gebhart/patrepeval huggingface dataset:
PfPK6, a novel cyclin-dependent kinase/mitogen-activated protein kinase-related protein kinase from Plasmodium falciparum (2000)

We have isolated a novel protein kinase cDNA, PfPK6, by differential display RT-PCR (DDRT-PCR) of mRNA obtained from different asexual erythrocytic stages of Plasmodium falciparum, which shows sequence similarity to both cyclin-dependent kinase (CDK) and mitogen-activated protein kinase (MAPK) family members. The 915 bp open reading frame (ORF) is interrupted by seven introns and encodes a 305-residue polypeptide with a predicted molecular mass of 35848 Da. Several cDNA clones with some of the intron sequences were isolated, indicating alternate or defective splicing of PfPK6 transcripts because the gene seems to be a single copy located on chromosome 13. The similarity of the catalytic domain of PfPK6 to those of CDK2 and MAPK is 57.3% and 49.6%, respectively. The signature PSTAIRE (single-letter amino acid codes) CDK motif is changed to SKCILRE in PfPK6. The TXY residues that are phosphorylated in MAPKs for their activation are T(173)PT in PfPK6. Three size classes of PfPK6 transcripts of 6.5, 2.0 and 1.1 kb are up-regulated during the transition of P. falciparum from ring to trophozoite. Western blot analysis suggested the expression of a 35 kDa polypeptide in trophozoites and schizonts. Immunofluorescence studies indicated both nuclear and cytoplasmic localization of PfPK6 in trophozoite, schizont and segmenter stages. In vitro, recombinant PfPK6 phosphorylated itself and also exogenous substrates, histone and the small subunit of the malarial ribonucleotide reductase (R2). The kinase activity of PfPK6 is sensitive to CDK inhibitors such as olomoucine and roscovitine. PfPK6 showed a preference for Mn(2+) over Mg(2+) ions as a cofactor. The Lys(38)-->Arg mutant is severely defective in its interaction with ATP and bivalent cations and somewhat defective in catalytic rate for R2 phosphorylation.
Color Centers Formation in Lithium Fluoride Nanocubes Doped with Different Elements (2013)

Nanocrystalline cubes of pure and doped LiF material were fabricated. They were doped with Cu, Ag, Dy, Tb, and Eu and studied for their PL properties. Shape of the obtained nanocubes was found to be modified by introducing dopants into the host of LiF. The crystallinity was also decreased by increasing the concentration of these dopants (i.e., Eu and Tb). These impurities could induce exothermic peaks at around 250°C in the measured DSC curves. Moreover, incorporating such impurities into the host of LiF was found to enhance intensity of the broad band at 370–550 nm that was observed in the pure one. Extra sharp emissions were also observed in Eu and Tb doped samples. These results showed that the active color centers created in pure LiF nanocubes can be enriched/enhanced by these impurities, mainly Eu and Tb. This implies that these nanocubes might be useful in the development of optical devices and advanced color center laser.
M-Phase High-Q Bandpass Filters (2013)

The four-phase high-Q bandpass filter introduced in the previous chapter can integrate external SAW filters in many narrowband RF applications such as cellular. In addition, the previous chapter described the design of a SAW-less quad-band GSM receiver integrated as part of 2.5G SoC in which the receiver uses four-phase on-chip high-Q bandpass filters to handle strong out-of-band blockers. The receiver passes all 3G blocker specifications with some margin, except for folding blockers that are located at the third, fifth, and other odd-order harmonics of the LO, where exceptions must be taken. Although useful in cellular receivers or other narrowband applications, for wideband applications such as TV reception, the four-phase filter is not a proper choice because of the blocker folding issue at the third, fifth, and all other odd harmonics. Therefore, the four-phase high-Q BPF must evolve further to move the closest folding components up to the higher frequencies that are much larger than the third harmonic of the clock. In this chapter, we will see that an M-phase high-Q bandpass filter is the solution [60, 67–69], which shifts the closest folding frequency components to the (M − 1)th harmonic.
The Synthesis and Structure of Stibaindoles (1990)

A simple route to stibaindoles, reaction (a), leads to monomeric 1-chloro- and 1-phenylstibaindoles in yields of 71–86%. Interest in heterocyclic compounds of heavy main-group elements has increased dramatically in recent years owing to their uses in materials science. Y,Z = H, OMe, C4H4
Crack formation in surface layers with strain gradients (2007)

Abstract The problem of crack formation in surface layers where a linear profile of elastic strain prevails through the thickness of a layer is investigated. Such strain gradients can be generated, for example, in graded alloy semiconductor layers or due to specific stress relaxation mechanisms in lattice mismatched layers or previously unanticipated dislocation-related strain gradients. The operation of the relaxation mechanisms related to threading dislocation inclination and leading to the strain gradients in nominally compressed Al x Ga 1 – x N layers grown on buffer layers with smaller lattice constants is discussed. A fracture mechanics model is developed for the calculation of the stress intensity factor of mode I cracks initiated at the surface of the layer exhibiting a linear strain dependence. The critical layer thickness for crack formation in such a gradient elastic field has been found in the framework of this fracture mechanics model. Results of the modeling are compared with experimental observations of crack onset in nominally compressed layers of Al x Ga 1− x N semiconductors. Good agreement between the model predictions and the experimental data is found.
Guest editorial: Selected papers from IEEE ICCC'12 (2013)

The papers in this special issue were presetned at the First IEEE International Conference on Communications in China (ICCC'12) that was held in Beijing, China, 15-17 August, 2012.
Sphericity and symmetry breaking in the formation of Frank–Kasper phases from one component materials (2014)

Frank-Kasper phases are tetrahedrally packed structures occurring in numerous materials, from elements to intermetallics to self-assembled soft materials. They exhibit complex manifolds of Wigner-Seitz cells with many-faceted polyhedra, forming an important bridge between the simple close-packed periodic and quasiperiodic crystals. The recent discovery of the Frank-Kasper σ-phase in diblock and tetrablock polymers stimulated the experiments reported here on a poly(isoprene-b-lactide) diblock copolymer melt. Analysis of small-angle X-ray scattering and mechanical spectroscopy exposes an undiscovered competition between the tendency to form self-assembled particles with spherical symmetry, and the necessity to fill space at uniform density within the framework imposed by the lattice. We thus deduce surprising analogies between the symmetry breaking at the body-centered cubic phase to σ-phase transition in diblock copolymers, mediated by exchange of mass, and the symmetry breaking in certain metals and alloys (such as the elements Mn and U), mediated by exchange of charge. Similar connections are made between the role of sphericity in real space for polymer systems, and the role of sphericity in reciprocal space for metallic systems such as intermetallic compounds and alloys. These findings establish new links between disparate materials classes, provide opportunities to improve the understanding of complex crystallization by building on synergies between hard and soft matter, and, perhaps most significantly, challenge the view that the symmetry breaking required to form reduced symmetry structures (possibly even quasiperiodic crystals) requires particles with multiple predetermined shapes and/or sizes.
Adaptation Across Extreme Variations using Unlabeled Domain Bridges (2019)

We tackle an unsupervised domain adaptation problem for which the domain discrepancy between labeled source and unlabeled target domains is large, due to many factors of inter and intra-domain variation. While deep domain adaptation methods have been realized by reducing the domain discrepancy, these are difficult to apply when domains are significantly unalike. In this work, we propose to decompose domain discrepancy into multiple but smaller, and thus easier to minimize, discrepancies by introducing unlabeled bridging domains that connect the source and target domains. We realize our proposal through an extension of the domain adversarial neural network with multiple discriminators, each of which accounts for reducing discrepancies between unlabeled (bridge, target) domains and a mix of all precedent domains including source. We validate the effectiveness of our method on several adaptation tasks including object recognition and semantic segmentation.
Bile Acid Profile and its Changes in Response to Cefoperazone Treatment in MR1 Deficient Mice (2020)

Mucosal associated invariant T-cells (MAIT cells) are activated following recognition of bacterial antigens (riboflavin intermediates) presented on major histocompatibility complex class I-related molecule (MR1). Our previous study showed that MR1<sup>-/-</sup> knock-out (KO) mice (lacking MAIT cells) harbor a unique microbiota that is resistant to antibiotic disruption and <i>Clostridioides</i> <i>difficile</i> colonization. While we have characterized the microbiota of this mouse strain, changes in global metabolic activity in these KO mice have not been assessed. Here, LC/MS-based untargeted metabolomics was applied to investigate the differences in the metabolome, specifically in the bile acid (BA) profile of wild-type (WT) and MR1<sup>-/-</sup> KO mice, as well as how antibiotics change these profiles. BA changes were evaluated in the intestinal content, cecum content, and stool samples from MR1<sup>-/-</sup> mice and WT mice treated with cefoperazone (Cef). Fecal pellets were collected daily and both intestinal and cecal contents were harvested at predetermined endpoints on day 0 (D0), day 1 (D1), day 3 (D3), and day 5 (D5). KO mice exhibited no changes in 6-hydroxymethyl-8-D-ribityllumazine (rRL-6-CH2OH; an MR1-restricted riboflavin derivative) in the stool samples at either time point vs. D0, while WT mice showed significant decreases in rRL-6-CH2OH in the stool samples on all treatment days vs. D0. Metabolomics analysis from cecal and stool samples showed that KO mice had more total BA intensity (KO/WT = ~1.7 and ~3.3 fold higher) than that from WT mice prior to Cef treatment, while the fold change difference (KO/WT = ~4.5 and ~4.4 fold) increased after five days of Cef treatment. Both KO and WT mice showed decreases in total BA intensity in response to Cef treatment, however, less dramatic decreases were present in KO vs. WT mice. Increases in taurocholic acid (TCA) intensity and decreases in deoxycholic acid (DCA) intensity in the stool samples from WT mice were associated with the depletion of certain gut bacteria, which was consistent with the previously reported microbiome data. Furthermore, the non-detected TCA and relatively higher DCA intensity in the KO mice might be related to <i>Clostridioides</i> <i>difficile</i> infection resistance, although this needs further investigation.
A practical synthesis of ATB-[2-3H] BMPA, a photolabelling reagent for exofacial glucose transporters (1997)

Major improvements in the efficiency of ATB-[2-3H]BMPA synthesis were achieved by using 1,3-dichloro-2-propanone O-benzyloxime (6) as the linking reagent. © 1997 John Wiley & Sons, Ltd.
Taccalonolide Binding to Tubulin Imparts Microtubule Stability and Potent In Vivo Activity (2013)

The taccalonolides are highly acetylated steroids that stabilize cellular microtubules and overcome multiple mechanisms of taxane resistance. Recently, two potent taccalonolides, AF and AJ, were identified that bind to tubulin directly and enhance microtubule polymerization. Extensive studies were conducted to characterize these new taccalonolides. AF and AJ caused aberrant mitotic spindles and bundling of interphase microtubules that differed from the effects of either paclitaxel or laulimalide. AJ also distinctly affected microtubule polymerization in that it enhanced the rate and extent of polymerization in the absence of any noticeable effect on microtubule nucleation. In addition, the resulting microtubules were found to be profoundly cold stable. These data, along with studies showing synergistic antiproliferative effects between AJ and either paclitaxel or laulimalide, suggest a distinct binding site. Direct binding studies demonstrated that AJ could not be displaced from microtubules by paclitaxel, laulimalide, or denaturing conditions, suggesting irreversible binding of AJ to microtubules. Mass spectrometry confirmed a covalent interaction of AJ with a peptide of β-tubulin containing the cyclostreptin-binding sites. Importantly, AJ imparts strong inter-protofilament stability in a manner different from other microtubule stabilizers that covalently bind to tubulin, consistent with the distinct effects of the taccalonolides as compared with other stabilizers. AF was found to be a potent and effective antitumor agent that caused tumor regression in the MDA-MB-231 breast cancer xenograft model. The antitumor efficacy of some taccalonolides, which stabilize microtubules in a manner different from other microtubule stabilizers, provides the impetus to explore the therapeutic potential of this site.
Role of Air in Growth and Production of Toxic Shock Syndrome Toxin 1 by Staphylococcus aureus in Experimental Cotton and Rayon Tampons (1989)

Rayon and cotton fibers of the type used in the manufacture of tampons were extracted for 6 hours in isopropyl alcohol in a soxhlet apparatus to remove all finishes from the fiber surface. The fibers were used to produce experimental tampons of commercial design. Using a syringe method, the tampons were saturated with diluted staphylococci in brain-heart infusion medium and incubated at 37 degrees C. Spent medium was expressed from the tampons and analyzed for growth of staphylococci and production of toxic shock syndrome toxin 1 (TSST-1). Results revealed no statistical difference in the production of TSST-1 by cells grown in rayon or cotton. However, a significant increase in TSST-1 production was observed in tampon cultures when compared with medium controls. When similar experiments were performed with tampons saturated with nitrogen, a significant decrease in TSST-1 production was observed when compared with air-saturated tampons. The results indicate that the oxygen normally present in tampons plays a significant role in modulating the production of TSST-1.
An open-source environmental chamber for materials-stability testing using an optical proxy (2023)

Designs for an open source environmental chamber for stability testing of metal halide perovskites and other materials using optical degradation fingerprints. The design suite can accommodate bulk samples, thin films or full photovoltaic devices.
Exciton transfer and propagation in carbon nanotubes studied by near‐field optical microscopy (2008)

Abstract We studied transfer and propagation of excitons in single semiconducting carbon nanotubes using high resolution tip‐enhanced near‐field photoluminescence microscopy. Exciton energy transfer is found to occur from a larger band gap nanotube to a smaller band gap nanotube. Efficient transfer however is found to be limited to a few nanometers because of competing fast non‐radiative relaxation and can be explained in terms of electromagnetic near‐field coupling. Towards the end of a nanotube, photoluminescence decay is observed on a length scale of 50–90 nm which is attributed to exciton propagation followed by additional non‐radiative relaxation at the nanotube end. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Comparative analysis of influence of non-linear distortion in power amplifier in wireless communications systems with single and multiple orthogonal carrier frequencies (2010)

The paper considers the impact of power amplifier’s non-linearity on wireless communication systems with a single carrier (SC) and multiple orthogonal subcarriers (OFDM). Detailed analysis is provided for the impact of non-linearity on generation accuracy of the transmitted signal and the shape of the output spectrum. It is demonstrated that in order to meet standard requirements to the signal generation accuracy and the spectrum mask compliance, a SC system typically has a moderate gain of 1–1.5 dB in comparison with an OFDM system. It is concluded that a decision on the modulation type selection for a wireless communication system should include additional factors beyond the power amplifier non-linearity impact analysis.
Contribution of Modeling Tools to Aeronautic NDT (2005)

The evaluation and adaptation of NDT simulation tools has been investigated for several years at EADS Corporate Research Center and has covered till now a number of applications. General simulation objectives, the modeling contribution to NDT domain and the deployment of NDT simulation tools in the aeronautical domain are discussed and illustrated on applications.
Supplementary Table 2 from Exploiting the Mutanome for Tumor Vaccination (2023)

&lt;p&gt;XLS file - 56K&lt;/p&gt;
Testing Models of Early Infant Habituation: A Reply to Slater and Morison. (1986)

Dannemiller and Banks (1983) proposed a model of habituation during early in fancy that was based on the selective adaptation of feature detectors. In reply, Slater and Morison (1985) presented evidence that they claimed argued against such a model. The Slater and Morison evidence is weighed against the five cri teria that Dannemiller and Banks originally listed for rejecting the model and it is concluded that the model has failed to receive adequate testing on four of these five criteria. One result presented by Slater and Morison, however, argues that the simple selective adaptation model may eventually have to be rejected as an adequate model of habituation and recovery effects during early infancy.
Development of third generation anti-EGFRvIII chimeric T cells and EGFRvIII-expressing artificial antigen presenting cells for adoptive cell therapy for glioma (2018)

Glioblastoma multiforme (GBM) is the most aggressive and deadly form of adult brain cancer. Despite of many attempts to identify potential therapies for this disease, including promising cancer immunotherapy approaches, it remains incurable. To address the need of improved persistence, expansion, and optimal antitumor activity of T-cells in the glioma milieu, we have developed an EGFRvIII-specific third generation (G3-EGFRvIII) chimeric antigen receptor (CAR) that expresses both co-stimulatory factors CD28 and OX40 (MR1-CD8TM-CD28-OX40-CD3ζ). To enhance ex vivo target specific activation and optimize T-cell culturing conditions, we generated artificial antigen presenting cell lines (aAPC) expressing the extracellular and transmembrane domain of EGFRvIII (EGFRVIIIΔ654) with costimulatory molecules including CD32, CD80 and 4-1BBL (EGFRVIIIΔ654 aAPC and CD32-80-137L-EGFRVIIIΔ654 aAPC). We demonstrate that the highest cell growth was achieved when G3-EGFRvIII CAR T-cells were cocultured with both co-stimulatory aAPCs and with exposure to EGFRvIII (CD32-80-137L-EGFRVIIIΔ654 aAPCs) in culturing periods of three to six weeks. G3-EGFRvIII CAR T-cells showed an increased level of IFN-γ when cocultured with CD32-80-137L-EGFRVIIIΔ654 aAPCs. Evaluation of G3-EGFRvIII CAR T-cells in an orthotropic human glioma xenograft model demonstrated a prolonged survival of G3-EGFRvIII CAR treated mice compared to control mice. Importantly, we observed survival of G3-EGFRvIII CAR T-cells within the tumor as long as 90 days after implantation in low-dose and single administration, accompanied by a marked tumor stroma demolition. These findings suggest that G3-EGFRvIII CAR cocultured with CD32-80-137L-EGFRVIIIΔ654 aAPCs warrants itself as a potential anti-tumor therapy strategy for glioblastoma.
Development of (quinolinyl)amido-based pincer palladium complexes: a robust and phosphine-free catalyst system for C–H arylation of benzothiazoles (2017)

Well-defined (quinolinyl)amido-pincer palladium complexes are developed and employed for the catalytic C–H bond arylation of benzothiazoles with aryl iodides, which can be recycled and reused for several cycles.
Superficial dosimetry imaging based on Čerenkov emission for external beam radiotherapy with megavoltage x‐ray beam (2013)

This study indicates that Čerenkov emission imaging might provide a valuable way to superficial dosimetry imaging in real time for external beam radiotherapy with megavoltage x-ray beams.
Exploring the performance benefits of end-to-end path switching (2004)

No abstract available.
Cranial bone apposition and ingrowth in a porous nickel–titanium implant (1995)

A 5 x 5 x 1-mm uncoated porous nickel-titanium (nitinol) implant was placed 4 mm to either side of the midsection of the frontal bone and 4 mm anterior to the coronal suture of the cranial bone of New Zealand White rabbits. In the other frontal location, a 5 x 5 x 1-mm coralline hydroxyapatite (HA) (Interpore 200, a well-known craniofacial implant material) implant was fitted. Rabbits were killed at each of three postsurgical intervals (2, 6, and 12 weeks), and the implants were evaluated for gross biocompatibility, bony contact, and ingrowth. No adjacent macrophage cells were observed for either implant type, and overlaying soft tissues and connective tissues readily adhered to the implants even after 2 weeks. Both materials made bone contact with the surrounding cranial hard tissue, and percent ingrowth increased with surgical recovery time. Measurements of microhardness and bone histologic parameters indicated that bone in contact with and grown into the implants was similar in properties to the surrounding cranial bone. Porous nitinol implants therefore appear to allow for significant cranial bone ingrowth after as few as 12 weeks, and thus nitinol appears to be suitable for craniofacial applications. Compared to HA, the nitinol implants demonstrated a trend for less total apposition and more total ingrowth after 6 and 12 weeks of implantation.
Micro- and Macrothermal Analysis of a Bioactive Surface-Engineered Polymer Formed by Physical Entrapment of Poly(ethylene glycol) into Poly(lactic acid) (2003)

Poly(dl-lactic acid) (PLA) materials have been surface engineered via an entrapment method to present high densities of poly(ethylene glycol) (PEG) to control protein adsorption. The resultant change in physical properties was characterized on the surface and bulk of the entrapped PEG/PLA system through microthermal analysis by scanning thermal microscopy (SThM). It was found that the inclusion of the PEG significantly reduced the glass transition temperature (Tg) of the modified PLA and that the magnitude of this Tg reduction remained unchanged throughout the PEG-modified PLA regions. This suggests that the entrapped PEG was in a miscible state with, and homogeneously distributed into, the PLA. This finding was confirmed using macrothermal analysis by differential scanning calorimetry. The amount of the PEG entrapped in the modified region was calculated to be 18 wt %. In addition, a sharp contrast was observed in the SThM thermal conductivity data on cross-sectioned samples designed to reveal the boundary between the modified and unmodified regions of the PLA. This unambiguously demonstrates that the physical properties of the PLA surface and near surface have been modified by the entrapment of PEG. We propose that the observed thermal contrast results from the temperature dependency of thermal conductivity (λ) of the parent PLA being altered by the inclusion of miscible PEG.