gebhart/patrepeval huggingface dataset:
Carrier dynamics and surface vibration-assisted Auger recombination in porous silicon (2018)

Excitation and recombination dynamics of the photoexcited charge carriers in porous silicon membranes were studied using a femtosecond pump-probe technique. Near-infrared pulses (800 nm, 60 fs) were used for the pump while, for the probe, we employed different wavelengths in the range between 3.4 and $5\phantom{\rule{0.28em}{0ex}}\ensuremath{\mu}\text{m}$ covering the medium wavelength infrared range. The data acquired in these experiments consist of simultaneous measurements of the transmittance and reflectance as a function of the delay time between the pump and probe for different pump fluences and probe wavelengths. To evaluate the results, we developed an optical model based on the two-dimensional Maxwell-Garnett formula, incorporating the free-carrier Drude contribution and nonuniformity of the excitation by the Wentzel-Kramers-Brillouin model. This model allowed the retrieval of information about the carrier density as a function of the pump fluence, time, and wavelength. The carrier density data were analyzed to reveal that the recombination dynamics is governed by Shockley-Read-Hall and Auger processes, whereas the diffusion has an insignificant contribution. We show that, in porous silicon samples, the Auger recombination process is greatly enhanced at the wavelength corresponding to the infrared-active vibrational modes of the molecular impurities on the surface of the pores. This observation of surface-vibration-assisted Auger recombination is not only for porous silicon in particular, but for low-dimension and bulk semiconductors in general. We estimate the time constants of Shockley-Read-Hall and Auger processes, and demonstrate their wavelength dependence for the excited carrier density in the range of ${10}^{18}--{10}^{19}\phantom{\rule{0.28em}{0ex}}1/{\text{cm}}^{3}$. We demonstrate that both processes are enhanced by up to three orders of magnitude with respect to the bulk counterpart. In addition, we provide a plethora of the physical parameters evaluated from the experimental data, such as the dielectric function and its dependence on the injection level of the free carriers, charge-carrier scattering time related high-frequency conductivity, and the free-carrier absorption at the midwave infrared range.
Fast hybrid parallel carry look-ahead adder (1990)

A new optical parallel arithmetic processing scheme using a nonholographic optoelectronic content-addressable memory (CAM) is discussed. The design of a four-bit CAM-based optical carry look-ahead adder (CLA) is presented. Compared with existing optoelectronic binary addition approaches, this nonholographic CAM scheme offers a number of practical advantages, such as faster processing speed and ease of optical implementation and alignment. For the addition of numbers longer than four bits, by incorporating the previous stages' carry, a number of four-bit CLA's can be cascaded. Experimental results are also presented.
A stabilizing gyroscopic obstacle avoidance controller for underactuated systems (2016)

This work addresses the problem of controlling an underactuated system to a goal state in a cluttered environment. To this end, a gyroscopic obstacle avoidance controller is proposed for a class of underactuated systems, which take as inputs body torques and a thrust force along some known body-fixed axis. The Lyapunov stability of the controller in the presence of obstacles is shown in theory and verified through simulations. Care is taken to ensure stability even when the system has only a finite obstacle detection radius, and a novel gyroscopic obstacle avoidance gain selection is designed which smoothly attenuates the steering force as the robot heads away from an obstacle. Furthermore, a gyroscopic steering force tailored to two primitive obstacles, namely cylinders and spheres, is proposed. Simulations of a quadrotor system and a nanosatellite system validate that the controller is stable under a large number of obstacles and smoothly converges to the goal state.
Switching processes and switching reproducibility in ferromagnetic ring structures (2004)

We present an experimental study of the reproducibility of the different switching processes occurring in rings. Using superconducting quantum interference device and magnetoresistance measurements, we can measure hysteresis loops of arrays of rings and single structures at varying temperatures and thereby separate the influence of thermal excitations and defects (extrinsic and intrinsic). We find that the temperature dependence of the switching fields and their distributions can be correlated with the different physical processes occurring during different transitions. Measurements of the angular dependence of the switching fields of a single ring allow us to distinguish the contributions of extrinsic and intrinsic defects to the switching field distributions and, counterintuitively, it is established that transitions involving nucleation processes are less prone to defects and thermal excitations than processes involving domain-wall or vortex core depinning and propagation.
Is polypharmacy the future for pharmacological management of obesity? (2022)

Despite the rapidly increasing prevalence and associated costs of obesity, treatment options have remained remarkably limited. Some 650 million people are estimated to be living with obesity, but until recently the lipase inhibitor orlistat was the only mainstay pharmacological option, alongside dietary restriction. However, with FDA approval of the glucagon-like peptide 1 receptor (GLP-1R) agonists, liraglutide and semaglutide, for the management of obesity, it is hoped the tide is beginning to turn. Roux-en-Y gastric bypass (RYGB) surgery remains the most effective intervention for weight loss, being attributable to changes in energy intake/expenditure. This is largely driven by substantial post-surgical modulation of circulating gut hormones, including GLP-1, as well as peptide tyrosine–tyrosine (PYY), oxyntomodulin (OXM), glucose-dependent insulinotropic hormone (GIP), cholecystokinin (CCK) and ghrelin. In order to mimic these effects of RYGB, there has been a recent surge of interest in pursuit of both administration of individual peptide combinations as well as development of unimolecular peptide hormone-based polypharmacy; single peptidic agents that co-activate several different receptor signalling pathways. Dual agonist therapies such as the GLP-1/GIP co-agonist Tirzepatide, are nearing regulatory approval for management of non-alcoholic fatty liver disease (NAFLD) and type 2 diabetes mellitus (T2DM). Given the significant appetite and weight reductions attained with these agents, it is hoped that such unimolecular peptide hormone drugs, along with similar molecules in development, will ultimately yield successful modern polypharmacy to help manage the current obesity epidemic.
Methods for neural circuit inference from population calcium imaging data (2010)

Frontiers Events is a rapidly growing calendar management system dedicated to the scheduling of academic events. This includes announcements and invitations, participant listings and search functionality, abstract handling and publication, related events and post-event exchanges. Whether an organizer or participant, make your event a Frontiers Event!
A new heuristic for rectilinear Steiner trees (2003)

The minimum rectilinear Steiner tree (RST) problem is one of the fundamental problems in the field of electronic design automation. The problem is NP-hard, and much work has been devoted to designing good heuristics and approximation algorithms; to date, the champion in solution quality among RST heuristics is the Batched Iterated 1-Steiner (BI1S) heuristic of Kahng and Robins (1992). In a recent development, exact RST algorithms have witnessed spectacular progress: the new release of the GeoSteiner code of Warme, Winter, and Zachariasen (1998) has average running time comparable to that of the fastest available Bl1S implementation, due to Robins. We are thus faced with the paradoxical situation that an exact algorithm for an NP-hard problem is competitive in speed with a state-of-the-art heuristic for the problem. The main contribution of this paper is a new RST heuristic, which has at its core a recent 3/2 approximation algorithm of Rajagopalan and Vazirani (1999) for the metric Steiner tree problem on quasi-bipartite graphs-these are graphs that do not contain edges connecting pairs of Steiner vertices. The RV algorithm is built around the linear programming relaxation of a sophisticated integer program formulation, called the bidirected cut relaxation. Our heuristic achieves a good running time by combining an efficient implementation of the RV algorithm with simple, but powerful geometric reductions. Experiments conducted on both random and real VLSI instances show that the new RST heuristic runs significantly faster than Robins' implementation of BI1S and than the GeoSteiner code. Moreover, the new heuristic typically gives higher-quality solutions than Bl1S.
Studies With Human Coronaviruses II. Some Properties of Strains 229E and OC43 (1972)

SummaryWhen the human coronaviruses, OC43 and 229E, are grown in the absence of calf serum, they have similar thermal inactivation rates and similar UV inactivation rates. When they are grown in the presence of serum, the thermal inactivation rate of OC43, and the UV inactivation rate of both OC43 and 229E are reduced, and evidence suggests this is because the viruses are in aggregates. The UV inactivation rate of serum-free OC43 and 229E is very similar to that of influenza A2 suggesting that the genomes are of comparable size. The shutoff temperatures for OC43 and 229E are 35-36° and 36-37°, respectively.The authors wish to thank Mr. A. R. Kalica for preparing and examining the electron microscope specimens.
Chemoselective Electrosynthesis Using Rapid Alternating Polarity (2021)

Challenges in the selective manipulation of functional groups (chemoselectivity) in organic synthesis have historically been overcome using either reagents/catalysts that tunably interact with a substrate or through modification to shield undesired sites of reactivity (protecting groups). Although electrochemistry offers precise redox control to achieve unique chemoselectivity, this approach often becomes challenging in the presence of multiple redox-active functionalities. Historically, electrosynthesis has been performed almost solely by using direct current (DC). In contrast, utilization of alternating current (AC) has been considered as an option to improve reaction efficiency rather than a way to achieve distinctly different reaction outcomes. Here we show how a unique type of waveform employed to deliver electric current – rapid alternating polarity (rAP) – enables control over reaction outcomes in the chemoselective reduction of carbonyl compounds, one of the most widely used reaction manifolds. The reactivity observed cannot be recapitulated using DC electrolysis or chemical reagents. The synthetic value brought by this new method for controlling chemoselectivity is vividly demonstrated in the context of classical reactivity problems such as chiral auxiliary removal and cutting-edge medicinal chemistry topics such as the synthesis of PROTACs.
DNA methylation age calculators reveal association with diabetic neuropathy in type 1 diabetes (2020)

Various methods of measuring DNAm age are sub-optimal in detecting people at higher risk of developing diabetic complications although some work better than the others.
<title>Application of variational calculus to nonimaging optics: design for small sources in three dimensions</title> (1999)

In this work the variational calculus will be applied to the design with axisymmetric sequential optical surfaces for small sources directly in 3D. This method is proven to be useful even in the case in which the skewness distributions of output bundle and emitter do not fit. The tool provides both the optimum 3D ray bundles at the exit aperture of a rotational collimator and the best 2D assignation of rays allowing the collimation reach its limit. Once this best assignation has been obtained, the optical profiles can be designed easily using only the central ray of the bundles. Afterwards, the actual device is obtained by rotation. As a consequence of the kind of method aforementioned, the angular performance of the collimators can be nearly error- free predicted before ray tracing.
Figure S1 from High Detection Rates of Pancreatic Cancer Across Stages by Plasma Assay of Novel Methylated DNA Markers and CA19-9 (2023)

&lt;p&gt;Supplemental Figure 1 shows the predicted probability of cancer from the cross-validated MDM rForest model, demonstrating no significant difference in model performance based on tumor size, tumor location, presence of symptoms at the time of diagnosis, or timing of biopsy in relationship to blood draw.&lt;/p&gt;
Negative Regulation of the Pseudomonas aeruginosa Outer Membrane Porin OprD Selective for Imipenem and Basic Amino Acids (1999)

Pseudomonas aeruginosa OprD is a specific porin which facilitates the uptake of basic amino acids and imipenem, a carbapenem antibiotic. Resistance to imipenem due to the loss of OprD is an important mechanism for the loss of clinical effectiveness. To investigate the negative regulatory mechanisms influencing oprD expression, a gene upstream of the coregulated mexEF-oprN efflux operon, designated mexT, was cloned. The predicted 304-amino-acid mature MexT protein showed strong homology to LysR-type regulators. When overexpressed it induced the expression of the mexEF-oprN efflux operon while decreasing the level of expression of OprD. The use of an oprD::xylE transcriptional fusion indicated that it acted by repressing the transcription of oprD. Salicylate, a weak aromatic acid known to reduce porin expression and induce low levels of multiple antibiotic resistance in Escherichia coli, was able to induce imipenem resistance and reduce the expression of OprD but not multiple antibiotic resistance or OprN expression in P. aeruginosa. This was also demonstrated to occur at the level of transcription. Acetyl salicylate and benzoate, but not catechol, were also able to reduce the levels of OprD in the P. aeruginosa outer membranes. These OprD-suppressing compounds increased imipenem resistance even in a mexT-overexpressing and nfxC mutant backgrounds, suggesting that such resistance is independent of the MexT repressor and that oprD is influenced by more than a single mechanism of repression.
Convergence in Optical and Digital Pattern Recognition: introduction to the feature issue (2010)

This Applied Optics feature issue, in addition to optical and digital pattern recognition, includes their convergence in the form of computational imaging.
Validating temporal properties of a deployed application with an MDA approach (2005)

International audience
Evaluation of a dual-frequency VECSEL emitting at 852 nm for cesium atomic clocks using coherent population trapping (2013)

2nd Workshop on VECSEL, Oct 2013, Montpellier, France
Defective activation of mitogen-activated protein kinase after allogeneic bone marrow transplantation (1996)

Allogeneic bone marrow transplant (BMT) recipients have increased susceptibility to infections for prolonged periods after phenotypic reconstitution of donor cells. This immunodeficiency status is characterized by multiple T-cell functional abnormalities. This study was designed to investigate several signaling pathways involved in T-cell activation during this period of immune deficiency. In initial experiments using equal numbers of CD3+ cells or highly purified T-cell subpopulations obtained from normal controls and BMT recipients, we confirmed that abnormal T-cell proliferation after CD3 cross-linking, phytohemagglutinin stimulation, or phorbol myristate acetate (PMA) stimulation of peripheral blood mononuclear cells from BMT recipients was due to a qualitative T-cell deficiency rather than to low numbers of circulating T cells. We next investigated the ability of the T-cell receptor/CD3 complex to transduce signals via receptor-associated protein tyrosine kinases. In all BMT recipients, CD3 cross-linking induced protein tyrosine phosphorylation of several proteins in a similar fashion to that seen in controls, including phosphorylation of a 21-kD protein that represents the zeta subunit of the receptor itself. Further investigation showed that CD3 cross-linking and PMA stimulation did not increase 42-44-kD mitogen-activated protein kinase (MAPK) activity. The failure of MAPK activation in BMT recipients occurred despite tyrosine phosphorylation of the 42-44-kD proteins, which, in normal controls, parallels enzyme activation. Our results indicate that T-cell immunodeficiency in BMT recipients is associated with a selective failure of MAPK activation, possibly related to abnormal posttranslational positive regulation of this enzyme.
Data from Selective Modulation of a Pan-Essential Protein as a Therapeutic Strategy in Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Cancer dependency maps, which use CRISPR/Cas9 depletion screens to profile the landscape of genetic dependencies in hundreds of cancer cell lines, have identified context-specific dependencies that could be therapeutically exploited. An ideal therapy is both lethal and precise, but these depletion screens cannot readily distinguish between gene effects that are cytostatic or cytotoxic. Here, we use a diverse panel of functional genomic screening assays to identify &lt;i&gt;NXT1&lt;/i&gt; as a selective and rapidly lethal &lt;i&gt;in vivo&lt;/i&gt; relevant genetic dependency in &lt;i&gt;MYCN&lt;/i&gt;-amplified neuroblastoma. NXT1 heterodimerizes with NXF1, and together they form the principal mRNA nuclear export machinery. We describe a previously unrecognized mechanism of synthetic lethality between NXT1 and its paralog NXT2: their common essential binding partner NXF1 is lost only in the absence of both. We propose a potential therapeutic strategy for tumor-selective elimination of a protein that, if targeted directly, is expected to cause widespread toxicity.&lt;/p&gt;Significance:&lt;p&gt;We provide a framework for identifying new therapeutic targets from functional genomic screens. We nominate NXT1 as a selective lethal target in neuroblastoma and propose a therapeutic approach where the essential protein NXF1 can be selectively eliminated in tumor cells by exploiting the NXT1–NXT2 paralog relationship.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Wang and Abdel-Wahab, p. 2129&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;i&gt;This article is highlighted in the In This Issue feature, p. 2113&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Background-Free Protein Detection in Polyacrylamide Gels and on Electroblots Using Transition Metal Chelate Stains (2003)

Electrophoretically separated proteins may be visualized using organic dyes such as Ponceau Red, Amido Black, Fast Green, or most commonly Coomassie Brilliant Blue (,). Alternatively, sensitive detection methods have been devised using metal ions and colloids of gold, silver, copper, carbon, or iron (-). Metal chelates form a third class of stains, consisting of transition metal complexes that bind avidly to proteins resolved in polyacrylamide gels or immobilized on solid-phase membrane supports (-). In recent years, metal chelate stains have been designed and optimized specifically for compatibility with commonly used microchemical characterization procedures employed in proteomics. The metal chelate stains are simple to implement, and do not contain extraneous chemicals such as glutaraldehyde, formaldehyde, or Tween-20 that are well known to interfere with many downstream protein characterization procedures.
Resilient Distributed Estimation: Exponential Convergence Under Sensor Attacks (2018)

This paper studies fully distributed parameter estimation under measurement attacks. A connected network of agents makes measurements of a parameter while an adversary manipulates a subset of the measurements. The goal of the agents is to recover the parameter in the presence of measurement attacks. This paper presents an iterative consen-sus+innovations algorithm for resilient distributed estimation. The algorithm ensures that all agents correctly recover the parameter of interest, with exponentially fast rate of convergence, so long as less than [3/10] of the agents' measurements are under attack, regardless of the (connected) network topology. We demonstrate the performance of the algorithm through numerical examples.
Direct Visualization of Oxygen Distribution in Operating Fuel Cells (2008)

Zelldiagnose: Die Sauerstoffverteilung innerhalb einer arbeitenden Brennstoffzelle kann visualisiert werden, wenn man ein durchsichtiges Gasflussfeld mit Farbstoff-Filmen überzieht (siehe Bild; räumliche Auflösung: 300 μm, Zeitauflösung: 500 ms). Die Sauerstoffverteilung in einer Polymerelektrolytmembran-Brennstoffzelle stimmte nicht mit den erwarteten Werten überein, was auf einen Beitrag durch Wasser schließen lässt.
External control of the scattering properties of a single optical nanoantenna (2010)

We present a mechanism to control the scattering properties of individual optical nanoantennas by applying an external electric field. We find that by electrically tuning an anisotropic load medium the scattered intensity becomes voltage-dependent. We also demonstrate that the scattering diagram of the antenna can be externally adjusted. This on-demand command opens up the possibility to tune an antenna without changing its geometrical parameters.
Deep-level emissions influenced by O and Zn implantations in ZnO (2005)

A set of bulk ZnO samples implanted with O and Zn at various densities were investigated by photoluminescence. The implantation concentration of O and Zn is varied between 1×1017∕cm3 and 5×1019∕cm3. The samples were thermally treated in an oxygen gas environment after the implantation. The results clearly show the influence of O and Zn implantations on the deep-level emission. By comparing the photoluminescence spectra for the samples with different implantations, we can conclude that the VZn is responsible to the observed deep-level emission. In addition, a novel transition at the emission energy of 3.08eV at 77K appears in the O-implanted sample with 5×1019∕cm3 implantation concentration. The novel emission is tentatively identified as O-antisite OZn.
Proteomics of a plant pathogen: Agrobacterium tumefaciens (2011)

Agrobacterium tumefaciens is an important plant pathogen which belongs to the α-proteobacteria. In addition, it has served as the main tool for plant molecular genetics. Here we focus on three major aspects: (i) proteomic mapping, (ii) the use of proteomics for the understanding of the response of A. tumefaciens to changes in environmental conditions and (iii) the analysis of the changes in genome expression following interaction with the host. These studies convey a global outlook on the functional genomics of A. tumefaciens and help to understand the physiology of this important organism.
Jet-associated deuteron production in pp collisions at s=13 TeV (2021)

Deuteron production in high-energy collisions is sensitive to the space-time evolution of the collision system, and is typically described by a coalescence mechanism. For the first time, we present results on jet-associated deuteron production in pp collisions at s = 13 TeV, providing an opportunity to test the established picture for deuteron production in events with a hard scattering. Using a trigger particle with high transverse-momentum (p T > 5 GeV/c) as a proxy for the presence of a jet at midrapidity, we observe a measurable population of deuterons being produced around the jet proxy. The associated deuteron yield measured in a narrow angular range around the trigger particle differs by 2.4-4.8 standard deviations from the uncorrelated background. The data are described by PYTHIA model calculations featuring baryon coalescence.