Showing papers by "University of Grenoble published in 2021"

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

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.

Graph Convolutional Networks for Hyperspectral Image Classification

Abstract: Convolutional neural networks (CNNs) have been attracting increasing attention in hyperspectral (HS) image classification due to their ability to capture spatial–spectral feature representations. Nevertheless, their ability in modeling relations between the samples remains limited. Beyond the limitations of grid sampling, graph convolutional networks (GCNs) have been recently proposed and successfully applied in irregular (or nongrid) data representation and analysis. In this article, we thoroughly investigate CNNs and GCNs (qualitatively and quantitatively) in terms of HS image classification. Due to the construction of the adjacency matrix on all the data, traditional GCNs usually suffer from a huge computational cost, particularly in large-scale remote sensing (RS) problems. To this end, we develop a new minibatch GCN (called miniGCN hereinafter), which allows to train large-scale GCNs in a minibatch fashion. More significantly, our miniGCN is capable of inferring out-of-sample data without retraining networks and improving classification performance. Furthermore, as CNNs and GCNs can extract different types of HS features, an intuitive solution to break the performance bottleneck of a single model is to fuse them. Since miniGCNs can perform batchwise network training (enabling the combination of CNNs and GCNs), we explore three fusion strategies: additive fusion, elementwise multiplicative fusion, and concatenation fusion to measure the obtained performance gain. Extensive experiments, conducted on three HS data sets, demonstrate the advantages of miniGCNs over GCNs and the superiority of the tested fusion strategies with regard to the single CNN or GCN models. The codes of this work will be available at https://github.com/danfenghong/IEEE_TGRS_GCN for the sake of reproducibility.

NASH limits anti-tumour surveillance in immunotherapy-treated HCC

Abstract: Hepatocellular carcinoma (HCC) can have viral or non-viral causes1-5. Non-alcoholic steatohepatitis (NASH) is an important driver of HCC. Immunotherapy has been approved for treating HCC, but biomarker-based stratification of patients for optimal response to therapy is an unmet need6,7. Here we report the progressive accumulation of exhausted, unconventionally activated CD8+PD1+ T cells in NASH-affected livers. In preclinical models of NASH-induced HCC, therapeutic immunotherapy targeted at programmed death-1 (PD1) expanded activated CD8+PD1+ T cells within tumours but did not lead to tumour regression, which indicates that tumour immune surveillance was impaired. When given prophylactically, anti-PD1 treatment led to an increase in the incidence of NASH-HCC and in the number and size of tumour nodules, which correlated with increased hepatic CD8+PD1+CXCR6+, TOX+, and TNF+ T cells. The increase in HCC triggered by anti-PD1 treatment was prevented by depletion of CD8+ T cells or TNF neutralization, suggesting that CD8+ T cells help to induce NASH-HCC, rather than invigorating or executing immune surveillance. We found similar phenotypic and functional profiles in hepatic CD8+PD1+ T cells from humans with NAFLD or NASH. A meta-analysis of three randomized phase III clinical trials that tested inhibitors of PDL1 (programmed death-ligand 1) or PD1 in more than 1,600 patients with advanced HCC revealed that immune therapy did not improve survival in patients with non-viral HCC. In two additional cohorts, patients with NASH-driven HCC who received anti-PD1 or anti-PDL1 treatment showed reduced overall survival compared to patients with other aetiologies. Collectively, these data show that non-viral HCC, and particularly NASH-HCC, might be less responsive to immunotherapy, probably owing to NASH-related aberrant T cell activation causing tissue damage that leads to impaired immune surveillance. Our data provide a rationale for stratification of patients with HCC according to underlying aetiology in studies of immunotherapy as a primary or adjuvant treatment.

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles.

Abstract: JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.

Accelerated global glacier mass loss in the early twenty-first century

Abstract: Glaciers distinct from the Greenland and Antarctic ice sheets are shrinking rapidly, altering regional hydrology1, raising global sea level2 and elevating natural hazards3. Yet, owing to the scarcity of constrained mass loss observations, glacier evolution during the satellite era is known only partially, as a geographic and temporal patchwork4,5. Here we reveal the accelerated, albeit contrasting, patterns of glacier mass loss during the early twenty-first century. Using largely untapped satellite archives, we chart surface elevation changes at a high spatiotemporal resolution over all of Earth’s glaciers. We extensively validate our estimates against independent, high-precision measurements and present a globally complete and consistent estimate of glacier mass change. We show that during 2000–2019, glaciers lost a mass of 267 ± 16 gigatonnes per year, equivalent to 21 ± 3 per cent of the observed sea-level rise6. We identify a mass loss acceleration of 48 ± 16 gigatonnes per year per decade, explaining 6 to 19 per cent of the observed acceleration of sea-level rise. Particularly, thinning rates of glaciers outside ice sheet peripheries doubled over the past two decades. Glaciers currently lose more mass, and at similar or larger acceleration rates, than the Greenland or Antarctic ice sheets taken separately7–9. By uncovering the patterns of mass change in many regions, we find contrasting glacier fluctuations that agree with the decadal variability in precipitation and temperature. These include a North Atlantic anomaly of decelerated mass loss, a strongly accelerated loss from northwestern American glaciers, and the apparent end of the Karakoram anomaly of mass gain10. We anticipate our highly resolved estimates to advance the understanding of drivers that govern the distribution of glacier change, and to extend our capabilities of predicting these changes at all scales. Predictions robustly benchmarked against observations are critically needed to design adaptive policies for the local- and regional-scale management of water resources and cryospheric risks, as well as for the global-scale mitigation of sea-level rise. Analysis of satellite stereo imagery uncovers two decades of mass change for all of Earth’s glaciers, revealing accelerated glacier shrinkage and regionally contrasting changes consistent with decadal climate variability.

Observation of Gravitational Waves from Two Neutron Star–Black Hole Coalescences

Abstract: We report the observation of gravitational waves from two compact binary coalescences in LIGO’s and Virgo’s third observing run with properties consistent with neutron star–black hole (NSBH) binaries. The two events are named GW200105_162426 and GW200115_042309, abbreviated as GW200105 and GW200115; the first was observed by LIGO Livingston and Virgo and the second by all three LIGO–Virgo detectors. The source of GW200105 has component masses 8.9−1.5+1.2 and 1.9−0.2+0.3M⊙ , whereas the source of GW200115 has component masses 5.7−2.1+1.8 and 1.5−0.3+0.7M⊙ (all measurements quoted at the 90% credible level). The probability that the secondary’s mass is below the maximal mass of a neutron star is 89%–96% and 87%–98%, respectively, for GW200105 and GW200115, with the ranges arising from different astrophysical assumptions. The source luminosity distances are 280−110+110 and 300−100+150Mpc , respectively. The magnitude of the primary spin of GW200105 is less than 0.23 at the 90% credible level, and its orientation is unconstrained. For GW200115, the primary spin has a negative spin projection onto the orbital angular momentum at 88% probability. We are unable to constrain the spin or tidal deformation of the secondary component for either event. We infer an NSBH merger rate density of 45−33+75Gpc−3yr−1 when assuming that GW200105 and GW200115 are representative of the NSBH population or 130−69+112Gpc−3yr−1 under the assumption of a broader distribution of component masses.

Small-cell lung cancer.

Abstract: Small-cell lung cancer (SCLC) represents about 15% of all lung cancers and is marked by an exceptionally high proliferative rate, strong predilection for early metastasis and poor prognosis. SCLC is strongly associated with exposure to tobacco carcinogens. Most patients have metastatic disease at diagnosis, with only one-third having earlier-stage disease that is amenable to potentially curative multimodality therapy. Genomic profiling of SCLC reveals extensive chromosomal rearrangements and a high mutation burden, almost always including functional inactivation of the tumour suppressor genes TP53 and RB1. Analyses of both human SCLC and murine models have defined subtypes of disease based on the relative expression of dominant transcriptional regulators and have also revealed substantial intratumoural heterogeneity. Aspects of this heterogeneity have been implicated in tumour evolution, metastasis and acquired therapeutic resistance. Although clinical progress in SCLC treatment has been notoriously slow, a better understanding of the biology of disease has uncovered novel vulnerabilities that might be amenable to targeted therapeutic approaches. The recent introduction of immune checkpoint blockade into the treatment of patients with SCLC is offering new hope, with a small subset of patients deriving prolonged benefit. Strategies to direct targeted therapies to those patients who are most likely to respond and to extend the durable benefit of effective antitumour immunity to a greater fraction of patients are urgently needed and are now being actively explored.

Planck 2018 results - VI. Cosmological parameters (Corrigendum)

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.

Relationships between changes in self-reported physical activity, sedentary behaviour and health during the coronavirus (COVID-19) pandemic in France and Switzerland.

Abstract: To assess whether changes in physical activity and sedentary behaviour during the COVID-19 lockdown are associated with changes in mental and physical health. Observational longitudinal study. Participants living in France or Switzerland responded to online questionnaires measuring physical activity, physical and mental health, anxiety, and depressive symptoms. Paired sample t-tests were used to assess differences in physical activity and sedentary behaviour before and during lockdown. Multiple linear regressions were used to investigate associations between changes in physical activity and changes in mental and physical health during lockdown. 267 (wave1) and 110 participants (wave2; 2 weeks later) were recruited. Lockdown resulted in higher time spent in walking and moderate physical activity (~10min/day) and in sedentary behaviour (~75min/day), compared to pre COVID-19. Increased physical activity during leisure time from week 2 to week 4 of lockdown was associated with improved physical health (β=.24, p=.002). Additionally, an increase in sedentary behaviour during leisure time was associated with poorer physical health (β=-.35, p=.002), mental health (β=-.25, p=.003), and subjective vitality (β=-.30, p=.004). Ensuring sufficient levels of physical activity and reducing sedentary time can play a vital role in helping people to cope with a major stressful event, such as the COVID-19 pandemic.

THE CONCISE GUIDE TO PHARMACOLOGY 2021/22: G protein-coupled receptors

Abstract: The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. Although the Concise Guide constitutes over 500 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/bph.15538. G protein-coupled receptors are one of the six major pharmacological targets into which the Guide is divided, with the others being: ion channels, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2021, and supersedes data presented in the 2019/20, 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate.

Global Incidence of Neurological Manifestations Among Patients Hospitalized With COVID-19-A Report for the GCS-NeuroCOVID Consortium and the ENERGY Consortium.

Abstract: Importance The COVID-19 pandemic continues to affect millions of people globally, with increasing reports of neurological manifestations but limited data on their incidence and associations with outcome. Objective To determine the neurological phenotypes, incidence, and outcomes among adults hospitalized with COVID-19. Design, Setting, and Participants This cohort study included patients with clinically diagnosed or laboratory-confirmed COVID-19 at 28 centers, representing 13 countries and 4 continents. The study was performed by the Global Consortium Study of Neurologic Dysfunction in COVID-19 (GCS-NeuroCOVID) from March 1 to September 30, 2020, and the European Academy of Neurology (EAN) Neuro-COVID Registry (ENERGY) from March to October 2020. Three cohorts were included: (1) the GCS-NeuroCOVID all COVID-19 cohort (n = 3055), which included consecutive hospitalized patients with COVID-19 with and without neurological manifestations; (2) the GCS-NeuroCOVID COVID-19 neurological cohort (n = 475), which comprised consecutive patients hospitalized with COVID-19 who had confirmed neurological manifestations; and (3) the ENERGY cohort (n = 214), which included patients with COVID-19 who received formal neurological consultation. Exposures Clinically diagnosed or laboratory-confirmed COVID-19. Main Outcomes and Measures Neurological phenotypes were classified as self-reported symptoms or neurological signs and/or syndromes assessed by clinical evaluation. Composite incidence was reported for groups with at least 1 neurological manifestation. The main outcome measure was in-hospital mortality. Results Of the 3055 patients in the all COVID-19 cohort, 1742 (57%) were men, and the mean age was 59.9 years (95% CI, 59.3-60.6 years). Of the 475 patients in the COVID-19 neurological cohort, 262 (55%) were men, and the mean age was 62.6 years (95% CI, 61.1-64.1 years). Of the 214 patients in the ENERGY cohort, 133 (62%) were men, and the mean age was 67 years (95% CI, 52-78 years). A total of 3083 of 3743 patients (82%) across cohorts had any neurological manifestation (self-reported neurological symptoms and/or clinically captured neurological sign and/or syndrome). The most common self-reported symptoms included headache (1385 of 3732 patients [37%]) and anosmia or ageusia (977 of 3700 patients [26%]). The most prevalent neurological signs and/or syndromes were acute encephalopathy (1845 of 3740 patients [49%]), coma (649 of 3737 patients [17%]), and stroke (222 of 3737 patients [6%]), while meningitis and/or encephalitis were rare (19 of 3741 patients [0.5%]). Presence of clinically captured neurologic signs and/or syndromes was associated with increased risk of in-hospital death (adjusted odds ratio [aOR], 5.99; 95% CI, 4.33-8.28) after adjusting for study site, age, sex, race, and ethnicity. Presence of preexisting neurological disorders (aOR, 2.23; 95% CI, 1.80-2.75) was associated with increased risk of developing neurological signs and/or syndromes with COVID-19. Conclusions and Relevance In this multicohort study, neurological manifestations were prevalent among patients hospitalized with COVID-19 and were associated with higher in-hospital mortality. Preexisting neurological disorders were associated with increased risk of developing neurological signs and/or syndromes in COVID-19.

A massive rock and ice avalanche caused the 2021 disaster at Chamoli, Indian Himalaya

Abstract: On 7 Feb 2021, a catastrophic mass flow descended the Ronti Gad, Rishiganga, and Dhauliganga valleys in Chamoli, Uttarakhand, India, causing widespread devastation and severely damaging two hydropower projects. Over 200 people were killed or are missing. Our analysis of satellite imagery, seismic records, numerical model results, and eyewitness videos reveals that ~27x106 m3 of rock and glacier ice collapsed from the steep north face of Ronti Peak. The rock and ice avalanche rapidly transformed into an extraordinarily large and mobile debris flow that transported boulders >20 m in diameter, and scoured the valley walls up to 220 m above the valley floor. The intersection of the hazard cascade with downvalley infrastructure resulted in a disaster, which highlights key questions about adequate monitoring and sustainable development in the Himalaya as well as other remote, high-mountain environments.

Fat1 deletion promotes hybrid EMT state, tumour stemness and metastasis.

Abstract: FAT1, which encodes a protocadherin, is one of the most frequently mutated genes in human cancers1-5. However, the role and the molecular mechanisms by which FAT1 mutations control tumour initiation and progression are poorly understood. Here, using mouse models of skin squamous cell carcinoma and lung tumours, we found that deletion of Fat1 accelerates tumour initiation and malignant progression and promotes a hybrid epithelial-to-mesenchymal transition (EMT) phenotype. We also found this hybrid EMT state in FAT1-mutated human squamous cell carcinomas. Skin squamous cell carcinomas in which Fat1 was deleted presented increased tumour stemness and spontaneous metastasis. We performed transcriptional and chromatin profiling combined with proteomic analyses and mechanistic studies, which revealed that loss of function of FAT1 activates a CAMK2-CD44-SRC axis that promotes YAP1 nuclear translocation and ZEB1 expression that stimulates the mesenchymal state. This loss of function also inactivates EZH2, promoting SOX2 expression, which sustains the epithelial state. Our comprehensive analysis identified drug resistance and vulnerabilities in FAT1-deficient tumours, which have important implications for cancer therapy. Our studies reveal that, in mouse and human squamous cell carcinoma, loss of function of FAT1 promotes tumour initiation, progression, invasiveness, stemness and metastasis through the induction of a hybrid EMT state.

LDpred2: better, faster, stronger.

Abstract: Motivation Polygenic scores have become a central tool in human genetics research. LDpred is a popular method for deriving polygenic scores based on summary statistics and a matrix of correlation between genetic variants. However, LDpred has limitations that may reduce its predictive performance. Results Here we present LDpred2, a new version of LDpred that addresses these issues. We also provide two new options in LDpred2: a "sparse" option that can learn effects that are exactly 0, and an "auto" option that directly learns the two LDpred parameters from data. We benchmark predictive performance of LDpred2 against the previous version on simulated and real data, demonstrating substantial improvements in robustness and predictive accuracy compared to LDpred1. We then show that LDpred2 also outperforms other polygenic score methods recently developed, with a mean AUC over the 8 real traits analyzed here of 65.1%, compared to 63.8% for lassosum, 62.9% for PRS-CS and 61.5% for SBayesR. Note that LDpred2 provides more accurate polygenic scores when run genome-wide, instead of per chromosome. Availability LDpred2 is implemented in R package bigsnpr. Supplementary information Supplementary data are available at Bioinformatics online.

Semiconductor qubits in practice

Abstract: In the past decade, semiconducting qubits have made great strides in overcoming decoherence, improving the prospects for scalability and have become one of the leading contenders for the development of large-scale quantum circuits. In this Review, we describe the current state of the art in semiconductor charge and spin qubits based on gate-controlled semiconductor quantum dots, shallow dopants and colour centres in wide-bandgap materials. We frame the relative strengths of the different semiconductor qubit implementations in the context of applications such as quantum simulation, computing, sensing and networks. By highlighting the status and future perspectives of the basic types of semiconductor qubits, this Review aims to serve as a technical introduction for non-specialists and a forward-looking reference for scientists intending to work in this field. Semiconductor qubits are expected to have diverse future quantum applications. This Review discusses semiconductor qubit implementations from the perspective of an ecosystem of applications, such as quantum simulation, sensing, computation and communication.

A gravitational-wave measurement of the Hubble constant following the second observing run of Advanced LIGO and Virgo

Abstract: This paper presents the gravitational-wave measurement of the Hubble constant (H 0) using the detections from the first and second observing runs of the Advanced LIGO and Virgo detector network. The presence of the transient electromagnetic counterpart of the binary neutron star GW170817 led to the first standard-siren measurement of H 0. Here we additionally use binary black hole detections in conjunction with galaxy catalogs and report a joint measurement. Our updated measurement is H 0 = km s−1 Mpc−1 (68.3% of the highest density posterior interval with a flat-in-log prior) which is an improvement by a factor of 1.04 (about 4%) over the GW170817-only value of km s−1 Mpc−1. A significant additional contribution currently comes from GW170814, a loud and well-localized detection from a part of the sky thoroughly covered by the Dark Energy Survey. With numerous detections anticipated over the upcoming years, an exhaustive understanding of other systematic effects are also going to become increasingly important. These results establish the path to cosmology using gravitational-wave observations with and without transient electromagnetic counterparts.

More Diverse Means Better: Multimodal Deep Learning Meets Remote-Sensing Imagery Classification

Abstract: Classification and identification of the materials lying over or beneath the earth’s surface have long been a fundamental but challenging research topic in geoscience and remote sensing (RS), and have garnered a growing concern owing to the recent advancements of deep learning techniques. Although deep networks have been successfully applied in single-modality-dominated classification tasks, yet their performance inevitably meets the bottleneck in complex scenes that need to be finely classified, due to the limitation of information diversity. In this work, we provide a baseline solution to the aforementioned difficulty by developing a general multimodal deep learning (MDL) framework. In particular, we also investigate a special case of multi-modality learning (MML)—cross-modality learning (CML) that exists widely in RS image classification applications. By focusing on “what,” “where,” and “how” to fuse, we show different fusion strategies as well as how to train deep networks and build the network architecture. Specifically, five fusion architectures are introduced and developed, further being unified in our MDL framework. More significantly, our framework is not only limited to pixel-wise classification tasks but also applicable to spatial information modeling with convolutional neural networks (CNNs). To validate the effectiveness and superiority of the MDL framework, extensive experiments related to the settings of MML and CML are conducted on two different multimodal RS data sets. Furthermore, the codes and data sets will be available at https://github.com/danfenghong/IEEE_TGRS_MDL-RS , contributing to the RS community.

Gaia Early Data Release 3 - Catalogue validation

Abstract: Context. The third Gaia data release is published in two stages. The early part, Gaia EDR3, gives very precise astrometric and photometric properties for nearly two billion sources together with seven million radial velocities from Gaia DR2. The full release, Gaia DR3, will add radial velocities, spectra, light curves, and astrophysical parameters for a large subset of the sources, as well as orbits for solar system objects.Aims. Before the publication of the catalogue, many different data items have undergone dedicated validation processes. The goal of this paper is to describe the validation results in terms of completeness, accuracy, and precision for the Gaia EDR3 data and to provide recommendations for the use of the catalogue data.Methods. The validation processes include a systematic analysis of the catalogue contents to detect anomalies, either individual errors or statistical properties, using statistical analysis and comparisons to the previous release as well as to external data and to models. Results. Gaia EDR3 represents a major step forward, compared to Gaia DR2, in terms of precision, accuracy, and completeness for both astrometry and photometry. We provide recommendations for dealing with issues related to the parallax zero point, negative parallaxes, photometry for faint sources, and the quality indicators.

NADPH Oxidases (NOX): An Overview from Discovery, Molecular Mechanisms to Physiology and Pathology.

Abstract: The reactive oxygen species (ROS)-producing enzyme NADPH oxidase (NOX) was first identified in the membrane of phagocytic cells. For many years, its only known role was in immune defense, where its ROS production leads to the destruction of pathogens by the immune cells. NOX from phagocytes catalyzes, via one-electron trans-membrane transfer to molecular oxygen, the production of the superoxide anion. Over the years, six human homologs of the catalytic subunit of the phagocyte NADPH oxidase were found: NOX1, NOX3, NOX4, NOX5, DUOX1, and DUOX2. Together with the NOX2/gp91phox component present in the phagocyte NADPH oxidase assembly itself, the homologs are now referred to as the NOX family of NADPH oxidases. NOX are complex multidomain proteins with varying requirements for assembly with combinations of other proteins for activity. The recent structural insights acquired on both prokaryotic and eukaryotic NOX open new perspectives for the understanding of the molecular mechanisms inherent to NOX regulation and ROS production (superoxide or hydrogen peroxide). This new structural information will certainly inform new investigations of human disease. As specialized ROS producers, NOX enzymes participate in numerous crucial physiological processes, including host defense, the post-translational processing of proteins, cellular signaling, regulation of gene expression, and cell differentiation. These diversities of physiological context will be discussed in this review. We also discuss NOX misregulation, which can contribute to a wide range of severe pathologies, such as atherosclerosis, hypertension, diabetic nephropathy, lung fibrosis, cancer, or neurodegenerative diseases, giving this family of membrane proteins a strong therapeutic interest.

A New Benchmark Based on Recent Advances in Multispectral Pansharpening: Revisiting Pansharpening With Classical and Emerging Pansharpening Methods

Abstract: Pansharpening refers to the fusion of a multispectral (MS) image and panchromatic (PAN) data aimed at generating an outcome with the same spatial resolution of the PAN data and the spectral resolution of the MS image. In the last 30 years, several approaches to deal with this issue have been proposed. However, the reproducibility of these methods is often limited, making the comparison with the state of the art hard to achieve. Thus, to fill this gap, we propose a new benchmark consisting of recent advances in MS pansharpening. In particular, optimized classical approaches [multiresolution analysis (MRA) and component substitution (CS)] are compared with methods belonging to the third generation of pansharpening, represented by variational optimization-based (VO) and machine learning (ML) techniques. The benchmark is tested on different scenarios (from urban to rural areas) acquired by different commercial sensors [i.e., IKONOS (IK), GeoEye-1 (GE-1), and WorldView-3 (WV-3)]. Both quantitative and qualitative assessments and the computational burden are analyzed in this article, and all of the implementations have been collected in a MATLAB toolbox that is made available to the community.

Upper limits on the isotropic gravitational-wave background from Advanced LIGO and Advanced Virgo’s third observing run

Abstract: We report results of a search for an isotropic gravitational-wave background (GWB) using data from Advanced LIGO’s and Advanced Virgo’s third observing run (O3) combined with upper limits from the earlier O1 and O2 runs. Unlike in previous observing runs in the advanced detector era, we include Virgo in the search for the GWB. The results of the search are consistent with uncorrelated noise, and therefore we place upper limits on the strength of the GWB. We find that the dimensionless energy density Ω GW ≤ 5.8 × 10 − 9 at the 95% credible level for a flat (frequency-independent) GWB, using a prior which is uniform in the log of the strength of the GWB, with 99% of the sensitivity coming from the band 20–76.6 Hz; Ω GW ( f ) ≤ 3.4 × 10 − 9 at 25 Hz for a power-law GWB with a spectral index of 2 / 3 (consistent with expectations for compact binary coalescences), in the band 20–90.6 Hz; and Ω GW ( f ) ≤ 3.9 × 10 − 10 at 25 Hz for a spectral index of 3, in the band 20–291.6 Hz. These upper limits improve over our previous results by a factor of 6.0 for a flat GWB, 8.8 for a spectral index of 2 / 3 , and 13.1 for a spectral index of 3. We also search for a GWB arising from scalar and vector modes, which are predicted by alternative theories of gravity; we do not find evidence of these, and place upper limits on the strength of GWBs with these polarizations. We demonstrate that there is no evidence of correlated noise of magnetic origin by performing a Bayesian analysis that allows for the presence of both a GWB and an effective magnetic background arising from geophysical Schumann resonances. We compare our upper limits to a fiducial model for the GWB from the merger of compact binaries, updating the model to use the most recent data-driven population inference from the systems detected during O3a. Finally, we combine our results with observations of individual mergers and show that, at design sensitivity, this joint approach may yield stronger constraints on the merger rate of binary black holes at z ≳ 2 than can be achieved with individually resolved mergers alone.

The emerging landscape of single-molecule protein sequencing technologies

Abstract: Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics. This Perspective describes new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell proteomics.

SEWA DB: A Rich Database for Audio-Visual Emotion and Sentiment Research in the Wild

Abstract: Natural human-computer interaction and audio-visual human behaviour sensing systems, which would achieve robust performance in-the-wild are more needed than ever as digital devices are increasingly becoming an indispensable part of our life. Accurately annotated real-world data are the crux in devising such systems. However, existing databases usually consider controlled settings, low demographic variability, and a single task. In this paper, we introduce the SEWA database of more than 2,000 minutes of audio-visual data of 398 people coming from six cultures, 50 percent female, and uniformly spanning the age range of 18 to 65 years old. Subjects were recorded in two different contexts: while watching adverts and while discussing adverts in a video chat. The database includes rich annotations of the recordings in terms of facial landmarks, facial action units (FAU), various vocalisations, mirroring, and continuously valued valence, arousal, liking, agreement, and prototypic examples of (dis)liking. This database aims to be an extremely valuable resource for researchers in affective computing and automatic human sensing and is expected to push forward the research in human behaviour analysis, including cultural studies. Along with the database, we provide extensive baseline experiments for automatic FAU detection and automatic valence, arousal, and (dis)liking intensity estimation.

Overview of KAGRA: Detector design and construction history

Abstract: KAGRA is a newly built gravitational-wave telescope, a laser interferometer comprising arms with a length of 3\,km, located in Kamioka, Gifu, Japan. KAGRA was constructed under the ground and it is operated using cryogenic mirrors that help in reducing the seismic and thermal noise. Both technologies are expected to provide directions for the future of gravitational-wave telescopes. In 2019, KAGRA finished all installations with the designed configuration, which we call the baseline KAGRA. In this occasion, we present an overview of the baseline KAGRA from various viewpoints in a series of of articles. In this article, we introduce the design configurations of KAGRA with its historical background.

Gaia Early Data Release 3 - The Gaia Catalogue of Nearby Stars

Abstract: Aims. We produce a clean and well-characterised catalogue of objects within 100 pc of the Sun from the Gaia Early Data Release 3. We characterise the catalogue through comparisons to the full data release, external catalogues, and simulations. We carry out a first analysis of the science that is possible with this sample to demonstrate its potential and best practices for its use.Methods. Theselection of objects within 100 pc from the full catalogue used selected training sets, machine-learning procedures, astrometric quantities, and solution quality indicators to determine a probability that the astrometric solution is reliable. The training set construction exploited the astrometric data, quality flags, and external photometry. For all candidates we calculated distance posterior probability densities using Bayesian procedures and mock catalogues to define priors. Any object with reliable astrometry and a non-zero probability of being within 100 pc is included in the catalogue.Results. We have produced a catalogue of 331 312 objects that we estimate contains at least 92% of stars of stellar type M9 within 100 pc of the Sun. We estimate that 9% of the stars in this catalogue probably lie outside 100 pc, but when the distance probability function is used, a correct treatment of this contamination is possible. We produced luminosity functions with a high signal-to-noise ratio for the main-sequence stars, giants, and white dwarfs. We examined in detail the Hyades cluster, the white dwarf population, and wide-binary systems and produced candidate lists for all three samples. We detected local manifestations of several streams, superclusters, and halo objects, in which we identified 12 members of Gaia Enceladus. We present the first direct parallaxes of five objects in multiple systems within 10 pc of the Sun.Conclusions. We provide the community with a large, well-characterised catalogue of objects in the solar neighbourhood. This is a primary benchmark for measuring and understanding fundamental parameters and descriptive functions in astronomy.