gebhart/patrepeval huggingface dataset:
Antagonism of CRTH2 ameliorates chronic epicutaneous sensitization-induced inflammation by multiple mechanisms (2008)

Prostaglandin D(2) (PGD(2)) and its receptor chemoattractant receptor homologous molecule expressed on T(h)2 cells (CRTH2) have been implicated in the pathogenesis of numerous allergic diseases. We investigated the role of PGD(2) and CRTH2 in allergic cutaneous inflammation by using a highly potent and specific antagonist of CRTH2. Administration of this antagonist ameliorated cutaneous inflammation caused by either repeated epicutaneous ovalbumin or FITC sensitization. Gene expression and ELISA analysis revealed that there was reduced pro-inflammatory cytokine mRNA or protein produced. Importantly, the CRTH2 antagonist reduced total IgE, as well as antigen-specific IgE, IgG1 and IgG2a antibody levels. This reduction in antibody production correlated to reduced cytokines produced by splenocytes following in vitro antigen challenge. An examination of skin CD11c(+) dendritic cells (DC) showed that in mice treated with the CRTH2 antagonist, there was a decrease in the number of these cells that migrated to the draining lymph nodes in response to FITC application to the skin. Additionally, naive CD4(+) T lymphocytes co-cultured with skin-derived DC from CRTH2 antagonist-treated mice showed a reduced ability to produce a number of cytokines compared with DC from vehicle-treated mice. Collectively, these findings suggest that CRTH2 has a pivotal role in mediating the inflammation and the underlying immune response following epicutaneous sensitization.
Activation of A3 adenosine receptors on human eosinophils elevates intracellular calcium (1996)

Adenosine (ADO) is a potent bronchoconstrictor in allergic patients and has been shown to increase the release of histamine from human lung tissues. Antagonists of ADO A1 and A2A receptors are not effective in attenuating these effects. Therefore, involvement of ADO A3 receptors in the bronchoconstrictor and/or inflammatory effects have to be considered. Eosinophils also play a pivotal role in allergic diseases such as asthma, thus it is natural to consider a link between the A3 receptor and eosinophils. Human peripheral blood eosinophils express the ADO A3 receptor as indicated by detection of the transcript for A3 receptors in polymerase chain reaction-amplified cDNA derived from the cells. A3 receptors on eosinophil membranes were characterized using the A3 receptor agonist radioligand 125I-labeled AB-MECA, which yielded Bmax and Kd values of 1.31 pmol/mg protein and 3.19 nmol/L, respectively. Treatment of eosinophils with the highly potent and selective A3 receptor agonist CI-IB-MECA clearly induced Ca2+ release from intracellular Ca2+ pools followed by Ca2+ influx, suggesting the presence of phospholipase C-coupled A3 receptors. In contrast, the ADO receptor agonists CPA and CGS 21680, selective for A1 and A2A receptors, respectively, at concentrations of < or = 30 mumol/ L did not elevate the intracellular Ca2+ level. These results attest to the existence of ADO A3 receptors on eosinophils and suggest that ADO stimulates these cells to release Ca2+ from intracellular stores via the activation of A3 receptors.
Genome Sequences of Nine Gram-Negative Vaginal Bacterial Isolates (2016)

The vagina is home to a wide variety of bacteria that have great potential to impact human health. Here, we announce reference strains (now available through BEI Resources) and draft genome sequences for 9 Gram-negative vaginal isolates from the taxa Citrobacter, Klebsiella, Fusobacterium, Proteus, and Prevotella.
Nanocavity enhanced diamond nitrogen-vacancy center zero phonon line emission (2011)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text P. E. Barclay, K. C. Fu, A. Faraon, C. Santori, and R. G. Beausoleil, "Nanocavity enhanced diamond nitrogen-vacancy center zero phonon line emission," in CLEO:2011 - Laser Applications to Photonic Applications, OSA Technical Digest (CD) (Optica Publishing Group, 2011), paper QFG6. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Effect of Energy Conversion, Turbulence and Fluid Dynamics on the Transient Heat Transfer and thus on the Scavenging of the Two Stroke Engine (2006)

Investigations on the working cycle and also the predictive simulation of the two stroke engine require knowledge about the energy flows especially in the exhaust system. As these processes are highly transient, a methodology was set up to be able to investigate these processes. Especially near the exhaust port, the temperature and composition of the fluid is changing from high temperature burned gas to cold fresh charge within one revolution. Also there is the radiation and convective heat transfer from the hot exhaust pipe metal to the surrounding. On the basis of measurements on a high performance 1000cc two stroke engine, a 1-dimensional (1D) simulation model was built up and validated. Further on 3D CFD models were set up, using the 1D results as boundary condition data. These 3D models were used for analysis of the 3-dimensional effects and also the transient heat transfer over the pipe wall.
Computing and querying datacubes (2001)

Datacube queries compute aggregates over database relations at a variety of granularities, and they constitute an important class of decision support queries. In this thesis we study problems pertaining to the computation of datacubes and frameworks for querying them. 
Often one wants only datacube output tuples whose aggregate value satisfies a certain condition, such as exceeding a given threshold. For example, one might ask for all combinations of model, color, and year of cars (including the special value “ALL” for each of the dimensions) for which the total sales exceeded a given amount of money. 
Computing a selection over a datacube can naively be done by computing the entire datacube and checking if the selection condition holds for each tuple in the result. However, it is often the case that selections are relatively restrictive, meaning that a lot of work computing datacube tuples is “wasted” since those tuples don't satisfy the selection condition. 
Our approach is to develop algorithms for processing a datacube query using the selection condition internally during the computation. By making use of the selection condition within the datacube computation, we can safely prune parts of the computation and end up with a more efficient computation of the answer. Our first technique, called “specialization”, uses the fact that a tuple in the datacube does not meet the given threshold to infer that all finer level aggregates cannot meet the threshold. We propose a scheme of specialization transformations on the underlying data sets, using properties of the aggregates and threshold functions. 
Our second technique is called “generalization”, and applies in the case where the actual value of the aggregate is not needed in the output, but used just to compare with the threshold. We refer to these as “projected datacube” queries. Generalization uses the fact that a tuple meets the given threshold to infer that all coarser level aggregates also meet the threshold. We also propose a scheme of generalization transformations. We demonstrate that computing the median is easier for projected datacubes. 
In the second major piece of work we study a main memory based framework for querying datacubes. For large datasets with many dimensions, the complete datacube may be very large. In order to support on-line access to datacube results, one would like to perform some precomputation to enhance query performance. 
We propose a main memory based framework which provides rapid response to queries and requires considerably less maintenance cost than a disk based scheme in an append-only environment. (Abstract shortened by UMI.)
The identification of bacillaene, the product of the PksX megacomplex in Bacillus subtilis (2007)

The approximately 80-kb pksX gene cluster in Bacillus subtilis encodes an unusual hybrid polyketide/nonribosomal peptide synthase that has been linked to the production of the uncharacterized antibiotic bacillaene. Multiple copies of this synthase, each similar in size to the ribosome, assemble into a single organelle-like complex with a mass of tens to hundreds of megadaltons. The resource requirements of the assembled megacomplex suggest that bacillaene has an important biological role. By coupling a differential NMR spectroscopic technique with genetically manipulated strains of B. subtilis, we were able to characterize the structure of this unusual secondary metabolite, which could not be predicted by using bioinformatic analysis. We report that bacillaene is a linear molecule with two amide bonds: the first links an alpha-hydroxy carboxylic acid to a omega-amino carboxylic acid containing a conjugated hexaene, and the second links the hexaene-containing carboxylic acid to an (omega-1) amino carboxylic acid containing a conjugated triene. Knowledge of bacillaene's structure has enabled us to annotate the pksX gene cluster and should facilitate the study of bacillaene's biosynthesis as well as its biological role in B. subtilis.
Functions of olfactory receptors are decoded from their sequence (2020)

Abstract G protein-coupled receptors (GPCRs) conserve common structural folds and activation mechanisms, yet their ligand spectra and functions are highly diversified. This work investigated how the functional variations in olfactory GPCRs (ORs)-the largest GPCR family-are encoded in the primary sequence. With the aid of site-directed mutagenesis and molecular simulations, we built machine learning models to predict OR-ligand pairs as well as basal activity of ORs. In vitro functional assay confirmed 20 new OR-odorant pairs, including 9 orphan ORs. Residues around the odorant-binding pocket dictate the odorant selectivity/specificity of the ORs. Residues that encode the varied basal activities of the ORs were found to mostly surround the conserved motifs as well as the binding pocket. The machine learning approach, which is readily applicable to mammalian OR families, will accelerate OR-odorant mapping and the decoding of combinatorial OR codes for odors.
Ionic Transport and Thermodynamic Interaction in Precision Polymer Blend Electrolytes for Lithium Batteries (2021)

Abstract Single‐ion conducting polymer electrolytes are of interest for use with advanced battery electrodes such as lithium metal, but achieving sufficiently high conductivity has been challenging. In this work, a model system containing charged sites that are precisely spaced along the polymer backbone is explored. Precision sulfonated poly(4‐phenylcyclopentene) lithium salt ( p 5PhS‐Li) with a high degree of sulfonation (&gt; 90%) is synthesized and blended with poly(ethylene oxide) (PEO) to investigate the thermodynamic and transport properties. Melting point depression is measured via differential scanning calorimetry, ionic conductivity, κ , is determined using electrochemical impedance spectroscopy, and the fraction of current carried by Li + is estimated based on steady‐state current measurements. In conjunction with a density measurement, melting point depression is used to find an effective Flory–Huggins interaction parameter, χ eff = − 0.21, suggesting miscibility of the blend. κ spans a large range from 2 × 10 −11 to 2 × 10 −7 S cm −1 over the composition and temperature range investigated. The fraction of charge carried by lithium ions also spans a significant range from 0.12 in majority PEO blend to 0.98 in majority p 5PhS‐Li blend. This study addresses several limitations of sulfonated polystyrene and opens up the possibility of precisely controlling the spacing of other anion types.
Supplementary Figure 2 from NEDD9 Promotes Oncogenic Signaling in Mammary Tumor Development (2023)

Supplementary Figure 2 from NEDD9 Promotes Oncogenic Signaling in Mammary Tumor Development
ChemInform Abstract: Synthesis of Fluorescent Pyrrolo[3,4‐b]quinolizine Derivatives and Evaluations as a Protein‐Labeling Probe. (2012)

Abstract The new fluorescent compounds (III), (V), (VII), and (VIII) are synthesized via an one‐pot condensation reaction.
ChemInform Abstract: Catalytic and Enantioselective Route to Medium‐Ring Heterocycles. Asymmetric Zirconium‐Catalyzed Ethylmagnesation of Seven‐ and Eight‐ Membered Rings. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Immobilization of trypsin onto “molded” macroporous poly(glycidyl methacrylate-co-ethylene dimethacrylate) rods and use of the conjugates as bioreactors and for affinity chromatography (2000)

Trypsin immobilization onto continuous "molded" rods of porous poly(glycidyl methacrylate-co-ethylene dimethacrylate) and some applications of the conjugate have been studied. The rods polymerized within a tubular mold (chromatographic column), were treated in situ with ethylenediamine, activated with glutaraldehyde and finally modified with trypsin. The performance of the trypsin-modified rods was evaluated and compared to that of poly(glycidyl methacrylate-co-ethylene dimethacrylate) beads, modified with the same enzyme. Overall the enzyme-modified rods performed substantially better than the corresponding beads. In particular, the performance of the molded supports as enzymatic reactors or as chromatographic media benefits greatly from the enhanced mass transfer that is characteristic of the molded rod at high flow rates. (c) 1996 John Wiley & Sons, Inc.
Development of Conductive Gelatine-Methacrylate Inks for Two-Photon Polymerisation (2021)

Conductive hydrogel-based materials are attracting considerable interest for bioelectronic applications due to their ability to act as more compatible soft interfaces between biological and electrical systems. Despite significant advances that are being achieved in the manufacture of hydrogels, precise control over the topographies and architectures remains challenging. In this work, we present for the first time a strategy to manufacture structures with resolutions in the micro-/nanoscale based on hydrogels with enhanced electrical properties. Gelatine methacrylate (GelMa)-based inks were formulated for two-photon polymerisation (2PP). The electrical properties of this material were improved, compared to pristine GelMa, by dispersion of multi-walled carbon nanotubes (MWCNTs) acting as conductive nanofillers, which was confirmed by electrochemical impedance spectroscopy and cyclic voltammetry. This material was also confirmed to support human induced pluripotent stem cell-derived cardiomyocyte (hPSC-CMs) viability and growth. Ultra-thin film structures of 10 µm thickness and scaffolds were manufactured by 2PP, demonstrating the potential of this method in areas spanning tissue engineering and bioelectronics. Though further developments in the instrumentation are required to manufacture more complex structures, this work presents an innovative approach to the manufacture of conductive hydrogels in extremely low resolution.
Evolution of contact bounces in MEMS switches under cycling (2014)

The reliability of Micro Electro Mechanical Switches (MEMS switches) still remains the main focus of attention, but only a few studies have dealt with their bouncing behavior. In this paper we investigate and compare contact bounces in three different types of electrostatic RF MEMS switches tested under similar hot switching conditions (5V/500μA). An instrumented test bench has been developed for monitoring and recording the contact closing voltage during several millions of cycles. The results point out that contact bounces are never observed during the early cycles with new components and may first appear after a few millions (or more) of cycles. They typically occur a few microseconds after contact closure and their duration is on the order of microseconds. Once a contact bounce appears, the number of contact bounces and their duration keep on increasing with the number of cycles. The origin of contact bounces is discussed in the paper and we show that this phenomenon is closely linked to the degradation of the electrical contacts that announces the failure of MEMS switches. Finally, the analysis of the experimental results reveals that contact bounces could be considered as a relevant indicator to predict the end of life of MEMS switches.
CD40L COSTIMULATORY PATHWAY IS REQUIRED FOR HOST SENSITIZATION AND ITS BLOCKADE ABROGATES ACCELERATED GRAFT REJECTION IN PRESENSITIZED HOSTS. (2000)

Kupiec-Weglinski, Jerzy W.1; Shen, Xiu-Da1; Gao, Feng1; Coito, Ana J.1; Sayegh, Mohamed H.2 Author Information
Spatial multiplexing over a line-of-sight millimeter-wave MIMO link: A two-channel hardware demonstration at 1.2Gbps over 41m range (2008)

This paper presents recent experimental results from a novel hardware prototype of an outdoor millimeter-wave line-ofsight (LOS) MIMO link. The system architecture establishes multiple parallel data channels using antenna element spacing derived from the principles of diffraction-limited optics. A millimeter-wave carrier frequency reduces the antenna array size to reasonably compact dimensions. In principle, this system architecture is scalable to larger one-dimensional and twodimensional arrays supporting data rates &gt;320Gbps. A twochannel LOS hardware prototype has been constructed and tested in an outdoor environment. The hardware prototype achieved bit error rates (BER) &lt;2x10 <sub>-6</sub> for two channels operating at 600Mbps each over a link range of 41m.
Bi-2212 and Y123 highly curved single-crystal-like objects: whiskers, bows and ring-like structures (2012)

High-temperature superconducting objects of Bi2Sr2CaCu2O8 and Y Ba2Cu3O7 highly curved in the ab-plane, such as curved/kinked whiskers, bows and ring-like structures, were obtained within a solid–liquid–solid (SLS) grass-like growth mechanism. As-grown objects are crystals with three-dimensional epitaxy similar to conventional single crystals: they can be viewed as crystal parts 'cut' from a conventional rectangular crystal. Between our curved objects and conventional crystals, whiskers or thin films there are some differences in the superconducting properties induced only by the shape factors and no new physics is observed. Some details of the growth mechanism are discussed, emphasizing curved-line formation.
Modeling ultrasound interaction with cancellous bone: investigation on the nature of the two compressional waves (2012)

Although ultrasound might be useful to assess bone quality, the mechanisms of ultrasound propagation in trabecular bone are still poorly understood. For example the propagation of a short pulse that leads, under some conditions, to two transmitted longitudinal waves, a fast and a slow one, is not well explained yet. The objective of this work is to further investigate the nature of these two longitudinal waves in simplified bone model media. The approach is to determine if the fast wave could result from a guided propagation in the solid matrix, the slow wave being due to the propagation in the surrounding fluid (bone marrow). In this context, we study the propagation of the coherent waves through simplified and customizable binary structures, obtained by a random addition of scatterers, with characteristic dimensions, material properties and anisotropy similar to those of bone. The benefit of such simplified structures is that ultrasound propagation in the entire medium can be theoretically studied from the properties of a single scatterer.
Using Mode Connectivity for Loss Landscape Analysis (2018)

Mode connectivity is a recently introduced frame- work that empirically establishes the connected- ness of minima by finding a high accuracy curve between two independently trained models. To investigate the limits of this setup, we examine the efficacy of this technique in extreme cases where the input models are trained or initialized differently. We find that the procedure is resilient to such changes. Given this finding, we propose using the framework for analyzing loss surfaces and training trajectories more generally, and in this direction, study SGD with cosine annealing and restarts (SGDR). We report that while SGDR moves over barriers in its trajectory, propositions claiming that it converges to and escapes from multiple local minima are not substantiated by our empirical results.
Criticality Uncertainty Dependence on Nuclear Data Library in Fast Molten Salt Reactors (2015)

To increase the sustainability of the nuclear fuel cycle, and increase security of nuclear energy, we have been inves- tigating Molten Salt Fast Reactors (MSFR) for transmutation of Minor actinoid (MA) isotopes. In the present work we describe the reactor physics analysis of a Th-TRU MSFR using a LiF-ThF4-TRUF3-fuel salt. We investigated the uncertainty of major reactor physics parameters using 3 sets of evaluated nuclear data: JENDL-4.0, JEFF-3.1.2, and ENDF/B-VII.1. The result of our work is that the spread in the multiplication factor is rather large between the sets of nuclear data, while other parameters are by and large the same. The uncertainties due to cross section covariance are large, with Th-232, U-233, and F-19 giving the most important contributions. The isotopic contributions to the uncertainties are quite different between the sets of nuclear data, giving a suspicion that the covariance data may is very different between the evaluations, and a review of the covariance data may be needed.
Oncogenic role of sFRP2 in P53-mutant osteosarcoma development via autocrine and paracrine mechanism (2018)

Abstract Osteosarcoma (OS), the most common primary bone tumor, is highly metastatic with high chemotherapeutic resistance and poor survival rates. Using induced pluripotent stem cells (iPSCs) generated from Li-Fraumeni syndrome (LFS) patients, we investigated an oncogenic role of secreted frizzled-related protein 2 (sFRP2) in P53 mutation-associated OS development. Interestingly, we found that high sFRP2 expression in OS patient samples correlates with poor survival. Systems-level analyses identified that expression of sFRP2 increases during LFS OS development and can induce angiogenesis. Ectopic sFRP2 overexpression in normal osteoblast precursors is sufficient to suppress normal osteoblast differentiation and to promote OS phenotypes through induction of oncogenic molecules such as FOXM1 and CYR61 in a β-catenin independent manner. Conversely, inhibition of sFRP2, FOXM1 or CYR61 represses the tumorigenic potential. In summary, these findings demonstrate the oncogenic role of sFRP2 in P53 mutation-associated OS development and that inhibition of sFRP2 is a potential therapeutic strategy.