gebhart/patrepeval huggingface dataset:
Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures (2007)

Mimotopes mimic the three-dimensional topology of an antigen epitope, and are frequently recognized by antibodies with affinities comparable to those obtained for the original antibody-antigen interaction. Peptides and anti-idiotypic antibodies are two classes of protein mimotopes that mimic the topology (but not necessarily the sequence) of the parental antigen. In this study, we combine these two classes by selecting mimotopes based on single domain IgNAR antibodies, which display exceptionally long CDR3 loop regions (analogous to a constrained peptide library) presented in the context of an immunoglobulin framework with adjacent and supporting CDR1 loops. By screening an in vitro phage-display library of IgNAR variable domains (V(NAR)s) against the target antigen monoclonal antibody MAb5G8, we obtained four potential mimotopes. MAb5G8 targets a linear tripeptide epitope (AYP) in the flexible signal sequence of the Plasmodium falciparum Apical Membrane Antigen-1 (AMA1), and this or similar motifs were detected in the CDR loops of all four V(NAR)s. The V(NAR)s, 1-A-2, -7, -11, and -14, were demonstrated to bind specifically to this paratope by competition studies with an artificial peptide and all showed enhanced affinities (3-46 nM) compared to the parental antigen (175 nM). Crystallographic studies of recombinant proteins 1-A-7 and 1-A-11 showed that the SYP motifs on these V(NAR)s presented at the tip of the exposed CDR3 loops, ideally positioned within bulge-like structures to make contact with the MAb5G8 antibody. These loops, in particular in 1-A-11, were further stabilized by inter- and intra- loop disulphide bridges, hydrogen bonds, electrostatic interactions, and aromatic residue packing. We rationalize the higher affinity of the V(NAR)s compared to the parental antigen by suggesting that adjacent CDR1 and framework residues contribute to binding affinity, through interactions with other CDR regions on the antibody, though of course definitive support of this hypothesis will rely on co-crystallographic studies. Alternatively, the selection of mimotopes from a large (<4 x 10(8)) constrained library may have allowed selection of variants with even more favorable epitope topologies than present in the original antigenic structure, illustrating the power of in vivo selection of mimotopes from phage-displayed molecular libraries.
FORMATION OF MEGACHROMOSOMES FROM HETEROCHROMATIC BLOCKS OF NICOTIANA TOMENTOSIFORMIS (1973)

A heterochromatic block (HB) from N. otophora occasionally undergoes great enlargement to form a "megachromosome" in hybrids and hybrid derivatives with N. tabacum. This paper shows that the two large HB's of closely related N. tomentosiformis, and perhaps a smaller one, also have the same capability. The evidence that both large HB's form megachromosomes is twofold. In a segregating backcross population from a parent possessing the two large HB's, all segregants with one block produced megachromosomes at metaphase or large heterochromatic clumps at interphase. Second, those segregants which possessed both heterochromatic blocks produced megachromosomes of two visibly different types. Proliferation to make megachromosomes thus may not be the property of merely one particular segment but a more common property of heterochromatin in a hybrid or otherwise disturbed background.
Serum-Soluble B7x Is Elevated in Renal Cell Carcinoma Patients and Is Associated with Advanced Stage (2008)

B7x is the newest member of the B7-CD28 family and is thought to dampen immune responses via negative costimulation. Tumor expression of B7x was recently described in renal cell carcinoma (RCC) and was associated with poor outcome. We developed an assay to detect serum-soluble B7x (sB7x) and investigated 101 patients with clear cell RCC who underwent nephrectomy between 2003 and 2007. For controls, we obtained serum from 101 sex-matched blood donors within the same age range. Following an ELISA for sB7x, detectable levels (>0.1 ng/mL) of sB7x were observed in 53 RCC patients compared with 18 controls (P < 0.001). Median (range) concentrations of sB7x for RCC patients and controls were 14.4 ng/mL (0.1-56.9) and 2.7 ng/mL (0.2-37.1), respectively. For RCC patients with detectable sB7x, median levels were significantly higher for patients with a tumor thrombus (19.2 versus 6.6 ng/mL; P = 0.007), positive lymph nodes (41.3 versus 10.3 ng/mL; P = 0.018), and distant metastases at nephrectomy (43.3 versus 8.5 ng/mL; P = 0.002) and tended to be higher in patients with high-grade tumors (18.8 versus 8.5; P = 0.090). Additionally, median sB7x levels for tumor-node-metastasis stage I to IV RCC were 6.6, 10.3, 14.5, and 43.3 ng/mL, respectively (P = 0.012). In this first evaluation of sB7x in RCC, we show that RCC patients are more likely to have detectable sB7x compared with controls and higher sB7x levels correlate with advanced tumor stage. These early results merit further investigation of this serum marker for potential diagnostic and prognostic purposes.
Systemic treatment of xenografts with vaccinia virus GLV-1h68 reveals the immunologic facet of oncolytic therapy (2009)

This study provides the first prospective validation of a universal mechanism associated with TSD. Thus, xenograft infection by oncolytic VACV, beyond offering a promising therapy of established cancers, may represent a reliable pre-clinical model to test therapeutic strategies aimed at modulating the central pathways leading to TSD; this information may lead to the identification of principles that could refine the treatment of cancer and chronic infection by immune stimulation or autoimmunity and allograft rejection through immune tolerance.
Hedgehog Signaling: Networking to Nurture a Promalignant Tumor Microenvironment (2011)

In addition to its role in embryonic development, the Hedgehog pathway has been shown to be an active participant in cancer development, progression, and metastasis. Although this pathway is activated by autocrine signaling by Hedgehog ligands, it can also initiate paracrine signaling with cells in the microenvironment. This creates a network of Hedgehog signaling that determines the malignant behavior of the tumor cells. As a result of paracrine signal transmission, the effects of Hedgehog signaling most profoundly influence the stromal cells that constitute the tumor microenvironment. The stromal cells in turn produce factors that nurture the tumor. Thus, such a resonating cross-talk can amplify Hedgehog signaling, resulting in molecular chatter that overall promotes tumor progression. Inhibitors of Hedgehog signaling have been the subject of intense research. Several of these inhibitors are currently being evaluated in clinical trials. Here, we review the role of the Hedgehog pathway in the signature characteristics of cancer cells that determine tumor development, progression, and metastasis. This review condenses the latest findings on the signaling pathways that are activated and/or regulated by molecules generated from Hedgehog signaling in cancer and cites promising clinical interventions. Finally, we discuss future directions for identifying the appropriate patients for therapy, developing reliable markers of efficacy of treatment, and combating resistance to Hedgehog pathway inhibitors.
Electrochemical Generation of a Hydrogen Bubble at a Recessed Platinum Nanopore Electrode (2015)

We report the electrochemical generation of a single hydrogen bubble within the cavity of a recessed Pt nanopore electrode. The recessed Pt electrode is a conical pore in glass that contains a micrometer-scale Pt disk (1-10 μm radius) at the nanopore base and a nanometer-scale orifice (10-100 nm radius) that restricts diffusion of electroactive molecules and dissolved gas between the nanopore cavity and bulk solution. The formation of a H2 bubble at the Pt disk electrode in voltammetric experiments results from the reduction of H(+) in a 0.25 M H2SO4 solution; the liquid-to-gas phase transformation is indicated in the voltammetric response by a precipitous decrease in the cathodic current due to rapid bubble nucleation and growth within the nanopore cavity. Finite element simulations of the concentration distribution of dissolved H2 within the nanopore cavity, as a function of the H(+) reduction current, indicate that H2 bubble nucleation at the recessed Pt electrode surface occurs at a critical supersaturation concentration of ∼0.22 M, in agreement with the value previously obtained at (nonrecessed) Pt disk electrodes (∼0.25 M). Because the nanopore orifice limits the diffusion of H2 out of the nanopore cavity, an anodic peak corresponding to the oxidation of gaseous and dissolved H2 trapped in the recessed cavity is readily observed on the reverse voltammetric scan. Integration of the charge associated with the H2 oxidation peak is found to approach that of the H(+) reduction peak at high scan rates, confirming the assignment of the anodic peak to H2 oxidation. Preliminary results for the electrochemical generation of O2 bubbles from water oxidation at a recessed nanopore electrode are consistent with the electrogeneration of H2 bubbles.
Immunohistologic and immunoelectron microscopic characterization of the mucosal lymphocytes of human small intestine by the use of monoclonal antibodies. (1983)

Monoclonal antibodies reactive with T cells, T cell subsets, B cells, monocytes, and natural killer cells were used to characterize the nature of mucosal lymphocytes in the human small intestine by application of the immunoperoxidase technique to tissue sections for light and electron microscopic examination. In addition, for comparison, peripheral blood mononuclear cells (PBL) were studied by immunoelectron microscopy. Most of the intraepithelial lymphocytes (IEL) were T cells (Leu-1+, T3+) and expressed the phenotype associated with cytotoxic/suppressor T cells (Leu-2a+, T8+). In contrast, a majority of T lymphocytes in the lamina propria expressed the phenotype associated with helper/inducer T cells (Leu-3a+, T4+). These observations confirm and extend the findings previously reported. In addition, a small number of cells in the lamina propria with the ultrastructural features of macrophages were found to react with anti-Leu-3a and anti-T4 antibodies. Although many IEL contained cytoplasmic granules and had ultrastructural features similar to those of circulating granular lymphocytes, none of these cells reacted with anti-Leu-7 (HNK-1), anti-T10, or anti-M1 antibodies. This suggests that IEL may not be related to circulating large granular lymphocytes, which are Leu-7+, T10+, M1+ and are associated with natural killer activity. Not only Leu-7+ PBL, but T8+, T4+, or T3+ mucosal lymphocytes or PBL also may contain cytoplasmic granules. Therefore, the cytoplasmic granules are not restricted to one cell type, in particular, to Leu-7+ cells.
Hyperosmolar Hyperglycemic State. (2005)

Hyperosmolar hyperglycemic state is a life-threatening emergency manifested by marked elevation of blood glucose and hyperosmolarity with little or no ketosis. Although there are multiple precipitating causes, underlying infections are the most common. Other causes include certain medications, nonadherence to therapy, undiagnosed diabetes mellitus, substance abuse, and coexisting disease. In children and adolescents, hyperosmolar hyperglycemic state is often present when type 2 diabetes is diagnosed. Physical findings include profound dehydration and neurologic symptoms ranging from lethargy to coma. Treatment begins with intensive monitoring of the patient and laboratory values, especially glucose, sodium, and potassium levels. Vigorous correction of dehydration is critical, requiring an average of 9 L of 0.9% saline over 48 hours in adults. After urine output is established, potassium replacement should begin. Once dehydration is partially corrected, adults should receive an initial bolus of 0.1 units of intravenous insulin per kg of body weight, followed by a continuous infusion of 0.1 units per kg per hour (or a continuous infusion of 0.14 units per kg per hour without an initial bolus) until the blood glucose level decreases below 300 mg per dL. In children and adolescents, dehydration should be corrected at a rate of no more than 3 mOsm per hour to avoid cerebral edema. Identification and treatment of underlying and precipitating causes are necessary.
Blood Pool MR Angiography of Aortic Stent-Graft Endoleak (2004)

Blood pool MR angiography using Ferumoxytol reveals more aortic stent-graft endoleaks than does CT angiography and depicts more endoleaks 24 hr after administration than during the immediate arterial phase because of a 50-fold increase in the volume of enhancement in the aneurysmal sac outside the stent-graft.
Electrode-derived myocardial pH measurements reflect intracellular myocardial metabolism assessed by phosphorus 31-nuclear magnetic resonance spectroscopy during normothermic ischemia. (1992)

To determine the ability of extracellular myocardial tissue pH measured with an intramural electrode to reflect myocardial intracellular metabolic status during normothermic ischemia, we studied 14 open-chest dogs with in vivo phosphorus 31-nuclear magnetic resonance spectroscopy during left anterior descending coronary artery occlusion (experimental group, group I, n = 7) or after a sham operation (control group, nonischemic, group II, n = 7). Phosphorus nuclear magnetic resonance spectra were acquired every 5 minutes at 4.7 tesla (256 averages, TR = 1000 msec, pulse width = 30 microseconds) with a 2 cm two-turn radiofrequency surface coil. Intracellular myocardial adenosine triphosphate peak area was normalized to an external phosphate standard. The change in adenosine triphosphate peak area was expressed as percent of baseline value. During 3 hours of normothermic ischemia the observed extracellular myocardial pH correlated with nuclear magnetic resonance-calculated myocardial pH in the ischemic dogs with an average r value of 0.94 (p less than 0.0001). During this same interval, the fall in extracellular myocardial pH correlated with the loss of adenosine triphosphate peak in each ischemic dog, with an average r value of 0.91 (p less than 0.0001). Thus extracellular myocardial pH, measured with an intramural electrode, correlated with nuclear magnetic resonance-derived myocardial pH and loss of myocyte adenosine triphosphate peak content and reflected the metabolic status of the myocyte during ischemia. These data validate the use of extracellular myocardial pH to assess the adequacy of myocardial preservation during aortic crossclamping for cardiac operations.
Exosome-encapsulated antibiotic against intracellular infections of methicillin-resistant <em>Staphylococcus aureus</em> (2018)

Exosomes provide an effective alternative for intracellular antibiotic delivery of antibiotic that is efficacious, cost-effective, and safe. This regimen can be viewed as a potential antimicrobial agent for use against intracellular infections.
Use of arbitrarily primed polymerase chain reaction to investigate Mycoplasma bovis outbreaks (2001)

Colony lineages from three Mycoplasma bovis outbreaks representing different husbandry conditions in the United States were characterized with arbitrarily primed polymerase chain reaction (AP-PCR). Cases studied included a closed beef herd, a dairy calf ranch, and a feedlot. The DNA was obtained from colony lineages and used for AP-PCR with primers REP1R-I and REP2-I. Case A and C lineages were uniform by AP-PCR analysis. Lineages from case B showed heterogeneity with AP-PCR. Outbreaks A and C were therefore both infected by one source, while the ranch (case B) was infected by multiple calf shipments. The AP-PCR typing method provides genotypic epidemiological information to successfully characterize M. bovis from sequential sampling of outbreaks and different husbandry conditions.
Microencapsulation of human growth hormone within biodegradable polyester microspheres: Protein aggregation stability and incomplete release mechanism (1999)

Recombinant human growth hormone (rhGH) was encapsulated within poly(d,l-lactic-co-glycolic acid) microspheres by a double emulsion solvent evaporation method. A mixture of methylene chloride and ethyl acetate in varying volume ratios was used for the microsphere preparation. Protein release profiles from three different microsphere formulations demonstrated initial burst effects ranging from 28.2% to 54.7% after a 1-day incubation and exhibited no further significant releases up to 19 days. This was because the encapsulated rhGH with the microspheres was largely aggregated in a noncovalent fashion during the formulation. Nonaggregated water soluble rhGH species within the microspheres are likely to be responsible for the rapid release upon incubation. The initially released rhGH in the incubation medium, however, was composed of mostly monomer species with a small amount of dimer as probed by size-exclusion chromatography. Circular dichroism spectra of the initially released rhGH in the medium revealed that the conformation of the released rhGH was correctly folded relative to that of native rhGH, with little variation in α-helix contents depending on the formulations. The “nonrelease” mechanism after the initial burst release was attributed to nonspontaneously dissociable noncovalent protein aggregation and surface adsorption of rhGH present within the microspheres. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 65: 659–667, 1999.
Monoclonal Antibody to Cardiac Myosin: Imaging of Experimental Myocardial Infarction (1984)

Monoclonal antibody R11D10 to human cardiac myosin, which also cross-reacted with canine cardiac myosin, was used to demonstrate in vivo localization and visualization by gamma scintigraphy of experimental myocardial infarction. R11D10 Fab with a Ka of 5 X 10(8) M-1 was labeled with technetium-99m (99mTc) by the dithionite reduction method of technetium pertechnetate, via a bifunctional chelating agent, diethylene triamine pentaacetic acid (DTPA). Uptake of 99mTc R11D10 Fab in the infarct can be visualized as early as 2 h after intravenous administration. Comparison of R11D10 uptake to thallium-201, an analogue of potassium which is sequestered by normal myocardium, showed an inverse relation (r = -0.75, -0.87, -0.89), similar to that obtained with 125I labeled polyclonal antimyosin Fab. Ratios of R11D10 Fab in the infarct to normal myocardium were as high as 30:1 where access of antibody to antigen was not blood flow limited. However, with severe blood-flow restriction, the ratios were lower at about 10:1. Despite the theoretical limitation of a single epitope per myosin molecule available for binding by R11D10 Fab, the immense excess of myosin in the infarcted myocardium allowed adequate concentration of radiolabeled R11D10 for visualization of the infarct by external gamma scintiscanning.
PFI-1, a Highly Selective Protein Interaction Inhibitor, Targeting BET Bromodomains (2013)

Bromo and extra terminal (BET) proteins (BRD2, BRD3, BRD4, and BRDT) are transcriptional regulators required for efficient expression of several growth promoting and antiapoptotic genes as well as for cell-cycle progression. BET proteins are recruited on transcriptionally active chromatin via their two N-terminal bromodomains (BRD), a protein interaction module that specifically recognizes acetylated lysine residues in histones H3 and H4. Inhibition of the BET-histone interaction results in transcriptional downregulation of a number of oncogenes, providing a novel pharmacologic strategy for the treatment of cancer. Here, we present a potent and highly selective dihydroquinazoline-2-one inhibitor, PFI-1, which efficiently blocks the interaction of BET BRDs with acetylated histone tails. Cocrystal structures showed that PFI-1 acts as an acetyl-lysine (Kac) mimetic inhibitor efficiently occupying the Kac binding site in BRD4 and BRD2. PFI-1 has antiproliferative effects on leukemic cell lines and efficiently abrogates their clonogenic growth. Exposure of sensitive cell lines with PFI-1 results in G1 cell-cycle arrest, downregulation of MYC expression, as well as induction of apoptosis and induces differentiation of primary leukemic blasts. Intriguingly, cells exposed to PFI-1 showed significant downregulation of Aurora B kinase, thus attenuating phosphorylation of the Aurora substrate H3S10, providing an alternative strategy for the specific inhibition of this well-established oncology target.
Polarization colours of collagen fibres: a sign of collagen production activity in fibrotic processes. (1984)

The maturation process of collagen fibres was investigated by the picro-sirius red/polarization light technique in experimental wound healing, in allyl-alcohol induced subacute and chronic liver fibrosis and in human biopsy material. Evidence was obtained that collagen fibres undergo a rapid maturation in fibrotic processes; the intensity of their birefringence increases and, at the same time, their polarization colour changes. Newly formed collagen fibres appear on the 4-6 mum thick sections in green polarization colour. Later, in a more mature stage, they became yellow, orange or red under crossed polaroids. The findings suggest that the simple picro-sirius red/polarizing light technique may be useful to form an opinion about the activity of the fibrotic process.
The effect of soluble complement receptor type 1 on acute humoral xenograft rejection in hDAF‐transgenic pig‐to‐primate life‐supporting kidney xenografts (2004)

The inclusion of TP10 in the immunosuppressive protocol does not clearly lead to improved xenograft survival. Despite effective neutralization of anti-Gal antibodies and effective inhibition of systemic complement activity, AHXR was apparent in four of six animals under chronic TP10 treatment, including deposits of complement activation products in the graft. Apparently, effective systemic complement inhibition by TP10 in combination with local complement regulation by the hDAF transgene product does not necessarily result in effective inhibition of complement activation at locations in the xenograft upon binding of anti-porcine antibodies to the grafted endothelium.
Effects of sonicated eosinophils on the in vitro sensitivity of human lymphoma cells to glucose oxidase. (1994)

We report here that cultured human lymphoma cells in the absence of sonicated eosinophils are sensitive to killing by glucose oxidase (beta-D-glucose:oxygen-oxido reductase; EC 1.1.3.4) at concentrations as low as 0.025 microgram/ml, a level that can be rapidly attained in s.c. tumor implants in mice that receive a single nonlethal injection of enzyme. Multiple clonogenic assays were used to measure the survival of human lymphoma cell lines (H9 and ARH-77) cultured for 14 days in complete RPMI 1640 supplemented with exogenous glucose oxidase (0.025-2.5 micrograms/ml) or an immunoconjugate containing glucose oxidase (0.25-25 micrograms/ml) in the presence or absence of catalase (10 micrograms/ml) or an equal number of sonicated human eosinophils with or without supplemental 100 microM Br-, I-, or SCN-. In addition, we used an immunoassay to measure the concentration of glucose oxidase in s.c. implants of the Sp 2/0 myeloma tumor at 0-30 min after an i.v. injection of 50 micrograms of enzyme into 21 BALB/c mice. Doses of glucose oxidase as small as 0.025 microgram/ml killed more than 3 logs of tumor cells. Catalase completely inhibited, and sonicated human eosinophils partially inhibited, the killing by glucose oxidase or immunoconjugate, whereas supplemental halides had no effect. Glucose oxidase i.v. produced levels > 0.04 microgram/g of tumor for 30 min after injection with a peak concentration of 0.079 microgram/g of tumor within 5 min of injection. These results are important because certain human lymphomas contain extensive extracellular deposits of eosinophil peroxidase, thereby making these tumors potentially less susceptible to killing by otherwise therapeutic doses of glucose oxidase.