gebhart/patrepeval huggingface dataset:
Sequences responsible for the distinctive hemolytic potentials of Friend and Moloney murine leukemia viruses are dispersed but confined to the psi-gag-PR region (1993)

Friend and Moloney murine leukemia viruses (F- and M-MuLV) induce distinct diseases in hematopoietic tissues following inoculation of newborn mice of susceptible strains. F-MuLV induces erythroleukemia preceded by severe early hemolytic anemia; M-MuLV induces thymomas and only very mild hemolysis. The major viral determinant of severe early hemolytic anemia residues in the env gene, but sequences located outside this gene can modulate this effect. By means of genetic chimeras of F- and M-MuLV, we have found that although they are confined to the 5' portion of the env gene intron, sequences that determine the distinctive hemolytic potentials of F- and M-MuLV are widely distributed over a region spanning the RNA encapsidation domain, the gag gene, and the portion of the pol gene encoding the viral protease. Within this large region, two fragments of M-MuLV, a 1.3-kb region encoding the matrix, pp12, and capsid proteins and a 0.8-kb region encoding the nucleocapsid and the viral protease, were capable, individually, of partially attenuating the capacity of F-MuLV for induction of severe early hemolytic anemia. In association, these two fragments conferred complete attenuation. Moreover, a second pair of adjacent fragments within this large region appeared to behave cooperatively to confer complete attenuation; a 0.36-kb region roughly corresponding to the encapsidation domain, although not detectably altering hemolytic potential on its own, deepened the attenuation conferred by the adjacent 1.3-kb region. Whether capable of inducing severe early hemolytic anemia or not and despite different efficiencies of induction of recombinant polytropic viruses, all chimeric viruses retained the erythroleukemogenicity of the F-MuLV parent.
Cross-Platform Access Control for Mobile Web Applications (2012)

Web browsers are a common platform for delivering cross-platform applications. However, they currently fail to provide consistent access control for security and privacy sensitive JavaScript APIs, such as geolocation and local storage. This problem is exacerbated by new HTML5 APIs and the increasing number of personal devices people own and use. In this paper we present the webinos platform which aims to provide a single, cross-device policy system for web applications on a wide range of web-enabled devices including TVs, smartphones, in-car systems and PCs. webinos solves the existing deficiencies in web authorisation by introducing the concept of a personal zone, the set of all devices and services owned by a particular user. All devices in this zone can synchronize their access control policies through interoperable middleware and can create flexible rules which may refer to an individual user, device or the entire zone. We provide details of the architecture and explain how our experience during design highlighted several conceptual challenges.
Qualitative and quantitative ultrastructural analysis of the membrane rearrangements induced by coronavirus (2010)

Coronaviruses (CoV) are enveloped positive-strand RNA viruses that induce different membrane rearrangements in infected cells in order to efficiently replicate and assemble. The origin, the protein composition and the function of these structures are not well established. To shed further light on these structures, we have performed a time-course experiment in which the mouse hepatitis virus (MHV)-induced membrane rearrangements were examined qualitatively and quantitatively by (immuno)-electron microscopy. With our approach we were able to confirm the appearance of 6, previously reported, membranous structures during the course of a complete infection cycle. These structures include the well-characterized double-membrane vesicles (DMVs), convoluted membranes (CMs) and virions but also the more enigmatic large virion-containing vacuoles (LVCVs), tubular bodies (TBs) and cubic membrane structures (CMSs). We have characterized the LVCVs, TBs and CMSs, and found that the CoV-induced structures appear in a strict order. By combining these data with quantitative analyses on viral RNA, protein synthesis and virion release, this study generates an integrated molecular and ultrastructural overview of CoV infection. In particular, it provides insights in the role of each CoV-induced structure and reveals that LVCVs are ERGIC/Golgi compartments that expand to accommodate an increasing production of viral particles.
Hydrophobic radicals embedded in neutral surfactants for dynamic nuclear polarization of aqueous environments at 9.4 Tesla (2014)

We show how large DNP enhancements of NMR signals can be obtained from several hydrophobic radicals that are solubilised in aqueous environments by a variety of biologically compatible neutral amphiphiles. In particular we show that the bi-radical TEKPOL can be incorporated into micelles formed by the surfactant polysorbate 80 (Tween-80), where we obtain large DNP enhancements (∼60) at 9.4 T and ∼100 K.
Fatty acids increase hepatitis B virus X protein stabilization and HBx‐induced inflammatory gene expression (2014)

The protein level of human hepatitis B virus (HBV) in infection is variable, depending on patient context. We previously reported that HBV X protein (HBx) induces hepatic lipid accumulation and inflammation. Here, we show that abnormal levels of hepatic fatty acids increase HBx protein stability during HBV expression, resulting in the potentiation of HBx-induced inflammation. Reactive oxygen species, Ca(2+) signaling and expression levels of various lipid metabolic genes were investigated in HBx-expressing cells and in HBx transgenic mice. Fatty acids, including palmitate, stearate and oleate, increased HBx protein stability by preventing proteasome-dependent degradation. Hepatic inflammation induced by a high fat diet (HFD) and HBx was measured based on the expression of interleukin-6 and tumor necrosis factor α. In addition, the protein level of HBx increased in HFD-HBx transgenic mice. Reactive oxygen species production and intracellular Ca(2+) signal activation play critical roles in fatty-acid-induced HBx stabilization. Abnormal levels of hepatic fatty acids resulted in synergistic induction of HBx protein and liver inflammatory gene expression through HBx protein stabilization. These results indicate that different fatty acid levels in the liver might affect HBV-induced pathogenesis.
A 125-163 GHz Power Amplifier in 28-nm FD-SOI CMOS with 20 dB Gain and 15 dBm Psat for D-Band Applications (2022)

International audience
Development of Automated Micro-Sampling System and Application to Semiconductor Devices (2018)

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A large-scale and low-power CAM architecture featuring a one-hot-spot block code for IP-address lookup in a network router (2005)

We propose a new CAM architecture for the large-scale integration and low-power operation of a network router application. This CAM reduces entry count by an average of 52%, using a newly developed one-hot-spot block code. This code eliminates redundancy in a memory cell and improves the efficiency of IP address compression. To implement the proposed code, a hierarchical match-line structure and an on-chip entry compression/extraction scheme are introduced. With this architecture, a search-depth control scheme deactivates unnecessary search lines and reduces power consumption by 45%. Using a DRAM cell, our new content addressable memory (CAM) can achieve 1.5 million entries in 0.13-/spl mu/m technology, which is six times more than a conventional static ternary CAM.
Power spectral analysis of mammographic parenchymal patterns (2006)

Mammographic density and parenchymal patterns have been shown to be associated with the risk of developing breast cancer. Two groups of women: gene-mutation carriers and low-risk women were included in this study. Power spectral analysis was performed within parenchymal regions of 172 digitized craniocaudal normal mammograms of the BRCA1/BRCA2 gene-mutation carriers and those of women at low-risk of developing breast cancer. The power law spectrum of the form, <i>P</i>(<i>f</i>)=<i>B</i>/<i>f</i><sup>&#946;</sup> was evaluated for the mammographic patterns. Receiver Operating Characteristic (ROC) analysis was used to assess the performance of exponent <i>&#946;</i> as a decision variable in the task of distinguishing between high and low-risk subjects. Power spectral analysis of mammograms demonstrated that mammographic parenchymal patterns have a power-law spectrum of the form, <i>P</i>(<i>f</i>)=<i>B</i>/<i>f</i><sup>&#946;</sup> where <i>f</i> is radial spatial frequency, with the average &#946; values of 2.92 and 2.47 for the gene-mutation carriers and for the low-risk women, respectively. A<sub>z</sub> values of 0.90 and 0.89 were achieved in distinguishing between the gene-mutation carriers and the low-risk women with the individual image &#946; value as the decision variable in the entire database and the age-matched group, respectively.
Rapid identification of specific mutations in the sequence of an enzyme variant produced by protein engineering using high-performance liquid chromatographic/fast atom bombardment mass spectrometric techniques (1994)

Unknown, specific mutations in the sequence of an enzyme variant (a Bacillus subtilisin protease) produced by protein engineering were identified using High-performance Liquid Chromatographic/Fast Atom Bombardment Mass Spectrometric (HPLC/FAB MS) techniques. The variant and the highly homologous wild-type enzyme were treated with CNBr followed by tryptic digestion. The resulting peptides were analysed using HPLC/frit FAB MS. The peptides with molecular masses beyond the range of the HPLC/MS system under the chosen scanning conditions were collected using HPLC and subsequently analysed 'off-line' using static FAB MS. This procedure allowed the complete amino acid sequence determination of the variant protease using the known amino acid sequence of the wild-type enzyme as reference.
Characterization of Resistances of a Capacitive Deionization System (2015)

Capacitive deionization (CDI) is a promising desalination technology, which operates at low pressure, low temperature, requires little infrastructure, and has the potential to consume less energy for brackish water desalination. However, CDI devices consume significantly more energy than the theoretical thermodynamic minimum, and this is at least partly due to resistive power dissipation. We here report our efforts to characterize electric resistances in a CDI system, with a focus on the resistance associated with the contact between current collectors and porous electrodes. We present an equivalent circuit model to describe resistive components in a CDI cell. We propose measurable figures of merit to characterize cell resistance. We also show that contact pressure between porous electrodes and current collectors can significantly reduce contact resistance. Lastly, we propose and test an alternative electrical contact configuration which uses a pore-filling conductive adhesive (silver epoxy) and achieves significant reductions in contact resistance.
Pseurotin B, C, D, and E. Further New Metabolites of Pseudeurotium ovalis STOLK (1981)

Abstract The structures 2–5 are assigned to the pseurotin B, C, D and E, which are new metabolites of Pseudeutorium ovalis S TOLK , based on spectroscopic data and chemical transformations.
Kinase‐mediated quasi‐dimers of EGFR (2010)

ABSTRACT Ligand‐induced dimerization of the epidermal growth factor receptor (ErbB‐1/EGFR) involves conformational changes that expose an extracellular dimerization interface. Subsequent alterations within the cytoplasmic kinase domain, which culminate in tyrosine phosphorylation, are less understood. Our study addressed this question by using two strategies: a chimeric receptor approach employed ErbB‐3, whose defective kinase domain was replaced by the respective part of EGFR. The implanted full‐length kinase, unlike its subdomains, conferred dimerization and catalysis. The data infer that the kinase function of EGFR is restrained by the carboxyl tail; once grafted distally to the ectopic tail of ErbB‐3, the kinase domain acquires quasi‐dimerization and activation. In an attempt to alternatively refold the cytoplasmic tail, our other approach employed kinase inhibitors. Biophysical measurements and covalent cross‐linking analyses showed that inhibitors targeting the active conformation of EGFR, in contrast to a compound recognizing the inactive conformation, induce quasi‐dimers in a manner similar to the chimeric ErbB‐3 molecule. Collectively, these observations unveil ki‐nase domain‐mediated quasi‐dimers, which are regulated by an autoinhibitory carboxyl tail. On the basis of these observations, we propose that quasi‐dimers precede formation of ligand‐induced, fully active dimers, which are stabilized by both extracellular and intracellular receptor‐receptor interactions.—Bublil, E. M., Pines, G., Patel, G., Fruhwirth, G., Ng, T., Yosef Yarden. Kinase‐mediated quasi‐dimers of EGFR. FASEB J. 24, 4744–4755 (2010). www.fasebj.org
Modeling broadcasting using omnidirectional and directional antenna in delay tolerant networks as an epidemic dynamics (2010)

We study broadcasting of information in a system of moving agents equipped with omnidirectional as well as directional antenna. The agent communication protocol is inspired by the classical SIRS epidemics dynamics. We assume that the antennas of all agents have a fixed transmitting power, while signal reception only occurs when the receivers sense signals with power exceeding a certain threshold. Thus, information exchange is a local phenomenon which depends on the relative distance and antenna orientation between the transmitting and the receiving agent. We derive an expression for the mean broadcasting time and study the information dissemination robustness of the system using elements of classical epidemiology and physics. In particular, we show that the mean broadcasting time depends upon ¿ which quantifies the area the radiation pattern of the antenna sweeps as it moves. We report three important observations (a) directional antennas perform better than omnidirectional antennas, (b) directional antennas whose beam-width is narrower perform even better, and (c) the performance enhances a lot if directional antennas rotate. These behaviors can be understood in the light of the reported analytical findings.
Moment-Based Adjustments of Statistical Inference in High-Dimensional Generalized Linear Models (2023)

We developed a statistical inference method applicable to a broad range of generalized linear models (GLMs) in high-dimensional settings, where the number of unknown coefficients scales proportionally with the sample size. Although a pioneering inference method has been developed for logistic regression, which is a specific instance of GLMs, we cannot apply this method directly to other GLMs because of unknown hyper-parameters. In this study, we addressed this limitation by developing a new inference method designed for a certain class of GLMs. Our method is based on the adjustment of asymptotic normality in high dimensions and is feasible in the sense that it is possible even with unknown hyper-parameters. Specifically, we introduce a novel convex loss-based estimator and its associated system, which are essential components of inference. Next, we devise a moment-based method for estimating the system parameters required by the method. Consequently, we construct confidence intervals for GLMs in a high-dimensional regime. We prove that our proposed method has desirable theoretical properties, such as strong consistency and exact coverage probability. Finally, we experimentally confirmed its validity.
Transcriptional approach to study porcine tracheal epithelial cells individually or dually infected with swine influenza virus and Streptococcus suis (2014)

Influenza virus would replicate in the respiratory epithelium and induce an inflammatory infiltrate comprised of mononuclear cells and neutrophils. In a co-infection situation, although these cells would be unable to phagocyte and kill S. suis, they are highly activated by this pathogen. S. suis is not considered a primary pulmonary pathogen, but an exacerbated production of proinflammatory mediators during a co-infection with influenza virus may be important in the pathogenesis and clinical outcome of S. suis-induced respiratory diseases.
Anionic coordinated polymerization ofɛ-caprolactone with aluminium, zirconium and some rare earths alkoxides as initiators in the presence of alcohols (1999)

The kinetics of the polymerization of ε-caprolactone initiated with various Lewis acid metal alkoxides (Al, Zr and rare earths such as Y, Sm, Nd) in the presence of excess alcohol has been investigated. Whatever the metal, the activity depends strongly on the [Alcohol]/[Metal] ratio and goes through a maximum, except for Zr, for which the increase of alcohol concentration leads to a continuous decrease of the reaction rate. The activities obtained for zirconium butoxide as initiator are lower than for aluminium isopropoxide at room temperature but the activation energy is higher. No transesterification reactions have been noticed during polymerization. The polymerization can be described according to a living process with fast transfer reaction, so that the molecular weight is easily controlled by the [Monomer]/[Alcohol] ratio. Rare earths alkoxides (Y, Sm, Nd) result in higher activities. Although some transesterification reactions are observed if leaving the polymer chains in contact with the active centers, functionalized oligomers can be obtained within less than 5 min with yttrium or samarium isopropoxide as initiators and benzyl alcohol in excess.
CO2 electroreduction on bimetallic Pd–In nanoparticles (2020)

The interaction of In and Pd in bimetallic particles causes dramatic changes in the CO<sub>2</sub> reduction behavior.
Cuff Tear Arthropathy (2004)

Visotsky, Jeffrey L. MD; Basamania, Carl MD; Seebauer, Ludwig MD; Rockwood, Charles A. MD; Jensen, Kirk L. MD Author Information
Reactivity of shape-controlled crystals and metadynamics simulations locate the weak spots of alumina in water (2019)

The kinetic stability of any material in water relies on the presence of surface weak spots responsible for chemical weathering by hydrolysis. Being able to identify the atomistic nature of these sites and the first steps of transformation is therefore critical to master the decomposition processes. This is the challenge that we tackle here: combining experimental and modeling studies we investigate the stability of alumina in water. Exploring the reactivity of shape-controlled crystals, we identify experimentally a specific facet as the location of the weak spots. Using biased ab initio molecular dynamics, we recognize this weak spot as a surface exposed tetra-coordinated Al atom and further provide a detailed mechanism of the first steps of hydrolysis. This understanding is of great importance to heterogeneous catalysis where alumina is a major support. Furthermore, it paves the way to atomistic understanding of interfacial reactions, at the crossroad of a variety of fields of research.
Therapeutic vaccination with Ad48/MVA and TLR7 stimulation in SIV-infected, ART-treated infant rhesus macaques (2020)

Abstract Antiretroviral therapy (ART) improves outcomes for the 2.1 million children living with HIV globally but is not a cure. Therefore strategies to reduce, eliminate, or control the persistent HIV reservoir would be highly beneficial. In this study, we sought to evaluate the impact of a therapeutic vaccine and TLR7 agonist in SIV-infected, ART-treated infant rhesus macaques (RMs). Four-week-old RMs (n=16) were infected orally with SIVmac251 then after an additional 4 weeks placed on a daily ART regimen. After 22 weeks post-infection (wpi) 8 RMs received 2 doses of Ad48 vectors expressing SIVgag-pol-env 8 weeks apart and 2 doses of MVA vectors expressing SIVgag-pol-env at 38 and 50 wpi; 10 oral doses of the TLR7 agonist (GS-986) were administered every other week beginning at 40 wpi. The remaining 8 RMs served as experimental controls. The magnitude of SIV-specific cellular immune responses, measured by IFN-γ ELISPOT and multiparametric intracellular cytokine staining, was increased in vaccinated RMs following Ad48-prime and was boosted by MVA. GS-986 induced an elevation of CD14+CD169+ monocytes 24 h after doses 1, 5, and 10. Four weeks after the last GS-986 dose daily ART was stopped to assess efficacy and animals were evaluated for 8 weeks. A similar time to rebound was observed in treated and control RMs. Despite the fact that SIV-infected ART-treated infant RMs are capable of mounting a robust vaccine response and immune activation by the TLR7 agonist this regimen was not sufficient to impact viral rebound. These results are distinct from previous studies performed in acutely infected adult RMs and highlight the importance of a pediatric model to evaluate HIV cure interventions during the unique period of immune development.
Contents Vol. 55, 2012 (2012)

and/or infrequently employed drug.
Robust Shape Reconstruction and Optimal Transportation (2014)

We describe a framework for robust shape reconstruction from raw point sets, based on optimal transportation between measures, where the input point sets are seen as distribution of masses. In addition to robustness to defect-laden point sets, hampered with noise and outliers, our approach can reconstruct smooth closed shapes as well as piecewise smooth shapes with boundaries.
Unsupervised Feature Learning from Temporal Data (2015)

Current state-of-the-art classification and detection algorithms rely on supervised training. In this work we study unsupervised feature learning in the context of temporally coherent video data. We focus on feature learning from unlabeled video data, using the assumption that adjacent video frames contain semantically similar information. This assumption is exploited to train a convolutional pooling auto-encoder regularized by slowness and sparsity. We establish a connection between slow feature learning to metric learning and show that the trained encoder can be used to define a more temporally and semantically coherent metric.
Synthesis of some cyclopropyl-γ-lactones as analogues of cytotoxic α-methylene-γ-lactones (1979)

Five novel α-cyclopropyl-γ-lactones [(5), (8), (12), (18), and (19)] have been prepared. The spirocyclopropyl lactones (5), (8), and (12) were prepared by addition of a keten to an alkene followed by a series of reactions involving reduction, 1,4-dehydrohalogenation, and Baeyer–Villiger oxidation. The optimum order for the last three steps depends upon the structure of the final product. The 2-oxatricyclo[3.3.0.04,6]octanones (18) and (19) were prepared in high yield from the corresponding 2-bromobicycloheptanone by Baeyer–Villiger oxidation and dehydrobromination.