gebhart/patrepeval huggingface dataset:
Juxtaposition of an Active Promoter to vsp Genes via Site-Specific DNA Inversions Generates Antigenic Variation in Mycoplasma bovis (2001)

Mycoplasma bovis, the most important etiological agent of bovine mycoplasmosis, undergoes extensive antigenic variation of major and highly immunogenic surface lipoprotein antigens (Vsps). A family of 13 related but divergent vsp genes, which occur as single chromosomal copies, was recently found in the chromosome of M. bovis. In the present study, the molecular mechanism mediating the high-frequency phase variation of two Vsps (VspA and VspC) as representatives of the Vsp family was investigated. Analysis of clonal isolates exhibiting phase transitions of VspA or of VspC (i.e., ON-->OFF-->ON) has shown that DNA inversions occur during Vsp phase variation. The upstream region of each vsp gene contains two sequence cassettes. The first (cassette no. 1), a 71-bp region upstream of the ATG initiation codon, exhibits 98% homology among all vsp genes, while the second (cassette no. 2), upstream of cassette no. 1, ranges in size from 50 to 180 bp and is more divergent. Examination of the ends of the inverted fragments during VspA or VspC phase variation revealed that in both cases, a change in the organization of vsp upstream cassettes involving three vsp genes had occurred. Primer extension and Northern blot analysis have shown that a specific cassette no. 2, designated A(2), is an active promoter and that juxtaposition of this regulatory element to a silent vsp gene by DNA inversions allows transcription initiation of the recipient gene. Further genetic analysis revealed that phase variation of VspA or of VspC involves two site-specific DNA inversions occurring between inverted copies of a specific 35-bp sequence present within the conserved cassette no. 1. A model for the control of Vsp phase variation is proposed.
Cloning and complete sequence of an HLA-A2 gene: analysis of two HLA-A alleles at the nucleotide level. (1985)

The gene for the HLA-A2 antigen has been cloned from the human lymphoblastoid cell line 721. Comparison of this sequence with the published sequence for HLA-A3 permits the examination of two alleles at the extremely polymorphic HLA-A locus. A high degree of sequence conservation was seen in both coding and noncoding DNA, 97.2% and 94.5%, respectively. Interestingly, the 3' untranslated region was the most conserved, with 99.5% homology. The polymorphism of the HLA-A antigens results from a high proportion of amino acid substitutions relative to the total nucleotide changes in exons 2 and 3. Unlike the clustered differences seen in this region on comparison of two H-2K alleles of mouse, nucleotide substitutions between the HLA-A2 and A3 alleles are evenly distributed. Substitutions at silent sites and within introns were used to calculate an intra-allelic divergence time of at least 10 to 15 million years for these two HLA-A alleles.
Increased accumulation of the glycoxidation product N(epsilon)-(carboxymethyl)lysine in human tissues in diabetes and aging. (1997)

N(epsilon)-(Carboxymethyl)lysine (CML), a major product of oxidative modification of glycated proteins, has been suggested to represent a general marker of oxidative stress and long-term damage to proteins in aging, atherosclerosis, and diabetes. To investigate the occurrence and distribution of CML in humans an antiserum specifically recognizing protein-bound CML was generated. The oxidative formation of CML from glycated proteins was reduced by lipoic acid, aminoguanidine, superoxide dismutase, catalase, and particularly vitamin E and desferrioxamine. Immunolocalization of CML in skin, lung, heart, kidney, intestine, intervertebral discs, and particularly in arteries provided evidence for an age-dependent increase in CML accumulation in distinct locations, and acceleration of this process in diabetes. Intense staining of the arterial wall and particularly the elastic membrane was found. High levels of CML modification were observed within atherosclerotic plaques and in foam cells. The preferential location of CML immunoreactivity in lesions may indicate the contribution of glycoxidation to the processes occurring in diabetes and aging. Additionally, we found increased CML content in serum proteins in diabetic patients. The strong dependence of CML formation on oxidative conditions together with the increased occurrence of CML in diabetic serum and tissue proteins suggest a role for CML as endogenous biomarker for oxidative damage.
Carbohydrate malabsorption and the effect of dietary restriction on symptoms of irritable bowel syndrome and functional bowel complaints. (2000)

Combined sugar malabsorption patterns are common in functional bowel disorders and may contribute to symptomatology in most patients. Dietary restriction of the offending sugar(s) should be implemented before the institution of drug therapy.
CTL responses of HLA-A2.1-transgenic mice specific for hepatitis C viral peptides predict epitopes for CTL of humans carrying HLA-A2.1. (1995)

Vaccine development in animal models depends on ability to recognize epitopes seen by human T cells. In this work, we show that CTL responses in transgenic mice expressing human HLA-A2.1 prospectively predict the same four of 11 hepatitis C virus (HCV) structural protein-derived peptides, expressing a sequence motif for HLA-A2.1 binding, that are actually recognized by human A2.1-restricted CTLs. The CTLs also recognized targets endogenously expressing these proteins. Human CTLs from HCV-infected patients, tested by using the same peptides, revealed a virtually identical response repertoire. A highly conserved HCV core peptide was the most immunogenic, and may be a valuable component of a vaccine against a broad range of HCV isolates in HLA-A2-positive patients. These results suggest that, in spite of species differences, the T cell repertoire is plastic enough to allow a similar response when the same class I MHC molecule is presenting the peptide. Thus, the HLA molecule plays the primary role in determining which peptides are recognized by CTLs. This transgenic mouse model is important for the study of HLA-restricted CTL determinants and for an approach to design a potential HCV vaccine.
Survival Signaling by Notch1: Mammalian Target of Rapamycin (mTOR)–Dependent Inhibition of p53 (2006)

Notch signaling is believed to promote cell survival in general. However, the mechanism is not clearly understood. Here, we show that cells expressing intracellular domain of human Notch1 (NIC-1) are chemoresistant in a wild-type p53-dependent manner. NIC-1 inhibited p53 by inhibiting its activating phosphorylations at Ser(15), Ser(20), and Ser(392) as well as nuclear localization. In addition, we found that inhibition of p53 by NIC-1 mainly occurs through mammalian target of rapamycin (mTOR) using phosphatidylinositol 3-kinase (PI3K)-Akt/protein kinase B (PKB) pathway as the mTOR inhibitor, rapamycin treatment abrogated NIC-1 inhibition of p53 and reversed the chemoresistance. Consistent with this, rapamycin failed to reverse NIC-1-induced chemoresistance in cells expressing rapamycin-resistant mTOR. Further, ectopic expression of eukaryotic initiation factor 4E (eIF4E), a translational regulator that acts downstream of mTOR, inhibited p53-induced apoptosis and conferred protection against p53-mediated cytotoxicity to similar extent as that of NIC-1 overexpression but was not reversed by rapamycin, which indicates that eIF4E is the major target of mTOR in Notch1-mediated survival signaling. Finally, we show that MCF7 (breast cancer) and MOLT4 (T-cell acute lymphoblastic leukemia) cells having aberrant Notch1 signaling are chemoresistant, which can be reversed by both PI3K and mTOR inhibitors. These results establish that Notch1 signaling confers chemoresistance by inhibiting p53 pathway through mTOR-dependent PI3K-Akt/PKB pathway and imply that p53 status perhaps is an important determinant in combination therapeutic strategies, which use mTOR inhibitors and chemotherapy.
Determination of oil content in oilseeds by analytical supercritical fluid extraction (1993)

The total oil content of soyflakes, canola seed and wetmilled corn germ were determined by analytical supercritical fluid extraction (SFE) with carbon dioxide as the extraction solvent. Results obtained by SFE were in excellent agreement with those obtained by a conventional Soxhlet technique with organic solvents. The analytical‐scale SFE technique yielded average means within one standard deviation of the means derived from the organic solvent‐based methodology. Matrices containing both high and low oil content were successfully extracted with carbon dioxide at comparable precision to that obtained with the standard procedure. The supercritical fluid‐based technique appears to be a suitable replacement for traditional extraction methods with organic solvents, thereby potentially eliminating the costs associated with solvent disposal and exposure of laboratory personnel to toxic and flammable solvents.
Intestinal absorption of heparin (1969)

Dimethylsulfoxide and diethylsulfone, and their homologues, induced the absorption of heparin from the rabbit intestine.Using the criterion of prolongation of whole blood clotting time, it was found that the quantitative absorption of heparin, as induced by di-n-propylsulfoxide or di-n-propylsulfone, increased with increasing amount of sodium heparinate administered to the intestine.
Synthesis of Single Crystals of Calcite with Complex Morphologies (2002)

Calcium carbonate single crystal structures (see Figure) have been precipitated in polymer membranes with bicontinuous structures whereby the morphologies are dictated by the polymer membrane. The single crystals exhibit intricate, sponge-like morphologies, demonstrating that synthesis of single crystals with complex structure is not restricted to the realm of biomineralization.
The 3-Deoxy Analogue of α-GalCer: Disclosing the Role of the 4-Hydroxyl Group for CD1d-Mediated NKT Cell Activation (2011)

KRN7000, or α-GalCer, is a potent agonist for natural killer T (NKT) cells. The 3-hydroxyl group of its phytosphingosine moiety is important for activating NKT cells, whereas its 4-hydroxyl group is perceived to be less crucial. To experimentally determine the role of the 4-hydroxyl group, we synthesized the 3-deoxy analogue of α-GalCer. It was found that 3-deoxy-α-GalCer induced potent cytokine responses from NKT cells, comparable to those of both α-GalCer and 4-deoxy-α-GalCer. This result and our docking studies suggest that the effects of an absence of the 3-hydroxyl group are compensated by the presence of a hydroxyl group at the C-4 position. Thus, we conclude that the 4-hydroxyl group of α-GalCer is as important to the mechanism of action as the 3-hydroxyl group and that the two hydroxyl groups could play individual and cooperative roles in orienting the glycolipid into the proper position in CD1d to be recognized by the T cell receptor of NKT cells.
Harmonic inversion of time signals and its applications (1997)

New methods of high resolution spectral analysis of short time signals are presented. These methods utilize the filter-diagonalization approach of Wall and Neuhauser [J. Chem. Phys. 102, 8011 (1995)] that extracts the complex frequencies ωk and amplitudes dk from a signal C(t)=∑kdke−itωk in a small frequency interval by recasting the harmonic inversion problem as the one of a small matrix diagonalization. The present methods are rigorously adapted to the conventional case of the signal available on a sparse equidistant time grid and use a more efficient boxlike filter. Various applications are discussed, such as iterative diagonalization of large Hamiltonian matrices for calculating bound and resonance states, scattering calculations in the presence of narrow resonances, etc. For the scattering problem the harmonic inversion is directly applied to the signal cn=(χf,Tn(Ĥ)χi), generated by the dynamical system governed by a modified Chebyshev recursion, avoiding the usual recasting the problem to the time domain. Some challenging numerical examples are presented. The general filter-diagonalization method is shown to be stable and efficient for the extraction of thousands of complex frequencies ωk and amplitudes dk from a signal. When the model signal is “spoiled” by a moderate amount of an additive Gaussian noise the obtained spectral estimate is still superior to the conventional Fourier spectrum.
Immunological responses to fed protein antigens in mice. II. Oral tolerance for CMI is due to activation of cyclophosphamide-sensitive cells by gut-processed antigen. (1983)

Mice fed ovalbumin develop specific systemic hyporesponsiveness. This oral tolerance is abrogated by cyclophosphamide pretreatment, and the mechanism of abrogation could be either via T suppressor cells or via damage to the gut epithelium. A serum transfer protocol was used to examine the site of action of cyclophosphamide in this system. Serum was collected from ovalbumin-fed mice and transferred into recipients which were then parenterally immunized with ovalbumin in Freund's complete adjuvant. Serum transfer suppressed the delayed-type hypersensitivity (DTH) responses but not the antibody responses of the recipients. Cyclophosphamide pretreatment (100 mg/kg) of recipients (but not of donors) abrogated this suppressor effect. Parenteral administration of ovalbumin in a range of doses did not induce immunological hyporesponsiveness. It is suggested that absorption across the gut mucosa leads to generation of fragments of ovalbumin that induce suppressor cells selective for DTH.
Anti-CD3 scFv-B7.1 fusion protein expressed on the surface of HeLa cells provokes potent T-lymphocyte activation and cytotoxicityThis paper is one of a selection of papers in this Special Issue, entitled International Symposium on Recent Advances in Molecular, Clinical, and Social Medicine, and has undergone the Journal's usual peer-review process. (2007)

The targeting of tumor cells by cytotoxic T lymphocytes is a promising strategy for biotherapy, but T cells require 2 signals via the T-cell receptor - CD3 complex and CD28 molecules for activation. To bridge the gap between cytotoxic T lymphocytes and tumor cells, our objective in this study was to describe the construction and the cell surface-anchored expression of a fusion protein, anti-CD3 scFv-B7.1, derived from inserting a fusion gene encoding anti-CD3 scFv and the extra-cellular domain of B7.1 fused by the splicing by overlap extension method into a mammalian expression vector, pDisplay. Transfection of the recombinant vector by electroporation into HeLa cells resulted in the production of protein migrating at approximately 57 kDa under reducing conditions. The expressed fusion protein could bind to T lymphocytes and induce strong T-cell activation. Meanwhile, a potent cytotoxicity was induced in the mixed culture of T-cell-modified tumor cells in a 96 h methyl-thiazolyl-diphenyl tetrazolium bromide assay. Our results indicate that this bifunctional protein, through activating T lymphocytes to lyse homologous human carcinomas, may be of potential value for T-cell-based immunotherapeutical treatment protocols in vivo.
Arabidopsis Proteins Containing Similarity to the Universal Stress Protein Domain of Bacteria (2003)

We have collected a set of 44 Arabidopsis proteins with similarity to the USPA (universal stress protein A of Escherichia coli) domain of bacteria. The USPA domain is found either in small proteins, or it makes up the N-terminal portion of a larger protein, usually a protein kinase. Phylogenetic tree analysis based upon a multiple sequence alignment of the USPA domains shows that these domains of protein kinases 1.3.1 and 1.3.2 form distinct groups, as do the protein kinases 1.4.1. This indicates that their USPA domain structures have diverged appreciably and suggests that they may subserve distinct cellular functions. Two USPA fold classes have been proposed: one based on Methanococcus jannaschii MJ0577 (1MJH) that binds ATP, and the other based on the Haemophilus influenzae universal stress protein (1JMV), highly similar to E. coli UspA, which does not bind ATP. A set of common residues involved in ATP binding in 1MJH and conserved in similar bacterial sequences is also found in a distinct cluster of Arabidopsis sequences. Threading analysis, which examines aspects of secondary and tertiary structure, confirms this Arabidopsis sequence cluster as highly similar to 1MJH. This structural approach can distinguish between the characteristic fold differences of 1MJH-like and 1JMV-like bacterial proteins and was used to assign the complete set of candidate Arabidopsis proteins to one of these fold classes. It is clear that all the plant sequences have arisen from a 1MJH-like ancestor.
Induction of Manganous Superoxide Dismutase by Tumor Necrosis Factor: Possible Protective Mechanism (1988)

Manganous superoxide dismutase (MnSOD) scavenges potentially toxic superoxide radicals produced in the mitochondria. Tumor necrosis factor-alpha (TNF-alpha) was found to induce the messenger RNA for MnSOD, but not the mRNAs for other antioxidant or mitochondrial enzymes tested. The increase in MnSOD mRNA occurred rapidly and was blocked by actinomycin D, but not by cycloheximide. Induction of MnSOD mRNA was also observed with TNF-beta, interleukin-1 alpha (IL-1 alpha), and IL-1 beta but not with other cytokines or agents tested. TNF-alpha induced MnSOD mRNA in all cell lines and normal cells examined in vitro and in various organs of mice in vivo. These effects of TNF-alpha and IL-1 on target cells may contribute to their reported protective activity against radiation as well as their ability to induce resistance to cell killing induced by the combination of TNF-alpha and cycloheximide.
AMYLOIDOSIS ASSOCIATED WITH JUVENILE RHEUMATOID ARTHRITIS (1982)

Clinical and pathological findings are reported in a Japanese girl who died of secondary amyloidosis associated with juvenile rheumatoid arthritis two years after the onset of symptoms. The patient had intermittent high fever, rheumatoid rash, polyarthralgia, and hepatosplenomegaly. The joints showed the typical histologic changes of juvenile rheumatoid arthritis. Amyloid deposition was found in various tissues; however, remarkable deposition of amyloid was observed in the gastrointestinal tract, especially in the ileum. The amyloid protein in this patient was identified as protein AA using the methods of potassium permanganate treatment and the peroxidase-antiperoxidase unlabeled antibody technique.
Influence of S-adenosylmethionine on DAPI-induced fluorescence of polyphosphate in the yeast vacuole (1980)

Use of the fluorochrome 4',6-diamidino-2-phenylindole.2 HCl (DAPI) in ultraviolet microscopy revealed fluorescent objects in Brownian motion within the vacuoles of seven species of yeast. The abundance of these bodies increased when cells of Saccharomyces cerevisiae were transferred from growth medium to a glucose-phosphate solution, indicating that they contain polyphosphate. In addition, the effect on vacuolar fluorescence of supplementing a defined growth medium with amino acids provided evidence that they also contained S-adenosylmethionine. These deductions were supported by in vitro studies of the interaction and fluorescence of polyphosphate, S-adenosylmethionine, and DAPI. Vacuolar fluorescence of cells in suspension in flucose-phosphate solution was less after addition of exogenous arginine, lysine, or glutamine but not after addition of alanine, aspartic acid, or methionine. Mithramycin was superior to DAPI as a fluorochrome for ultraviolet demonstration of yeast nuclei since it stained the nuclei much more intensely and did not fluoresce with other material in the cells.
Synergistic Effects in Aqueous Solutions of Mixed Wormlike Micelles and Hydrophobically Modified Polymers (2005)

The linear and nonlinear rheological properties of a hydrophobically modified guar (hm-HPG) and a surfactant forming wormlike micelles, the erucyl bis(hydroxyethyl)methylammonium chloride, have been investigated in 0.4 M KCl aqueous solution. The comparison between the zero-shear viscosity behaviors of the nonmodified guar and the hm-HPG shows a decrease of the intermolecular associations upon increasing the temperature. Significant synergistic effects were observed between the modified polymer and the wormlike micelles in a range of concentrations extending from 0.1 to 1 wt % and for temperatures up to 60 °C. The optimal synergy for the zero-shear viscosity is obtained for mixtures with an overall concentration ≈ 0.35 wt % and a surfactant/polymer ratio equal to 1/4 (w/w). The terminal time of the stress relaxation, the zero-shear viscosity as well as the viscosity at a shear rate of 100 s-1 and the lifetime of the associations show a maximum at this composition. The experimental observations suggest the formation of very efficient cross-links between the wormlike micelles and the polymer chains.
Nitric/Nitrous Acid Equilibria in Supercritical Water (1999)

UV−vis spectroscopy was utilized to measure the decomposition of aqueous HNO3 solutions above 300 °C, in some cases with added NaOH, H2O2, and/or NaNO2, to form NO2, HNO2, NO, N2O, and oxygen. Individual bands corresponding to HNO2 and NO2 were deconvoluted from the spectra up to 400 °C. With constrained nonlinear optimization, areas of these bands were used to determine extinction coefficients of NO2 and HNO2 and equilibrium constants for the reactions: HNO3 ⇌ H+ + NO3-; 2HNO3 ⇌ H2O + 2NO2 + (1/2)O2; 2NO2 + H2O ⇌ HNO3 + HNO2; 2HNO2 ⇌ H2O + 2NO + (1/2)O2; 2NO ⇌ N2O + (1/2)O2; (Na+)(NO3-) ⇌ Na+ + NO3-.
Recombinant viral-like particles of parvovirus B19 as antigen carriers of anthrax protective antigen. (2006)

Viral-like particles (VLPs) of parvovirus B19 were employed as an antigen carrier to present antigenic determinants of Bacillus anthracis. The small-loop peptide and the full-length domain 4 of protective antigen (PA) were chosen as immunogens for presentation on the VLP-capsid surface and subsequent immunization of BALB/c mice. The recombinant VLPs induced anti-PA IgG titers of up to 2.5 x 10(4). Neutralization assays showed that the recombinant VLPs elicited neutralizing anti-PA antibody titers of up to 1:400 and showed potential for the prevention of lethal toxin-induced mortality of mouse-macrophage cells (RAW264.7). In postimmune sera, no anti-PA titers were detected against synthetic small-loop peptide. Recombinant VLPs demonstrated the capacity to retain the immunogenicity of the displayed microbial PA-epitopes and elicited robust levels of anti-PA antibody titers. These findings suggest that the recombinant VLPs of parvovirus B19 have potential as an additional tool in the development of sub-unit vaccines.
Closed form expressions for crack mouth displacements and stress intensity factors for chevron notched short bar and short rod specimens based on experimental compliance measurements (1992)

A set of equations are presented describing certain fracture mechanics parameters for chevron notch bar and rod specimens. They are developed by fitting compliance calibration data reported earlier. The equations present the various parameters in their most useful forms. The data encompass the entire range of the specimen geometries most commonly used. Their use will facilitate the testing and analysis of brittle metals, ceramics, and glasses.
Administration of human inter-α-inhibitors maintains hemodynamic stability and improves survival during sepsis* (2002)

Human IalphaI/PalphaI appears to be a useful agent for maintaining hemodynamic stability and improving survival during the progression of polymicrobial sepsis.