gebhart/patrepeval huggingface dataset:
Investigation of annealed, thin(∼2.6 nm)-Al2O3/AlGaN/GaN metal-insulator-semiconductor heterostructures on Si(111) via capacitance-voltage and current-voltage studies (2019)

Annealed, thin(∼2.6 nm)-Al2O3/AlGaN/GaN metal-insulator-semiconductor (MIS) heterostructures on Si(111) are fabricated and studied via capacitance–voltage (C–V) measurements to quantify densities of fast and slow interface trap states and via current–voltage (I–V) measurements to investigate dominant gate current leakage mechanisms. Dual-sweep C–V measurements reveal small voltage hysteresis (∼1 mV) around threshold voltage, indicating a low density of slow interface trap states of ∼109 cm−2. Frequency-dependent conductance measurements show fast interface trap state density ranging from 8 × 1012 to 5 × 1011 eV−1 cm−2 at energies from 0.275 to 0.408 eV below the GaN conduction band edge. Temperature-dependent I–V characterizations reveal that trap-assistant tunneling (TAT) dominates the reverse-bias carrier transport while the electric field across the Al2O3 ranges from 3.69 to 4.34 MV cm−1, and the dominant Al2O3 trap state energy responsible for such carrier transport is identified as 2.13 ± 0.02 eV below the Al2O3 conduction band edge. X-ray photoelectron spectroscopy measurements on Al2O3 before and after annealing suggest an annealing-enabled reaction between Al-O bonds and inherent H atoms. Overall, we report that annealed, thin-Al2O3 dielectric is an effective (Al)GaN surface passivation alternative when minimizing passivation-associated parasitic capacitance is required, yet non-ideal for significantly suppressing gate leakage current in MIS structures due to the governing TAT carrier transport mechanism.
Computational design of thermostabilizing point mutations for G protein-coupled receptors (2018)

Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational approach to effective prediction of stabilizing mutations in GPCRs, named CompoMug, which employs sequence-based analysis, structural information, and a derived machine learning predictor. Tested experimentally on the serotonin 5-HT<sub>2C</sub> receptor target, CompoMug predictions resulted in 10 new stabilizing mutations, with an apparent thermostability gain ~8.8°C for the best single mutation and ~13°C for a triple mutant. Binding of antagonists confers further stabilization for the triple mutant receptor, with total gains of ~21°C as compared to wild type apo 5-HT<sub>2C</sub>. The predicted mutations enabled crystallization and structure determination for the 5-HT<sub>2C</sub> receptor complexes in inactive and active-like states. While CompoMug already shows high 25% hit rate and utility in GPCR structural studies, further improvements are expected with accumulation of structural and mutation data.
Ibritumomab Tiuxetan Radioimmunotherapy Improves Quality of Life in Patients With Low-Grade, Follicular, or Transformed Non-Hodgkin’s Lymphoma (2001)

The impact of anticancer therapy on quality of life has been receiving increasing attention, particularly with diseases such as low-grade non-Hodgkin’s lymphoma (NHL), where palliation rather than cure is the primary objective of therapy. The
Real-Time Formation Evaluation and Contamination Prediction Through Inversion of Downhole Fluid Sampling Measurements (2017)

Abstract Acquisition of fluid samples using wireline formation testers (WFT) is an integral part of reservoir evaluation and fluid characterization. Recent developments in formation tester hardware have enabled wireline-based fluid sampling in a wide range of downhole conditions. However, accurate quantification of oil-based mud (OBM) filtrate contamination using data from downhole fluid analysis (DFA) sensors alone remains challenging, especially in difficult sampling environments and for advanced sampling tools which have complex inflow geometries and active guarding of filtrate flows. Such tools and conditions lead to contamination behaviors that do not follow simple power-law models which are commonly assumed in OBM contamination monitoring (OCM) algorithms. In this paper, we introduce a new OCM algorithm based on inversion of DFA data using a full 3D numerical flow model of the contamination cleanup process. Based on formation and fluid properties and operational tool settings, the model predicts the evolution of filtrate contamination as a function of time and pumped volume and can thus be used to forward-model the DFA sensor responses. Sensor data are then inverted in real time to provide contamination predictions. Real-time computation is enabled through fast, high-fidelity proxy models for the cleanup process. The proxy models are trained on and thoroughly vetted against a large number of full-scale numerical simulations. Compared to existing algorithms, the new OCM method is now applicable for all types of sampling hardware and a wider set of operating conditions. By directly relying on a model of the cleanup process, the physical properties of the formation and fluids (such as porosity, permeability, viscosity, and depth of filtrate invasion) are estimated during the inversion, thus providing additional valuable information for formation evaluation. The new method is demonstrated by practical application in both synthetic and field examples of oil sampling in OBM. The synthetic examples demonstrate the robustness of the algorithm and show that the true formation and fluid properties can be recovered from noise-corrupted sensor data. The field example presented demonstrates that contamination predictions are in good agreement with results from laboratory analysis, and the inverted formation properties are consistent with estimates based on openhole logs and pressure measurements.
Multi-scale user migration on Reddit (2021)

Migration is a natural phenomenon in online social networks where users move across virtual spaces within or across platforms. Platforms such as Reddit drive migration behaviour by facilitating the formation of communities around discussion topics. However, migration also occurs in relation to the emergence of cyber-social threats. For example, 'trolling' involves users intentionally moving in and out of spaces to provoke conflict. In extreme cases, platforms move to shut down spaces due to user behaviour, forcing those users to migrate elsewhere. This paper provides a set of methods to help study migration at two scales: micro-scale involving individual users moving between spaces over relatively short time periods (between posts), and macro-scale involving groups of users moving over relatively longer time periods (changing their posting habits). We take Reddit as an example platform due to its community orientation, and COVID-19 as a means of qualitatively illustrating the results of our methods. We show how micro-scale analyses reveal sub-network structures indicative of overlapping user communities and how macroscale analyses provide important context to understand the micro-scale patterns, while also revealing consequences of platform moderation on user migration. For COVID-19, the micro-scale analyses reveal an interplay of controversies, politics and humour, while the macro-scale analyses point to increasing politicisation of the pandemic and a rise of conspiracy theories.
Supplementary Figure 4 from Reversal of NK-Cell Exhaustion in Advanced Melanoma by Tim-3 Blockade (2023)

&lt;p&gt;PDF file - 87K, Fig. S4. Tim-3 is up-regulated in MD NK cells.&lt;/p&gt;
Two-dimensional non-Abelian topological insulators and the corresponding edge/corner states from an eigenvector frame rotation perspective (2022)

We propose the concept of two-dimensional (2D) non-Abelian topological insulators which can explain the energy distributions of the edge states and corner states in systems with parity-time symmetry. From the viewpoint of non-Abelian band topology, we establish the constraints on the 2D Zak phase and polarization. We demonstrate that the corner states in some 2D systems can be explained as the boundary mode of the one-dimensional edge states arising from the multiband non-Abelian topology of the system. We also propose the use of the off-diagonal Berry phase as complementary information to assist the prediction of edge states in non-Abelian topological insulators. Our work provides an alternative approach to study edge and corner modes and this idea can be extended to three-dimensional systems.
Ultra-wide Field Retinal Imaging in Detection, Classification, and Management of Diabetic Retinopathy (2012)

Current ultra-wide field (UWF) retinal imaging systems utilize scanning laser ophthalmoscope technology combined with an ellipsoidal mirror to capture up to 200 degrees of the retina in a single image. When compared with mydriatic ETDRS-protocol, 7 standard field photographs and clinical examination, nonmydriatic UWF images appear to have excellent agreement in allowing the detection and classification of diabetic retinopathy (DR), although larger, definitive validation studies are still forthcoming. UWF imaging and angiography allow visualization of peripheral retinal nonperfusion, vascular leakage and neovascularization in patients with DR that may not be captured on 7 standard fields. Prospective randomized controlled trials are needed to evaluate whether modified laser treatment algorithms based on improved visualization of the retinal periphery might improve patient outcomes. Nonmydriatic UWF imaging has potential applications for ocular diabetic telehealth programs, but validation of newer, more portable, and more affordable UWF imaging models is needed.
Effet des métallisations réelles dans les lignes GaAs pour les circuits microondes monolithiques (1989)

Cet article traite les effets des métallisations réelles dans les lignes GaAs pour circuits intégrés microondes. Une approche théorique originale, qui est en fait une extension de la Méthode Spectrale classique, est présentée dans cette communication. Cette approche est appliquée à une ligne Metal-Isolant-Semiconducteur (MIS) sur GaAs. On montre l'effet de l'épaisseur des rubans sur les caractéristiques de propagation : permittivité effective, pertes de propagation et impédance caractéristique.
Three-dimensional light microscopy for the analysis of chromosome organization in Drosophila embryo (1991)

We are interested in the three-dimensional physical relationships among chromosomes in mitotically active nuclei. Using high-resolution, three-dimensional optical sectioning microscopy incorporating a charge-coupled device (CCD), we have analyzed the spatial arrangements of chromosomes in nuclei from Drosophila melanogaster embryos. During early stages of nuclear division, these embryos exist as syncytial blastoderms, with up to 5000 nuclei forming a single layer near the embryo's surface and dividing essentially synchronously. This greatly facilitates the analysis of chromosome organization because of the simple monolayer arrangement of nuclear structures at defined mitotic stages. From prophase to anaphase, three-dimensional paths of condensed chromosomes stained with a DNA-specific fluorescent dye can be traced using an interactive computer program. We have used this method to ask the specific biological question of whether pairs of homologous chromosomes have a consistent, ordered arrangement in diploid nuclei. Our results have shown that homologous chromosomes are not associated with each other from prophase to anaphase in syncytial blastoderm stage embryos.
Abstract 11 (2015)

AMERICAN SOCIETY OF PLASTIC SURGEONS PLASTIC & RECONSTRUCTIVE SURGERY PRS GLOBAL OPEN ASPS EDUCATION NETWORK AMERICAN SOCIETY OF PLASTIC SURGEONS PLASTIC & RECONSTRUCTIVE SURGERY PRS GLOBAL OPEN ASPS EDUCATION NETWORK
Inhibition of hexokinase-2 with targeted liposomal 3-bromopyruvate in an ovarian tumor spheroid model of aerobic glycolysis (2015)

SKOV-3 spheroids developed by the hanging drop method can be used as a tumor aerobic glycolysis model for evaluation of therapies targeting the glycolytic pathway in cancer cells. Encapsulation of 3-BPA in a liposomal formulation improved permeability, HK2 inhibition, and cytotoxicity in the multicellular spheroid model.
Real-time imaging of the Schlemm's canal by Fourier-Domain Optical Coherence Tomography for glaucoma laser surgery (2012)

National audience
Edge wave enabled diffractive optical elements for Augmented Reality glasses (2021)

International audience
Supported Ir and Pt Clusters:  Reactivity with Oxygen Investigated by Extended X-ray Absorption Fine Structure Spectroscopy (1996)

Extended X-ray absorption fine structure (EXAFS) spectroscopy was used to investigate the effects of oxidation and reduction on supported noble metal clusters. After long-term exposure to laboratory air at room temperature, platinum clusters with an average diameter of approximately 7 Å inside the pores of BaKLTL zeolite were almost completely fragmented. The EXAFS data indicate small, highly disordered platinum−platinum contributions but no bulk platinum oxides. Treatment in H2 at 450 °C led to the formation of platinum clusters about 10 Å in average diameter, and exposure of these to air at room temperature led to the formation of a disordered platinum-oxide-like phase covering a core of platinum atoms. The reactivity of platinum clusters with oxygen is size-dependent, and platinum cluster growth by oxidation−reduction cycles may be inhibited by the size of the zeolite pores. Similarly, iridium clusters on MgO, approximated as Ir4, were fragmented by treatment in O2, but treatment of the oxidized iridium clusters with H2 at 573 K resulted in the formation of clusters with an Ir−Ir coordination number of 2.7 (and an Ir−Ir distance of 2.68 Å), indicating slightly less than four Ir atoms per cluster. These data are nearly the same as those characterizing the original sample prior to oxidation, suggesting that the clusters had been reformed into almost their original state. This is the first evidence of supported metal clusters being oxidized and then regenerated nearly intact. The near reversibility of the oxidation−reduction process may be unique to iridium, being related to its slight but non-negligible oxophilicity and its resistance to sintering.
Atomic force microscope observation of MoS2 particles synthesized on mica, MoS2, and graphite (2003)

Nanometer-sized particles of molybdenum oxide were thermally deposited and then sulfided on mica, MoS2, and highly oriented pyrolytic graphite (HOPG) to simulate MoS2 catalysts for the hydrodesulfurization reaction of petroleum. The topography of the particles observed by AFM reflected the interaction force dominant at the particle-substrate interfaces. Oxide particles ionically interacted with mica which restricted the mobility of the deposit and led to particles smaller in lateral dimension, whereas aggregated oxide was observed on the other non-ionic substrates. Basal-bonded MoS2 crystals were observed on the three substrates when sulfided at 673 K. [DOI: 10.1380/ejssnt.2003.80]
Profiling of immune dysfunction in COVID-19 patients allows early prediction of disease progression (2020)

With a rising incidence of COVID-19-associated morbidity and mortality worldwide, it is critical to elucidate the innate and adaptive immune responses that drive disease severity. We performed longitudinal immune profiling of peripheral blood mononuclear cells from 45 patients and healthy donors. We observed a dynamic immune landscape of innate and adaptive immune cells in disease progression and absolute changes of lymphocyte and myeloid cells in severe versus mild cases or healthy controls. Intubation and death were coupled with selected natural killer cell KIR receptor usage and IgM+ B cells and associated with profound CD4 and CD8 T-cell exhaustion. Pseudo-temporal reconstruction of the hierarchy of disease progression revealed dynamic time changes in the global population recapitulating individual patients and the development of an eight-marker classifier of disease severity. Estimating the effect of clinical progression on the immune response and early assessment of disease progression risks may allow implementation of tailored therapies.
Cell-cell interactions are essential for maintenance of hepatocyte function in collagen gel but not on matrigel (1997)

The objective of this study was to examine the importance of cellular aggregation for the maintenance of liver-specific functions in hepatocytes. We used two culture matrix systems (collagen sandwich and Matrigel) to examine the responsiveness of albumin secretory function in cultured rat hepatocytes under various seeding conditions. With high cell seeding, both culture systems elicited comparable levels of elevated function. Under conditions of sparse seeding, however, their responses were quite distinct: collagen sandwiched cells exhibited a significant deterioration in secretion, while Matrigel-cultured cells retained their basal levels of function. This indicates that a critical degree of cell-cell interactions is essential for promoting function in the collagen sandwich, and in the Matrigel-cultured cells functions may be preserved by constitutive matrix-related phenomena, even in the absence of aggregation. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 706-711, 1997.
Abstract 5513: An immune-active tumor microenvironment favors clinical response to ipilimumab (2011)

Abstract Ipilimumab, a fully human monoclonal antibody specific to CTLA-4, has shown improvement in overall survival in previously treated advance melanoma patients. As a consequence of blockade of the T cell regulatory molecule CTLA-4, ipilimumab treatment is associated with proliferation and activation of peripheral T cells. An important factor for impacting tumor growth however, is whether these T cells can successfully migrate into the tumor. In order to gain a better understanding of the various tumor-associated components that determine the clinical activity of ipilimumab in melanoma tumors, Affymetrix gene expression profiling and pathway analysis were retrospectively performed on 46 primary or metastatic melanoma tumors, collected in a complete phase II clinical trial in advanced melanoma patients. In biopsies obtained at baseline (before treatment), there were 361 differentially genes expressed (≥ 1.5 fold difference in expression, p ≤ 0.01); most over-expressed transcripts and pathways associated with favorable clinical activity were immune-related. Furthermore, differential analysis of mRNA from pre- and post-treatment tumor biopsies pointed to additional increase in the expression of these genes after treatment. Interestingly, ipilimumab treatment was associated with down-regulation of a number of melanoma-associated transcripts in the tumors within a short time (3 weeks after the first dose). Our preliminary results suggest that high pre-existing immune-activity favors clinical response to ipilimumab. These analyses also provide a list of candidate biomarkers with potential predictive value for response to ipilimumab, to be confirmed in a larger, placebo controlled clinical trial. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5513. doi:10.1158/1538-7445.AM2011-5513
Data from A Multigene Assay Is Prognostic of Survival in Patients with Early-Stage Lung Adenocarcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Clinical staging does not adequately risk stratify patients with early stage non–small cell lung cancer. We sought to generate a real-time PCR (RT-PCR)–based prognostic model in patients with early stage lung adenocarcinoma, the dominant histology of lung cancer in the United States.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We studied gene expression of 61 candidate genes in 107 patients with completely surgically resected lung adenocarcinoma using RT-PCR. We used crossvalidation methods to select and validate a prognostic model based on the expression of a limited number of genes. A risk score was generated based on model coefficients, and survival of patients with high- and low-risk scores were analyzed.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We generated a four-gene model based on expression of &lt;i&gt;WNT3a, ERBB3, LCK&lt;/i&gt;, and &lt;i&gt;RND3&lt;/i&gt;. Risk score predicted mortality better than clinical stage or tumor size (adjusted hazard ratio, 6.7; 95% confidence interval, 1.6-28.9; &lt;i&gt;P&lt;/i&gt; = 0.001). Among 70 patients with stage I disease, 5-year overall survival was 87% among patients with low-risk scores, and 38% among patients with high-risk scores (&lt;i&gt;P&lt;/i&gt; = 0.0002). Among all patients, 5-year overall survival was 62% and 41%, respectively (&lt;i&gt;P&lt;/i&gt; = 0.0054). Disease-free survival was also significantly different among low- and high-risk score patients.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; This multigene assay predicts overall and disease-free survival significantly better than clinical stage and tumor size in patients with early stage lung adenocarcinoma and performs especially well in patients with stage I disease. Prospective clinical trials are needed to determine whether high-risk patients with stage I disease benefit from adjuvant chemotherapy.&lt;/p&gt;&lt;/div&gt;
Novel principle for flux sensing in the application of a DC + AC current sensor (2014)

Magnetostriction describes the geometrical change in length of a ferromagnetic material in dependence of its internal magnetic flux density value. By detecting the vibrations caused by these dimensional changes with a piezo-electric transducer, the instantaneous value of the magnetic flux inside a magnetic core can be sensed from DC up to a few kilohertz. This principle, together with a high bandwidth current transformer, was utilized in order to construct a current sensor capable of measuring currents ranging from DC to several MHz. As will be shown in this paper, an additional sinusoidal AC-excitation of the core material provides higher sensitivity of the length measurement and overcomes the high-pass characteristic of the piezo sensor. In order to prove the principle and to demonstrate the capabilities of this new sensor, a series of experimental measurements and implementation results are presented.
Automated Measurement and Control of Slump and Water Content for Concrete Quality Assurance (2013)

This paper presents an analysis of data on 8,226 loads of ready mixed concrete as measured by truck-mounted, automated slump management equipment. This equipment measures and controls slump and water content from batching to final discharge, and also records concrete temperature, admixture use, drum rotation speed and number of revolutions, and time. The data indicate that the use of this equipment resulted in concrete arriving at the jobsite at the correct slump for discharge, reduced variability in slump at discharge, and more consistent mixing after loading. Data also showed that water additions can be made, uniformly mixed, and fully documented while the truck is in transit. The paper describes how the documentation and control provided by such equipment can be part of a quality assurance program.
Linearization of Gamma Energy Spectra in Scintillator-Based Commercial Instruments (2010)

This paper presents a novel technique developed for linearizing the energy spectra of radiation detectors in commercial radioisotope identification devices. Based on few spectrum measurements with standard radio-nuclide sources, this method allows generation of individual nonlinear calibration functions at minimum expense in the routine instrument setup. Instead of fitting peak positions, the measured raw data are compared with simulated spectrum templates, and local gain factors providing the best correspondence are taken as reference points for the calibration function. This approach avoids the problem of fitting multiple peaks with intensity ratios influenced by absorbing layers and assures an accuracy of 1% in the energy range of 30 keV to 3 MeV.