gebhart/patrepeval huggingface dataset:
Phase I Clinical Evaluation of rDEN4Δ30-200,201: A Live Attenuated Dengue 4 Vaccine Candidate Designed for Decreased Hepatotoxicity (2008)

The rDEN4Delta30-200,201 is a live attenuated DENV-4 vaccine candidate specifically designed to further attenuate the rDEN4Delta30 parent virus. In the present study, 28 healthy adult volunteers were randomized to receive either 10(5) plaque-forming unit (PFU) of vaccine (20) or placebo (8) as a single subcutaneous injection. Volunteers were evaluated for safety every other day for 16 days. Serum neutralizing antibody titer against DEN4 was determined at study day 28, 42, and 180. The vaccine infected all vaccinees and was well tolerated without inducing alanine aminotransferase (ALT) elevations. Although virus was not recovered from the serum of any vaccinee, moderate levels of neutralizing antibody were induced in all volunteers. Thus the restricted replication of rDEN4Delta30-200,201 previously documented in animal models was confirmed in humans. The rDEN4Delta30-200,201 is a promising candidate and can be considered for inclusion in a tetravalent dengue virus (DENV) vaccine.
Sensemaking in the personal health space (2015)

Purpose – Service alignment between health service provider and patient is changing. Instead of placing responsibilities into the hands of a provider, new forms of co-operation are emerging in which patients are regarded as a resource and a partner. In order to see this vision come to life, mechanisms that: first, support patient’s health decision making; and second, integrate matters of health into a wider ensemble that is health space; the overarching state of health-related affairs, are needed. In the following, these kinds of mechanisms are investigated and their applicability is discussed in relation to a national project. The paper aims to discuss these issues. Design/methodology/approach – The work is exploratory and conceptual, focussing more on people than on technology. In the work, findings related to a concept of a health navigator; an artefact of personal health decision support, are assembled into a framework that bases on key sociological theories. The empirical elements focus on observations made on applicability of the concept, and the underlying framework of citizen-centric electronic health services. Findings – The authors argue that the discussed concept, when applied to personal health decision making according to the underlying framework, has a potential to change health service provisioning. In addition to stimulating new kind of co-operation between the health service provider and the citizen, the concept gives form to, somewhat idealized, notions of patient choice and empowerment. Research limitations/implications – The work described here is exploratory and forward-looking. Even though the concept and the framework are tested to a degree in a national project, more practice-oriented work is needed in terms of real-world applicability. It follows from this that the work is a conceptual elaboration on the future of personal health decision making. Originality/value – The findings, including the discussed challenges and needs, stem from real-world observations; from the needs of citizens. As such, they indicate a direction into which the development of personal health records and health decision support aids should go.
New Monordens Produced by Amidepsine-producing Fungus Humicola sp. FO-2942 (2003)

Based on UV spectrum-guided purification, new monordens C, D and E, known monordens A (radicicol) and B and 5-O-methylsclerone were isolated from the fermentation broth of amidepsine-producing Humicola sp. FO-2942 by solvent extraction, silica-gel column chromatography, ODS column chromatography and HPLC. All monordens cause the cell cycle arrest at G1 and G2/M phases in Jurkat cells. But among them, monordens A and E show antifungal activity only against Aspergillus niger.
Environmental Barrier Coatings for SiCf/SiC (2014)

Ceramic matrix composite (CMCs) are not viable in gas turbine engines without mitigating rapid surface recession resulting from water vapor–induced vaporization of silica scale. Currently, external barrier coatings, known as environmental barrier coatings (EBCs), are the most promising approach to protecting CMCs from surface recession. The first generation EBCs, silicon mullite or mullite + BSAS BSAS, developed in the NASA HSCT-EPM Program enabled the world's first successful engine test of a CMC component in a Solar Turbines industrial gas turbine with one engine completing a 14 000-hour field test. The second generation EBCs with temperature capabilities >1482°C (2700°F) were developed in the NASA UEET Program. The first generation and second generation EBCs laid the foundation for next generation EBCs. APS is currently the most successful and widely used process to fabricate EBCs. Other potential coating processes include EB-PVD, DVD, PS-PVD, CVD, and slurry-based processes. Non-line-of-sight EBC processes are desirable for complex-shaped CMC components because EBC is a prime reliant coating. Three key components for validating EBCs are water vapor, gas velocity, and temperature gradient. Currently combinations of steam cycling rig, high velocity–high steam burner rig, laser rig, and high pressure burner rig are used to validate EBCs. Sources for EBC degradation can be categorized into three groups: chemical, mechanical, and physical. Strong interactions between various degradation modes are expected, and therefore, a model that incorporates all these factors needs to be developed to successfully project the life of EBC. An industry standard or a model system, which is relevant to various versions of EBCs, needs to be established on which the life modeling effort can be focused.
Insight into particle production mechanisms via angular correlations of identified particles in pp collisions at $$\sqrt{\mathrm{s}}=7$$s=7 TeV (2017)

Two-particle angular correlations were measured in pp collisions at s = 7 TeV for pions, kaons, protons, and lambdas, for all particle/anti-particle combinations in the pair. Data for mesons exhibit an expected peak dominated by effects associated with mini-jets and are well reproduced by general purpose Monte Carlo generators. However, for baryon-baryon and anti-baryon-anti-baryon pairs, where both particles have the same baryon number, a near-side anticorrelation structure is observed instead of a peak. This effect is interpreted in the context of baryon production mechanisms in the fragmentation process. It currently presents a challenge to Monte Carlo models and its origin remains an open question.
Ground current control scheme for back‐to‐back three‐phase T‐type rectifier and inverter systems (2018)

This paper presents a method to control the ground current in a back‐to‐back connection of three‐phase T‐type rectifier and inverter stages if operated from a three‐phase mains with a grounded neutral point and a star‐connected three‐phase load with grounded star point. The proposed control scheme requires a ground current sensor and a single control loop, achieves a closed‐loop control system bandwidth of 1.7 kHz, and does not interact with the existing input phase current control system that is used to achieve sinusoidal mains currents. According to the presented experimental results, an effective reduction of the rms ground current from more than 200 mA (without controller) to less than 3 mA (with the proposed control scheme) is realized. © 2018 Institute of Electrical Engineers of Japan. Published by John Wiley &amp; Sons, Inc.
Report on the SIGIR 2013 Workshop on Adaptive Retrieval and Recommender Systems (2013)

In recent years, immense progress has been made in the development of recommendation, retrieval, and personalisation techniques. The evaluation of these systems is still based on traditional information retrieval and statistics metrics, e.g., precision, recall and/or RMSE, often not taking the use-case and situation of the actual system into consideration. However, the rapid evolution of recommender and adaptive IR systems in both their goals and their application domains foster the need for new evaluation methodologies and environments. In the Workshop on Benchmarking Adaptive Retrieval and Recommender Systems, we aimed to provide a platform for discussions on novel evaluation and benchmarking approaches.
Temporal Information Transformed into a Spatial Code by a Neural Network with Realistic Properties (1995)

Neurons exhibit a wide range of properties in addition to postsynaptic potential (PSP) summation and spike generation. Although other neuronal properties such as paired-pulse facilitation (PPF) and slow PSPs are well characterized, their role in information processing remains unclear. It is possible that these properties contribute to temporal processing in the range of hundreds of milliseconds, a range relevant to most complex sensory processing. A continuous-time neural network model based on integrate-and-fire elements that incorporate PPF and slow inhibitory postsynaptic potentials (IPSPs) was developed here. The time constants of the PPF and IPSPs were estimated from empirical data and were identical and constant for all elements in the circuit. When these elements were incorporated into a circuit inspired by neocortical connectivity, the network was able to discriminate different temporal patterns. Generalization emerged spontaneously. These results demonstrate that known time-dependent neuronal properties enable a network to transform temporal information into a spatial code in a self-organizing manner--that is, with no need to assume a spectrum of time delays or to custom-design the circuit.
Genome-wide CRISPR screens reveal a specific ligand for the glycan-binding immune checkpoint receptor Siglec-7 (2021)

<i>Glyco-immune checkpoint receptors</i>, molecules that inhibit immune cell activity following binding to glycosylated cell-surface antigens, are emerging as attractive targets for cancer immunotherapy. Defining biologically relevant ligands that bind and activate such receptors, however, has historically been a significant challenge. Here, we present a CRISPRi genomic screening strategy that allowed unbiased identification of the key genes required for cell-surface presentation of glycan ligands on leukemia cells that bind the glyco-immune checkpoint receptors Siglec-7 and Siglec-9. This approach revealed a selective interaction between Siglec-7 and the mucin-type glycoprotein CD43. Further work identified a specific N-terminal glycopeptide region of CD43 containing clusters of disialylated O-glycan tetrasaccharides that form specific Siglec-7 binding motifs. Knockout or blockade of CD43 in leukemia cells relieves Siglec-7-mediated inhibition of immune killing activity. This work identifies a potential target for immune checkpoint blockade therapy and represents a generalizable approach to dissection of glycan-receptor interactions in living cells.
Inherently Selective Water-Free Deposition of Titanium Dioxide on the Nanoscale: Implications for Nanoscale Patterning (2022)

Water-free inherent selective deposition of TiO2 on Si and SiO2 in preference to SiCOH has been studied via atomic layer deposition (ALD) and pulsed chemical vapor deposition (CVD). SiCOH is a nonreactive low-k dielectric material, consisting of highly porous alkylated SiO2. Water-free deposition was studied to protect SiCOH and increase selectivity. The titanium precursor used in all studies was Ti(OiPr)4 [titanium(IV) isopropoxide] and contains four oxygen atoms enabling it to form TiO2 through single-precursor CVD. At 250 °C substrate temperature, selective water-free ALD of TiO2 using Ti(OiPr)4 and either acetic acid (AcOH) or formic acid (HCO2H) as a second precursor was studied. By both ALD processes, around 2 nm of TiO2 was deposited on Si and SiO2 without any deposition on SiCOH. The TiO2 ALD films had a root-mean-square roughness of 2–3 Å. In situ X-ray photoelectron spectroscopy showed that Ti(OiPr)4 + AcOH ALD occurred via ligand exchange between −OiPr and AcO–. ALD with formic acid, which is a 10× stronger proton donor than acetic acid, displayed similar selectivity but with a 10× higher growth rate than ALD with acetic acid. Single-precursor pulsed CVD with Ti(OiPr)4 was also studied at 250 and 295 °C substrate temperatures. At 250 °C, TiO2 growth on all substrates was minuscule (<1 nm for 400 pulses). Single-precursor pulsed CVD (2000 pulses) at 295 °C displayed the highest selectivity among all processes studied: 16.9 and 40.1 nm TiO2 molecules were deposited on Si and SiO2, respectively, while less than a monolayer of TiO2 was deposited on SiCOH. The pulsed CVD at 295 °C showed ∼20 nm of selective TiO2 deposition on nanoscale patterned samples. It is expected that the selective TiO2 CVD can be applicable in the nanoscale patterning process in metal-oxide-semiconductor field-effect transistor fabrication.
Oligonucleotide Flexibility Dictates Crystal Quality in DNA-Programmable Nanoparticle Superlattices* (2020)

Superlattices composed of noble metal nanoparticles display considerable promise for the development of optical metamaterials [1–5], and architectures with tunable permittivity [3], permeability [4], negative indices of refraction [2, 4, 5], and even some with chiral [5, 6] and active [7] responses have been explored. However, the realization of such architectures using nanoparticles has proven synthetically challenging because these structures typically require both high metallic volume fraction (approaching or exceeding 20%) [3, 8] and large diameter particles (i.e., 30–100 nm). While super-lattices have been formed using electrostatic [9], entropic [10] and molecular interactions [11], DNA-mediated assembly [12, 13] offers unprecedented levels of control over the interparticle distance and superlattice symmetry. The development of metamaterials from DNA-nanoparticle superlattices, however, has been impeded by the difficulty in synthesizing periodic structures with suitably high metallic volume fractions, as they are more prone to kinetic jamming and often form non-crystalline arrangements regardless of annealing conditions. Here, we show that incorporating flexible spacers along with annealing DNA-nanoparticle systems close to their melting transitions improves crystalline quality in terms of domain size and microstrain. These insights allow for the crystallization of nano-particle superlattices with up to 34% volume fraction, up from the previously reported maximum of 14% [14]. Importantly, this paper does not focus on metamaterials per se, but rather on the scientific underpinnings required to assemble large AuNPs into structures with high inorganic volume fractions.
Photoaffinity Labeling and Mass Spectrometry Identify Ribosomal Protein S3 as a Potential Target for Hybrid Polar Cytodifferentiation Agents (1999)

The ability of a novel class of hybrid polar compounds (HPCs) to induce differentiation and consequent cessation of proliferation of transformed cells has led to their development as potential chemotherapeutic agents in the treatment of cancer. Suberoylanilide hydroxamic acid (SAHA) is a prototype of a family of hydroxamic acid based compounds (SAHA-like HPCs) that can, at micromolar concentrations, induce a variety of transformed cell lines to differentiate. The mechanism of action of the HPCs is not entirely understood. Searching for a cellular target of the SAHA-like HPCs, we synthesized a photoaffinity labeling reagent structurally based on SAHA, and probed for SAHA-binding proteins in murine erythroleukemia (MEL) cells. Photoaffinity labeling in cell free extracts identified a 32-kDa protein (p32) that was specifically labeled by the photoaffinity reagent. Cell fractionation assays localized p32 to the P100 fraction. p32 was partially purified and identified by mass spectrometry as the 40 S ribosomal protein S3. Expression of epitope-tagged S3 in bacterial lysates followed by photoaffinity labeling confirmed its specific labeling. Identification of a cytodifferentiation agent target may shed light on the mechanism by which the SAHA-like HPCs exert their antitumor effects.
Cloning of a <i>Schizosaccharomyces pombe</i> homologue of elongation factor 1 alpha by two-hybrid selection of calmodulin-binding proteins (1999)

This study reports the cloning and characterization of a cDNA encoding elongation factor 1-alpha (EF1alpha) from the yeast Schizosaccharomyces pombe. The cDNA was cloned from an Schizosaccharomyces pombe expression library by a two-hybrid selection for clones encoding calmodulin (CaM)-binding proteins. The predicted protein is highly homologous to mammalian EF1alpha, indicating a strong tendency towards conservation of the primary amino acid sequence. The protein was expressed as a glutathione S-transferase fusion in both bacteria and in Schizosaccharomyces pombe. The bacterial protein was shown by solution assay to compete with CaM kinase II for CaM. The CaM binding domain was localized to the C-terminus of the protein by this method. Expression of full-length EF1alpha in vivo caused an increase in cell cycle length and a decreased rate of growth as evidenced by a lack of elongated cells in slowly dividing cultures. This effect appears to involve CaM binding because a truncation mutant version of EF1alpha lacking the CaM binding domain did not cause cell cycle delay.
Transport of Long-Chain Native Fatty Acids across Lipid Bilayer Membranes Indicates That Transbilayer Flip-Flop Is Rate Limiting (1997)

Evidence from a number of laboratories suggests that membrane proteins may meditate the transport of physiologic fatty acids (FA) across cell membranes. However, studies using lipid membranes indicate that FA are capable of spontaneous flip-flip, raising the possibility that rapid transport through the lipid phase obviates the need for a transport protein. Determining the rate-limiting steps for transport of FA across lipid membranes, therefore, is central to understanding FA transport across cell membranes. The transport of long-chain FA across lipid membranes, from the aqueous compartment on one side of the lipid bilayer to the aqueous phase on the other side, has not been measured previously. In this study, we have used the fluorescent probe ADIFAB to monitor the time course of FA movement from the outer to the inner aqueous compartments and from the lipid membrane to the outer aqueous compartment of lipid vesicles. These two measurements, together with measurements of the lipid:aqueous partition coefficients, allowed the determination of the rate constants for binding (kon), flip-flop (kff), and dissociation (koff) for the transport of long-chain natural FA across lipid vesicles. These rates were determined using large unilamellar vesicles (LUV) of approximately 1000 A diameter, prepared by extrusion and giant unilamellar vesicles (GUV), prepared by detergent dialysis, that are >/=2000 A diameter. The results of these studies for vesicles composed of egg phosphatidylcholine (EPC) and cholesterol reveal kff values that range from 3 to 15 s-1 for LUV and from 0.1 to 1.0 s-1 for GUV, depending upon temperature and FA type. For these same vesicles, dissociation rate constants range from 4 to 40 s-1 for LUV and from 0.3 to 2.5 s-1 for GUV. In all instances, the rate constant for flip-flop is smaller than koff, and because the rate of binding is greater than the rate of transport, we conclude that flip-flop is the rate-limiting step for transport. These results demonstrate that (1) kff and koff are smaller for GUV than for LUV, (2) the rate constants increase with FA type according to oleate (18:1) < palmitate (16:0) < linoleate (18:2), and (3) the barrier for flip-flop has a significant enthalpic component. Comparison of the flip-flop rates determined for GUV with values estimated from previously reported metabolic rates for cardiac myocytes, raises the possibility that flip-flop across the lipid phase alone may not be able to support metabolic requirements.
Neoantigen Identification and Response to Adoptive Cell Transfer in Anti–PD-1 Naïve and Experienced Patients with Metastatic Melanoma (2022)

These results indicate that decreases in TMB and targeted neoantigens partially account for the difference in response to ACT and that additional factors likely influence responses in these patients. See related commentary by Blass and Ott, p. 2980.
Separation And Measurement Of Surface Scatter And Volume Scatter From Transparent Optics (1989)

A prototype instrument has been developed that separates light scattered from transparent optics into light scattered from the surface and light scattered from the bulk. The instrument also calculates the loss coefficient for transparent materials. The method has been combined with a raster scanning technique to produce a sensitive method of detecting component contamination in the presence of surface scatter.
La chirurgie orthopédique et traumatologique guidée par l’image. De la naissance à l’âge adulte. (2018)

Trois défis chirurgicaux sont à la base de la naissance de la chirurgie orthopédique guidée par l’image :réaliser une visée linéaire à l’intérieur d’un organe ; faire des coupes osseuses pour construire un alignement physiologique,remplacer une articulation ou réséquer une tumeur ; enfin, détecter des conflits potentiels entre structuresanatomiques et/ou prothétiques. Les mutations principales sur le plan des technologies logicielles ou matérielles concernentla nature des informations utilisées pour planifier et guider le geste : données préopératoires anatomiques 3D,fluoroscopie peropératoire, données peropératoires fonctionnelles (axes des membres, centre de rotation des articulations),modèles statistiques de formes anatomiques et plus récemment imagerie intra-opératoire 3D. Le choix de cesmodalités impacte la nécessité (ou pas) de méthodes de recalage et leurs choix d’implémentation. L’étroite collaborationentre les scientifiques du laboratoire TIMC-IMAG et les chirurgiens orthopédistes grenoblois, entre 1995et 2002, a permis aux équipes françaises d’être à l’origine de nombreuses innovations et de premières réalisationschirurgicales, même si des équipes étrangères étaient déjà presque aussi avancées. C’est ainsi que les applicationscliniques au niveau du rachis, du remplacement prothétique de l’articulation du genou et de la hanche, de la réparationdes ligaments du genou ou de la correction des déformations des membres ont vu le jour. Malgré leur coût et le tempsadditionnel opératoire, ces systèmes ont eu un effet parfaitement compensé par la diminution significative de la dispersiondes résultats anatomiques.
Model Diagnostic Analysis of Global Coverage Satellites (2014)

We investigate the ability of a reduction in the complexity of a model to enable a more rapid optimization of that model, with minimal reduction in accuracy, if critical parameters and features are identified and contained within the reduced model. We present a Model Diagnostics analysis of the Draim global coverage constellations and the underlying coverage model used to analyze their performance using Sobol’s method of sensitivity indices. We propose complexity reduction based on the diagnostic analysis. Two separate optimizations are run using a Multi-Objective Evolutionary Algorithm optimization tool. One optimization uses the original problem formulation while the other uses a reduced-complexity formulation. We demonstrate that subtle behavior in the interaction of all parameters (not only the critical ones) dramatically affects performance of the optimization.