gebhart/patrepeval huggingface dataset:
Characterizing a Murine Model for Astrovirus Using Viral Isolates from Persistently Infected Immunocompromised Mice (2019)

Human astroviruses are single-stranded RNA enteric viruses that cause a spectrum of disease ranging from asymptomatic infection to systemic extragastrointestinal spread; however, they are among the least-characterized enteric viruses, and there is a lack of a well-characterized small animal model. Finding that immunocompromised mice were resistant to human astrovirus infection via multiple routes of inoculation, our studies aimed to determine whether murine astrovirus (MuAstV) could be used to model human astrovirus disease. We experimentally infected wild-type mice with MuAstV isolated from immunocompromised mice and found that the virus was detected throughout the gastrointestinal tract, including the stomach, but was not associated with diarrhea. The virus was also detected in the lung. Although virus levels were higher in recently weaned mice, the levels were similar in male and female adult mice. Using two distinct viruses isolated from different immunocompromised mouse strains, we observed virus strain-specific differences in the duration of infection (3 versus 10 weeks) in wild-type mice, indicating that the within-host immune pressure from donor mice shaped the virus kinetics in immunocompetent recipient hosts. Both virus strains elicited minimal pathology and a lack of sustained immunity. In summary, MuAstV represents a useful model for studying asymptomatic human infection and gaining insight into the astrovirus pathogenesis and immunity.<b>IMPORTANCE</b> Astroviruses are widespread in both birds and mammals; however, little is known about the pathogenesis and the immune response to the virus due to the lack of a well-characterized small-animal model. Here we describe two distinct strains of murine astrovirus that cause infections in immunocompetent mice that mirror aspects of asymptomatic human infections, including minimal pathology and short-lived immunity. However, we noted that the duration of infection differed greatly between the strains, highlighting an important facet of these viruses that was not previously appreciated. The ubiquitous nature and diversity of murine astroviruses coupled with the continuous likelihood of reinfection raise the possibility of viral interference with other mouse models of disease.
Development and validation of RAYDOSE: a Geant4-based application for molecular radiotherapy (2013)

We developed and validated a Monte-Carlo-based application (RAYDOSE) to generate patient-specific 3D dose maps on the basis of pre-treatment imaging studies. A CT DICOM image is used to model patient geometry, while repeated PET scans are employed to assess radionuclide kinetics and distribution at the voxel level. In this work, we describe the structure of this application and present the tests performed to validate it against reference data and experiments. We used the spheres of a NEMA phantom to calculate S values and total doses. The comparison with reference data from OLINDA/EXM showed an agreement within 2% for a sphere size above 2.8 cm diameter. A custom heterogeneous phantom composed of several layers of Perspex and lung equivalent material was used to compare TLD measurements of gamma radiation from (131)I to Monte Carlo simulations. An agreement within 5% was found. RAYDOSE has been validated against reference data and experimental measurements and can be a useful multi-modality platform for treatment planning and research in MRT.
Structure, viscoelasticity, and interfacial dynamics of a model polymeric bicontinuous microemulsion (2015)

We have systematically studied the equilibrium structure and dynamics of a polymeric bicontinuous microemulsion (BμE) composed of poly(cyclohexylethylene) (PCHE), poly(ethylene) (PE), and a volumetrically symmetric PCHE-PE diblock copolymer, using dynamic mechanical spectroscopy, small angle X-ray and neutron scattering, and transmission electron microscopy. The BμE was investigated over an 80 °C temperature range, revealing a structural evolution and a rheological response not previously recognized in such systems. As the temperature is reduced below the point associated with the lamellar-disorder transition at compositions adjacent to the microemulsion channel, the interfacial area per chain of the BμE approaches that of the neat (undiluted) lamellar diblock copolymer. With increasing temperature, the diblock-rich interface swells through homopolymer infiltration. Time-temperature-superposed linear dynamic data obtained as a function of frequency show that the viscoelastic response of the BμE is strikingly similar to that of the fluctuating pure diblock copolymer in the disordered state, which we associate with membrane undulations and the breaking and reforming of interfaces. This work provides new insights into the structure and dynamics that characterize thermodynamically stable BμEs in the limits of relatively weak and strong segregation.
Circulating Donor-Specific Anti-HLA Antibodies Associate With Immune Activation Independent of Kidney Transplant Histopathological Findings (2022)

Despite the critical role of cytokines in allograft rejection, the relation of peripheral blood cytokine profiles to clinical kidney transplant rejection has not been fully elucidated. We assessed 28 cytokines through multiplex assay in 293 blood samples from kidney transplant recipients at time of graft dysfunction. Unsupervised hierarchical clustering identified a subset of patients with increased pro-inflammatory cytokine levels. This patient subset was hallmarked by a high prevalence (75%) of donor-specific anti-human leukocyte antigen antibodies (HLA-DSA) and histological rejection (70%) and had worse graft survival compared to the group with low cytokine levels (HLA-DSA in 1.7% and rejection in 33.7%). Thirty percent of patients with high pro-inflammatory cytokine levels and HLA-DSA did not have histological rejection. Exploring the cellular origin of these cytokines, we found a corresponding expression in endothelial cells, monocytes, and natural killer cells in single-cell RNASeq data from kidney transplant biopsies. Finally, we confirmed secretion of these cytokines in HLA-DSA-mediated cross talk between endothelial cells, NK cells, and monocytes. In conclusion, blood pro-inflammatory cytokines are increased in kidney transplant patients with HLA-DSA, even in the absence of histology of rejection. These observations challenge the concept that histology is the gold standard for identification of ongoing allo-immune activation after transplantation.
Retraction: Anomalies in growth of electrodeposited Ni–Fe nanogranular films (2019)

Retraction of ‘Anomalies in growth of electrodeposited Ni–Fe nanogranular films’ by T. I. Zubar <italic>et al.</italic>, <italic>CrystEngComm</italic>, 2018, <bold>20</bold>, 2306–2315.
“Calix[4]-box” cages promote the formation of amide bonds in water in the absence of coupling reagents (2018)

The present work shows that encapsulation can be used to promote amide bond formation in water under mild conditions, in the absence of carbodiimide coupling agents.
Web spam identification through content and hyperlinks (2008)

We present an algorithm, witch, that learns to detect spam hosts or pages on the Web. Unlike most other approaches, it simultaneously exploits the structure of the Web graph as well as page contents and features. The method is efficient, scalable, and provides state-of-the-art accuracy on a standard Web spam benchmark.
The pioneer factor PBX1 is a novel driver of metastatic progression in ERα-positive breast cancer (2015)

Over 30% of ERα breast cancer patients develop relapses and progress to metastatic disease despite treatment with endocrine therapies. The pioneer factor PBX1 translates epigenetic cues and mediates estrogen induced ERα binding. Here we demonstrate that PBX1 plays a central role in regulating the ERα transcriptional response to epidermal growth factor (EGF) signaling. PBX1 regulates a subset of EGF-ERα genes highly expressed in aggressive breast tumours. Retrospective stratification of luminal patients using PBX1 protein levels in primary cancer further demonstrates that elevated PBX1 protein levels correlate with earlier metastatic progression. In agreement, PBX1 protein levels are significantly upregulated during metastatic progression in ERα-positive breast cancer patients. Finally we reveal that PBX1 upregulation in aggressive tumours is partly mediated by genomic amplification of the PBX1 locus. Correspondingly, ERα-positive breast cancer patients carrying PBX1 amplification are characterized by poor survival. Notably, we demonstrate that PBX1 amplification can be identified in tumor derived-circulating free DNA of ERα-positive metastatic patients. Metastatic patients with PBX1 amplification are also characterized by shorter relapse-free survival. Our data identifies PBX1 amplification as a functional hallmark of aggressive ERα-positive breast cancers. Mechanistically, PBX1 amplification impinges on several critical pathways associated with aggressive ERα-positive breast cancer.
Supplementary Table 1 from Exome Sequencing to Predict Neoantigens in Melanoma (2023)

&lt;p&gt;Cell line information and Sanger sequence confirmed mutations in each cell line.&lt;/p&gt;
Les pistolets LIBS : Applications au patrimoine et à la géologie (2020)

Les sources laser nanosecondes ainsi que les spectromètres optiques ont atteint un niveau de compacité tel que cela a conduit au développement et à la commercialisation de pistolets LIBS. Avec une autonomie de plusieurs heures, ces dispositifs permettent de réaliser, hors du laboratoire, de nombreuses analyses élémentaires semiquantitatives de la plupart des éléments d’intérêt. Le patrimoine et la géologie font partie des domaines qui ont d’ores et déjà tiré profit de ces nouveaux outils.
Resistance of optical and colored glasses to 3-nsec laser pulses (1982)

In the experimental setup, the pulse of a Nd:YAG glass laser (1060-nm wavelength, 3-nsec pulse duration, output energy up to 1 J) generated damage at the surface and in the bulk of optical glasses. The slightly focused beam exhibited a 2-mm diam in the sample plane with a peak energy density of up to 50 J/cm(2). The surface damage was investigated on 5-mm thick samples with a differential interference microscope (Nomar-ski). In most cases, the damage was small pits probably caused by absorption centers in the polishing layer. Thresholds were more dependent on the polishing method than on the chemical composition of the glass. Typical values ranged from 15 to 25 J/cm(2) for optical glasses and from 8 to 25 J/cm(2) for colored glasses. Studies of internal damage using 20-mm thick samples showed two phenomena: threadlike and pointlike damage at different thresholds. Threadlike damage was caused by self-focusing of the laser beam and was therefore correlated with the nonlinear refractive index of the sample. Inclusions within the glass are responsible for the pointlike damage. Internal damage thresholds varied from 7 to more than 45 J/cm(2). Glass types BK-1, BK-7, TiK-1, BaK-2, ZK-1, PSK-50, and BaLK-3 show high resistance.
Synthesis of <i>P</i>-Chiral Dihydrobenzooxaphospholes Through Negishi Cross-Coupling (2015)

An efficient Negishi cross-coupling was developed for the synthesis of the biaryl axes present in useful P-chiral dihydrobenzooxaphosphole ligands. This approach has allowed for the synthesis of new derivatives of these ligands that were not accessible by the previous route employing Suzuki-Miyaura cross-coupling. The use of Pd2(dba)3/BI-DIME as the catalyst system affords the desired biaryl compounds in good yields with excellent rates and with catalyst loadings as low as 0.25 mol %.
Neuroenergetic response to prolonged cerebral glucose depletion after severe brain injury and the role of lactate (2015)

In patients with acute brain injury (ABI), increased cerebral energy demand is frequent, potentially leading to cerebral glucose depletion (GD) and poor outcome. In this setting, lactate may act as supplemental fuel. We examined dynamics of cerebral lactate supply during prolonged GD in ABI.
Thermoacoustic instabilities of highly premixed flames in combustors and boilers (1999)

The attempt to reduce the formation of pollutants from combustion processes has led in recent years to the development of novel low-temperature combustion processes. Confined flames of this type exhibit a number of instability mechanisms, which can lead to unacceptable combustion noise or even to severe damage. The instability mechanisms, which appear in cases of technical interest, are reviewed and explained. It is shown that a realistic model for the description of the instability requires a proper representation of the contribution of the flame as the driving element. To date, nonlinear transfer functions have to be deduced from combustion experiments, but attempts to derive transfer functions numerically have already been published. In the past, modeling efforts were strongly focused on longitudinal modes. Although circumferential modes are of technical importance, they have not yet been fully understood. In this case, a complex interaction of the nonlinear flame with the linear acoustic system has to be taken into account and the transition between modes becomes more important. Since a satisfactory description of the interaction is not yet available, active instability control techniques have been proposed. Their limit in cases of technical interest will be discussed.
Synthesis and Surface Attachment of ABC Triblock Copolymers Containing Glassy and Rubbery Segments (2004)

Abstract Summary: The synthesis of an ABC triblock copolymer containing glassy and rubbery segments was conducted using a combination of living anionic and atom transfer radical polymerizations (ATRP). A poly(dimethylsiloxane) (pDMS) macroinitiator ( $\overline M _{{\rm n}\quad {\rm SEC}\;}$ = 6 200; $\overline M _{\rm w} /\overline M _{\rm n}$ = 1.19) was prepared by living anionic ring‐opening polymerization, followed by hydrosilation reactions to incorporate 2‐bromoisobutyrate end groups for initiation of ATRP. The ATRP of styrene (S) using the pDMS macroinitiator yielded a diblock copolymer ( $\overline M _{{\rm n}\quad {\rm SEC}\;}$ = 66 730; $\overline M _{\rm w} /\overline M _{\rm n}$ = 1.38). Chain extension of the pDMS‐ b ‐pS macroinitiator with 3‐(dimethoxymethylsilyl)propyl acrylate (DMSA) by ATRP yielded an ABC triblock copolymer. The latter reactive segment was covalently attached to silanol groups on a silicon wafer. The presentation of either glassy pS or flexible pDMS segments of the brushes attached to the surface was reversibly controlled by treatment with selective solvents for each segment. Surface immobilization of pDMS‐ b ‐pS‐ b ‐pDMSA triblock copolymer to Si wafer. Treatment of brush with toluene, methanol, or annealing yields brush with hard pS surface. Treatment with hexane selectively solvates pDMS, and the soft layer is presented to the brush surface. magnified image Surface immobilization of pDMS‐ b ‐pS‐ b ‐pDMSA triblock copolymer to Si wafer. Treatment of brush with toluene, methanol, or annealing yields brush with hard pS surface. Treatment with hexane selectively solvates pDMS, and the soft layer is presented to the brush surface.
Control of formation of viscoelastic droplets and distribution of nano-inclusions in functional deposition for lithium–sulfur batteries (2019)

The electrospray process produces micro/nanodroplets for various applications such as thin and uniform coatings, drug carriers and mass spectrometry. In this paper, we study the spray processes of viscoelastic jets using simulations and experiments. In discretized modeling, the jet is perturbed with axisymmetric instability and the growth of this instability causes the jet to break into droplets. For the experiments, a solution of polyvinyl alcohol in water is sprayed and is visualized using a high-speed camera. The droplet size distribution is studied from simulations with experiments for three spray cases: electrospray, air spray, and air-controlled electrospray. Our simulations and experiments reveal that the electric field is effective in reducing the droplet size, while air flow offers more jet break-ups and thus a larger number of droplets. As a result, air-controlled electrospray where these two driving forces are synergistically combined leads to a larger number of smaller droplets than electrospray or air spray. Finally, we applied three spray processes to obtain a deposition of sulfur/mesoporous carbon/graphene/polymer binder composites as a lithium sulfur battery cathode and demonstrated that air-controlled electrospray leads to a higher capacity and rate capability than other processes, exhibiting 800 mA h g<sup>-1</sup> at 0.5C and 600 mA h g<sup>-1</sup> at 2C.
Tissue engineered heart valves re-endothelialized under simulated physiological conditions: Preclinical testing (2006)

Introduction: The regenerative ability of implanted decellularized heart valves is still discussed controversial. The aim of this study was to evaluate the in-vivo integration capacity of decellularized in comparison to re-endothelialized pulmonary valves (PV) in the sheep model.
[P1–281]: DIAGNOSTIC PERFORMANCE USING CSF YKL‐40 IN ALZHEIMER'S DISEASE AND FRONTOTEMPORAL DEMENTIA (2017)

Cerebrospinal fluid (CSF) YKL-40 − a marker for microglial differentiation and activation − has emerged as a relevant neuroinflammatory biomarker for Alzheimer's disease (AD). The aim of this study was two-fold. First, we examined, in a purely clinical level of analysis, the diagnostic accuracy of CSF YKL-40 in discriminating: AD dementia from cognitively healthy controls (HC) and frontotemporal dementia (FTD). Then, we tested the classificatory performance of CSF YKL-40 using a novel unbiased biomarker-guided descriptive categorization system for AD, the “A/T/N” classification. This approach includes three binary biomarker categories reflecting AD pathophysiology, where “A” refers to “amyloid-beta (Aβ) pathology”, “T” to “tau pathology”, and “N” to neurodegeneration. We measured CSF YKL-40 in a cross-sectional multicenter study of 108 participants classified as AD dementia (n=35), FTD (n=9), mild cognitive impairment (MCI; n=41), according to clinical diagnostic criteria; a group of HC (n=23) was also included. In the clinical level, CSF YKL-40 was compared among HC subjects, MCI, AD dementia, and FTD patients. Adopting the unbiased biomarker-based classification system, we classified subjects as AD pathophysiology-negative (n=15), tau-positive (n=15), amyloid-beta (Aβ)-positive (n=13), AD pathophysiology-positive (n=33), FTD (n=9) and HC (n=23). AUROCs were computed through logistic regression within a Leave-One-Out Cross-Validation (LOO-CV) approach to assess the discriminatory performance of YKL-40. Correlations of CSF YKL-40 with the core AD biomarkers were investigated in the entire sample using Spearman's rank-order correlation test. CSF YKL-40 distinguished AD dementia group from HC subjects and FTD cases with AUROCs of 0.69 and 0.70, respectively. CSF YKL-40 discriminated tau-positive and AD pathophysiology-positive individuals from HC, and AD pathophysiology-positive patients from FTD with AUROCs of 0.76, 0.72, and 0.73, respectively. CSF YKL-40 significantly correlated with hyperphosphorylated tau (ρs=0.574, P<0.001) and total-tau (ρs=0.554, P<0.001) but not with Aβ (ρs=0.002, P=0.980). CSF YKL-40 exhibits a fair performance in distinguishing patients with tau-positive pathophysiological mechanisms. In addition, we reported a positive correlation between CSF YKL-40 and tau protein. Overall, these data suggest a potential useful role of this biomarker in the clinical diagnosis of AD and support a biomarker-guided pathophysiological stratification.
Effect of weaning, week postweaning and diet composition on pancreatic and small intestinal luminal lipase response in young swine. (1990)

The effects of weaning, week postweaning and diet composition on concentration of lipase in the pancreas and small intestinal lumen were investigated in weanling swine. In Exp. 1, lipase levels were evaluated in suckling pigs from 2 to 35 d of age and in pigs weaned at 21 or 35 d of age. Pigs weaned at 21 d of age were fed a corn-soybean meal diet with lipase levels measured from 3 to 28 d postweaning. Pancreas weights increased during the suckling period; they were lowered at 3 d postweaning and were lower at 7 d postweaning than in suckling pigs but increased linearly from 3 to 28 d postweaning. Lipase level per unit wet tissue and total pancreatic levels increased from 2 to 35 d of age in suckling pigs (P less than .01). Weaning at 21 d of age resulted in a decline (P less than .05) in lipase levels in the pancreas at 3 and 7 d postweaning, but the levels subsequently tended to increase between 7 and 28 d postweaning. Whereas relative lipase levels in the intestinal lumen increased from 2 to 35 d of age in suckling pigs, total luminal enzyme did not decline upon weaning when pigs were weaned at either 21 or 35 d of age. Total luminal lipase per unit empty body increased linearly (P less than .01) each week postweaning. In Exp. 2, a 2 X 2 factorial arrangement of corn oil (0 or 6%) and dried whey (0 or 25%) was used to evaluate digestive lipase levels in pigs weaned at 21 d of age.(ABSTRACT TRUNCATED AT 250 WORDS)
Tensile modulus modeling of carbon‐filled nylon 6,6 and polycarbonate‐based resins (2003)

Abstract Electrically and thermally conductive resins can be produced by adding conductive fillers to insulating polymers. Mechanical properties, such as tensile modulus, are also important. This research focused on performing compounding runs followed by injection molding and tensile testing of carbon‐filled nylon 6,6 and polycarbonate‐based resins. The three carbon fillers investigated included an electrically conductive carbon black, synthetic graphite particles, and a milled pitch–based carbon fiber. For each polymer, resins were produced and tested that contained varying amounts of these single‐carbon fillers. In addition, combinations of fillers were investigated by conducting a full 2 3 factorial design and a complete replicate in each polymer. These tensile modulus experimental results were then compared to results predicted by several different models. For the composites containing only one filler type, the Nielsen model with the modified Ψ term provided the best prediction of the actual experimental values. For the composites containing more than one filler type, a new parameter, which includes the vibrated bulk density (VBD) of the fillers, was incorporated into the Nielsen model with the modified Ψ term. This model with the new VBD parameter provided the best estimate of experimental tensile modulus for composites containing multiple‐filler types. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 1716–1728, 2003
"Contribution to the mapping of customer's requirements and process parameters" (2010)

International audience
3D large-signal analysis in beam optics analyzer (2013)

The standard approach to obtain the spent beam exiting an IOT output cavity is to assume a beam profile at the cavity entrance and use a 2D large signal code such as Tesla or Nemesis to modulate the beam. These codes rely on integration of equivalent circuit equations coupled with the Lorentz force equations for particle trajectories. They employ a 2D model for the circuit fields and a 2D Poisson solver. They are very efficient and give very good results. However, they are not convenient to use for IOT devices. An injected RF modulated beam profile is either provided analytically or computed elsewhere by another code. More complex 3D geometries such as a multiple beam configuration could not be analyzed by such 2D large signal codes.