gebhart/patrepeval huggingface dataset:
The Vitamin D Receptor Interacts with General Transcription Factor IIB (1995)

The vitamin D receptor (VDR) heterodimerizes with retinoid X receptors (RXR) on many vitamin D-responsive promoter elements, suggesting that this complex is the active factor in vitamin D-mediated transcription. However, the mechanism of transcriptional regulation following VDR-RXR binding to DNA is not well characterized. Using a yeast two-hybrid protein interaction assay, we demonstrate that VDR forms specific protein: protein contacts with the basal transcription factor TFIIB. Deletion analysis indicated that the carboxyl-terminal ligand binding domain of VDR interacted with a 43-residue amino-terminal domain in TFIIB. The interaction with TFIIB showed selectivity for the ligand binding domain of VDR as similar regions of RXR alpha or of retinoic acid receptor alpha did not couple with TFIIB. Binding assays with purified proteins showed a direct interaction between VDR and TFIIB in vitro. These data suggest a mechanism for VDR-dependent transcription in which protein contacts between VDR and TFIIB may impart regulatory information to the transcription preinitiation complex.
Dual-Plateau Capnogram Caused by Cracked Sample Filter (2000)

While providing anesthesia for a patient with severe emphysematous lung disease undergoing thoracoscopic lung volume reduction surgery, a capnogram wave form similar to that shown in Figure 1 was observed. Although recognized as unusual, it was felt to perhaps represent the patient’s severe ventilation abnormality. A similar capnogram was observed on the two subsequent patients, despite an unsuccessful search for causes of the abnormality. We observed that the second increase in the expired CO2 wave form was in time with the commencement of inspiration. By inference, a leak in the gas sample line and adapters was sought. Eventually a microscopic crack (Figure 2) was found in the filter (#6050-0001-669 Membrane Separator Cartridge) of the Ohmeda RGM 5250 gas analyzer (Datex-Ohmeda, Madison, WI).Figure 1: Capnogram demonstrating wave form with two plateaus.Figure 2: Ohmeda filter (Datex-Ohmeda, Madison, WI) showing crack.To explain this observation, we hypothesize that, during the initial phase of expiration, aspiration of the gas sample by the analyzer produced a negative pressure at the cracked sample filter that aspirated room air. With the commencement of inspiration, positive pressure in the anesthesia circuit reduced the negative pressure at the sample filter and eliminated or reduced the aspiration of ambient air, thus, allowing a second plateau that more accurately reflected alveolar PCO2. A gas analyzer capable of monitoring nitrogen would have perhaps enabled more rapid identification of the source of the wave form by showing contamination with air. Discussion with the manufacturer revealed that this cause of an abnormal capnogram had not been previously described. Simon C. Body MB, ChB Kevin Taylor MSc(Eng), PEng James H. Philip MD, ME
Downlink Non-Orthogonal Multiple Access (NOMA) Combined with Single User MIMO (SU-MIMO) (2015)

This paper investigates a downlink non-orthogonal multiple access (NOMA) combined with single user MIMO (SU-MIMO) for future LTE (Long-Term Evolution) enhancements. In particular, we propose practical schemes to efficiently combine NOMA with open-loop SU-MIMO (Transmission Mode 3: TM3) and closed-loop SU-MIMO (Transmission Mode 4: TM4) specified in LTE. The goal is also to clarify the performance gains of NOMA combined with SU-MIMO transmission, taking into account the LTE radio interface such as frequency-domain scheduling, adaptive modulation and coding (AMC), and NOMA specific functionalities such as, multi-user pairing/ordering, transmit power allocation and successive interference cancellation (SIC) at the receiver side. Based on computer simulations, we evaluate NOMA link-level performance and show that the impact of error propagation associated with SIC is marginal when the power ratio of cell-edge and cell-center users is sufficiently large. In addition, we evaluate NOMA system-level performance gains for different granularities of scheduling and MCS (modulation and coding scheme) selection, for both genie-aided channel quality information (CQI) estimation and approximated CQI estimation, and using different number of power sets. Evaluation results show that NOMA combined with SU-MIMO can still provide a hefty portion of its expected gains even with approximated CQI estimation and limited number of power sets, and also when LTE compliant subband scheduling and wideband MCS is applied.
Correction: Prospective on using fibre mid-infrared supercontinuum laser sources for in vivo spectral discrimination of disease (2020)

Correction for ‘Prospective on using fibre mid-infrared supercontinuum laser sources for <italic>in vivo</italic> spectral discrimination of disease’ by Angela B. Seddon <italic>et al., Analyst</italic>, 2018, <bold>143</bold>, 5874–5887.
Hot electron target interaction experiments at the GOL-3 facility (1997)

At the GOL-3 facility, experiments on the interaction of powerful hot electron streams with various materials have been performed. For energy densities of the hot electron stream above 10 MJ/m2 an explosive-like erosion was observed, which at energy densities of 30 MJ/m2 reaches 500 mu m for fine grain graphite and 200 mu m for tungsten. Under these conditions, the corona of the carbon vapour cloud has temperatures below 1.2 eV and densities up to 1017 cm-3. It propagates along the magnetic field lines with maximum velocities of 2.1*106 cm/s. The longitudinal and transverse (along and across magnetic field lines) vapour velocities of the colder bulk plasma are about 106 cm/s. A model for explosive-like erosion was developed and tested against the GOL-3 results. For graphite the destruction threshold is 10 kJ/g. This value is considerably lower than the vaporization enthalpy of 20.5 kJ/g for three atomic vaporization. The validated model was applied to a numerical analysis of the occurrence of explosive-like erosion for ITER disruptions and runaway electrons. If the energy density of the runaways remains below 30 MJ/m2, explosive-like erosion of graphite occurs for electron energies below 20 MeV. For the energetic tail of Maxwellian plasma electrons with temperatures up to 20 keV and power densities of 10 MW/cm2 without any angular spread, explosive-like erasion becomes comparable to erosion by vaporization
Temperature dependence of tunneling magnetoresistance in epitaxial magnetic tunnel junctions using aCo2FeAlHeusler alloy electrode (2010)

Spin-valve-type epitaxial magnetic tunnel junctions (MTJs) consisting of a full-Heusler alloy ${\text{Co}}_{2}\text{FeAl}$ (CFA) and a MgO tunnel barrier were fabricated on a single-crystal MgO(001) substrate using sputtering method for all the layers. Experimental temperature-dependent tunnel magnetoresistance in the MTJs was revealed to be fitted well using spin wave excitation model for tunneling spin polarization, $P(T)={P}_{0}(1\ensuremath{-}\ensuremath{\alpha}{T}^{3/2})$ up to room temperature, where ${P}_{0}$ is the spin polarization at 0 K and $\ensuremath{\alpha}$ is a fitting parameter. The determined $P$ and $\ensuremath{\alpha}$ are shown to be significantly different between bottom and top CFA electrodes facing a MgO barrier. It is demonstrated that the bottom CFA deposited on a Cr buffer has a low $\ensuremath{\alpha}$ and behaves as a half-metal with $P\ensuremath{\sim}1$ in terms of the ${\ensuremath{\Delta}}_{1}$ symmetry due to the coherent tunneling through a MgO barrier.
Apoptotic Death of CD8+ T Lymphocytes After Immunization: Induction of a Suppressive Population of Mac-1+/Gr-1+ Cells (1998)

Following an infection or immunization, a primary CD8+ T cell response generally rises then falls rapidly before giving rise to a "memory" response. When we immunized mice with recombinant viral immunogens optimized to enhance the lytic capability of CD8+ T cells, we measured a profound depression in Ag-specific effector function after early restimulation. Indeed, a "mirror image" cytolytic capability was observed: the most powerful immunogens, as measured by cytolytic capacity 6 days after immunization, elicited the weakest secondary immune response when evaluated following an additional 6 days after restimulation. To understand the mechanism of this suppression, we examined the fate of splenocytes immunized with a vaccinia virus encoding Ag and IL-2 then restimulated ex vivo. We found that these splenocytes underwent an apoptotic cell death, upon early restimulation, that was not dependent on the engagement of the FasR (CD95). Unlike previously described mechanisms of "propriocidal cell death" and "clonal exhaustion," the cell death we observed was not an inherent property of the CD8+ T cells but rather was due to a population of splenocytes that stained positive for both the Mac-1 and Gr-1 surface markers. Deletion of these cells in vitro or in vivo completely abrogated the observed suppression of cytolytic reactivity of Ag-specific CD8+ T cells. These observations could account for the apparent absence of Ag-specific immune responses after some current vaccination regimens employing powerful immunogens. Finally, our results may shed new light on a mechanism for the suppression of CD8+ T cell responses and its effect on vaccine efficacy and on immune memory.
A Quasi‐Chemical Kinetics Model for the Growth and Death of Staphylococcus aureus in Intermediate Moisture Bread (2003)

ABSTRACT: The “quasi‐chemical” kinetics model accounts for all 4 phases of the microbial lifecycle based on a proposed series of chemical rate equations. The model fits continuous growth‐death kinetics for Staphylococcus aureus in intermediate moisture bread in various conditions of water activity, pH, and temperature. Growth rates evaluated using the quasi‐chemical model are compared with values obtained with the Gompertz model. Kinetics data obtained with the quasi‐chemical model are integrated with a probabilistic approach to estimate the boundary between growth and no‐growth conditions. Continuous modeling of microbial growth/death kinetics in actual foods advances predictive modeling that conventionally separates growth and death models.
PAPR Reduction Using Cyclic-Selective Mapping with Delayed Correlation in Time Domain (2015)

In this paper, a peak-to-average power ratio (PAPR) reduction scheme without side information (SI) is propossed. Cyclic-selective mapping (cyclic-SLM) has been applied to reduce the PAPR of a transmit orthogonal frequency division multiplexing (OFDM) signal. The cyclic-SLM generates a signal candidate by combining an original signal and its cyclic shifted signal. The Cyclic SLM requires side information regarding the cyclic shift to recover the signal while it will reduce the throughput of a wireless OFDM system. The propossed scheme applies delayed correlation based estimation to omit the transmision of the SI. In the receiver side, the amount of the cyclic shift is estimated with exploiting the correlation between a guard interval sequence and a received signal. Numerical results show that the cyclic-SLM with the delayed correlation (DC) provides significant PAPR reduction while it realizes the accuracy of the shift estimation close to 100% at E_b/N_0 of 8 dB. It also achieves the PAPR that is equivalent to the conventional SLM and the bit error rate degradation is slightly different from that with perfect shift estimation.
Real-time monitoring of video quality in IP networks (2005)

This paper investigates the problem of assessing the quality of video transmitted over IP networks. Our goal is to develop a methodology that is both reasonably accurate and simple enough to support the large-scale deployments that the increasing use of video over IP are likely to demand. For that purpose, we focus on developing an approach that is capable of mapping network statistics, e.g., packet losses, available from simple measurements, to the quality of video sequences reconstructed by receivers. A first step in that direction is a loss-distortion model that accounts for the impact of network losses on video quality, as a function of application-specific parameters such as the video codec and loss recovery technique, coded bit rate, packetization, video characteristics, etc. The model, although accurate, is poorly suited to large-scale, on-line monitoring, because of its dependency on many parameters that are difficult to estimate in real-time. As a result, we introduce a "relative quality" metric that bypasses this problem by measuring video quality against a quality benchmark that the network is expected to provide. The approach offers a lightweight video quality monitoring solution that is suitable for large-scale deployments. We assess its feasibility and accuracy through extensive simulations and experiments.
Abstract PL02-03: The zinc-finger degrome (2019)

Abstract The small molecule drugs thalidomide, lenalidomide, and pomalidomide induce the ubiquitination and proteasomal degradation of Ikaros (IKZF1) and Aiolos (IKZF3) by mediating their interaction with Cereblon (CRBN), the substrate receptor of the CRL4CRBN ubiquitin ligase. Here we screened the human Cys2-His2 (C2H2) zinc finger (ZF) proteome for degradation by CRL4CRBN in the presence of thalidomide analogues, identifying 11 ZF targets. Structural and functional characterization of the C2H2 zinc finger degron demonstrates how diverse ZF domains bind the drug-CRBN interface. Computational ZF docking, in conjunction with biochemical analysis, predicts that at least 50 zinc-fingers bind the drug-CRBN complex in vitro, a larger number than previously anticipated. These results provide strategies to degrade other zinc finger transcription factors. Citation Format: Quinlan L. Sievers, Georg Petzold, Richard D. Bunker, Aline Renneville, Brian Liddicoat, Wassim Abdulrahman, Tarjei Mikkelsen, Benjamin L. Ebert, Nicolas H. Thoma. The zinc-finger degrome [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr PL02-03. doi:10.1158/1535-7163.TARG-19-PL02-03
Effectiveness of Model-Based Defenses for Digitally Controlled Industrial Systems: Nuclear Reactor Case Study (2019)

Model-based defenses have been promoted over the past decade as essential defenses against intrusion and data deception attacks into the control network used to digitally regulate the operation of critical industrial systems such as nuclear reactors. The idea is that physics-based models could differentiate between genuine, i.e., unaltered by adversaries, and malicious network engineering data, e.g., flowrates, temperatures, etc. Machine learning techniques have also been proposed to further improve the differentiating power of model-based defenses by constantly monitoring the engineering data for any possible deviations that are not consistent with the physics. While this is a sound premise, critical systems, such as nuclear reactors, chemical plants, oil and gas plants, etc., share a common disadvantage: almost any information about them can be obtained by determined adversaries, such as state-sponsored attackers. Thus, one must question whether model-based defenses would be resilient under these extreme adversarial conditions. This paper represents a first step toward answering this question. Specifically, we introduce self-learning techniques, including both pure data-driven, e.g., deep neural networks, and physics-based techniques able to predict dynamic behavior for a nuclear reactor model. The results indicate that if attackers are technically capable, they can learn very accurate models for reactor behavior, which raises concerns about the effectiveness of model-based defenses.
IAPMA 2011: 2nd Workshop on information access to personal media archives (2011)

Towards e-Memories: challenges of capturing, summarising, presenting, understanding, using, and retrieving relevant information from heterogeneous data contained in personal media archives.&#13;\n&#13;\nWelcome to IAPMA 2011, the second international workshop on "Information Access for Personal Media Archives". It is now possible to archive much of our life experiences in digital form using a variety of sources, e.g. blogs written, tweets made, social network status updates, photographs taken, videos seen, music heard, physiological monitoring, locations visited and environmentally sensed data of those places, details of people met, etc. Information can be captured from a myriad of personal information devices including desktop computers, PDAs, digital cameras, video and audio recorders, and various sensors, including GPS, Bluetooth, and biometric devices.
Determination of the cubic to hexagonal fraction in GaN nucleation layers using grazing incidence x-ray scattering (1998)

Recent electron diffraction and microscopy studies of GaN nucleation layers have shown that faults in the stacking of the close-packed planes result in the coexistence of cubic and hexagonal phases within the layers. Using grazing incidence x-ray scattering, we have quantified the proportion of the cubic and hexagonal phases throughout the nucleation layer. We compare the structure of a 20 nm nucleation layer grown on sapphire by atmospheric pressure metal-organic chemical vapor deposition at 525 °C to that of an identical layer heated to 1060 °C. The fractions of cubic and hexagonal phases in the layers are determined by a comparison of the scattering data with a Hendricks–Teller model. High temperature exposure results in a decrease of the cubic fraction from 0.56 to 0.17. The good agreement with the Hendricks–Teller model indicates that the positions of the stacking faults are uncorrelated.
Scale-up and process integration of sugar production by acidolysis of municipal solid waste/corn stover blends in ionic liquids (2017)

Results indicate that MSW blends are viable and valuable resource to consider when assessing biomass availability and affordability for lignocellulosic biorefineries. This scale-up evaluation demonstrates that the acid-assisted IL deconstruction technology can be effectively scaled up to larger operations and the current study established the baseline of scaling parameters for this process.
Foldable Perovskite Solar Cells Using Carbon Nanotube‐Embedded Ultrathin Polyimide Conductor (2021)

Recently, foldable electronics technology has become the focus of both academic and industrial research. The foldable device technology is distinct from flexible technology, as foldable devices have to withstand severe mechanical stresses such as those caused by an extremely small bending radius of 0.5 mm. To realize foldable devices, transparent conductors must exhibit outstanding mechanical resilience, for which they must be micrometer-thin, and the conducting material must be embedded into a substrate. Here, single-walled carbon nanotubes (CNTs)-polyimide (PI) composite film with a thickness of 7 µm is synthesized and used as a foldable transparent conductor in perovskite solar cells (PSCs). During the high-temperature curing of the CNTs-embedded PI conductor, the CNTs are stably and strongly <i>p</i>-doped using MoO <i><sub>x</sub></i> , resulting in enhanced conductivity and hole transportability. The ultrathin foldable transparent conductor exhibits a sheet resistance of 82 Ω sq.<sup>-1</sup> and transmittance of 80% at 700 nm, with a maximum-power-point-tracking-output of 15.2% when made into a foldable solar cell. The foldable solar cells can withstand more than 10 000 folding cycles with a folding radius of 0.5 mm. Such mechanically resilient PSCs are unprecedented; further, they exhibit the best performance among the carbon-nanotube-transparent-electrode-based flexible solar cells.
Towards Training Probabilistic Topic Models on Neuromorphic Multi-chip Systems (2018)

Probabilistic topic models are popular unsupervised learning methods, including probabilistic latent semantic indexing (pLSI) and latent Dirichlet allocation (LDA). By now, their training is implemented on general purpose computers (GPCs), which are flexible in programming but energy-consuming. Towards low-energy implementations, this paper investigates their training on an emerging hardware technology called the neuromorphic multi-chip systems (NMSs). NMSs are very effective for a family of algorithms called spiking neural networks (SNNs). We present three SNNs to train topic models. The first SNN is a batch algorithm combining the conventional collapsed Gibbs sampling (CGS) algorithm and an inference SNN to train LDA. The other two SNNs are online algorithms targeting at both energy- and storage-limited environments. The two online algorithms are equivalent with training LDA by using maximum-a-posterior estimation and maximizing the semi-collapsed likelihood, respectively. They use novel, tailored ordinary differential equations for stochastic optimization. We simulate the new algorithms and show that they are comparable with the GPC algorithms, while being suitable for NMS implementation. We also propose an extension to train pLSI and a method to prune the network to obey the limited fan-in of some NMSs.
Recent progress in distributed feedback InGaN/GaN laser diodes (2019)

Laser diodes based on Gallium Nitride (GaN) are useful devices in a wide range of applications including atomic spectroscopy, data storage and optical communications. To fully exploit some of these application areas there is a need for a GaN laser diode with high spectral purity, e.g. in atomic clocks, where a narrow linewidth blue laser source can be used to target the atomic cooling transition. We report on the continuous wave, room temperature operation of a distributed feedback laser diode (DFB-LD) with high-order notched gratings. The design, fabrication and characterization of DFB devices based on the (Al,In) GaN material system is described. A single peak emission at 408.6 nm with an optical power of 20 mW at 225 mA and a side mode suppression ratio (SMSR) of 35 dB was achieved. Additionally, we demonstrate the use of a GaN DFB-LD as a transmitter in visible optical communications system. We also present results from a DFB-LD optimized for laser cooling of Sr+.