gebhart/patrepeval huggingface dataset:
Expression of Human Herpesvirus 6B <i>rep</i> within Infected Cells and Binding of Its Gene Product to the TATA-Binding Protein In Vitro and In Vivo (2000)

We have characterized the human herpesvirus 6B (HHV-6B) rep gene, which is a homologue of the adeno-associated virus type 2 rep and is unique in the herpesvirus family. Three transcripts, 9.0, 5.0, and 2. 7 kb (the major transcript), were detected by Northern blotting using an HHV-6B rep probe under late conditions. We investigated the expression kinetics of the rep gene using cycloheximide (CHX) and phosphonoformic acid (PFA), which are inhibitors of protein synthesis and viral DNA synthesis, respectively. The 5.2-kb transcript was mainly detected in the absence of protein biosynthesis upon infection, and none of the 9.0-, 5.0-, and 2.7-kb transcripts detected under the late conditions were detected in the presence of CHX and PFA. Sequences obtained from a cDNA library showed that the 5.0- and 2.7-kb transcripts were spliced from two and three exons, respectively, and the 2.7-kb transcript was more abundant. Immunohistochemistry using an antibody raised against the HHV-6 rep gene product (REP) revealed that REP was mainly present in the nucleus of MT-4 cells within 24 h after infection with HHV-6B. Using pull-down assays, coimmunoprecipitation, and a mammalian two hybrid system, we showed that HHV-6 REP binds to a transcription factor, human TATA-binding protein, through its N-terminal region.
Borrelia burgdorferi binds plasminogen, resulting in enhanced penetration of endothelial monolayers (1995)

Several strains of Borrelia burgdorferi and Borrelia hermsii can bind human Lys-plasminogen specifically. Affinity blots using 125I-labeled plasminogen showed that numerous polypeptides of all the strains and species tested could bind via lysine residues to the plasminogen molecule since binding could be completely inhibited by the lysine analog epsilon-aminocaproic acid. Binding analysis using 125I-labeled plasminogen on live intact organisms showed that the organisms possess two binding sites for plasminogen: a high-affinity site with a Kd of 24 +/- 12 pM and 106 +/- 14 binding sites per spirochete and a low-affinity site with a Kd of 20 +/- 4 nM and 2,683 +/- 36 binding sites per spirochete. Indirect immunofluorescence and confocal microscopy showed a generalized but punctate pattern of plasminogen binding to the spirochete surface. Exogenously provided urokinase-type plasminogen activator converted B. burgdorferi surface-bound plasminogen to enzymatically active plasmin as demonstrated by the breakdown of the chromogenic plasmin substrate S2251. Plasmin-coated organisms showed an enhanced ability to penetrate endothelial cell monolayers grown on connective tissue substrates compared to untreated controls (P < 0.001). This functional assay demonstrated that enzymatically active plasmin on the surface of spirochetes can lead to greater invasion of tissues.
Phase-Transfer Synthesis of Optically Pure Oxetanes Obtained from 1,2,2-Trisubstituted 1,3-Propanediols (1995)

Treatment of the 3-monomethanesulfonates of 1,2,2-trisubstituted 1,5-propanediols under phase-transfer conditions affords 2-aryl (or alkyl)-3,3-dialkyloxetanes. Twelve oxetanes have been obtained by this method; three of these oxetanes have been obtained enantiomerically pure as both enantiomers starting from the appropriate enantiomerically pure 1,3-diols. In these reactions the chiral center does not undergo inversion and the oxetanes have the same absolute configuration as the starting 1,3-diols.
Mismatching design method for RFID tag antenna (2010)

This paper presents an original design method (mismatching design method) for RFID tag antenna application through the analysis of the Radar Cross Section (RCS) in RFID system. This design method can achieve the largest delta RCS than traditional way so that it optimizes the stability of the RFID system. The Thevenin equivalent circuit model of the tag antenna is discussed which displays the limit of the mismatching design method. Finally, a design example is given by using the method presented and the result verifies the validity of the analysis in this paper.
15.3: <i>Invited Paper</i> : Volume Holographic Components for Display Applications (2000)

Abstract Volume holographic components are being used to enhance the performance of a variety of liquid crystal and projection display systems. Holographic components address the ever‐present need within display systems for more efficient light management. With proper design, holographic components address this need with higher light throughput, reduced thickness and weight, reduced energy consumption, and additional opportunities for unique system functions. This paper describes design parameters and examples of improved devices by introducing the unique features of diffractive holographic components. These features include angular and spectral selectivity, high efficiency, and multiple optical functions designed into single components. Holographic reflectors, front diffusers, and compensations films have been developed and used in direct view liquid crystal displays. Holographic color filters and projection screens have also been developed based on this technology. For these applications the holographic component and system will be discussed. Finally, design considerations will be discussed that relate to the development of new display systems and components.
Addition of Pullulan to Trehalose Glasses Improves the Stability of β-Galactosidase at High Moisture Conditions (2017)

Incorporation of therapeutic proteins in a matrix of sugar glass is known to enhance protein stability, yet protection is often lost when exposed to high relative humidity (RH). We hypothesized that especially in these conditions the use of binary glasses of a polysaccharide and disaccharide might yield advantages for protein stability. Therefore, different amounts of the polysaccharide pullulan were introduced in freeze-dried trehalose glasses. In these homogeneous blends, the presence of pullulan above 50 weight % prevented crystallization of trehalose when exposed to high RH. Storage stability testing up to 4 weeks of the model protein β-galactosidase incorporated in pullulan/trehalose blends showed superior behavior of pure trehalose at 30°C/0% RH, while pullulan/trehalose blends yielded the best stability at 30°C/56% RH. In conclusion, binary glasses of pullulan and trehalose may provide excellent stability of proteins under storage conditions that may occur in practice, namely high temperature and high RH.
Ocular gene therapy: The basic science and current state of research (1997)

Recent technical advances have led to the demonstration of the molecular basis of many genetic eye diseases. Methods now in use have been able to both suppress and insert genes in vitro and in vivo in ocular cells. The combination of this new knowledge and these techniques offers the potential for a new therapeutic approach to diseases that currently have no treatments. The scientific basis of gene therapy is introduced and then the current state of research is discussed in relation to the eye and ocular tissues.
Skin colour, skin redness and melanin biometric measurements: comparison study between Antera<sup>®</sup> 3D, Mexameter<sup>®</sup> and Colorimeter<sup>®</sup> (2015)

Antera 3D(®) , such as Mexameter(®) MX-18 and Colorimeter(®) CL-400, are robust, sensitive and precise equipment for the skin colour analysis.
<i>Porphyromonas gingivalis</i> Genes Involved in <i>fimA</i> Regulation (2004)

Porphyromonas gingivalis is an important component of the complex plaque biofilm that is a direct precursor of periodontal disease. The major fimbriae are required for attachment to oral surfaces and are an important virulence factor. Fimbrillin (FimA) expression in P. gingivalis is inhibited by surface molecule of Streptococcus cristatus, an early colonizer of dental plaque. In this study, differential display PCR was used to identify P. gingivalis genes that are regulated in response to S. cristatus. Of several differentially expressed genes, pg2131 and pg2167 were upregulated by S. cristatus signaling molecules. A null mutant of pg2167 did not transcriptionally regulate fimA following exposure to S. cristatus. In fact, fimA transcription was enhanced in the pg2167 mutant, suggesting that pg2167 may act to repress fimA expression. In contrast, a mutation in pg2131 did not affect transcription of fimA in the presence of S. cristatus. However, production of fimbrillin was significantly diminished in the pg2131 mutant, implicating involvement in posttranscriptional regulation in fimbriation. These data suggest that P. gingivalis fimbriation is controlled by more than one regulation mechanism, involving both transcriptional and posttranscriptional processes.
Linoleate Impairs Collagen Synthesis in Primary Cultures of Avian Chondrocytes (1996)

The effects of supplemental fatty acids, vitamin E (VIT E), and iron-induced oxidative stress on collagen synthesis, cellular injury, and lipid peroxidation were evaluated in primary cultures of avian epiphyseal chondrocytes. The treatments included oleic and linoleic acids (O or 50 microM) complexed with BSA and dl-alpha-tocopheryl acetate (VIT E at 0 or 100 microM). After 14 days of preculture, the chondrocytes were enriched with fatty acids for 8 days then cultured with VIT E for 2 days. The chondrocytes were then treated with ferrous sulfate (O or 20 microM) for 24 hr to induce oxidative stress. Collagen synthesis was the lowest and the activity of lactate dehydrogenase (LDH) was the highest in chondrocyte cultures treated with 50 microM linoleic acid and 0 VIT E. In contrast, VIT E supplemented at 100 microM partially restored collagen synthesis in the chondrocytes enriched with linoleic acid and lowered LDH activity in the media. The iron oxidative inducer significantly increased the values of thiobarbituric acid-reactive substances (TBARS) in the culture medium. The data showed that linoleic acid impaired chondrocyte cell function and caused cellular injury but that VIT E reversed these effects. Results from a previous study demonstrated that VIT E stimulated bone formation in chicks fed unsaturated fat, and the present findings in cultures of epiphyseal chondrocytes suggest that VIT E is important for chondrocyte function in the presence of polyunsaturated fatty acids. VIT E appears to be beneficial for growth cartilage biology and in optimizing bone growth.
Cation−π Interactions in Ligand Recognition by Serotonergic (5-HT<sub>3A</sub>) and Nicotinic Acetylcholine Receptors:  The Anomalous Binding Properties of Nicotine (2002)

A series of tryptophan analogues has been introduced into the binding site regions of two ion channels, the ligand-gated nicotinic acetylcholine and serotonin 5-HT(3A) receptors, using unnatural amino acid mutagenesis and heterologous expression in Xenopus oocytes. A cation-pi interaction between serotonin and Trp183 of the serotonin channel 5-HT(3A)R is identified for the first time, precisely locating the ligand-binding site of this receptor. The energetic contribution of the observed cation-pi interaction between a tryptophan and the primary ammonium ion of serotonin is estimated to be approximately 4 kcal/mol, while the comparable interaction with the quaternary ammonium of acetylcholine is approximately 2 kcal/mol. The binding mode of nicotine to the nicotinic receptor of mouse muscle is examined by the same technique and found to differ significantly from that of the natural agonist, acetylcholine.
Wireless wearable biomonitors for lifetime wellness optimization (2005)

A wearable physiological and environmental monitoring system and a practical implementation are presented. The technical requirements for wearable electronics and sensors have been specified with an example of ECG, oxygenometer, and wireless network-based bidirectional communication. A presented system includes micro-device design, wireless network based on TCP/IP protocol and software application. The result samples from monitoring in ambulatory environment confirm the performance and usefulness of the proposed methodology.
Synthetic TRuC receptors engaging the complete T cell receptor for potent anti-tumor response (2019)

T cells expressing CD19-targeting chimeric antigen receptors (CARs) reveal high efficacy in the treatment of B cell malignancies. Here, we report that T cell receptor fusion constructs (TRuCs) comprising an antibody-based binding domain fused to T cell receptor (TCR) subunits can effectively reprogram an intact TCR complex to recognize tumor surface antigens. Unlike CARs, TRuCs become a functional component of the TCR complex. TRuC-T cells kill tumor cells as potently as second-generation CAR-T cells, but at significant lower cytokine release and despite the absence of an extra co-stimulatory domain. TRuC-T cells demonstrate potent anti-tumor activity in both liquid and solid tumor xenograft models. In several models, TRuC-T cells are more efficacious than respective CAR-T cells. TRuC-T cells are shown to engage the signaling capacity of the entire TCR complex in an HLA-independent manner.
One Pot Multi-Component Synthesis of N-Substituted Decahydroacridine- 1, 8-Diones Catalyzed by MoO3/SiO2 as an Efficient and Reusable Heterogeneous Catalyst (2012)

A simple, efficient and ecofriendly one pot synthesis protocol has been developed for the synthesis of N-substituted decahydroacridine-1,8-diones by using an efficient and recyclable solid acidic silica supported MoO3/SiO2 catalyst from a condensation of aldehyde, amine and cyclic 1,3-diketone in THF. The reaction using MoO3/SiO2 catalyst was carried out under mild condition with very high yields up to 92%. The present approach of this methodology offers several advantages such as shorter reaction times, good yields, low cost, environmentally benign, milder reaction conditions, easy recovery of catalyst and reusability.
Sequence comparison methods (2003)

This chapter discusses the evolutionary mechanisms giving rise to changes in protein sequences and the challenges faced when aligning protein sequences. It considers accurate methods for automatically aligning protein sequences, based on dynamic programming. The chapter assesses the performance of the existing database search methods in recognizing proteins which are homologs, i.e. evolutionarily related sequences. It also considers the challenges and strategies involved in multiple sequence alignment. The chapter describes the concepts underlying automated methods for comparing protein sequences and also discusses the reliability of these methods. The best way of understanding how dynamic programming works is to consider a simple computer implementation of it applied to sequence alignment. The chapter also describes the percentage of relatives identified by any of the sequence search methods that can also be increased by scanning against protein family libraries or intermediate sequence libraries rather than scanning the basic sequence repositories like GenBank, EMBL or Trembl.
Influenza Viral Vectors Expressing Two Kinds of HA Proteins as Bivalent Vaccine Against Highly Pathogenic Avian Influenza Viruses of Clade 2.3.4.4 H5 and H7N9 (2018)

The H5 and H7N9 subtypes of highly pathogenic avian influenza viruses (HPAIVs) in China pose a serious challenge to public health and the poultry industry. In this study, a replication competent recombinant influenza A virus of the Í5N1 subtype expressing the H7 HA1 protein from a tri-cistronic NS segment was constructed. A heterologous dimerization domain was used to combine with the truncated NS1 protein of 73 amino acids to increase protein stability. H7 HA1, nuclear export protein coding region, and the truncated NS1 were fused in-frame into a single open reading frame via 2A self-cleaving peptides. The resulting PR8-H5-NS1(73)H7 stably expressed the H5 HA and H7 HA1 proteins, and exhibited similar growth kinetics as the parental PR8-H5 virus <i>in vitro</i>. PR8-H5-NS1(73)H7 induced specific hemagglutination inhibition (HI) antibody against H5, which was comparable to that of the combination vaccine of PR8-H5 and PR8-H7. The HI antibody titers against H7 virus were significantly lower than that by the combination vaccine. PR8-H5-NS1(73)H7 completely protected chickens from challenge with both H5 and H7 HPAIVs. These results suggest that PR8-H5-NS1(73)H7 is highly immunogenic and efficacious against both H5 and H7N9 HPAIVs in chickens. <b>Highlights</b>: - PR8-H5-NS1(73)H7 simultaneously expressed two HA proteins of different avian influenza virus subtypes. - PR8-H5-NS1(73)H7 was highly immunogenic in chickens. - PR8-H5-NS1(73)H7 provided complete protection against challenge with both H5 and H7N9 HPAIVs.
Vehicle Acoustic Solutions (2003)

<div class="htmlview paragraph">Vehicles are faced with a variety of airborne and structure-borne noise sources, such as wind, road, tire, engine and powertrain. To minimize the noise intrusion into the passenger compartment, a system level approach must be taken. This system level approach requires a focused effort to minimize noise at the primary sources, and an engineering initiative to desensitize the transfer paths through proper body design, sealing, and the implementation of noise control materials. This paper looks at different innovative materials applied to the body structure, their design and placement of them to support a quiet interior. A series of vehicle case studies details the in-vehicle performance and benefits of both preformed and bulk material solutions that are applied to the body structure: baffles, sealers, barriers, dampers and structural reinforcements. An emphasis is placed on low cost, low mass and high performance optimized solutions.</div>
Peptide methionine sulfoxide reductase from<i>Escherichia coli</i>and<i>Mycobacterium tuberculosis</i>protects bacteria against oxidative damage from reactive nitrogen intermediates (2001)

Inducible nitric oxide synthase (iNOS) plays an important role in host defense. Macrophages expressing iNOS release the reactive nitrogen intermediates (RNI) nitrite and S-nitrosoglutathione (GSNO), which are bactericidal in vitro at a pH characteristic of the phagosome of activated macrophages. We sought to characterize the active intrabacterial forms of these RNI and their molecular targets. Peptide methionine sulfoxide reductase (MsrA; EC ) catalyzes the reduction of methionine sulfoxide (Met-O) in proteins to methionine (Met). E. coli lacking MsrA were hypersensitive to killing not only by hydrogen peroxide, but also by nitrite and GSNO. The wild-type phenotype was restored by transformation with plasmids encoding msrA from E. coli or M. tuberculosis, but not by an enzymatically inactive mutant msrA, indicating that Met oxidation was involved in the death of these cells. It seemed paradoxical that nitrite and GSNO kill bacteria by oxidizing Met residues when these RNI cannot themselves oxidize Met. However, under anaerobic conditions, neither nitrite nor GSNO was bactericidal. Nitrite and GSNO can both give rise to NO, which may react with superoxide produced by bacteria during aerobic metabolism, forming peroxynitrite, a known oxidant of Met to Met-O. Thus, the findings are consistent with the hypotheses that nitrite and GSNO kill E. coli by intracellular conversion to peroxynitrite, that intracellular Met residues in proteins constitute a critical target for peroxynitrite, and that MsrA can be essential for the repair of peroxynitrite-mediated intracellular damage.
Broad-spectral-range synchronized flat-top arrayed-waveguide grating applied in a 225-channel cascaded spectrometer (2012)

We present a new synchronized design for flattening the passband of an arrayed-waveguide grating (AWG) over a broad wavelength range of 90 nm. A wavelength-insensitive 3-dB balanced coupler is designed to be used in duplicate in a Mach-Zehnder interferometer (MZI); the phase deviation created by one of the balanced couplers is cancelled by flipping the other coupler around. This MZI is arranged in tandem with the AWG such that the output signal of the MZI is the input signal of the AWG. We demonstrate a 5-channel, 18-nm-spacing AWG with a 0.5-dB bandwidth of 12 nm over a 90-nm spectral range. A low-loss cascaded AWG system is demonstrated by using the MZI-synchronized flat-top AWG as a primary filter.
Eight New Species of Mandevilla Lindley (Apocynaceae, Apocynoideae) from Brazil (2006)

Eight new species of Mandevilla Lindley are described and illustrated. The new species, six of them rare and endemic, occur in eastern Brazil. Three of the new species (M. fistulosa, M. grazielae, and M. harleyi) are shrubs growing on the upper slopes of granitic inselbergs in Minas Gerais and Espírito Santo in southeastern Brazil. Two species, M. semirii and M. rubra, are woody lianas growing on rock outcrops of quartzite in campo rupestre vegetation of Minas Gerais. Mandevilla hatschbachii, a distinctive shrub known only from three collections, occurs in the campo rupestre formations in eastern Brazil in Bahia. Mandevilla guanabarica, a suffrutescent liana generally misidentified as M. funiformis (Vellozo) K. Schumman, is found at the borders of the Atlantic rainforest in Espírito Santo and Rio de Janeiro. Mandevilla dardanoi is a small shrub endemic to Maciço da Borborema, in northeastern Brazil.
Children with Autism and Asperger Syndrome: A Guide for Practitioners and Carers (1998)

The Spectrum of Disorders in Autism. Recent Advances in Understanding the Causes of Autism. Approaches to Treatment for Children with Autism. Developing Communications Skills. Social and Play Skills. Obsessional and Ritualistic Disorders. Education Provision for Children with Autism. Medical Intervention. Issues for Families.
Straining strained molecules. III. The spectral and mutagenic properties and an alternate synthesis of diaceperylene and dicyclopenta[1,2,3-<i>cd</i>:1′,2′,3′-<i>lm</i>]perylene (1992)

The synthesis of diaceperylene (1) from 5,6-dilithioacenaphthene via nickel or cobalt catalysed couplings proceeded in better yield than a multistep synthesis involving formation of 5,5′-diacenaphthene first. Dehydrogenation of 1 to dicyclopenta[1,2,3-cd:1′,2′,3′-lm]perylene (2) proved a better route than coupling of 5,6-disubstituted acenaphthylene derivatives. Ultraviolet, proton, and carbon nuclear magnetic resonance spectra and electrode reduction potential data of 1 and 2 are discussed with respect to molecular mechanics calculations of strain in these and related bridged naphthalenes. Both 1 and 2 were found to be weakly mutagenic in an Ames microsome test, in contrast to cyclopenta[cd]pyrene.
Organic Syntheses Using Polymeric Supports, Polymeric Reagents, and Polymeric Catalysts (1976)

Abstract In conventional organic syntheses, organic molecules are treated with a reagent or reagents and the transformed organic molecules, now termed the product, are isolated. The various steps in a conventional organic synthesis may be represented schematically as in Fig. 1. In this scheme a low molecular weight molecule (A) is treated with a low molecular weight reagent (B). When the reaction has gone to the maximum extent (reactions seldom proceed to 100% completion), the desired product (C) is isolated from the reaction mixture. The isolation is done by conventional procedures of extraction precipitation, distillation, sublimation, and various chromatographic methods. In this way the desired product (C) is separated from the reaction by-products, solvents, and any catalysts (D) which might be present in the final reaction mixture. Frequently the isolation process involves one or more of the above operations to obtain the pure product (C).