gebhart/patrepeval huggingface dataset:
Shigellaeffector IpaH4.5 targets 19S regulatory particle subunit RPN13 in the 26S proteasome to dampen cytotoxic T lymphocyte activation (2018)

Subversion of antigen-specific immune responses by intracellular pathogens is pivotal for successful colonisation. Bacterial pathogens, including Shigella, deliver effectors into host cells via the type III secretion system (T3SS) in order to manipulate host innate and adaptive immune responses, thereby promoting infection. However, the strategy for subverting antigen-specific immunity is not well understood. Here, we show that Shigella flexneri invasion plasmid antigen H (IpaH) 4.5, a member of the E3 ubiquitin ligase effector family, targets the proteasome regulatory particle non-ATPase 13 (RPN13) and induces its degradation via the ubiquitin-proteasome system (UPS). IpaH4.5-mediated RPN13 degradation causes dysfunction of the 19S regulatory particle (RP) in the 26S proteasome, inhibiting guidance of ubiquitinated proteins to the proteolytically active 20S core particle (CP) of 26S proteasome and thereby suppressing proteasome-catalysed peptide splicing. This, in turn, reduces antigen cross-presentation to CD8+ T cells via major histocompatibility complex (MHC) class I in vitro. In RPN13 knockout mouse embryonic fibroblasts (MEFs), loss of RPN13 suppressed CD8+ T cell priming during Shigella infection. Our results uncover the unique tactics employed by Shigella to dampen the antigen-specific cytotoxic T lymphocyte (CTL) response.
The Flash Memory Cell for the Nodes to Come: Material Requirements from a Device Perspective (2009)

The quest for mass storage and the diversity of end-user applications led to an aggressive scaling of the NAND Flash memory. A key factor to its success is the high density integration potential, which allows fabrication of large memory arrays. Reduction of the feature size below 40 nm may, however, require modifications of the conventional floating gate cell architecture, due to lack of physical space between neighboring cells, which no longer allows wrapping of the control gate over the floating gate. This has consequences on both intra- as well as inter-cell levels, calling for the introduction of high-k dielectrics in Flash memory. In this paper, we take a top-down stance and translate device characteristics into material requirements and/or points of attention that need to be addressed in order to ensure a successful continued scaling of the Flash memory for the upcoming technology generations.
Carrier generation in polycrystalline MgIn2O4 thin films by proton implantation (2002)

Abstract Thin films of polycrystalline MgIn2O4 (spinel structure; bandgap, 3.5 eV) were prepared on silica glass by the rf sputtering technique. The thin films were insulating in the as-deposited state, and proton implantation was carried out in the fluence range from 1 × 1015 to 1 × 1018 cm−2 at room temperature to introduce carrier electrons in the films. Upon implantation at a fluence of 1 × 1015 cm−2, the electrical conductivity increased to as high as approximately 3 × 1015 cm−1 and saturated at this level even for higher fluences. Carrier generation efficiency was about 100 % at a fluence of 1 × 1015 cm−2 but monotonically decreased with increasing fluence. Nuclear reaction analysis on deuteron-implanted specimens revealed that the depth profile of D concentration for all specimens was almost the same in the as-implanted state, and the D fraction retained in the films was about 80 % for a D+ fluence of 1 × 1016 cm−2, about 70 % for 1 × 1017 cm−2, and about 65 % for 1 × 1018 cm−2. After post-annealing at 300°C, the width of the D distribution became broader, and the retained D fraction was reduced to 50 % for a D+ fluence of 1 × 1017 cm−2 or 17 % for 1 × 1018 cm−2. These results strongly suggest that the majority of H+ ions implanted at high fluences are present in the films as neutral species such as H2 molecules. Therefore, the formation of these species, which are inactive for carrier generation, is responsible for the decrease in carrier generation efficiency.
Continuous quantitative mapping of multi-organ T1 relaxation times with ShMOLLI to assess dose response in respiratory challenges at 3T (2013)

Background The performance of T1 mapping as a stable biomarker depends on its sensitivity to pathological changes and relative insensitivity to normal physiological variations or common clinical interventions, such as oxygen administration. We address the impact of breathing air supplemented with oxygen (O2) and/or carbon dioxide (CO2) on T1 values in healthy myocardium and selected extra-cardiac tissues.
Impact of the channel direction on the 1/f noise in SOI-MOSFETs fabricated on (100) and (110) silicon oriented wafers (2007)

In this paper we present the study of 1/f noise in SOI n‐ and p‐MOSFET fabricated on Si(100) and Si(110) oriented wafers. A comparison of noise performances are first presented, then the impact of the in‐plane channel direction on the low frequency noise for each device is investigated. A particular attention is made for transistors fabricated on Si(110) oriented substrates.
Introducing descending control of nociception: a measure of diffuse noxious inhibitory controls in conscious animals (2021)

Bannister, Kirsty; Kucharczyk, Mateusz W.; Graven-Nielsen, Thomas; Porreca, Frank Author Information
Flexible and Simple Route for the Stereoselective Synthesis of Trisubstituted γ-Butyrolactones: Total Synthesis of (+)-Blastomycinone and its Analogs (2004)

A flexible route for the stereoselective synthesis of trisubstituted γ-butyrolactones, namely (+)-blastomycinone and its analogs, is devised by the Sharpless asymmetric epoxidation and the regioselective ring opening reaction with dibutylcopper lithium as the key steps to introduce the requisite alkyl chain.
Detection of pulsed-amplitude and phase-modulated signals (2003)

We review the detection of pulsed optical data formats, focusing on on/off keying (OOK) and differential phase shift keying (DPSK). We point out the benefits of pulsed signal reception, and explain why balanced rather than single-ended detection should be used for DPSK.
Online experts for admission control in SDN (2016)

SDN unleashes the potential to perform computational intensive machine learning algorithms to solve complex routing problems. This demo presents an architecture for the SDN controller that integrates several online routing algorithms for the real-time admission control of new connection requests. The demonstrator permits to compare the evolution of the network according to the admission decisions taken by different online algorithms and to simulate future scenarios to support strategic decisions aimed at improving the infrastructure.
The effect of particle size on the biodistribution of low-modulus hydrogel PRINT particles (2020)

There is a growing recognition that the deformability of particles used for drug delivery plays a significant role on their biodistribution and circulation profile. Understanding these effects would provide a crucial tool for the rational design of drug delivery systems. While particles resembling red blood cells (RBCs) in size, shape and deformability have extended circulation times and altered biodistribution profiles compared to rigid, but otherwise similar particles, the in vivo behavior of such highly deformable particles of varied size has not been explored. We report the fabrication of a series of discoid, monodisperse, low-modulus hydrogel particles with diameters ranging from 0.8 to 8.9 μm, spanning sizes smaller than and larger than RBCs. We injected these particles into healthy mice, and tracked their concentration in the blood and their distribution into major organs. These deformable particles all demonstrated some hold up in filtration tissues like the lungs and spleen, followed by release back into the circulation, characterized by decreases in particles in these tissues with concomitant increases in particle concentration in blood. Particles similar to red blood cells in size demonstrated longer circulation times, suggesting that this size and shape of deformable particle is uniquely suited to avoid clearance.
Iterative scheme for 1- and 2- dimensional d.c.-transistor simulation (1969)

A numerical iterative scheme is presented for the solution of the 1- and 2-dimensional semiconductor d.c. transport equations. This scheme is applied to an n-p-n transistor structure. Input data are geometry, doping profile, boundary conditions and, optionally, mobility dependencies and generation-recombination law.
ChemInform Abstract: RATES OF THIOL‐DISULFIDE INTERCHANGE REACTIONS BETWEEN MONO‐ AND DITHIOLS AND ELLMAN′S REAGENT (1977)

Abstract Die Geschwindigkeitskonstanten des Thiol‐Disulfid‐Austausches zwischen Mono‐ und Dithiolen sowie Ellman′s Reagens (I) werden in Beziehung zu 1A den pK a ‐Werten der Thiol‐Gruppen gesetzt.
An Unbiased Signal-to-Interference Ratio Estimator for the High Speed Downlink Packet Access System (2003)

We propose an unbiased signal-to-interference ratio (SIR) estimator for the high speed downlink packet access (HSDPA) system. The proposed SIR estimator solves the problem of underestimation present in conventional SIR estimators and is suitable for channel quality measurement in the adaptive modulation and coding scheme of HSDPA, which requires accurate SIR estimation for optimum adaptive modulation and coding selection. Our analysis and simulation results demonstrate the improved estimation performance of the proposed SIR estimator.
Supplemental Figure S5 from <sup>18</sup>F-FAZA PET Imaging Response Tracks the Reoxygenation of Tumors in Mice upon Treatment with the Mitochondrial Complex I Inhibitor BAY 87-2243 (2023)

&lt;p&gt;Supplemental Figure S5. Bar graphs showing effect of BAY 87-2243 on RT-PCR expression profiles for (A) SLC16A, (B) ITGB1, (C) IGF-2 and (D) TK-1&lt;/p&gt;
Supplementation with Red Palm Oil Increases β‐Carotene and Vitamin A Blood Levels in Patients with Cystic Fibrosis (2015)

Patients with cystic fibrosis (CF) show decreased plasma concentrations of antioxidants due to malabsorption of lipid soluble vitamins and consumption by chronic pulmonary inflammation. β-Carotene is a major source of retinol and therefore is of particular significance in CF. The aim of this study was to investigate the effect of daily intake of red palm oil (RPO) containing high amounts of β-carotene on the antioxidant levels in CF patients. Sixteen subjects were recruited and instructed to enrich their food with 2 to 3 tablespoons of RPO (~1.5 mg of β-carotene) daily over 8 weeks. Carotenoids, retinol, and α-tocopherol were measured in plasma at baseline and after intervention. In addition β-carotene, lycopene, α-tocopherol, and vitamin C were measured in buccal mucosa cells (BMC) to determine the influence of RPO on antioxidant tissue levels. Eleven subjects completed the study properly. Plasma β-carotene, retinol, and α-carotene of these patients increased, but plasma concentrations of other carotenoids and α-tocopherol as well as concentrations of β-carotene, lycopene, α-tocopherol, and vitamin C in BMC remained unchanged. Since RPO on a daily basis did not show negative side effects the data suggest that RPO may be used to elevate plasma β-carotene in CF.
Faculty Opinions recommendation of Identification of the DNA binding sites of PerA, the transcriptional activator of the bfp and per operons in enteropathogenic Escherichia coli. (2003)

Read the full review for this Faculty Opinions recommended article: Identification of the DNA binding sites of PerA, the transcriptional activator of the bfp and per operons in enteropathogenic Escherichia coli.
OP024 Agreement among central readers in the evaluation of endoscopic disease activity in Crohn's disease (2014)

of a biomarker test that can identify and stratify young IBD patients. Methods Samples from well-characterized patients were collected from 15 North American GI centers. Median age was 15 (IQR: 13-16). Samples from 251 patients were used: 147 Crohn's disease (CD), 47 ulcerative colitis (UC) and 57 non-IBD disease controls. A combination of serological markers (ASCA-IgA, ASCA-IgG, ANCA, pANCA, anti-OmpC, anti-Fla2, anti-FlaX and anti-CBir1), four gene variants (ATG16L1, NKX2-3, ECM1, and STAT3) and five inflammatory markers (CRP, SAA, ICAM, VCAM, and VEGF) were used in this evaluation. Identification of IBD, CD, and UC and was made with the aid of a machine learning model. Sensitivity, specificity, NPV, PPV and accuracy statistics were calculated for both the IBD vs. Non-IBD component of the diagnostic model, and separately for the CD vs. UC component (for patients called IBD by the model). Results The multi-marker biomarker diagnostic model performed in classifying IBD, CD and UC in pediatric patients as reported in Table 1. We observed a sensitivity of 86.1% and a specificity of 86% for identifying young adults with IBD. The sensitivity and specificity for classifying CD in patients called IBD by the model was 91.9% and 75.8%, respectively. UC sensitivity and specificity was 82.1% and 90.5%, respectively. Diagnostic accuracy of the biomarkers was 86.1% for IBD vs. non-IBD, 88.2% for CD and 88.9% for UC. The IBD NPV and PPV were 64.5% and 95.4% respectively. CD NPV and PPV were 73.5% and 92.7%, respectively. UC NPV and PPV were and 95.5% and 67.6%, respectively. Conclusion Our results demonstrate that a combination of serological, genetic, and inflammatory markers may be utilized for classifying non-IBD, CD, and UC in the young adult patient population. Further studies are required to further investigate the clinical utility of this biomarker test. Table 1
Long‐term tolerability, immunogenicity and efficacy of Nuwiq® (human‐cl rhFVIII) in children with severe haemophilia A (2018)

Long-term treatment with Nuwiq<sup>®</sup> for the prevention of bleeds in children with severe haemophilia A was well tolerated, effective and reduced spontaneous bleeding by up to 70% compared with GENA-03.
Denoising by Higher Order Statistics (2011)

A standard approach for deducing a variational denoising method is the maximum a posteriori strategy. Here, the denoising result is chosen in such a way that it maximizes the conditional density function of the reconstruction given its observed noisy version. Unfortunately, this approach does not imply that the empirical distribution of the reconstructed noise components follows the statistics of the assumed noise model. In this paper, we propose to overcome this drawback by applying an additional transformation to the random vector modeling the noise. This transformation is then incorporated into the standard denoising approach and leads to a more sophisticated data fidelity term, which forces the removed noise components to have the desired statistical properties. The good properties of our new approach are demonstrated for additive Gaussian noise by numerical examples. Our method shows to be especially well suited for data containing high frequency structures, where other denoising methods which assume a certain smoothness of the signal cannot restore the small structures.
Light-induced annihilation of Frenkel defects in organo-lead halide perovskites (2016)

The photoinduced removal of trap states due to Frenkel defects is found to enhance the PLQE of perovskite thin films.
Seamless spectrum handover improving cell outage in cognitive radio systems (2009)

In cognitive radio systems, there is a concern of service disruption because of spectrum handover. Spectrum handover occurs when a secondary user changes frequency due to the appearance of a primary user. Spectrum handover can be frequent if a cognitive radio system operates in a wide spectrum band. In this case, spectrum handover may drastically degrade the performance of cognitive radio systems because of the different propagation loss according to the usage of different frequency. Here, we propose a seamless spectrum handover scheme. The proposed handover scheme can avoid service disruption and can reduce redundant handovers. The efficiency of the proposed scheme is validated by simulation results.
Microstructure dependence of the c-axis critical current density in second-generation YBCO tapes (2011)

C-axis current flow in high temperature superconductor (HTS) tape-shaped wires arises in configurations where the local wire axis is not perpendicular to the local magnetic field, such as in power cables with helically wound HTS tapes. The c-axis critical current density Jcc has been recently found to be orders of magnitude lower than the ab-plane critical current density Jcab. Here we report on Jcc (77 K, sf) values of various YBa2Cu3O7-based (YBCO) tapes with different microstructures. Our results show that the value of Jcc (77 K, sf) decreases significantly with increasing concentration of ab-plane stacking faults in YBCO thin films and that the critical current anisotropy γ = Jcab/Jcc can reach values as high as 2070, implying that in the highest-anisotropy tape, ∼20% of the tape width carries c-axis current in a helically wound power cable.
Does polypharmacy shape dependency transitions in the very old? Findings from the Newcastle 85+ Study (2022)

when a relatively able person visits the GP or clinical pharmacist, careful consideration should be given to whether the potential benefits from adding a new medication outweigh the risk to reduced recovery of independence.
Solution-processed Bii<inf>3</inf> solar cells (2016)

We present a proof-of-concept solid state solar cell with an efficiency of 1.0 % using solution-processed BÍI3 absorber layer. Spin-coated BiI3 thin films show stability in air for over one month. The films were integrated into an all-inorganic photovoltaic device with a transition-metal oxide hole transport layer. Thermal annealing BiL· films at 100 °C in a solvent vapor led to the highest short circuit current value of 6.9 ± 0.5 mA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . In general, these devices have a large open circuit voltage deficit. EQE measurements show low collection efficiency at the BiI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> -TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> interface, indicating a potential pathway toward improved power conversion efficiencies.
LAMP3 inhibits autophagy and contributes to cell death by lysosomal membrane permeabilization (2021)

A253-control: A253 control for LAMP3 stable overexpression; A253- LAMP3: A253 LAPM3 stable overexpression; CASP1: caspase 1; CASP3: caspase 3; CHX: cycloheximide; CTSB: cathepsin B; CTSD: cathepsin D; CQ: chloroquine; DCs: dendritic cells; ER: endoplasmic reticulum; LGALS3: galectin 3; HCV: hepatitis C virus; HSG-control: HSG control for LAMP3 stable overexpression; HSG-LAMP3: HSG LAMP3 stable overexpression; HSP: heat shock protein; HTLV-1: human T-lymphocyte leukemia virus-1; IXA: ixazomib; LAMP: lysosomal associated membrane protein; MHC: major histocompatibility complex; mAb: monoclonal antibody; OE: overexpression; pepA: pepstatin A; pAb: polyclonal antibody; pSS: primary Sjögren syndrome; qRT-PCR: quantitative real- time reverse transcriptase polymerase chain reaction; SLE: systemic lupus erythematosus; SS: Sjögren syndrome; UPR: unfolded protein response; V-ATPase: vacuolar-type proton- translocating ATPase; Y-VAD: Ac-YVAD-cmk; Z-DEVD; Z-DEVD-fmk; Z-VAD: Z-VAD- fmk.
A novel architecture for robust video transmission in MC-CDMA cellular networks over slow fading channels (2004)

Reliable interactive video transmission in CDMA cellular networks is difficult since residual channel errors cannot be avoided and the available bandwidth is scarce. In order to improve quality of the decoded video, this paper introduces a novel architecture for reliable transmission in multicode DS-CDMA (MC-CDMA) systems. Unlike previous protection schemes, the new architecture not only improves video quality, but it also achieves an efficient use of the available resources in the network. As an application of this concept, we propose a robust scheme for reliable video communication from wired users to mobile users in slow fading environments. Our approach consists of two main ingredients: a novel closed-loop error control technique to reduce packet loss and interference, and a new scheme to stop error propagation in the decoded sequence originating from residual channel errors. Based both on theoretical analysis and numerical results, we show that our approach achieves important improvements in the quality of the decoded video with low additional complexity.
Effective conductivity due to continuous polarization reorientation in fluid ferroelectrics (2011)

A smectic-A (SmA) liquid crystal phase of fluid layers with in-plane polarization P is shown to exhibit effective conductivity in the semiconducting range during electric-field-induced polarization reorientation, but becomes insulating once the polarization is aligned with the field. Such fluid ferroelectrics sandwiched between highly insulating layers enable electro-optic devices with long-term dc electrostatic control of polarization and optic axis orientation.
Empirical Centroid Fictitious Play: An Approach for Distributed Learning in Multi-Agent Games (2015)

The paper is concerned with distributed learning in large-scale games. The well-known fictitious play (FP) algorithm is addressed, which, despite theoretical convergence results, might be impractical to implement in large-scale settings due to intense computation and communication requirements. An adaptation of the FP algorithm, designated as the empirical centroid fictitious play (ECFP), is presented. In ECFP players respond to the centroid of all players' actions rather than track and respond to the individual actions of every player. Convergence of the ECFP algorithm in terms of average empirical frequency (a notion made precise in the paper) to a subset of the Nash equilibria is proven under the assumption that the game is a potential game with permutation invariant potential function. A more general formulation of ECFP is then given (which subsumes FP as a special case) and convergence results are given for the class of potential games. Furthermore, a distributed formulation of the ECFP algorithm is presented, in which, players endowed with a (possibly sparse) preassigned communication graph, engage in local, non-strategic information exchange to eventually agree on a common equilibrium. Convergence results are proven for the distributed ECFP algorithm.
Communication-Efficient Distributed Reinforcement Learning (2018)

This paper deals with distributed reinforcement learning (DRL), which involves a central controller and a group of learners. In particular, two DRL settings encountered in several applications are considered: multi-agent reinforcement learning (RL) and parallel RL, where frequent information exchanges between the learners and the controller are required. For many practical distributed systems, however, such as those involving parallel machines for training deep RL algorithms, and multi-robot systems for learning the optimal coordination strategies, the overhead caused by these frequent communication exchanges is considerable, and becomes the bottleneck of the overall performance. To address this challenge, a novel policy gradient method is developed here to cope with such communication-constrained DRL settings. The proposed approach reduces the communication overhead without degrading learning performance by adaptively skipping the policy gradient communication during iterations. It is established analytically that i) the novel algorithm has convergence rate identical to that of the plain-vanilla policy gradient for DRL; while ii) if the distributed computing units are heterogeneous in terms of their reward functions and initial state distributions, the number of communication rounds needed to achieve a desirable learning accuracy is markedly reduced. Numerical experiments on a popular multi-agent RL benchmark corroborate the significant communication reduction attained by the novel algorithm compared to alternatives.