gebhart/patrepeval huggingface dataset:
Étude structurale de l'amino-5 dibenzyl-4,4 one-3 2H-thiadiazine-1,2,6 dioxyde-1,1 (1988)

5-Amino-4,4-dibenzyl-3-one-2H-1,2,6-thiadiazine-1,1-dioxide was structurally characterized in the solid state by X-ray diffraction. The structure shows that the title compound exists in the solid in a sheet-packed form and as the amino tautomer. The unconjugated heterocyclic ring, which in the structures of related compounds is usually folded, is planar in the present structure. 1 H nuclear magnetic resonance and dipole moment data indicate that the title compound has the same structure in the solid state and in solution.
Abstract 235: Preclinical activity of an antibody drug conjugate targeting tumor specificmuc1 structural peptide-glycotope (2019)

Abstract SAR566658 antibody drug conjugate (ADC) is a humanized DS6 (huDS6) antibody conjugated through a cleavable linker to the cytotoxic maytansinoid derivative DM4 that has been evaluated in the clinical setting. The purpose of our work was; 1) characterize the epitope targeted by anti DS6 on mucin1, 2) determine the prevalence of antigen expression in a patient population and 3) further explore preclinical activities of the ADC. Murine DS6 monoclonal antibody (muDS6) was generated from serous ovary adenocarcinoma immunization of immunocompetent mice. It specifically recognizes a MUC-1 tandem repeat domain in the context of cancer associated glycosylation. CA6-positive MUC-1 carries mucin-type O-linked glycans with α2,3-sialylated and β1,4-galactosylated termini, and antibody binding was abrogated by treating MUC-1 with specific glycosidases that remove either one of these glycan structures. However, the antibody did not bind to synthetic glycans modeled according to the major O-glycans of MUC-1. Our characterization of the peptide-glycotope leads us to conclude that tumor associated glycosylation is essential for the formation of the epitope on the peptide sequence of the MUC-1 tandem repeat domain. CA6 expression was evaluated by immunohistochemistry in paraffin embedded tumor tissue samples: 35.2% of breast cancer patients, 70,1% of ovarian cancer patients and 58,5% of bladder cancer patients have at least 30% of CA6 positive cells with an intensity of 2+/3+ in a multinational population-based study. In pre-clinical in vivo models, SAR566658 induced anti-tumor activity against CA6 positive tumor models of human pancreas, cervix and bladder cancer as well as and 3 Breast Patient-Derived Xenografts (PDX). Efficacy was correlated with MUC1-CA6 expression levels. In 3 additional models, SAR566658 showed anti-tumor activity that was more potent when compared to 3 conventional tubulin cytotoxic agents, docetaxel, vinorelbine and vinblastine. Citation Format: Marc Trombe, Anne Caron, Alexia Tellier, Chantal Carrez, Stephane Guérif, Severine Clavier, Nathalie Karst, Juhani Saarinen, Tero Satomaa, Virve Pitkänen, Olli Aitio, Annamari Heiskanen, Matteo Fassan, Jan Pinkas, Raffaele Baffa, Veronique Blanc, Celine Nicolazzi. Preclinical activity of an antibody drug conjugate targeting tumor specificmuc1 structural peptide-glycotope [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 235.
Room temperature operation of 1.55.MU.m wavelength-range GaN/AlN quantum well intersubband photodetectors (2005)

The room-temperature operation of a GaN/AlN quantum well infrared photodetector (QWIP) using the intersubband transition (ISBT) in a GaN/AlN multiple quantum well (MQW) was demonstrated for the first time. The GaN/AlN QWIP was operated under DC biasing with a vertically conductive geometry to the MQW layer. A clear photoinduced response was observed for P polarized 1.47µm light irradiation. Dependencies of the photoresponse on the applied DC bias voltage, and the polarization and wavelength of incident light were evaluated for the GaN/AlN QWIP. The maximum responsivity was estimated to be 0.11mA/W for a DC bias of 15V at room temperature.
Supplementary Tables 1-3 from High Frequency of <i>PIK3R1</i> and <i>PIK3R2</i> Mutations in Endometrial Cancer Elucidates a Novel Mechanism for Regulation of PTEN Protein Stability (2023)

Supplementary Tables 1-3 from High Frequency of &lt;i&gt;PIK3R1&lt;/i&gt; and &lt;i&gt;PIK3R2&lt;/i&gt; Mutations in Endometrial Cancer Elucidates a Novel Mechanism for Regulation of PTEN Protein Stability
Local Epiphyseal Growth Modulation for the Early Treatment of Progressive Scoliosis (2016)

5.
Synthesis of Nanosized TiO2 by Cationic Polymerization of (µ4‐oxido)‐hexakis(µ‐furfuryloxo)‐octakis(furfuryloxo)‐tetra‐titanium (2008)

Interpenetrated inorganic–organic composite materials can be synthesized by twin polymerization of (µ4-oxido)-hexakis(µ-furfuryloxo)-octakis(furfuryloxo)-tetra-titanium. Poly(furfuryl alcohol)/titanium dioxide composites are formed in which the titania species are uniform dispersed. Pure nanosized titanium dioxide (anatase) is obtained after heat and water treatment and removing the organic layer of the composite materials by oxidation.
Electric Vehicle Charging: A Noncooperative Game Using Local Measurements (2014)

A distributed control algorithm is proposed to manage the electrical power demand for the purpose of charging electric vehicles so that (a) the overall power demand remains within the limitations of the distribution network and (b) each vehicle obtains a sufficiently charged battery at the end of the charging cycle. The charging algorithm utilises only local measurements to determine the charge current. The control problem is modelled as a non-cooperative game with weakly coupled cost functions for each vehicle. The cost function for each vehicle consist of an individual cost term and a group cost term. The group cost term expresses the aggregated demand of all vehicles and serves the purpose of ensuring that the infrastructure capacity constraints are respected. It is shown that this term can be estimated from local voltage measurements. The individual cost term reflects the need to achieve a desired charge level in the battery. Sufficient conditions for the overall system to admit a unique Nash Equilibrium are identified. Convergence and stability properties for a particular greedy algorithm implementation are described. To illustrate the efficacy of the proposed charging methodology, the algorithm is simulated in the context of an Australian suburban low voltage electricity distribution network.
The Synthesis of Certain Phomentrioloxin A Analogues and Their Evaluation as Herbicidal Agents (2016)

A series of 28 analogues of the phytotoxic geranylcyclohexentriol (-)-phomentrioloxin A (1) has been synthesized through cross-couplings of various enantiomerically pure haloconduritols or certain deoxygenated derivatives with either terminal alkynes or borylated alkenes. Some of these analogues display modest herbicidal activities, and physiological profiling studies suggest that analogue 4 inhibits photosystem II in isolated thylakoids in vitro.
Improved Electrical Properties and Thermal Stability of GeON Gate Dielectrics Formed by Plasma Nitridation of Ultrathin Oxides on Ge(100) (2011)

We demonstrated the impact of plasma nitridation on thermally grown GeO2 for the purposes of obtaining high-quality germanium oxynitride (GeON) gate dielectrics. Physical characterizations revealed the formation of a nitrogen-rich surface layer on the ultrathin oxide, while keeping an abrupt GeO2/Ge interface without a transition layer. The thermal stability of the GeON layer was significantly improved over that of the pure oxide. We also found that although the GeO2 layer is vulnerable to air exposure, a nitrogen-rich layer suppresses electrical degradation and provides excellent insulating properties. Consequently, we were able to obtain Ge-MOS capacitors with GeON dielectrics of an equivalent oxide thickness (EOT) as small as 1.7 nm. Minimum interface state density (Dit) values of GeON/Ge structures, i.e., as low as 3 x 1011 cm-2eV-1, were successfully obtained for both the lower and upper halves of the bandgap.
Pseudoparticle Neutralization Assay for Detecting Ebola- Neutralizing Antibodies in Biosafety Level 2 Settings (2015)

To the Editor:

Ebola virus is currently causing an unprecedented outbreak in West Africa. The pathogen is classified as a biosafety level 4 (BSL-4)1 pathogen and should be handled only in high-level biosafety settings (1). Virus neutralization is considered to be the gold standard serological assay for infections, but in the case of Ebola, this test requires culturing of live virus in a BSL-4 facility. Because of these stringent biosafety requirements, options for clinical diagnosis or epidemiological studies of Ebola cases are limited. For this reason, we developed a pseudoviral particle neutralization (PPNT) assay that can detect neutralizing antibody to Ebola virus in BSL-2 containments.

Ebola glycoprotein (GP) is a major target of neutralizing antibodies in humans. The pseudoviral particle generated in this study is a lentiviral vector carrying the GP of Zaire ebolavirus detected in the current outbreak (2). Methods for the pseudoviral particle production and PPNT assay were essentially identical to those for Middle East respiratory syndrome (MERS) and influenza, as previously described (3, 4). Briefly, a codon-optimized GP sequence was chemically synthesized (Genscript) and subcloned into a protein-expressing vector, pcDNA3.1+. The resulting …
1189: TRANSCRIPTOMIC ENDOTYPES IMPLICATE A UNIQUE RISK PROFILE FOR KIDNEY-RELATED OUTCOMES IN SEPSIS (2022)

Introduction: Acute kidney injury (AKI) is the most frequent organ dysfunction in critically ill patients with sepsis. Optimal clinical management, including the timing of renal replacement therapy (RRT), is still unclear, caused by the inherent heterogeneity of the syndrome. We sought to apply transcriptomic endotypes to a cohort of critically ill patients with sepsis and associate it with the risk for kidney-related endpoints. Methods: Secondary analysis of a cohort of 200 adult critically ill patients meeting Sepsis-3 criteria. Patients with a prior or immediate need for RRT, decompensated liver cirrhosis, or moribund condition were excluded. Whole-blood RNA (within 12h from ICU admission) was available from 167 patients for Nanostring gene expression analysis of 33 signature mRNAs to allocate patients into one of three pre-described endotypes (inflammopathic (IE), adaptive (AE), coagulopathic (CE)). Clinical outcomes were recorded over a follow-up period of 30d (RRT, persisting AKI, 7/30d all-cause mortality). Results: Fifty-seven patients were allocated to IE, 70 to AE, and 40 to CE, with no significant differences in demographic variables. IE group was enriched for patients in septic shock (87.7%, vs. 40 and 65%; p< 0.001), associated with higher mean lactate levels (65mg/dL, vs. 36 and 36.6mg/dL; p< 0.001) and pronounced positive fluid balance within the first 24h (5.73L, vs. 3.4 and 4.45L; p=0.019). 24.1%, 17.4%, and 7.7% of patients (IE, AE, CE, respectively) required RRT within 7d after admission (p=0.118). In contrast, there was a trend for a higher occurrence of persistent AKI in IE and CE (60.7 and 69.6%) compared to AE (42.8%; p=0.156). IE patients showed the highest early (7d) mortality of 15.8%, followed by 8.6% and 2.5% for AE and CE, respectively (p=0.084). Similar 30d mortality rates of 26.3 and 27.1% were observed for IE and AE, while mortality was low in CE (10.0%; p=0.078). Conclusions: Patients with IE exhibited the highest need for RRT accompanied by elevated early and delayed mortality. In contrast, CE patients - despite exhibiting a high incidence of persistent AKI – show the lowest incidences for all other clinical outcomes. Transcriptomic endotyping seems to be a promising strategy for renal risk refinement in future trials.
5.8 GHz Highly Sensitive and Linear Doppler Radar Using Digital Self-Injection-Locking Technology (2022)

This paper presents a 5.8 GHz low-IF Doppler radar that uses digital self-injection-Iocking (DSIL) technology to achieve high sensitivity and high linearity. The system consists of an RF up-down converter, an IF image rejector, and an IF DSIL radar. To verify its high sensitivity and high linearity, an experiment of the proposed radar was conducted to detect a slightly vibrating object that was moved over a large range by two stacked actuators, showing satisfactory and promising results.
Optical and X-ray attenuation properties of hafnium oxide nanoparticles surface functionalized with fucoidan: toward the early diagnosis of atherothrombotic diseases (2023)

HfO 2 NPs surface functionalized with fucoidan show specific targeting of aggregated platelets and appear as a new candidate for X-ray imaging for the molecular-scale diagnosis of atherothrombosis.
Modeling and multi-objective optimization of 2.5D inductor-based Fully Integrated Voltage Regulators for microprocessor applications (2015)

This work presents the modeling and the multi-objective optimization of a 2.5D inductor-based Fully Integrated Voltage Regulator (FIVR) with respect to efficiency η and/or chip area power density α, i.e. based on the η-α-Pareto-front, for microprocessor applications. The Voltage Regulator consists of a four-phase interleaved buck converter operated in Continuous Conduction Mode (CCM). The rated power of the considered converter is 1W, and input and output voltages are constant and equal to V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in</sub> = 1.7V and V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">out</sub> = 0.85V. The optimization employs analytical models for the switches, which reside on chip and are manufactured in a 32nm CMOS SOI process, and for the passive components, i.e. racetrack inductors with magnetic core material and deep-trench capacitors that are fabricated in a silicon interposer. The optimization procedure considers thermal aspects and disregards solutions that lead to excessive component temperatures. According to the optimization results, either high efficiencies, greater than 90%, or high area power densities, with chip power densities greater than 20W/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and interposer power densities higher than 1.5W/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> are achievable. The optimized design point, selected from the η-α-Pareto-front, features an efficiency of 90.1%, interposer power density of 0.309W/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , and a chip power density of 27.4W/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
DNA-binding mechanism and evolution of Replication Protein A (2022)

ABSTRACT Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair, in both eukaryotic and archaeal cells. By using an integrative approach that combines three crystal structures, four cryo-EM structures in complex with single-stranded DNA (ssDNA) of different lengths, we extensively characterized RPA from Pyrococcus abyssi in different states. These structures show two essential features conserved in eukaryotes: a trimeric core and a module that promotes cooperative binding to ssDNA, as well as a newly identified archaeal-specific domain. These structures reveal for the first time how ssDNA is handed over from one RPA complex to the other, and uncover an unanticipated mechanism of self-association on ssDNA tracts. This work constitutes a significant step forward in the molecular understanding of the structure and DNA-binding mechanism of RPA, with far-reaching implications for the evolution of this primordial replication factor in Archaea and Eukarya.
Hessenberg Reduction with Transient Error Resilience on GPU-Based Hybrid Architectures (2016)

Graphics Processing Units (GPUs) have been seeing widespread adoption in the field of scientific computing, owing to the performance gains provided on computation-intensive applications. In this paper, we present the design and implementation of a Hessenberg reduction algorithm immune to simultaneous soft-errors, capable of taking advantage of hybrid GPU-CPU platforms. These soft-errors are detected and corrected on the fly, preventing the propagation of the error to the rest of the data. Our design is at the intersection between several fault tolerant techniques and employs the algorithm-based fault tolerance technique, diskless checkpointing, and reverse computation to achieve its goal. By utilizing the idle time of the CPUs, and by overlapping both host-side and GPU-side workloads, we minimize the resilience overhead. Experimental results have validated our design decisions as our algorithm introduced less than 2% performance overhead compared to the optimized, but fault-prone, hybrid Hessenberg reduction.
A multiple source, or, is a striped apple more striped than a striped orange? (1989)

An abstract is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.
Optimization of Single-Molecule Fluorescence Burst Detection of ds-DNA: Application to Capillary Electrophoresis Separations of 100–1000 Basepair Fragments (1997)

Methods for optimizing the dye labeling, laser excitation, and data analysis for single-molecule fluorescence burst detection of ds-DNA have been developed and then validated through capillary electrophoresis (CE) separations of 100–1000 basepair (bp) DNA. Confocal microscopy is used to observe fluorescence bursts from individual DNA fragments labeled with the intercalation dye TO6 as they pass through the ∼ 2-μm-diameter focused laser beam. The dye concentration and laser power were optimized by studying fluorescence burst intensities from pBluescript DNA fragments. The optimal TO6 concentration was ≤100 nM, and the optimal laser power was ≤1 mW. Single-molecule counting was then used to detect CE separations of a 100–1000 bp DNA sizing ladder in 3% linear polyacrylamide. Discrete and baseline-resolved fluorescence bursts were observed in bands as small as 100 bp, and the average burst size within each band increased linearly with fragment size. By counting events using a single optimally chosen discriminator level, we achieve maximum signal-to-noise ratio (S/N) for each fragment size. If the discriminator level is ramped linearly with fragment size to achieve a constant detection efficiency, then the number of events properly reflects the relative fragment concentrations.
COVID-19 Severity Is Associated with Differential Antibody Fc-Mediated Innate Immune Functions (2021)

Beyond neutralization, antibodies binding to their Fc receptors elicit several innate immune functions including antibody-dependent complement deposition (ADCD), antibody-dependent cell-mediated phagocytosis (ADCP), and antibody-dependent cell-mediated cytotoxicity (ADCC). These functions are beneficial, as they contribute to pathogen clearance; however, they also can induce inflammation. We tested the possibility that qualitative differences in SARS-CoV-2-specific antibody-mediated innate immune functions contribute to coronavirus disease 2019 (COVID-19) severity. We found that anti-S1 and anti-RBD antibodies from hospitalized COVID-19 patients elicited higher ADCD but lower ADCP compared to antibodies from nonhospitalized COVID-19 patients. Consistently, higher ADCD was associated with higher systemic inflammation, whereas higher ADCP was associated with lower systemic inflammation during COVID-19. Our study points to qualitative, differential features of anti-SARS-CoV-2 specific antibodies as potential contributors to COVID-19 severity. Understanding these qualitative features of natural and vaccine-induced antibodies will be important in achieving optimal efficacy and safety of SARS-CoV-2 vaccines and/or COVID-19 therapeutics.<b>IMPORTANCE</b> A state of hyperinflammation and increased complement activation has been associated with coronavirus disease 2019 (COVID-19) severity. However, the pathophysiological mechanisms that contribute to this phenomenon remain mostly unknown. Our data point to a qualitative, rather than quantitative, difference in SARS-CoV-2-specific antibodies' ability to elicit Fc-mediated innate immune functions as a potential contributor to COVID-19 severity and associated inflammation. These data highlight the need for further studies to understand these qualitative features and their potential contribution to COVID-19 severity. This understanding could be essential to develop antibody-based COVID-19 therapeutics and SARS-CoV-2 vaccines with an optimal balance between efficacy and safety.
Atomic and Electronic Structures of Ni/YSZ(111) Interface (2004)

Thin Ni films were deposited on the (111) surface of YSZ at 1073 K by a pulsed laser deposition technique. The interfacial atomic structure of Ni/YSZ was investigated by high-resolution transmission electron microscopy (HRTEM). It was found that Ni was epitaxially oriented to the YSZ surface, and the following orientation relationship (OR) was observed: (111)Ni || (111)YSZ, [110]Ni || [110]YSZ. Geometrical coherency of the Ni/YSZ system was also evaluated by the coincidence of reciprocal lattice points (CRLP) method. It was found that the most coherent OR predicted by CRLP method was (705)Ni || (111)YSZ, [010]Ni || [110]YSZ, which was not consistent with the experimentally observed OR. To understand the detailed atomic structure, HRTEM image simulations were performed. However, simulated images based on both O-terminated and Zr-terminated interface models were quite similar to the experimental image, and thus it was hard to determine which model is comparable with the actual interface only by the HRTEM image simulations. In order to clarify the termination layer at the interface, electronic structures of the Ni/YSZ interface were investigated by electron energy-loss spectroscopy. It was found that significant differences were observed in O-K edge spectra between the interface and the YSZ crystal interior, and the spectrum from the interface showed similar features to the reference spectrum of bulk NiO. This indicates that the Ni-O interaction occurs at the interface to terminate the oxygen {111} plane of YSZ at the Ni/YSZ interface. In addition, the density of Ni-O bonds across the interface in the experimental OR was larger than that in the most coherent OR predicted by CRLP method, which also suggests that the on-top Ni-O bonds stabilize the Ni/YSZ(111) interface.