gebhart/patrepeval huggingface dataset:
The Sushi Domains of Secreted GABAB1 Isoforms Selectively Impair GABAB Heteroreceptor Function (2008)

GABA(B) receptors are the G-protein-coupled receptors for gamma-aminobutyric acid (GABA), the main inhibitory neurotransmitter in the brain. GABA(B) receptors are promising drug targets for a wide spectrum of psychiatric and neurological disorders. Receptor subtypes exhibit no pharmacological differences and are based on the subunit isoforms GABA(B1a) and GABA(B1b). GABA(B1a) differs from GABA(B1b) in its ectodomain by the presence of a pair of conserved protein binding motifs, the sushi domains (SDs). Previous work showed that selectively GABA(B1a) contributes to heteroreceptors at glutamatergic terminals, whereas both GABA(B1a) and GABA(B1b) contribute to autoreceptors at GABAergic terminals or to postsynaptic receptors. Here, we describe GABA(B1j), a secreted GABA(B1) isoform comprising the two SDs. We show that the two SDs, when expressed as a soluble protein, bind to neuronal membranes with low nanomolar affinity. Soluble SD protein, when added at nanomolar concentrations to dissociated hippocampal neurons or to acute hippocampal slices, impairs the inhibitory effect of GABA(B) heteroreceptors on evoked and spontaneous glutamate release. In contrast, soluble SD protein neither impairs the activity of GABA(B) autoreceptors nor impairs the activity of postsynaptic GABA(B) receptors. We propose that soluble SD protein scavenges an extracellular binding partner that retains GABA(B1a)-containing heteroreceptors in proximity of the presynaptic release machinery. Soluble GABA(B1) isoforms like GABA(B1j) may therefore act as dominant-negative inhibitors of heteroreceptors and control the level of GABA(B)-mediated inhibition at glutamatergic terminals. Of importance for drug discovery, our data also demonstrate that it is possible to selectively impair GABA(B) heteroreceptors by targeting their SDs.
Introduction (2011)

Pour que l’objet existe en tant que tel, il faut que l’homme reconnaisse qu’ils font deux et que, l’ayant posé comme distinct de lui, il le pose également dans une altérité absolue. Ce partage est toujours précaire. Jeté au-devant de nous, l’objet s’offre à la perception humaine comme une altérité première : il est un autre corps occupant un autre espace, forme familière ou étrangère qui devient « objet » à part entière en se dotant de contours. Entre la forme et l’objet, il y a l’enveloppe, ...
Subdural electrodes in the presurgical evaluation for surgery of epilepsy. (1992)

This article gives first an overview of the advantages and disadvantages of electrodes of progressively greater invasiveness used in the evaluation of patients who are candidates for surgery of epilepsy. The following sections discuss the design of subdural electrodes, their clinical indications, and the relative advantages and disadvantages of subdural electrodes when compared with other invasive techniques.
(Invited) Influence of Vibrations on the Emission Properties of Single Graphene Quantum Dots (2022)

Recent years have shown an increasing number of studies dedicated to new light emitters for diverse applications such as optoelectronics, bio-imaging, and quantum technologies. In this context, graphene quantum dots (GQD) have important assets since bottom-up chemistry allows complete control of the structure, opening the way to wide customization of their electronic, optical, and spin properties [1-3]. The full benefit from these opportunities requires addressing GQD’s intrinsic photophysical properties.To do so, single molecule photoluminescence experiment is a powerfull tool [4]. Here, we highlight the influence of vibrations on GQDs’ optical properties, by comparing optical studies to extensive DFT/TDDFT calculations combined with molecular dynamics simulations. Specifically, we discussed their role in the transitions' oscillator strengths [5]. In order to get deeper in the photophysics of GQD, we investigate the spectroscopy of single GQDs at cryogenic temperatures. In particular, we show a narrowing of the emission lines at low temperature, that allows us to characterize and identify vibrational replicas that are characteristic to GQDs [6]. [1] M. G. Debije, J. Am. Chem. Soc . 2004, 126, 4641 [2] X. Yan, X. Cui, and L.-s. Li, J. Am. Chem. Soc . 2010 132, 5944 [3] A. Konishi et al , J. Am. Chem. Soc. 2010, 132, 11021 [4] S. Zhao et al , Nature Communications , 2018 , 9, 3470 [5] T. Liu et al , under review [6] T. Liu et al , in preparation
Lossless Predictive Coding (2009)

For typical images, the values of adjacent pixels are highly correlated; that is, a great deal of information about a pixel value can be obtained by inspecting its neighboring pixel values. This property is exploited in predictive coding techniques where an attempt is made to predict the value of a given pixel based on the values of the surrounding pixels. We first describe a general, but impractical, predictive coding scheme and then discuss modifications that yield a practical scheme.
DART: A Framework for Determining Approximation Levels in an Approximable Memory Hierarchy (2019)

In this article, we propose a framework for determining approximation levels of approximable memories in a memory hierarchy for executing error resilient applications. The framework aims at optimizing the configuration for employing approximate memories in a computing system. It is based on considering data footprints at different memory hierarchy levels and an expected output quality to determine the amount of approximations at each memory hierarchy level. The problem of finding a suitable memory approximation configuration is performed using a branch-and-bound algorithm considering all possible memory approximation arrangements. The best configuration leading to the lowest power consumption when meeting the expected output quality is selected. The efficacy of the proposed framework for two memory hierarchies with different cache topologies is evaluated by comparing energy consumptions of approximate memories with those of the exact memory units in the memory hierarchy under different output accuracy level targets. For example, with 28 dB as a peak signal to noise ratio (PSNR) constraint, the study, which is performed for four image processing applications, indicates up to 54% and 22% power consumption improvements for the SRAM cache and the DRAM memory, respectively.
Subcell Modeling of Frequency-Dependent Thin Layers in the FDTD Method (2016)

A subcell modeling technique for frequency-dependent thin layers in finite-difference time-domain method is introduced. The proposed method is based on the application of the integral form of the Maxwell-Ampere equation and the solution of a set of auxiliary equations to advance the field components. It has the ability to handle one or several frequency-dependent thin layers embedded in a frequency-dependent medium without solving high-order differential equations. To validate our proposed method, we compare the obtained results with analytical solutions and with numerical references in both time domain and frequency domain.
Extraction of large valence-band energy offsets and comparison to theoretical values for strained-Si/strained-Ge type-II heterostructures on relaxed SiGe substrates (2012)

Metal-oxide-semiconductor capacitors were fabricated on type-II staggered gap strained-Si/strained-Ge heterostructures epitaxially grown on relaxed SiGe substrates of various Ge fractions. Quasistatic quantum-mechanical capacitance-voltage (CV) simulations were fit to experimental CV measurements to extract the band alignment of the strained layers. The valence-band offset of the strained-Si/strained-Ge heterostructure was found to be 770, 760, and 670 meV for 35, 42, and 52$%$ Ge in the relaxed SiGe substrate, respectively. These values are approximately 100 meV larger than the usually recommended band offsets for modeling Si/Ge structures. It is shown that the larger valence-band offsets found here are consistent with an 800-meV average valence-band offset between Si and Ge, which also explains the type-II band alignment observed in strained-Si${}_{1\ensuremath{-}x}$Ge${}_{x}$ on unstrained-Si heterostructures.
Classification of emotional content of sighs in dyadic human interactions (2012)

Emotions are an important part of human communication and are expressed both verbally and non-verbally. Common nonverbal vocalizations such as laughter, cries and sighs carry important emotional content in conversations. Sighs often are associated with negative emotion. In this work, we show that emotional sighs exist along both ends of the valence axis (positive-emotion vs. negative-emotion sighs) in spontaneous affective dialogs and that they have certain distinct multimodal characteristics. Classification results show that it is possible to differentiate between the two types of emotionally valenced sighs, using a combination of acoustic and gestural features with an overall unweighted accuracy of 58.26%.
Predictive Value and Cost-Effectiveness Analysis of a Rapid Polymerase Chain Reaction for Preoperative Detection of Nasal Carriage of<i>Staphylococcus aureus</i> (2003)

Rapid real-time PCR is an accurate, rapid, and cost-effective method for identifying S. aureus carriers for preoperative intervention.
Society for Immunotherapy of Cancer clinical and biomarkers data sharing resource document: Volume II—practical challenges (2020)

The development of strongly predictive validated biomarkers is essential for the field of immuno-oncology (IO) to advance. The highly complex, multifactorial data sets required to develop these biomarkers necessitate effective, responsible data-sharing efforts in order to maximize the scientific knowledge and utility gained from their collection. While the sharing of clinical- and safety-related trial data has already been streamlined to a large extent, the sharing of biomarker-aimed clinical trial derived data and data sets has been met with a number of hurdles that have impaired the progression of biomarkers from hypothesis to clinical use. These hurdles include technical challenges associated with the infrastructure, technology, workforce, and sustainability required for clinical biomarker data sharing. To provide guidance and assist in the navigation of these challenges, the Society for Immunotherapy of Cancer (SITC) Biomarkers Committee convened to outline the challenges that researchers currently face, both at the conceptual level (Volume I) and at the technical level (Volume II). The committee also suggests possible solutions to these problems in the form of professional standards and harmonized requirements for data sharing, assisting in continued progress toward effective, clinically relevant biomarkers in the IO setting.
(Invited) Photoelectrocatalysis: Solar-Assisted Hydrogen Production in Microgravity Environments (2017)

Artificial photosynthesis systems, which follow the concept of the Z-scheme of natural photosynthesis, are presently being realized as catalyst-functionalized photovoltaic tandem devices for the photoelectrochemical oxidation of water and the simultaneous generation of hydrogen as a so-called “solar fuel”. The successful implementation of an efficient photoelectrochemical (PEC) water splitting cell is not only a highly desirable approach to solving the energy challenge on earth: an effective air revitalization system generating a constant flux of O 2 while simultaneously recycling CO 2 and providing a sustainable fuel supply is also essential for the International Space Station and long-term space missions, where a regular resupply from earth is not possible. Here, we present the photoelectrochemical production of hydrogen in microgravity environments on p-type indium phosphide electrodes with deposited rhodium electrocatalysts. Our findings indicate that microgravity has a significant impact on the gas bubble evolution behaviour and the mass transfer rate of the evolved hydrogen gas on the electrode surface. Furthermore, microgravity influences the current-voltage characteristics and the overall solar-to-hydrogen efficiency of the catalyst functionalized semiconductor-based half-cell. Further experiments with nanostructured rhodium catalysts fabricated by shadow nanosphere lithography on the InP surface suggest that the structure of the electrode surface plays a significant role for the gas bubble evolution behaviour and for the further the development of efficient prototypes for solar-assisted water splitting and hydrogen production that operate in micro- and hypergravity environments.
Small‐Molecule Screening and Profiling by Using Automated Microscopy (2004)

Automated fluorescence microscopy provides a powerful tool for analyzing the physiological state of single cells with high throughput and high information content. Here I discuss two types of experiments in which this technology was used to discover and characterize bioactive small molecules. In phenotypic-screening experiments, the goal is to find "hits" with specific effects on cells by screening large libraries of small molecules. An example is screening for small molecules that perturb mitosis by novel mechanisms. In cytological-profiling experiments, the goal is to characterize the bioactivity of a limited number of small molecules in considerable depth, and thus understand their mechanism and toxicities at the cellular level. I discuss an example in which 100 small molecules with known bioactivity were profiled by using multiple fluorescent probes, and clustered into mechanistic classes by automated statistical analysis.
A Nested Association Mapping Panel in <i>Arabidopsis thaliana</i> for Mapping and Characterizing Genetic Architecture (2020)

Linkage and association mapping populations are crucial public resources that facilitate the characterization of trait genetic architecture in natural and agricultural systems. We define a large nested association mapping panel (NAM) from 14 publicly available recombinant inbred line populations (RILs) of <i>Arabidopsis thaliana</i>, which share a common recurrent parent (Col-0). Using a genotype-by-sequencing approach (GBS), we identified single nucleotide polymorphisms (SNPs; range 563-1525 per population) and subsequently built updated linkage maps in each of the 14 RIL sets. Simulations in individual RIL populations indicate that our GBS markers have improved power to detect small effect QTL and enhanced resolution of QTL support intervals in comparison to original linkage maps. Using these robust linkage maps, we imputed a common set of publicly available parental SNPs into each RIL linkage map, generating overlapping markers across all populations. Though ultimately depending on allele frequencies at causal loci, simulations of the NAM panel suggest that surveying between 4 to 7 of the 14 RIL populations provides high resolution of the genetic architecture of complex traits, relative to a single mapping population.
Integrating planning and execution for a team of heterogeneous robots with time and communication constraints (2018)

International audience
Coupled TM surface plasmon features of graphene-metal layered structure in the sub-THz frequency range (2015)

TM surface plasmon (SP) characteristics of a four-layer structure, consisting of air as the superstrate, a monolayer of graphene, a dielectric buffer layer and metal as the substrate are analyzed at sub-THz frequencies. TM SPs in such case are represented by metal-like and graphene-like branches. For small frequencies the metal-like plasmon splits up into two branches depending on the graphene electron concentration; one of the branches goes into cutoff at the point where the branch features Brewster-type characteristics. Graphene-like plasmon modes are converted into short-range modes for small buffer thicknesses. Brewster-type SP modes can be effectively modulated in the vicinity of their cutoff thicknesses by means of the graphene electron concentration.
Statistical physics and Alzheimer’s disease (1998)

We discuss the possible utility of statistical physics in elucidating some of the puzzling phenomena that seem to occur in the brains of patients affected with Alzheimer’s disease. Further, we report three specific results from this approach: (i) The size distribution of senile plaques appears to be log-normal, (ii) We develop a model for growth of senile plaques that is characterized by both aggregation and disaggregation, and (iii) We quantify neuron architecture and find quantitative evidence for the existence of microcolumns positioned at right angles to the known lamina.
Redesign of a protein–peptide interaction: Characterization and applications (2009)

The design of protein-peptide interactions has a wide array of practical applications and also reveals insight into the basis for molecular recognition. Here, we present the redesign of a tetratricopeptide repeat (TPR) protein scaffold, along with its corresponding peptide ligand. We show that the binding properties of these protein-peptide pairs can be understood, quantitatively, using straightforward chemical considerations. The recognition pairs we have developed are also practically useful for the specific identification of tagged proteins. We demonstrate the facile replacement of these proteins, which we have termed T-Mods (TPR-based recognition module), for antibodies in both detection and purification applications. The new protein-peptide pair has a dissociation constant that is weaker than typical antibody-antigen interactions, yet the recognition pair is highly specific and we have shown that this affinity is sufficient for both Western blotting and affinity purification. Moreover, we demonstrate that this more moderate affinity is actually advantageous for purification applications, because extremely harsh conditions are not required to dissociate the T-Mod-peptide interaction. The results we present are important, not only because they represent a successful application of protein design but also because they help define the properties that should be sought in other scaffolds that are being developed as antibody replacements.
Effects of in-situ TiB2 particles on machinability and surface integrity in milling of TiB2/2024 and TiB2/7075 Al composites (2020)

In-situ ceramics particle reinforced aluminum matrix composites are favored in the aerospace industry due to excellent properties. However, the hard ceramic particles as the reinforcement phase bring challenges to machining. To study the effect of in-situ TiB2 particles on machinability and surface integrity of TiB2/2024 composite and TiB2/7075 composite, milling experiments were performed, and compared with conventional 2024 and 7075 aluminum alloys. In-situ TiB2 particles clustered at the grain boundaries and dispersed inside the matrix alloy grains hinder the dislocation movement of the matrix alloy. Therefore, the milling force and temperature of the composites are higher than those of the aluminum alloys due to the increase of the strength and the decrease of the plasticity. In the milling of composites, abrasive wear is the main wear form of carbide tools, due to the scratching of hard nano-TiB2 particles. The composites containing in-situ TiB2 particles have machining defects such as smearing, micro-scratches, micro-pits and tail on the machined surface. However, in-situ TiB2 particles impede the plastic deformation of the composites, which greatly reduces cutting edge marks on the machined surface. Therefore, under the same milling parameters, the surface roughness of TiB2/2024 composite and TiB2/7075 composite is much less than that of 2024 and 7075 aluminum alloy respectively. Under the milling conditions of this experiment, the machined subsurface has no metamorphic layer, and the microhardness of the machined surface is almost the same as that of the material. Besides, compared with 2024 and 7075 aluminum alloy, machined surfaces of TiB2/2024 composite and TiB2/7075 composite both show tensile residual stress or low magnitude of compressive residual stress.
Low Temperature Serpentinite Replacement by Carbonates during Seawater Influx in the Newfoundland Margin (2020)

Serpentinite replacement by carbonates in the seafloor is one of the main carbonation processes in nature providing insights into the mechanisms of CO2 sequestration; however, the onset of this process and the conditions for the reaction to occur are not yet fully understood. Preserved serpentine rim with pseudomorphs of carbonate after serpentine and lobate-shaped carbonate grains are key structural features for replacement of serpentinite by carbonates. Cathodoluminescence microscopy reveals that Ca-rich carbonate precipitation in serpentinite is associated with a sequential assimilation of Mn. Homogeneous δ18O values at the µm-scale within grains and host sample indicate low formation temperature (&lt;20 °C) from carbonation initiation, with a high fluid to rock ratio. δ13C (1–3 ± 1‰) sit within the measured values for hydrothermal systems (−3–3‰), with no systematic correlation with the Mn content. δ13C values reflect the inorganic carbon dominance and the seawater source of CO2 for carbonate. Thermodynamic modeling of fluid/rock interaction during seawater transport in serpentine predicts Ca-rich carbonate production, at the expense of serpentine, only at temperatures below 50 °C during seawater influx. Mg-rich carbonates can also be produced when using a model of fluid discharge, but at significantly higher temperatures (150 °C). This has major implications for the setting of carbonation in present-day and in fossil margins.
Type II superlattice technology for LWIR detectors (2016)

SCD has developed a range of advanced infrared detectors based on III-V semiconductor heterostructures grown on GaSb. The XB<i>n</i>/XB<i>p</i> family of barrier detectors enables diffusion limited dark currents, comparable with MCT Rule-07, and high quantum efficiencies. This work describes some of the technical challenges that were overcome, and the ultimate performance that was finally achieved, for SCD’s new 15 &mu;m pitch “Pelican-D LW” type II superlattice (T2SL) XB<i>p</i> array detector. This detector is the first of SCD's line of high performance two dimensional arrays working in the LWIR spectral range, and was designed with a ~9.3 micron cut-off wavelength and a format of 640 x 512 pixels. It contains InAs/GaSb and InAs/AlSb T2SLs, engineered using k &bull; p modeling of the energy bands and photo-response. The wafers are grown by molecular beam epitaxy and are fabricated into Focal Plane Array (FPA) detectors using standard FPA processes, including wet and dry etching, indium bump hybridization, under-fill, and back-side polishing. The FPA has a quantum efficiency of nearly 50%, and operates at 77 K and F/2.7 with background limited performance. The pixel operability of the FPA is above 99% and it exhibits a stable residual non uniformity (RNU) of better than 0.04% of the dynamic range. The FPA uses a new digital read-out integrated circuit (ROIC), and the complete detector closely follows the interfaces of SCD’s MWIR Pelican-D detector. The Pelican- D LW detector is now in the final stages of qualification and transfer to production, with first prototypes already integrated into new electro-optical systems.