gebhart/patrepeval huggingface dataset:
Subtyping of major SARS-CoV-2 variants reveals different transmission dynamics based on 10 million genomes (2022)

SARS-CoV-2 continues to evolve, causing waves of the pandemic. Up to May 2022, 10 million genome sequences have accumulated, which are classified into five major variants of concern. With the growing number of sequenced genomes, analysis of the big dataset has become increasingly challenging. Here we developed systematic approaches based on sets of correlated single nucleotide variations (SNVs) for comprehensive subtyping and pattern recognition of transmission dynamics. The approach outperformed single-SNV and spike-centric scans. Moreover, the derived subtypes elucidate the relationship of signature SNVs and transmission dynamics. We found that different subtypes of the same variant, including Delta and Omicron exhibited distinct temporal trajectories. For example, some Delta and Omicron subtypes did not spread rapidly, while others did. We identified sets of characteristic SNVs that appeared to enhance transmission or decrease efficacy of antibodies for some subtypes. We also identified a set of SNVs that appeared to suppress transmission or increase viral sensitivity to antibodies. For the Omicron variant, the dominant type in the world, we identified the subtypes with enhanced and suppressed transmission in an analysis of eight million genomes as of March 2022 and further confirmed the findings in a later analysis of ten million genomes as of May 2022. While the "enhancer" SNVs exhibited an enriched presence on the spike protein, the "suppressor" SNVs are mainly elsewhere. Disruption of the SNV correlation largely destroyed the enhancer-suppressor phenomena. These results suggest the importance of fine subtyping of variants, and point to potential complex interactions among SNVs.
Antistatic protection in wafer drying process by spin-drying (1992)

As part of an effort to produce a static-free wafer spin-dryer the authors developed an ionizer for use with spin-dryers and evaluated its charge removing and particle rejecting effects. Particle generation due to sputtering of the discharge electrodes themselves was prevented. The protection of the discharge electrodes with quartz glass completely prevents particle generation by ion and electron sputters, and the concentration of ozone generated is reduced to less than 1/10 of the usual level. This ionizer is excellent in its charge-removing performance taking only about 1 s to reduce the wafer potential from +or-5 kV to +or-0.1 kV. The residual potential due to the imbalance of ion polarity is extremely low, only 10 V at the maximum. The ionizer's charge removing effect to prevent particle deposition was also evaluated, and almost complete success is reported in preventing the statically induced deposition of particles to wafers while they are being dried by a spin-dryer.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Capacitance and bandwidth tradeoffs in a cross-coupled CMOS negative capacitor (2013)

Recent advances in technology have driven renewed interest in the design of CMOS negative capacitance circuits for diverse applications such as wideband metamaterials and radio frequency integrated circuits. In practice, the particular CMOS fabrication process generally limits the practical range of capacitance values and bandwidths that can be achieved. In addition, the reactive component of the desired impedance is often accompanied by a parasitic resistive component. To address these issues, a CMOS cross-coupled negative capacitance circuit is designed and simulated in a 0.5 micron CMOS process. Results are presented for -5 pF, -10 pF, and -20 pF designs with ten-percent bandwidths of approximately 140 MHz, 100 MHz, and 80 MHz respectively.
Conjugation of Specifically Developed Antibodies for High- and Low-Molecular-Weight Glutenins with Fluorescent Quantum Dots as a Tool for Their Detection in Wheat Flour Dough (2018)

The importance of gluten proteins, gliadins and glutenins, is well-known in the quality of wheat products. To gain more specific information about the role of glutenins in wheat dough, the two major subunits of glutenin, high- and low-molecular-weight (HMW and LMW) glutenins, were extracted, isolated, and identified by mass spectrometry. Antibodies for HMW and LMW glutenins were developed using the proteomic information on the characterized glutenin subunits. The antibodies were found to be specific to each subunit by western immunoblots and were then conjugated to quantum dots (QDs) using site-click conjugation, a new method to keep antibody integrity. A fluorescence-link immunosorbent assay tested the successful QD conjugation. The QD-conjugated antibodies were applied to dough samples, where they recognized glutenin subunits and were visualized using a confocal laser scanning microscope.
Multi-Scale Characterization of Electronic and Ionic Limitations to Power Performance of Composite Electrodes Toward Ultra-High Surface Capacities (2016)

International audience
Designing a debugging interaction language for cognitive modelers (2012)

In this paper, we investigate how a debugging environment should support a population doing work at the core of HCI research: cognitive modelers. In conducting this investigation, we extended the Natural Programming methodology (a user-centered design method for HCI researchers of programming environments), to add an explicit method for mapping the outcomes of NP's empirical investigations to a language design. This provided us with a concrete way to make the design leap from empirical assessment of users' needs to a language. The contributions of our work are therefore: (1) empirical evidence about the content and sequence of cognitive modelers' information needs when debugging, (2) a new, empirically derived, design specification for a debugging interaction language for cognitive modelers, and (3) an initial case study of our "Natural Programming Plus" methodology.
Oxidation Behavior of Mo-Si-B In Situ Composites (2007)

Isothermal oxidation behavior of Al added Mo-Si-B in-situ composites was investigated under Ar-20%O2 and air atmosphere over the temperature range of 1073–1673 K. The Al added Mo-Si-B composites ((Mo-8.7mol%Si-17.4mol%B)-1mol%Al) were prepared by arc-melting, and homogenized at 2073 K for 24 h in an Ar-flow atmosphere. The ternary Mo-Si-B in-situ composite exhibited a rapid mass loss at the initial oxidation stage and then the passive oxidation after the substrates were sealed with borosilicate glass in the temperature range of 1173–1473 K, whereas it exhibited a rapid mass gain around 1073 K. On the other hand, the Al addition significantly improved the oxidation resistance of Mo-Si-B in-situ composites at temperatures from 1073–1573 K. These excellent oxidation resistances are considered to be due to the rapid formation of a continuous, dense scale of Al-Si-O complex oxides.
A wavelength multiplexer using cascaded three-dimensional vertical couplers (2000)

A four-channel wavelength multiplexer/demultiplexer for sparse wavelength division multiplexing was demonstrated using cascaded three-dimensional (3D) vertical couplers. 17 nm channel spacing with crosstalk less than 15 dB was achieved. Strong coupled vertical couplers were fabricated using wafer bonding to invert a conventionally processed epitaxial layer and bond to a new host substrate. This technology makes the fabrication of 3D photonic integrated circuits and the realization of multilevel optical interconnects possible.
Multifunctional hybrid materials for combined photo and chemotherapy of cancer (2012)

Combined chemo and photothermal therapy in in vitro testing has been achieved by means of multifunctional nanoparticles formed by plasmonic gold nanoclusters with a protecting shell of porous silica that contains an antitumor drug. We propose a therapeutic nanoplatform that associates the optical activity of small gold nanoparticles aggregates with the cytotoxic activity of 20(S)-camptothecin simultaneously released for the efficient destruction of cancer cells. For this purpose, a method was used for the controlled assembly of gold nanoparticles into stable clusters with a tailored absorption cross-section in the vis/NIR spectrum, which involves aggregation in alkaline medium of 15 nm diameter gold colloids protected with a thin silica layer. Clusters were further encapsulated in an ordered homogeneous mesoporous silica coating that provides biocompatibility and stability in physiological fluids. After internalization in 42-MG-BA human glioma cells, these protected gold nanoclusters were able to produce effective photothermolysis under femtosecond pulse laser irradiation of 790 nm. Cell death occurred by combination of a thermal mechanism and mechanical disruption of the membrane cell due to induced generation of micrometer-scale bubbles by vaporizing the water inside the channels of the mesoporous silica coating. Moreover, the incorporation of 20(S)-camptothecin within the pores of the external shell, which was released during the process, provoked significant cell death increase. This therapeutic model could be of interest for application in the treatment and suppression of non-solid tumors.
Efficient delivery of quantum dots in live cells by gold nanoparticle mediated photoporation (2015)

There is considerable interest in using Quantum Dots (QDs) as fluorescent probes such for cellular imaging due to unique advantages in comparison with conventional molecular dyes. However, cytosolic delivery of QDs into live cells remains a major challenge. Here we demonstrate highly efficient delivery of PEG-coated QDs into live cells by means of laser-induced vapour nanobubbles. Using this procedure we succeeded in high-throughput loading of ~80% of cells while maintaining a cell viability of ~85%.
Potentiation of Glucose-induced Insulin Release by Glucose in the Isolated Pancreas of Fed and Fasted Rats (1976)

Glucose, apart from its acute insulin-releasing effect, exerts a time-dependent potentiating action on subsequent stimulations of the pancreas. The influence of a 24-hour starvation on these two actions of glucose was studied with the completely isolated, perfused rat pancreas preparation. Starvation had no effect on the time kinetics of the insulin response, but the magnitudes of the early and late insulin-secretion phases were reduced to similar extents. It was demonstrated by using a wide glucose concentration range that the maximal insulin response is not significantly modified by starvation. In contrast, both the threshold of stimulation by and the Km for glucose were higher in the pancrease from fasted rats. Thus, starvation reduces the sensitivity of the islet for the insulin-releasing action of glucose. When the stimulatory concentrations of glucose were preceded for 40 minutes by the perfusion of 8.3 mM instead of the basal, 4.4 mM glucose, insulin secretion from the pancreas of fed animals was not modified. In contrast, raising the glucose concentration of the equilibrium period to 8.3 mM potentiated markedly the insulin response to subsequent stimulations in the pancreas from fasted rats. This potentiation expressed itself as increase in the maximal response: the Km for glucose was not reduced. Thus a 40-minute pretreatment with 8.3 mM glucose does not correct the diminished sensitivity induced by a 24-hour starvation. It is concluded that in starvation (1) the sensitivity for glucose of the mechanisms that initiate insulin release is diminished; (2) the sensitivity of the pancreas for the potentiation-inducing action of glucose is augumented. (3) In both respects, the insulin response of fasted rats is similar to that of mildly diabetic subjects. These and other findings suggest that the effect of glucose in initiation of insulin release and on generation of a state of potentiation in the islet are mediated by different mechanisms.
Time reversal in ultrasound focusing transmitters and receivers (2010)

The ability of a single-channel time reversal acoustic systems to focus and receive ultrasound radiation is considered. The basic element of these systems is a liquid-filled acoustic reverberator. Two types of the reverberators have been experimentally studied; one of them is a thin-wall cylindrical balloon used in ultrasound catheters for treatment of cardiac fibrillation, and the other consists of plane-parallel foil layers. It is demonstrated that such systems can effectively focus ultrasound using only one radiation channel. Random deformation of balloon walls and foil layers leads to a noticeable improvement of focusing quality and helps to overcome the limitations imposed by a spatial symmetry of a system. The use of a binary radiation mode increases the focal field intensity as compared to the conventional mode. The possibility of spatial localization of external sources with the use of the time reversal focusing system as a receiver is demonstrated.
Identification of Troponin C Antagonists from a Phage-displayed Random Peptide Library (2021)

Affinity purification of a phage-displayed library, expressing random peptide 12-mers at the N terminus of protein III, has identified 10 distinct novel sequences which bind troponin C specifically. The troponin C-selected peptides yield a consensus binding sequence of (V/L)(D/E)XLKXXLXXLA. Sequence comparison revealed as much as a 62.5% similarity between phiT5, the peptide sequence of the phage clone with the highest level of binding to troponin C, and the N-terminal region of troponin I isoforms. Biotinylated peptides corresponding to library-derived sequences and similar sequences from various isoforms of troponin I were synthesized shown to bind troponin C specifically. Alkaline phosphatase fusion proteins of two of the phage clone sequences bound troponin C specifically, and were specifically competed by both library-derived and native troponin I peptides. Measurement of equilibrium dissociation constants of the peptides by surface plasmon resonance yielded dissociation constants for troponin C as low as 0.43 microM for pT5; in contrast, dissociation constants for calmodulin were greater than 6 microM for all peptides studied. Nondenaturing polyacrylamide gel electrophoresis demonstrated that pT5 formed a stable complex with troponin C in the presence of calcium. We also found that the pT5 peptide inhibited the maximal calcium-activated tension of rabbit psoas muscle fibers.
Number of People Blind or Visually Impaired by Glaucoma Worldwide and in World Regions 1990 – 2010: A Meta-Analysis (2016)

By 2010, one out of 15 blind people was blind due to glaucoma, and one of 45 visually impaired people was visually impaired, highlighting the increasing global burden of glaucoma.
Near-field wire-based passive probe antenna for the selective detection of the longitudinal electric field at terahertz frequencies (2009)

A passive probe antenna for cw near-field microscopy at millimeter and submillimeter wavelengths is defined. It is based on the coupling between a free-space linearly polarized propagating beam to a wire mode. This is obtained efficiently owing to a discontinuous phase plate. This passive “optical” structure allows either the generation of a subwavelength confinement of the longitudinal electric field (polarized along the wire antenna) or, due to reciprocity, the collection of the longitudinal component of the electric field (along the wire antenna) with subwavelength resolution. The emission and collection properties of the proposed antenna have been demonstrated experimentally using a preliminary realization designed to work at 0.1 THz. Experimental results are well supported by calculations.
The transparent crab: preparation and nanostructural implications for bioinspired optically transparent nanocomposites (2011)

An optically transparent crab-shell with an intact original shape and substantial morphological detail is presented. Inorganic calcium carbonate particles, proteins, lipids and pigments are removed from a native crab-shell, and the remaining chitin nanofibrous structure is impregnated by a monomer and polymerized. The nanostructural implications for man-made nanocomposites are discussed. An important application of the finding is demonstrated as heterogeneous micro-scale crab shell chitin particles are successfully used to process transparent nanocomposites. The incorporation of nanostructured chitin macro-particles not only retains transparency of the matrix resin but also drastically reduces the coefficient of thermal expansion of the polymer. Moreover, the optical transmittance of the composite is stable over a large range of temperatures despite significant inhomogeneity at the mm scale and the large temperature changes in the refractive index of the resin in its isolated state. This class of materials is an interesting candidate for transparent substrates in next-generation electronic devices such as flexible displays and solar cells.
Two-Dimensional Direct-Reading Fluorescence Spectrograph for DNA Sequencing by Capillary Array Electrophoresis (2001)

We report a compact, two-dimensional direct-reading fluorescence spectrograph and demonstrate its application to DNA sequencing by capillary array electrophoresis. The detection cuvette is based on sheath flow, wherein the capillaries terminate in a two-dimensional array in a fluid-filled chamber that is pressurized with buffer. A thin metal plate is located downstream from the capillaries. This barrier plate has an array of holes that precisely matches the location of the capillaries. Buffer flows through the holes, drawing analyte from the capillaries in a well-defined array of thin filaments. Fluorescence is excited in the upper chamber with an elliptically shaped laser beam. The bottom chamber is sealed with a glass window and drained from the side. Fluorescence is detected by imaging the illuminated sample streams through the holes in the barrier plate. A prism is used to disperse fluorescence from each sample across a CCD camera so that the emission spectrum is monitored simultaneously from each capillary. The instrument is demonstrated in a 32-capillary configuration but can be scaled to several thousand capillaries.
Cyclic Sulfamidates as Vehicles for the Synthesis of Substituted Lactams (2004)

[reaction: see text] A structurally diverse series of mono- and disubstituted 1,2- and 1,3-cyclic sulfamidates react with stabilized enolates, including malonate and phosphonoacetate variants, to provide, after lactamization, substituted and alpha-functionalized pyrrolidinone and piperidinone derivatives.
A new apparatus for measuring high viscosities (1988)

A new viscometer especially designed for the high viscosity region is presented. The magnetoviscometer uses Stokes' falling sphere principle, where the gravitational force is substituted by a magnetic one. The working principle and set-up of the apparatus are described; some results obtained on technical polymers are given and special features of the magnetoviscometer (such as measurement under pressure and the use of disposable cells) are emphasised.
Reliability of directional information in unsorted spikes and local field potentials recorded in human motor cortex (2014)

NCT00912041.).
Akuszitikai Példatár (Acoustic Problems) (1989)

First Page
2‐Phenoxy‐nicotinamides are Potent Agonists at the Bile Acid Receptor GPBAR1 (TGR5) (2012)

Potency with potential: 2-Phenoxy-nicotinamides were identified as potent agonists at the GPBAR1 receptor, a target in the treatment of obesity, type 2 diabetes and metabolic syndrome. Extensive structure-activity relationship studies supported by homology modeling and docking resulted in the identification of optimized GPBAR1 agonists, potent against both human and mouse receptors, endowed with favorable physicochemical properties and good metabolic stability.
Multiprocessor system with multiple concurrent modes of execution (2023)

A multiprocessor system supports multiple concurrent modes of speculative execution. Speculation identification numbers (IDs) are allocated to speculative threads from a pool of available numbers. The pool is divided into domains, with each domain being assigned to a mode of speculation. Modes of speculation include TM, TLS, and rollback. Allocation of the IDs is carried out with respect to a central state table and using hardware pointers. The IDs are used for writing different versions of speculative results in different ways of a set in a cache memory.
New routes to control nanoparticle synthesis: general discussion (2015)

Yangwei Liu opened a general discussion of the paper by A. Paul Alivisatos: In the in situ TEM experiment, the NPs are actually moving in 3D with a range of several hundred nanometers. In the images and videos that were shown in the presentation,1 I was quite surprised that during the movement,
Cutting Edge: NK Cells Mediate IgG1-Dependent Hyperacute Rejection of Xenografts (2004)

Classic hyperacute rejection is dependent on the activation of the terminal components of complement. Recently, xenoantibodies with limited abilities to activate the classical pathway of complement in vitro have been implicated in the acute vascular rejection of xenografts. It is unclear how these Abs affect their pathogenic activities in vivo. In this study, we demonstrate the ability of an anti-Gal-alpha1,3Gal (Gal) IgG1, with modest complement-activating abilities in vitro, to induce xenograft rejection. This rejection was dependent on the activation of complement, on FcgammaR-mediated interactions, and on the presence of NK cells. Inhibition of any one of these factors resulted in the abrogation of IgG1-mediated rejection. In contrast, an anti-Gal IgG3 mAb induced classic, hyperacute rejection that was solely dependent on complement activation. Our observations implicate two types of IgG-mediated rejection; one that is dependent on complement activation, and a second that is uniquely dependent on complement, FcgammaR, and NK cells.
Loran Data Modulation: A Primer [AESS Tutorial IV] (2007)

Loran has provided navigation service since 1958. Though not originally designed with data broadcast capabilities, Loran's versatility has enabled data to be broadcast with great benefits. Research in the last two decades has resulted in a tremendous increase in the data capacity of Loran thereby increasing its utility. Currently, a modernized Loran is being evaluated for its capability to backup GPS and data modulation is an integral part of this Loran design. An overview and analysis of Loran modulation techniques is provided.
What’s Next for Me? (2012)

Few things are impossible to diligence and skill. Great works are performed not by strength, but perseverance.
Analysis of Safe Operating Area of NLDMOS and PLDMOS Transistors Subject to Transient Stresses (2010)

Transient safe operating area (TSOA) of n-type and p-type laterally diffused metal-oxide-semiconductor (LDMOS) subject to transient stresses is presented for electrostatic discharge applications. LDMOS devices connected in the gate-grounded and gate-biased configurations are stressed with 1-, 2-, 5-, 10-, and 100-ns duration transmission line pulses, and a methodology to develop an effective and accurate TSOA based on these measurements is discussed. Two-dimensional technology computer-aided design simulations are also used to discuss critical physical mechanisms governing the current conduction during the transients and the condition that finally leads to device failure beyond the TSOA.
DIRECTOR CONFIGURATION OF A NEMATIC LIQUID CRYSTAL AROUND A SPHERICAL PARTICLE: NUMERICAL ANALYSIS USING ADAPTIVE MESH REFINEMENT (2004)

We investigate numerically the orientational configuration of a nematic liquid crystal around a spherical particle. The use of adaptive mesh refinement scheme proves quite useful to overcome the numerical difficulty arising from large scale difference between a particle and a topological defect. Our scheme reproduces successfully the hedgehog and the Saturn ring configurations that have been observed experimentally. To demonstrate that dynamical behaviors can also be investigated using our scheme, we present a simulation result which exhibits a transition from a hedgehog to a Saturn ring under the application of an external field.