gebhart/patrepeval huggingface dataset:
Identification of an enhancer agonist cytotoxic T lymphocyte peptide from human carcinoembryonic antigen. (1997)

A vaccination strategy designed to enhance the immunogenicity of self-antigens that are overexpressed in tumor cells is to identify and slightly modify immunodominant epitopes that elicit T-cell responses. The resultant T cells, however, must maintain their ability to recognize the native configuration of the peptide-MHC interaction on the tumor cell target. We used a strategy to enhance the immunogenicity of a human CTL epitope directed against a human self-antigen, which involved the modification of individual amino acid residues predicted to interact with the T-cell receptor; this strategy, moreover, required no prior knowledge of these actual specific interactions. Single amino acid substitutions were introduced to the CAP1 peptide (YLSGANLNL), an immunogenic HLA-A2+-binding peptide derived from human carcinoembryonic antigen (CEA). In this study, four amino acid residues that were predicted to potentially interact with the T-cell receptor of CAP1-specific CTLs were systematically replaced. Analogues were tested for binding to HLA-A2 and for recognition by an established CTL line directed against CAP1. This line was obtained from peripheral blood mononuclear cells from an HLA-A2+ individual vaccinated with a vaccinia-CEA recombinant. An analogue peptide was identified that was capable of sensitizing CAP1-specific CTLs 10(2)-10(3) times more efficiently than the native CAP1 peptide. This enhanced recognition was shown not to be due to better binding to HLA-A2. Therefore, the analogue CAP1-6D (YLSGADLNL, Asn at position 6 replaced by Asp) meets the criteria of a CTL enhancer agonist peptide. Both the CAP1-6D and the native CAP1 peptide were compared for the ability to generate specific CTL lines in vitro from unimmunized apparently healthy HLA-A2+ donors. Whereas CAP1 failed to generate CTLs from normal peripheral blood mononuclear cells, the agonist peptide was able to generate CD8+ CTL lines that recognized both the agonist and the native CAP1 sequence. Most importantly, these CTLs were capable of lysing human tumor cells endogenously expressing CEA. The use of enhancer agonist CTL peptides may thus represent a new efficient direction for immunotherapy protocols.
A test method of a PEFC single cell with reference electrodes (2010)

Abstract A test method is proposed for obtaining correct polarization curves of PEFC single cells with reference electrodes, which in principle should have identical anode polarization curves for both H 2 /O 2 and H 2 /Air. Measured anode polarization curves are usually linear to the current density but not ohmic. Leak current between cathode and reference electrode causes voltage shift on the anode polarization curve. In order to obtain the ohmic anode polarization, the measured anode polarization curve should be moved vertically up to overlap with the base point. Configuration of the electrode edge adjacent to the reference electrode gives a significant effect on the anode and cathode potential. Polarization of an electrode which is 0.5 mm nearer to the reference electrode than the other electrode does not include the ohmic loss of the membrane. Instead, polarization of the other electrode includes the ohmic loss of the membrane. © 2010 Wiley Periodicals, Inc. Electr Eng Jpn, 172(1): 10–18, 2010; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/eej.20979
Exendin-4 and Glucagon-like-peptide-1:  NMR Structural Comparisons in the Solution and Micelle-Associated States (2001)

Exendin-4, a 39 amino acid peptide originally isolated from the oral secretions of the lizard Heloderma suspectum, has been shown to share certain activities with glucagon-like-peptide-1 (GLP-1), a 30 amino acid peptide. We have determined the structuring preferences of exendin-4 and GLP-1 by NMR in both the solution and dodecylphosphocholine (DPC) micelle-associated states. Based on both chemical shift deviations and the pattern of intermediate range NOEs, both peptides display significant helicity from residue 7 to residue 28 with greater fraying at the N-terminus. Thornton and Gorenstein [(1994) Biochemistry 33, 3532-3539] reported that the presence of a flexible, helix-destabilizing, glycine at residue 16 in GLP-1 was an important feature for membrane and receptor binding. Exendin-4 has a helix-favoring glutamate as residue 16. In the micelle-associated state, NMR data indicate that GLP-1 is less helical than exendin-4 due to the presence of Gly16; chemical shift deviations along the peptide sequence suggest that Gly16 serves as an N-cap for a second, more persistent, helix. In 30 vol-% trifluoroethanol (TFE), a single continuous helix is evident in a significant fraction of the GLP-1 conformers present. Exendin-4 has a more regular and less fluxional helix in both media and displays stable tertiary structure in the solution state. In the micelle-bound state of exendin-4, a single helix (residues 11-27) is observed with residues 31-39 completely disordered and undergoing rapid segmental motion. In aqueous fluoroalcohol or aqueous glycol, the Leu21-Pro38 span of exendin-4 forms a compact tertiary fold (the Trp-cage) which shields the side chain of Trp25 from solvent exposure and produces ring current shifts as large as 3 ppm. This tertiary structure is partially populated in water and fully populated in aqueous TFE. The Leu21-Pro38 segment of exendin-4 may be the smallest protein-like folding unit observed to date. When the Trp-cage forms, fraying of the exendin-4 helix occurs exclusively from the N-terminus; backbone NHs for the C-terminal residues of the helix display H/D exchange protection factors as large as 10(5) at 9 degrees C. In contrast, no tertiary structure is evident when exendin-4 binds to DPC micelles. An energetically favorable insertion of the tryptophan ring into the DPC micelle is suggested as the basis for this change. With the exception of exendin-4 in media containing fluoro alcohol cosolvents, NMR structure ensembles generated from the NOE data do not fully reflect the conformational averaging present in these systems. Secondary structure definition from chemical shift deviations may be the most appropriate treatment for peptides that lack tertiary structure.
Glutathione‐S‐transferase‐green fluorescent protein fusion protein reveals slow dissociation from high site density beads and measures free GSH (2006)

Glutathione in cellular lysates and GST-fusion protein affinity chromatography eluates can be measured by flow cytometry. Many interactions between GST fusion proteins and their fluorescent binding partners should be quantifiable by flow cytometry. Although a system may have the disadvantage that it has a low affinity and a correspondingly quick off-rate in solution, it may remain on beads if the site density can be increased to offer a slow apparent off rate.
Determinants of specific RNA interference-mediated silencing of human β-globin alleles differing by a single nucleotide polymorphism (2006)

A single nucleotide polymorphism (SNP) in the sickle beta-globin gene (beta(S)) leads to sickle cell anemia. Sickling increases sharply with deoxy sickle Hb concentration and decreases with increasing fetal gamma-globin concentration. Measures that decrease sickle Hb concentration should have an antisickling effect. RNA interference (RNAi) uses small interfering (si)RNAs for sequence-specific gene silencing. A beta(S) siRNA with position 10 of the guide strand designed to align with the targeted beta(S) SNP specifically silences beta(S) gene expression without affecting the expression of the gamma-globin or normal beta-globin (beta(A)) genes. Silencing is increased by altering the 5' end of the siRNA antisense (guide) strand to enhance its binding to the RNA-induced silencing complex (RISC). Specific beta(S) silencing was demonstrated by using a luciferase reporter and full-length beta(S) cDNA transfected into HeLa cells and mouse erythroleukemia cells, where it was expressed in the context of the endogenous beta-globin gene promoter and the locus control region enhancers. When this strategy was used to target beta(E), silencing was not limited to the mutant gene but also targeted the normal beta(A) gene. siRNAs, mismatched with their target at position 10, guided mRNA cleavage in all cases except when two bulky purines were aligned. The specific silencing of the beta(S)-globin gene, as compared with beta(E), as well as studies of silencing SNP mutants in other diseases, indicates that siRNAs developed to target a disease-causing SNP will be specific if the mutant residue is a pyrimidine and the normal residue is a purine.
Optical clearing in photoacoustic flow cytometry (2013)

Clinical applications of photoacoustic (PA) flow cytometry (PAFC) for detection of circulating tumor cells in deep blood vessels are hindered by laser beam scattering, that result in loss of PAFC sensitivity and resolution. We demonstrate biocompatible and rapid optical clearing (OC) of skin to minimize light scattering and thus, increase optical resolution and sensitivity of PAFC. OC effect was achieved in 20 min by sequent skin cleaning, microdermabrasion, and glycerol application enhanced by massage and sonophoresis. Using 0.8 mm mouse skin layer over a blood vessel in vitro phantom we demonstrated 1.6-fold decrease in laser spot blurring accompanied by 1.6-fold increase in PA signal amplitude from blood background. As a result, peak rate for B16F10 melanoma cells in blood flow increased 1.7-fold. By using OC we also demonstrated the feasibility of PA contrast improvement for human hand veins.
Analysis and partial epitope mapping of human T cell responses to Trypanosoma cruzi cysteinyl proteinase. (1993)

Human infection with Trypanosoma cruzi (Chagas' disease) is usually accompanied by humoral and cellular immune responses to GP57/51, a major antigen that was recently identified as a prominent cysteinyl proteinase (cruzipain). The PBMC responses of 11 chronic chagasic patients and the properties of anti-cruzipain T cell lines are reported herein. GP57/51, isolated from Y strain epimastigotes (n-cruzipain) or the recombinant protein expressed in E. coli (r-cruzipain), elicited proliferative responses of variable intensity from the patient's PBMC. T cell lines were then generated using each of these antigens. These lines, which always carried the CD4+ phenotype, were reciprocally stimulated by n-cruzipain or r-cruzipain, the responses to the former being usually stronger. The analysis of cytokine production suggested that Th1-like subsets dominate the patient's responses: IFN-gamma was consistently induced on stimulation with either n-cruzipain or r-cruzipain. In contrast, IL-4 was present in very small concentrations or was undetectable. We then sought to define T cell epitopes of cruzipain using synthetic peptides spanning portions of the central (catalytic) domain and COOH-terminal extension. From a panel of 11 peptides, only one 33 mer peptide (P214) elicited a strong proliferative response on anti-cruzipain T cell lines, the intensity being comparable to that induced by r-cruzipain. Conversely, T cell lines started with P214 were responsive to either n-cruzipain or r-cruzipain, the proliferative responses again being accompanied by IFN-gamma production, but not IL-4. Interestingly, P214 is located in a conserved region of the catalytic domain of cruzipain, hence may propitiate opportunities for cross-recognition of other members of the papain superfamily. Fine epitope mapping should reveal whether structurally similar regions of host thiol-cathepsins can be potential targets for cross-reactive T cell responses during chronic human infection.
The role of extended defects on the performance of optoelectronic devices in nitride semiconductors (2012)

Abstract In this paper I am addressing the fundamental question as to why the performance of optoelectronic devices based on nitride semiconductors is insensitive to high concentration of extended defects, which is not the case for traditional III–V compounds. There are three important differences between these two families of semiconductors, which contribute to this finding: (a) the chemical bonds in nitrides are strongly ionic while are mostly covalent in III–V compounds. This leads to the bunching of the surface states as well as the states associated with dangling bonds in edge dislocations near the band edges, which prevents them from being non‐radiative recombination centers. Furthermore, the surface states have less effect on the surface Fermi level position; (b) the nitrides can exist in the wurtzite structure (equilibrium) and the cubic structure (metastable) and the enthalpy of formation of the two allotropic forms differs only by a few meV. Thus, conversions between the two phases occur easily by creation of stacking faults along the closed packed (0001) and (111) planes. As a result basal plane stacking faults are abundant in both compounds and alloys. This leads to strong band structure potential fluctuations; (c) additional band structure potential fluctuations exist in InGaN and AlGaN alloys, due to phase separation and alloy ordering. Both types of potential fluctuations contribute to exciton localization and thus efficient radiative recombination even at room temperature.
Phosphorylation of the α Subunit of Rat Brain Sodium Channels by cAMP-dependent Protein Kinase at a New Site Containing Ser686 and Ser687 (1989)

The alpha subunit of the rat brain sodium channel is phosphorylated by cAMP-dependent protein kinase in vitro and in situ at multiple sites which yield seven tryptic phosphopeptides. Phosphopeptides 1-4 and 7 are derived from phosphorylation sites between residues 554 and 623 in a single large CNBr fragment from the cytoplasmic segment connecting homologous domains I and II of the alpha subunit (Rossie, S., Gordon, D., and Catterall, W. A. (1987) J. Biol. Chem. 262, 17530-17535). In the present work, antibodies were prepared against a synthetic peptide corresponding to residues 676-692 (AbSP15), which contain one additional potential phosphorylation site at Ser686-Ser687 in a different predicted CNBr fragment of this same intracellular segment. AbSP15 recognizes native and denatured sodium channels specifically and immunoprecipitates phosphorylated CNBr fragments of low molecular mass that contain a new site phosphorylated by cAMP-dependent protein kinase. Comparison of tryptic phosphopeptides derived from intact alpha subunits with those derived from the phosphorylated CNBr fragments isolated by immunoprecipitation with AbSP15 indicates that the two previously unidentified phosphopeptides 5 and 6 derived from the intact alpha subunit arise from phosphorylation of the site containing Ser686-Ser687. These results identify a new cAMP-dependent phosphorylation site and show that the major cAMP-dependent phosphorylation sites of the rat brain sodium channel, which are phosphorylated both in vitro and in intact neurons, are all located in a cluster between residues 554 and 687 in the intracellular segment between domains I and II.
Antigen-Antibody Immune Complexes Empower Dendritic Cells to Efficiently Prime Specific CD8+ CTL Responses In Vivo (2002)

Dendritic cells (DCs) require a maturation signal to acquire efficient CTL-priming capacity. In vitro FcgammaR-mediated internalization of Ag-Ab immune complexes (ICs) can induce maturation of DCs. In this study, we show that IC-induced DC maturation in vitro enables DCs to prime peptide-specific CD8+ CTLs in vivo, independently of CD4+ Th cells. Importantly, OVA/anti-OVA IC-treated DCs not only primed CD8+ CTLs to an exogenously loaded peptide nonrelated to OVA, but also efficiently primed CTLs against the dominant CTL epitope derived from the OVA Ag present in the ICs. Our studies show that ICs fulfill a dual role in priming of CD8+ CTL responses to exogenous Ags: enhancement of Ag uptake by DCs and activation of DCs, resulting in "license to kill." These findings indicate that the presence of specific Abs can crucially affect the induction of cytotoxic cellular responses.
Learnability and Complexity of Quantum Samples (2020)

Given a quantum circuit, a quantum computer can sample the output distribution exponentially faster in the number of bits than classical computers. A similar exponential separation has yet to be established in generative models through quantum sample learning: given samples from an n-qubit computation, can we learn the underlying quantum distribution using models with training parameters that scale polynomial in n under a fixed training time? We study four kinds of generative models: Deep Boltzmann machine (DBM), Generative Adversarial Networks (GANs), Long Short-Term Memory (LSTM) and Autoregressive GAN, on learning quantum data set generated by deep random circuits. We demonstrate the leading performance of LSTM in learning quantum samples, and thus the autoregressive structure present in the underlying quantum distribution from random quantum circuits. Both numerical experiments and a theoretical proof in the case of the DBM show exponentially growing complexity of learning-agent parameters required for achieving a fixed accuracy as n increases. Finally, we establish a connection between learnability and the complexity of generative models by benchmarking learnability against different sets of samples drawn from probability distributions of variable degrees of complexities in their quantum and classical representations.
Harzianin HB I, an 11-residue peptaibol from Trichoderma harzianum: isolation, sequence, solution synthesis and membrane activity (1997)

Harzianin HB I is a minor component of the peptaibol mixture biosynthesized by a Trichoderma harzianum strain. It is isolated by a multi-step chromatography procedure, including HPLC; its sequence has been elucidated by LSIMS and two-dimensional 1H NMR experiments. This 11-residue peptaibol is an analogue of the 14-residue peptaibol harzianin HC IX, resulting from the deletion of the tripeptide Aib-Pro-Ala. The CD and NMR data (NOE data and amide proton temperature coefficients) are similar to those of HC IX, suggesting a right-handed helix-type conformation for the two peptides. Harzianin HB I was synthesized by the solution-phase method using BOP as coupling reagent. The membrane properties examined on liposomes are compared with those of other known peptaibols.
Dynamics of anti-Stokes photoluminescence in type-IIAlxGa1−xAs−GaInP2heterostructures: The important role of long-lived carriers near the interface (1997)

We have studied the anti-Stokes photoluminescence (ASPL) of a type-II ${\mathrm{Al}}_{x}{\mathrm{Ga}}_{1\ensuremath{-}x}{\mathrm{A}\mathrm{s}\ensuremath{-}\mathrm{G}\mathrm{a}\mathrm{I}\mathrm{n}\mathrm{P}}_{2}$ heterojunction. We have found that the ASPL can appear in both layers adjacent to the heterojunction when the excitation photon energy is higher than the energy of below-band-gap (BBG) luminescence. The intensity of ${\mathrm{GaInP}}_{2}$-related ASPL shows an almost linear dependence on the excitation intensity. Time-resolved photoluminescence experiments reveal that the ASPL can be sustained as long as the BBG luminescence remains. Our results suggest that the energy up conversion for the ASPL is via a two-step two-photon absorption process involving localized, long-lived carriers near the type-II interface.
A Prospective Study of Triglyceride Level, Low-Density Lipoprotein Particle Diameter, and Risk of Myocardial Infarction (1996)

These findings indicate that nonfasting triglyceride levels appear to be a strong and independent predictor of future risk of MI, particularly when the total cholesterol level is also elevated. In contrast, LDL particle diameter is associated with risk of MI, but not after adjustment for triglyceride level. Increased triglyceride level, small LDL particle diameter, and decreased HDL-C levels appear to reflect underlying metabolic perturbations with adverse consequences for risk of MI; elevated triglyceride levels may help identify high-risk individuals.
Rabbit model for Chlamydia pneumoniae infection (1997)

A rabbit model was established for Chlamydia pneumoniae infection that may be helpful to understand the pathogenesis of disease in humans. Twelve, pathogen-free, 1-month-old New Zealand White rabbits were inoculated with 1.0 x 10(7) to 5.0 x 10(7) CFU of purified C. pneumoniae (ATCC strain VR 1310) via the nasopharynx (1 rabbit died immediately postinoculation, and 11 were available for study). Five controls were inoculated with the carrier buffer. Ten of the 11 study rabbits demonstrated serological evidence of acute infection (immunoglobulin G antibodies, 1:8 to > 1:16), with the weakest response at 7 days and the strongest response at 28 days, whereas none of the controls showed any seroconversion. Study animals were sacrificed in batches of three, on days 7, 14, 21, and 28, but controls were sacrificed on days 7 and 28. Two-thirds of the animals demonstrated evidence of bronchiolitis and pneumonia on days 7 and 14 and resolution by day 21. Two study rabbits demonstrated, on histology, early and intermediate lesions of atherosclerosis: one animal (day 7) showed the accumulation of foamy macrophages (fatty streak) in the arch of the aorta, and the other animal (day 14) showed spindle cell proliferation of smooth muscle cells (intermediate lesion). Focal periaortitis was seen in the same animal (day 7). C. pneumoniae elementary bodies were demonstrated by immunocytochemical stain in the lungs (n = 2), liver (n = 3), spleen (n = 5), and aorta (n = 2), one of which corresponded to the intermediate lesion. C. pneumoniae was cultured from the lungs (n = 2), liver (n = 2), spleen (n = 2), and aortic arch (n = 1). All histopathological, immunocytochemical, and cultural studies were negative in the controls. Hence, the rabbit provides a useful animal model for the study of C. pneumoniae infection and its complications, particularly atherosclerosis.