gebhart/patrepeval huggingface dataset:
Development of a High-Throughput Quantitative Assay for Detecting Herpes Simplex Virus DNA in Clinical Samples (1999)

We have developed a high-throughput, semiautomated, quantitative fluorescence-based PCR assay to detect and type herpes simplex virus (HSV) DNA in clinical samples. The detection assay, which uses primers to the type-common region of HSV glycoprotein B (gB), was linear from <10 to 10(8) copies of HSV DNA/20 microl of sample. Among duplicate samples in reproducibility runs, the assay showed less than 5% variability. We compared the fluorescence-based PCR assay with culture and gel-based liquid hybridization system with 335 genital tract specimens from HSV type 2 (HSV-2)-seropositive persons attending a research clinic and 380 consecutive cerebrospinal fluid (CSF) samples submitted to a diagnostic virology laboratory. Among the 162 culture-positive genital tract specimens, TaqMan PCR was positive for 157 (97%) specimens, whereas the quantitative-competitive PCR was positive for 144 (89%) specimens. Comparisons of the mean titer of HSV DNA detected by the two assays revealed that the mean titer detected by the gel-based system was slightly higher (median, 1 log). These differences in titers were in part related to the fivefold difference in the amount of HSV DNA used in the amplicon standards with the two assays. Among the 380 CSF samples, 42 were positive by both assays, 13 were positive only by the assay with the agarose gel, and 3 were positive only by the assay with the fluorescent probe. To define the subtype of HSV DNA detected in the screening assay, we also designed one set of primers which amplifies the gG regions of both types of HSV and probes which are specific to either HSV-1 (gG1) or HSV-2 (gG2). These probes were labeled with different fluorescent dyes (6-carboxyfluorescein for gG2 and 6-hexachlorofluorescein for gG1) to enable detection in a single PCR. In mixing experiments the probes discriminated the correct subtype in mixtures with up to a 7-log-higher concentration of the opposite subtype. The PCR typing results showed 100% concordance with the results obtained by assays with monoclonal antibodies against HSV-1 or HSV-2. Thus, while the real-time PCR is slightly less sensitive than the gel-based liquid hybridization system, the high throughput, the lack of contamination during processing, the better reproducibility, and the better ability to type the isolates rapidly make the real-time PCR a valuable tool for clinical investigation and diagnosis of HSV infection.
Chemical recycling of poly(thiourethane) thermosets enabled by dynamic thiourethane bonds (2020)

Herein, we introduce a detailed investigation of the dynamic nature of the thiourethane bond and subsequently apply this dynamic character to formation, recycling and even additive manufacturing using cross-linked networks.
The EBP50-moesin interaction involves a binding site regulated by direct masking on the FERM domain (2004)

Members of the ezrin-radixin-moesin (ERM) protein family serve as regulated microfilament-membrane crosslinking proteins that, upon activation, bind the scaffolding protein ERM-phosphoprotein of 50 kDa (EBP50). Here we report a 3.5 A resolution diffraction analysis of a complex between the active moesin N-terminal FERM domain and a 38 residue peptide from the C terminus of EBP50. This crystallographic result, combined with sequence and structural comparisons, suggests that the C-terminal 11 residues of EBP50 binds as an alpha-helix at the same site occupied in the dormant monomer by the last 11 residues of the inhibitory moesin C-terminal tail. Biochemical support for this interpretation derives from in vitro studies showing that appropriate mutations in both the EBP50 tail peptide and the FERM domain reduce binding, and that a peptide representing just the C-terminal 14 residues of EBP50 also binds to moesin. Combined with the recent identification of the I-CAM-2 binding site on the ERM FERM domain (Hamada, K., Shimizu, T., Yonemura, S., Tsukita, S., and Hakoshima, T. (2003) EMBO J. 22, 502-514), this study reveals that the FERM domain contains two distinct binding sites for membrane-associated proteins. The contribution of each ligand to ERM function can now be dissected by making structure-based mutations that specifically affect the binding of each ligand.
Better Key Sizes (and Attacks) for LWE-Based Encryption. (2010)

We analyze the concrete security and key sizes of theoretically sound lattice-based encryption schemes based on the “learning with errors ” (LWE) problem. Our main contributions are: (1) a new lattice attack on LWE that combines basis reduction with an enumeration algorithm admitting a time/success tradeoff, which performs better than the simple distinguishing attack considered in prior analyses; (2) concrete parameters and security estimates for an LWE-based cryptosystem that is more compact and efficient than the well-known schemes from the literature. Our new key sizes are up to 10 times smaller than prior examples, while providing even stronger concrete security levels.
Enterococcus faecalis antigens in human infections (1997)

Genomic libraries of two Enterococcus faecalis strains, OG1RF and TX52 (an isolate from an endocarditis patient), were constructed in cosmid vectors pBeloBAC11 and pLAFRx, and screened with a serum from a rabbit immunized with surface proteins of an E. faecalis endocarditis isolate and sera from four patients with enterococcal endocarditis. Seventy-five cosmid clones reacted with at least two of the sera. Thirty-eight of the 75 immunopositive clones were considered to contain distinct inserts based on their DNA restriction patterns and were chosen for further subcloning into a pBluescript vector. Each sublibrary was screened with one of the five sera, and the DNA sequence of the immunopositive subclones was determined. Analysis of these sequences revealed similarities to a range of proteins, including bacterial virulence factors, transporters, two-component regulators, metabolic enzymes, and membrane or cell surface proteins. Fourteen subclones did not show significant similarity to any sequence in the databases and may contain novel genes. Thirteen of the immunopositive cosmid clones did not yield immunopositive subclones, and one such cosmid clone produced a nonprotein antigen in Escherichia coli.
Luminescence of Zn- and Cd-doped GaN (1972)

The luminescence of epitaxial GaN layers doped with Zn or Cd during growth is characterized, at low doping levels, by the presence of an I1-type line at 3.455 eV at 4.2 K which is attributed to the decay of excitons bound to neutral [inverted lazy s] 190-meV deep Zn or Cd acceptors on Ga sites. In addition, a broad and very efficient (&amp;gt; 12% at 300 K) band centered around 2.85 eV is observed in both vapor- and solution-grown samples and completely dominates the spectrum at high doping levels. Contrary to the usual band-gap dependence, this ``blue'' emission band shifts to slightly higher energies with increasing temperature.
Functional characterization of human blood coagulation factor XIa using hybridoma antibodies. (1985)

During the initiation of intrinsic coagulation factors XI and XIa interact intimately with several other coagulation proteins (factor XIIa, high Mr kininogen, and factor IX) as well as with the platelet surface. To help elucidate these complex intramolecular interactions, we have prepared a collection of monoclonal antibodies directed against various epitopes in factor XI. We have utilized these reagents to isolate factor XI and the light chain of factor XIa on affinity columns, and to probe structure-function relationships involved in the interactions of factor XIa with factor IX. The isolated light chain of factor XIa retained greater than 90% of its amidolytic activity against the oligopeptide substrate pyro-Glu-Pro-Arg-pNA (S-2366), but only 3.8% of its clotting activity in a factor XIa assay and 1% of its factor IX activating activity in an activation peptide release assay. This suggests that regions of the heavy chain are required for development of coagulant activity and specifically for the interaction of factor XIa with factor IX. To test this hypothesis, the effects of three of the monoclonal antibodies (5F4, 1F1, and 3C1) on the function of factor XIa were examined. The results show that in a clotting assay the light chain-specific antibody (5F4) inhibits 100% of the factor XIa activity, whereas of the heavy chain-specific antibodies, one (3C1) inhibits 75% and another (1F1) only 17%. Similarly in the factor IX activation peptide release assay, antibody 5F4 inhibits 100% of the factor XIa activity, whereas 3C1 inhibits 75% and 1F1 inhibits 33%. We conclude that regions located in the heavy chain, in addition to those in the light chain, are involved in the interaction of factor XIa with factor IX and in the expression of the coagulant activity of factor XI.
Prostaglandin D2 Selectively Induces Chemotaxis in T Helper Type 2 Cells, Eosinophils, and Basophils via Seven-Transmembrane Receptor Crth2 (2001)

Prostaglandin (PG)D2, which has long been implicated in allergic diseases, is currently considered to elicit its biological actions through the DP receptor (DP). Involvement of DP in the formation of allergic asthma was recently demonstrated with DP-deficient mice. However, proinflammatory functions of PGD2 cannot be explained by DP alone. We show here that a seven-transmembrane receptor, CRTH2, which is preferentially expressed in T helper type 2 (Th2) cells, eosinophils, and basophils in humans, serves as the novel receptor for PGD2. In response to PGD2, CRTH2 induces intracellular Ca2+mobilization and chemotaxis in Th2 cells in a Galphai-dependent manner. In addition, CRTH2, but not DP, mediates PGD2-dependent cell migration of blood eosinophils and basophils. Thus, PGD2 is likely involved in multiple aspects of allergic inflammation through its dual receptor systems, DP and CRTH2.
Spatial redundancy in Higher Order Ambisonics and its use for lowdelay lossless compression (2009)

When Higher Order Ambisonics (HOA) is used to represent a sound field, the channels might contain a lot of redundancy in some cases. This redundancy can be exploited in order to provide more efficient network transmission and storage. In this work the amount of inter-channel redundancy for Higher Order Ambisonics is investigated. Furthermore, lossless compression techniques that build on this redundancy are studied, with a focus on low-delay algorithms for real-time, or two-way, applications. The presented encoding scheme results in a delay of 256 samples, but with a rather high computational complexity both for encoding and decoding. The system also preserves the desired features of the HOA format, such as the scalability and the ability to reproduce over arbitrary loudspeaker layouts.
Purification and Characterization of Neutral Sphingomyelinase from Helicobacter pylori (2000)

Phospholipase activities of human gastric bacterium, Helicobacter pylori, are regarded as the pathogenic factors owing to their actions on epithelial cell membranes. In this study, we purified and characterized neutral sphingomyelinase (N-SMase) from the superficial components of H. pylori strains for the first time. N-SMase was purified 2083-fold with an overall recovery of 37%. The purification steps included acid glycine extraction, ammonium sulfate precipitation, CM-Sepharose, Mono-Q, and Sephadex G-75 column chromatography. Approximate molecular mass for the native N-SMase was around 32 kDa. When N-omega-trinitrophenylaminolauryl sphingomyelin (TNPAL-SM) was used as a substrate, the purified enzyme exhibited a K(m) of 6.7 microM and a V(max) of 15.6 nmol of TNPAL-sphingosine/h/mg of protein at 37 degrees C in 50 mM phosphate-buffered saline, pH 7.4. N-SMase reaches optimal activity at pH 7.4 and has a pI of 7.15. The enzyme activity is magnesium dependent and specifically hydrolyzed sphingomyelin and phosphatidylethanolamine. The enzyme also exhibits hemolytic activity on human erythrocytes. According to Western blot analysis, a rabbit antiserum against purified N-SMase from H. pylori cross-reacted with SMase from Bacillus cereus. Sera from individuals with H. pylori infection but not uninfected ones recognizing the purified N-SMase indicated that it was produced in vivo. In enzyme-linked immunosorbent assays, the purified N-SMase used as an antigen was as effective as crude protein antigens in detecting human antibodies to H. pylori.
A T-cell dormant state in the autoimmune process of nonobese diabetic mice treated with complete Freund's adjuvant. (1992)

Three experimental manipulations showed the suppressive effect of injection of complete Freund's adjuvant (CFA) in the diabetic state of nonobese diabetic (NOD) mice. (i) Diabetes was inhibited in young NOD mice injected with the adjuvant. (ii) Recurrence of diabetes in mice transplanted with pancreatic islets was also inhibited when the recipients were injected with CFA. (iii) Injection of spleen lymphocytes from diabetic mice into male NOD mice transferred the diabetic state, but this transfer was markedly suppressed when the recipients were treated with CFA. In all three cases the spleen cells from the normoglycemic mice treated with CFA induced diabetes when transferred into NOD male mice. CFA, therefore, induces a state of T-cell dormancy, in which the islets are no longer subject to an immune attack.
Localization of BmpA on the Exposed Outer Membrane ofBorrelia burgdorferiby Monospecific Anti-Recombinant BmpA Rabbit Antibodies (2004)

BmpA (P39) is an immunodominant chromosomally encoded Borrelia burgdorferi protein. The potential strong cross-reactivity of anti-BmpA antibodies with the other members of this paralogous protein family and the previous use of antibodies whose reactivity to the other Bmp proteins was uncharacterized have resulted in continued controversy over its localization in B. burgdorferi. In an effort to provide a definitive demonstration of the localization of BmpA, rabbit antibodies raised to recombinant BmpA (rBmpA) were rendered monospecific by absorption with rBmpB. This reagent did not react with rBmpB, rBmpC, or rBmpD in dot immunobinding, detected only a single 39-kDa band and a single 39-kDa, pI 5.0 spot on one- and two-dimensional immunoblots of B. burgdorferi lysates, respectively, and immunoprecipitated a single 39-kDa protein from these lysates. It detected BmpA in the Triton X-114-soluble and -insoluble fractions of B. burgdorferi, suggesting association with both inner and outer bacterial cell membranes. Treatment of intact B. burgdorferi with proteinase K partially digested BmpA, consistent with a limited surface exposure on the outer bacterial membrane, a suggestion confirmed by immunofluorescence of unfixed B. burgdorferi cultured in vitro and in vivo. Anti-rBmpA antibody was bacteriostatic for B. burgdorferi B31 in culture, again suggesting localization of BmpA on the exposed spirochetal outer surface. Surface localization of BmpA, growth inhibition by anti-rBmpA antibodies, and the previously reported conservation of bmpA in different B. burgdorferi sensu lato strains may indicate that BmpA plays an essential role in B. burgdorferi biology.
Vaccinia Virus Recombinants: Expression of VSV Genes and Protective Immunization of Mice and Cattle (1985)

Vesicular stomatitis virus (VSV) causes a contagious disease of horses, cattle, and pigs. When DNA copies of messenger RNA's for the G or N proteins of VSV were linked to a vaccinia virus promoter and inserted into the vaccinia genome, the recombinants retained infectivity and synthesized VSV polypeptides. After intradermal vaccination with live recombinant virus expressing the G protein, mice produced VSV-neutralizing antibodies and were protected against lethal encephalitis upon intravenous challenge with VSV. In cattle, the degree of protection against intradermalingually injected VSV was correlated with the level of neutralizing antibody produced following vaccination.
Enhanced Performance in Fluorene‐Free Organometal Halide Perovskite Light‐Emitting Diodes using Tunable, Low Electron Affinity Oxide Electron Injectors (2015)

Fluorene-free perovskite light-emitting diodes (LEDs) with low turn-on voltages, higher luminance and sharp, color-pure electroluminescence are obtained by replacing the F8 electron injector with ZnO, which is directly deposited onto the CH3NH3PbBr3 perovskite using spatial atmospheric atomic layer deposition. The electron injection barrier can also be reduced by decreasing the ZnO electron affinity through Mg incorporation, leading to lower turn-on voltages.
Brain-Cell Protein Synthesis Specifically Related to Learning (1970)

The study takes up the problem whether synthesis of certain protein fractions in nerve cells of the hippocampus in rats during the transfer of handedness may be specific for this learning process. Electrophoretic separation of protein was carried out on polyacrylamide gels at the microscale. The investigation encompasses the brain-specific, acidic protein S100 and two protein fractions moving close to the S100 protein during electrophoresis. The protein synthesis was studied during one month of intermittent training of the animals. The temporal link between behavior and an increase in the synthesis of nerve-cell protein indicates that the protein response is specific for the processes occurring in the hippocampus during learning.
Multi-WDM-channel, Gbit/s pulse generation from a single laser source utilizing LD-pumped supercontinuum in optical fibers (1994)

More than 40 wavelength-division-multiplexed (WDM) channels of 5-10 ps pulse streams are generated over 1530-1570 nm at 6.3 Gbit/s from a single laser source utilizing laser-diode (LD)-pumped supercontinuum in optical fibers for the first time. The time-bandwidth products of the generated pulses are within the range of 0.3-0.6, and it has been verified that the generated WDM picosecond pulses are capable of being interleaved to produce up to 40 WDM channels, each consisting of 50 Gbit/s time-division-multiplexed (TDM) pulse streams, in one optical fiber.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Generation of a broadband single-mode supercontinuum in a conventional dispersion-shifted fiber by use of a subnanosecond microchiplaser (2003)

We report the experimental generation, simply by use of a subnanosecond microchip laser at 532 nm and a conventional dispersion-shifted fiber, of a supercontinuum that spans more than 1100 nm. We show by detailed spectral analysis that this supercontinuum originates from a preliminary four-wave mixing process with multimode phase matching and subsequent double-cascade stimulated Raman scattering and is transversely single mode as a result of Raman-induced mode competition. This technique is believed to be the simplest configuration that allows one to generate a stable supercontinuum.
Endorepellin, a Novel Inhibitor of Angiogenesis Derived from the C Terminus of Perlecan (2003)

Perlecan, a ubiquitous basement membrane heparan sulfate proteoglycan, plays key roles in blood vessel growth and structural integrity. We discovered that the C terminus of perlecan potently inhibited four aspects of angiogenesis: endothelial cell migration, collagen-induced endothelial tube morphogenesis, and blood vessel growth in the chorioallantoic membrane and in Matrigel plug assays. The C terminus of perlecan was active at nanomolar concentrations and blocked endothelial cell adhesion to fibronectin and type I collagen, without directly binding to either protein; henceforth we have named it "endorepellin." We also found that endothelial cells possess a significant number of high affinity (K(d) of 11 nm) binding sites for endorepellin and that endorepellin binds endostatin and counteracts its anti-angiogenic effects. Thus, endorepellin represents a novel anti-angiogenic product, which may retard tumor neovascularization and hence tumor growth in vivo.
Specific Binding of High-Mobility-Group I (HMGI) Protein and Histone H1 to the Upstream AT-Rich Region of the Murine Beta Interferon Promoter: HMGI Protein Acts as a Potential Antirepressor of the Promoter (1999)

The high-mobility-group I (HMGI) protein is a nonhistone component of active chromatin. In this work, we demonstrate that HMGI protein specifically binds to the AT-rich region of the murine beta interferon (IFN-beta) promoter localized upstream of the murine virus-responsive element (VRE). Contrary to what has been described for the human promoter, HMGI protein did not specifically bind to the VRE of the murine IFN-beta promoter. Stably transfected promoters carrying mutations on this HMGI binding site displayed delayed virus-induced kinetics of transcription. When integrated into chromatin, the mutated promoter remained repressed and never reached normal transcriptional activity. Such a phenomenon was not observed with transiently transfected promoters upon which chromatin was only partially reconstituted. Using UV footprinting, we show that the upstream AT-rich sequences of the murine IFN-beta promoter constitute a preferential binding region for histone H1. Transfection with a plasmid carrying scaffold attachment regions as well as incubation with distamycin led to the derepression of the IFN-beta promoter stably integrated into chromatin. In vitro, HMGI protein was able to displace histone H1 from the upstream AT-rich region of the wild-type promoter but not from the promoter carrying mutations on the upstream high-affinity HMGI binding site. Our results suggest that the binding of histone H1 to the upstream AT-rich region of the promoter might be partly responsible for the constitutive repression of the promoter. The displacement by HMGI protein of histone H1 could help to convert the IFN-beta promoter from a repressed to an active state.
Metastatic basal cell carcinoma: rapid symptomatic response to Cisplatin and Paclitaxel (2004)

This regimen is an active combination for the rare patient with metastatic BCC. The combination of carboplatin and paclitaxel causes less neurotoxicity and may therefore be a superior regimen.
Smart Card Developer's Kit (1998)

From the Publisher:
Smart Card Developer's Kit is designed to provide the practical information you need to design and build applications that incorporate smart cards. Using a combination of detailed exposition, technical reference summaries, and extended examples, this book familiarizes you with the unique strengths and capabilities of this emerging computer technology.
The Masking of Clicks by Pure Tones and Bands of Noise (1950)

Pure tones and various bands of noise were used to mask impulsive acoustic stimuli (clicks) that were produced by electrical square pulses through a moving-coil type earphone. Results indicate that it is difficult to generalize about the masking of clicks by pure tones from observations on only a few observers because of sizeable individual differences. The masking of clicks by noise, however, is related unambiguously to the intensity and the spectral distribution of the noise. Both pure tones and narrow bands of noise provide maximum masking in the region between 1000 and 3000 c.p.s. Generally speaking, noise is a more efficient masker of clicks than are single pure tones. Although the present measurements were made with masking frequencies below 6500 c.p.s., there is some preliminary evidence to suggest that the audibility of certain clicks in noise is markedly dependent on frequencies above 6500 c.p.s. The linear (slope = 1) relation between the masking of speech or pure tones by noise and the intensity of the noise does not apply here. Rather a trimodal function indicates that the masking of unfiltered clicks by “pinkish-white” noise does not change over a 30-db range of moderate intensities. Below and above this range masking increases with the intensity of noise, sometimes at a slope greater than one.