FA) profiles of the myxobacteria Stigmatella aurantiaca and Myxococcus xanthus were investigated by acidic methanolysis of total cell extracts and GC or GC-MS analysis. The main components were 13-methyltetradecanoic acid (iso-15:0) and (Z)-hexadec-11-enoic acid (16:1, omega-5 cis). The biosynthesis of iso-FAs was investigated in several feeding experiments. Feeding of isovaleric acid (IVA) to a mutant impaired in the degradation of leucine to isovaleryl-CoA (IV-CoA)(bkd mutant) of M. xanthus only increased the amount of iso-odd FAs, whereas feeding of isobutyric acid (IBA) gave increased amounts only of iso-even FAs. In contrast, a bkd mutant of S. aurantiaca gave increased amounts of iso-odd and iso-even fatty acids in both experiments. We assumed that in S. aurantiacaalpha-oxidation takes place. [D(7)]-15-Methylhexadecanoic acid was synthesised and fed to S. aurantiaca as well as [D(10)]leucine and [D(8)]valine to elucidate this pathway in more detail. The iso-fatty acid was degraded by alpha- and beta-oxidation steps. [D(10)]Leucine was strongly incorporated into iso-odd and iso-even fatty acids, whereas the incorporation rates for [D(8)]valine into both types of fatty acids were low. Thus alpha-oxidation plays an important role in the biosynthesis of iso-fatty acids in S. aurantiaca. The incorporation rates observed after feeding of [D(10)]leucine and [D(8)]valine are the highest for iso-17:0 compared to the other acids. This indicates the central role of iso-17:0 in the biosynthesis of iso-FAs. The shorter homologues seem to be formed mainly by alpha-oxidation and beta-oxidation of this acid. After feeding of traces of unsaturated counterparts of this labelled FA occurred in the extracts indicating that desaturases are active in the biosynthesis of unsaturated fatty acids in S. aurantiaca.
Induction of Potent CD8 + T-Cell Responses by Novel Biodegradable Nanoparticles Carrying Human Immunodeficiency Virus Type 1 gp120 (2007)

The mainstream of recent anti-AIDS vaccines is a prime/boost approach with multiple doses of the target DNA of human immunodeficiency virus type 1 (HIV-1) and recombinant viral vectors. In this study, we have attempted to construct an efficient protein-based vaccine using biodegradable poly(gamma-glutamic acid) (gamma-PGA) nanoparticles (NPs), which are capable of inducing potent cellular immunity. A significant expansion of CD8+ T cells specific to the major histocompatibility complex class I-restricted gp120 epitope was observed in mice intranasally immunized once with gp120-carrying NPs but not with gp120 alone or gp120 together with the B-subunit of cholera toxin. Both the gp120-encapsulating and -immobilizing forms of NPs could induce antigen-specific spleen CD8+ T cells having a functional profile of cytotoxic T lymphocytes. Long-lived memory CD8+ T cells could also be elicited. Although a substantial decay in the effector memory T cells was observed over time in the immunized mice, the central memory T cells remained relatively constant from day 30 to day 238 after immunization. Furthermore, the memory CD8+ T cells rapidly expanded with boosting with the same immunogen. In addition, gamma-PGA NPs were found to be a much stronger inducer of antigen-specific CD8+ T-cell responses than nonbiodegradable polystyrene NPs. Thus, gamma-PGA NPs carrying various HIV-1 antigens may have great potential as a novel priming and/or boosting tool in current vaccination regimens for the induction of cellular immune responses.
Perioperative gabapentin for the prevention of persistent pain after thoracotomy: a randomized controlled trial (2014)

We found no evidence for the superiority of gabapentin over placebo for the treatment of acute pain following thoracotomy or for the prevention of persistent post-thoracotomy pain.
Graduated response and the emergence of a European surveillance society (2010)

Purpose This paper seeks to offer an alternative critique to graduated response, a warning and sanction mechanism aimed at fighting online piracy. Design/methodology/approach This paper reflects on and frames graduated response in terms of theories on surveillance society and code. In particular, it analyses the graduated response debate in the European Union and the current initiatives in France and the UK. Findings The paper argues that graduated response portrays rights holders as being in a state of emergency, is a form of social sorting, and has a technological bias. Originality/value This paper contends that many objections raised to graduated response have been reduced to issues concerning the procedure rather than the principle, and that important societal questions concerning graduated response remain un(der)explored.
Dye-Sensitized Core−Shell Nanocrystals:  Improved Efficiency of Mesoporous Tin Oxide Electrodes Coated with a Thin Layer of an Insulating Oxide (2002)

Coating nanocrystalline SnO2 electrodes for dye-sensitized solar cell applications with a thin layer of ZnO, TiO2, ZrO2, MgO, Al2O3, Y2O3, or other insulating oxides was found to improve dye adsorption and increase the sensitized photocurrent. The surface of the oxide coating is more basic than SnO2, which renders dye attachment by its carboxyl groups more favorable. At the same time, the photovoltage and fill factor are strongly enhanced, resulting in much better energy conversion efficiencies. This change is ascribed to inhibition of electron back transfer from SnO2 to the redox electrolyte (I3-) by the insulating oxide. The optimum coating thickness is only a few angstroms, suggesting that electron transfer from the excited dye attached to the oxide surface to the underlying SnO2 occurs by tunneling through the insulator layer. Different methods for coating SnO2 nanocrystals with a thin layer of an insulating oxide were compared. The best results were obtained by adding a soluble metal salt to the SnO2 colloid, which is converted to the oxide on firing of the electrode. Specific adsorption of the metal ions on the SnO2 surface guarantees homogeneous coating at near-monolayer coverage. Although the energy conversion efficiency of such modified SnO2 electrodes is still inferior to that of the usually employed TiO2 electrodes, the larger band gap of SnO2 offers the advantage of better long-term stability of the solar cell in the presence of UV light. Surface modification of nanocrystalline TiO2 electrodes with very thin insulating oxide layers also improves the photovoltage but diminishes the current. Because of a blue shift in the photocurrent onset of insulator-coated TiO2, the solar cell stability in UV light is again enhanced.
Contrast mechanisms in polarization-sensitive Mueller-matrix optical coherence tomography and application in burn imaging (2003)

We investigate the various contrast mechanisms provided by polarization-sensitive (PS) Mueller-matrix optical coherence tomography (OCT). Our PS multichannel Mueller-matrix OCT is the first, to our knowledge, to offer simultaneously comprehensive polarization-contrast mechanisms, including the amplitude of birefringence, the orientation of birefringence, and the diattenuation in addition to the polarization-independent intensity contrast, all of which can be extracted from the measured Jones or the equivalent Mueller matrix. Theoretical analysis shows that when diattenuation is negligible, the round-trip Jones matrix represents a linear retarder, which is the foundation of conventional PS-OCT, and can be calculated with a single incident polarization state, although the one-way Jones matrix generally represents an elliptical retarder; otherwise, two incident polarization states are needed. The experimental results obtained from rat skin samples, which conform well with the histology, show that Mueller OCT provides complementary structural and functional information on biological samples and reveal that polarization contrast is more sensitive to thermal degeneration of biological tissue than amplitude-based contrast. Thus, Mueller OCT has significant potential for application in the noninvasive assessment of burn depth.
Objective autorefraction in posterior chamber pseudophakia. (1990)

Automated refraction with the Canon RK-1 Autoref keratometer was evaluated in 110 eyes (110 patients) six to eight weeks after they had undergone extracapsular cataract extraction with posterior chamber intraocular lens implantation and achieved a best corrected visual acuity of at least 6/12. Autorefraction readings were obtained in 100 (91%) of these eyes. The agreement between autorefraction and clinical refraction data was 98% for spherical equivalence less than 0.51 dioptres (D), 95% for sphere power less than 0.51D, 94% for cylinder power less than 0.51D, and 85% for cylinder axis less than 11 degrees. Autorefraction can provide acceptably accurate postoperative refraction values in pseudophakic eyes.
Prenatal protein malnutrition alters the proportion but not numbers of parvalbumin-immunoreactive interneurons in the hippocampus of the adult Sprague-Dawley rat (2011)

Prenatal protein malnutrition alters the structure and function of the adult rat hippocampal formation. The current study examines the effect of prenatal protein malnutrition on numbers of parvalbumin-immunoreactive (PV-IR) GABAergic interneurons, which are important for perisomatic inhibition of hippocampal pyramidal neurons. Brain sections from prenatally protein malnourished and normally nourished rats were stained for parvalbumin and PV-IR neurons were quantified using stereology in the dentate gyrus, CA3/2 and CA1 subfields, and the subiculum for both cerebral hemispheres. Results demonstrated that prenatal malnutrition did not affect the number of PV-IR interneurons in the hippocampus. Since prenatal protein malnutrition reduces total neuron numbers in the CA1 subfield (1), this results in an altered ratio of PV-IR interneurons to total neuronal numbers (from 1:22.9 in controls to 1:20.5 in malnourished rats). Additionally, there was no hemispheric asymmetry of either PV-IR neuron numbers or ratio of PV-IR:total neuron numbers.
Factors influencing proximal dental contact strengths (2000)

The aim of this study was to systematically measure proximal contact strength in complete natural dentitions of 30 adults (25.3 +/- 3.0 years of age), and to analyze its relationship to tooth type, tooth location, chewing effort and time of day variation. The contact strengths were measured dynamically during removal of a calibrated 0.05-mm-thick metal strip between the proximal contacts of adjacent teeth. Proximal contact strengths were lower in the maxilla (2.51 +/- 1.36 N) compared to the mandible (4.26 +/- 1.88 N). Within the jaws, the lowest proximal contact strength was measured between canine and first premolar (2.91 +/- 1.79 N) and the highest between second premolar and first molar (3.73 +/- 1.95 N). Chewing increased the proximal contact strength within the maxilla (before: 2.51 +/- 1.36 N, after: 3.02 +/- 1.45 N) but it remained unchanged in the mandible (before: 4.26 +/- 1.88 N, after: 4.22 +/- 1.85 N). The proximal contact strength increased significantly from morning (3.39 +/- 1.86 N) to noon (3.61 +/- 1.77 N), and then decreased in the afternoon (3.43 +/- 1.60 N). It was concluded that proximal contact strength can be significantly influenced by location, tooth type, chewing and time of day variation. Based on the differences in distribution due to the effect of chewing and time of day, it is speculated that proximal contact strength is a physiological entity of multifactorial origin.
MHC class II molecules deliver costimulatory signals in human T cells through a functional linkage with IL-2-receptors (1993)

MHC class II-positive T cells are found in tissues involved in autoimmune and infectious disorders. Because stimulation of class II molecules by mAb or bacterial superantigens induces protein tyrosine phosphorylation through activation of PTK3 in T cells, we hypothesized that class II signals play a regulatory function in T cell activation. Here, we show that cross-linking HLA-DR and -DP but not -DQ molecules by immobilized mAb enhanced proliferative T cell responses to IL-2. In contrast, class II stimulation had no effect on IL-4-induced proliferation. The costimulatory effect was most pronounced at low concentrations of IL-2, was blocked by IL-2R mAb, and was at least partly mediated through an up-regulation of IL-2 high affinity receptors. As expected, activation of IL-2R by IL-2 induced tyrosine phosphorylation of several proteins including p56lck, and class II cross-linking by mAb induced tyrosine phosphorylation of specific substrates including PLC-gamma 1. Combined stimulation of IL-2R and class II molecules had an additive effect on tyrosine phosphorylation. Pretreatment of T cells with a protein tyrosine kinase inhibitor, herbimycin A, inhibited IL-2 and class II-induced proliferation suggesting that class II costimulation of IL-2 responses may involve activation of tyrosine kinases. Taken together, the present data suggest that extensive cross-linking of class II molecules delivers costimulatory signals that enhance IL-2 sensitivity in human T cells.
Gene expression microarray analysis reveals YKL-40 to be a potential serum marker for malignant character in human glioma. (2002)

We have identified a potential serum marker for glioblastoma multiforme (GBM) using microarray analysis from samples of GBM. We compared the gene expression profile of 19 gliomas to pooled normal brain by competitive hybridization of RNA from each tumor sample to a pooled sample of RNA isolated from normal brain tissue using the Incyte 10,000 gene expression array. The most differentially expressed gene in this analysis encodes a secreted glycoprotein and is referred to as YKL-40. YKL-40 mRNA was detected in the GBM samples with a range of 3- to 62-fold elevation over normal brain. It has been reported previously that this protein is expressed in pathologic conditions of extracellular matrix degradation and angiogenesis, such as rheumatoid arthritis, severe osteoarthritis, hepatic fibrosis, primary colorectal cancer, and metastatic breast cancer. These data suggest YKL-40 may be involved in extracellular matrix degradation and/or angiogenesis. Western blot analysis of glioma samples for YKL-40 protein levels revealed substantial elevation in approximately 65% of GBMs and undetectable levels in lower-grade gliomas (grade II and III) or normal brain tissue. We performed ELISA analysis on serum samples of glioma patients to determine whether this protein would correlate with the presence of tumor and tumor grade or burden. YKL-40 serum levels were substantially elevated in many of the GBM patients. Statistical analysis of these data indicates that in patients with glioma, serum YKL-40 levels correlate with tumor grade and potentially tumor burden in GBM.
Acute kidney injury during the COVID-19 outbreak (2020)

The novel coronavirus disease 2019 is the first coronavirus pandemic in human history. Europe and the USA have become epicenters of the COVID-19 pandemic. Acute kidney injury (AKI) is one of the most common complications during COVID-19, which increases the risk of in-hospital death. In-depth analysis of the occurrence, underlying mechanisms and clinical evidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced AKI helps clinicians to be alert to kidney damage. We believe that people will triumph in this war and save as many lives as possible.
Identification of Biochemical Defects in Pancreatic Islets of fa/fa Rats: A Developmental Study (1995)

Adult obese (fa/fa) Zucker rats hypersecrete insulin in response to glucose and other secretagogues. Functional changes in islet alpha 2-adrenoceptors (8) and glycolytic regulation (9) have been reported. In this study, the development of these biochemical lesions in islets isolated from suckling (3 week old) and weanling (5 week old) lean and fa/fa rats was investigated and compared to results in adult animals. Glucose (15 mM)-induced insulin secretion was inhibited by mannoheptulose (MH) in lean (n = 8) but not fa/fa (n = 10) adult rats, indicating loss of sensitivity of glucokinase to competitive inhibition. Sensitivity to MH was somewhat reduced in the islets of 3- and 5-week-old fa/fa (n = 7 and 12) compared to lean (n = 15 and 9) rats, requiring 30-100 fold higher concentrations to achieve significant inhibition. At 3 weeks of age fa/fa rats did not differ from lean controls in either islet insulin content or body weight, but both parameters were increased in fa/fa rats by 5 weeks. The presence of altered alpha 2-adrenoceptor function in fa/fa rats could not be confirmed in this study. Unlike the previous report, prazosin did not antagonize alpha 2-agonist mediated inhibition of insulin secretion. The presence of defective regulation of the glycolytic pathway by mannoheptulose in suckling and weanling rats may contribute to development of hyperinsulinemia in fa/fa rats.
Isolation and characterization of lon mutants in Salmonella typhimurium (1986)

In this paper we report the isolation and characterization of lon mutants in Salmonella typhimurium. The mutants were isolated by using positive selection by chlorpromazine resistance. The physiological and biochemical properties of the lon mutants in S. typhimurium are very similar to those of Escherichia coli lon mutants. Mutants altered at this locus contain little or no activity of the ATP-dependent protease La and show a number of pleiotropic phenotypes, including increased production of capsular polysaccharides, increased sensitivity to UV light and other DNA-damaging agents, and a decreased ability to degrade abnormal proteins.
Aberrant methylation of NPY, PENK, and WIF1 as a promising marker for blood-based diagnosis of colorectal cancer (2013)

We showed the potential of NPY, PENK, and WIF1 as combined epigenetic markers for CRC diagnosis, both in tissue and serum and tested their use as serum biomarkers in other cancers. We optimized a QM-MSP for simultaneously quantifying their methylation levels. Our assay can be an effective blood test for patients where CRC risk is present but difficult to assess (e.g. mild symptoms with no CRC family history) and who would therefore not necessarily choose to go for further examination. This panel of markers, if validated, can also be a cost effective screening tool for the detection of asymptomatic cancer patients for colonoscopy.