gebhart/patrepeval huggingface dataset:
Interleukin 2 receptor gene expression in normal human T lymphocytes. (1985)

We have used cDNAs for the human interleukin 2 (IL-2) receptor to study IL-2 receptor gene expression in normal activated T cells. Resting T cells do not contain detectable IL-2 receptor mRNA. Within 1 hr after stimulation with phytohemagglutinin (PHA), a large, presumably nuclear precursor RNA species is seen, which then gradually disappears. Mature IL-2 receptor mRNA forms appear within 8 hr after stimulation, reach peak levels between 8 and 24 hr, and then decline. Thus, in PHA-activated lymphocytes the rise and fall in IL-2 receptor mRNA levels precede by more than 24 hr the peak and decline of IL-2 receptor protein expression occurring at the cell surface. 4 beta-Phorbol 12-myristate 13-acetate (PMA) also stimulates IL-2 receptor mRNA and protein expression by T cells. Combinations of optimal concentrations of PHA and PMA produce an additive effect on IL-2 receptor mRNA levels, suggesting that PHA and PMA may induce IL-2 receptor gene expression through different, complementary mechanisms. Nuclease S1-protection assays indicate that IL-2 receptor mRNAs may differ in length due to the use of three different polyadenylylation signals. Further, these assays demonstrate the presence of transcripts that lack a 216-base segment within the protein-coding region and thus do not encode a functional IL-2 receptor. Nuclear transcription assays indicate that the increase in IL-2 receptor mRNA is reflected at the level of transcription. Thus, IL-2 receptor gene regulation controls IL-2 receptor expression at the cell surface and is intimately linked to the control of T-cell proliferation.
Calibrating atomic-scale force sensors installed at the tip apex of a scanning tunneling microscope (2013)

Scanning tunneling microscopy (STM) tips decorated with either a single carbon monoxide molecule or a single xenon atom are characterized by simultaneous force and conductance measurements using a combined low-temperature noncontact atomic force and scanning tunneling microscope (NC-AFM/STM). It is shown that in both cases the particle decorating the tip simultaneously performs the function of an atomic-scale force sensor and transducer which couples the short-range force acting on the tip to the tunneling conductance of the junction. On the basis of the experimental data, two distinct coupling regimes are identified; in one of them the force sensor-transducer function is calibrated quantitatively.
Selective-absorption cross section of CF_3CHCl_2 and CF_3CDCl_2 at 102 and 106 μm of a TEA CO_2 laser (1979)

A selective absorption cross section of 100:1 was measured for Freon 123-d and natural Freon 123 at the 10.2- and 10.6-microm lines of a TEA CO(2) laser. Multiple-photon absorption occurs at low fluence (0.1 J/cm(2)) at 10.2microm but not at 10.6 microm.
A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits (2019)

The shoot apical meristem (SAM) orchestrates the balance between stem cell proliferation and organ initiation essential for postembryonic shoot growth. Meristems show a striking diversity in shape and size. How this morphological diversity relates to variation in plant architecture and the molecular circuitries driving it are unclear. By generating a high-resolution gene expression atlas of the vegetative maize shoot apex, we show here that distinct sets of genes govern the regulation and identity of stem cells in maize versus <i>Arabidopsis.</i> Cell identities in the maize SAM reflect the combinatorial activity of transcription factors (TFs) that drive the preferential, differential expression of individual members within gene families functioning in a plethora of cellular processes. Subfunctionalization thus emerges as a fundamental feature underlying cell identity. Moreover, we show that adult plant characters are, to a significant degree, regulated by gene circuitries acting in the SAM, with natural variation modulating agronomically important architectural traits enriched specifically near dynamically expressed SAM genes and the TFs that regulate them. Besides unique mechanisms of maize stem cell regulation, our atlas thus identifies key new targets for crop improvement.
Progesterone Interacts with P-Glycoprotein in Multidrug-resistant Cells and in the Endometrium of Gravid Uterus (1989)

P-Glycoprotein (P-GP) plays a pivotal role in maintaining the multidrug-resistant (MDR) phenotype. This membrane glycoprotein is overproduced in MDR cells and the endometrium of the mouse gravid uterus (Arceci, R.J., Croop, J.M., Horwitz, S.B., and Housman, D. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 4350-4354). This latter observation and an interest in endogenous substrates for P-GP led to a study of the interaction of steroids with P-GP found in the endometrium of the mouse gravid uterus and in MDR cells derived from the murine macrophage-like cell J774.2. [3H]Azidopine labeling of P-GP from these two sources was inhibited by various steroids, particularly progesterone. Progesterone also markedly inhibited [3H]vinblastine binding to membrane vesicles prepared from MDR cells, enhanced vinblastine accumulation in MDR cells, and increased the sensitivity of MDR cells to vinblastine. In addition, we have demonstrated that the hydrophobicity of a steroid is important in determining its effect on inhibition of drug binding to P-GP. It is concluded that progesterone, a relatively nontoxic endogenous steroid, interacts with P-GP and is capable of reversing drug resistance in MDR cells.
Polarization Dependent Loss Monitor and Compensation for Digital Coherent Transmission System (2018)

This paper is a summary of Mueller matrix method based polarization dependent loss monitor and compensation in digital coherent transmission system. The experimental demonstration shows that the scheme can achieve high Q improvement of 1.6dB for a polarization-dependent-loss of 5dB.
Effect of the Brugada syndrome mutation A39V on calmodulin regulation of Cav1.2 channels (2014)

Our data indicate that caution must be exercised when interpreting the effects of CaM mutants on ion channel gating.
Additional methods for putative drive genes discovery and oaCGH results from <i>SETD2</i> Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma (2023)

&lt;p&gt;File contains additional information regarding methods for identifying putative driver genes with MutSigCV and high-impact mutations based analysis. Also methods for predicting impacts of TP53 and SETD2 genes. And further information about the oaCGH analysis for somatic copy number aberrations across a subset of 22 dogs.&lt;/p&gt;
Development of -N4-NIM for Molecular Imaging of Tumor Hypoxia (2012)

The nitro group of 2-nitroimidazole (NIM) enters the tumor cells and is bioreductively activated and fixed in the hypoxia cells. 1,4,8,11-tetraazacyclotetradecane (N4) has shown to be a stable chelator for (99m)Tc. The present study was aimed to develop (99m)Tc-cyclam-2-nitroimidazole ((99m)Tc-N4-NIM) for tumor hypoxia imaging. N4-NIM precursor was synthesized by reacting N4-oxalate and 1,3-dibromopropane-NIM, yielded 14% (total synthesis). Cell uptake of (99m)Tc-N4-NIM and (99m)Tc-N4 was obtained in 13762 rat mammary tumor cells and mesothelioma cells in 6-well plates. Tissue distribution of (99m)Tc-N4-NIM was evaluated in breast-tumor-bearing rats at 0.5-4 hrs. Tumor oxygen tension was measured using an oxygen probe. Planar imaging was performed in the tumor-bearing rat and rabbit models. Radiochemical purity of (99m)Tc-N4-NIM was >96% by HPLC. Cell uptake of (99m)Tc-N4-NIM was higher than (99m)Tc-N4 in both cell lines. Biodistribution of (99m)Tc-N4-NIM showed increased tumor-to-blood and tumor-to-muscle count density ratios as a function of time. Oxygen tension in tumor tissue was 6-10 mmHg compared to 40-50 mmHg in normal muscle tissue. Planar imaging studies confirmed that the tumors could be visualized clearly with (99m)Tc-N4-NIM in animal models. Efficient synthesis of N4-NIM was achieved. (99m)Tc-N4-NIM is a novel hypoxic probe and may be useful in evaluating cancer therapy.
Medical Events on Board Aircraft: Reducing Confusion and Misinterpretation in the Scientific Literature (2021)

<b>INTRODUCTION:</b> A topic in aviation medicine that attracts much attention from the scientific community as well as from the media concerns medical incidents on board commercial airline flights. It was noticed that many papers on the subject were written by authors whose specialization was outside that of aviation medicine and that they sometimes made basic errors concerning the application of scientific principles of the subject. A review was undertaken to determine if there were any patterns to the observed errors and, if so, to consider whether recommendations might be provided that could reduce their frequency.<b>METHOD:</b> A literature search was undertaken of MEDLINE using PubMed for English-only articles published between January 1, 1974, and February 1, 2019, employing the following search terms: air emergency, air emergencies, air passenger, air travel, aircraft, airline, aviation, commercial air, flight, and fitness to fly. In addition, other relevant papers held in the personal collection of the authors were reviewed.<b>RESULTS:</b> Many cases of misinterpretation or misunderstanding of aviation medicine were found, which could be classified into eight main categories: references; cabin altitude; pressure/volume relationship; other technical aspects of aircraft operations; regulations; medical events; in-flight deaths; and automated external defibrillator.<b>CONCLUSION:</b> Papers were identified as having questionable statements of fact or of emphasis. Such instances often appeared to result from authors being unfamiliar with the subject of aviation medicine and/or the commercial aviation environment. Simple steps could be taken by authors to reduce the future rate of such instances and recommendations are provided.<b>Thibeault C, Evans AD. <i>Medical events on board aircraft: reducing confusion and misinterpretation in the scientific literature.</i> Aerosp Med Hum Perform. 2021; 92(4):265273.</b>
Can You Fix My Neural Network? Real-Time Adaptive Waveform Synthesis for\n Resilient Wireless Signal Classification (2021)

Thanks to its capability of classifying complex phenomena without explicit\nmodeling, deep learning (DL) has been demonstrated to be a key enabler of\nWireless Signal Classification (WSC). Although DL can achieve a very high\naccuracy under certain conditions, recent research has unveiled that the\nwireless channel can disrupt the features learned by the DL model during\ntraining, thus drastically reducing the classification performance in\nreal-world live settings. Since retraining classifiers is cumbersome after\ndeployment, existing work has leveraged the usage of carefully-tailored Finite\nImpulse Response (FIR) filters that, when applied at the transmitter's side,\ncan restore the features that are lost because of the the channel actions,\ni.e., waveform synthesis. However, these approaches compute FIRs using offline\noptimization strategies, which limits their efficacy in highly-dynamic channel\nsettings. In this paper, we improve the state of the art by proposing Chares, a\nDeep Reinforcement Learning (DRL)-based framework for channel-resilient\nadaptive waveform synthesis. Chares adapts to new and unseen channel conditions\nby optimally computing through DRL the FIRs in real-time. Chares is a DRL agent\nwhose architecture is-based upon the Twin Delayed Deep Deterministic Policy\nGradients (TD3), which requires minimal feedback from the receiver and explores\na continuous action space. Chares has been extensively evaluated on two\nwell-known datasets. We have also evaluated the real-time latency of Chares\nwith an implementation on field-programmable gate array (FPGA). Results show\nthat Chares increases the accuracy up to 4.1x when no waveform synthesis is\nperformed, by 1.9x with respect to existing work, and can compute new actions\nwithin 41us.\n
Improving single-input polarization-sensitive OCT using maximum likelihood estimation (2022)

Polarization sensitivity is a powerful extension of conventional OCT, providing additional contrast for birefringent structures. However, its widespread clinical adoption is complicated by increased system complexity and cost. Single-input polarization-sensitive OCT provides an alternative which bypasses some of the hardware requirements but is prone to artifacts. Here we present a method utilizing existing polarization mode dispersion within the catheter in combination with optimization algorithms to accurately estimate the sample retardance. This strategy has been shown to suppress artifacts and improve agreement with conventional two-state PS-OCT, facilitating the clinical adoption using optimization methods to overcome hardware limitations.
Sensor-less force control for injection molding machine using reaction torque observer (2008)

In recent years, the industrial researchers have paid attention to the not only position control but also force control. The one target of force control researches is the injection molding machine. The conventional force control system uses the force sensor to detect the inserted force. However, the force control system using force sensor has some problems such as the noise, the frequency band and so on. This paper newly proposes that the reaction torque observer is applied to the injection molding machine using ball screw. The reaction torque observer solves this problem of force sensor. However, it is well-known that the ball screw system has the resonant frequency caused by the torsion phenomenon. Hence, this torsion vibration affects both performances of force control and reaction torque estimation. This paper proposes a new reaction torque observer considering the torsion phenomenon and the friction torque. The proposed reaction torque observer estimates the reaction torque accurately. Moreover, as the outside of proposed reaction torque observer has its friction model, this friction model can be tuned without considering the stability condition of force control feedback system. The validity of proposed force control system is confirmed by the experimental results. This paper realizes the low cost and space-saving injection molding machine by using the proposed force sensor-less control method.
Establishment and characterization of continuous helper T cell lines specific to poly(lTyr,lGlu)-poly(dlAla)–poly(lLys). (1981)

Abstract Murine helper T cells activated to the synthetic polypeptide (T.G)-A–L have been established in vitro as continuous cell lines. In vitro educated cells were obtained by culturing nonadherent spleen cells for 6 days on antigen-pulsed splenic adherent cells. In cases when the initial activation procedure was suboptimal, the helper activity of the cells harvested was further potentiated by reculturing the cells for an additional 24 hr on (T,G)-A–L bearing splenic adherent cells. The educated T cells were further cultivated in medium containing a T cell growth factor (TCGF), without additional antigenic stimulation, and the helper T cell lines obtained have been in culture now for more than 18 mo. The characteristics of 1 of the lines, designated E-9M(+), are described in this paper. The proliferating blast-like cells of this line bear the Thy-1.2 antigen, and they also reacted with antibodies against the variable region of the immunoglobulin heavy chain (VH) as well as with an antiserum against (T,G)-A–L. specific idiotypes (Id), as detected by the fluorescence-activated cell sorter (FACS II). The active helper T cells of the E-9M(+) bear Ly-1.1 determinants, and they efficiently activated hapten-primed B cells in an in vitro antibody production system. Culture fluids of this (T,G)-A–L specific helper T cell line could specifically replace the function of T cells in inducing antibody responses. In addition, it was found that the E-9M(+)-derived specific helper factor was absorbed on and eluted from affinity columns of immobilized (T,G)-A–L, anti H-2b, anti-VH, and anti-Id. Thus, this antigen-binding specific helper factor possesses MHC as well as V-region gene determinants.
Waveguide excitation and collection of surface‐enhanced Raman scattering from a single plasmonic antenna (2018)

Abstract The integration of plasmonic antennas on single‐mode silicon nitride waveguides offers great perspective for integrated surface‐enhanced Raman spectroscopy (SERS). However, the few reported experimental demonstrations still require multiple plasmonic antennas to obtain a detectable SERS spectrum. Here, we show, for the first time, SERS signal detection by a single nanoplasmonic antenna integrated on a single‐mode SiN waveguide. For this purpose, we investigated a backscattering detection scheme in combination with background noise reduction, which allowed an optimization of the signal‐to‐noise ratio (SNR) of this platform. Furthermore, a comparison with the free‐space SERS spectrum of the same antenna shows that the conversion efficiency from pump power to total radiated Stokes power is twice as efficient in the case of waveguide excitation. As such, we explored several important aspects in the optimization of on‐chip SERS sensors and experimentally demonstrated the power of exciting nanoplasmonic antennas using the evanescent field of a waveguide. This observation not only is useful for Raman sensing but also could be beneficial for any process involving plasmonic enhancement.
Temperature-dependent magnetization reversal in(Co∕Pt)∕Rumultilayers (2008)

Antiferromagnetically coupled $(\mathrm{Co}∕\mathrm{Pt})∕\mathrm{Ru}$ multilayers with perpendicular anisotropy have been shown to exhibit both vertically and laterally correlated magnetization reversal modes. In this work, the magnetization reversal of a multilayer film whose layer thicknesses have been tuned to be at the phase boundary between the two reversal modes has been investigated as a function of temperature, using the first-order reversal curve (FORC) method. At high temperatures, reversal via vertically correlated stripe domains throughout the film thickness is observed, similar to that in $\mathrm{Co}∕\mathrm{Pt}$ films without the Ru spacers. At low temperatures, antiferromagnetic (AF) interlayer exchange coupling dominates, and laterally correlated reversal is observed with an AF coupled remanent state. Under magnetic field cycling, dipolar fields can transform the sample back into a vertically correlated domain state, thus leading to an exotic behavior with FORC's existing outside the major hysteresis loop. Calculations show that the laterally correlated reversal mode is indeed slightly more stable, and the crossover to vertically correlated reversal can be induced by temperature as well as magnetic field.
Abstract 623: CLU inhibition using OGX-011 is a new adjuvant therapeutic strategy for HSP90 inhibition in prostate cancer (2011)

Abstract Introduction and Objective: Prostate cancer (PCa) responds initially to anti-androgen therapies, however, progression to castration resistant disease (CRPC) frequently occurs. Several small molecule inhibitors of HSP90 show promise in CRPC and other cancers. However, most HSP90 inhibitors (17-AAG or PF-04928473 and its prodrug PF-04929113) trigger the elevation of HSPs (HSP90, 70, 27 and clusterin), which lead to tumor cell survival and treatment resistance. We hypothesized that targeting clusterin (CLU) using siRNA or the antisense drug, OGX-011, may enhance HSP90 inhibitors-induced cell death in PCa. Methods: Inducible and constitutive CLU and other HSP mRNA and protein levels were measured by real-time RT-PCR and immunoblot assays. The combination of OGX-011 with PF-04928473 or 17-AAG was evaluated in vitro on LNCaP and PC3 cells growth and apoptosis. The HSP90 inhibitor PF-04929113 was evaluated in combination with OGX-011 in vivo in athymic mice bearing castration resistant LNCaP xenografts, while the combination of OGX-011 with 17-AAG was evaluated in PC3 xenografts. Results: In prostate tumor cell lines, PF-04928473 and 17-AAG induced expression of HSPs in a dose and time dependent manner, and especially CLU at RNA and protein level, by increasing HSF-1 nuclear translocation and transcription activity. In vitro, OGX-011 synergistically enhanced the activity of HSP90 inhibitors on cell growth and apoptosis with increased sub-G1 fraction and PARP cleavage. These biologic events were accompanied by decreased expression of HSPs, Akt, AR and PSA, and HSF-1 transcriptional activity. In vivo, OGX-011, administered 3 times a week (IP, 15mg/kg), potentiated the effect of orally administered HSP90 inhibitors (PF-04929113: 25mg/kg; 17-AAG: 50mg/kg), significantly inhibiting tumor growth by 80% and prolonging survival in PC3 and castrate resistant LNCaP xenograft model compared to the HSP90 inhibitors alone. Conclusions: These results indicate that HSP90 inhibitor-mediated induction of CLU expression can be attenuated by OGX-011, with synergistic effects on delaying progression of CRPC. This work was supported by the Canadian Institutes of Health Research fellowship and Association pour la Recherche sur le Cancer, France. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 623. doi:10.1158/1538-7445.AM2011-623
Glycerol Selective Oxidation to Lactic Acid over AuPt Nanoparticles; Enhancing Reaction Selectivity and Understanding by Support Modification (2020)

Abstract A high surface area mesoporous TiO 2 material (110 m 2 /g) was synthesised using a nanocasting methodology, utilizing SBA‐15 as a hard template. This material was subsequently used as a support to prepare a series of 1 wt.% AuPt/TiO 2 catalysts, synthesised by conventional impregnation and sol‐immobilisation. Catalysts were tested for the oxidation of glycerol to lactic acid and their performance was compared with corresponding catalysts supported on TiO 2 −P25, TiO 2 ‐anatase and TiO 2 ‐rutile. Higher rates of reaction and higher selectivity to lactic acid were observed over nanocast TiO 2 supported catalysts. The increased performance of these catalysts was attributed to the presence of Si on the surface of the support, which likely arose from inefficient etching of the SBA‐15 template. The presence of Si in these catalysts was confirmed by X‐ray photoelectron spectroscopy and electron energy loss spectroscopy. It was proposed that the residual Si present increases the Brønsted acidity of the TiO 2 support, which can lead to the formation of Lewis acid sites under reaction conditions; both sites are known to catalyse the dehydration of a primary alcohol in glycerol. Typically, under alkaline conditions, lactic acid is formed by the nucleophilic abstraction of a hydrogen. Thus, we propose that the improved selectivity to lactic acid over the nanocast TiO 2 supported catalyst is attributed to the co‐operation of heterogeneous and homogeneous dehydration reactions, as both compete directly with a direct oxidation pathway, which leads to the formation of oxidation products such as glyceric and tartronic acid.