gebhart/patrepeval huggingface dataset:
Synthesis of fluorescein-labelled O-mannosylated peptides as components for synthetic vaccines: comparison of two synthetic strategies (2007)

Mannose-binding proteins on the surface of antigen-presenting cells (APCs) are capable of recognizing and internalizing foreign agents in the early stages of immune response. These receptors offer a potential target for synthetic vaccines, especially vaccines designed to stimulate T cells. We set out to synthesize a series of fluorescein-labelled O-mannosylated peptides using manual solid phase peptide synthesis (SPPS) on pre-loaded Wang resin, in order to test their ability to bind mannose receptors on human APCs in vitro. A flexible and reliable method for the synthesis of fluorescein-labelled O-mannosylated glycopeptides was desired in order to study their lectin-binding properties using flow cell cytometry. Two synthetic strategies were investigated: incorporation of a fluorescein label into the peptide chain via a lysine side chain epsilon-amino group at the final stage of standard Fmoc solid phase peptide synthesis or attachment of the fluorescein label to the N(alpha)-amino group of a lysine with further incorporation of a mannosylated peptide unit through the side chain N(epsilon)-amino group. The latter strategy proved more effective in that it facilitated SPPS by positioning the growing mannosylated peptide chain further removed from the fluorescein label.
Transformed Social Interaction: Decoupling Representation from Behavior and Form in Collaborative Virtual Environments (2004)

Computer-mediated communication systems known as collaborative virtual environments (CVEs) allow geographically separated individuals to interact verbally and nonverbally in a shared virtual space in real time. We discuss a CVE-based research paradigm that transforms (i.e., filters and modifies) nonverbal behaviors during social interaction. Because the technology underlying CVEs allows a strategic decoupling of rendered behavior from the actual behavior of the interactants, conceptual and perceptual constraints inherent in face-to-face interaction need not apply. Decoupling algorithms can enhance or degrade facets of nonverbal behavior within CVEs, such that interactants can reap the benefits of nonverbal enhancement or suffer nonverbal degradation. Concepts underlying transformed social interaction (TSI), the ethics and implications of such a research paradigm, and data from a pilot study examining TSI are discussed.
Microenvironments of Basic Amino Acids in Amphipathic .alpha.-Helixes Bound to Phospholipid: 13C NMR Studies Using Selectively Labeled Peptides (1995)

The lipid-binding properties of serum apolipoproteins are mediated by class A amphipathic alpha-helices in which basic and acidic amino acid residues tend to be localized at the helix polar-nonpolar boundary and the center of the polar face, respectively. To better understand the role of the interfacial basic residues, the microenvironments and titration characteristics of lysine (Lys) residues have been examined using two 18-residue peptides. The parent 18A molecule (AspTrpLeuLysAlaPheTyrAspLysValAlaGluLysLeuLysGluAlaPhe) binds phospholipid relatively well because of its class A amphipathic helix, whereas 18R, which has the positions of basic and acidic residues reversed, binds to phospholipid relatively weakly. Lys residues were 13C-dimethylated, and NMR spectra were obtained of the peptides complexed with dimyristoylphosphatidylcholine (1/1 (w/w) DMPC/peptide). The four [13C]-epsilon-dimethyl-Lys in 18A gave four resonances at chemical shifts (delta) of 42-43 ppm, whereas only a single resonance at delta 42.70 ppm was observed from the four Lys in 18R. Measurements of delta as a function of pH gave pKa values. The four Lys in 18R had a common pKa of 10.3, indicating that the Lys in the polar face of the amphipathic helix have the pKa expected for noninteracting, fully hydrated groups. In contrast, the four Lys in Ac-18A-NH2 had pKa's in the range 9.4-11.0, indicating that they exist in various microenvironments at the polar-nonpolar boundary of the 18A helix. To examine individual Lys, 18A was synthesized with various Lys selectively labeled. Lys-4, -9, -13, and -15 in Ac-18A-NH2 associated with DMPC had pKa values of 11.0, 9.4, 9.4, and 10.3, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Super-Resolution TOA Estimation With Diversity for Indoor Geolocation (2004)

This paper presents an in-depth investigation of frequency-domain super-resolution time-of-arrival (TOA) estimation with diversity techniques for indoor geolocation applications. A methodology for performance evaluation of super-resolution techniques based on the measurements of indoor radio propagation channels is presented. The performance of super-resolution techniques is compared with the performance of conventional TOA estimation techniques. The effects of diversity techniques on the performance of super-resolution techniques are evaluated. The measurement and simulation methods presented in this paper can be used to establish empirical performance bounds for real implementation of super-resolution indoor geolocation systems.
Effect of interfacial structures on spin dependent tunneling in epitaxial <i>L</i>1-FePt/MgO/FePt perpendicular magnetic tunnel junctions (2015)

Epitaxial FePt(001)/MgO/FePt magnetic tunnel junctions with L10-FePt electrodes showing perpendicular magnetic anisotropy were fabricated by molecular beam epitaxial growth. Tunnel magnetoresistance ratios of 21% and 53% were obtained at 300 K and 10 K, respectively. Our previous work, based on transmission electron microscopy, confirmed a semi-coherent interfacial structure with atomic steps (Kohn et al., APL 102, 062403 (2013)). Here, we show by x-ray photoemission spectroscopy and first-principles calculation that the bottom FePt/MgO interface is either Pt-terminated for regular growth or when an Fe layer is inserted at the interface, it is chemically bonded to O. Both these structures have a dominant role in spin dependent tunneling across the MgO barrier resulting in a decrease of the tunneling magnetoresistance ratio compared with previous predictions.
Structure Determination and Dynamics of Peptides Overlapping the Catalytic Hairpin of the Ras-Specific GEF Cdc25<sup>Mm</sup> (2003)

Ras proteins are small G proteins playing a major role in eukaryotic signal transduction. Guanine nucleotide exchange factors (GEF) stimulate GDP/GTP exchange, resulting in the formation of the active Ras-GTP complex. In mammalian cells, two major Ras-specific GEF exist: Sos-like and Cdc25-like. To date, structural data are available only for Cdc25(Mm). We designed and synthesized Cdc25(Mm)-derived peptides spanning residues corresponding to the hSos1 HI helical hairpin that has been implicated in the GEF catalytic mechanism. NMR experiments on a chemically synthesized Cdc25(Mm)(1178-1222) peptide proved that helix I readily reaches a conformation very similar to the corresponding helix in hSos1, while residues corresponding to helix H in hSos1 show higher conformational flexibility. Molecular dynamics studies with the appropriate solvent model showed that different conformational spaces are available for the peptide. Since helix H is making several contacts with Ras and a Cdc25(Mm)(1178-1222) peptide is able to bind nucleotide-free Ras in a BIAcore assay, the peptide must be able to obtain the proper Ras-interacting conformation, at least transiently. These results indicate that rational design and improvement of the Ras-interacting peptides should take into account conformational and flexibility features to obtain molecules with the appropriate biochemical properties.
COMPARISON BETWEEN CONVENTIONAL AND TWO-DIMENSIONAL XRD (2003)

A comparison between the conventional Bragg-Brentano diffractometer and the two-dimensional (2D) diffractometer is made in terms of diffraction geometry, diffraction pattern, and various applications. A two-dimensional XRD system for combinatorial screening in transmission mode is introduced. IINTRODUCTION A two-dimensional X-ray diffraction (XRD 2 ) system has both the capability of acquiring diffraction patterns in 2D space simultaneously, and analyzing the 2D diffraction data accordingly [1-3]. In recent years, usage of two-dimensional (2D) detectors has dramatically increased due to the advances in detector technology, point beam X-ray optics, and computing power. The integrated data gives better intensity and statistics for phase identification and quantitative analysis, especially for those samples with texture, large grain size, or small quantity. 2D detectors can collect diffraction data in a large 2θ range simultaneously without sample or detector movement. This is extremely important for high-throughput diffraction screening [4]. Figure 1 is a comparison between the conventional diffractometer and the two-dimensional diffractometer. The diffraction data collection in the conventional diffractometer is confined within a plane, here referred to as diffractometer plane. With a 2D detector, the measurable diffraction is no longer limited in the diffractometer plane. Instead, the whole or a large portion of the diffraction rings (as called Debye ring) can be measured simultaneously.
Enasidenib for the treatment of acute myeloid leukemia (2018)

In August 2017, the United States Federal Drug Administration (FDA) approved enasidenib (Idhifa, Celgene/Agios) for adults with relapsed and refractory acute myelogenous leukemia (AML) with an IDH2 mutation. Enasidenib targets cells with mutant copies of isocitrate dehydrogenase-2 (IDH2), inhibiting the oncometabolite 2-hydroxyglutarte (2-HG) formed by the mutant IDH2. Areas covered: We review the studies leading to enasidenib's approval, as well as common side effects and safety issues experienced during the clinical trials. There is a focus on the diagnosis and treatment of these side effects including differentiation syndrome. Expert commentary: We are experiencing a revolution in the understanding of the mechanism of AML. A majority of the effort has been concentrated on targeting gene mutations or pathway activations with precision therapeutics. Enasidenib is beneficial in a patient population that previously had limited treatment options. However, given the fact that enasidenib is a highly specific inhibitor of an early stable mutation, it is questionable whether a strategy of targeting a single mutation or pathway in relapsed AML will allow for better than the 20% complete remission (CR) rate observed with this therapy. The proper role for single mutation targeting in AML needs to be carefully considered.
A New Dawn for CO2 EOR (2005)

Abstract A range of techniques have been developed to improve the recovery efficiency of oil reservoirs. Of these, gas injection is currently the second most common EOR process after thermal methods that is practiced on a material scale with some 250 mbd directly attributable. Initial exploration of gas injection focused on use of a hydrocarbon injectant. However, competitive sales markets for hydrocarbon gas led to the identification of CO2 as a potential injectant. There is now over thirty years experience with the injection of CO2 for Enhanced Oil Recovery. Although initially developed as a means to improve oil recovery, there is renewed interest in the potential for CO2 EOR as an option to reduce global emissions of Greenhouse Gases. This may lead both to a significant expansion in the level of application as well as to some significant changes in the way in which CO2 EOR is applied. Introduction Many areas of the world are actively implementing gas injection to maximise the potential of extensive oil reserves. A successful gas flood requires two key criteria be satisfied. Firstly, the injected gas must be able to mobilise additional oil. Secondly, the flood must be able to sweep the mobilised oil to producers. Additional oil may be mobilized in two ways. Firstly, gas may be able to access parts of the reservoir that have been bypassed by water. Second, gas may enable some incremental recovery from those parts of the reservoir already swept by water by virtue of the fact that the residual oil saturation to gas is usually somewhat lower than for water. Many of the current gas injection schemes operate near to miscibility conditions to mobilise the maximum amount of incremental oil. The injected gas is often used in combination with water in order to get the joint benefits of mobilising oil with the miscible gas while using water to sweep mobilized oil to producing wells.
Chemotaxis Inhibitory Protein of <i>Staphylococcus aureus</i>, a Bacterial Antiinflammatory Agent (2004)

Leukocyte migration is a key event both in host defense against invading pathogens as well as in inflammation. Bacteria generate chemoattractants primarily by excretion (formylated peptides), complement activation (C5a), and subsequently through activation of leukocytes (e.g., leukotriene B4, platelet-activating factor, and interleukin 8). Here we describe a new protein secreted by Staphylococcus aureus that specifically impairs the response of neutrophils and monocytes to formylated peptides and C5a. This chemotaxis inhibitory protein of S. aureus (CHIPS) is a 14.1-kD protein encoded on a bacteriophage and is found in >60% of clinical isolates. CHIPS reduces the neutrophil recruitment toward C5a in a mouse peritonitis model, even though its activity is much more potent on human than on mouse cells. These findings suggest a new immune escape mechanism of S. aureus and put forward CHIPS as a potential new antiinflammatory therapeutic compound.
Measuring Skewness and Kurtosis (1984)

The question of how to measure the degree of skewness of a continuous random variable is addressed. In van Zwet (1964) a method for ordering two distributions with regard to skewness is given. Here, using the concept of comparative skewness, we consider properties that a measure of skewness should satisfy. Several extensions of the Bowley measure of skewness taking values on (-1, 1) are discussed. How well these measures reflect one's intuitive idea of skewness is examined. These measures of skewness are extended to measures of kurtosis for symmetric distributions.
Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas (2016)

Single-cell genome, DNA methylome, and transcriptome sequencing methods have been separately developed. However, to accurately analyze the mechanism by which transcriptome, genome and DNA methylome regulate each other, these omic methods need to be performed in the same single cell. Here we demonstrate a single-cell triple omics sequencing technique, scTrio-seq, that can be used to simultaneously analyze the genomic copy-number variations (CNVs), DNA methylome, and transcriptome of an individual mammalian cell. We show that large-scale CNVs cause proportional changes in RNA expression of genes within the gained or lost genomic regions, whereas these CNVs generally do not affect DNA methylation in these regions. Furthermore, we applied scTrio-seq to 25 single cancer cells derived from a human hepatocellular carcinoma tissue sample. We identified two subpopulations within these cells based on CNVs, DNA methylome, or transcriptome of individual cells. Our work offers a new avenue of dissecting the complex contribution of genomic and epigenomic heterogeneities to the transcriptomic heterogeneity within a population of cells.
Antimony Tin Oxide (ATO) Nanoparticle Formation from H<sub>2</sub>O<sub>2</sub> Solutions: a New Generic Film Coating from Basic Solutions (2010)

A generic method for conductive film coating of minerals and acid-sensitive materials by antimony-doped tin oxide (ATO) is introduced. The coating was performed from a hydrogen peroxide stabilized stannate and antimonate precursor solution. This is the first demonstration of ATO coating from an organic ligand-free solution. Uniform coating of different clays and other irregular configurations by monosized 5 nm ATO particles was demonstrated. The deposition mechanism and the observed preference for mineral surface coating over homogeneous agglomeration of the tin oxide particles are explained by a hydrogen peroxide capping mechanism and hydrogen bonding of the hydroperoxo nanoparticles to the H(2)O(2)-activated mineral surfaces.
The Oxidation of Substituted Toluenes by Cobalt(III) Acetate in Acetic Acid Solution (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Oxidation of Substituted Toluenes by Cobalt(III) Acetate in Acetic Acid SolutionCharles F. Hendriks, Hendrik C. A. van Beek, and Pieter M. HeertjesCite this: Ind. Eng. Chem. Prod. Res. Dev. 1978, 17, 3, 256–260Publication Date (Print):September 1, 1978Publication History Published online1 May 2002Published inissue 1 September 1978https://pubs.acs.org/doi/10.1021/i360067a016https://doi.org/10.1021/i360067a016research-articleACS PublicationsRequest reuse permissionsArticle Views327Altmetric-Citations28LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Increased durability of optical fiber through the use of compressive cladding (1982)

Durable fibers having a thin Ti-doped silica surface layer were fabricated by using the refined fabrication process of compressive cladding. High surface-compressive stresses up to 0.69 GPa (100 kpsi) resulted in significant improvement in fatigue resistance of optical-fiber waveguides.
Basic polypeptides accelerate the hydrolysis of ribonucleic acids (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBasic polypeptides accelerate the hydrolysis of ribonucleic acidsBernard. Barbier and Andre. BrackCite this: J. Am. Chem. Soc. 1988, 110, 20, 6880–6882Publication Date (Print):September 1, 1988Publication History Published online1 May 2002Published inissue 1 September 1988https://doi.org/10.1021/ja00228a045Request reuse permissionsArticle Views186Altmetric-Citations56LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (464 KB) Get e-Alertsclose Get e-Alerts
Multiple limbic regions mediate the disruption of prepulse inhibition produced in rats by the noncompetitive NMDA antagonist dizocilpine. (1998)

Prepulse inhibition (PPI), a phenomenon in which a weak prestimulus decreases the startle response to an intense stimulus, provides an operational measure of sensorimotor gating (a process by which an organism filters sensory information) and is diminished in schizophrenia and schizotypal patients. The psychotomimetic phencyclidine and its potent congener dizocilpine are noncompetitive antagonists of the NMDA receptor complex, and they disrupt PPI in rodents, mimicking the clinically observed PPI deficit. The neuroanatomical substrates mediating the PPI-disruptive effects of noncompetitive NMDA antagonists are unknown. The present study sought to identify brain regions subserving the disruption of PPI produced by noncompetitive NMDA antagonists in rats. PPI was measured in startle chambers immediately after bilateral infusion of dizocilpine (0, 0.25, 1.25, and 6.25 microgram/0.5 microliter/side) into one of six brain regions: amygdala, dorsal hippocampus, medial prefrontal cortex, nucleus accumbens, ventral hippocampus, and dorsomedial thalamus. Dizocilpine significantly decreased PPI after infusion into the amygdala or dorsal hippocampus. A trend toward PPI disruption was observed with administration into medial prefrontal cortex. In contrast, no change in PPI was produced by dizocilpine infusion into nucleus accumbens, ventral hippocampus, or dorsomedial thalamus. Startle reactivity was increased by dizocilpine infusion into amygdala, dorsal hippocampus, nucleus accumbens, and dorsomedial thalamus, but not medial prefrontal cortex. These findings indicate that multiple limbic forebrain regions mediate the ability of noncompetitive NMDA antagonists to disrupt PPI and that the PPI-disruptive and the startle-increasing effects of dizocilpine are mediated by different central sites.
Modulation of cardiac autonomic activity during and immediately after exercise (1989)

Fluctuations in heart rate above 0.03 Hz reflect autonomic modulation of sinoatrial node activity. To assess the dynamics of autonomic nervous activity during and immediately after exercise, we determined the power spectrum of heart rate and respiratory fluctuations in 43 normal subjects without known cardiac disease, 8 patients with severe congestive heart failure, and 6 patients status-post cardiac transplantation before, during, and after graded-work load exercise on a cycle ergometer. Before exercise, heart rate fluctuations (spectral power) at both high (0.15-0.80 Hz) and low (0.03-0.15 Hz) frequencies were significantly higher in normal subjects than in either heart failure or transplant patients but were not different between the two groups with heart disease. During exercise, heart rate power at all frequencies rapidly and progressively decreased in normal subjects, until at peak exercise it was not different from the other two groups. During recovery, heart rate power increased in normal subjects but remained significantly below base line. The findings demonstrate a marked reduction of autonomic modulation of heart rate in patients with heart failure and after cardiac transplant and support a progressive withdrawal of vagal activity during exercise with a gradual increase during recovery in normal subjects.