gebhart/patrepeval huggingface dataset:
Comprehensive Epitope Analysis of Human Immunodeficiency Virus Type 1 (HIV-1)-Specific T-Cell Responses Directed against the Entire Expressed HIV-1 Genome Demonstrate Broadly Directed Responses, but No Correlation to Viral Load (2003)

Cellular immune responses play a critical role in the control of human immunodeficiency virus type 1 (HIV-1); however, the breadth of these responses at the single-epitope level has not been comprehensively assessed. We therefore screened peripheral blood mononuclear cells (PBMC) from 57 individuals at different stages of HIV-1 infection for virus-specific T-cell responses using a matrix of 504 overlapping peptides spanning all expressed HIV-1 proteins in a gamma interferon-enzyme-linked immunospot (Elispot) assay. HIV-1-specific T-cell responses were detectable in all study subjects, with a median of 14 individual epitopic regions targeted per person (range, 2 to 42), and all 14 HIV-1 protein subunits were recognized. HIV-1 p24-Gag and Nef contained the highest epitope density and were also the most frequently recognized HIV-1 proteins. The total magnitude of the HIV-1-specific response ranged from 280 to 25,860 spot-forming cells (SFC)/10(6) PBMC (median, 4,245) among all study participants. However, the number of epitopic regions targeted, the protein subunits recognized, and the total magnitude of HIV-1-specific responses varied significantly among the tested individuals, with the strongest and broadest responses detectable in individuals with untreated chronic HIV-1 infection. Neither the breadth nor the magnitude of the total HIV-1-specific CD8+-T-cell responses correlated with plasma viral load. We conclude that a peptide matrix-based Elispot assay allows for rapid, sensitive, specific, and efficient assessment of cellular immune responses directed against the entire expressed HIV-1 genome. These data also suggest that the impact of T-cell responses on control of viral replication cannot be explained by the mere quantification of the magnitude and breadth of the CD8+-T-cell response, even if a comprehensive pan-genome screening approach is applied.
Preparation of sodium fluoride-loaded gelatin microspheres, characterization and cariostatic studies (2004)

Sodium fluoride-loaded gelatin microspheres (NaF-GMS) were prepared using double-phase emulsified condensation polymerization. The average diameter of microspheres was (11.33+/-5.56) microm. The drug content and encapsulation efficiency were 8.80% and 76.73%, respectively. The fluoride releasing profiles of NaF-GMS in physiological saline and artificial saliva (pH 4.5, pH 6.8) showed that NaF-GMS had a sustained-release property and fluoride release rate was increased in pH 4.5 artificial saliva. Experiments conducted in rabbits' oral cavity using NaF-GMS and NaF solution as control revealed NaF-GMS could maintain oral fluoride retention longer than NaF solution. Cariostatic abilities of NaF-GMS including demineralization prohibition in vitro, fluoride deposition in artificial dental plaque and the ability of targeting to cariogenic bacteria were investigated in artificial dental plaque. The results indicated NaF-GMS with lower fluoride concentrations could achieve equivalent cariostatic effect to the concentrated NaF solution, at the same time, could prolong fluoride retention in dental plaque. Microscopic observation showed that NaF-GMS carrying fusion protein of glucan-binding domain could adhere more bacteria than NaF-GMS and this might indicate the possibility of targeting to cariogenic bacteria when NaF-GMS were properly modified.
Interconversion between apolipoprotein A-I-containing lipoproteins of pre-beta and alpha electrophoretic mobilities. (1992)

Apolipoprotein (apo) A-I-containing lipoproteins can be separated into two subfractions, pre-beta HDL and alpha HDL (high density lipoproteins), based on differences in their electrophoretic mobility. In this report we present results indicating that these two subfractions are metabolically linked. When plasma was incubated for 2 h at 37 degrees C, apoA-I mass with pre-beta electrophoretic mobility disappeared. This shift in apoA-I mass to alpha electrophoretic mobility was blocked by the addition of either 1.4 mM DTNB or 10 mM menthol to the plasma prior to incubation, suggesting that lecithin:cholesterol acyltransferase (LCAT) activity was involved. There was no change in the electrophoretic mobility of either pre-beta HDL or alpha HDL when they were incubated with cholesterol-loaded fibroblasts. However, after exposure to the fibroblasts, the cholesterol content of the pre-beta HDL did increase approximately sixfold, suggesting that pre-beta HDL can associate with appreciable amounts of cellular cholesterol. Pre-beta HDL-like particles appear to be generated by the incubation of alpha HDL with cholesteryl ester transfer protein (CETP) and either very low density lipoproteins (VLDL) or low density lipoproteins (LDL). This generation of pre-beta HDL-like particles was documented both by immunoelectrophoresis and by molecular sieve chromatography. Based on these findings, we propose a cyclical model in which 1) apoA-I mass moves from pre-beta HDL to alpha HDL in connection with the action of LCAT and the generation of cholesteryl esters within the HDL, and 2) apoA-I moves from alpha HDL to pre-beta HDL in connection with the action of CETP and the movement of cholesteryl esters out of the HDL. Additionally, we propose that the relative plasma concentrations of pre-beta HDL and alpha HDL reflect the movement of cholesteryl esters through the HDL. Conditions that result in the accumulation of HDL cholesteryl esters will be associated with low concentrations of pre-beta HDL, whereas conditions that result in the depletion of HDL cholesteryl esters will be associated with elevated concentrations of pre-beta HDL. This postulate is consistent with published findings in patients with hypertriglyceridemia and LCAT deficiency.
THz generation using extrinsic photoconductivity at 1550 nm (2012)

1550-nm pulses from a fiber-mode-locked laser are used to drive an ErAs:GaAs photoconductive switch, resulting in easily measured THz radiation with average broadband (~0.1 to 1.0 THz) power of ≈0.1 mW. The new THz switching mechanism is attributed to fast extrinsic photoconductivity that generates photocarriers (probably electrons) from the ErAs nanoparticles embedded in the material with a lifetime of ~0.45 ps (354 GHz bandwidth). This is the first known demonstration of useful THz power generation by extrinsic photoconductivity.
Studies of a human T lymphocyte antigen recognized by a monoclonal antibody. (1981)

A monoclonal antibody (designated L17F12) detects an antigen present on 95-100% of human peripheral T lymphocytes, the majority of thymocytes, and acute lymphocytic leukemia T cells but not B cells, B-cell lines, or monocytes. Examination of frozen tissue sections by the immunoperoxidase method revealed that the cells expressing this antigen were found predominantly in the medulla of thymus and in T-cell zones of lymph node and spleen. The antigen recognized by L17F12 was associated with a cell-surface glycoprotein of 67,000 daltons. L17F12 was used to isolate this molecule from human thymocytes, normal peripheral T cells, leukemic T cells, and T-cell lines. Expression of this antigen on normal T cells was not diminished by prolonged exposure in vitro to various T-cell stimuli. In the absence of complement, L17F12 bound to T cells without altering proliferative functions, thus enabling rapid purification of functionally intact T cells. In the presence of complement, L17F12 was cytolytic for T cells, providing the basis for depletion of T cells from heterogeneous populations. These data suggest that the monoclonal antibody L17F12 recognizes a specific T-cell differentiation protein. This antibody will be useful in studies of the human immune system.
HLA‐DR typing by PCR amplification with sequence‐specific primers (PCR‐SSP) in 2 hours: An alternative to serological DR typing in clinical practice including donor‐recipient matching in cadaveric transplantation (1992)

In most PCR-based tissue typing techniques the PCR amplification is followed by a post-amplification specificity step. In typing by PCR amplification with sequence-specific primers (PCR-SSP), typing specificity is part of the amplification step, which makes the technique almost as fast as serological tissue typing. In the present study primers were designed for DR "low-resolution" typing by PCR-SSP, i.e. identifying polymorphism corresponding to the serologically defined series DR1-DRw18. This resolution was achieved by performing 19 PCR reactions per individual, 17 for assigning DR1-DRw18 and 2 for the DRw52 and DRw53 superspecificities. Thirty cell lines and 121 individuals were typed by the DR "low-resolution" PCR-SSP technique, TaqI DRB-DQA-DQB RFLP analysis and serology. The concordance between PCR-SSP typing and RFLP analysis was 100%. The reproducibility was 100% in 40 samples typed on two separate occasions. No false-positive or false-negative typing results were obtained. All homozygous and heterozygous combinations of DR1-DRw18 could be distinguished. Amplification patterns segregated according to dominant Mendelian inheritance. DNA preparation, PCR amplification and post-amplification processing, including gel detection, documentation and interpretation, were performed in 2 hours. In conclusion, PCR-SSP is an accurate typing technique with high sensitivity, specificity and reproducibility. The method is rapid and inexpensive. DR "low-resolution" typing by the PCR-SSP technique is ideally suited for analyzing small numbers of samples simultaneously and is an alternative to serological DR typing in routine clinical practice including donor-recipient matching in cadaveric transplantations.
693. A new synthesis of glutamine and of γ-dipeptides of glutamic acid from phthalylated intermediates (1949)

F. E. King and D. A. A. Kidd, J. Chem. Soc., 1949, 3315 DOI: 10.1039/JR9490003315
A DNA insulator prevents repression of a targeted X-linked transgene but not its random or imprinted X inactivation (2006)

Some genes on the inactive X chromosome escape silencing. One possible escape mechanism is that heterochromatization during X inactivation can be blocked by boundary elements. DNA insulators are candidates for blocking because they shield genes from influences of their chromosomal environment. To test whether DNA insulators can act as boundaries on the X chromosome, we inserted into the mouse X-linked Hprt locus a GFP transgene flanked with zero, one, or two copies of a prototypic vertebrate insulator from the chicken beta-globin locus, chicken hypersensitive site 4, which contains CCCTC binding factor binding sites. On the active X chromosome the insulators blocked repression of the transgene, which commences during early development and persists in adults, in a copy number-dependent manner. CpG methylation of the transgene correlated inversely with expression, but the insulators on the active X chromosome were not methylated. On the inactive X chromosome, insulators did not block random or imprinted X inactivation of the transgene, and both the insulator and transgene were almost completely methylated. Thus, the chicken hypersensitive site 4 DNA insulator is sufficient to protect an X-linked gene from repression during development but not from X inactivation.
Decreased salivary epidermal growth factor in rheumatoid disease: a possible mechanism for increased susceptibility to gastric ulceration. (1990)

Mean (SD) number of injections and insulin dose during days at home and during westward and eastward travel Insulin dose (units) Injections per day Intermediate actingt Short acting Total Westward travel: Normal day at home 3-3 (1-1) 23-7 (9-9) 11-3 (9-2) 35-0 (11 1) Day offlight 48(1-1) 25-1 (96) 175 (8.5)* 426(11 1)* Eastward travel: Normaltwodaysathome 6 4(1 8) 48-5 (19 2) 23 4 (6 8) 71 9(22 1) Dayofflightandnextday 63(14) 407(144)* 242(132) 649(190)* *p<0.001Compared with value on normal days at home (unpaired t test).tIncludes basal insulin dose in two patients using insulin pumps.
N-Arylpiperazine-1-carboxamide Derivatives: a Novel Series of Orally Active Nonsteroidal Androgen Receptor Antagonists (2005)

A novel series of N-arylpiperazine-1-carboxamide derivatives was synthesized and their androgen receptor (AR) antagonist activities and in vivo antiandrogenic properties were evaluated. Reporter assays indicated that trans-2,5-dimethylpiperazine derivatives are potent AR antagonists, and in this series trans-N-4-[4-cyano-3-(trifluoromethyl)phenyl]-N-(2,4-difluorophenyl)-2,5-dimethylpiperazine-1-carboxamide (18 g, YM-175735) exhibited the most potent antiandrogenic activity. Compared to bicalutamide, YM-175735 is an approximately 4-fold stronger AR antagonist and has slightly increased antiandrogenic activity, suggesting that YM-175735 may be useful in the treatment of prostate cancer.
An S/MAR-based infectious episomal genomic DNA expression vector provides long-term regulated functional complementation of LDLR deficiency (2007)

Episomal gene expression vectors offer a safe and attractive alternative to integrating vectors. Here we describe the development of a high capacity episomal vector system exploiting human episomal retention sequences to provide efficient vector maintenance and regulated gene expression through the delivery of a genomic DNA locus. The iBAC-S/MAR vector is capable of the infectious delivery and retention of large genomic DNA transgenes by exploiting the high transgene capacity of herpes simplex virus type 1 (HSV-1) and the episomal retention properties of the scaffold/matrix attachment region (S/MAR). The iBAC-S/MAR vector was used to deliver and maintain a 135 kb genomic DNA insert carrying the human low density lipoprotein receptor (LDLR) genomic DNA locus at high efficiency in CHO ldlr(-/-) a7 cells. Long-term studies on CHO ldlr(-/-) a7 clonal cell lines carrying iBAC-S/MAR-LDLR demonstrated low copy episomal stability of the vector for >100 cell generations without selection. Expression studies demonstrated that iBAC-S/MAR-LDLR completely restored LDLR function in CHO ldlr(-/-) a7 cells to physiological levels and that this expression can be repressed by approximately 70% by high sterol levels, recapitulating the same feedback regulation seen at the endogenous LDLR locus. This vector overcomes the major problems of vector integration and unregulated transgene expression.
Exploiting statistics on query expressions for optimization (2002)

Statistics play an important role in influencing the plans produced by a query optimizer. Traditionally, optimizers use statistics built over base tables and assume independence between attributes while propagating statistical information through the query plan. This approach can introduce large estimation errors, which may result in the optimizer choosing inefficient execution plans. In this paper, we show how to extend a generic optimizer so that it also exploits statistics built on expressions corresponding to intermediate nodes of query plans. We show that in some cases, the quality of the resulting plans is significantly better than when only base-table statistics are available. Unfortunately, even moderately-sized schemas may have too many relevant candidate statistics. We introduce a workload-driven technique to identify a small subset of statistics that can provide significant benefits over just maintaining base-table statistics. Finally, we present experimental results on an implementation of our approach in Microsoft SQL Server 2000.
Novel HLA-Cw8-Restricted T Cell Epitopes Derived from Tyrosinase-Related Protein-2 and gp100 Melanoma Antigens (1999)

The identification of T cell epitopes presented by alternative HLA-B and -C alleles may provide a means to counteract the tumor escape mechanism based on the selection of tumor cells no longer susceptible to HLA-A-restricted T cell recognition. Several T cell clones and lines were obtained from T lymphocytes purified from melanoma-infiltrated or noninfiltrated lymph nodes of a patient who remained disease free 8 yr after surgery. Selected T cells recognized the autologous melanoma as evaluated by direct cytolysis and production of cytokines. These effectors were directed against the tyrosinase-related protein-2 (TRP-2) and gp100 melanoma epitopes restricted by HLA-Cw8. The nonamer and decamer peptides containing the sequence ANDPIFVVL (residues 387-395) of TRP-2 and the octamer, nonamer, and decamer peptides containing the sequence SNDGPTLI (residues 71-78) of gp100 reconstituted the epitope for TRP-2- and gp100-specific T cell lines and clones, respectively. However, only the nonameric form of TRP-2 and the nonameric and octameric forms of gp100 were able to induce peptide-specific T cells recognizing the autologous tumor in an HLA-class I-restricted fashion from PBMC of the melanoma patient studied. Together these data indicate that HLA-Cw8 can restrict the recognition of gp100 and TRP-2 epitopes by CTL, and that such peptides could stimulate a patient's PBL, suggesting that these Ags could have contributed to a systemic immunity against melanoma.
The CIPIC HRTF database (2002)

This paper describes a public-domain database of high-spatial-resolution head-related transfer functions measured at the UC Davis CIPIC Interface Laboratory and the methods used to collect the data.. Release 1.0 (see http://interface.cipic.ucdavis.edu) includes head-related impulse responses for 45 subjects at 25 different azimuths and 50 different elevations (1250 directions) at approximately 5/spl deg/ angular increments. In addition, the database contains anthropometric measurements for each subject. Statistics of anthropometric parameters and correlations between anthropometry and some temporal and spectral features of the HRTFs are reported.
Antimicrobial activities of squalamine mimics (1997)

We investigated the antimicrobial properties of compounds with structural features that were designed to mimic those of squalamine, an antibiotic isolated from the stomach of the dogfish shark. The mimics, like squalamine, are sterol-polyamine conjugates. Unlike squalamine, the mimics were simple to prepare, at high yield, from readily available starting materials. Several squalamine mimics showed activity against gram-negative rods, gram-positive cocci including methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecium, and fungi. Some had little or no hemolytic activity. The hydrophobicity of the sterol backbone and the length and the cationic charge of the side chains appeared to be critical determinants of activity. One of the squalamine mimics, SM-7, was bactericidal against Escherichia coli, Pseudomonas aeruginosa, and S. aureus; its activity was decreased by divalent or monovalent cations and by bovine serum albumin. Subinhibitory concentrations of SM-7 markedly enhanced the antimicrobial activity of rifampin against gram-negative rods. These results suggest that the compounds may disrupt an outer membrane of gram-negative rods. Squalamine mimics are a new class of broad-spectrum antimicrobial agents. The antagonism of their activity by serum and albumin and their hemolytic properties may limit their use as systemic agents. The squalamine mimics, because of their potencies, broad spectra of antimicrobial activity, and potential for systemic toxicity, appear to be good candidates for development as topical antimicrobial agents.
A Monoclonal Antibody-Based Enzyme-Linked Immunosorben Assay for Quantitation of Plasma Thrombospondin (1986)

An enzyme-linked immunosorbent assay was developed to quantitate the platelet secretory glycoprotein, thrombospondin (TSP), in plasma. Specificity of the assay was provided by using an anti-TSP monoclonal antibody (McAb) to coat 96 well polystyrene assay plates. The effective range of the standard curve for the assay was between 2.5 ng/mL and 500 ng/mL. Interassay and intraassay variations were 6.9% and 7.5%, respectively. To avoid spontaneous release of TSP from platelets after the blood was drawn, and to obtain a valid measurement of plasma TSP concentration, it was essential to place and maintain blood samples on ice immediately after blood was drawn and to separate plasma from cellular constituents within two hours. The mean plasma TSP concentration of 24 healthy adults was 64.3 +/- 18.0 ng/mL (mean +/- SD). The TSP concentration of pooled normal human serum (n = 6) was 15.9 micrograms/mL. Interference occurred when undiluted plasma or serum samples were assayed. This interfering effect could be eliminated completely by a tenfold dilution of plasma or serum samples before the assay. The assay also was applied successfully to quantitate TSP release from platelets after induction of aggregation by different platelet-aggregating agents.
Electrogenerated Chemiluminescence Detection in Paper-Based Microfluidic Sensors (2011)

This paper describes the first approach at combining paper microfluidics with electrochemiluminescent (ECL) detection. Inkjet printing is used to produce paper microfluidic substrates which are combined with screen-printed electrodes (SPEs) to create simple, cheap, disposable sensors which can be read without a traditional photodetector. The sensing mechanism is based on the orange luminescence due to the ECL reaction of tris(2,2'-bipyridyl)ruthenium(II) (Ru(bpy)(3)(2+)) with certain analytes. Using a conventional photodetector, 2-(dibutylamino)ethanol (DBAE) and nicotinamide adenine dinucleotide (NADH) could be detected to levels of 0.9 μM and 72 μM, respectively. Significantly, a mobile camera phone can also be used to detect the luminescence from the sensors. By analyzing the red pixel intensity in digital images of the ECL emission, a calibration curve was constructed demonstrating that DBAE could be detected to levels of 250 μM using the phone.