gebhart/patrepeval huggingface dataset:
An In Vitro Microneutralization Assay for SARS‐CoV‐2 Serology and Drug Screening (2020)

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the city of Wuhan, Hubei Province, China, in late 2019. Since then, the virus has spread globally and caused a pandemic. Assays that can measure the antiviral activity of antibodies or antiviral compounds are needed for SARS-CoV-2 vaccine and drug development. Here, we describe in detail a microneutralization assay, which can be used to assess in a quantitative manner if antibodies or drugs can block entry and/or replication of SARS-CoV-2 in vitro. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Microneutralization assay to test inhibition of virus by antibodies (purified antibodies or serum/plasma) Basic Protocol 2: Screening of anti-SARS-CoV-2 compounds in vitro Support Protocol: SARS-CoV-2 propagation.
Association between IGF‐1 levels ranges and all‐cause mortality: A meta‐analysis (2022)

The association between IGF-1 levels and mortality in humans is complex with low levels being associated with both low and high mortality. The present meta-analysis investigates this complex relationship between IGF-1 and all-cause mortality in prospective cohort studies. A systematic literature search was conducted in PubMed/MEDLINE, Scopus, and Cochrane Library up to September 2019. Published studies were eligible for the meta-analysis if they had a prospective cohort design, a hazard ratio (HR) and 95% confidence interval (CI) for two or more categories of IGF-1 and were conducted among adults. A random-effects model with a restricted maximum likelihood heterogeneity variance estimator was used to find combined HRs for all-cause mortality. Nineteen studies involving 30,876 participants were included. Meta-analysis of the 19 eligible studies showed that with respect to the low IGF-1 category, higher IGF-1 was not associated with increased risk of all-cause mortality (HR = 0.84, 95% CI = 0.68-1.05). Dose-response analysis revealed a U-shaped relation between IGF-1 and mortality HR. Pooled results comparing low vs. middle IGF-1 showed a significant increase of all-cause mortality (HR = 1.33, 95% CI = 1.14-1.57), as well as comparing high vs. middle IGF-1 categories (HR = 1.23, 95% CI = 1.06-1.44). Finally, we provide data on the association between IGF-1 levels and the intake of proteins, carbohydrates, certain vitamins/minerals, and specific foods. Both high and low levels of IGF-1 increase mortality risk, with a specific 120-160 ng/ml range being associated with the lowest mortality. These findings can explain the apparent controversy related to the association between IGF-1 levels and mortality.
Simulation studies of persistent photoconductivity and filamentary conduction in opposed contact semi-insulating GaAs high power switches (1999)

A self-consistent, two-dimensional, time-dependent, drift-diffusion model is developed to simulate the response of high power photoconductive switches. Effects of spatial inhomogeneities associated with the contact barrier potential are incorporated and shown to foster filamentation. Results of the dark current match the available experiment data. Persistent photoconductivity is shown to arise at a high bias even under the conditions of spatial uniformity. Filamentary currents require an inherent spatial inhomogeneity, and are more likely to occur for low optical excitation. Under strong uniform illumination, the spatial nonuniformities were quenched as a result of a polarization-induced collapse in the internal fields. However, strong electric fields resulting at the contacts create a bipolar plasma, and hence, a virtual “double injection.”
Effects of Annealing Temperature on the Charge-Collection and Light-Harvesting Properties of TiO2 Nanotube-Based Dye-Sensitized Solar Cells (2010)

We report on the influence of annealing temperature (Ta) on the microstructure and dynamics of electron transport and recombination in dye-sensitized solar cells (DSSCs) incorporating oriented titanium oxide nanotube (NT) arrays. The morphology of the NT arrays was characterized by scanning and transmission electron microscopies and Raman and X-ray diffraction spectroscopies. Over the temperature range from 200 to 600 °C, the crystallinity, crystal phase, and structural integrity of the NT walls underwent pronounced changes whereas the overall film architecture remained intact. Increasing Ta from 200 to 400 °C transformed the as-deposited NT film from the amorphous phase to partially crystalline (300 °C) to fully crystalline anatase (400 °C). When the as-deposited NTs were detached from the underlying Ti substrate and then annealed, the anatase crystallites comprising the NT walls were stable to at least 600 °C in air. When the NTs remained attached to the substrate, thermal oxidation of the Ti metal initiated the growth and propagation of rutile crystallites in the NT walls at relatively low temperatures (ca. 500 °C). Once present in the NT walls, the rutile crystallites further catalyzed the anatase-to-rutile transformation, leading to partial degradation of the walls. The percent of rutile present in the TiO2 NT walls increased from 3% to 32% for samples annealed between 500 and 600 °C. Charge transport and recombination properties of dye-sensitized NT films were studied by frequency-resolved modulated photocurrent/photovoltage spectroscopies. Altering the microstructure of the NTs led to significant changes in the electron transport and recombination kinetics in DSSCs. At a fixed photoelectron density, the electron diffusion coefficient and recombination current density are found to change orders of magnitude in the opposite direction over the temperature range. DSSCs containing NT films annealed at 400 °C exhibited the fastest transport and slowest recombination kinetics. The various structural changes were also found to affect the light-harvesting, charge-injection, and charge-collection properties of DSSCs, which, in turn, altered the photocurrent density, photovoltage, and solar energy conversion efficiency.
NaviFields (2017)

Virtual Reality allow users to explore virtual environments naturally, by moving their head and body. However, the size of the environments they can explore is limited by real world constraints, such as the tracking technology or the physical space available. Existing techniques removing these limitations often break the metaphor of natural navigation in VR (e.g. steering techniques), involve control commands (e.g., teleporting) or hinder precise navigation (e.g., scaling user's displacements). This paper proposes NaviFields, which quantify the requirements for precise navigation of each point of the environment, allowing natural navigation within relevant areas, while scaling users' displacements when travelling across non-relevant spaces. This expands the size of the navigable space, retains the natural navigation metaphor and still allows for areas with precise control of the virtual head. We present a formal description of our NaviFields technique, which we compared against two alternative solutions (i.e., homogeneous scaling and natural navigation). Our results demonstrate our ability to cover larger spaces, introduce minimal disruption when travelling across bigger distances and improve very significantly the precise control of the viewpoint inside relevant areas.
ChemInform Abstract: Efficient Synthesis of Purines and Purine Nucleosides via an Inverse Electron Demand Diels—Alder Reaction. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Angle‐dependent utilization of gradient hardware for oblique MR imaging (1994)

A straightforward method for calculating maximum gradient amplitudes for the frequency-encoding, phase-encoding, and section-select functions in oblique magnetic resonance (MR) imaging is presented. The calculated amplitude values depend on the prescribed angulation and on which of the three functions are simultaneously active. The derived expressions are optimal in most cases, and when not optimal, they still offer substantial improvement over calculations that do not incorporate angular information. Both matrix-based and geometric interpretations are presented.
One-pass frame level budget allocation in video coding using inter-frame dependency (2009)

In this paper, a one-pass budget allocation algorithm is proposed for hybrid video coding. Taking the percentage of skipped MBs as the measure of inter-frame dependency, the optimal budget allocation is first modeled for a two-frame case. Then this model is extended to a practical method in slow movement scenario, where the information of inter-frame dependency is predicted based on the previously coded frames. Simulations show that the proposed algorithm outperforms the recommended MB and frame level rate control algorithms in H.264/AVC reference software JM 15.1. For eight CIF sequences with slow movement, significant gains of 0.91 dB and 0.43 dB on average (1.66 dB and 1.49 dB at maximum) were obtained over the reference MB and frame level rate control, respectively. Considering that the computational complexity by the proposed algorithm is quite low (less than 1% of the total coding time when fast motion estimation algorithm is enabled), it is quite appealing for real-time video applications.
LiNbO 3 resonant-type optical modulatorwith double-stub structure (2001)

A resonant-type LiNbO3 optical modulator with symmetric stubs and modulating electrodes was investigated. Modulation efficiency was enhanced by the resonance of the modulating electrode. The enhancement factor of the fabricated modulator was 3.41 at 10 GHz.
Phosphane Copper(I) Dicarboxylates: Synthesis and Their Potential Use as Precursors for the Spin‐coating Process in the Deposition of Copper (2010)

Abstract Dicopper dicarboxylates [( R 3 P) m Cu X Cu(P R 3 ) m ] ( 5a , X = O 2 CCO 2 , R = Ph, m = 2; 5b , X = O 2 CCO 2 , R = n Bu, m = 3) were prepared by treatment of [Cu 2 O] ( 1a ) with HO 2 CCO 2 H ( 2a ) in presence of P R 3 ( 4a , R = Ph; 4b , R = n Bu). A further synthesis approach to mono‐ and dicopper dicarboxylates is given using an electrolysis cell equipped with Cu electrodes and charged with acids H 2 X and phosphanes R 3 P. Without addition of a base mononuclear [( n Bu 3 P) m Cu X H] ( 6a , m = 3, X H = O 2 CCO 2 H, 6b , m = 3, X H = O 2 CCH 2 CO 2 H, 6c , m = 3, X H = O 2 CCH 2 CH 2 CO 2 H, 6d , m = 2, X H = O 2 C‐2‐C 5 H 4 N‐6‐CO 2 H) was formed, whereas in presence of NEt 3 ( 3 ), the dicopper systems [( R 3 P) m Cu X Cu(P R 3 ) m ] ( 5a , X = O 2 CCO 2 , R = Ph, m = 2; 5b , X = O 2 CCO 2 , R = n Bu, m = 3; 5c , X = O 2 CCH 2 CO 2 , R = n Bu, m = 3; 5d , X = O 2 CCH 2 CH 2 CO 2 , R = n Bu, m = 3; 5e , X = O 2 C‐2‐C 5 H 4 N‐6‐CO 2 , R = n Bu, m = 3) were produced. When 6a reacted with [(tmeda)Zn( n Bu) 2 ] ( 7 ), trimetallic [(tmeda)Zn(( n Bu 3 P) 3 CuO 2 CCO 2 ) 2 ] ( 8 ) was accessible. In this heterobimetallic complex the Zn(tmeda) unit spans two CuO 2 CCO 2 entities. The molecular structures of 5a , 6a and 6d in the solid state were determined by single X‐ray structure analysis. Complexes 5a and 6a are monomers, whereas 6d creates in the solid state a linear open chain coordination polymer by hydrogen bridge formation. Characteristic for 6d is the somewhat distorted trigonal bipyrimidal arrangement around the copper atom with the n Bu 3 P ligands in axial and the C 5 H 3 NCO 2 H oxygen and nitrogen atoms in equatorial positions. In 5a the oxalate connectivity binds in a μ ‐1,2,3,4 fashion being part of a planar Cu 2 (oxalate) core. TG studies of several mono‐ and dicopper dicarboxylates were carried out. Release of the P R 3 ligands is recognized and the remaining Cu‐(di)carboxylate unit decomposes to afford elemental copper and CO 2 . The deposition of copper onto pieces of PVD‐Cu oxidized silicon wafers by applying the spin‐coating process and using 5c and 5d as precursors is discussed.
Identifying Dynamic Structural Changes of Active Sites in Pt–Ni Bimetallic Catalysts Using Multimodal Approaches (2018)

Alloy nanoparticle catalysts are known to afford unique activities that can differ markedly from their parent metals, but there remains a generally limited understanding of the nature of their atomic (and likely dynamic) structures as exist in heterogeneously supported forms under reaction conditions. Notably unclear is the nature of their active sites and the details of the varying oxidation states and atomic arrangements of the catalytic components during chemical reactions. In this work, we describe multimodal methods that provide a quantitative characterization of the complex heterogeneity present in the chemical and electronic speciations of Pt–Ni bimetallic catalysts supported on mesoporous silica during the reverse water gas shift reaction. The analytical protocols involved a correlated use of in situ X-ray Absorption Spectroscopy (XAS) and Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS), complimented by ex-situ aberration corrected Scanning Transmission Electron Microscopy (STEM). The data reveal that complex reactions occur between the metals and support in this system under operando conditions. These reactions, and the specific impacts of strong metal–silica bonding interactions, prevent the formation of alloy phases containing Ni–Ni bonds. This feature of structure provides high activity and selectivity for the reduction of CO2 to carbon monoxide without significant competitive levels of methanation. We show how these chemistries evolve to the active state of the catalyst: bimetallic nanoparticles possessing an intermetallic structure (the active phase) that are conjoined with Ni-rich, metal-silicate species.
Practical Implementation of Robust State Space Obfuscation for Hardware IP Protection (2022)

&lt;p&gt;Hardware obfuscation is a design transformation technique that transforms a design to protect its confidentiality against untrusted parties. In particular, it aims at protecting proprietary hardware intellectual property (IP) blocks against reverse engineering (RE), piracy, and extraction of design secrets. A wide array of existing works on hardware obfuscation have demonstrated its security promises and theoretical robustness against diverse attacks. However, these techniques lack in (1) scalability to large commercial-scale designs, (2) ease of integration with existing electronic design automation (EDA) tool flow, (3) ability to protect against emergent attack modes, such as structural analysis-based attacks, and (4) ability to efficiently trade-off security with design overhead. The latter requires an effective metric to quantify robustness against RE attacks. In this paper, we introduce a practical state space obfuscation algorithm and associated automation tool, ProtectIP, that address the above shortcomings. The algorithmic steps have polynomial complexity and are scalable for large designs. We have developed a complete EDA tool flow that integrates ProtectIP. We show exponential resistance can be achieved against all known RE attacks while incurring modest area overhead (24% on average) with negligible impact (maximum 5% overhead) on critical-path delay. We quantify the level of achieved security using metrics and show that an intelligent attacker with partial knowledge of the obfuscation process has a low probability (maximum 0:33) of succeeding in RE attacks.&lt;/p&gt;
Spatial distribution and developmental appearance of postjunctional P2X1 receptors on smooth muscle cells of the mouse vas deferens (2001)

P2X1-type purinoceptors have been shown to mediate fast transmission between sympathetic varicosities and smooth muscle cells in the mouse vas deferens but the spatial organization of these receptors on the smooth muscle cells remains inconclusive. Voltage clamp techniques were used to estimate the amplitudes of spontaneous excitatory junction currents (SEJCs) in cells of the vas deferens longitudinal smooth muscle layer. These currents involved the activation of about 6% of the P2X-type channels present on the cell, as compared to whole cell currents produced when isolated smooth muscle cells were exposed to maximal concentrations of either ATP or alpha,beta-MeATP. Immunofluorescence staining of the vas deferens with antibodies against P2X1 receptor showed a diffuse, grainy distribution over the entire membrane of each smooth muscle cell. Anti-P2X1 staining was not markedly clustered beneath anti-SV2-stained sympathetic varicosities. Similar results were obtained for cells in the urinary bladder. During development, P2X1 mRNA was detected as early as embryonic day 15 (E15). Increasing intensities of diffuse immunostaining for P2X1 were observed in the walls of the bladder, tail artery, and aorta from E15 until 6 weeks postnatal. The vas deferens showed increasing intensities of diffuse staining of its smooth muscle layers between 2 and 6 weeks postnatal, consistent with the time-course of development of fast purinergic transmission described previously. Together, the results suggest that the response of smooth muscle of the vas deferens to ATP released from sympathetic varicosities relies on rapidly desensitizing P2X1 receptors, distributed diffusely across the smooth muscle cell surface.
A Design of Low MDL Scrambling-type PLC 6-mode Multiplexer (2019)

A low mode-dependent-loss scrambling-type 6-mode multi/demultiplexers (mode scramblers) together with the design methodology is proposed for mode-division multiplexing system. The condition for achieving low mode-dependent-loss characteristics is discussed through two-type of mode scramblers.
Glial Membranes at the Node of Ranvier Prevent Neurite Outgrowth (2005)

Nodes of Ranvier are regularly placed, nonmyelinated axon segments along myelinated nerves. Here we show that nodal membranes isolated from the central nervous system (CNS) of mammals restricted neurite outgrowth of cultured neurons. Proteomic analysis of these membranes revealed several inhibitors of neurite outgrowth, including the oligodendrocyte myelin glycoprotein (OMgp). In rat spinal cord, OMgp was not localized to compact myelin, as previously thought, but to oligodendroglia-like cells, whose processes converge to form a ring that completely encircles the nodes. In OMgp-null mice, CNS nodes were abnormally wide and collateral sprouting was observed. Nodal ensheathment in the CNS may stabilize the node and prevent axonal sprouting.
Advanced Data-Analytics-Based Fiber-Longitudinal Monitoring for Optical Transport Networks (2020)

We present a novel monitor that estimates distance-wise optical power profile along a transmission-line-longitudinal axis throughout multiple spans by using signal at the link end only. This monitor can localize anomaly point caused by unexpected optical attenuation with sub-km resolution.
Direct and Continuous Inhibition of ADAM17 Using a Novel Selective Inhibitor Restores Functional Platelet Yield From Human Pluripotent Stem Cells (2011)

Abstract Abstract 2323 Platelet transfusion is therapeutically important for patients with thrombocytopenia and/or bleeding disorders. Problems associated with a lack of donors and unknown infections in the blood have not been fully resolved, however. In that context, human induced pluripotent stem cells (hiPSCs) are a potentially abundant source of infection-free platelets. The pluripotent state of hiPSCs and their differentiation depend upon appropriate culture conditions defined in part by oxygen and temperature. We therefore initially examined whether temperatures at or below 24°C, which are required for preservation of platelet concentrates ex vivo, allow hiPSC differentiation to generate platelets. We found that only at 37°C were platelets generated. But at 37°C in vitro, platelets are subject to degradation exemplified by the shedding of GPIbα, a receptor for von Willebrand factor (vWF), which is caused by a disintegrin and metalloprotease (ADAM) 17. We therefore developed KP-457, a novel ADAM17 inhibitor that has a reverse hydroxamic acid structure and has been found safe in rats and dogs. Although inhibition of p38 MAP kinase, putatively upstream of ADAM17, reportedly inhibits GPIbα shedding in stored human platelets, even at 37°C, administration of the p38 inhibitor SB203580 induces cytotoxicity during differentiation, leading to a loss of platelet yield from hiPSCs. By contrast, KP-457 significantly protected GPIbα expression in platelets from hiPSCs and in aged human platelets in culture at 37°C. Moreover, iPSC-derived platelets generated in the presence of KP-457 displayed improved hemostatic function when studied using an imaging system that enables characterization of single-platelet kinetics during thrombus formation after laser-induced injury in vivo. We propose this new drug could markedly improve the maintenance of functional platelets generated in culture, particularly those derived from hiPSCs. Disclosures: No relevant conflicts of interest to declare.
Phase conjugate oscillators (1989)

Optical resonators containing a phase conjugate mirror (PCM) have been a subject of great interest, where the PCM is employed as an end mirror of the resonator cavity for intracavity aberration correction. 1 Recent theoretical analysis indicates that the insertion of a PCM inside a ring laser cavity results in a reduction of the lock-in threshold and reduces the imbalance between the amplitudes of the oppositely directed traveling waves. 2 In the extreme case of phase conjugate oscillation without conventional gain, lock-in can be completely eliminated. 3 We have developed a general theory for nondegenerate oscillations in a phase conjugate oscillator (PCO) i.e., an optical resonator with a PCM as an intracavity element. The PCM consists of a nonlinear transparent medium pumped by a pair of counterpropagating laser beams so that phase conjugation of an input beam with possible gain is achieved by nondegenerate four-wave mixing (NFWM). The linear absorption/gain in the medium is also taken into account. In the absence of any conventional mirrors so that the PCO behaves like an ordinary PCM, we recover the results of phase conjugation by NFWM. 4 Our study shows that the nonlinear gain required for oscillation is considerably increased/decreased due to the linear absorption/gain in the medium, while the bandwidth and the sidelobe structure of the bandpass filter are also affected. In the case when there is only one conventional mirror, the PCO reduces to a phase conjugate resonator (a resonator bounded by a conventional mirror and a PCM). Our theory shows that nondegenerate oscillation is possible in such a resonator. The theory can also be used to study the effects of linear absorption/gain on the filter operation.
Tree LSTMs for Learning Sentence Representations (2017)

In this work we obtain sentence embeddings with a recursive model using dependency graphs as network structure, trained with dictionary definitions. We compare the performance of our recursive Tree-LSTMs against other deep learning models: a recurrent version which considers a sequential connection between sentence elements, and a bag of words model which does not consider word ordering at all. We compare the approaches in an unsupervised similarity task in which general purpose embeddings should help to distinguish related content.