gebhart/patrepeval huggingface dataset:
Epitope-Specific Antibody Responses to a Plasmodium falciparum Subunit Vaccine Target in a Malaria-Endemic Population (2020)

Circumsporozoite protein (CSP) coats the Plasmodium falciparum sporozoite surface and is a major malaria subunit vaccine target. We measured epitope-specific reactivity to field-derived CSP haplotypes in serum samples from Malian adults and children on a custom peptide microarray. Compared to children, adults showed greater antibody responses and responses to more variants in regions proximal to and within the central repeat region. Children acquired short-lived immunity to an epitope proximal to the central repeat region but not to the central repeat region itself. This approach has the potential to differentiate immunodominant from protective epitope-specific responses when combined with longitudinal infection data.
Simulating Surfactant-Iron Oxide Interfaces: From Density Functional Theory to Molecular Dynamics (2019)

Understanding the behaviour of surfactant molecules on iron oxide surfaces is important for many industrial applications. Molecular dynamics (MD) simulations of such systems have been limited by the absence of a force-feild (FF) which accurately describes the molecule-surface interactions. In this study, interaction energies from density functional theory (DFT) + U calculations with a van der Waals functional are used to parameterize a classical FF for MD simulations of amide surfactants on iron oxide surfaces. The Original FF, which was derived using mixing rules and surface Lennard-Jones (LJ) parameters developed for nonpolar molecules, were shown to signi cantly underestimate the adsorption energy and overestimate the equilibrium adsorption distance compared to DFT. Conversely, the Optimized FF showed excellent agreement with the interaction energies obtained from DFT calculations for a wide range of surface coverages and molecular conformations near to and adsorbed on a-Fe2O3(0001). This was facilitated through the use of a Morse potential for strong chemisorption interactions, modi fied LJ parameters for weaker physisorption interactions, and adjusted partial charges for the electrostatic interactions. The Original FF and Optimized FF were compared in classical nonequilibrium molecular dynamics (NEMD) simulations of amide molecules con fined between iron oxide surfaces. When the Optimized FF was employed, the amide molecules were pulled closer to the surface and the orientation of the headgroups was more similar to that observed in the DFT calculations compared to the Original FF. The Optimized FF proposed here facilitates classical MD simulations of amide-iron oxide interfaces in which the interactions are representative of accurate DFT calculations.
Macro-Ring-Functionalised Poly(ether ether ketone): A New Molecular Architecture for Aromatic Polymers (2002)

Poly(ether ether ketone) terminated with 4-phenoxyphenoxy end groups undergoes essentially quantitative condensation with a novel carboxy-functionalised macrocyclic ether-ketone in trifluoromethanesulfonic acid to afford a semi-crystalline, bis(macrocycle)-terminated polyketone. This new molecular architecture, characterised by NMR spectroscopy, DSC, MALDI-TOF mass spectrometry and – for a model oligomer – by single-crystal X-ray analysis, opens up new possibilities for in-situ chain extension and crosslinking of high-performance polymers.
Classification of underwater targets from autonomous underwater vehicle sampled bistatic acoustic scattered fields (2015)

One of the long term goals of autonomous underwater vehicle (AUV) minehunting is to have multiple inexpensive AUVs in a harbor autonomously classify hazards. Existing acoustic methods for target classification using AUV-based sensing, such as sidescan and synthetic aperture sonar, require an expensive payload on each outfitted vehicle and post-processing and/or image interpretation. A vehicle payload and machine learning classification methodology using bistatic angle dependence of target scattering amplitudes between a fixed acoustic source and target has been developed for onboard, fully autonomous classification with lower cost-per-vehicle. To achieve the high-quality, densely sampled three-dimensional (3D) bistatic scattering data required by this research, vehicle sampling behaviors and an acoustic payload for precision timed data acquisition with a 16 element nose array were demonstrated. 3D bistatic scattered field data were collected by an AUV around spherical and cylindrical targets insonified by a 7-9 kHz fixed source. The collected data were compared to simulated scattering models. Classification and confidence estimation were shown for the sphere versus cylinder case on the resulting real and simulated bistatic amplitude data. The final models were used for classification of simulated targets in real time in the LAMSS MOOS-IvP simulation package [M. Benjamin, H. Schmidt, P. Newman, and J. Leonard, J. Field Rob. 27, 834-875 (2010)].
A chiral pyrene excimer in .gamma.-cyclodextrin cavity (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA chiral pyrene excimer in .gamma.-cyclodextrin cavityKoji Kano, Hitoshi Matsumoto, Shizunobu Hashimoto, Masahiko Sisido, and Yukio ImanishiCite this: J. Am. Chem. Soc. 1985, 107, 21, 6117–6118Publication Date (Print):October 1, 1985Publication History Published online1 May 2002Published inissue 1 October 1985https://pubs.acs.org/doi/10.1021/ja00307a055https://doi.org/10.1021/ja00307a055research-articleACS PublicationsRequest reuse permissionsArticle Views812Altmetric-Citations100LEARN 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 optionsGet e-Alertsclose Get e-Alerts
Design, Properties and Recent Application of Macrocycles in Medicinal Chemistry (2017)

Macrocyclic compounds have recently received increasing attention in drug discovery as these compounds offer the potential to modulate difficult targets and to access novel chemotypes. Approaches towards libraries of macrocyclic compounds based on modular organic synthesis and applications of these technology platforms to find and improve biologically active compounds are introduced in this minireview. Alternatively, lead compounds may be obtained by truncation and modification of macrocyclic natural products. Selected medicinal chemistry programs are discussed, illustrating a macrocyclization approach toward ligands with improved properties. The design of such ligands is often informed by X-ray crystal structures of protein-ligand complexes. Efforts to understand cellular permeability and oral bioavailability of cyclic peptides and non-peptidic macrocycles are summarized.
Economic Dispatch for an Agent-Based Community Microgrid (2015)

In this paper, an economic dispatch (ED) problem for a community microgrid is studied. In this microgrid, each agent pursues an ED for its personal resources. In addition, each agent is capable of trading electricity with other agents through a local energy market. In this paper, an energy market operating in the presence of the grid is introduced. The proposed market is mainly developed for an experimental community microgrid at the Missouri University of Science and Technology, Rolla, MO, USA, and can be applied to other distribution level microgrids. To develop the algorithm, first, the microgrid is modeled and a dynamic ED algorithm for each agent is developed. Afterwards, an algorithm for handling the market is introduced. Lastly, simulation results are provided to demonstrate the proposed community market, and show the effectiveness of the market in reducing the operation costs of passive and active agents.
Proton Nuclear Magnetic Resonance Spectral Resolution of Enantiomeric Amino Acid Tyrosine (2001)

Europium (S,S) ethylendiamine-N,N- disuccinate was utilized for NMR spectral resolution of enantiomeric amino acid tyrosine in aqueous solutions.
Diferències dialectals del català a partir de les oracions interrogatives absolutes amb «que» (2005)

Aquest estudi centra l?atencio en l?analisi dels parametres prosodics (entonacio,
durada i intensitat) que caracteritzen les oracions interrogatives absolutes
encapcalades per la conjuncio «que». El corpus emprat ha estat el constituit per
oracions completes de tres accents tonals obtingut en quatre punts d?enquesta
(Barcelona, Tarragona, Lleida i Tortosa) a partir de mostres recollides a parlants
femenines representatives del lloc en questio. Els resultats mostren clarament com
l?analisi de l?F0 caracteritza la parla de cadascun dels quatre indrets estudiats sense
confusio.
Inclusion of picolines by a substituted binaphthyl diol host: selectivity and structure (2013)

The host compound 3,3′-bis(9-hydroxy-9-fluorenyl)-2,2′-binaphthyl forms inclusion compounds with the isomers of picoline. Competition experiments show that the preferred selectivity is in the order 4PIC > 3PIC > 2PIC. The structures of the inclusion compounds formed with each picoline, as well as representative samples from the competition experiments, have been elucidated. The thermal stabilities of the inclusion compounds correlate with the selectivity results.
Hydroquinone‐Based Biarylic Polyphenols as Redox Organocatalysts for Dioxygen Reduction: Dramatic Effect of Orcinol Substituent on the Catalytic Activity (2017)

Abstract A series of 18 new biaryls has been synthesized and investigated with regard to their organocatalytic efficiency. They consist of a hydroquinone core linked to a phenol or a resorcinol moiety. It is shown that the resorcinol moiety substituted on its meta position has a strong impact on the catalytic activities of these compounds towards the reduction of dioxygen by diethylhydroxylamine (DEHA) in aqueous medium. While the derivative consisting of the two cores spaced by three methylene units is completely inactive, substitution on the hydroquinone part leads to tremendously active catalysts, especially the biaryl consisting of methoxyhydroquinone‐orcinol. Two mechanisms are proposed to explain the dramatic efficiency of the novel hydroquinone‐based biarylic polyphenols for the catalytic reduction of dioxygen, both considering the influence of the orcinol moiety on the semiquinone anion intermediate. As a first hypothesis, this substituent could promote its direct reduction by DEHA to regenerate the hydroquinone, which will react again to regenerate the semiquinone. On the other hand, an intramolecular hydrogen bond could enhance the reactivity of the semiquinone anion toward dioxygen by an addition–elimination mechanism. In this case, the elimination would provide the corresponding quinone but, since the reduction of the quinones by DEHA is much slower than the observed kinetics, a reduction by DEHA prior to the elimination has to be considered to generate the semiquinone anion instead of the quinone. magnified image
Using PCA and LVQ neural network for automatic recognition of five types of white blood cells (2010)

Designing an effective classifier has been a challenging task in the previous methods proposed in the literature. In this paper, we apply a combination of feature selection algorithm and neural network classifier in order to recognize five types of white blood cells in the peripheral blood. For this purpose, first nucleus and cytoplasm are segmented using Gram-Schmidt method and snake algorithm, respectively; second, three kinds of features are extracted from the segmented areas. Then the best features are selected using Principal Component Analysis (PCA). Finally, five types of white blood cells are classified using Learning Vector Quantization (LVQ) neural network. The performance analysis of the proposed algorithm is validated by an expert's classification results. The efficiency of the proposed algorithm is highlighted by comparing our results with those reported in a recent article which proposed a method based on the combination of Sequential Forward Selection (SFS) as the feature selection algorithm and Support Vector Machines (SVM) as the classifier.
Human Immunodeficiency Virus Type 1 Vpu Inhibitor, BIT225, in Combination with 3-Drug Antiretroviral Therapy: Inflammation and Immune Cell Modulation (2020)

BIT225 is a first-in-class inhibitor of human immunodeficiency virus (HIV) type 1 Vpu. A phase II trial enrolled 36 HIV-1-infected, treatment-naive participants in Thailand to receive standard-of-care antiretroviral therapy (ART), tenofovir disoproxil fumarate/emtricitabine/efavirenz (Atripla), with 100 or 200 mg of BIT225 or placebo (daily) for 12 weeks. Combined treatment with BIT225 and ART was found to be generally safe and well tolerated, with antiviral efficacy comparable to that of ART alone. The secondary end point-soluble CD163, a marker of monocyte/macrophage inflammation-was noted to be significantly decreased in the BIT225 arm. Plasma-derived activated CD4+ and CD8+ T cells, natural killer cells, and interleukin 21 were increased in those treated with BIT225. These findings are consistent with inhibition of the known effects of HIV Vpu and may reflect clinically important modulation of inflammatory and immune function. Further clinical study is planned to both confirm and extend these important findings in treatment-naive, and treatment-experienced individuals. Clinical Trials Registration. Australian New Zealand Clinical Trials Registry (Universal Trial Number U1111-1191-2194).
Flame quenching dynamics in a rectangular cross section channel for different velocity regimes (2017)

Understanding the efficiency of flame arresting devices in extreme conditions and critical locations, such as the inlets of fuel tanks, is required to guarantee that the system design is both safe and optimized. The efficiency of these flame arresting devices is influenced by various parameters such as fuel, mixture fraction, pressure, surface material, surface temperature, flame front velocity, etc. However the significance of flame front velocity to the quenching distance has yet to be quantified. In our preliminary study, it has been observed that the quenching distance is a strong function of flame front velocity. Previously, two different velocity regimes (20 m/s and 100 m/s) were studied; however, to develop a predictive model of this phenomenon, understanding this behavior over a wider range of velocities is required. Experiments were conducted in a 2D rectangular duct connecting an ignition chamber to a secondary chamber. Stoichiometric methane-air mixtures at initial conditions 1 bar and 298 K are used in this study. Different duct configurations with similar quenching elements are used for achieving flame front velocities in different regimes. The influence of flame front velocity on quenching distance is discussed in this paper.
Optimization of nonlinear stochastic uncertain relaxed controlled systems: entropy rate functionals and robustness (2004)

This paper is concerned with nonlinear stochastic uncertain relaxed controlled diffusions, in which the pay-off is described by the relative entropy between the nominal measure and the uncertain measure, when the uncertain measure satisfies certain energy inequality constraints. With respect to this formulation two problems are defined. The first, seeks to minimize the relative entropy over the set of unknown measures which satisfy inequality constraints. The second, seeks to maximize over the set of admissible relaxed control laws, the minimum value of relative entropy induced by the uncertain measures among those which satisfy inequality constraints. The second problem is equivalent to a minimax problem, while the first is an optimization problem with respect to a fix control law. Certain monotonicity properties of the optimal solution are discussed, while relations to the well-known Cramer's theorem of large deviations are introduced. In addition, the implication of these results to minimax games for fully observable stochastic systems in which the strategies are measures are delineated and relations to risk-sensitive control problems are investigated.
Demonstration of scalable, flat, and high-throughput data center architecture based on arrayed waveguide grating routers (2014)

We designed and experimentally demonstrated a scalable datacenter architecture with intra-cluster all-to-all topology and flat inter-cluster interconnection based on wavelength routing in AWGRs. Experiments show 97% intra-cluster throughput for uniform random traffic, and error-free inter-cluster communication at 10 Gb/s.
Ultrafine Magnetite Nanopowder: Synthesis, Characterization, and Preliminary Use as Filler of Polymethylmethacrylate Nanocomposites (2012)

Magnetite (Fe 3 O 4 ) nanoparticles prepared by microwave-assisted hydrothermal synthesis have been characterized in terms of morphological and structural features. Electron micrographs collected in both scanning (SEM) and transmission (TEM) modes and evaluations of X-ray powder diffraction (XRD) patterns have indicated the achievement of a monodispersed crystallite structure with particles having an average size around 15–20 nm. Structural investigations by Micro-Raman spectroscopy highlighted the obtainment of magnetite nanocrystals with a partial surface oxidation to maghemite ( γ -Fe 3 O 4 ). Preliminary attention has been also paid to the use of these magnetite nanoparticles as filler for a commercial polymethylmethacrylate resin. Hybrid formulations containing up to 3 wt% of nanoparticles were prepared by melt blending and characterized by calorimetric and thermogravimetric tests. For sake of comparison, same formulations containing commercial Fe 3 O 4 nanoparticles are also reported. Calorimetric characterization indicates an increase of both glass transition temperature and thermal stability of the nanocomposite systems when loaded with the synthesized magnetite nanoparticles rather then loaded with the same amount of commercial Fe 3 O 4 . This first observation represents just one aspect of the promising potentiality offered by the novel magnetic nanoparticles when mixed with PMMA.
Using spatially explicit, time‐dependent analysis to understand how social factors influence conservation outcomes (2019)

Conservation across human-dominated landscapes requires an understanding of the social and ecological factors driving outcomes. Studies that link conservation outcomes to social and ecological factors have examined temporally static patterns. However, there may be different social and ecological processes driving increases and decreases in conservation outcomes that can only be revealed through temporal analyses. Through a case study of the invasion of Falcataria moluccana in Hawaii, we examined the association of social factors with increases and decreases in invader distributions over time and space. Over 7 years, rates of invader decrease varied substantially (66-100%) relative to social factors, such as building value, whether land was privately or publically owned, and primary residence by a homeowner, whereas rates of increase varied only slightly (<0.1-3.6%) relative to such factors. These findings suggest that links between social factors and invasion in the study system may be driven more by landowners controlling existing invasive species, rather than by landowners preventing the spread of invasive species. We suggest that spatially explicit, time-dependent analyses provide a more nuanced understanding of the way social factors influence conservation outcomes. Such an understanding can help managers develop outreach programs and policies targeted at different types of landowners in human-dominated landscapes.
Solid‐Phase Synthesis of Oligo‐ADP‐Ribose (2016)

Solid-phase methodology for synthesis of adenosine diphosphate ribose oligomers (ADPr-oligomers) of defined length is described using an advanced 2-ribosyl adenosine phosphoramidite building block that is prepared in solution via an expeditious and high-yielding method. The methodology is based on phosphitylation of a phosphomonoester as the key condensation step in the solid-phase protocol. As ADP-ribosylation appears to be an important yet poorly understood post-translational modification of proteins, the presented methodology for rapid synthesis of ADPr-fragments of exactly defined length should be of interest for researchers in the field of structural biology and cell biology. © 2016 by John Wiley & Sons, Inc.
Anomalies in kinetics of hydrogen evolution from austenitic stainless steel from 300 to 1000 °C (2001)

The rate of rise method was arranged for monitoring the kinetics of hydrogen evolution from austenitic stainless steel (AISI 304) samples, inductively heated in the range from 300 to 1000 °C. After each heating cycle, the accumulated gases were analyzed by quadrupole mass spectroscopy and quantity of evolved hydrogen was determined. Three sample types were studied: “only cleaned,” hydrogen annealed (1050 °C), and vacuum annealed (950 °C). Below 800 °C, the effect of pretreatment was manifested very differently in kinetics. Fast release of approximately 2×1019 atoms H cm−3 from hydrogen annealed samples was recorded which was close to published data of solubility. By increasing the temperature above 800 °C for a prolonged time, much more hydrogen evolved from all sample types. The equivalent concentration change varied from 4 to 9×1019 atoms H cm−3, but the measurements were ceased before the “totally outgassed state” was reached. By repeated annealing of two samples in high vacuum, the rest of the hydrogen was again partially extracted and partially redistributed to the sites, from which it was easily released after intermediate cooling down. There is a lack of data in the literature about the amount and evolution kinetics of the trapped or tightly bound hydrogen. The present findings differ from existing theoretical models of outgassing and may explain the reason for the inefficiency of thermal treatment methods to prepare stainless steel for extreme high vacuum application.
Purification and properties of pyrimidine nucleoside monophosphate kinase from baker's yeast. (1983)

Pyrimidine nucleoside monophosphate kinase was purified from baker's yeast to 280-fold. The molecular weight of the enzyme was calculated to be 26, 000 by gel filtration. With ATP as a phosphate donor, UMP was the most active phosphate acceptor. Besides UMP, the kinase also phosphorylated CMP, dCMP and dUMP. Km values for UMP, CMP, dCMP and dUMP were 0.052, 0.071, 0.54 and 8.5mM, respectively. The kinase was activated by preincubation with dithiothreitol. The extent of the activation depended on the concentration of dithiothreitol and incubation time. HgCl2, p-CMB and N-ethylmaleimide inhibited this enzyme.