Constant entropy sampling and release waves of shock compressions

We present several equilibrium methods that allow to compute isentropic processes, either during the compression or the release of the material. These methods are applied to compute the isentropic release of a shocked monoatomic liquid at high pressure and temperature. Moreover, equilibrium results of isentropic release are compared to the direct nonequilibrium simulation of the same process. We show that due to the viscosity of the liquid but also to nonequilibrium effects, the release of the system is not strictly isentropic

Joint PDF modelling of turbulent flow and dispersion in an urban street canyon

The joint probability density function (PDF) of turbulent velocity and concentration of a passive scalar in an urban street canyon is computed using a newly developed particle-in-cell Monte Carlo method. Compared to moment closures, the PDF methodology provides the full one-point one-time PDF of the underlying fields containing all higher moments and correlations. The small-scale mixing of the scalar released from a concentrated source at the street level is modelled by the interaction by exchange with the conditional mean (IECM) model, with a micro-mixing time scale designed for geometrically complex settings. The boundary layer along no-slip walls (building sides and tops) is fully resolved using an elliptic relaxation technique, which captures the high anisotropy and inhomogeneity of the Reynolds stress tensor in these regions. A less computationally intensive technique based on wall functions to represent boundary layers and its effect on the solution are also explored. The calculated statistics are compared to experimental data and large-eddy simulation. The present work can be considered as the first example of computation of the full joint PDF of velocity and a transported passive scalar in an urban setting. The methodology proves successful in providing high level statistical information on the turbulence and pollutant concentration fields in complex urban scenarios.Comment: Accepted in Boundary-Layer Meteorology, Feb. 19, 200

Expression of ALS-linked SOD1 mutation in motoneurons or myotubes induces differential effects on neuromuscular function in vitro

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that selectively affects upper and lower motoneurons. Dismantlement of the neuromuscular junction (NMJ) is an early pathological hallmark of the disease whose cellular origin remains still debated. We developed an in vitro NMJ model to investigate the differential contribution of motoneurons and muscle cells expressing ALS-causing mutation in the superoxide dismutase 1 (SOD1) to neuromuscular dysfunction. The primary co-culture system allows the formation of functional NMJs and fosters the expression of the ALS-sensitive fast fatigable type II-b myosin heavy chain (MHC) isoform. Expression of SOD1(G93A) in myotubes does not prevent the formation of a functional NMJ but leads to decreased contraction frequency and lowers the slow type I MHC isoform transcript levels. Expression of SOD1(G93A) in both motoneurons and myotubes or in motoneurons alone however alters the formation of a functional NMJ. Our results strongly suggest that motoneurons are a major factor involved in the process of NMJ dismantlement in an experimental model of ALS

A versatile Plasmodium falciparum reporter line expressing NanoLuc enables highly sensitive multi-stage drug assays

Presentation of a versatile Plasmodium falciparum dual reporter line, expressing both a fluorescent protein and NanoLuc under a constitutive promoter, that can be used to screen for novel anti-malarial drugs effective against multiple stages of the parasite.Transgenic luciferase-expressing Plasmodium falciparum parasites have been widely used for the evaluation of anti-malarial compounds. Here, to screen for anti-malarial drugs effective against multiple stages of the parasite, we generate a P. falciparum reporter parasite that constitutively expresses NanoLuciferase (NanoLuc) throughout its whole life cycle. The NanoLuc-expressing P. falciparum reporter parasite shows a quantitative NanoLuc signal in the asexual blood, gametocyte, mosquito, and liver stages. We also establish assay systems to evaluate the anti-malarial activity of compounds at the asexual blood, gametocyte, and liver stages, and then determine the 50% inhibitory concentration (IC50) value of several anti-malarial compounds. Through the development of this robust high-throughput screening system, we identify an anti-malarial compound that kills the asexual blood stage parasites. Our study highlights the utility of the NanoLuc reporter line, which may advance anti-malarial drug development through the improved screening of compounds targeting the human malarial parasite at multiple stages.Host-parasite interactio

Development of a few TW Ti:Sa laser system at 100 Hz for proton acceleration

[EN] We report the development of a table-top high peak power Titanium:Sapphire (Ti:Sa) CPA laser working at 100 Hz capable of delivering 205 mJ, 55 fs pulses. Every amplification stage is pumped by Nd-doped solid-state lasers and fully powered by diodes. Thermal effects in the Ti:Sa amplifiers are compensated passively with optics. This system is intended to be used for proton acceleration experiments at high repetition rates.Centro para el Desarrollo Tecnológico Industrial (CDTI, Spain) within the INNPRONTA program, Grant no. IPT-20111027.Lera, R.; Bellido-Millán, PJ.; Sánchez, I.; Mur, P.; Seimetz, M.; Benlloch Baviera, JM.; Roso, L.... (2019). Development of a few TW Ti:Sa laser system at 100 Hz for proton acceleration. Applied Physics B. 125(1):1-8. https://doi.org/10.1007/s00340-018-7113-8S181251P. Zeitoun, G. Faivre, S. Sebban, T. Mocek, A. Hallou, M. Fajardo, D. Aubert, P. Balcou, F. Burgy, D. Douillet, S. Kazamias, G. de Lachèze-Murel, T. Lefrou, S. le Pape, P. Mercère, H. Merdji, A.S. Morlens, J.P. Rousseau, C. Valentin, Nature 431(7007), 426–429 (2004)V. Malka, S. Fritzler, E. Lefebvre, M.-M. Aleonard, F. Burgy, J.-P. Chambaret, J.-F. Chemin, K. Krushelnick, G. Malka, S.P.D. Mangles, Z. Najmudin, M. Pittman, J.-P. Rousseau, J.-N. Scheurer, B. Walton, A.E. Dangor, Science 298(5598), 1596–1600 (2002)H. Daido, M. Nishiuchi, A.S. Pirozhkov, Rep. Progress Phys. 75(5), 056401 (2012)A. Macchi, M. Borghesi, M. Passoni, Rev. Mod. Phys. 85, 751–793 (2013)T. Tajima, J.M. Dawson, Phys. Rev. Lett. 43, 267–270 (1979)M. Noaman-ul Haq, H. Ahmed, T. Sokollik, L. Yu, Z. Liu, X. Yuan, F. Yuan, M. Mirzaie, X. Ge, L. Chen, J. Zhang, Phys. Rev. Accel. Beams 20, 041301 (2017)D. Strickland, G. Mourou, Opt. Commun. 53(3), 219–221 (1985)G. Cheriaux, B. Walker, L.F. Dimauro, P. Rousseau, F. Salin, J.P. Chambaret, Opt. Lett. 21(6), 414–416 (1996)P. Tournois, Opt. Commun. 140(4), 245–249 (1997)R. Soulard, A. Brignon, S. Raby, E. Durand, R. Moncorgé, Appl. Phys. B 106(2), 295–300 (2012)J. Liu, L. Ge, L. Feng, H. Jiang, H. Su, T. Zhou, J. Wang, Q. Gao, J. Li, Chin. Opt. Lett. 14(5), 051404 (2016)A. Maleki, M.K. Tehrani, H. Saghafifar, M.H.M. Dindarlu, H. Ebadian, Laser Phys. 26(2), 025003 (2016)R. Lera, F. Valle-Brozas, S. Torres-Peiró, A.R. de-la Cruz, M. Galán, P. Bellido, M. Seimetz, J.M. Benlloch, L. Roso, Appl. Opt. 55(33), 9573–9576 (2016)R. Lausten, P. Balling, J. Opt. Soc. Am. B 20(7), 1479–1485 (2003)I. Nam, M. Kim, T.H. Lee, S.W. Lee, H. Suk, Curr. Appl. Phys. 15(4), 468–472 (2015)E. Treacy, IEEE J. Quantum Electron. 5(9), 454–458 (1969)A. Trisorio, S. Grabielle, M. Divall, N. Forget, C.P. Hauri, Opt. Lett. 37(14), 2892–2894 (2012)Y.-H. Cha, Y.-W. Lee, S.M. Nam, J.M. Han, Y.J. Rhee, B.D. Yoo, B.C. Lee, Y.U. Jeong, Appl. Opt. 46(28), 6854–6858 (2007)P. Bellido, R. Lera, M. Seimetz, A.R. de la Cruz, S. Torres-Peiró, M. Galán, P. Mur, I. Sánchez, R. Zaffino, L. Vidal, A. Soriano, S. Sánchez, F. Sánchez, M. Rodríguez-Álvarez, J. Rigla, L. Moliner, A. Iborra, L. Hernández, D. Grau-Ruiz, A. González, J. García-Garrigos, E. Díaz-Caballero, P. Conde, A. Aguilar, L. Roso, J. Benlloch, J. Instrum. 12(05), T05001 (2017

Multiple TORC1-Associated Proteins Regulate Nitrogen Starvation-Dependent Cellular Differentiation in Saccharomyces cerevisiae

The budding yeast Saccharomyces cerevisiae undergoes differentiation into filamentous-like forms and invades the growth medium as a foraging response to nutrient and environmental stresses. These developmental responses are under the downstream control of effectors regulated by the cAMP/PKA and MAPK pathways. However, the upstream sensors and signals that induce filamentous growth through these signaling pathways are not fully understood. Herein, through a biochemical purification of the yeast TORC1 (Target of Rapamycin Complex 1), we identify several proteins implicated in yeast filamentous growth that directly associate with the TORC1 and investigate their roles in nitrogen starvation-dependent or independent differentiation in yeast.We isolated the endogenous TORC1 by purifying tagged, endogenous Kog1p, and identified associated proteins by mass spectrometry. We established invasive and pseudohyphal growth conditions in two S. cerevisiae genetic backgrounds (Σ1278b and CEN.PK). Using wild type and mutant strains from these genetic backgrounds, we investigated the roles of TORC1 and associated proteins in nitrogen starvation-dependent diploid pseudohyphal growth as well as nitrogen starvation-independent haploid invasive growth.We show that several proteins identified as associated with the TORC1 are important for nitrogen starvation-dependent diploid pseudohyphal growth. In contrast, invasive growth due to other nutritional stresses was generally not affected in mutant strains of these TORC1-associated proteins. Our studies suggest a role for TORC1 in yeast differentiation upon nitrogen starvation. Our studies also suggest the CEN.PK strain background of S. cerevisiae may be particularly useful for investigations of nitrogen starvation-induced diploid pseudohyphal growth

Evolution of the TOR Pathway

The TOR kinase is a major regulator of growth in eukaryotes. Many components of the TOR pathway are implicated in cancer and metabolic diseases in humans. Analysis of the evolution of TOR and its pathway may provide fundamental insight into the evolution of growth regulation in eukaryotes and provide a practical framework on which experimental evidence can be compared between species. Here we performed phylogenetic analyses on the components of the TOR pathway and determined their point of invention. We find that the two TOR complexes and a large part of the TOR pathway originated before the Last Eukaryotic Common Ancestor and form a core to which new inputs have been added during animal evolution. In addition, we provide insight into how duplications and sub-functionalization of the S6K, RSK, SGK and PKB kinases shaped the complexity of the TOR pathway. In yeast we identify novel AGC kinases that are orthologous to the S6 kinase. These results demonstrate how a vital signaling pathway can be both highly conserved and flexible in eukaryotes

Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

A genome-scale specificity and interaction map for yeast SH3 domain-containing proteins reveal how family members show selective binding to target proteins and predicts the dynamic localization of new candidate endocytosis proteins

Virgo Detector Characterization and Data Quality during the O3 run

The Advanced Virgo detector has contributed with its data to the rapid growth of the number of detected gravitational-wave signals in the past few years, alongside the two LIGO instruments. First, during the last month of the Observation Run 2 (O2) in August 2017 (with, most notably, the compact binary mergers GW170814 and GW170817) and then during the full Observation Run 3 (O3): an 11 months data taking period, between April 2019 and March 2020, that led to the addition of about 80 events to the catalog of transient gravitational-wave sources maintained by LIGO, Virgo and KAGRA. These discoveries and the manifold exploitation of the detected waveforms require an accurate characterization of the quality of the data, such as continuous study and monitoring of the detector noise. These activities, collectively named {\em detector characterization} or {\em DetChar}, span the whole workflow of the Virgo data, from the instrument front-end to the final analysis. They are described in details in the following article, with a focus on the associated tools, the results achieved by the Virgo DetChar group during the O3 run and the main prospects for future data-taking periods with an improved detector.Comment: 86 pages, 33 figures. This paper has been divided into two articles which supercede it and have been posted to arXiv on October 2022. Please use these new preprints as references: arXiv:2210.15634 (tools and methods) and arXiv:2210.15633 (results from the O3 run