gebhart/patrepeval huggingface dataset:
Abstract 3512: Expanded human regulatory iNKT cells exhibit direct cytotoxicity against hematolymphoid tumor targets (2012)

Abstract CD1d-restricted invariant natural killer T (iNKT) cells are rare but potent innate regulatory cells capable of immune modulation via robust production of Th1/Th2 cytokines, as well as tumor immunosurveillance via direct cytotoxicity. Protocols to expand iNKT cells and augment their cytotoxicity would broaden their application in allogeneic transplantation and adjuvant anti-tumor immunotherapy. We have optimized a protocol for ex vivo expansion of highly purified human CD3+CD4negVα24+ iNKT cells from human peripheral blood mononuclear cells (PBMC). PBMCs were stimulated with an iNKT-specific glycolipid (α-GalCer), recombinant IL-2 and IL-7 and sorted to &amp;gt; 98% purity at day 7. Sorted iNKT cells were further expanded in the presence of irradiated allogeneic PBMCs, Vα24-specific TCR stimulation, and low-dose IL-2 and IL-7 for 21 days. This results in roughly 10^3-fold expansion, with peak yields of at day 21-28 of expansion (range 1.5 x 10^5 - 10.6 x 10^6 iNKT cells from 1 x 10^8 - 3.5 x 10^8 starting PBMC). At 28 days, these iNKT cells secrete high levels of IL-13, TNF-α, GM-CSF, and IL-4, moderate IL-2 and IFN-γ in anti-CD2/CD3/CD28 bead-stimulated Luminex supernatant assay. Day 28 expanded iNKT cells are dose-dependent suppressors of sorted autologous CD3+CD8+ effector T cells in 72-hr mixed leukocyte reaction (MLR). Anti-CD2/CD3/CD28 activation of these iNKT cells induced expression of high levels of key cytolytic effector molecules, including granzyme B. We therefore measured cytotoxicity of activated day 28 iNKT cells against various hematolymphoid tumor targets following co-incubation of iNKT cells versus control effector populations with firefly luciferase-transduced RS4:11 and Nalm6 (B-ALL), U937 (monocytic), and K562 (CML) targets. iNKT cell effectors (E) demonstrated dose-dependent cytotoxicity against B-lymphoid tumor targets (T) (e.g.: Nalm6: 37.7% at E:T 2:1, 17.7% at E:T 1:1, 7.7% at E:T 0.5:1), with no significant cytotoxicity against myeloid targets (e.g.: K562: 11.8% at E:T 2:1, 6.7 at E:T 1:1, 1.8 at E:T 0.5:1). Our results indicate that human iNKT cells expressing high levels of Th2 and regulatory cytokines can be potently expanded ex vivo and manifest cytotoxicity against B-ALL targets, supporting their potential application in tailored immunotherapy in the pre- and post-transplant setting. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3512. doi:1538-7445.AM2012-3512
An Efficient Time-Frequency Representation for Parametric-Based Audio Object Coding (2011)

Object-based audio coding can provide new music applications with interactivity. To efficiently compress a lot of target audio objects, a subband-based parametric coding scheme has been adopted for MPEG spatial audio object coding. In this letter, the time-frequency (T/F) subband analysis structure is investigated. A reconfigured T/F structure is also proposed to enhance the generating performance of sound scenes such as ‘karaoke’ and ‘solo’ play in interactive music scenarios. From the experimental results, it was confirmed that the proposed scheme remarkably improves the SNR and sound quality.
Geometric Calibration of Head-Mounted Displays and its Effects on Distance Estimation (2012)

Head-mounted displays (HMDs) allow users to observe virtual environments (VEs) from an egocentric perspective. However, several experiments have provided evidence that egocentric distances are perceived as compressed in VEs relative to the real world. Recent experiments suggest that the virtual view frustum set for rendering the VE has an essential impact on the user's estimation of distances. In this article we analyze if distance estimation can be improved by calibrating the view frustum for a given HMD and user. Unfortunately, in an immersive virtual reality (VR) environment, a full per user calibration is not trivial and manual per user adjustment often leads to mini- or magnification of the scene. Therefore, we propose a novel per user calibration approach with optical see-through displays commonly used in augmented reality (AR). This calibration takes advantage of a geometric scheme based on 2D point - 3D line correspondences, which can be used intuitively by inexperienced users and requires less than a minute to complete. The required user interaction is based on taking aim at a distant target marker with a close marker, which ensures non-planar measurements covering a large area of the interaction space while also reducing the number of required measurements to five. We found the tendency that a calibrated view frustum reduced the average distance underestimation of users in an immersive VR environment, but even the correctly calibrated view frustum could not entirely compensate for the distance underestimation effects.
Tratamiento superficial por láser de recubrimientos por proyección por plasma de ZrO2 8 % Y2O3 (2005)

Un equipo láser continuo de CO2, con potencia nominal de 1 kW, se utilizó para sellar la superficie revestida con ZrO2 8 % Y2O3 por proyección por plasma sobre un substrato de acero AISI 1045. Se investigaron los efectos del tratamiento de fusión con láser sobre la microestrutura y la resistencia a la corrosión del recubrimiento. La resistencia a la corrosión se analizó por medidas electroquímicas en una solución de NaCl al 3 %. Las micrografias mostraron que la superficie del revestimiento presentó varias grietas pequeñas, sin embargo, no fueron observados poros. La microestructura de la capa sellada presentó una estructura en forma de columnas con crecimiento perpendicular a la superficie libre. El sellado a láser mejora la resistencia a la corrosión de los recubrimientos y aumenta la microdureza.
Surface Composition Effects in Electrocatalysis:  Kinetics of Oxygen Reduction on Well-Defined Pt3Ni and Pt3Co Alloy Surfaces (2002)

The oxygen reduction reaction (ORR) has been studied on polycrystalline Pt3Ni and Pt3Co alloys in acid electrolytes using the rotating ring disk electrode (RRDE) method. Preparation and characterization of alloy surfaces were performed in ultrahigh vacuum (UHV). Clearly defined surface composition was determined via low-energy ion-scattering (LEIS) spectroscopy. Polycrystalline bulk alloys of Pt3Ni and Pt3Co were prepared in UHV having two different surface compositions: one with 75% Pt and the other with 100% Pt. The latter we call a “Pt-skin” structure and is produced by an exchange of Pt and Co in the first two layers. The base voltammetry in 0.1 M HClO4 solution of the 75% Pt alloy surface indicated a decrease of Hupd pseudocapacitance (ca. 30−40 μC/cm2) consistent with the surface composition determined in UHV. With the exception of the “Pt-skin” surface on Pt3Ni, all the alloy electrodes exhibited stable i−E curves with repeated cycling between 0.05 and 1.0 V at all temperatures. Activities of Pt-alloys for the ORR were compared to the polycrystalline Pt in 0.5 M H2SO4 and 0.1 M HClO4 electrolytes in the temperature range of 293 < T < 333 K. It was found that the order of activity is dependent on the nature of anions of supporting electrolytes: in H2SO4 the activity increased in the order Pt3Ni > Pt3Co > Pt; in HClO4, however, the order of activities at 333 K was “Pt-skin” > Pt3Co > Pt3Ni > Pt. The catalytic enhancement was greater in 0.1 M HClO4 than in 0.5 M H2SO4, with the maximum enhancement observed for the “Pt-skin” on Pt3Co in 0.1 M HClO4 being 3−4 times that for pure Pt. Catalytic enhancement of the ORR on Pt3Ni and Pt3Co vs Pt was attributed to the inhibition of Pt−OHad formation on Pt sites surrounded by “oxide” covered Ni and Co atoms beyond 0.8 V. Kinetic analyses of RRDE data revealed that kinetic parameters for the ORR and the production of H2O2 on the Pt3Ni, Pt3Co, and “Pt-skin” alloys are the same as on pure Pt: reaction order, m = 1, two identical Tafel slopes in HClO4, and a single Tafel slope in H2SO4, apparent activation energy ≈ 21−25 kJ/mol. The fact that essentially the same kinetic parameters are assessed from the analysis of the ORR data on all three surfaces implies that the reaction mechanism on Pt3Ni and Pt3Co alloy surfaces is the same as one proposed for pure Pt, i.e., a “series” 4e- reduction pathway.
Functional and applied aspects of the DOWNY MILDEW RESISTANT 1 and 6 genes in Arabidopsis (2012)

Plants are constantly exposed to micro-organisms including pathogens. They are resistant to the vast majority of potential pathogens due to a multilayered defence system. Plant disease susceptibility, on the other hand, is determined by virulence factors from the pathogen, their targets in the host and the successful suppression of plant defences. To gain insight into the molecular mechanisms underlying disease susceptibility, we study the interaction between the oomycete pathogen Hyaloperonospora arabidopsidis, causing downy mildew, and its host Arabidopsis. A forward genetic screen resulted in several downy mildew resistant (dmr) Arabidopsis mutants of which dmr1 and dmr6 were further characterized. Chapter 2 described the cloning of DMR1 that encodes for homoserine kinase (HSK), a key enzyme in the Aspartate pathway. Mutation of HSK in the dmr1 mutant resulted in accumulation of the amino acid homoserine. Exogenous application of homoserine proved to be sufficient to induce resistance against H. arabidopsidis. No known defence-related pathways were associated with the observed resistance, indicating homoserine accumulation triggers a novel form of plant resistance. HSK was further analysed in chapter 3 where a reverse genetics approach (TILLING) resulted in additional hsk alleles. One mutant accumulated homoserine and is resistant to downy mildew infection. Another mutant did not develop beyond the seedling stage suggesting HSK is an essential plant gene. We also identified HSK orthologs for a number of crop species making them candidates for mutagenesis to further explore dmr1-mediated resistance. Chapter 4 described the characterization of the DMR6 gene, coding for a 2-oxoglutarate Fe(II)-dependent oxygenase. Absence of a functional DMR6 gene resulted in resistance that requires a functional salicylic acid pathway. On the other hand, overexpression of DMR6 resulted in enhanced susceptibility towards biotrophic pathogens indicating DMR6 acts as negative regulator of defence. A 3-dimensional model was constructed of the DMR6 protein that facilitated in the identification of important residues in the substrate pocket. Chapter 5 described the family of DMR6-like oxygenases (DLOs) and their role in plant defence. Two Arabidopsis DLOs, identified through phylogenetic analysis, have a similar molecular function as DMR6. Also, we have identified DMR6 orthologs in several crop species that are able to complement the dmr6-mediated resistance. A DMR6/DLO-specific motif is identified that could be used for the identification of crop DMR6 or DLO proteins. The presence of this conserved motif could determine the specificity for a particular substrate that is shared between different species.
Tumor-Associated Lymphocytes and Increased FoxP3+ Regulatory T Cell Frequency Correlate with More Aggressive Papillary Thyroid Cancer (2010)

TAL and high Treg frequency in primary thyroid tumors correlates with more aggressive disease. Future prospective studies may identify Treg frequency as a predictive factor in PTC, and the suppressive effects of Treg should be considered in the design of immune-based therapies.
Identification and characterization of genes determining receptor binding and pilus length of Escherichia coli type 1 pili (1987)

We describe the identification and characterization of two genes and their gene products responsible for determining receptor binding and pilus length in type 1-piliated Escherichia coli. One gene, pilE, conferred the ability of piliated cells to agglutinate guinea pig erythrocytes. The other gene, pilF, determined pilus length, in that mutants having lesions in pilF had very long pili. The two genes were detected after Tn5 mutagenesis of a cloned segment of DNA that normally complemented a pilE lesion in the chromosome. Thus, lesions in pilE or pilF on the cloned segment resulted in mutants having the PilE- phenotype (piliated but unable to agglutinate erythrocytes). Introduction of the plasmid-encoded mutant alleles of pilE and pilF into the chromosome followed by electron microscopic examination of the mutants showed that only lesions in pilF conferred the striking increase in pilus length. Mutations in pilF could be complemented in trans by the original cloned segment to produce cells with parental-length pili. Minicell transcription and translation of the cloned pilE and pilF genes having representative Tn5 insertion mutations showed that the pilE gene product was a protein of ca. 31 kilodaltons and that the pilF gene product was a protein of ca. 18 kilodaltons. We believe that the pilF gene product may act as a competitive inhibitor of pilus polymerization. Thus, pilus length may be controlled by the ratio of pilin to pilF gene product present within the cell.
Electroabsorption spectroscopy of luminescent and nonluminescent π-conjugated polymers (1997)

We have measured the quadratic electroabsorption (EA) spectrum of a variety of soluble luminescent and nonluminescent \ensuremath{\pi}-conjugated polymer films in the spectral range of 1.5--4.5 eV. The luminescent polymers include MEH and DOO derivatives of poly(phenylene-vinylene), poly(phenylene ethylene), and polythiophene; the nonluminescent polymers include poly(diethynyl silane) and monosubstituted polyacetylene. All EA spectra show a Stark shift of the low-lying odd-parity exciton ${(1B}_{u})$ and imply the presence of phonon sidebands. There are also higher-energy bands due to transfer of oscillator strength to even-parity exciton states ${(A}_{g}),$ the strongest of which ${(mA}_{g})$ is located at an energy about 1.3 times that of the ${1B}_{u}$ exciton in both luminescent and nonluminescent polymers; in the luminescent polymers the EA spectra also show a second prominent ${A}_{g}$ state ${(kA}_{g})$ at an energy of about 1.6 times that of the ${1B}_{u}.$ We have successfully fitted the EA spectra by calculating the imaginary part of the third order optical susceptibility, $\mathrm{Im}[{\ensuremath{\chi}}^{3}(\ensuremath{-}\ensuremath{\omega};\ensuremath{\omega},0,0)],$ using a summation over states model dominated by the ground state, the ${1B}_{u}$ exciton, two strongly coupled ${A}_{g}$ states (${\mathrm{mA}}_{g}$ and ${\mathrm{kA}}_{g}$), and their most strongly coupled vibrations, using Frank-Condon overlap integrals. A distribution of conjugation lengths, which results in a distribution of excited state energies, was also incorporated into the model. The decomposition of the EA spectra due to the conjugation length distribution was then used to calculate the ${1B}_{u}$ exciton polarizability $(\ensuremath{\Delta}p)$ using first derivative analysis. For the longest conjugation lengths in our films, we found $\ensuremath{\Delta}p$ to be of order ${10}^{4}(\mathrm{\AA{}}{)}^{3}$ in luminescent polymers and ${10}^{3}{\mathrm{\AA{}}}^{3}$ in nonluminescent polymers, respectively, in good agreement with recent subnanosecond transient photoconductivity measurements. We also found that the Huang-Rhys parameter of the ${1B}_{u}$ exciton varies between 0.25 and 0.9, being in general smaller for the luminescent polymers. The consequent exciton relaxation energies were calculated to be of order 100 meV.
The Drosophila Broad-Complex encodes a family of related proteins containing zinc fingers. (1991)

The Broad-Complex (BR-C) is essential for metamorphosis in Drosophila melanogaster. This locus is coextensive with the 2B5 ecdysone-responsive early puff and is necessary for puffing and transcription of many subsequently activated late genes in the developing salivary gland. Mapping of 31 cDNA clones indicates that approximately 100 kb of the genome is devoted to the synthesis of many BR-C RNAs. Sequence analyses of these cDNA clones show that the BR-C encodes a family of related proteins characterized by a common core amino-terminal domain fused to alternate carboxy domains each containing a pair of zinc fingers. Most proteins also contain domains rich in distinctive amino acids located between the common core and zinc finger regions. BR-C mutant alleles resulting from chromosomal rearrangements at 2B5 are associated with deletions of 5'-untranslated sequences, separation of the core coding domain from the downstream zinc finger domains, or a P element insertional disruption of a zinc finger coding sequence. We infer that the BR-C directly regulates late gene expression by specifying the synthesis of a family of proteins with DNA binding potential.
Standardization of Microcomputed Tomography for Tracheal Tissue Engineering Analysis (2020)

Tracheal tissue engineering has become an active area of interest among clinical and scientific communities; however, methods to evaluate success of <i>in vivo</i> tissue-engineered solutions remain primarily qualitative. These evaluation methods have generally relied on the use of photographs to qualitatively demonstrate tracheal patency, endoscopy to image healing over time, and histology to determine the quality of the regenerated extracellular matrix. Although those generally qualitative methods are valuable, they alone may be insufficient. Therefore, to quantitatively assess tracheal regeneration, we recommend the inclusion of microcomputed tomography (μCT) to quantify tracheal patency as a standard outcome analysis. To establish a standard of practice for quantitative μCT assessment for tracheal tissue engineering, we recommend selecting a constant length to quantify airway volume. Dividing airway volumes by a constant length provides an <i>average</i> cross-sectional area for comparing groups. We caution against selecting a length that is unjustifiably large, which may result in artificially inflating the average cross-sectional area and thereby diminishing the ability to detect actual differences between a test group and a healthy control. Therefore, we recommend selecting a length for μCT assessment that corresponds to the length of the defect region. We further recommend quantifying the <i>minimum</i> cross-sectional area, which does not depend on the length, but has functional implications for breathing. We present empirical data to elucidate the rationale for these recommendations. These empirical data may at first glance appear as expected and unsurprising. However, these standard methods for performing μCT and presentation of results do not yet exist in the literature, and are necessary to improve reporting within the field. Quantitative analyses will better enable comparisons between future publications within the tracheal tissue engineering community and empower a more rigorous assessment of results. Impact statement The current study argues for the standardization of microcomputed tomography (μCT) as a quantitative method for evaluating tracheal tissue-engineered solutions <i>in vivo or ex vivo.</i> The field of tracheal tissue engineering has generally relied on the use of qualitative methods for determining tracheal patency. A standardized quantitative evaluation method currently does not exist. The standardization of μCT for evaluation of <i>in vivo</i> studies would enable a more robust characterization and allow comparisons between groups within the field. The impact of standardized methods within the tracheal tissue engineering field as presented in the current study would greatly improve the quality of published work.
Real-Time CARS Imaging Reveals a Calpain-Dependent Pathway for Paranodal Myelin Retraction during High-Frequency Stimulation (2011)

High-frequency electrical stimulation is becoming a promising therapy for neurological disorders, however the response of the central nervous system to stimulation remains poorly understood. The current work investigates the response of myelin to electrical stimulation by laser-scanning coherent anti-Stokes Raman scattering (CARS) imaging of myelin in live spinal tissues in real time. Paranodal myelin retraction at the nodes of Ranvier was observed during 200 Hz electrical stimulation. Retraction was seen to begin minutes after the onset of stimulation and continue for up to 10 min after stimulation was ceased, but was found to reverse after a 2 h recovery period. The myelin retraction resulted in exposure of Kv 1.2 potassium channels visualized by immunofluorescence. Accordingly, treating the stimulated tissue with a potassium channel blocker, 4-aminopyridine, led to the appearance of a shoulder peak in the compound action potential curve. Label-free CARS imaging of myelin coupled with multiphoton fluorescence imaging of immuno-labeled proteins at the nodes of Ranvier revealed that high-frequency stimulation induced paranodal myelin retraction via pathologic calcium influx into axons, calpain activation, and cytoskeleton degradation through spectrin break-down.
Mechanisms of hepatic triglyceride accumulation in non-alcoholic fatty liver disease (2013)

Non-alcoholic fatty liver disease (NAFLD) is characterized by hepatic lipid accumulation in the absence of excess alcohol intake. NAFLD is the most common chronic liver disease, and ongoing research efforts are focused on understanding the underlying pathobiology of hepatic steatosis with the anticipation that these efforts will identify novel therapeutic targets. Under physiological conditions, the low steady-state triglyceride concentrations in the liver are attributable to a precise balance between acquisition by uptake of non-esterified fatty acids from the plasma and by de novo lipogenesis, versus triglyceride disposal by fatty acid oxidation and by the secretion of triglyceride-rich lipoproteins. In NAFLD patients, insulin resistance leads to hepatic steatosis by multiple mechanisms. Greater uptake rates of plasma non-esterified fatty acids are attributable to increased release from an expanded mass of adipose tissue as a consequence of diminished insulin responsiveness. Hyperinsulinemia promotes the transcriptional upregulation of genes that promote de novo lipogenesis in the liver. Increased hepatic lipid accumulation is not offset by fatty acid oxidation or by increased secretion rates of triglyceride-rich lipoproteins. This review discusses the molecular mechanisms by which hepatic triglyceride homeostasis is achieved under normal conditions, as well as the metabolic alterations that occur in the setting of insulin resistance and contribute to the pathogenesis of NAFLD.
Hospitalized Patients with 2009 H1N1 Influenza in the United States, April–June 2009 (2009)

During the evaluation period, 2009 H1N1 influenza caused severe illness requiring hospitalization, including pneumonia and death. Nearly three quarters of the patients had one or more underlying medical conditions. Few severe illnesses were reported among persons 65 years of age or older. Patients seemed to benefit from antiviral therapy.
Rat Spleen Dendritic Cells Express Natural Killer Cell Receptor Protein 1 (NKR-P1) and Have Cytotoxic Activity to Select Targets via a Ca2+-dependent Mechanism (1997)

Dendritic cells (DC) are a subset of leukocytes whose major function is antigen presentation. We investigated the phenotype and function of enriched (95-98.5%) rat DC. We show that both spleen and thymus DC express the natural killer cell receptor protein 1 (NKR-P1) as a disulfide linked homodimer of 60 kD. Freshly isolated DC express a low level of NKR-P1, which is strongly upregulated after overnight culture. Spleen, but not thymus DC, were able to kill the NK-sensitive YAC-1 cell line in vitro, and since this killing was Ca2+ dependent, a Fas ligand-Fas interaction was probably not involved. Besides their potent antigen-presenting function, DC can thus be cytotoxic for some tumor targets.