Showing papers by "Russian Academy of Sciences published in 2021"
Daniel J. Klionsky1, Amal Kamal Abdel-Aziz2, Sara Abdelfatah3, Mahmoud Abdellatif4 +2980 more•Institutions (777)
TL;DR: In this article, the authors present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes.
Abstract: In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
1,129 citations
Université Paris-Saclay1, Autonomous University of Barcelona2, University of Cambridge3, National Institute for Occupational Safety and Health4, German Center for Neurodegenerative Diseases5, University of Bonn6, Harvard University7, University of Lausanne8, University of Padua9, National Research Council10, Heidelberg University11, Salk Institute for Biological Studies12, University of Minnesota13, Pasteur Institute14, Tel Aviv University15, Johns Hopkins University16, University of Portsmouth17, Katholieke Universiteit Leuven18, PSL Research University19, Trinity College, Dublin20, Baylor College of Medicine21, University College London22, University of Edinburgh23, Oregon Health & Science University24, National Institutes of Health25, Columbia University26, University of Copenhagen27, University of Rochester28, Ludwig Maximilian University of Munich29, University of Málaga30, Tufts University31, University of Freiburg32, Utrecht University33, Nihon University34, Max Delbrück Center for Molecular Medicine35, University of California, Los Angeles36, University of Yamanashi37, New York University38, University of British Columbia39, King Abdullah University of Science and Technology40, University of Wisconsin-Madison41, University of California, San Francisco42, McGill University43, University of Kentucky44, Kyushu University45, University of Bordeaux46, Polytechnic Institute of Cávado and Ave47, University of Minho48, University of Alabama at Birmingham49, University of Gothenburg50, University of Poitiers51, Cajal Institute52, King's College London53, University of Strasbourg54, Virginia Tech55, University of Düsseldorf56, I.M. Sechenov First Moscow State Medical University57, Russian Academy of Sciences58, University of Seville59, Georgia Institute of Technology60, University of Texas Health Science Center at Houston61, University of California, San Diego62, Universidade Federal do Rio Grande do Sul63, University of Ljubljana64, University of Manchester65, Ikerbasque66
TL;DR: In this article, the authors point out the shortcomings of binary divisions of reactive astrocytes into good-vs-bad, neurotoxic vs-neuroprotective or A1-vs.A2.
Abstract: Reactive astrocytes are astrocytes undergoing morphological, molecular, and functional remodeling in response to injury, disease, or infection of the CNS. Although this remodeling was first described over a century ago, uncertainties and controversies remain regarding the contribution of reactive astrocytes to CNS diseases, repair, and aging. It is also unclear whether fixed categories of reactive astrocytes exist and, if so, how to identify them. We point out the shortcomings of binary divisions of reactive astrocytes into good-vs-bad, neurotoxic-vs-neuroprotective or A1-vs-A2. We advocate, instead, that research on reactive astrocytes include assessment of multiple molecular and functional parameters-preferably in vivo-plus multivariate statistics and determination of impact on pathological hallmarks in relevant models. These guidelines may spur the discovery of astrocyte-based biomarkers as well as astrocyte-targeting therapies that abrogate detrimental actions of reactive astrocytes, potentiate their neuro- and glioprotective actions, and restore or augment their homeostatic, modulatory, and defensive functions.
797 citations
TL;DR: Developments in the ATSAS 3.0 release are described, including new programs for data simulation and for the structural modelling of lipids, nucleic acids and polydisperse systems.
Abstract: The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus-based concentration-independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi-atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy – a PyMOL plugin to run a subset of ATSAS tools – to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.
381 citations
University of Michigan1, Cornell University2, University of Pennsylvania3, University of Massachusetts Medical School4, University of Naples Federico II5, Baylor College of Medicine6, Spanish National Research Council7, Complutense University of Madrid8, New York University9, Boston Children's Hospital10, University of Rome Tor Vergata11, NewYork–Presbyterian Hospital12, University of Pittsburgh13, University of Paris14, French Institute of Health and Medical Research15, National University of Cuyo16, Albert Einstein College of Medicine17, University of New Mexico18, Goethe University Frankfurt19, Weizmann Institute of Science20, University of Turku21, Sapienza University of Rome22, Virginia Commonwealth University23, St. Jude Children's Research Hospital24, Discovery Institute25, University of Copenhagen26, University of Tromsø27, Eötvös Loránd University28, Merck & Co.29, University of Freiburg30, Babraham Institute31, University of South Australia32, University of Adelaide33, University of Oviedo34, University of Chicago35, University of Graz36, National Institutes of Health37, City University of New York38, Queens College39, University of Tokyo40, University of Zurich41, Austrian Academy of Sciences42, University of British Columbia43, University of California, San Francisco44, Russian Academy of Sciences45, University Medical Center Groningen46, University of Cambridge47, University of Glasgow48, Rutgers University49, University of Padua50, Kazan Federal University51, University of Bern52, University of Oxford53, Oslo University Hospital54, University of Oslo55, Foundation for Research & Technology – Hellas56, University of Crete57, Francis Crick Institute58, Osaka University59, Chinese Academy of Sciences60, Harvard University61, Icahn School of Medicine at Mount Sinai62, Shanghai Jiao Tong University63, Karolinska Institutet64
TL;DR: In this paper, preclinical data linking autophagy dysfunction to the pathogenesis of major human disorders including cancer as well as cardiovascular, neurodegenerative, metabolic, pulmonary, renal, infectious, musculoskeletal, and ocular disorders.
Abstract: Autophagy is a core molecular pathway for the preservation of cellular and organismal homeostasis. Pharmacological and genetic interventions impairing autophagy responses promote or aggravate disease in a plethora of experimental models. Consistently, mutations in autophagy-related processes cause severe human pathologies. Here, we review and discuss preclinical data linking autophagy dysfunction to the pathogenesis of major human disorders including cancer as well as cardiovascular, neurodegenerative, metabolic, pulmonary, renal, infectious, musculoskeletal, and ocular disorders.
365 citations
TL;DR: Aghanim et al. as mentioned in this paper used the same data set to derive a 95% upper bound of 0.020 using the principal component analysis (PCA) model and uniform priors on the PCA mode amplitudes.
Abstract: Author(s): Aghanim, N; Akrami, Y; Ashdown, M; Aumont, J; Baccigalupi, C; Ballardini, M; Banday, AJ; Barreiro, RB; Bartolo, N; Basak, S; Battye, R; Benabed, K; Bernard, JP; Bersanelli, M; Bielewicz, P; Bock, JJ; Bond, JR; Borrill, J; Bouchet, FR; Boulanger, F; Bucher, M; Burigana, C; Butler, RC; Calabrese, E; Cardoso, JF; Carron, J; Challinor, A; Chiang, HC; Chluba, J; Colombo, LPL; Combet, C; Contreras, D; Crill, BP; Cuttaia, F; De Bernardis, P; De Zotti, G; Delabrouille, J; Delouis, JM; DI Valentino, E; DIego, JM; Dore, O; Douspis, M; Ducout, A; Dupac, X; Dusini, S; Efstathiou, G; Elsner, F; Enslin, TA; Eriksen, HK; Fantaye, Y; Farhang, M; Fergusson, J; Fernandez-Cobos, R; Finelli, F; Forastieri, F; Frailis, M; Fraisse, AA; Franceschi, E; Frolov, A; Galeotta, S; Galli, S; Ganga, K; Genova-Santos, RT; Gerbino, M; Ghosh, T; Gonzalez-Nuevo, J; Gorski, KM; Gratton, S; Gruppuso, A; Gudmundsson, JE; Hamann, J; Handley, W; Hansen, FK; Herranz, D; Hildebrandt, SR; Hivon, E; Huang, Z; Jaffe, AH; Jones, WC; Karakci, A; Keihanen, E; Keskitalo, R; Kiiveri, K; Kim, J; Kisner, TS | Abstract: In the original version, the bounds given in Eqs. (87a) and (87b) on the contribution to the early-time optical depth, (15,30), contained a numerical error in deriving the 95th percentile from the Monte Carlo samples. The corrected 95% upper bounds are: τ(15,30) l 0:018 (lowE, flat τ(15, 30), FlexKnot), (1) τ(15, 30) l 0:023 (lowE, flat knot, FlexKnot): (2) These bounds are a factor of 3 larger than the originally reported results. Consequently, the new bounds do not significantly improve upon previous results from Planck data presented in Millea a Bouchet (2018) as was stated, but are instead comparable. Equations (1) and (2) give results that are now similar to those of Heinrich a Hu (2021), who used the same Planck 2018 data to derive a 95% upper bound of 0.020 using the principal component analysis (PCA) model and uniform priors on the PCA mode amplitudes.
344 citations
TL;DR: A review of the current understandings of NK cell biology, ongoing pre-clinical and clinical development of NK cells-based therapies and discuss the progress, challenges, and future perspectives is provided in this paper.
Abstract: Natural killer (NK) cell is a specialized immune effector cell type that plays a critical role in immune activation against abnormal cells. Different from events required for T cell activation, NK cell activation is governed by the interaction of NK receptors with target cells, independent of antigen processing and presentation. Due to relatively unsophisticated cues for activation, NK cell has gained significant attention in the field of cancer immunotherapy. Many efforts are emerging for developing and engineering NK cell-based cancer immunotherapy. In this review, we provide our current understandings of NK cell biology, ongoing pre-clinical and clinical development of NK cell-based therapies and discuss the progress, challenges, and future perspectives.
218 citations
TL;DR: In this paper, the authors discuss the CAR signaling and efficacy T in solid tumors and evaluate the most significant barriers in this process and describe the most novel therapeutic methods aiming to the acquirement of the promising therapeutic outcome in non-hematologic malignancies.
Abstract: CARs are simulated receptors containing an extracellular single-chain variable fragment (scFv), a transmembrane domain, as well as an intracellular region of immunoreceptor tyrosine-based activation motifs (ITAMs) in association with a co-stimulatory signal. Chimeric antigen receptor (CAR) T cells are genetically engineered T cells to express a receptor for the recognition of the particular surface marker that has given rise to advances in the treatment of blood disorders. The CAR T cells obtain supra-physiological properties and conduct as “living drugs” presenting both immediate and steady effects after expression in T cells surface. But, their efficacy in solid tumor treatment has not yet been supported. The pivotal challenges in the field of solid tumor CAR T cell therapy can be summarized in three major parts: recognition, trafficking, and surviving in the tumor. On the other hand, the immunosuppressive tumor microenvironment (TME) interferes with T cell activity in terms of differentiation and exhaustion, and as a result of the combined use of CARs and checkpoint blockade, as well as the suppression of other inhibitor factors in the microenvironment, very promising results were obtained from the reduction of T cell exhaustion. Nowadays, identifying and defeating the mechanisms associated with CAR T cell dysfunction is crucial to establish CAR T cells that can proliferate and lyse tumor cells severely. In this review, we discuss the CAR signaling and efficacy T in solid tumors and evaluate the most significant barriers in this process and describe the most novel therapeutic methods aiming to the acquirement of the promising therapeutic outcome in non-hematologic malignancies.
214 citations
TL;DR: In this article, the authors reported the detection of more than 530 photons at energies above 100 teraelectronvolts and up to 1.4 PeV from 12 sources in the Galaxy.
Abstract: The extension of the cosmic-ray spectrum beyond 1 petaelectronvolt (PeV; 1015 electronvolts) indicates the existence of the so-called PeVatrons—cosmic-ray factories that accelerate particles to PeV energies. We need to locate and identify such objects to find the origin of Galactic cosmic rays1. The principal signature of both electron and proton PeVatrons is ultrahigh-energy (exceeding 100 TeV) γ radiation. Evidence of the presence of a proton PeVatron has been found in the Galactic Centre, according to the detection of a hard-spectrum radiation extending to 0.04 PeV (ref. 2). Although γ-rays with energies slightly higher than 0.1 PeV have been reported from a few objects in the Galactic plane3–6, unbiased identification and in-depth exploration of PeVatrons requires detection of γ-rays with energies well above 0.1 PeV. Here we report the detection of more than 530 photons at energies above 100 teraelectronvolts and up to 1.4 PeV from 12 ultrahigh-energy γ-ray sources with a statistical significance greater than seven standard deviations. Despite having several potential counterparts in their proximity, including pulsar wind nebulae, supernova remnants and star-forming regions, the PeVatrons responsible for the ultrahigh-energy γ-rays have not yet been firmly localized and identified (except for the Crab Nebula), leaving open the origin of these extreme accelerators. Observations of γ-rays with energies up to 1.4 PeV find that 12 sources in the Galaxy are PeVatrons, one of which is the Crab Nebula.
184 citations
National Radio Astronomy Observatory1, Smithsonian Institution2, Massachusetts Institute of Technology3, University of Stuttgart4, Benedictine College5, Max Planck Society6, Goddard Space Flight Center7, Centre national de la recherche scientifique8, The Catholic University of America9, University of Virginia10, Russian Academy of Sciences11
TL;DR: Using spectral matched filtering of radio data from the Green Bank Telescope, this article detected two nitrile-group-functionalized polycyclic aromatic hydrocarbons (PAHs) in the interstellar medium.
Abstract: Unidentified infrared emission bands are ubiquitous in many astronomical sources. These bands are widely, if not unanimously, attributed to collective emissions from polycyclic aromatic hydrocarbon (PAH) molecules, yet no single species of this class has been identified in space. Using spectral matched filtering of radio data from the Green Bank Telescope, we detected two nitrile-group-functionalized PAHs, 1- and 2-cyanonaphthalene, in the interstellar medium. Both bicyclic ring molecules were observed in the TMC-1 molecular cloud. In this paper, we discuss potential in situ gas-phase PAH formation pathways from smaller organic precursor molecules.
168 citations
Russian Academy of Sciences1, Skolkovo Institute of Science and Technology2, National Research University – Higher School of Economics3, University of Chicago4, Donostia International Physics Center5, Spanish National Research Council6, University of the Basque Country7, University of Paris8, University of Trento9, Istituto Italiano di Tecnologia10, Sapienza University of Rome11, University of Tokyo12
TL;DR: In this paper, the synthesis of one of the best-known high-TC superconductors-yttrium hexahydride I m 3 ¯ m -YH6 is reported, which displays a superconducting transition at ≈224 K at 166 GPa.
Abstract: Pressure-stabilized hydrides are a new rapidly growing class of high-temperature superconductors, which is believed to be described within the conventional phonon-mediated mechanism of coupling. Here, the synthesis of one of the best-known high-TC superconductors-yttrium hexahydride I m 3 ¯ m -YH6 is reported, which displays a superconducting transition at ≈224 K at 166 GPa. The extrapolated upper critical magnetic field Bc2 (0) of YH6 is surprisingly high: 116-158 T, which is 2-2.5 times larger than the calculated value. A pronounced shift of TC in yttrium deuteride YD6 with the isotope coefficient 0.4 supports the phonon-assisted superconductivity. Current-voltage measurements show that the critical current IC and its density JC may exceed 1.75 A and 3500 A mm-2 at 4 K, respectively, which is higher than that of the commercial superconductors, such as NbTi and YBCO. The results of superconducting density functional theory (SCDFT) and anharmonic calculations, together with anomalously high critical magnetic field, suggest notable departures of the superconducting properties from the conventional Migdal-Eliashberg and Bardeen-Cooper-Schrieffer theories, and presence of an additional mechanism of superconductivity.
167 citations
Nanyang Technological University1, Far Eastern Federal University2, Xi'an Jiaotong University3, Sapporo Medical University4, Harvard University5, University of Vienna6, Russian Academy of Sciences7, Broad Institute8, National University of Mongolia9, National Cheng Kung University10, University of Washington11, Max Planck Society12, Pennsylvania State University13, Fudan University14, Minzu University of China15, Academia Sinica16, Altai State University17, Northwest University (China)18, Chinese Academy of Sciences19, Xiamen University20, Hainan Medical University21, Guangxi Medical University22, Tibet University for Nationalities23, Guangxi University for Nationalities24, Guangxi Normal University25, University of California, Santa Barbara26
TL;DR: In this paper, the authors report genome-wide data from 166 East Asian individuals dating to between 6000 and 1000 BC and 46 present-day groups, showing that hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during the Late Pleistocene epoch.
Abstract: The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people1,2. Here we report genome-wide data from 166 East Asian individuals dating to between 6000 bc and ad 1000 and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during the Late Pleistocene epoch. We also follow expansions during the subsequent Holocene epoch from four regions. First, hunter-gatherers from Mongolia and the Amur River Basin have ancestry shared by individuals who speak Mongolic and Tungusic languages, but do not carry ancestry characteristic of farmers from the West Liao River region (around 3000 bc), which contradicts theories that the expansion of these farmers spread the Mongolic and Tungusic proto-languages. Second, farmers from the Yellow River Basin (around 3000 bc) probably spread Sino-Tibetan languages, as their ancestry dispersed both to Tibet—where it forms approximately 84% of the gene pool in some groups—and to the Central Plain, where it has contributed around 59–84% to modern Han Chinese groups. Third, people from Taiwan from around 1300 bc to ad 800 derived approximately 75% of their ancestry from a lineage that is widespread in modern individuals who speak Austronesian, Tai–Kadai and Austroasiatic languages, and that we hypothesize derives from farmers of the Yangtze River Valley. Ancient people from Taiwan also derived about 25% of their ancestry from a northern lineage that is related to, but different from, farmers of the Yellow River Basin, which suggests an additional north-to-south expansion. Fourth, ancestry from Yamnaya Steppe pastoralists arrived in western Mongolia after around 3000 bc but was displaced by previously established lineages even while it persisted in western China, as would be expected if this ancestry was associated with the spread of proto-Tocharian Indo-European languages. Two later gene flows affected western Mongolia: migrants after around 2000 bc with Yamnaya and European farmer ancestry, and episodic influences of later groups with ancestry from Turan. Genome-wide data from 166 East Asian individuals dating to between 6000 bc and ad 1000 and from 46 present-day groups provide insights into the histories of mixture and migration of human populations in East Asia.
TL;DR: In this article, the authors acknowledge support from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan, the Japan Society for the Promotion of Science (JSPS), and the Tau-Lepton Physics Research Center of Nagoya University.
Abstract: We acknowledge support from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan, the Japan Society for the Promotion of Science (JSPS), and the Tau-Lepton Physics Research Center of Nagoya University; the Australian Research Council including Grants No. DP180102629, No. DP170102389, No. DP170102204, No. DP150103061, No. FT130100303; Austrian Science Fund (FWF); the National Natural Science Foundation of China under Contracts No. 11435013, No. 11475187, No. 11521505, No. 11575017, No. 11675166, No. 11705209; Key Research Program of Frontier Sciences, Chinese Academy of Sciences (CAS), Grant No. QYZDJ-SSWSLH011; the CAS Center for Excellence in Particle Physics (CCEPP); the Shanghai Pujiang Program under Grant No. 18PJ1401000; the Ministry of Education, Youth and Sports of the Czech Republic under Contract No. LTT17020; the Carl Zeiss Foundation, the Deutsche Forschungsgemeinschaft, the Excellence Cluster Universe, and the VolkswagenStiftung; the Department of Science and Technology of India; the Istituto Nazionale di Fisica Nucleare of Italy; National Research Foundation (NRF) of Korea Grants No. 2016R1D1A1B01010135, No. 2016R1D1A1B02012900, No. 2018R1A2B3003643, No. 2018R1A6A1A06024970, No. 2018R1D1A1B07047294, No. 2019K1A3A7A09033840, No. 2019R1I1A3A01058933; Radiation Science Research Institute, Foreign Large-size Research Facility Application Supporting project, the Global Science Experimental Data Hub Center of the Korea Institute of Science and Technology Information, and KREONET/GLORIAD the Polish Ministry of Science and Higher Education and the National Science Center; the Ministry of Science and Higher Education of the Russian Federation, Agreement No. 14.W03.31.0026; University of Tabuk research Grants No. S-1440-0321, No. S-0256-1438, and No. S-0280-1439 (Saudi Arabia); the Slovenian Research Agency; Ikerbasque, Basque Foundation for Science, Spain; the Swiss National Science Foundation; the Ministry of Education and the Ministry of Science and Technology of Taiwan; and the U.S. Department of Energy and the National Science Foundation.
TL;DR: The evolution of the adaptogenic concept has led back to basics of TMS and a new level of understanding of holistic approach, which provides a rationale for their use in stress‐induced and aging‐related diseases.
Abstract: Adaptogens comprise a category of herbal medicinal and nutritional products promoting adaptability, resilience, and survival of living organisms in stress. The aim of this review was to summarize the growing knowledge about common adaptogenic plants used in various traditional medical systems (TMS) and conventional medicine and to provide a modern rationale for their use in the treatment of stress-induced and aging-related disorders. Adaptogens have pharmacologically pleiotropic effects on the neuroendocrine-immune system, which explain their traditional use for the treatment of a wide range of conditions. They exhibit a biphasic dose-effect response: at low doses they function as mild stress-mimetics, which activate the adaptive stress-response signaling pathways to cope with severe stress. That is in line with their traditional use for preventing premature aging and to maintain good health and vitality. However, the potential of adaptogens remains poorly explored. Treatment of stress and aging-related diseases require novel approaches. Some combinations of adaptogenic plants provide unique effects due to their synergistic interactions in organisms not obtainable by any ingredient independently. Further progress in this field needs to focus on discovering new combinations of adaptogens based on traditional medical concepts. Robust and rigorous approaches including network pharmacology and systems pharmacology could help in analyzing potential synergistic effects and, more broadly, future uses of adaptogens. In conclusion, the evolution of the adaptogenic concept has led back to basics of TMS and a new level of understanding of holistic approach. It provides a rationale for their use in stress-induced and aging-related diseases.
TL;DR: In this paper, the authors proposed a method for combining predictions in ensembles of different object detection models: weighted boxes fusion, which significantly improves the quality of the fused predicted rectangles for an ensemble.
Belgian Institute for Space Aeronomy1, Royal Netherlands Meteorological Institute2, University of Bremen3, Norwegian Institute for Air Research4, University of Innsbruck5, Goddard Space Flight Center6, Université Paris-Saclay7, Aristotle University of Thessaloniki8, Wageningen University and Research Centre9, University of Toronto10, European Space Agency11, Max Planck Society12, Russian Academy of Sciences13, National Autonomous University of Mexico14, Chiba University15, Danish Meteorological Institute16, Japan Agency for Marine-Earth Science and Technology17, Finnish Meteorological Institute18, University of Science and Technology of China19, Instituto Nacional de Técnica Aeroespacial20, University of La Réunion21, National Institute of Water and Atmospheric Research22, University of Manchester23, Kyrgyz National University24
TL;DR: In this article, ground-based validation results of the atmospheric NO2 data produced operationally since April 2018 by the TROPOMI instrument on board of the ESA/EU Copernicus Sentinel-5 Precursor (S5p) satellite are compared to correlative measurements collected from, respectively, 19 Multi-Axis DOAS (MAX-DOAS), 26 NDACC Zenith-Scattered-Light DOAS, and 25 PGN/Pandora instruments distributed globally.
Abstract: This paper reports on consolidated ground-based validation results of the atmospheric NO2 data produced operationally since April 2018 by the TROPOMI instrument on board of the ESA/EU Copernicus Sentinel-5 Precursor (S5p) satellite. Tropospheric, stratospheric, and total NO2 column data from S5p are compared to correlative measurements collected from, respectively, 19 Multi-Axis DOAS (MAX-DOAS), 26 NDACC Zenith-Scattered-Light DOAS (ZSL-DOAS), and 25 PGN/Pandora instruments distributed globally. The validation methodology gives special care to minimizing mismatch errors due to imperfect spatio-temporal co-location of the satellite and correlative data, e.g., by using tailored observation operators to account for differences in smoothing and in sampling of atmospheric structures and variability, and photochemical modelling to reduce diurnal cycle effects. Compared to the ground-based measurements, S5p data show, on an average: (i) a negative bias for the tropospheric column data, of typically −23 to −37 % in clean to slightly polluted conditions, but reaching values as high as −51 % over highly polluted areas; (ii) a slight negative bias for the stratospheric column data, of about −0.2 Pmolec/cm2, i.e. approx. −2 % in summer to −15 % in winter; and (iii) a bias ranging from zero to −50 % for the total column data, found to depend on the amplitude of the total NO2 column, with small to slightly positive bias values for columns below 6 Pmolec/cm2 and negative values above. The dispersion between S5p and correlative measurements contains mostly random components, which remain within mission requirements for the stratospheric column data (0.5 Pmolec/cm2), but exceed those for the tropospheric column data (0.7 Pmolec/cm2). While a part of the biases and dispersion may be due to representativeness differences, it is known that errors in the S5p tropospheric columns exist due to shortcomings in the (horizontally coarse) a-priori profile representation in the TM5-MP chemistry transport model used in the S5p retrieval, and to a lesser extent, to the treatment of cloud effects. Although considerable differences (up to 2 Pmolec/cm2 and more) are observed at single ground-pixel level, the near-real-time (NRTI) and off-line (OFFL) versions of the S5p NO2 operational data processor provide similar NO2 column values and validation results when globally averaged, with the NRTI values being on average 0.79 % larger than the OFFL values.
TL;DR: In this article, the ATLAS particle-flow reconstruction method is used to reconstruct the topo-clusters of the proton-proton collision data with a center-of-mass energy of 13$ TeV collected by the LHC.
Abstract: Jet energy scale and resolution measurements with their associated uncertainties are reported for jets using 36-81 fb$^{-1}$ of proton-proton collision data with a centre-of-mass energy of $\sqrt{s}=13$ TeV collected by the ATLAS detector at the LHC. Jets are reconstructed using two different input types: topo-clusters formed from energy deposits in calorimeter cells, as well as an algorithmic combination of charged-particle tracks with those topo-clusters, referred to as the ATLAS particle-flow reconstruction method. The anti-$k_t$ jet algorithm with radius parameter $R=0.4$ is the primary jet definition used for both jet types. Jets are initially calibrated using a sequence of simulation-based corrections. Next, several $\textit{in situ}$ techniques are employed to correct for differences between data and simulation and to measure the resolution of jets. The systematic uncertainties in the jet energy scale for central jets ($|\eta| 2.5$ TeV). The relative jet energy resolution is measured and ranges from ($24 \pm 1.5$)% at 20 GeV to ($6 \pm 0.5$)% at 300 GeV.
TL;DR: In this paper, a brief overview of literature data on energy storage technologies utilising hydrogen and metal hydrides is presented along with results of the related R&D activities carried out by the authors.
Science for Life Laboratory1, Swedish Museum of Natural History2, University of Copenhagen3, Stockholm University4, Francis Crick Institute5, University of California, Santa Cruz6, University of Potsdam7, Middle East Technical University8, Natural History Museum9, China Agricultural University10, Russian Academy of Sciences11
TL;DR: In this paper, the authors report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old.
Abstract: Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780–560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution. Siberian mammoth genomes from the Early and Middle Pleistocene subepochs reveal adaptive changes and a key hybridization event, highlighting the value of deep-time palaeogenomics for studies of speciation and long-term evolutionary trends.
Vienna University of Technology1, Delft University of Technology2, Lund University3, University of California, Berkeley4, University of Bologna5, Forschungszentrum Jülich6, National Research Council7, Centre national de la recherche scientifique8, Spanish National Research Council9, Sungkyunkwan University10, Agricultural Research Service11, Finnish Meteorological Institute12, University of Copenhagen13, Universiti Teknologi Malaysia14, University of Graz15, Invertis University16, Argonne National Laboratory17, University of Colorado Boulder18, Chinese Academy of Sciences19, Ludwig Maximilian University of Munich20, University of Southern California21, University of Salamanca22, University of Chile23, University of Perugia24, National Oceanic and Atmospheric Administration25, National and Kapodistrian University of Athens26, Agriculture and Agri-Food Canada27, Rutgers University28, Monash University, Clayton campus29, United States Department of Agriculture30, University of Twente31, Russian Academy of Sciences32, Chengdu University of Information Technology33, Norwegian Water Resources and Energy Directorate34, International Sleep Products Association35, University of Dundee36, Tsinghua University37, Wuhan University38, University of Arizona39, Katholieke Universiteit Leuven40, European Space Agency41
TL;DR: The main scope of this paper is to inform readers about the evolution of the ISMN over the past decade, including a description of network and data set updates and quality control procedures.
Abstract: . In 2009, the International Soil Moisture Network (ISMN) was initiated as a community effort, funded by the European Space Agency, to serve as a centralised data hosting facility for globally available in situ soil moisture measurements ( Dorigo et al. , 2011 b , a ) . The ISMN brings together in situ soil moisture measurements collected and freely shared by a multitude of organisations, harmonises them in terms of units and sampling rates, applies advanced quality control, and stores them in a database. Users can freely retrieve the data from this database through an online web portal ( https://ismn.earth/en/ , last access: 28 October 2021). Meanwhile, the ISMN has evolved into the primary in situ soil moisture reference database worldwide, as evidenced by more than 3000 active users and over 1000 scientific publications referencing the data sets provided by the network. As of July 2021, the ISMN now contains the data of 71 networks and 2842 stations located all over the globe, with a time period spanning from 1952 to the present. The number of networks and stations covered by the ISMN is still growing, and approximately 70 % of the data sets contained in the database continue to be updated on a regular or irregular basis. The main scope of this paper is to inform readers about the evolution of the ISMN over the past decade, including a description of network and data set updates and quality control procedures. A comprehensive review of the existing literature making use of ISMN data is also provided in order to identify current limitations in functionality and data usage and to shape priorities for the next decade of operations of this unique community-based data repository.
Wouter van Rheenen1, Rick A.A. van der Spek1, Mark K Bakker1, Joke J.F.A. van Vugt1 +209 more•Institutions (82)
TL;DR: All ALS associated signals combined reveal a role for perturbations in vesicle mediated transport and autophagy, and provide evidence for cell-autonomous disease initiation in glutamatergic neurons.
Abstract: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a life-time risk of 1 in 350 people and an unmet need for disease-modifying therapies. We conducted a cross-ancestry GWAS in ALS including 29,612 ALS patients and 122,656 controls which identified 15 risk loci in ALS. When combined with 8,953 whole-genome sequenced individuals (6,538 ALS patients, 2,415 controls) and the largest cortex-derived eQTL dataset (MetaBrain), analyses revealed locus-specific genetic architectures in which we prioritized genes either through rare variants, repeat expansions or regulatory effects. ALS associated risk loci were shared with multiple traits within the neurodegenerative spectrum, but with distinct enrichment patterns across brain regions and cell-types. Across environmental and life-style risk factors obtained from literature, Mendelian randomization analyses indicated a causal role for high cholesterol levels. All ALS associated signals combined reveal a role for perturbations in vesicle mediated transport and autophagy, and provide evidence for cell-autonomous disease initiation in glutamatergic neurons.
TL;DR: In this article, the anomalous Hall effect was shown to be present in a three-dimensional topological magnetic superlattice structure when the Fermi energy is tuned into the correct energy window.
Abstract: The quantum anomalous Hall effect1,2 is a fundamental transport response of a topological insulator in zero magnetic field. Its physical origin is a result of an intrinsically inverted electronic band structure and ferromagnetism3, and its most important manifestation is the dissipationless flow of chiral charge currents at the edges of the system4, a property that has the potential to transform future quantum electronics5,6. Here, we report a Berry-curvature-driven4,7 anomalous Hall regime at temperatures of several Kelvin in the magnetic topological bulk crystals in which Mn ions self-organize into a period-ordered MnBi2Te4/Bi2Te3 superlattice. Robust ferromagnetism of the MnBi2Te4 monolayers opens a surface gap8–10, and when the Fermi level is tuned to be within this gap, the anomalous Hall conductance reaches an e2/h quantization plateau, which is a clear indication of chiral transport through the edge states. The quantization in this regime is not obstructed by the bulk conduction channels and therefore should be present in a broad family of topological magnets. A three-dimensional topological magnetic superlattice structure exhibits the quantum anomalous Hall effect when the Fermi energy is tuned into the correct energy window.
TL;DR: The updated version of the GTRD provides an integrated view of transcription regulation through a dedicated web interface with advanced browsing and search capabilities, an integrated genome browser, and table reports by cell types, transcription factors, and genes of interest.
Abstract: The Gene Transcription Regulation Database (GTRD; http://gtrd.biouml.org/) contains uniformly annotated and processed NGS data related to gene transcription regulation: ChIP-seq, ChIP-exo, DNase-seq, MNase-seq, ATAC-seq and RNA-seq. With the latest release, the database has reached a new level of data integration. All cell types (cell lines and tissues) presented in the GTRD were arranged into a dictionary and linked with different ontologies (BRENDA, Cell Ontology, Uberon, Cellosaurus and Experimental Factor Ontology) and with related experiments in specialized databases on transcription regulation (FANTOM5, ENCODE and GTEx). The updated version of the GTRD provides an integrated view of transcription regulation through a dedicated web interface with advanced browsing and search capabilities, an integrated genome browser, and table reports by cell types, transcription factors, and genes of interest.
TL;DR: In this article, the authors used T1-weighted magnetic resonance images to determine neurobiologic correlates of group differences in cortical thickness between cases and controls in 6 disorders: attention-deficit/hyperactivity disorder (ADHD), autism spectrum disorder (ASD), bipolar disorder (BD), major depressive disorder (MDD), obsessive-compulsive disorder (OCD), and schizophrenia.
Abstract: Importance Large-scale neuroimaging studies have revealed group differences in cortical thickness across many psychiatric disorders. The underlying neurobiology behind these differences is not well understood.
Objective To determine neurobiologic correlates of group differences in cortical thickness between cases and controls in 6 disorders: attention-deficit/hyperactivity disorder (ADHD), autism spectrum disorder (ASD), bipolar disorder (BD), major depressive disorder (MDD), obsessive-compulsive disorder (OCD), and schizophrenia.
Design, Setting, and Participants Profiles of group differences in cortical thickness between cases and controls were generated using T1-weighted magnetic resonance images. Similarity between interregional profiles of cell-specific gene expression and those in the group differences in cortical thickness were investigated in each disorder. Next, principal component analysis was used to reveal a shared profile of group difference in thickness across the disorders. Analysis for gene coexpression, clustering, and enrichment for genes associated with these disorders were conducted. Data analysis was conducted between June and December 2019. The analysis included 145 cohorts across 6 psychiatric disorders drawn from the ENIGMA consortium. The numbers of cases and controls in each of the 6 disorders were as follows: ADHD: 1814 and 1602; ASD: 1748 and 1770; BD: 1547 and 3405; MDD: 2658 and 3572; OCD: 2266 and 2007; and schizophrenia: 2688 and 3244.
Main Outcomes and Measures Interregional profiles of group difference in cortical thickness between cases and controls.
Results A total of 12 721 cases and 15 600 controls, ranging from ages 2 to 89 years, were included in this study. Interregional profiles of group differences in cortical thickness for each of the 6 psychiatric disorders were associated with profiles of gene expression specific to pyramidal (CA1) cells, astrocytes (except for BD), and microglia (except for OCD); collectively, gene-expression profiles of the 3 cell types explain between 25% and 54% of variance in interregional profiles of group differences in cortical thickness. Principal component analysis revealed a shared profile of difference in cortical thickness across the 6 disorders (48% variance explained); interregional profile of this principal component 1 was associated with that of the pyramidal-cell gene expression (explaining 56% of interregional variation). Coexpression analyses of these genes revealed 2 clusters: (1) a prenatal cluster enriched with genes involved in neurodevelopmental (axon guidance) processes and (2) a postnatal cluster enriched with genes involved in synaptic activity and plasticity-related processes. These clusters were enriched with genes associated with all 6 psychiatric disorders.
Conclusions and Relevance In this study, shared neurobiologic processes were associated with differences in cortical thickness across multiple psychiatric disorders. These processes implicate a common role of prenatal development and postnatal functioning of the cerebral cortex in these disorders.
National Institutes of Health1, University of California, San Diego2, Saint Petersburg State University3, University of Washington4, University of California, Berkeley5, Johns Hopkins University6, University of Connecticut7, University of California, Santa Cruz8, University of Geneva9, Stowers Institute for Medical Research10, Harvard University11, Wellcome Trust Sanger Institute12, University of Cambridge13, Howard Hughes Medical Institute14, Washington University in St. Louis15, University of Tennessee Health Science Center16, Yale University17, Pacific Biosciences18, University of Düsseldorf19, National Institute of Standards and Technology20, Max Planck Society21, Baylor College of Medicine22, University of California, Davis23, Institute for Systems Biology24, Duke University25, University of Pittsburgh26, Russian Academy of Sciences27
TL;DR: The T2T-CHM13 reference as mentioned in this paper contains gapless assemblies for all 22 autosomes plus Chromosome X, corrected numerous errors, and introduced nearly 200 million bp of novel sequence containing 2,226 paralogous gene copies, 115 of which are predicted to be protein coding.
Abstract: In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of the human genome, which revolutionized the field of genomics. While these drafts and the updates that followed effectively covered the euchromatic fraction of the genome, the heterochromatin and many other complex regions were left unfinished or erroneous. Addressing this remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium has finished the first truly complete 3.055 billion base pair (bp) sequence of a human genome, representing the largest improvement to the human reference genome since its initial release. The new T2T-CHM13 reference includes gapless assemblies for all 22 autosomes plus Chromosome X, corrects numerous errors, and introduces nearly 200 million bp of novel sequence containing 2,226 paralogous gene copies, 115 of which are predicted to be protein coding. The newly completed regions include all centromeric satellite arrays and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies for the first time.
TL;DR: In this paper, a photonic platform enables the observation of nonlinear topological corner states and solitons in a second-order topological insulator, as shown by experiments.
Abstract: Higher-order topological insulators are a novel topological phase beyond the framework of conventional bulk–boundary correspondence1,2. In these peculiar systems, the topologically non-trivial boundary modes are characterized by a co-dimension of at least two3,4. Despite several promising preliminary considerations regarding the impact of nonlinearity in such systems5,6, the flourishing field of experimental higher-order topological insulator research has thus far been confined to the linear evolution of topological states. As such, the observation of the interplay between nonlinearity and the dynamics of higher-order topological phases in conservative systems remains elusive. Here we experimentally demonstrate nonlinear higher-order topological corner states. Our photonic platform enables us to observe nonlinear topological corner states as well as the formation of solitons in such topological structures. Our work paves the way towards the exploration of topological properties of matter in the nonlinear regime, and may herald a new class of compact devices that harnesses the intriguing features of topology in an on-demand fashion. The nonlinear properties of photonic topological insulators remain largely unexplored, as band topology is linked to linear systems. But nonlinear topological corner states and solitons can form in a second-order topological insulator, as shown by experiments.
Saleh Abdalla1, Abdolnabi Abdeh Kolahchi, Michael Ablain, Susheel Adusumilli2 +357 more•Institutions (88)
TL;DR: In 2018, the 25th year of development of radar altimetry was celebrated and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences as discussed by the authors.
TL;DR: In this paper, a molecular understanding of molecular mechanisms of purinergic signalling provides new and exciting insights into the treatment of human diseases such as neurodegeneration, rheumatic immune diseases, inflammation, and cancer.
Abstract: Purines and their derivatives, most notably adenosine and ATP, are the key molecules controlling intracellular energy homoeostasis and nucleotide synthesis. Besides, these purines support, as chemical messengers, purinergic transmission throughout tissues and species. Purines act as endogenous ligands that bind to and activate plasmalemmal purinoceptors, which mediate extracellular communication referred to as “purinergic signalling”. Purinergic signalling is cross-linked with other transmitter networks to coordinate numerous aspects of cell behaviour such as proliferation, differentiation, migration, apoptosis and other physiological processes critical for the proper function of organisms. Pathological deregulation of purinergic signalling contributes to various diseases including neurodegeneration, rheumatic immune diseases, inflammation, and cancer. Particularly, gout is one of the most prevalent purine-related disease caused by purine metabolism disorder and consequent hyperuricemia. Compelling evidence indicates that purinoceptors are potential therapeutic targets, with specific purinergic agonists and antagonists demonstrating prominent therapeutic potential. Furthermore, dietary and herbal interventions help to restore and balance purine metabolism, thus addressing the importance of a healthy lifestyle in the prevention and relief of human disorders. Profound understanding of molecular mechanisms of purinergic signalling provides new and exciting insights into the treatment of human diseases.
TL;DR: The use of metal oxide nanoparticles (IONPs) is one of the promising ways for overcoming antibiotic resistance in bacteria and fungi as discussed by the authors, however, the effectiveness of IONPs has not yet been evaluated.
Abstract: The use of metal oxide nanoparticles is one of the promising ways for overcoming antibiotic resistance in bacteria. Iron oxide nanoparticles (IONPs) have found wide applications in different fields of biomedicine. Several studies have suggested using the antimicrobial potential of IONPs. Iron is one of the key microelements and plays an important role in the function of living systems of different hierarchies. Iron abundance and its physiological functions bring into question the ability of iron compounds at the same concentrations, on the one hand, to inhibit the microbial growth and, on the other hand, to positively affect mammalian cells. At present, multiple studies have been published that show the antimicrobial effect of IONPs against Gram-negative and Gram-positive bacteria and fungi. Several studies have established that IONPs have a low toxicity to eukaryotic cells. It gives hope that IONPs can be considered potential antimicrobial agents of the new generation that combine antimicrobial action and high biocompatibility with the human body. This review is intended to inform readers about the available data on the antimicrobial properties of IONPs, a range of susceptible bacteria, mechanisms of the antibacterial action, dependence of the antibacterial action of IONPs on the method for synthesis, and the biocompatibility of IONPs with eukaryotic cells and tissues.
TL;DR: In this paper, most research has concentrated around stomatal limitation to photosynthesis, while non-stomatal limitations to photosynthetic plants have been studied in agricultural sustainability and global food security.
Abstract: Soil salinity is a major threat to agricultural sustainability and a global food security. Until now, most research has concentrated around stomatal limitation to photosynthesis, while non-stomatal...
TL;DR: The therapeutical potential of new plants included in the modern edition of the Russian Pharmacopoeia, implemented in 2018, are highlighted, underlining their therapeutic potential and significance for global phytopharmacotherapy.