gebhart/patrepeval huggingface dataset:
Transport et diffusion d'atomes dans des milieux poreux. Modélisation et simulation par dynamique moléculaire (2013)

National audience
Pupil-segmentation-based adaptive optics for microscopy (2011)

Inhomogeneous optical properties of biological samples make it difficult to obtain diffraction-limited resolution in depth. Correcting the sample-induced optical aberrations needs adaptive optics (AO). However, the direct wavefront-sensing approach commonly used in astronomy is not suitable for most biological samples due to their strong scattering of light. We developed an image-based AO approach that is insensitive to sample scattering. By comparing images of the sample taken with different segments of the pupil illuminated, local tilt in the wavefront is measured from image shift. The aberrated wavefront is then obtained either by measuring the local phase directly using interference or with phase reconstruction algorithms similar to those used in astronomical AO. We implemented this pupil-segmentation-based approach in a two-photon fluorescence microscope and demonstrated that diffraction-limited resolution can be recovered from nonbiological and biological samples.
Antifungal study of substituted 4-pyridylmethylene-4′-aniline Schiff bases (2016)

Two substituted 4-pyridylmethylene-4′-aniline Schiff bases showed antifungal activity against.<italic>Aspergillus niger</italic>and<italic>Candida albicans</italic>. They may be useful for the development of safe drug candidates for<italic>A. niger</italic>and<italic>C. albicans</italic>cases of otomycosis.
Correlation between lung inflammatory cells, viral load and cytokines in fatal COVID-19 (2022)

SARS-CoV2 infection induces a complex interaction between virus and host immune system, activating multiple inflammatory pathways and leading to hyperinflammation, diffuse alveolar damage (DAD), ARDS, and multiorgan failure. We aimed to correlate the quantification of viral load, inflammatory cells and cytokines in lung tissue of fatal COVID-19. We assessed inflammatory cells by multiplex immunohistochemistry, cytokines by Luminex xMAP Assay and viral load by real time PCR in autopsy lung tissue of 18 COVID-19 patients. Correlations were considered statistically significant if p&lt;0.05. Macrophages correlated with IL-1β (r=0.54), IL-10 (r=0.5), IFN-α2 (r=0.72), IFN-γ (r=0.6), CCL20 (r=0.5), TGF-β1 (r=0.6), TGF-β2 (r=0.6). CD4+T cells correlated with CCL20 (r=0.6), MDC/CCL2 (r=0.53), CCL17 (r=0.5), IP-10 (r=0.6), CXCL9 (r=0.6). CD8+T cells correlated with IL-1β (r=0.54), IL-4 (r=0.63), IL-6 (r=0.7), IL-8 (r=0.63), IL-10 (r=0.6), TNF-α (r=0.6), IFN-γ (r=0.74), CCL20 (r=0.7), TGF-β1 (r=0.7), TGF-β2 (r=0.56), TGF-β3 (r=0.54), MDC/CCL2 (r=0.7), CCL17 (r=0.64). Langerin dendritic cells (DC) correlated with symptom onset to death interval (r=0.6), hospitalization length (r=0.65), mechanical ventilation (MV) length (r=0.6), ICU stay (r=0.6), exudative DAD (r=-0.5), viral load (r=-0.6). Myeloid DC correlated with symptom onset to death interval (r=0.8), hospitalization length (r=0.8), MV length (r=0.8), ICU stay (r=0.8), exudative DAD (r=-0.5), viral load (r=-0.7). Viral load correlated with symptom onset to death interval (r=-0.7), hospitalization length (r=-0.8), MV length (r=-0.7), ICU stay (r=-0.8), exudative DAD (r=0.6). There is a complex temporal inflammatory modulation in severe COVID-19.
What Is a Host? Incorporating the Microbiota into the Damage-Response Framework (2014)

Since proof of the germ theory of disease in the late 19th century, a major focus of the fields of microbiology and infectious diseases has been to seek differences between pathogenic and nonpathogenic microbes and the role that the host plays in microbial pathogenesis. Remarkably, despite the increasing recognition that host immunity plays a role in microbial pathogenesis, there has been little discussion about what constitutes a host. Historically, hosts have been viewed in the context of their fitness or immunological status and characterized by adjectives such as immune, immunocompetent, immunosuppressed, immunocompromised, or immunologically impaired. However, in recent years it has become apparent that the microbiota has profound effects on host homeostasis and susceptibility to microbial diseases in addition to its effects on host immunity. This raises the question of how to incorporate the microbiota into defining a host. This definitional problem is further complicated because neither host nor microbial properties are adequate to predict the outcome of host-microbe interaction because this outcome exhibits emergent properties. In this essay, we revisit the damage-response framework (DRF) of microbial pathogenesis and demonstrate how it can incorporate the rapidly accumulating information being generated by the microbiome revolution. We use the tenets of the DRF to put forth the following definition of a host: a host is an entity that houses an associated microbiome/microbiota and interacts with microbes such that the outcome results in damage, benefit, or indifference, thus resulting in the states of symbiosis, colonization, commensalism, latency, and disease.
Immunohistochemical detection of p53, PTEN, Rb, and p16 in canine osteosarcoma using tissue microarray (2018)

Although inactivating mutations of tumor suppressor genes are well described in cell lines of canine osteosarcoma (OS), expression of tumor suppressor proteins in spontaneous disease is poorly characterized. We determined the immunohistochemical expression of p53, PTEN, Rb, and p16 in a large cohort of dogs with OS. Formalin-fixed, paraffin-embedded samples of canine OS were analyzed retrospectively. Primary tumor samples from 145 dogs, collected between 2003 and 2008, were evaluated by tissue microarray. Streptavidin-biotin complex immunohistochemistry was performed using monoclonal antibodies for Rb and PTEN and polyclonal antibodies for p16 and p53. The average age of dogs was 7.6 y, and 118 of 145 (81%) were purebred. Most commonly represented purebreds were Greyhound (23%), Rottweiler (11%), and Labrador Retriever (10%). Immunohistochemical detection of p53, PTEN, Rb, and p16 was 81%, 61%, 66%, and 66%, respectively. The staining pattern for p16 was primarily cytoplasmic; the predominant pattern for PTEN, Rb, and p53 was cytoplasmic and nuclear. Exclusively cytoplasmic staining was noted in 19% of samples positive for p53 and 8% of samples positive for Rb. Kaplan-Meier curves showed that protein expression was not associated with significant differences in overall survival ( p > 0.191). We documented heterogeneity in both immunostaining and subcellular localization of tumor suppressor proteins, providing further characterization of canine OS.
Advancing a Comprehensive Approach to the Study of Lower Urinary Tract Symptoms (2016)

We propose a new framework for future urology research, which should help to reduce the medical and economic burden of lower urinary tract symptoms in the United States population.
Variable Region Identical IgA and IgE to Cryptococcus neoformans Capsular Polysaccharide Manifest Specificity Differences (2015)

In recent years several groups have shown that isotype switching from IgM to IgG to IgA can affect the affinity and specificity of antibodies sharing identical variable (V) regions. However, whether the same applies to IgE is unknown. In this study we compared the fine specificity of V region-identical IgE and IgA to Cryptococcus neoformans capsular polysaccharide and found that these differed in specificity from each other. The IgE and IgA paratopes were probed by nuclear magnetic resonance spectroscopy with (15)N-labeled peptide mimetics of cryptococcal polysaccharide antigen (Ag). IgE was found to cleave the peptide at a much faster rate than V region-identical IgG subclasses and IgA, consistent with an altered paratope. Both IgE and IgA were opsonic for C. neoformans and protected against infection in mice. In summary, V-region expression in the context of the ϵ constant (C) region results in specificity changes that are greater than observed for comparable IgG subclasses. These results raise the possibility that expression of certain V regions in the context of α and ϵ C regions affects their function and contributes to the special properties of those isotypes.
EUV lithography : historical perspective and road ahead (2014)

Lithography, in the form of carved type printing, can be dated as far back as the 3rd century AD. Starting from the 19th century it played a major role as the basis for dissemination and preservation of knowledge in the form of printed books, maps, newspapers, etc. In the mid 20th century, with the invention of the micro- and nanoelectronics, it took on a new meaning and became the basis for the patterning solutions of the modern day semiconductor industry. New challenges for further scaling of semiconductor devices in the 21th century brought Extreme Ultraviolet Lithography (EUVL) under close scrutiny of both hightech companies and scientific institutes. This growing interest has developed new insights into the science and technology of EUV production and EUV related processes in the areas of plasma physics, optics, surface physics and chemistry as well as many others. In his lecture he will describe his continuing voyage to explore this exciting world where these areas come together and he will sketch the possible technological developments that are still\nahead of us.
Absorption, Metabolism, and Excretion of ACT-1004-1239, a First-In-Class CXCR7 Antagonist: In Vitro, Preclinical, and Clinical Data (2022)

ACT-1004-1239 is a potent, selective, first-in-class CXCR7 antagonist, which shows a favorable preclinical and clinical profile. Here we report the metabolites and the metabolic pathways of ACT-1004-1239 identified using results from <i>in vitro</i> and <i>in vivo</i> studies. Two complementary <i>in vitro</i> studies (incubation with human liver microsomes in the absence/presence of cytochrome P450- [CYP] specific chemical inhibitors and incubation with recombinant CYPs) were conducted to identify CYPs involved in ACT-1004-1239 metabolism. For the <i>in vivo</i> investigations, a microtracer approach was integrated in the first-in-human study to assess mass balance and absorption, distribution, metabolism, and excretion (ADME) characteristics of ACT-1004-1239. Six healthy male subjects received orally 100 mg non-radioactive ACT-1004-1239 together with 1 μCi <sup>14</sup>C-ACT-1004-1239. Plasma, urine, and feces samples were collected up to 240 h post-dose and <sup>14</sup>C-drug-related material was measured with accelerator mass spectrometry. This technique was also used to construct radiochromatograms of pooled human samples. Metabolite structure elucidation of human-relevant metabolites was performed using high performance liquid chromatography coupled with high resolution mass spectrometry and facilitated by the use of rat samples. CYP3A4 was identified as the major CYP catalyzing the formation of M1 <i>in vitro</i>. In humans, the cumulative recovery from urine and feces was 84.1% of the dose with the majority being eliminated via the feces (69.6%) and the rest via the urine (14.5%). In human plasma, two major circulating metabolites were identified, i.e., M1 and M23. Elimination <i>via</i> M1 was the only elimination pathway that contributed to ≥25% of ACT-1004-1239 elimination. M1 was identified as a secondary amine metabolite following oxidative N-dealkylation of the parent. M23 was identified as a difluorophenyl isoxazole carboxylic acid metabolite following central amide bond hydrolysis of the parent. Other metabolites observed in humans were A1, A2, and A3. Metabolite A1 was identified as an analog of M1 after oxidative defluorination, whereas both, A2 and A3, were identified as a reduced analog of M1 and parent, respectively, after addition of two hydrogen atoms at the isoxazole ring. In conclusion, CYP3A4 contributes to a relevant extent to ACT-1004-1239 disposition and two major circulating metabolites were observed in humans. <b>Clinical Trial Registration:</b> (https://clinicaltrials.gov/ct2/show/NCT03869320) ClinicalTrials.gov Identifier NCT03869320.
Next steps in AAV preclinical and translational R&D (2021)

<div class="authors authors-lg"><div class="author"><div class="author-img"><img src="https://cdn.insights.bio/uploads/Anna Tretiakova pic sa.png" data-image="1"></div><div class="author-det"> <b>Anna Tretiakova</b>, PhD, is a Senior Vice President of Product Development, leading the company’s research and translational programs to deliver clinical candidate vectors. Anna is an industry veteran with more than 30 years of of research and development experience that spans basic research and non-clinical translational sciences, progressing from a bench scientist in academia to senior leadership roles with biotechnology and pharmaceutical organizations. She has spent over a decade exclusively focused on AAV gene therapy for monogenic and non-monogenic diseases in various therapeutic areas at the University of Pennsylvania Gene Therapy Program, Pfizer Rare Disease Research Unit, SwanBio Therapeutics, and, most recently, at AskBio. She completed her graduate education in molecular biology and biochemistry with a PhD from Thomas Jefferson University in Philadelphia and diploma from Novosibirsk State University in Russia. </div></div></div><div class="authors authors-lg"><div class="author"><div class="author-img"><img src="https://cdn.insights.bio/uploads/Shari Gordon pic sq.png" data-image="1"></div><div class="author-det"> <b>Shari Gordon</b> is the Senior Director of Immunology at Asklepios Biopharmaceutical (Ask Bio). Shari is a viral immunologist with 18 years of experience in infectious diseases. Shari’s passion for science began with her graduate work at Emory University focused on HIV pathogenesis and continued with her post graduate work that evaluated novel vaccine approaches using viral vectors. Shari had an illustrious career at GlaxoSmithKline and then ViiV Healthcare advancing biologics for the treatment of HIV and Cancer before joining Ask Bio. At Ask Bio Shari leads the clinical immunology and immunoassays teams that characterize the immune response to AAV gene therapy and immune modulatory approaches. </div></div></div>
Minimally Invasive Cervical Microendoscopic Foraminotomy: An Initial Clinical Experience (2002)

The MEF technique yielded clinical results equivalent to those of the open surgical group as well as to those described in the literature. MEF patients, however, had less blood loss, shorter hospitalizations, and a much lower postoperative pain medication requirement.
Skewed distribution of natural killer cells in psoriasis skin lesions (2012)

Psoriasis is a hyper-proliferative disease of the skin in which immunological mechanisms play a direct pathogenetic role. There have been limited studies of natural killer (NK) cells in psoriasis. The aim of this study was to examine the phenotype of NK cells in skin biopsies and peripheral blood mononuclear cells from patients with psoriasis and healthy controls. CD56(+) CD16(-) and CD56(+) CD16(+) NK cells were isolated from lesional skin, unaffected skin and PBMC of psoriasis patients, and normal skin and PBMC from healthy controls. The expression of CD57, NKG2A and NKG2C was assessed by flow cytometry. NK cells in psoriasis skin lesions were skewed in their expression of CD57, a marker of NK cell maturity, with CD57 expression significantly reduced and NKG2A expression increased on NK cells in lesional and unaffected skin compared to controls. These data suggest that in this patient cohort, NK cells could be isolated from psoriasis lesions and exhibit an immature phenotype.
Annealing Kinetic Model Using Fast and Slow Metastable Defects for Hydrogenated-Amorphous-Silicon-Based Solar Cells (2007)

The two-component kinetic model employing “fast” and “slow” metastable defects for the annealing behaviors in pin-type hydrogenated-amorphous-silicon- (a-Si:H-) based solar cells is simulated using a normalized fill factor. Reported annealing data on pin-type a-Si:H-based solar cells are revisited and fitted using the model to confirm its validity. It is verified that the two-component model is suitable for fitting the various experimental phenomena. In addition, the activation energy for annealing of the solar cells depends on the definition of the recovery time. From the thermally activated and high electric field annealing behaviors, the plausible microscopic mechanism on the defect removal process is discussed.
Electric and Magnetic Field Galvanic Distortion Decomposition of BC87 Data. (1997)

The BC87 magnetotelluric data exhibit distortions due to three-dimensional structures at all scale sizes, from very local to regional. Previous work has shown that these distortions can sometimes, but not always, be described by an electric field galvanic distortion model, and hence can be removed using a tensor decomposition approach. This work extends the analysis to include galvanic distortion of the magnetic field, and shows its importance for many of the BC87 sites. However, even a combined electric and magnetic field galvanic distortion approach fails for quite a few of the sites studied. This is pervasive for periods shorter than 10 s, suggesting local 3D inductive effects, but model inadequacy at longer periods may indicate a breakdown of the model assumptions, particularly the requirement that the regional electric field be both uniform across the distorting body and comparable to that at the observation point.
Single-electron transistor structures based on silicon-on-insulator silicon nanowire fabrication by scanning probe lithography and wet etching (2002)

We propose a promising fabrication technology for single-electron transistors based on a silicon-on-insulator (SOI) nanowire fabricated by scanning probe lithography and KOH wet etching. The 10-nm-wide and 10-nm-high silicon nanowire is defined by scanning probe lithography and KOH wet etching process technology. Along the [100] direction on a (100) SOI silicon wafer, local oxidation was performed in ambient using highly doped Si cantilevers with a resistivity of 0.01–0.0025 Ω cm and a commercial atomic force microscope/scanning tunneling microscope instrument. Using the oxide pattern as a Si etching mask, the Si substrate was dipped in aqueous KOH solution, in which unoxidized regions are selectively etched by aqueous KOH orientation-dependent etching. The silicon nanowire was obtained by well-controlled overetching of 34 wt % at 40 °C for 50 s. The top gate, back gates and contact pads were defined by photolithography and dry etching. Statistics showing the reproducibility of this technique are also demonstrated.
Iridium-alloy processing experience in FY 1990 (1991)

Iridium-alloy blanks and foil are produced at the Oak Ridge National Laboratory for use as fuel cladding material in radioisotope thermoelectric generators for space power sources. Until 1984, the material was produced from small, 500-g drop castings. A new process has been developed in which consumable electrodes of about 10 kg are melted, extruded, and then rolled to produce the sheet products. The work performed during FY 1990 included the consumable-electrode arc melting of four ingots and the extruding and rolling to sheet of four billets. Significant improvements made in the extruding and arc-melting processes during FY 1989 have been demonstrated to dramatically increase the rate of blank acceptance in nondestructive evaluations. Efforts to improve the rolling practice and to better characterize intermetallic particle distributions in the sheet are also described.
Decision Support System for Constantly Monitoring Patients in a Comorbid Condition (2013)

In this paper, we present the design of a telecommunication and computer technology based system for monitoring patients in the presence of a comorbid condition. Specifically, we take the monitoring of patients with both atrial fibrillation (AF) and Wolff Parkinsons White (WPW) as an example to clarify the process of system design. This system performs combining of guidelines for different diseases in view of the potential conflict occuring. The architecture of our system, including this decision support system, is detailed in this paper. To show system accuracy, we theoretically evaluate the ability of a decision support system to correctly make decisions as well as to detect the conflict between guidelines.
Complex double-binary-offset-carrier modulation for a unitary characterisation of Galileo and GPS signals (2006)

The authors introduce a new class of modulation, the complex double-binary-offset-carrier (CDBOC) modulation class, which covers most of the modulation types proposed so far for Galileo and GPS signals, namely the binary and quaternary phase shift keying, sine BOC, cosine BOC and alternate BOC modulations. At the same time, the CDBOC class provides a more general framework, with the potential for new applications of wide-band code division multiple access systems and/or future satellite navigation systems. The theoretical derivations of the power spectral density and the auto-correlation function of the CDBOC-modulated signals are introduced, and the theoretical analysis is compared with the results obtained via simulations. The advantage of our method in the context of Galileo and GPS signals is its simplicity and the fact that it provides unified analytical formulas for most of the existent GPS/Galileo signals.
Thermal Stability of a Thin HfO2/Ultrathin SiO2/Si Structure: Interfacial Si Oxidation and Silicidation (2003)

We examine the thermal stability of a 2.6-nm-HfO2/0.3-nm-SiO2/Si structure in O2 pressure and in an ultrahigh vacuum. The temperature and O2-pressure dependence of Si oxidation at the HfO2/Si interface indicates that high-vacuum conditions are required to suppress interfacial oxidation (order of 10-7 Torr at 800°C). The void nucleation of Hf silicide (<1000 cm-2) takes place at temperatures higher than 900°C, which raises the issue of failure when HfO2 film is used in metal-insulator-semiconductor devices.
A Real Sea Test of Wave Powered Generation Buoys Using Dielectric Elastomers (2012)

For the practical application of wave powered generation, it is necessary that an epoch-making technology or performance have to be developed. This paper describes an actual sea test for application of the dielectric elastomer to wave powered generation. The power generation device using the dielectric elastomer of a floating buoy is installed to the fishery harbor of Suzaki in the IZU peninsula [1]. In the actual sea test, accelerations in three degree of freedom and output energy due to motion of the powered buoy are measured. Incident waves are measured using an ultrasonic wave meter. Expected acquirable power of the powered buoy with the dielectric elastomer is from 25 mW to 56 mW in observation time which is one minutes. Relationship between motion of the buoy transferred from the accelerations and the output power is investigated from the results. From the results, it is proven that a small wave powered generation buoy system is available with the dielectric elastomer.
Inverter Device Nonlinearity Characterization Technique for Use in a Motor Drive System (2014)

This paper introduces a detailed nonlinearity characterization technique for insulated-gate bipolar transistor inverters in a drive system which is able to measure device nonlinearities. Methods are derived from measurements of the voltage on the inverter phases. These measurements are obtained while applying a set of direct currents to an electrical machine. These methods are then applied to tests using alternating current. The study of inverter nonlinearities is useful in order to conduct condition monitoring. These methods fulfill the need to characterize each device in an inverter. In addition to characterizing every device using either ac or dc current, the method is resistant to noise; for these reasons, the method is applicable in the field. Simulations and experimental work demonstrate the benefits and applicability of the methods.