gebhart/patrepeval huggingface dataset:
516 Caspase-8 regulated senescence as an immune checkpoint in T lymphocytes for adoptive cell therapy (2020)

<h3>Background</h3> The development of immunotherapies holds great promise for the treatment of refractory infections and cancer. Current approaches, although effective in many settings, have limitations that prevent their widespread use. Hence, several aspects require improvements, including the re-wiring of T-cell fates and function. T-cell dysfunction is central to the persistence of several chronic viral infections and the progression of malignancies. Upon activation, T cells can follow several paths of differentiation, leading to terminal effector differentiation and/or exhaustion which are widely recognized as dysfunctional features limiting human immune competence. Furthermore, dysfunctional features induced during laboratory-based manipulations of T-cell products prior to adoptive cell transfer has a determining effect on outcomes. Similarly, repeated antigen encounters after transfer in vivo favors the development of T-cell dysfunction. However, the nature and underlying mechanisms of T-cell dysfunction are still incompletely understood. <h3>Methods</h3> Combining genomics, phenotypic and functional analyses in various physiologically and clinically relevant settings, we investigated the key factors leading to T-cell dysfunction. Specifically, we evaluated the impact of repeated stimulations using CD3/CD28-coated beads or antigen-loaded dendritic cells in human T-cell long term cultures, and BCMA-expressing cells for anti-BCMA CAR T cells. We also examined mouse antigen-specific T cells during chronic lymphocytic choriomeningitis virus (LCMV) infection as well as datasets obtained from circulating T cells from acute myeloid leukemia (AML) patients. <h3>Results</h3> We identified telomere-independent cellular senescence as a central aspect of exhausted PD-1-expressing T cells following repeated stimulations. Mechanistically, it is associated the induction of p16INK4a. Additionally, we found that cellular senescence features are partly regulated by the activation of caspase-8, through a non-apoptotic function of this molecule not previously described in T cells. <h3>Conclusions</h3> We thus conclude that caspase-8 may regulate the balance between apoptosis and proliferation by protecting T cells from cellular senescence. Senescence-associated mechanisms may be seen as key players in T-cell dysfunction occurring following repeated stimulations and as such should be considered as novel immune checkpoints impeding the success of T-cell adoptive immunotherapy in humans. <h3>Ethics Approval</h3> This study was approved by the local Maisonneuve-Rosemont Hospital research ethics authorities and participants’ informed consent was obtained (CÉR2020-2141 and CÉR13030).
Ultrathin self-powered artificial skin (2014)

Herein, we introduce an ultra-thin self-powered artificial skin (SPAS) based on a piezoelectric nanogenerator, which harvests stored elastic deformation energy produced by the bending and stretching actions of the skin. This finding is an important step toward building a self-powered “smart skin”.
Parity-time-symmetry breaking in double-slab surface-plasmon-polariton waveguides (2015)

We theoretically demonstrate spontaneous PT-symmetry breaking behavior of surface-plasmon polaritons (SPP) in coupled double-slab (DS) waveguides. By virtue of a flat-top field at critical wavelength, the imaginary index of a DS-SPP mode can be controlled via changing the core thickness, while the real index is kept constant. Therefore, a waveguide coupler that consists of a pair of DS-SPP waveguides with different core thicknesses can represent a passive PT-symmetric system, which always maintains symmetry under a real potential. This set-up also represents a good opportunity to investigate the underlying physics of PT-symmetry breaking in non-Hermitian Hamiltonian systems.
Tuning the p-type doping of GaN over three orders of magnitude via efficient Mg doping during halide vapor phase epitaxy (2022)

The precise control of Mg concentration ([Mg]) in p-type GaN layers from 2.3 × 1016 to 2.0 × 1019 cm−3 was demonstrated by halide vapor phase epitaxy (HVPE) on n-type GaN (0001) freestanding substrates. [Mg] in GaN layers could be controlled well by varying the input partial pressure of MgCl2 formed by a chemical reaction between MgO solid and HCl gas under the thermodynamic equilibrium condition. In the sample with [Mg] of 2.0 × 1019 cm−3, a step-bunched surface was observed because the surface migration of Ga adatoms was enhanced by the surfactant effect of Mg atoms. The samples show high structural qualities determined from x-ray rocking curve measurements. The acceptor concentration was in good agreement with [Mg], indicating that almost all Mg atoms act as acceptors. The compensating donor concentrations in the samples were higher than the concentrations of Si, O, and C impurities. We also obtained the Mg acceptor level at a sufficiently low net acceptor concentration of 245 ± 2 meV. These results show that the HVPE method is promising for fabricating GaN vertical power devices, such as n-channel metal–oxide–semiconductor field-effect transistors.
Supplementary Figure 1 from An Improved Bioluminescence Resonance Energy Transfer Strategy for Imaging Intracellular Events in Single Cells and Living Subjects (2023)

Supplementary Figure 1 from An Improved Bioluminescence Resonance Energy Transfer Strategy for Imaging Intracellular Events in Single Cells and Living Subjects
Changing the subject in teacher education: Centering Indigenous, diasporic, and settler colonial relations (2013)

This paper suggests that, so long as we are focused on racism and colonialism as an exclusively Indigenous struggle, we fail to engage non-Indigenous peoples as “allies” of Indigenous education and sovereignty. My goal is to place a developing literature on settler-Indigenous alliances into a productive and more explicit dialogue with anti-oppressive educational theory and praxis. I address two critical questions: 1) How might we engage structurally privileged learners, some of whom are non-Indigenous peoples, to think about colonial dominance and racism in Canada? and 2) How might we work in coalition with privileged learners—and especially with new Canadians—to consider matters of land, citizenship, and colonization? I conclude by identifying a series of pedagogical practices aimed at the troubling of normalcy—an approach to teaching that disrupts the binary of self/Other. I consider briefly in turn the implications of this pedagogy for decolonization, the invigoration of teacher education programs in Canada, and the building and rejuvenation of relationships between Indigenous peoples and settler, diasporic, and migrant Indigenous populations.
P166 VEDOLIZUMAB MARKET ACCESS ANALYSIS OF HEALTH INSURANCE IBD POLICIES (2018)

risk or protection in each IBD gene in order to highlight opportune therapeutic targets. Results: We have already completed exomes of 13,000 IBD cases providing a high-resolution view of coding variation at each GWAS hit and demonstrated a convincing excess of rare exome signal collectively. The cases are drawn from individual substudies that focus on isolated populations (Ashkenazi, Finnish, French-Canadian), admixed populations and clinical extremes, each providing unique opportunities for discovery. Early findings include novel protective truncating variants, the complete allelic series (including unique founder population alleles), non-additive inheritance models at known genes such as NOD2, overlooked low-frequency coding variants that explain GWAS hits (PRDM1, NRIP1). The integration of low frequency and rare functional variants with GWAS is moving us much closer towards completion of the genetic architecture of IBD. Conclusion: Early analyses of the data have revealed novel non-coding associations in known IBD genes as well as coding variants that implicate genes at loci in which the 'causative' gene was unknown. Furthermore, initial results have suggested variation in enrichment of different processes across different ethnicities.
Matching drug transcriptional signatures to rare losses disrupting synaptic gene networks identifies known and novel candidate drugs for schizophrenia (2018)

ABSTRACT Schizophrenia is a complex neuropsychiatric disorder. The etiology is not fully understood, but genetics plays an important role. Pathway analysis of genetic variants have suggested a central role for neuronal synaptic processes. Currently available antipsychotic medications successfully control positive symptoms (hallucinations and delusions) largely by inhibiting the dopamine D2 receptors; however, these drugs have more limited impact on negative symptoms (social withdrawal, flat affections, anhedonia) and cognitive deterioration. Drug development efforts have focused on a wide range of neurotransmitter systems and other agents, with conflicting or inconclusive results. New drug development paradigms are needed. A recent analysis, using common variant association results to match drugs based on their transcriptional perturbation signature, found drugs enriched in known antipsychotics plus novel candidates. We followed a similar approach, but started our analysis from a synaptic gene network implicated by rare copy number loss variants. We found that a significant number of antipsychotics (p-value = 0.0002) and other psychoactive drugs (p-value = 0.0004) upregulate synaptic network genes. Based on global gene expression similarity, active drugs formed two main clusters: one with many known antipsychotics and antidepressants, the other with various drug categories including two nootropics. We specifically recommend further examination of nootropics with limited side effects ( meclofenoxate , piracetam and vinpocetine ) for combination therapy with antipsychotics to improve cognitive performance. Detailed experimental follow-up is required to further evaluate other candidate drugs lacking an official nervous system indication, although, for at least a few of these, psychoactive effects have been reported in the literature.
High power N-face GaN high electron mobility transistors grown by molecular beam epitaxy with optimization of AlN nucleation (2009)

We investigated the effect of AlN nucleation layers (NLs) on the structural and electrical properties of N-face GaN grown on C-face 6H-SiC substrates by plasma-assisted molecular beam epitaxy. The GaN films were characterized by secondary ion mass spectroscopy, x-ray diffraction, and transistor electrical measurements. It was found that an AlN NL grown in the N-rich regime was essential for realizing highly resistive GaN buffers. The mosaic structure of the GaN epilayers was systematically correlated with the AlN nucleation conditions. N-face high electron mobility transistors fabricated on these low-leakage buffers demonstrated the highest output power density at 4 GHz to date of 8.1 W/mm with an associated power-added efficiency of 54%.
Re-examination of Flat-Band Voltage Shift for High-k MOS Devices (2007)

We have systematically investigated the V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">FB</inf> shift in the case of the stacked bi-layer high-k dielectrics with paying attention to the high-k/IL-SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> interface. We demonstrate for the first time that V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">FB</inf> shifts are determined predominantly by the high-k/IL-SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> interface, while the gate/high-k interface plays little role.
Supplemental Figure 4 from Short- and Long-Term Effects of CDK4/6 Inhibition on Early-Stage Breast Cancer (2023)

&lt;p&gt;Palbociclib in the MIND Model&lt;/p&gt;
Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer (2011)

Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in select prostate tissues and cell lines using MethylPlex-next-generation sequencing (M-NGS). Hidden Markov model-based next-generation sequence analysis identified ∼68,000 methylated regions per sample. While global CpG island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation significantly increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively (P-value < 2 × 10(-16)). We found distinct patterns of promoter methylation around transcription start sites, where methylation occurred not only on the CGIs, but also on flanking regions and CGI sparse promoters. Among the 6691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer-specific, including numerous novel DMRs. A novel cancer-specific DMR in the WFDC2 promoter showed frequent methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization, and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion-positive and -negative cancers, and we confirmed this observation using pyrosequencing on a tissue panel. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression.
Ultra low energy arsenic implant limits on sheet resistance and junction depth (2002)

We have investigated the limits on sheet resistance, junction depth and abruptness using ultra low energy As implants and RTA annealing. We report on anomalous diffusion of 1 keV arsenic implants where the same RTA anneal can result in a deeper junction compared to a 5 keV implant of similar dose. A range of anneal times and temperatures in an RTA from 1020C to 1175C, including spike anneals, have been studied. The effect of junction abruptness in reducing the external resistance of the S/D extension for these 5 and 1 keV As implants has been investigated. We show that because of a trade off between junction depth and sheet resistance limits, 1 keV As implants and RTA anneals cannot meet the technology roadmap requirements beyond 2005, though the junction abruptness will meet the requirements till 2011.
Controlling the state of a motorway using express lanes (2015)

An algorithm for controlling the state of a motorway using express lanes is proposed. The aim of the control is to support the maximum speed on the express lanes by redistributing flows at the entrances. This is achieved with regard to the state of general purpose lanes and the condition of minimal growth of queues at the entrances. To describe the algorithm and its properties, the discretized hydrodynamic traffic flow model of Lighthill, Whitham, and Richards is used.
Rigorose Modellierung von Reaktivabsorptionsprozessen (2002)

Die Absorption von Gasen in flüssigen Waschmitteln mit begleitenden chemischen Reaktionen (reaktive Absorption) stellt eines der wichtigsten industriellen Verfahren dar. Vorteilhaft erweisen sich dabei Eigenschaften wie hohe Beladbarkeit der Waschflüssigkeit, Entfernung von gasförmigen Komponenten bis in den ppm-Bereich, moderate Betriebsdrücke und selektive Entfernung von Schadkomponenten. Die reaktive Absorption beruht auf einer Kombination verschiedener kinetisch kontrollierter Phänomene, wobei im Mittelpunkt die Wechselwirkungen zwischen chemischen Reaktionen und Stofftransport in Mehrkomponentengemischen stehen. Daher ist eine Beschreibung auf der Basis des Gleichgewichtsmodells häufig unzutreffend und eine kinetisch basierte Modellierung von entscheidender Bedeutung. In diesem Beitrag werden die Grundlagen der rigorosen Modellierung von Reaktivabsorptionsprozessen erläutert. Anhand mehrerer Fallbeispiele werden detaillierte Modelle validiert. Darüber hinaus werden für die Simulation unerlässliche Modellparameter wie Diffusionskoeffizienten oder Reaktionskinetiken diskutiert. Basierend auf gezielten Sensitivitätsanalysen kann eine Modellreduktion mit einhergehender Verkürzung der Rechenzeiten vorgenommen werden. Das somit erhaltene Modell wird erfolgreich bei der dynamischen Simulation angewendet. Dabei erscheint die Berücksichtigung von Filmreaktionen als unerlässlich. Rigorous Modeling of Reactive Absorption Processes Absorption of gases in liquid solutions accompanied by chemical reactions or reactive absorption, represents one of the most important industrial operations. The advantages of this process are enhanced solution capacity, low impurity concentrations up to the ppm-range, moderate operation pressure, and selective removal of contaminants. Reactive absorption is based on a combination of several kinetically controlled phenomena, the focus being on the coupling of chemical reactions and mass transfer in multicomponent mixtures. Therefore, a process description using the equilibrium concept is often insufficient and kinetic modeling is required. This paper describes the basics of rigorous modeling of reactive absorption processes. Several case studies are used in order to validate the models. In addition, a discussion of necessary model parameters, such as diffusion coefficients and reaction kinetics, is given. A reduced model with lower computation time is obtained via detailed sensitivity analysis. This model is successfully used in dynamic simulations. In this respect a proper consideration of the film reactions appears to be crucial.
Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage (2013)

OP9 is a yet-uncultivated bacterial lineage found in geothermal systems, petroleum reservoirs, anaerobic digesters and wastewater treatment facilities. Here we use single-cell and metagenome sequencing to obtain two distinct, nearly complete OP9 genomes, one constructed from single cells sorted from hot spring sediments and the other derived from binned metagenomic contigs from an in situ-enriched cellulolytic, thermophilic community. Phylogenomic analyses support the designation of OP9 as a candidate phylum for which we propose the name 'Atribacteria'. Although a plurality of predicted proteins is most similar to those from Firmicutes, the presence of key genes suggests a diderm cell envelope. Metabolic reconstruction from the core genome suggests an anaerobic lifestyle based on sugar fermentation by Embden-Meyerhof glycolysis with production of hydrogen, acetate and ethanol. Putative glycohydrolases and an endoglucanase may enable catabolism of (hemi)cellulose in thermal environments. This study lays a foundation for understanding the physiology and ecological role of the 'Atribacteria'.
Smoke Development and Suppression (2004)

No AccessPlastics Flammability HandbookJan 2004Smoke Development and SuppressionM. Le Bras, D. Price, S. BourbigotM. Le Bras, D. Price, S. Bourbigothttps://doi.org/10.3139/9783446436695.007SectionsAboutPDF ToolsAdd to FavoritesDownload CitationTrack CitationsCopy LTI LinkPDF key 'share (en)' returned an object instead of string.FacebookTwitterEmailLinkedIn previous chapternext chapter FiguresReferencesRelatedDetailsCited BySmoke Development and SuppressionJürgen Troitzsch, Edith Antonatus10 March 2021 2004Pages: 189-205Print ISBN: 978-3-446-21308-1eISBN: 978-3-446-43669-5 Copyright & Permissions© 2004 Carl Hanser Verlag GmbH & Co. KGPDF DownloadLoading ...
Rapid Identification of Mycobacteria to the Species Level Using INNO-LiPA Mycobacteria, a Reverse Hybridization Assay (2001)

INNO-LiPA Mycobacteria (LiPA; Innogenetics, Zwijnaarde, Belgium) is a kit for the simultaneous detection and identification of Mycobacterium species in culture and identifies the Mycobacterium tuberculosis complex, the M. avium complex (MAC), and the following Mycobacterium species: M. kansasii, M. avium, M. intracellulare, M. scrofulaceum, M. gordonae, M. xenopi, and the M. chelonae-M. abscessus complex. The assay, which targets the 16S-23S rRNA spacer region, was evaluated on 157 mycobacterial strains that had been identified by conventional techniques and PCR-restriction enzyme analysis of the hsp65 gene (PRA). Forty-seven reference strains consisting of 37 different species and 110 human clinical isolates were submitted to the test, and all were hybridized with the Mycobacterium genus probe (MYC) on the LiPA strip (100% sensitivity). Ninety-four isolates hybridized to their corresponding species- or complex-specific probes; only one isolate phenotypically identified as M. gordonae did not react with its specific probe (99.4% accuracy). Thirty-seven MAC strains were phenotypically identified to the complex level and to the species level by LiPA as M. avium (n = 18) or M. intracellulare (n = 7) or as belonging to the M. avium-M. intracellulare-M. scrofulaceum complex (n = 12). Of the last 12 strains, 10 had M. avium PRA patterns and 2 had M. intracellulare PRA patterns. Three isolates that had been identified as a single species by conventional identification were proven to be mixed cultures by the LiPA assay. The whole procedure can be performed in 1 working day, starting with the supernatant of a small amount of bacterial mass that had been treated by freezing and then boiling.
The Effects of Silica Nanoparticles in Toughened Epoxy Resins and Fiber-Reinforced Composites (Print-on-Demand) (2015)

Kurzzusammenfassung 7 3.2.5.References 83 3.3.Property improvements of fiber-reinforced composites based on epoxy resins modified with SiO2 nanoparticles 86 3.3.1.
Intensity clamping measurement of laser filaments in air at 400 and 800 nm (2010)

Molecular ${\mathrm{N}}_{2}$ fluorescence excited by laser filaments formed from laser pulses at 400 and 800 nm propagating in air is investigated. A comparison showed that, when excited with 400 nm photons, the fluorescence from the first negative band of ${\mathrm{N}}_{2}{}^{+}$ was enhanced by a factor of 6.4 while that of the second positive band of neutral ${\mathrm{N}}_{2}$ remained relatively constant. The enhanced ${\mathrm{N}}_{2}{}^{+}$ signal is attributed to a more efficient inner-shell multiphoton process (to the ${B}^{2}$${\ensuremath{\Sigma}}_{u}^{+}$ state) at 400 nm leaving a larger population of ${\mathrm{N}}_{2}{}^{+}$ ions in the excited state. On the other hand, the stable fluorescence from neutral ${\mathrm{N}}_{2}$ is due to the fact that the plasma density is more or less the same at both wavelengths. Using these results, a theoretical model is developed to determine the clamped intensities of the laser filaments at 400 and 800 nm.