gebhart/patrepeval huggingface dataset:
Strategy of Fc-Recognizable Peptide Ligand Design for Oriented Immobilization of Antibody (2014)

A new strategy for designing a short-chain peptide ligand with high affinity to the Fc region of an antibody was proposed. The targeted antibody is human prostate specific antibody (PSA) derived from Mouse IgG2a. The ligand design strategy involves two major parts: binding site selection and peptide ligand design. One of the exposed hydrophobic patches near the bottom of the antibody's Fc region, identified from the molecular docking of naphthelene and end-capped tryptophan, was selected as the binding site. After examining the charge distribution around the binding site, various peptide ligands were designed according to the possible hydrophobic and electrostatic interactions. A peptide ligand, RRGW, was found to have high Fc binding affinity by the analysis of molecular dynamics (MD) simulation. The first two residues, two arginines, play an important role in electrostatic interaction between the peptide and the Fc region of the antibody. The fourth residue, the tryptophan, provides the VDW force; and the flexibility of peptide is achieved through the help of the third residue, the glycine. The binding affinity, recognition efficiency, and orientation factor were calculated from the results of surface plasmon resonance (SPR) measurements. The result shows that the dissociation constant is 5.56 × 10(-10) M(-1). We also found that the recognition efficiency and orientation factor on the ligand attached surface were much higher than those on negatively and positively charged surfaces. This approach provides a simple and fast strategy for small ligands design on oriented antibody immobilization.
THE EFFECT OF PROTEASE INHIBITOR ON REPERFUSION INJURY AFTER UNILATERAL PULMONARY ISCHEMIA (1993)

Reperfusion injury is a large problem in the early stage after lung transplantation. Its prevention by protease inhibitor was evaluated experimentally. Warm ischemic models were made with the left lungs of adult mongrel dogs. The time for the warm ischemic procedure was set at 2 hr, and the lungs were reperfused for 2 hr. The experimental group was divided into a control group, a UTI (urinary trypsin inhibitor) group and a GM (gabexate mecilate) group. To the UTI group, 10,000 units/kg of UTI was administrated during reperfusion, and to the GM group, 20 mg/kg of gabexate mecilate was administrated similarly. In the control group, the pulmonary vascular resistance and the lung tissue wet and dry weight ratios (W/D ratios) increased significantly, and thickened interstitium and infiltration of neutrophils were observed histologically after reperfusion. In the GM group, W/D ratios increased significantly, and histological appearances were similar to the control group. In the UTI group, the pulmonary vascular resistance increased slightly, but the W/D ratio did not increase significantly, and no changes were seen histologically after reperfusion. In the survival experiment, only two of the five dogs survived for more than seven days in the control and GM groups, while all five dogs survived for more than seven days in the UTI group. These results indicate that UTI significantly attenuates reperfusion injury, perhaps by inhibiting neutrophil proteases.
β-Endorphin-Induced Stimulation of Central Sympathetic Outflow: β-Endorphin Increases Plasma Concentrations of Epinephrine, Norepinephrine, and Dopamine in Rats* (1981)

Intracisternal administration of synthetic human beta-endorphin (0.058-7.25 nmol) in chronically cannulated, conscious, freely moving, adult male rats increased plasma concentrations of epinephrine, norepinephrine, and dopamine in a dose-related manner. Epinephrine secretion was the most sensitive to the stimulatory effect of intracerebral beta-endorphin; plasma epinephrine increased transiently in response to 0.058 nmol. Of the three catecholamines, plasma epinephrine showed the greatest and most rapid response to the largest dose (7.25 nmol) studied. Plasma norepinephrine increased significantly in response to 1.45 nmol, peaking later than plasma epinephrine. Plasma dopamine increased only in response to the highest dose examined. These beta-endorphin effects on plasma catecholamines were inhibited by intraarterial naloxone (1.1 mumol/kg), supporting mediation at opioid receptors. Pretreatment with the ganglionic blocking agent chlorisondamine inhibited the responses of all three catecholamines to intracisternal beta-endorphin. Bilateral adrenal denervation completely prevented the plasma epinephrine response to beta-endorphin and blunted the plasma norepinephrine and dopamine responses. Prior intracisternal administration of hemicholinium-3 blocked the plasma responses of all three catecholamines to intracisternal beta-endorphin, providing evidence for the involvement of central cholinergic neurons in the mechanism mediating beta-endorphin-induced increases in plasma catecholamines. The data are consistent with the hypothesis that endorphins act at a presently unknown brain site(s) to increase the central sympathetic outflow to adrenal medulla and peripheral sympathetic nerve endings, thus stimulating peripheral catecholamine release and increasing plasma concentrations of epinephrine, norepinephrine, and dopamine.
Phenotypic Analysis of Yellow Fever Virus Derived from Complementary DNA (1995)

A thorough phenotypic characterization of yellow fever (YF) virus generated from cDNA is a necessary prerequisite for mapping virulence/attenuation determinants and exploring the potential of YF attenuated virus 17D as a carrier for heterologous protective epitopes. In this study, YF virus was produced from 17D cDNA clones after lipofectin-mediated RNA transfection of certified primary cultures of chicken embryo fibroblasts (YFiv5.2/SL). This virus was passaged once in embryonated chicken eggs according to current YF vaccine manufacture methodology to produce the experimental virus (YFiv5.2/VL). These viruses were characterized in established monkey neurovirulence safety tests and quantitative clinical and histologic scores were derived for each virus. The experimental vaccine viruses (YFiv5.2/SL and VL) compared favorably with another well-known YF vaccine strain (17DD) used as control virus for the histologic score. Although slightly higher clinical neurovirulence was observed for YFiv5.2 as compared with the 17DD virus, it should not preclude the use of YFiv5.2 for mapping YF virus virulence determinants.
The Optical File Cabinet: a random-access file system for write-once optical disks (1988)

The Optical File Cabinet (OFC) is patterned after a conventional office file cabinet where all versions of a stored item are retained, but the current version of each item is the easiest to find. The OFC retains the favorable aspects of write-once optical disks while preserving the existing relationship between the operating system and the file system. Alternate approaches to write-once storage and the characteristics of write-once optical disks are described. The salient features of the OFC are examined, namely, the file system tree, growing data structures, and the large memory requirement. The relationship between the OFC and the operating system is discussed. Also considered are reliability, the user-level software interface, long-term storage, simulating the OFC, and implementation of the OFC on a Tektronix 4404 engineering workstation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparison of oral estrogens and estrogens plus androgen on bone mineral density, menopausal symptoms, and lipid-lipoprotein profiles in surgical menopause (1995)

Oral estrogen-androgen increased vertebral bone mineral density compared with pre-treatment values and relieved somatic symptoms. Safety indices, including lipoprotein levels, indicated that the combination was well tolerated over the 2 years of treatment.
Isolated diffuse type B-cell lymphoma of the palate: an unusual entity (2013)

Lymphomas frequently occur as extranodal lesions in the head and neck, but are rarely seen in the palate. We present a case of isolated diffuse type B-cell lymphoma of the palate, which occurred in a 28-year-old man. The patient had no history of immune compromise, and he presented to the emergency department with a 7-month history of a painful, non-healing ulcerative mass in the hard and soft palate. Positron emission tomography facilitated pretreatment assessment of the extent and activity of the lesion. Histopathological and immunohistochemical analyses of biopsied tissue confirmed a diagnosis of diffuse type B-cell lymphoma. The clinical findings and therapeutic challenges in this heterogeneous group of malignancies are discussed.
New Light on a "Forgotten War": The Diplomacy of the Korean Conflict (2000)

New Light on a “Forgotten War”: The Diplomacy of the Korean Conflict Get access Priscilla Roberts Priscilla Roberts Priscilla Roberts is a lecturer in history and the director of the Centre of American Studies at the University of Hong Kong. She has published extensively on United States diplomatic history and is an associate editor of The Encyclopedia of the Korean War, to be released in June 2000 by ABC-CLIO. Her 1997 article, “The Anglo-American Theme,” published in the Summer 1997 issue of Diplomatic History won the 1997 Arthur Miller Prize for the best British article in American Studies. Search for other works by this author on: Oxford Academic Google Scholar OAH Magazine of History, Volume 14, Issue 3, Spring 2000, Pages 10–14, https://doi.org/10.1093/maghis/14.3.10 Published: 01 March 2000
Simultaneous Molecular Detection and Confirmation of Influenza AH5, with Internal Control (2010)

Influenza viruses continue to be a major cause of respiratory tract infection, resulting in substantial morbidity and mortality throughout the world. Accurate and rapid differential diagnosis of influenza virus infections, particularly associated with zoonotic infections, is important for public health actions, patient management, and treatment. Real-time PCR is widely considered the gold standard for molecular detection of influenza viruses owing to its high assay specificity, extreme detection sensitivity, and wide linear dynamic range. This protocol describes the use of a real-time RT-PCR assay for identification of influenza A and B viruses, detection of H5 subtype viruses, and an internal control, in a multiplexed, single-tube format. The inclusion of an internal bacteriophage control allows the efficiency of the extraction and amplification process to be monitored, so that false-negative results may be avoided. The primers and probe sets in this multiplex assay have been validated with a panel of influenza A viruses of different subtypes (including swine influenza viruses), and influenza B viruses, and specificity further confirmed with non-related respiratory viruses.
Pembrolizumab for Advanced Melanoma (2016)

PD-1 blockade therapy with the anti-programmed-death-receptor-1 antibody pembrolizumab has shown promise for patients with advanced melanoma in prior
Plastid enzymes of terpenoid biosynthesis. Purification and characterization of gamma-tocopherol methyltransferase from Capsicum chromoplasts. (1985)

gamma-Tocopherol methyltransferase was solubilized and purified from Capsicum chromoplast membranes by a combination of standard fractionation techniques. The purified enzyme was electrophoretically homogeneous, and its molecular weight, determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, was 33,000. In the absence of detergent, the enzyme formed high molecular weight aggregates. Several properties of the enzyme have been determined. The Km values were 2.5 and 13.7 microM for S-adenosylmethionine and gamma-tocopherol, respectively. The enzyme was able to transfer the methyl group S-adenosylmethionine to N-4-azido-2-nitrophenyl-beta-alanyl-gamma-tocopherol. The rate of transfer was less efficient compared to gamma-tocopherol. In the presence of ultraviolet light, this analog inhibited the gamma-tocopherol methyltransferase activity.
The fast multipole method for periodic structures (2002)

The fast multipole method (FMM) can be applied to the computation of radiation and scattering from infinite periodic structures by applying the Ewald summation technique to the FMM translation operator. When the, FMM group is taken to be a unit cell in the structure, this results in a large saving in the setup times compared to a straightforward FFT approach.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Studies on B lymphoid tumors treated with monoclonal anti-idiotype antibodies: correlation with clinical responses (1987)

Monoclonal anti-idiotype antibodies can be made which are exquisitely specific for B lymphocytic malignancies. We have conducted a clinical trial in which some patients' tumors regressed after infusion of such antibodies. Here, we evaluated characteristics of the antibodies, the tumors, and the patients to determine which features best correlated with the clinical response. Neither the isotype of the murine antibodies, nor their avidity were predictive of clinical outcome. The specific epitope to which the antibodies bound was characterized by immunochemical techniques. Reactivity with a heavy-light chain combinatorial determinant correlated somewhat with clinical effect. Variations in the characteristics of the individual tumors such as antigen sites per cell and ability to modulate the surface immunoglobulin were not predictive of response. In one patient with prolymphocytic leukemia the anti-idiotype antibody had a direct antiproliferative effect on tumor cells in vitro. This patient's tumor response was explainable by such a direct mechanism. In the other patients, who had lymphomas, therapeutic outcome correlated with the number of host nontumor cells infiltrating the tumor. The vast majority of these nontumor cells were mature T lymphocytes of the Leu 4, Leu 3 (T3, T4) phenotype. Thus, a preexistent host-tumor interaction seems to be important in the in vivo effect of anti-idiotype antibodies in B cell tumors.
Electrotonic interactions between aggregates of chick embryo cardiac pacemaker cells (1986)

Synchronization of spontaneously active heart cell aggregates occurs shortly after they are brought into contact. The synchronous rate is determined by pacemaker phase resetting and passive subthreshold electrotonic interactions. To further study the effects of passive electrical interactions, we have used 150-microns diameter aggregates prepared from cells of 4d (4-day ventricle + 1 day in vitro), 7d, and 14d embryonic chick ventricle as models of primary, latent, and nonpacemaker tissues, respectively. Coupling of 4d and 7d aggregates (4d/7d pairs) leads to intermediate synchronous rates. We show here that elevating external K+ from 1.3 to 2.8 mM, which has no effect on 4d/4d pairs but selectively reduces the beat rate of 7d/7d pairs by 42%, slows the synchronous beat rate of 4d/7d pairs by 23%. Increases in electrical coupling in newly joined 4d/14d pairs cause the 4d rate to slow to a minimum value (16 +/- 13 beats/min, n = 16) just prior to the onset of synchronous activity. The rate slowly recovers to a final value of 40 +/- 12 beat/min. We conclude that the spontaneous beat rate of a primary pacemaker is modulated by both active and passive interactions with latent or nonpacemaker tissues.
Human B cells secrete migration inhibition factor (MIF) and present a naturally processed MIF peptide on HLA‐DRB1*0405 by a FXXL motif (1999)

A better knowledge of peptide structures interacting with major histocompatibility complex (MHC) molecules is of great interest for better understanding of the molecular basis of immune recognition. We have isolated naturally processed peptides from a continuously growing antigen-presenting Epstein-Barr virus-transformed human B-cell line. HLA-DR complexes were purified by specific affinity chromatography and complexed peptides were released by acid treatment. The isolated peptides were separated by reversed phase chromatography and fractions were analysed by Edman degradation at picomolar ranges. From 30 fractions that were examined seven peptides bound to the HLA-DRB1*0405 and two peptides from the human leucocyte antigen (HLA) class II associated invariant chain bound to HLA-DRB1*1302. In addition, a N-terminal beta-chain peptide of the 0405 allele was identified. Evaluation of amino acid sequences revealed a refined FXXL motif for the 0405 allele, in which F (phenylalanine) stands for any aromatic amino acid and L (leucine) can be exchanged by either I (isoleucine) or V (valine). In total, three fractions contained a peptide derived from the human migration inhibition factor (MIF), a pro-inflammatory cytokine that is normally produced by activated T lymphocytes and monocytes/macrophages. Indeed, cytokine analysis revealed high amounts of MIF secreted by the B-cell line, confirming that MHC class II expressing cells can present any intrinsic peptide that contains the distinct motif for HLA-binding. For MIF, the amino acid sequence Y36IAV39 represents the required binding motif for HLA-DRB1*0405. Nevertheless, it is the first time that cytokine fragments were found to bind to HLA molecules on human B cells.
Enhanced induction of antitumor T-cell responses by cytotoxic T lymphocyte-associated molecule-4 blockade: the effect is manifested only at the restricted tumor-bearing stages. (1997)

Cytotoxic T lymphocyte-associated molecule-4 (CTLA-4), a second counterreceptor for the B7 family of costimulatory molecules, functions as a negative regulator of T-cell activation. Here, we investigated whether the blockade of the CTLA-4 function leads to enhancement of antitumor T-cell responses at various stages of tumor growth. Unfractionated spleen cells taken from CSAIM fibrosarcoma-bearing mice 1-2 weeks after CSA1M cell implantation (early tumor-bearing mice) contained tumor-primed T cells that produced interleukin 2 and IFN-gamma through collaboration with antigen-presenting cell-binding tumor antigens when cultured in vitro. However, this initial lymphokine-producing capacity decreased at later stages of tumor growth (7-10 weeks after tumor cell implantation). Anti-CTLA-4 monoclonal antibody (mAb) was added to whole-spleen cell cultures from early or late tumor-bearing mice. Spleen cells from early tumor-bearing mice exhibited enhanced production of interleukin 2 and IFN-gamma upon in vitro culture in the presence of anti-CTLA-4 mAb. However, addition of anti-CTLA-4 mAb to whole-spleen cell cultures from late tumor-bearing mice failed to display such an enhancement. Consistent with these in vitro results, the in vivo antitumor effect of anti-CTLA-4 administration was observed in a tumor-bearing stage-restricted manner; in vivo administration of anti-CTLA-4 (1 mg/mouse, three times at 1-week intervals) into early tumor-bearing mice resulted in regression of growing tumors, whereas the same treatment did not affect tumor growth when performed for late tumor-bearing mice. Similar anti-CTLA-4 effect was observed in another tumor (OV-HM ovarian carcinoma) model. These in vitro and in vivo results indicate that CTLA-4 blockade in tumor-bearing individuals enhances the capacity to generate antitumor T-cell responses, but the expression of such an enhancing effect is restricted to early stages of tumor growth.
Interactions of thrombospondin with extracellular matrix proteins: selective binding to type V collagen. (1984)

Thrombospondin (TS), a protein first described in platelets, was recently shown to be synthesized and secreted by endothelial cells, fibroblasts, and smooth muscle cells. The presence of TS in the extracellular matrix of cultured cells has prompted us to examine the associations of this protein with matrix macromolecules. Interactions of TS with both matrix and serum proteins were tested using an enzyme-linked immunosorbent assay. With this assay we assessed the binding of TS in solution to proteins adsorbed to polystyrene microtiter plates. Among collagens, platelet TS bound to type V but not to types I, III, or IV. This selective interaction was confirmed in experiments using proteins linked to cyanogen bromide-activated Sepharose. TS released from platelets in response to thrombin activation, as well as that secreted by endothelial cells in culture, bound to type V but not to type I collagen-Sepharose. No binding was observed to denatured type V collagen-Sepharose. The binding region for type V collagen was located in a chymotrypsin-produced fragment of TS with chains of Mr = 70,000, after reduction. Interactions of TS with a number of other proteins, including fibronectin, fibrinogen, and laminin, could be demonstrated using the enzyme-linked immunosorbent assay technique but the interpretation of these findings is difficult since comparable binding to protein-Sepharose was not always observed. Our findings suggest that both the extravascular distribution and function of TS in vivo may involve an interaction with type V collagen.
Determination of kinetic constants for the interaction between a monoclonal antibody and peptides using surface plasmon resonance (1992)

Differences in the affinity of a monoclonal antibody raised against the protein of tobacco mosaic virus for 15 related peptides (residues 134-146) carrying single-residue modifications were investigated using a novel biosensor technology (Pharmacia BIAcore). Analysis of the peptide-antibody interaction in real time allowed fast and reproducible measurements of both association and dissociation rate constants. Out of 15 mutant peptides analyzed, five were not recognized by the antibody at all, and seven were recognized as well as the wild-type peptide. For three of the peptides, the rate constants were different for the mutant and wild-type peptides. The pattern of residue recognition suggests that the epitope is formed by three residues (140, 143, and 144) in a helical conformation that mimics the structure in the protein. Even a minor modification of these residues totally abolishes recognition by the antibody. Modifications of adjacent residues result in small but significant differences in association and/or dissociation rate constants. One of the recognized residues is totally buried in the three-dimensional structure of TMV protein, suggesting that a structural rearrangement next to the helix occurs during protein-antibody interaction.