gebhart/patrepeval huggingface dataset:
Anti‐IFN‐α/‐ω neutralizing antibodies from COVID‐19 patients correlate with downregulation of IFN response and laboratory biomarkers of disease severity (2022)

A significant number of COVID-19 patients were shown to have neutralizing antibodies (NAB) against IFN; however, NAB specificity, fluctuation over time, associations with biochemical and hematological parameters, and IFN gene expression are not well characterized. Binding antibodies (BAB) to IFN-α/-β were screened in COVID-19 patients' serum. All BAB positive sera, and a subset of respiratory samples, were tested for NAB against IFN-α/-β/-ω, using an antiviral bioassay. Transcript levels of IFN-α/-β/-ω and IFN-stimulated genes (ISGs) were quantified. Anti-IFN-I BAB were found in 61 out of 360 (17%) of patients. Among BAB positive sera, 21.3% had a high NAB titer against IFN-α. A total of 69.2% of anti-IFN-α NAB sera displayed cross-reactivity to IFN-ω. Anti-IFN-I NAB persisted in all patients. NAB to IFN-α were also detected in 3 out of 17 (17.6%) of respiratory samples. Anti-IFN-I NAB were higher in males (p = 0.0017), patients admitted to the ICU (p < 0.0001), and patients with a fatal outcome (p < 0.0001). NAB were associated with higher levels of CRP, LDH, d-Dimer, and higher counts of hematological parameters. ISG-mRNAs were reduced in patients with persistently NAB titer. NAB are detected in a significant proportion of severe COVID-19. NAB positive patients presented a defective IFN response and increased levels of laboratory biomarkers of disease severity.
A proteomic screen reveals novel Fas ligand interacting proteins within nervous system Schwann cells (2007)

Fas ligand (FasL) binds Fas (CD95) to induce apoptosis or activate other signaling pathways. In addition, FasL transduces bidirectional or 'reverse signals'. The intracellular domain of FasL contains consensus sequences for phosphorylation and an extended proline rich region, which regulate its surface expression through undetermined mechanism(s). Here, we used a proteomics approach to identify novel FasL interacting proteins in Schwann cells to investigate signaling through and trafficking of this protein in the nervous system. We identified two novel FasL interacting proteins, sorting nexin 18 and adaptin beta, as well as two proteins previously identified as FasL interacting proteins in T cells, PACSIN2 and PACSIN3. These proteins are all associated with endocytosis and trafficking, highlighting the tight regulation of cell surface expression of FasL in the nervous system.
Visualization Of 3-D Finite Element Model Analysis Of Defibrillation (2005)

Construction and solution of 3-D finite element models of the thorax experiencing defibrillatory shock generates several 3-D data sets: tomographic scans, tissue classification, thoracic voltages, thoracic voltage gradients, and thoracic current densities. The requirements for a set of visualization tools to aid in interpreting these data are identified, and an implementation/development plan is presented.
A novel class of nucleolar RNAs from Tetrahymena (1992)

We describe a family of at least four nucleolar RNAs (snoRNAs) from the ciliate, Tetrahymena. The snoRNAs are 120-140 nucleotides long, moderately AU-rich and contain no modified nucleotides. Their 5' ends are blocked by a cap of unknown nature. The snoRNAs can be folded into similar secondary structures consisting of two hairpins separated by a single-stranded AU-rich spacer. The sequences and secondary structures show no extensive sequence or secondary structure resemblance to any other small RNAs in the public databases.
Direct Synthesis of Hydrogen Peroxide and Benzyl Alcohol Oxidation Using Au−Pd Catalysts Prepared by Sol Immobilization (2010)

We report the preparation of Au-Pd nanocrystalline catalysts supported on activated carbon prepared via a sol-immobilization technique and explore their use for the direct synthesis of hydrogen peroxide and the oxidation of benzyl alcohol. In particular, we examine the synthesis of a systematic set of Au-Pd colloidal nanoparticles having a range of Au/Pd ratios. The catalysts have been structurally characterized using a combination of UV-visible spectroscopy, transmission electron microscopy, STEM HAADF/XEDS, and X-ray photoelectron spectroscopy. The Au-Pd nanoparticles are found in the majority of cases to be homogeneous alloys, although some variation is observed in the AuPd composition at high Pd/Au ratios. The optimum performance for the synthesis of hydrogen peroxide is observed for a catalyst having a Au/Pd 1:2 molar ratio. However, the competing hydrogenation reaction of hydrogen peroxide increases with increasing Pd content, although Pd alone is less effective than when Au is also present. Investigation of the oxidation of benzyl alcohol using these materials also shows that the optimum selective oxidation to the aldehyde occurs for the Au/Pd 1:2 molar ratio catalyst. These measured activity trends are discussed in terms of the structure and composition of the supported Au-Pd nanoparticles.
<title>Effects of carrier transport on relative intensity noise and modulation response in quantum-well lasers</title> (1992)

The maximum possible intrinsic modulation in semiconductor lasers is conventionally written in terms of the K factor. Although this is often sufficient in bulk lasers, it is usually not true in quantum well lasers where carrier transport can significantly affect the high speed properties. Here we present analytical expressions, which include the effects of carrier transport, for the modulation response and the relative intensity noise in quantum well lasers. We show that in the presence of significant transport effects, the K factor is not an accurate measure of the maximum possible intrinsic modulation bandwidth.
Gas‐Sorption Properties of Cobalt(II)–Carborane‐Based Coordination Polymers as a Function of Morphology (2009)

Infinite pores! Three structurally and topologically distinct infinite coordination-polymer (ICP) materials are synthesized from 1,12-dihydroxycarbonyl-1,12-dicarba-closo-dodecaborane and CoII salts (see image). All three have markedly different porosities and, consequently, different N2, H2, and CO2 uptakes. This work emphasizes the importance of morphological control in tailoring the properties of ICP structures. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Review: Infection, fever, and exogenous and endogenous pyrogens: some concepts have changed (2004)

For many years, it was thought that bacterial products caused fever via the intermediate production of a host-derived, fever-producing molecule, called endogenous pyrogen (EP). Bacterial products and other fever-producing substances were termed exogenous pyrogens. It was considered highly unlikely that exogenous pyrogens caused fever by acting directly on the hypothalamic thermoregulatory center since there were countless fever-producing microbial products, mostly large molecules, with no common physical structure. In vivo and in vitro, lipopolysaccharides (LPSs) and other microbial products induced EP, subsequently shown to be interleukin-1 (IL-1). The concept of the `endogenous pyrogen' cause of fever gained considerable support when pure, recombinant IL-1 produced fever in humans and in animals at subnanomolar concentrations. Subsequently, recombinant tumor necrosis factor-α (TNF-α), IL-6 and other cytokines were also shown to cause fever and EPs are now termed pyrogenic cytokines. However, the concept was challenged when specific blockade of either IL-1 or TNF activity did not diminish the febrile response to LPS, to other microbial products or to natural infections in animals and in humans. During infection, fever could occur independently of IL-1 or TNF activity. The cytokine-like property of Toll-like receptor (TLR) signal transduction provides an explanation by which any microbial product can cause fever by engaging its specific TLR on the vascular network supplying the thermoregulatory center in the anterior hypothalamus. Since fever induced by IL-1, TNF-α, IL-6 or TLR ligands requires cyclooxygenase-2, production of prostaglandin E 2 (PGE 2 ) and activation of hypothalamic PGE 2 receptors provides a unifying mechanism for fever by endogenous and exogenous pyrogens. Thus, fever is the result of either cytokine receptor or TLR triggering; in autoimmune diseases, fever is mostly cytokine mediated whereas both cytokine and TLR account for fever during infection.
Experiences with locking in a NUMA multiprocessor operating system kernel (1994)

We describe the locking architecture of a new operating system, HURRICANE, designed for large scale shared-memory multiprocessors. Many papers already describe kernel locking techniques, and some of the techniques we use have been previously described by others. However, our work is novel in the particular combination of techniques used, as well as several of the individual techniques themselves. Moreover, it is the way the techniques work together that is the source of our performance advantages and scalability. Briefly, we use: • a hybrid coarse-grain/fine-grain locking strategy that has the low latency and space overhead of a coarse-grain locking strategy while having the high concurrency of a fine-grain locking strategy; • replication of data structures to increase access bandwidth and improve concurrency; • a clustered kernel that bounds the number of processors that can compete for a lock so as to reduce second order effects such as memory and interconnect contention; • Distributed Locks to further reduce second order effects, with modifications that reduce the uncontended latency of these locks to close to that of spin locks.
Can Low-Dose Unenhanced Multidetector CT Be Used for Routine Evaluation of Suspected Renal Colic? (2003)

Can Low-Dose Unenhanced Multidetector CT Be Used for Routine Evaluation of Suspected Renal Colic?Douglas S. Katz1, N. Venkataramanan1, Sandy Napel2 3 and F. Graham Sommer2Audio Available | Share
MOF modified pencil electrode for hydrogen peroxide detections (2018)

Background: Hydrogen peroxide is a key component of fungal biomass degradation. Fungal extracellular enzymes can produce this reactive oxygen species or depend on it as a co-substrate. The measurement of H2O2 in proximity of enzymes bound to biomass is important to elucidate its production rate by oxidases, its consumption rate by peroxidases. Objectives This work reports the fabrication and characterization of pencil graphite electrode (PGE) and its application to measure the H2O2 production by cellobiose dehydrogenase (CDH). Methods: The limit of detection (LOD) and the sensitivity of pencil graphite electrode were detected for both of bare and modified PGE, respectively. The H2O2 generation of cellulose immobilized CDH was measured using the MOF modified PGE. CDH produces H2O2 in the presence of cellobiose as a substrate. Results: MOF modified PGE exhibited low LODs (571 μM) and high sensitivities (2.35μA mM-1mm-1). The lower acquisition costs and higher simplicity compensate for the higher LODs and lower sensitivities when compared to platinum electrodes. Conclusions: PGE was easy to fabricate, multiply usable and cost effective which make it a strong and promising tool for H2O2 measuring.
Probabilistic Inference in Graphical Models (1998)

This chapter contains sections titled: 2.1 Exact Inference Using Probability Propagation (The Sum-Product Algorithm), 2.2 Monte Carlo Inference: Gibbs Sampling and Slice Sampling, 2.3 Variational Inference, 2.4 Helmholtz Machines
Performance of physical cell ID detection using PVS based transmit diversity for NB-IoT (2017)

The Narrowband (NB)-Internet-of-Things (IoT) radio interface by the 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> generation partnership project (3GPP) achieves efficient low-cost transmission of IoT traffic with low power consumption for a set of user equipment (UE). Transmit diversity at a base station is effective in achieving a high detection probability for the NB primary synchronization signal (NPSS) and NB secondary synchronization signal (NSSS) without increasing computational complexity at the UE. This paper investigates the effect of precoding vector switching (PVS) based transmit diversity employing up to 8 transmitter antennas on the physical cell ID (PCID) detection probability for NB-IoT. Computer simulation results show when the fading among transmitter antennas is uncorrelated, and that the NPSS detection probability using PVS based transmit diversity with N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">tx</sub> = 4 antennas is improved by approximately 14% compared to that with N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">tx</sub> = 2 at the average received signal-to-noise power ratio of -5 dB. Moreover, the PCID detection probability with N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">tx</sub> = 4 is improved by approximately 10% compared to that with N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">tx</sub> = 2 even for a high fading correlation among transmitter antennas such as 0.6. When increasing the N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">tx</sub> value to 8, the PCID detection probability increases by approximately 8% compared to that with N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">tx</sub> = 4 for the large frequency offset of A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</sub> = 70 kHz. Therefore, we conclude that the PVS based transmit diversity with more antennas up to N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">tx</sub> = 8 is effective in improving the PCID detection probability when considering the actual impairments including fading correlation among transmitter antennas and frequency offset due to the frequency error of the oscillator in the IoT equipment.
A Modular Plasmid Assembly Kit for Multigene Expression, Gene Silencing and Silencing Rescue in Plants (2014)

The Golden Gate (GG) modular assembly approach offers a standardized, inexpensive and reliable way to ligate multiple DNA fragments in a pre-defined order in a single-tube reaction. We developed a GG based toolkit for the flexible construction of binary plasmids for transgene expression in plants. Starting from a common set of modules, such as promoters, protein tags and transcribed regions of interest, synthetic genes are assembled, which can be further combined to multigene constructs. As an example, we created T-DNA constructs encoding multiple fluorescent proteins targeted to distinct cellular compartments (nucleus, cytosol, plastids) and demonstrated simultaneous expression of all genes in Nicotiana benthamiana, Lotus japonicus and Arabidopsis thaliana. We assembled an RNA interference (RNAi) module for the construction of intron-spliced hairpin RNA constructs and demonstrated silencing of GFP in N. benthamiana. By combination of the silencing construct together with a codon adapted rescue construct into one vector, our system facilitates genetic complementation and thus confirmation of the causative gene responsible for a given RNAi phenotype. As proof of principle, we silenced a destabilized GFP gene (dGFP) and restored GFP fluorescence by expression of a recoded version of dGFP, which was not targeted by the silencing construct.
Germanium nMOSFETs with GeO2 Passivation and n+/p Junctions Formed by Spin-On Dopants (2012)

In this work, Ge devices are fabricated with a gate stack consisting of an Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> high-k dielectric with GeO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> interfacial passivation layer and a TaN metal gate. Diodes and nFETs contain n+ layers formed via a “spin-on dopant” (SOD), using Ni source and drain contacts.
MIMO Detection Methods: How They Work [Lecture Notes] (2009)

The goal of this lecture has been to provide an overview of approaches, in the communications receiver context. Which method is the best in practice? This depends much on the purpose of solving : what error rate can be tolerated, what is the ultimate measure of performance (e.g., frame-error-rate, worst-case complexity, or average complexity), and what computational platform is used. Additionally, the bits in s may be part of a larger code word and different s vectors in that code word may either see the same H (slow fading) or many different realizations of H (fast fading). This complicates the picture, because notions that are important in slow fading (such as spatial diversity) are less important in fast fading, where diversity is provided anyway by time variations. Detection for MIMO has been an active field for more than ten years, and this research will probably continue for some time.
Comparison of Isoflurane and α-Chloralose in an Anesthetized Swine Model of Acute Pulmonary Embolism Producing Right Ventricular Dysfunction (2015)

Pulmonary embolism (PE) is a leading cause of sudden cardiac death, and a model is needed for testing potential treatments. In developing a model, we compared the hemodynamic effects of isoflurane and α-chloralose in an acute swine model of PE because the choice of anesthesia will likely affect the cardiovascular responses of an animal to PE. At baseline, swine that received α-chloralose (n = 6) had a lower heart rate and cardiac output and higher SpO2, end-tidal CO2, and mean arterial pressure than did those given isoflurane (n = 9). After PE induction, swine given α-chloralose compared with isoflurane exhibited a lower heart rate (63 ± 10 compared with 116 ± 15 bpm) and peripheral arterial pressure (52 ± 12 compared with 61 ± 12 mm Hg); higher SpO2 (98% ± 3% compared with 95% ± 1%), end-tidal CO2 (35 ± 4 compared with 32 ± 5), and systolic blood pressure (121 ± 8 compared with 104 ± 20 mm Hg); and equivalent right ventricular:left ventricular ratios (1.32 ± 0.50 compared with 1.23 ± 0.19) and troponin I mean values (0.09 ± 0.07 ng/mL compared with 0.09 ± 0.06 ng/mL). Isoflurane was associated with widely variable fibrinogen and activated partial thromboplastin time. Intraexperiment mortality was 0 of 6 animals for α-chloralose and 2 of 9 swine for isoflurane. All swine anesthetized with α-chloralose survived with sustained pulmonary hypertension, RV-dilation-associated cardiac injury without the confounding vasodilatory or coagulatory effects of isoflurane. These data demonstrate the physiologic advantages of α-chloralose over isoflurane for anesthesia in a swine model of severe submassive PE.
MicroRNAs Related to Cognitive Impairment After Hearing Loss (2020)

These results indicate that miR-376a-3p and miR-598-3p were related to cognitive impairment after hearing loss.
Ferroelectric thin films for monolithic optical devices (1995)

Abstract Though many technical barriers must be crossed, current trends in materials fabrication suggest several routes to integrating electrooptic and nonlinear optical materials monolithically with silicon and III-V semiconductor technology. These approaches include poled organic polymers, poled fused silica, and polycrystalline or epitaxially grown dielectric and ferroelectric oxide thin films. Optical waveguides fabricated from these materials may enable applications in integrated optics such as frequency doublers and modulators. Although the principal work in our laboratory is on oxide heterostructures on GaAs and sapphire, the introduction highlights the progress of other approaches. Because optical losses limit the feasibility of many device structures, considerable discussion is devoted to this topic. The use of atomic force microscopy to predict scattering losses. The summary is preceeded by some brief remarks about poling.
Unilateral Problems in Structural Analysis IV : Proceedings of the fourth meeting on Unilateral Problems in Structural Analysis, Capri, June 14-16, 1989 (1991)

Elementary Solutions for Equilibrium Problems of Masonry-Like Materials.- Finite Element Analysis of Nonlinear Laminated Composite Plates.- Holonomic Versus Rate Relations in Plasticity.- A Unified Treatment of Damage and Plasticity Based on a New Definiton of Microfracture.- Shape Optimization in Unilateral Boundary Value Problems.- Dynamics of Rigid Bodies with Dry Friction and Partially Elastic Collisions.- Calculation of the Evolution of the Form of a Railway Wheel Profile through Wear.- A Global Existence Result for the Quasistatic Frictional Contact Problem with Normal Compliance.- Debonding of Bimodular Plates.- Remarks on a Numerical Method for Unilateral Contact Including Friction.- Recent Research on Elastic-Plastic Oscillators.- Optimal Control of Systems Governed by Variational-Hemivariational Inequalities.- Theorems of the Alternative in Unilateral Structural Mechanics.- Quasi-Static Signorini's Contact Problem with Friction and Duality.- Dynamics of Unilateral Systems on a Finite-Dimensional Riemannian Manifold.
Microbiome and Metabolome driven differentiation of TGF-β producing Tregs leads to Senescence and HIV latency (2020)

Summary Current therapeutic interventions to eradicate latent HIV (“reservoir”) and restore immune function in ART-treated HIV infection have yet to show efficacy. To explore mechanisms of HIV persistence, we apply an integrated systems biology approach and identify a distinct group of individuals with poor CD4 T-cell reconstitution (Immunologic non-responders, “INRs”) and high frequencies of cells with inducible HIV. Contrary to the prevailing notion that immune activation drives HIV persistence and immune dysfunction, peripheral blood leukocytes from these subjects have enhanced expression of a network of genes regulated by cellular senescence driving transcription factors (TFs) FOXO3, SMAD2 and IRF3. In these subjects, increased frequencies of regulatory T cells and expression of the TGF-β signaling cascade are complimented by the downregulation of cell cycle, metabolic and pro-inflammatory pathways. Lactobacillaceae family and metabolites (members of the butyrate family – i.e. α-ketobutyrate) were correlated with Treg frequencies in “Senescent-INRs” ex vivo, triggered the differentiation of TGF-β producing Tregs and promoted HIV latency establishment in vitro. These cascades, downstream of PD-1/TGF-β, prevent memory T cell differentiation and are associated with an increase in frequencies of cells with inducible HIV ex vivo. Our findings identify cellular senescence responses that can be targeted by PD-1 or TGF-β specific interventions that have shown safety and efficacy in cancer, and may prove to be crucial for HIV eradication.
Complete analytical solution of electromagnetic field problem of high-speed spinning ball (2012)

In this article, a small sphere spinning in a rotating magnetic field is analyzed in terms of the resulting magnetic flux density distribution and the current density distribution inside the ball. From these densities, the motor torque and the eddy current losses can be calculated. An analytical model is derived, and its results are compared to a 3D finite element analysis. The model gives insight into the torque and loss characteristics of a solid rotor induction machine setup, which aims at rotating the sphere beyond 25 Mrpm.