Metashooting: a novel tool for free energy reconstruction from polymorphic phase transition mechanisms

We introduce a novel scheme for the mechanistic investigation of solid-solid phase transitions, which we dub extit{metashooting}. Combining transition path sampling molecular dynamics and metadynamics, this scheme allows for both a complete mechanistic analysis and a detailed mapping of the free energy surface. This is illustrated by performing extit{metashooting} calculations on the pressure-induced B4/B3 $ightarrow$ B1 phase transition in ZnO. The resulting free energy map helps to clarify the role of intermediate configurations along this activated process and the competition between different mechanistic regimes with superior accuracy. We argue that extit{metashooting} can be efficiently applied to a broader class of activated processes

Many-particle Li Ion dynamics in LiMPO4 olivine phosphates (M = Mn, Fe)

LiMPO4 (M = Mn, Fe) olivine phosphates are important materials for battery applications due to their stability, safety, and reliable recharge cycle. Despite continuous experimental and computational investigations, several aspects of these materials remain challenging, including conductivity dimensionality and how it maps onto Li pathways. In this work, we use a refined version of our finite temperature molecular dynamics “shooting” approach, originally designed to enhance Li hopping probability. We perform a comparative analysis of ion mobility in both materials, focused on many-particle effects. Therein, we identify main [010] diffusion channels, as well as means of interchannel couplings, in the form of Li lateral [001] hopping, which markedly impact the overall mobility efficiency as measured by self-diffusion coefficients. This clearly supports the need of many-particle approaches for reliable mechanistic investigations and for battery materials benchmarking due to the complex nature of the diffusion and transport mechanisms

Tox2 is required for the maintenance of GC TFH cells and the generation of memory TFH cells

効率よい抗体反応の形成に必要なTリンパ球因子の発見. 京都大学プレスリリース. 2021-10-15.Molecules for building stronger antibodies. 京都大学プレスリリース. 2021-10-15.Memory T follicular helper (TFH) cells play an essential role to induce secondary antibody response by providing help to memory and naïve B cells. Here, we show that the transcription factor Tox2 is vital for the maintenance of TFH cells in germinal centers (GCs) and the generation of memory TFH cells. High Tox2 expression was almost exclusive to GC TFH cells among human tonsillar and blood CD4+ T cell subsets. Tox2 overexpression maintained the expression of TFH-associated genes in T cell receptor–stimulated human GC TFH cells and inhibited their spontaneous conversion into TH1-like cells. Tox2-deficient mice displayed impaired secondary TFH cell expansion upon reimmunization with an antigen and upon secondary infection with a heterologous influenza virus. Collectively, our study shows that Tox2 is highly integrated into establishment of durable GC TFH cell responses and development of memory TFH cells in mice and humans

The recent progress on silver nanoparticles: Synthesis and electronic applications

Nanoscience enables researchers to develop new and cost-effective nanomaterials for energy, healthcare, and medical applications. Silver nanoparticles (Ag NPs) are currently increasingly synthesized for their superior physicochemical and electronic properties. Good knowledge of these characteristics allows the development of applications in all sensitive and essential fields in the service of humans and the environment. This review aims to summarize the Ag NPs synthesis methods, properties, applications, and future challenges. Generally, Ag NPs can be synthesized using physical, chemical, and biological routes. Due to the great and increasing demand for metal and metal oxide nanoparticles, researchers have invented a new, environmentally friendly, inexpensive synthetic method that replaces other methods with many defects. Studies of Ag NPs have increased after clear and substantial support from governments to develop nanotechnology. Ag NPs are the most widely due to their various potent properties. Thus, this comprehensive review discusses the different synthesis procedures and electronic applications of Ag NPs

Dissociation Protocols Used for Sarcoma Tissues Bias the Transcriptome Observed in Single-Cell and Single-Nucleus RNA Sequencing

BACKGROUND: Single-cell RNA-seq has emerged as an innovative technology used to study complex tissues and characterize cell types, states, and lineages at a single-cell level. Classification of bulk tumors by their individual cellular constituents has also created new opportunities to generate single-cell atlases for many organs, cancers, and developmental models. Despite the tremendous promise of this technology, recent evidence studying epithelial tissues and diverse carcinomas suggests the methods used for tissue processing, cell disaggregation, and preservation can significantly bias gene expression and alter the observed cell types. To determine whether sarcomas - tumors of mesenchymal origin - are subject to the same technical artifacts, we profiled patient-derived tumor explants (PDXs) propagated from three aggressive subtypes: osteosarcoma (OS), Ewing sarcoma (ES), desmoplastic small round cell tumor (DSRCT). Given the rarity of these sarcoma subtypes, we explored whether single-nuclei RNA-seq from more widely available archival frozen specimens could accurately be identified by gene expression signatures linked to tissue phenotype or pathognomonic fusion proteins. RESULTS: We systematically assessed dissociation methods across different sarcoma subtypes. We compared gene expression from single-cell and single-nucleus RNA-sequencing of 125,831 whole-cells and nuclei from ES, DSRCT, and OS PDXs. We detected warm dissociation artifacts in single-cell samples and gene length bias in single-nucleus samples. Classic sarcoma gene signatures were observed regardless of the dissociation method. In addition, we showed that dissociation method biases could be computationally corrected. CONCLUSIONS: We highlighted transcriptional biases, including warm dissociation and gene-length biases, introduced by the dissociation method for various sarcoma subtypes. This work is the first to characterize how the dissociation methods used for sc/snRNA-seq may affect the interpretation of the molecular features in sarcoma PDXs

Preclinical Efficacy of Endoglin-Targeting Antibody–Drug Conjugates for the Treatment of Ewing Sarcoma

[EN] Endoglin (ENG; CD105) is a coreceptor of the TGFb family that is highly expressed in proliferating endothelial cells. Often coopted by cancer cells, ENG can lead to neo-angiogenesis and vasculogenic mimicry in aggressive malignancies. It exists both as a transmembrane cell surface protein, where it primarily interacts with TGFb, and as a soluble matricellular protein (sENG) when cleaved by matrix metal-loproteinase 14 (MMP14). High ENG expression has been associated with poor prognosis in Ewing sarcoma, an aggressive bone cancer that primarily occurs in adolescents and young adults. However, the therapeutic value of ENG targeting has not been fully explored in this disease. Experimental Design: We characterized the expression pattern of transmembrane ENG, sENG, and MMP14 in preclinical and clinical samples. Subsequently, the antineoplastic potential of two novel ENG-targeting monoclonal antibody–drug conjugates (ADC), OMTX503 and OMTX703, which differed only by their drug payload (nigrin-b A chain and cytolysin, respectively), was assessed in cell lines and preclinical animal models of Ewing sarcoma. Results: Both ADCs suppressed cell proliferation in proportion to the endogenous levels of ENG observed in vitro. Moreover, the ADCs significantly delayed tumor growth in Ewing sarcoma cell line–derived xenografts and patient-derived xenografts in a dose-dependent manner. Conclusions: Taken together, these studies demonstrate potent preclinical activity of first-in-class anti-ENG ADCs as a nascent strategy to eradicate Ewing sarcoma

Measuring the atmospheric neutrino oscillation parameters and constraining the 3+1 neutrino model with ten years of ANTARES data

The ANTARES neutrino telescope has an energy threshold of a few tens of GeV. This allows to study the phenomenon of atmospheric muon neutrino disappearance due to neutrino oscillations. In a similar way, constraints on the 3+1 neutrino model, which foresees the existence of one sterile neutrino, can be inferred. Using data collected by the ANTARES neutrino telescope from 2007 to 2016, a new measurement of m2 32 and 23 has been performed | which is consistent with world best- t values | and constraints on the 3+1 neutrino model have been derived.Centre National de la Recherche Scienti que (CNRS)Commissariat a l' energie atomique et aux energies alternatives (CEA)Commission Européenne (FEDER fund and Marie Curie Program)Institut Universitaire de France (IUF)IdEx program and UnivEarthS Labex program at Sorbonne Paris Cité (ANR-10-LABX-0023 and ANR-11-IDEX-0005-02)Labex OCEVU (ANR-11-LABX-0060) and the A*MIDEX project (ANR-11-IDEX-0001-02)Région ÎIle-de- France (DIM-ACAV)Région Alsace (contrat CPER)Région Provence-Alpes-Côte d'Azur, Département du Var and Ville de La Seyne-sur-MerBundesministerium für Bildung und Forschung (BMBF)Istituto Nazionale di Fisica Nucleare (INFN)Nederlandse organisatie voor Wetenschappelijk Onderzoek (NWO)Council of the President of the Russian Federation for young scientists and leading scientific schools supporting grantsExecutive Unit for Financing Higher Education, Research, Development and Innovation (UEFISCDIÇ)Ministerio de Economía y Competitividad (MINECO): Plan Estatal de Investigación (refs. FPA2015-65150-C3-1-P, -2-P and -3-P, (MINECO/FEDER))Severo Ochoa Centre of Excellence and Red Consolider MultiDark (MINECO), and Prometeo and Grisolía programs (Generalitat Valenciana)Ministry of Higher Education, Scienti c Research and Professional Trainin

ANTARES and IceCube Combined Search for Neutrino Point-like and Extended Sources in the Southern Sky

[EN] A search for point-like and extended sources of cosmic neutrinos using data collected by the ANTARES and IceCube neutrino telescopes is presented. The data set consists of all the track-like and shower-like events pointing in the direction of the Southern Sky included in the nine-year ANTARES point-source analysis, combined with the throughgoing track-like events used in the seven-year IceCube point-source search. The advantageous ¿eld of view of ANTARES and the large size of IceCube are exploited to improve the sensitivity in the Southern Sky by a factor of ~2 compared to both individual analyses. In this work, the Southern Sky is scanned for possible excesses of spatial clustering, and the positions of preselected candidate sources are investigated. In addition, special focus is given to the region around the Galactic Center, whereby a dedicated search at the location of SgrA* is performed, and to the location of the supernova remnant RXJ 1713.7-3946. No signi¿cant evidence for cosmic neutrino sources is found, and upper limits on the ¿ux from the various searches are presented.The authors of the IceCube Collaboration acknowledge the support from the following agencies and institutions: USA-U.S. National Science Foundation-Office of Polar Programs, U.S. National Science Foundation-Physics Division, Wisconsin Alumni Research Foundation, Center for High Throughput Computing (CHTC) at the University of Wisconsin-Madison, Open Science Grid (OSG), Extreme Science and Engineering Discovery Environment (XSEDE), U.S. Department of Energy-National Energy Research Scientific Computing Center, Particle astrophysics research computing center at the University of Maryland, Institute for Cyber-Enabled Research at Michigan State University, and Astroparticle physics computational facility at Marquette University; Belgium-Funds for Scientific Research (FRS-FNRS and FWO), FWO Odysseus and Big Science programmes, and Belgian Federal Science Policy Office (Belspo); Germany-Bundesministerium fur Bildung und Forschung (BMBF), Deutsche Forschungsgemeinschaft (DFG), Helmholtz Alliance for Astroparticle Physics (HAP), Initiative and Networking Fund of the Helmholtz Association, Deutsches Elektronen Synchrotron (DESY), and High Performance Computing Cluster of the RWTH Aachen; Sweden-Swedish Research Council, Swedish Polar Research Secretariat, Swedish National Infrastructure for Computing (SNIC), and Knut and Alice Wallenberg Foundation; Australia - Australian Research Council; Canada-Natural Sciences and Engineering Research Council of Canada, Calcul Quebec, Compute Ontario, Canada Foundation for Innovation, WestGrid, and Compute Canada; Denmark-Villum Fonden, Danish National Research Foundation (DNRF), Carlsberg Foundation; New Zealand-Marsden Fund; Japan-Japan Society for Promotion of Science (JSPS) and Institute for Global Prominent Research (IGPR) of Chiba University; Korea-National Research Foundation of Korea (NRF); Switzerland-Swiss National Science Foundation (SNSF); United Kingdom-Department of Physics, University of Oxford.Albert, A.; Andre, M.; Anghinolfi, M.; Anton, G.; Ardid Ramírez, M.; Aubert, J.; Aublin, J.... (2020). ANTARES and IceCube Combined Search for Neutrino Point-like and Extended Sources in the Southern Sky. The Astrophysical Journal. 892(2):1-12. https://doi.org/10.3847/1538-4357/ab7afbS112892

The global burden of cancer attributable to risk factors, 2010-19 : a systematic analysis for the Global Burden of Disease Study 2019

Background Understanding the magnitude of cancer burden attributable to potentially modifiable risk factors is crucial for development of effective prevention and mitigation strategies. We analysed results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 to inform cancer control planning efforts globally. Methods The GBD 2019 comparative risk assessment framework was used to estimate cancer burden attributable to behavioural, environmental and occupational, and metabolic risk factors. A total of 82 risk-outcome pairs were included on the basis of the World Cancer Research Fund criteria. Estimated cancer deaths and disability-adjusted life-years (DALYs) in 2019 and change in these measures between 2010 and 2019 are presented. Findings Globally, in 2019, the risk factors included in this analysis accounted for 4.45 million (95% uncertainty interval 4.01-4.94) deaths and 105 million (95.0-116) DALYs for both sexes combined, representing 44.4% (41.3-48.4) of all cancer deaths and 42.0% (39.1-45.6) of all DALYs. There were 2.88 million (2.60-3.18) risk-attributable cancer deaths in males (50.6% [47.8-54.1] of all male cancer deaths) and 1.58 million (1.36-1.84) risk-attributable cancer deaths in females (36.3% [32.5-41.3] of all female cancer deaths). The leading risk factors at the most detailed level globally for risk-attributable cancer deaths and DALYs in 2019 for both sexes combined were smoking, followed by alcohol use and high BMI. Risk-attributable cancer burden varied by world region and Socio-demographic Index (SDI), with smoking, unsafe sex, and alcohol use being the three leading risk factors for risk-attributable cancer DALYs in low SDI locations in 2019, whereas DALYs in high SDI locations mirrored the top three global risk factor rankings. From 2010 to 2019, global risk-attributable cancer deaths increased by 20.4% (12.6-28.4) and DALYs by 16.8% (8.8-25.0), with the greatest percentage increase in metabolic risks (34.7% [27.9-42.8] and 33.3% [25.8-42.0]). Interpretation The leading risk factors contributing to global cancer burden in 2019 were behavioural, whereas metabolic risk factors saw the largest increases between 2010 and 2019. Reducing exposure to these modifiable risk factors would decrease cancer mortality and DALY rates worldwide, and policies should be tailored appropriately to local cancer risk factor burden. Copyright (C) 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license.Peer reviewe

Search for dark matter towards the Galactic Centre with 11 years of ANTARES data

Neutrino detectors participate in the indirect search for the fundamental constituents of dark matter (DM) in form of weakly interacting massive particles (WIMPs). In WIMP scenarios, candidate DM particles can pair-annihilate into Standard Model products, yielding considerable fluxes of high-energy neutrinos. A detector like ANTARES, located in the Northern Hemisphere, is able to perform a complementary search looking towards the Galactic Centre, where a high density of dark matter is thought to accumulate. Both this directional information and the spectral features of annihilating DM pairs are entered into an unbinned likelihood method to scan the data set in search for DM-like signals in ANTARES data. Results obtained upon unblinding 3170 days of data reconstructed with updated methods are presented, which provides a larger, and more accurate, data set than a previously published result using 2101 days. A non-observation of dark matter is converted into limits on the velocity-averaged cross section for WIMP pair annihilation