gebhart/patrepeval huggingface dataset:
Circulating human dendritic cells differentially express high levels of a 55-kd actin-bundling protein. (1996)

This study was initiated to examine the differential expression of an evolutionary conserved human 55-kd actin-bundling (p55) protein that is induced in B lymphocytes by Epstein-Barr virus infection. Our study demonstrates that p55 is specifically expressed at constitutively high levels in human peripheral blood dendritic cells and lymph node (interdigitating) dendritic cells. Blood dendritic cells constitute a minority (< 2%) of all blood leukocytes but are a distinct population of potent antigen-presenting cells. Immunofluorescence microscopy with a monoclonal antibody specific for p55 showed that 87% of peripheral blood dendritic cells stained brightly in the cytoplasm and in the veiled cytoplasmic extensions. In contrast, monocytes, granulocytes, T cells, and B lymphocytes showed no expression of the p55 protein. Western blot analysis confirmed that only the dendritic cell component of peripheral blood expressed high levels of p55. Staining of human lymph node sections demonstrated selective expression of the p55 antigen by dendritic cells in the T-cell-dependent areas but not in the B cell follicles. p55 is likely to be involved in the organization of a specialized microfilament cytoskeleton in the dendritic cells, and the anti-p55 antibody should be useful for further characterization of this important population of antigen-presenting cells in clinical transplantation, HIV-1 pathogenesis, and autoimmune diseases.
The Inhibition Mechanism of Serpins (1995)

Inhibitors that belong to the serine protease inhibitor or serpin family have reactive centers that constitute a mobile loop with P1-P1' residues acting as a bait for cognate protease. Current hypotheses are conflicting as to whether the native serpin-protease complex is a tetrahedral intermediate with an intact inhibitor or an acyl-enzyme complex with a cleaved inhibitor P1-P1' peptide bond. Here we show that the P1' residue of the plasminogen activator inhibitor type 1 mutant (P1' Cys) became more accessible to radiolabeling in complex with urokinase-type plasminogen activator (uPA) compared with its complex with catalytically inactive anhydro-uPA, indicating that complex formation with cognate protease leads to a conformational change whereby the P1' residue becomes more accessible. Analysis of chemically blocked NH2 termini of serpin-protease complexes revealed that the P1-P1' peptide bonds of three different serpins are cleaved in the native complex with their cognate protease. Complex formation and reactive center cleavage were found to be rapid and coordinated events suggesting that cleavage of the reactive center loop and the subsequent loop insertion induce the conformational changes required to lock the serpin-protease complex.
Turbo equalization (2004)

Turbo equalization is an iterative equalization and decoding technique that can achieve equally impressive performance gains for communication systems that send digital data over channels that require equalization, i.e., those that suffer from intersymbol interference (ISI). In this article, we discuss the turbo equalization approach to coded data transmission over ISI channels, with emphasis on the basic ideas and some of the practical details. The original system introduced by Douillard et al. can be viewed as an extension of the turbo decoding algorithm by considering the effect of the ISI channel as another form of error protection, i.e., as a rate-1 convolutional code.
Characterization of the Taxol Binding Site on the Microtubule (1999)

Photoaffinity labeling methods have allowed a definition of the sites of interaction between Taxol and its cellular target, the microtubule, specifically beta-tubulin. Our previous studies have indicated that [(3)H]3'-(p-azidobenzamido)Taxol photolabels the N-terminal 31 amino acids of beta-tubulin (Rao, S., Krauss, N. E., Heerding, J. M., Swindell, C. S., Ringel, I., Orr, G. A., and Horwitz, S. B. (1994) J. Biol. Chem. 269, 3132-3134) and [(3)H]2-(m-azidobenzoyl)Taxol photolabels a peptide containing amino acid residues 217-233 of beta-tubulin (Rao, S., Orr, G. A., Chaudhary, A. G., Kingston, D. G. I., and Horwitz, S. B. (1995) J. Biol. Chem. 270, 20235-20238). The site of photoincorporation of a third photoaffinity analogue of Taxol, [(3)H]7-(benzoyldihydrocinnamoyl) Taxol, has been determined. This analogue stabilizes microtubules polymerized in the presence of GTP, but in contrast to Taxol, does not by itself enhance the polymerization of tubulin to its polymer form. CNBr digestion of [(3)H]7-(benzoyldihydrocinnamoyl)Taxol-labeled tubulin, with further arginine-specific cleavage by clostripain resulted in the isolation of a peptide containing amino acid residues 277-293. Amino acid sequence analysis indicated that the photoaffinity analogue cross-links to Arg(282) in beta-tubulin. Advances made by electron crystallography in understanding the structure of the tubulin dimer have allowed us to visualize the three sites of photoincorporation by molecular modeling. There is good agreement between the binding site of Taxol in beta-tubulin as determined by photoaffinity labeling and electron crystallography.
Molecular modeling of protein-glycosaminoglycan interactions. (1989)

Forty-nine regions in 21 proteins were identified as potential heparin-binding sites based on the sequence organizations of their basic and nonbasic residues. Twelve known heparin-binding sequences in vitronectin, apolipoproteins E and B-100, and platelet factor 4 were used to formulate two search strings for identifying potential heparin-binding regions in other proteins. Consensus sequences for glycosaminoglycan recognition were determined as [-X-B-B-X-B-X-] and [-X-B-B-B-X-X-B-X-] where B is the probability of a basic residue and X is a hydropathic residue. Predictions were then made as to the heparin-binding domains in endothelial cell growth factor, purpurin, and antithrombin-III. Many of the natural sequences conforming to these consensus motifs show prominent amphipathic periodicities having both alpha-helical and beta-strand conformations as determined by predictive algorithms and circular dichroism studies. The heparin-binding domain of vitronectin was modeled and formed a hydrophilic pocket that wrapped around and folded over a heparin octasaccharide, yielding a complementary structure. We suggest that these consensus sequence elements form potential nucleation sites for the recognition of polyanions in proteins and may provide a useful guide in identifying heparin-binding regions in other proteins. The possible relevance of protein-glycosaminoglycans interactions in atherosclerosis is discussed.
Designing environments - more than furniture arrangement (2012)

As early childhood educators move away from 'boxed-style' programs to more 'child-centred', emergent curricula; thought, planning and collaboration are needed in designing the environment.
FIH-1 is an asparaginyl hydroxylase enzyme that regulates the transcriptional activity of hypoxia-inducible factor (2002)

Mammalian cells adapt to hypoxic conditions through a transcriptional response pathway mediated by the hypoxia-inducible factor, HIF. HIF transcriptional activity is suppressed under normoxic conditions by hydroxylation of an asparagine residue within its C-terminal transactivation domain, blocking association with coactivators. Here we show that the protein FIH-1, previously shown to interact with HIF, is an asparaginyl hydroxylase. Like known hydroxylase enzymes, FIH-1 is an Fe(II)-dependent enzyme that uses molecular O(2) to modify its substrate. Together with the recently discovered prolyl hydroxylases that regulate HIF stability, this class of oxygen-dependent enzymes comprises critical regulatory components of the hypoxic response pathway.
Frequency-Offset Estimation for MIMO and OFDM Systems Using Orthogonal Training Sequences (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We propose a training-sequence-based frequency-offset estimator for a multiple transmit-and-receive antenna system in frequency-flat fading channels. The estimator is based on the maximum likelihood (ML) criterion and does not require channel information. To reduce the computational load, they propose to use special training sequences—the periodic orthogonal codes. Using these codes, we get a closed form estimator which requires much lower computational load (some additions and multiplications). For the high signal-to-noise ratio and small frequency offset, the proposed estimator achieves the performance of the optimal ML estimator, which locates the peak of the likelihood function. We also apply the proposed estimator to a multiple antenna system in frequency-selective channels and an orthogonal-frequency-division-multiplexing system. With theoretical analysis and simulations, we evaluate the performance of the proposed estimator. </para>
Theiler's murine encephalomyelitis virus induces tumour necrosis factor-alpha in murine astrocyte cell cultures. (1993)

Cytokines have been postulated to exert an important modulatory and recruiting role in demyelination induced by Theiler's murine encephalomyelitis virus (TMEV) in SJL/J mice. Using a cytolytic bioassay and ELISA, we have detected and quantified a cytokine, tumour necrosis factor-alpha (TNF-alpha), in supernatants from astrocyte cultures infected in vitro with TMEV. TNF was detected only after TMEV-specific infection of astrocyte cultures (approximately 200-400 U/ml). In vitro TNF synthesis appeared in a dose- and time-dependent manner and was produced by both SJL/J (a strain susceptible to TMEV-induced demyelination) and BALB/c (a resistant strain) astrocytes. The precise nature of TNF activity was further assessed by fast protein liquid chromatography (FPLC) and antibody neutralization. These results indicate an active role for astrocytes as accessory immune cells in our experimental model for multiple sclerosis.
Cooling for Acute Ischemic Brain Damage (COOL AID) (2001)

Induced hypothermia appears feasible and safe in patients with acute ischemic stroke even after thrombolysis. Refinements of the cooling process, optimal target temperature, duration of therapy, and, most important, clinical efficacy, require further study.
Comparison of Antibiotic Beads and Intravenous Antibiotics in Open Fractures (2000)

This study compared the efficacy of antibiotic impregnated beads with conventional intravenous antibiotics in the treatment of open fractures. A randomized prospective study was designed and conducted during a 29-month period. Sixty-seven patients with 75 open fractures were treated similarly, with the exception of the method of antibiotic administration, and were followed up for at least 1 year after injury. Infection occurred in two of 24 (8.3%) fractures treated with antibiotic beads alone and in two of 38 (5.3%) fractures treated with conventional intravenous antibiotics. In an unanticipated nonrandomized third cohort group, patients received antibiotic beads and intravenous antibiotics administered for nonorthopaedic reasons or limb threatening injury, or both. Two of 13 (15.4%) fractures in this high risk group became infected. Infection ultimately resolved in all fractures treated with antibiotic beads alone or antibiotic beads in conjunction with conventional intravenous antibiotics. This study was unable to achieve statistical significance; however, the data suggest antibiotic beads may be useful in preventing infection in open fractures. Thus, a larger multicenter randomized prospective study of isolated open fractures, eliminating other variables, is justified.
Analysis of CpG C‐to‐T mutations in neurofibromatosis type 1 (1998)

Neurofibromatosis type 1 (NF1) is a dominant disorder caused by mutations in the NF1 gene; approximately 100 NF1 gene mutations have been published. The CpG C-to-T transition is a frequent mutation mechanism in genetic disorders. To estimate its frequency in NF1, we employed a PCR-restriction digestion method to examine 17 CpGs in 65 patients, and also screened for a CpG nonsense transition (R1947X) that occurs in 1-2% of patients. The analysis revealed disease-related CpG C-to-T transitions (including a nonsense mutation that may be as frequent as R1947X) as well as a benign variant and another mutation at a CpG. Four patients showed CpG mutations in analysis of 18 sites (17 surveyed by restriction digest, plus the R1947X assay), including three C-to-T transitions and one C-to-G transversion. These 18 sites represent one-fifth of the 91 CpGs at which a C-to-T transition would result in a nonsense or nonconservative missense mutation. Thus, it is feasible that the CpG mutation rate at NF1 might be similar to that seen in other disorders with a high mutation rate, and that recurrent NF1 mutations may frequently reside at CpG sites. Hum Mutat 11:411, 1998. © 1998 Wiley-Liss, Inc.
Synthesis of Helix 69 of Escherichia coli 23S rRNA Containing Its Natural Modified Nucleosides, m3Ψ and Ψ (2002)

The synthesis of 3-methylpseudouridine (m(3)Psi) phosphoramidite, 5'-O-[benzhydryloxybis(trimethylsilyloxy)silyl]-2'-O-[bis(2-acetoxyethoxy)methyl]-3-methylpseudouridine-3'-(methyl-N,N-diisopropyl)phosphoramidite, is reported. Selective pivaloyloxymethyl protection of the Psi N1 followed by methylation at N3 was used to generate the naturally occurring pseudouridine analogue. The m(3)Psi phosphoramidite was used in combination with pseudouridine (Psi) and standard base phosphoramidites to synthesize a 19-nucleotide RNA representing helix 69 of Escherichia coli 23S ribosomal RNA (rRNA) (residues 1906-1924), containing a single m(3)Psi at position 1915 and two Psi's at positions 1911 and 1917. Our synthesis of the fully modified helix 69 RNA demonstrates the ability to make milligram quantities of RNA that can be used for further high-resolution structure studies. Site-selective introduction of the methyl group at the N3 position of pseudouridine at position 1915 causes a slight increase in the thermodynamic stability of the RNA hairpin relative to pseudouridine; RNAs containing either uridine or 3-methyluridine at position 1915 have similar stability. One-dimensional imino proton NMR and circular dichroism spectra of the modified RNAs reveal that the methyl group does not cause any substantial changes in the RNA hairpin structure.
A measurement-based model for predicting coverage areas of urban microcells (1993)

The authors have performed data reductions on 900 MHz signal attenuations measured on numerous streets in Manhattan. The database consists of both local spatial averages of signal attenuation and the short-term fluctuations about this average. The former, which is termed the local mean attenuation (LMA), is the primary focus. The database is used to obtain contours of constant LMA for two neighborhoods. It is shown that the contours have the shapes of convex diamonds. The authors propose that squares inscribed within these contours be used as the building blocks of microcellular environments. A theory is developed that explains the contours and predicts, with reasonable accuracy, the sizes of the inscribed squares. It is also shown that the prediction method can be applied without the need for measured data. The short-term fluctuation statistics of the signal attenuation are examined. They are shown to be Rayleigh-like in the non-line-of-sight regions of a microcell and Rice-like in the line-of-sight region. Possible extensions to other frequency bands and other urban environments are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Screening Phage Display Peptide Libraries on Nitrocellulose Membranes (2003)

The procedure of using phage display libraries involves several cycles of phage biopanning (, , ). In each of these cycles, a selector protein is incubated with the phage library, and members of the library displaying peptides that interact with the selector protein are selected and amplified in E. coli cells. Multiple cycles of biopanning are required in order to increase the number of the specific clones over the background levels, since the imtial ratio between nonspecific members of the library (the size of the library repertoire) and members that are specific for a single binding protein is usually in the order of 106 or more.
Butyrate Improves Insulin Sensitivity and Increases Energy Expenditure in Mice (2009)

OBJECTIVE We examined the role of butyric acid, a short-chain fatty acid formed by fermentation in the large intestine, in the regulation of insulin sensitivity in mice fed a high-fat diet. RESEARCH DESIGN AND METHODS In dietary-obese C57BL/6J mice, sodium butyrate was administrated through diet supplementation at 5% wt/wt in the high-fat diet. Insulin sensitivity was examined with insulin tolerance testing and homeostasis model assessment for insulin resistance. Energy metabolism was monitored in a metabolic chamber. Mitochondrial function was investigated in brown adipocytes and skeletal muscle in the mice. RESULTS On the high-fat diet, supplementation of butyrate prevented development of insulin resistance and obesity in C57BL/6 mice. Fasting blood glucose, fasting insulin, and insulin tolerance were all preserved in the treated mice. Body fat content was maintained at 10% without a reduction in food intake. Adaptive thermogenesis and fatty acid oxidation were enhanced. An increase in mitochondrial function and biogenesis was observed in skeletal muscle and brown fat. The type I fiber was enriched in skeletal muscle. Peroxisome proliferator–activated receptor-γ coactivator-1α expression was elevated at mRNA and protein levels. AMP kinase and p38 activities were elevated. In the obese mice, supplementation of butyrate led to an increase in insulin sensitivity and a reduction in adiposity. CONCLUSIONS Dietary supplementation of butyrate can prevent and treat diet-induced insulin resistance in mouse. The mechanism of butyrate action is related to promotion of energy expenditure and induction of mitochondria function.
Simulation of terahertz generation at semiconductor surfaces (2002)

A three-dimensional semiclassical Monte Carlo model is presented to describe fast carrier dynamics in semiconductors after photoexcitation. Far-field terahertz (THz) radiation patterns are calculated for both InAs and GaAs with, and without, application of external magnetic fields. This analysis distinguishes between surface depletion field and photo-Dember mechanisms for generating THz radiation. The theoretical model reproduces experimental data from GaAs and InAs, and demonstrates that a magnetic field enhances THz emission by rotating the emitting dipole with respect to the sample surface, leading to an increased coupling of radiation through the surface.
Surface-chemistry technology for microfluidics (2003)

A new technology to pattern surface charges, either negatively or positively, using a standard photolithography process is introduced. A positively charged poly(allylamine hydrochloride) (PAH) layer is coated onto a negatively charged silicon oxide surface by electrostatic self-assembly (ESA). Combined with photolithography in a lift-off-based process, several different surface charge patterns were successfully produced. Due to definition of the pattern by photolithography, no limitations in the pattern geometry exist. Any surface charge pattern can be created to enable fine control of fluid motion in microfluidic devices. Physical properties of this PAH layer were characterized. The generation of a bi-directional shear flow was demonstrated by using alternating longitudinal surface charge pattern with a single driving force, i.e. an externally applied electric field inside a microchannel.
Lack of RNA-DNA oligonucleotide (chimeraplast) mutagenic activity in mouse embryos (2005)

There are numerous reports of the use of RNA-DNA oligonucleotides (chimeraplasts) to correct point mutations in vitro and in vivo, including the human apolipoprotein E gene (ApoE). Despite the absence of selection for targeting, high efficiency conversion has been reported. Although mainly used to revert deleterious mutations for gene therapy applications, successful use of this approach would have the potential to greatly facilitate the production of defined mutations in mice and other species. We have attempted to create a point mutation in the mouse ApoE gene by microinjection of chimeraplast into the pronuclei of 1-cell mouse eggs. Following transfer of microinjected eggs we analysed 139 E12.5 embryos, but obtained no evidence for successful conversion.
Preparation and anti-HIV activities of aurintricarboxylic acid fractions and analogs: direct correlation of antiviral potency with molecular weight (1991)

Aurintricarboxylic acid (ATA) was fractionated by a combination of dialysis, ultrafiltration, and gel permeation chromatography. The number average and weight average molecular weights of the ATA fractions were determined by the universal calibration method. The sulfonic acid analogue of ATA was prepared and separated in high and low molecular weight fractions. The phosphonic acid analogue of ATA was also synthesized. All of the ATA fractions were tested for prevention of the cytopathic effect of HIV-1 and HIV-2 in MT-4 cell culture as well as against HIV-1 in CEM cell culture. The abilities of the fractions and analogues to inhibit syncytium formation between HIV-1- and HIV-2-infected HUT-78 cells and uninfected MOLT-4 cells were evaluated. In addition, the fractions and analogues were tested for cytotoxicity in mock-infected MT-4 cells, prevention of the binding of the OKT4A monoclonal antibody to the CD4 receptor, inhibition of the binding of anti-gp120 monoclonal antibody to gp120, inhibition of attachment of HIV-1 virions to MT-4 cells, and inhibition of HIV-1 reverse transcriptase. In all of these assays except cytotoxicity, there was a correlation of potency with molecular weight. The higher the molecular weight, the higher the activity. Several of the lower molecular weight fractions of ATA, which bound to gp120 but not to CD4, prevented HIV-1 and HIV-2 cytopathicity. A similar profile was observed for the phosphonic acid analogue of ATA and the lower molecular weight fraction of the sulfonic acid analogue. The results on the ATA fractions indicate that the binding of ATA to gp120 in the absence of CD4 binding is sufficient for anti-HIV activity. The active compounds bind more avidly to gp120 than to CD4. The anti-HIV activity of the ATA fractions is due to inhibition of virus binding due to an interference with the gp120-CD4 interaction.
Refractive Index of Silver Chloride for Visible and Infra-Red Radiant Energy* (1950)

The refractive indices of a 31° prism of silver chloride were measured at 30 wave-lengths at a constant room temperature of 23.9°C, from 0.578 to 20.6μ by use of a minimum-deviation spectrometer and a Perkin-Elmer infra-red spectrometer equipped with a calibrated screw for operation of the Littrow mirror. A cadmium-mercury lamp was the source from 1 to 2μ. From 2 to 20μ a Globar was used as the source with various Baird’s reflection interference filters and the absorption bands of carbon dioxide, carbon disulfide, water, methylcyclohexane, polystyrene, trichlorobenzene, and chlorobenzotrifluoride for the identification of wave-lengths. In the visible region two prisms, one pressed and polished, the other sawed and lapped, were used and the results compared. The sensitivity of index to temperature is approximately −6.1 × 10−5 per centigrade degree for wave-length 0.610μ.
Adrenaline in the treatment of anaphylaxis: what is the evidence? (2003)

Adrenaline (epinephrine) is the recommended first line treatment for patients with anaphylaxis. This review discusses the safety and efficacy of adrenaline in the treatment of anaphylaxis in the light of currently available evidence. A pragmatic approach to use of adrenaline auto-injectors is suggested.