gebhart/patrepeval huggingface dataset:
Down-Regulation of CD1 on Antigen-Presenting Cells by Infection with Mycobacterium tuberculosis (1998)

Intracellular pathogens have developed efficient evasion strategies to survive the defenses of the host immune system. In this study, we describe a new escape mechanism utilized by Mycobacterium tuberculosis that involves the down-regulation of the Ag-presenting molecule CD1 from the cell surface of CD1+ APCs. The loss of CD1 from the cell surface is associated with a complete inhibition of the ability of the infected cells to present Ag to CD1-restricted T cells. The down-regulation of Ag-presenting molecules on CD1+ APC by infection with M. tuberculosis is unique for CD1, since the expression of the classical Ag-presenting molecules MHC class I and MHC class II is not influenced. Our data show that efficient down-regulation of CD1 requires infection of the cells with live mycobacteria, since heat killing of the bacteria completely abrogates the effect. The observed down-regulation is not due to the secretion of cytokines or other host- or pathogen-derived factors. Investigation of upstream events responsible for the down-regulation of CD1 revealed that infection with live M. tuberculosis decreased the steady state CD1-mRNA levels. This study introduces a novel evasion mechanism of M. tuberculosis that could contribute to persistence of intracellular infection by avoiding immune recognition.
Analysis of bioconversion from apogossypol hexaacetate to apogossypol, a novel proapoptotic compound (2005)

2259 Overexpression of anti-apoptotic Bcl-2-family proteins Bcl-2 or Bcl-X L occurs during apoptosis dysregulation in many malignancies, resulting in resistance to cytotoxic anticancer drugs. Recent studies showed that Bcl-2 and Bcl-X L are targets of (±)Gossypol (Kitada, et al. J Med Chem 46: 4258, 2003), which has then tested for treatment of metastatic adrenal cancer, glioblastoma and breast cancer with low but measurable responses. (-)Gossypol was also developed and showed improved efficacy and pharmacokinetic properties to some extent (Jia, et al. 2003 AACR-NCI-EORTC). It seems that the presence of two highly reactive aldehyde groups in Gossypol may be a limitation to its therapeutic successes. By using a combination of molecular modeling and structural biology techniques, Apogossypol (AG), which lacks the aldehydic groups and retains pro-apoptototic activity, has recently been synthesized and shown to bind to and inhibit the Bcl-2-family proteins, Bcl-2 and Bcl-X L , inducing apoptosis of the tumor cell lines (Becattini et. al ., Chem Biol. 11:389-9, 2004). However, due to the inherent instability of AG in the solid form, the compound has been synthesized as a hexaacetate prodrug form, a very stable compound both in solution and in solid form. Apogossypol hexaacetate (AGA) lacks apoptotic activity because the acetate groups hinder the binding of the compound to the Bcl-2 proteins. Therefore, the acetates must be cleaved for the molecule to exhibit activity in vivo . In preparation for preclinical studies, a method was developed and validated for the analysis of AG in mouse plasma from mice dosed with AGA. The methodology involves protein precipitation of plasma samples followed by LC/MS/MS analysis. The validated concentration range extends from 10-2,000 ng/mL using 100 μL of mouse plasma, with extraction recoveries averaging 90%. The quantitation is based on internal standardization using apigenin as the internal standard. This method was used to determine the short-term stability of AG in mouse plasma stored at room temperature, on ice, and at 37 degrees C. AG was found to be stable for at least 1 hour at room temperature and 3 hours when stored on ice, however, it appeared degraded in plasma in less than 30 minutes at 37 °C. The stability of AG at 37 °C was increased by the addition 1% ascorbic acid to plasma. Incubation of AGA at 0.2, 1 and 5 μg/ml with mouse plasma for 30 min at 37 °C resulted in essentially complete conversion of AGA in AG (>100%). The conversion appears to be temperature-dependent because lowering temperatures delayed the conversion rate. The addition of 1% ascorbic acid to the incubation also delayed the conversion rate. The bioconversion was also demonstrated in mice after administration of AGA. These results suggest that AGA will be a useful prodrug form of apogossypol and may have considerable theoretical and practical significance (Supported by NCI Contract No. N01-CM-07110).
Ellipsometry measurement of the complex refractive index and thickness of polysilicon thin films (1990)

A scheme to measure precisely the complex refractive index, N − iK, and the thickness of polycrystalline silicon (poly-Si) film is proposed and demonstrated. The measurement is made by scanning the ellipsometer light beam along a beveled surface of the poly-Si film and by adopting a zero-layer model to derive the Nse − T plot, where Nse is the equivalent real refractive index and T is the thickness of the measured poly-Si film. The complex refractive index, N − iK, is obtained from the Nse − T plot, and the thickness is computed from the ellipsometry equation. Error analyses have been done on both the conventional ellipsometry method and the proposed method, and results show that the proposed method has more than an order-of-magnitude improvement in accuracy compared with the conventional method. Experimental results of applying this method to measure the complex refractive index of poly-Si films prepared at different processing conditions are also shown.
Purely Spin‐Vibronic Coupling Assisted Triplet to Singlet Up‐Conversion for Real Deep Blue Organic Light‐Emitting Diodes with Over 20% Efficiency and y Color Coordinate of 0.05 (2021)

Finding narrow-band, ultrapure blue thermally activated delayed fluorescence (TADF) materials is extremely important for developing highly efficient organic light-emitting diodes (OLEDs). Here, spin-vibronic coupling (SVC)-assisted ultrapure blue emitters obtained by joining two carbazole-derived moieties at a para position of a phenyl unit and performing substitutions using several blocking groups are presented. Despite a relatively large singlet-triplet gap (∆E<sub>ST</sub> ) of >0.2 eV, efficient triplet-to-singlet crossover can be realized, with assistance from resonant SVC. To enhance the spin crossover, electronic energy levels are fine-tuned, thereby causing ∆E<sub>ST</sub> to be in resonance with a triplet-triplet gap (∆E<sub>TT</sub> ). A sizable population transfer between spin multiplicities (>10<sup>3</sup> s<sup>-1</sup> ) is achieved, and this result agrees well with theoretical predictions. An OLED fabricated using a multiple-resonance-type SVC-TADF emitter with CIE color coordinates of (0.15, 0.05) exhibits ultrapure blue emissions, with a narrow full-width-at-half-maximum of 21 nm and a high external quantum efficiency of 23.1%.
Photonic crystal coupled plasmonic hybrid nanosensors (2016)

We present an approach to enhance particle nanoplasmonics by using coupling to the high-Q dielectric photonic crystal (PC) resonance. The PC-coupled gold nanorods (AuNRs) exhibit strong amplification (>9x) of the SERS signal compared to the PC-uncoupled AuNRs.
Two-photon frequency division multiplexing for functional in vivo imaging: a feasibility study (2019)

Recently, we presented a new approach to create high-speed amplitude modulation of femtosecond laser pulses and tag multiple excitation beams with specific modulation frequencies. In this work, we discuss the utility of this method to record calcium signals in brain tissue with two-photon frequency-division multiplexing (2P-FDM) microscopy. While frequency-multiplexed imaging appears slightly inferior in terms of image quality as compared to conventional two-photon laser scanning microscopy due to shot noise-induced cross-talk between frequency channels, applying this technique to record average signals from regions of interest (ROI) such as neuronal cell bodies was found to be promising. We use phase information associated with each pixel or waveform within a selected ROI to phase-align and recombine the signals into one extended amplitude-modulated waveform. This procedure narrows the frequency detection window, effectively decreasing noise contributions from other frequency channels. Using theoretical analysis, numerical simulations, and in vitro imaging, we demonstrate a reduction of cross-talk by more than an order of magnitude and predict the usefulness of 2P-FDM for functional studies of brain activity.
Figure S4 (A,B) from Dual Targeting of EGFR and IGF1R in the TNFAIP8 Knockdown Non–Small Cell Lung Cancer Cells (2023)

&lt;p&gt;EGFR localization to early endosomes&lt;/p&gt;
Quantitative kinetic analysis of the bacteriophage λ genetic network (2005)

The lysis-lysogeny decision of bacteriophage lambda has been a paradigm for a developmental genetic network, which is composed of interlocked positive and negative feedback loops. This genetic network is capable of responding to environmental signals and to the number of infecting phages. An interplay between CI and Cro functions suggested a bistable switch model for the lysis-lysogeny decision. Here, we present a real-time picture of the execution of lytic and lysogenic pathways with unprecedented temporal resolution. We monitor, in vivo, both the level and function of the CII and Q gene regulators. These activators are cotranscribed yet control opposite developmental pathways. Conditions that favor the lysogenic response show severe delay and down-regulation of Q activity, in both CII-dependent and CII-independent ways. Whereas CII activity correlates with its protein level, Q shows a pronounced threshold before its function is observed. Our quantitative analyses suggest that by regulating CII and CIII, Cro plays a key role in the ability of the lambda genetic network to sense the difference between one and more than one phage particles infecting a cell. Thus, our results provide an improved framework to explain the longstanding puzzle of the decision process.
Studies on the interactions between human replication factor C and human proliferating cell nuclear antigen (1999)

Proliferating cell nuclear antigen (PCNA) is a processivity factor required for DNA polymerase delta (or epsilon)-catalyzed DNA synthesis. When loaded onto primed DNA templates by replication factor C (RFC), PCNA acts to tether the polymerase to DNA, resulting in processive DNA chain elongation. In this report, we describe the identification of two separate peptide regions of human PCNA spanning amino acids 36-55 and 196-215 that bind RFC by using the surface plasmon resonance technique. Site-directed mutagenesis of residues within these regions in human PCNA identified two specific sites that affected the biological activity of PCNA. Replacement of the aspartate 41 residue by an alanine, serine, or asparagine significantly impaired the ability of PCNA to (i) support the RFC/PCNA-dependent polymerase delta-catalyzed elongation of a singly primed DNA template; (ii) stimulate RFC-catalyzed DNA-dependent hydrolysis of ATP; (iii) be loaded onto DNA by RFC; and (iv) activate RFC-independent polymerase delta-catalyzed synthesis of poly dT. Introduction of an alanine at position 210 in place of an arginine also reduced the efficiency of PCNA in supporting RFC-dependent polymerase delta-catalyzed elongation of a singly primed DNA template. However, this mutation did not significantly alter the ability of PCNA to stimulate DNA polymerase delta in the absence of RFC but substantially lowered the efficiency of RFC-catalyzed reactions. These results are in keeping with a model in which surface exposed regions of PCNA interact with RFC and the subsequent loading of PCNA onto DNA orients the elongation complex in a manner essential for processive DNA synthesis.
Towards a 99% Efficient Three-Phase Buck-Type PFC Rectifier for 400-V DC Distribution Systems (2011)

In telecom applications, the vision for a total power conversion efficiency from the mains to the output of point-of-load (PoL) converters of 95% demands optimization of every conversion step, i.e., the power factor correction (PFC) rectifier front-end should show an outstanding efficiency in the range of 99%. For recently discussed 400-V dc distribution bus voltages, a buck-type PFC rectifier is a logical solution. In this paper, an efficiency-optimized, 98.8% efficient, 5-kW three-phase buck-type PFC rectifier with 400-V output is presented. Methods for calculating losses of all components are described and are used to optimize the converter design for efficiency at full load. Special attention is paid to semiconductor losses, which are shown to be dominant, with the parasitic device capacitance losses being a significant component. The calculation of these parasitic capacitance losses is treated in detail, and the charge-balance approach used is verified. A prototype of the proposed rectifier is constructed which verifies the accuracy of the models used for loss calculation and optimization.
In vitro simulation of immunosuppression caused by Trypanosoma brucei: active involvement of gamma interferon and tumor necrosis factor in the pathway of suppression (1996)

Experimental infections of mice with the African trypanosome Trypanosoma brucei lead to a profound state of T-cell unresponsiveness in the lymph node cell (LNC) compartment. This suppression is mediated by macrophage-like cells which inhibit interleukin 2 (IL-2) secretion and down-regulate IL-2 receptor expression (M. Sileghem, A. Darji, R. Hamers, M. Van de Winkel, and P. De Baetselier, Eur. J. Immunol. 19:829-835, 1989). Similar suppressive cells can be generated in vitro by pulsing 2C11-12 macrophage hybridoma cells with opsonized T. brucei parasites (2C11-12P cells). Cocultures of 2C11-12P cells and LNCs secrete higher levels of gamma interferon (IFN-gamma), and the hyperproduction of IFN-gamma was found to be confined to CD8+ lymphoid cells. Elimination of CD8+ cells from cocultures of 2C11-12P cells and LNCs restores the T-cell proliferative response. Furthermore, addition of neutralizing anti-IFN-gamma antibodies to the cocultures reduces the level of suppression and concomitantly restores the level of IL-2 receptor expression. Hence, IFN-gamma plays a cardinal role in this in vitro model for T. brucei-elicited immunosuppression. Cocultures of LNCs and 2C11-12P cells in a two-chamber culture system further demonstrated that cell-cell contact is required for hyperproduction of IFN-gamma and, moreover, that IFN-gamma cooperates with a 2C11-12P-derived diffusible factor to exert its suppressive activity. Finally, tumor necrosis factor alpha (TNF-alpha produced by 2C11-12P cells was found to be implicated in the hyperproduction of IFN-gamma, since addition of neutralizing anti-TNF-alpha antibodies to cocultures reduced the level of suppression and concomitantly abrogated the hyperproduction of IFN-gamma. Collectively, our findings indicate that T. brucei-elicited suppressive 2C11-12 macrophage cells differentially influence T-cell subpopulations: (i) CD8+ cells are signaled via cell-cell contact to produce IFN-gamma, and TNF-alpha is implicated in this process, and (ii) locally produced IFN-gamma and macrophage-released factors act in concert to inhibit CD4+ and CD8+ T-cell proliferative responses.
Chemical modification of mammalian cell surfaces (2003)

The mammalian cell surface is a highly heterogeneous chemical environment with proteins, carbohydrates, lipids and composite molecules controlling vital cell functions. Chemical modification of this environment is a challenge due to the complexity of the surface chemistry and the fragility of the cell. Here, we review recent attempts to perform targeted, non-genetically controlled, changes to cell surface chemistry. Potential applications of cell surface engineering are presented.
Analytical In Situ Gas Transmission Electron Microscopy Enabled with Ultrathin Silicon Nitride Membranes (2023)

Journal Article Analytical In Situ Gas Transmission Electron Microscopy Enabled with Ultrathin Silicon Nitride Membranes Get access Kunmo Koo, Kunmo Koo Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USAThe NUANCE Center, Northwestern University, Evanston, IL, USA Search for other works by this author on: Oxford Academic Google Scholar Paul J M Smeets, Paul J M Smeets Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USAThe NUANCE Center, Northwestern University, Evanston, IL, USA Search for other works by this author on: Oxford Academic Google Scholar Xiaobing Hu, Xiaobing Hu Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USAThe NUANCE Center, Northwestern University, Evanston, IL, USA Corresponding authors: xbhu@northwestern.edu; v-dravid@northwestern.edu Search for other works by this author on: Oxford Academic Google Scholar Vinayak P Dravid Vinayak P Dravid Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USAThe NUANCE Center, Northwestern University, Evanston, IL, USA Corresponding authors: xbhu@northwestern.edu; v-dravid@northwestern.edu Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 29, Issue Supplement_1, 1 August 2023, Pages 1597–1598, https://doi.org/10.1093/micmic/ozad067.820 Published: 22 July 2023
Radiosensitivity of Human Bone Marrow Granulocyte-Macrophage Progenitor Cells and Stromal Colony-Forming Cells: Effect of Dose Rate (1986)

Study of the radiation biology of human bone marrow hematopoietic cells has been difficult since unseparated bone marrow cell preparations also contain other nonhematopoietic stromal cells. We tested the clonogenic survival after 0.05 or 2 Gy/min X irradiation using as target cells either fresh human bone marrow or nonadherent hematopoietic cells separated from stromal cells by the method of long-term bone marrow culture (LTBMC). Sequential nonadherent cell populations removed from LTBMC were enriched for hematopoietic progenitors forming granulocyte-macrophage colony-forming unit culture (GM-CFUc) that form colonies at Day 7, termed GM-CFUc7, or Day 14 termed GM-CFUc14. The results demonstrated no effect of dose rate on the D0 or n of fresh marrow GM-CFUc (colonies greater than or equal to 50 cells) after plating in a source of their obligatory growth factor, colony-stimulating factor (CSF) (GM-CFUc7 irradiated at 2 Gy/min, D0 = 1.02 +/- 0.05, n = 1.59 +/- 0.21; at 0.05 Gy/min, D0 = 1.07 +/- 0.03, n = 1.50 +/- 0.04; GM-CFUc14 at 2 Gy/min, D0 = 1.13 +/- 0.03, n = 1.43 +/- 0.03; at 0.05 Gy/min, D0 = 1.16 +/- 0.04, n = 1.34 +/- 0.05). There was a decrease in the radiosensitivity of GM-CFUc7 and GM-CFUc14 derived from nonadherent cells of long-term bone marrow cultures compared to fresh marrow that was observed at both dose rates. In contrast, adherent stromal cells irradiated at low compared to high dose rate showed a significantly greater radioresistance (Day 19 colonies of greater than or equal to 50 cells; at 2 Gy/min, D0 = 0.99 Gy, n = 1.03; at 0.05 Gy/min D0 = 1.46 Gy, n = 2.00). These data provide strong evidence for a difference in the radiosensitivity of human marrow hematopoietic progenitor compared to adherent stromal cells.
Figure S1 from Growth of Triple-Negative Breast Cancer Cells Relies upon Coordinate Autocrine Expression of the Proinflammatory Cytokines IL-6 and IL-8 (2023)

&lt;p&gt;Figure S1 - PDF file 76K, Flow chart outlining the analyses and selection criteria utilized for the identification of inflammatory genes with differential expression in both patient and cell line datasets&lt;/p&gt;
Development of a magnetic resonance sensor for on-line monitoring of {sup 99}Tc and {sup 23}Na in tank waste cleanup processes: Final report and implementation plan (2000)

In response to US Department of Energy (DOE) requirements for advanced cross-cutting technologies, Argonne National Laboratory is developing an on-line sensor system for the real-time monitoring of {sup 99}Tc and {sup 23}Na in various locations throughout radioactive-waste processing facilities. Based on nuclear magnetic resonance spectroscopy, the highly automated sensor system can provide near-real-time response with minimal sampling. The technology, in the form of a flow-through nuclear-magnetic-resonance-based on-line process sensing and control system, can rapidly monitor {sup 99}Tc speciation and concentration (from 0.1 molar to 10 micro molar) in the feedstocks and eluents of radioactive-waste treatment processes. The system is nonintrusive, capable of withstanding harsh plant environments, and reasonably immune to contaminants. Furthermore, the system is capable of operating over large variations in pH, conductivity, and salinity. This document describes design parameters, results from sensitivity studies, and initial results obtained from oxidation-reduction studies that were conducted on technetium standards and waste specimens obtained from DOE's Hanford site. A cursory investigation of the system's capabilities to monitor {sup 23}Na at high concentrations are also reported, as are descriptions of site requirements, implementation recommendations, and testing techniques.
Electrochemically Induced Maskless Metal Deposition on Micropore Wall (2012)

By applying an external electric field across a micropore via an electrolyte, metal ions in the electrolyte can be reduced locally onto the inner wall of the micropore, which was fabricated in a silica-covered silicon membrane. This maskless metal deposition on the silica surface is a result of the pore membrane polarization in the electric field.
Synthesis of Manganite Perovskites by Reverse Homogeneous Precipitation Method in the Presence of Alkylammonium Cations (2000)

Abstract A single-phase LaMnO3+δ perovskite with high surface area could be synthesized after air-calcining the hydroxide precursor at 650 °C and above. The precursor was easily obtained by dropping a mixed aqueous solution of La and Mn nitrates into highly basic aq. NH3 with and without the presence of N(CH3)4Br. The addition of N(CH3)4Br was effective in increasing the specific surface area of the products as well as in stabilizing the colloidal solution of the hydroxide precursor.
Embedded Real-Time Control via MATLAB, Simulink, and xPC Target (2005)

This article shows how xPC Target [44] facilitates embedded control system design by turning general-purpose personal computer (PC) hardware into a rapid prototyping platform. The PC-based platform used is the MathWorks xPC TargetBox™ [45], an industrial PC. xPC Target is integrated in Simulink® [31], enabling the use of Simulink as a graphical front end with Math-Works tools for parameter estimation, response optimization, and linearization throughout the design cycle.
Ferroic Multipolar Order and Disorder in Cyanoelpasolite Molecular Perovskites (2018)

&lt;div&gt;We use a combination of variable-temperature high-resolution synchrotron X-ray powder diffraction measurements and Monte Carlo simulations to characterise the evolution of two different types of ferroic multipolar order in a series of cyano elpasolite molecular perovskites. We show that ferroquadrupolar order in [C3N2H5]2Rb[Co(CN)6] is a first-order process that is well described by a 4-state Potts model on the simple cubic lattice. Likewise, ferrooctupolar order in [NMe4]2B[Co(CN)6] (B = K, Rb, Cs) also emerges via a first-order transition that now corresponds to a 6-state Potts model. Hence, for these particular cases, the dominant symmetry breaking mechanisms are well understood in terms of simple statistical mechanical models. By varying composition, we find that the effective coupling between multipolar degrees of freedom—and hence the temperature at which ferromultipolar order emerges—can be tuned in a chemically sensible manner.&lt;/div&gt;&lt;div&gt;&lt;br&gt;&lt;/div&gt;