Analysis of protein chameleon sequence characteristics

Conversion of local structural state of a protein from an α-helix to a β-strand is usually associated with a major change in the tertiary structure. Similar changes were observed during the self assembly of amyloidogenic proteins to form fibrils, which are implicated in severe diseases conditions, e.g., Alzheimer disease. Studies have emphasized that certain protein sequence fragments known as chameleon sequences do not have a strong preference for either helical or the extended conformations. Surprisingly, the information on the local sequence neighborhood can be used to predict their secondary at a high accuracy level. Here we report a large scale-analysis of chameleon sequences to estimate their propensities to be associated with different local structural states such as α -helices, β-strands and coils. With the help of the propensity information derived from the amino acid composition, we underline their complexity, as more than one quarter of them prefers coil state over to the regular secondary structures. About half of them show preference for both α-helix and β-sheet conformations and either of these two states is favored by the rest

CHIC: Corporate Document for Visual question Answering

The massive use of digital documents due to the substantial trend of paperless initiatives confronted some companies to find ways to process thousands of documents per day automatically. To achieve this, they use automatic information retrieval (IR) allowing them to extract useful information from large datasets quickly. In order to have effective IR methods, it is first necessary to have an adequate dataset. Although companies have enough data to take into account their needs, there is also a need for a public database to compare contributions between state-of-the-art methods. Public data on the document exists as DocVQA[2] and XFUND [10], but these do not fully satisfy the needs of companies. XFUND contains only form documents while the company uses several types of documents (i.e. structured documents like forms but also semi-structured as invoices, and unstructured as emails). Compared to XFUND, DocVQA has several types of documents but only 4.5% of them are corporate documents (i.e. invoice, purchase order, etc). All of this 4.5% of documents do not meet the diversity of documents required by the company. We propose CHIC a visual question-answering public dataset. This dataset contains different types of corporate documents and the information extracted from these documents meet the right expectations of companies

Nanoindentation cartography in Al/Al-Cu-Fe composites: Correlation between chemical heterogeneities and mechanical properties

During the last two decades, nanoindentation testing has become a commonly used technique for measuring surface mechanical properties such as hardness or elastic modulus. With devices equipped with a motorized X-Y table, it is now possible to perform large regular nanoindentation arrays in order to make an accurate statistics of the mechanical properties. This method is particularly interesting to study heterogeneous materials. The statistical analysis, associated to mathematical deconvolution methods allows identifying the properties of each individual phase. Furthermore, hardness or elastic modulus maps can be then established and compared to other local properties such as microstructure, crystallographic orientation or chemical composition. The nanoindentation cartography method has been used to study the mechanical properties of a metal matrix composite (Aluminum matrix with ω-Al-Cu-Fe reinforcement particles, synthesized by sparking plasma sintering) (cf. figure 1). Emphasize has been placed on the Aluminum matrix properties, where the detailed analysis of the individual nanoindentation curves shows serrated behavior characteristic of Portevin-Le Chatelier effect associated to dislocation pinning by solute atoms. The comparison between chemical (SEM – EDXS analysis) and hardness maps as well as the quantitative analysis of the deformation curves gives evidence of a strong correlation between the chemical heterogeneities and mechanical properties of the Aluminum matrix

Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis

Background: High throughput single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for exploring cellular heterogeneity among complex human cancers. scRNA-Seq studies using fresh human surgical tissue are logistically difficult, preclude histopathological triage of samples, and limit the ability to perform batch processing. This hindrance can often introduce technical biases when integrating patient datasets and increase experimental costs. Although tissue preservation methods have been previously explored to address such issues, it is yet to be examined on complex human tissues, such as solid cancers and on high throughput scRNA-Seq platforms. Methods: Using the Chromium 10X platform, we sequenced a total of ~ 120,000 cells from fresh and cryopreserved replicates across three primary breast cancers, two primary prostate cancers and a cutaneous melanoma. We performed detailed analyses between cells from each condition to assess the effects of cryopreservation on cellular heterogeneity, cell quality, clustering and the identification of gene ontologies. In addition, we performed single-cell immunophenotyping using CITE-Seq on a single breast cancer sample cryopreserved as solid tissue fragments. Results: Tumour heterogeneity identified from fresh tissues was largely conserved in cryopreserved replicates. We show that sequencing of single cells prepared from cryopreserved tissue fragments or from cryopreserved cell suspensions is comparable to sequenced cells prepared from fresh tissue, with cryopreserved cell suspensions displaying higher correlations with fresh tissue in gene expression. We showed that cryopreservation had minimal impacts on the results of downstream analyses such as biological pathway enrichment. For some tumours, cryopreservation modestly increased cell stress signatures compared to freshly analysed tissue. Further, we demonstrate the advantage of cryopreserving whole-cells for detecting cell-surface proteins using CITE-Seq, which is impossible using other preservation methods such as single nuclei-sequencing. Conclusions: We show that the viable cryopreservation of human cancers provides high-quality single-cells for multiomics analysis. Our study guides new experimental designs for tissue biobanking for future clinical single-cell RNA sequencing studies

Review of the Accomplishments of Mid-latitude Super Dual Auroral Radar Network (SuperDARN) HF Radars

The Super Dual Auroral Radar Network (SuperDARN) is a network of High Frequency (HF) radars located in the high- and mid-latitude regions of both hemispheres that is operated under international cooperation. The network was originally designed for monitoring the dynamics of the ionosphere and upper atmosphere in the high-latitude regions. However, over the last approximately 15 years SuperDARN has expanded into the mid-latitude regions. With radar coverage that now extends continuously from auroral to sub-auroral and mid-latitudes a wide variety of new scientific findings have been obtained. In this paper, the background of mid-latitude SuperDARN is presented at first. Then the accomplishments made with mid-latitude SuperDARN radars are reviewed in five specified scientific and technical areas: convection, ionospheric irregularities, HF propagation analysis, ion-neutral interactions and magnetohydrodynamic (MHD) waves. Finally, the present status of mid-latitude SuperDARN is updated and directions for future research are discussed

A new isoquinoline and ceramide from the stem barks of Discoglypremna caloneura (Pax) Prain (Euphorbiaceae) with antiproteinase and cytotoxic activities.

peer reviewedTwo new compounds, an isoquinoline (1) and caloneuramide (2), a ceramide were isolated from the stem bark of Discoglypremna caloneura together with seven known compounds namely aurantiamide acetate (3), acetylaleuritolic acid (4), 3α-hydroxylaleuritolic acid 2α-p-hydroxybenzoate (5), mixture of stigmasterol (6) and β-sitosterol (7), mixture of 7-oxo-stigmasterol (8) and 7-oxo-β-sitosterol (9). Their structures were determined based on data from literature and spectroscopic methods. Derivatization reactions on the isoquinoline led to two new compounds, the methylated (10) and acetylated (11) derivatives. Some compounds and extracts were evaluated for their cytotoxic and antiproteinase activity. Antiproteinase effect of compounds 1, 10 and 11 exhibited IC(50) values of 10.77, 1.19 and 3.61 μg/mL respectively; significantly low compared to the standard drug, acetyl salicylic acid (IC(50) = 20.28 μg/mL). Ethyl acetate and methanol extract exhibited moderate cytotoxicity activity on Chang liver cells with CC(50) values of 167.90 ± 2.20 and 106.30 ± 2.03 μg/mL compared to the reference drug cucurmin (CC(50) = 11.05 ± 1.04 μg/mL)

Inborn errors of OAS-RNase L in SARS-CoV-2-related multisystem inflammatory syndrome in children

Funding Information: The Laboratory of Human Genetics of Infectious Diseases is supported by the Howard Hughes Medical Institute, the Rockefeller University, the St. Giles Foundation, the National Institutes of Health (NIH) (R01AI088364 and R21AI160576), the National Center for Advancing Translational Sciences (NCATS), NIH Clinical and Translational Science Award (CTSA) program (UL1TR001866), the Yale Center for Mendelian Genomics and the GSP Coordinating Center funded by the National Human Genome Research Institute (NHGRI) (UM1HG006504 and U24HG008956), the Yale High-Performance Computing Center (S10OD018521), the Fisher Center for Alzheimer's Research Foundation, the Meyer Foundation, the JBP Foundation, the French National Research Agency (ANR) under the "Investments for the Future" program (ANR-10-IAHU-01), the Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence (ANR-10-LABX-62-IBEID), the French Foundation for Medical Research (FRM) (EQU201903007798), the ANR GenMISC (ANR-21-COVR-039), the ANRS-COV05, ANR GENVIR (ANR-20-CE93-003) and ANR AABIFNCOV (ANR-20-CO11-0001) projects, the ANR-RHU program (ANR-21-RHUS-08), the European Union's Horizon 2020 research and innovation program under grant agreement 824110 (EASI-genomics), the HORIZON-HLTH-2021-DISEASE-04 program under grant agreement 01057100 (UNDINE), the ANR-RHU Program ANR-21-RHUS-08 (COVIFERON), the Square Foundation, Grandir - Fonds de solidarité pour l'enfance, the Fondation du Souffle, the SCOR Corporate Foundation for Science, the French Ministry of Higher Education, Research, and Innovation (MESRI-COVID-19), Institut National de la Santé et de la Recherche Médicale (INSERM), and Paris Cité University. We acknowledge support from the National Institute of Allergy and Infectious Diseases (NIAID) of the NIH under award R01AI104887 to R.H.S. and S.R.W. The Laboratory of Human Evolutionary Genetics (Institut Pasteur) is supported by the Institut Pasteur, the Collège de France, the French Government's Investissement d'Avenir program, Laboratoires d'Excellence "Integrative Biology of Emerging Infectious Diseases" (ANR-10-LABX-62-IBEID) and "Milieu Intérieur" (ANR-10-LABX-69-01), the Fondation de France (no. 00106080), the FRM (Equipe FRM DEQ20180339214 team), and the ANR COVID-19-POPCELL (ANR-21-CO14-0003-01). A. Puj. is supported by ACCI20-759 CIBERER, EasiGenomics H2020 Marató TV3 COVID 2021-31-33, the HORIZON-HLTH-2021-ID: 101057100 (UNDINE), the Horizon 2020 program under grant no. 824110 (EasiGenomics grant no. COVID-19/PID12342), and the CERCA Program/Generalitat de Catalunya. The Canarian Health System sequencing hub was funded by the Instituto de Salud Carlos III (COV20-01333 and COV20-01334), the Spanish Ministry of Science and Innovation (RTC-2017-6471-1; AEI/FEDER, UE), Fundación MAPFRE Guanarteme (OA21/131), and Cabildo Insular de Tenerife (CGIEU0000219140 and "Apuestas científicas del ITER para colaborar en la lucha contra la COVID-19"). The CoV-Contact Cohort was funded by the French Ministry of Health and the European Commission (RECOVER project). Our studies are also funded by the Ministry of Health of the Czech Republic Conceptual Development of Research Organization (FNBr, 65269705) and ANID COVID0999 funding in Chile. G. Novelli and A. Novelli are supported by Regione Lazio (Research Group Projects 2020) No. A0375-2020-36663, GecoBiomark. A.M.P., M.L.D., and J.P.-T. are supported by the Inmungen-CoV2 project of CSIC. This work was supported in part by the Intramural Research Program of the NIAID, NIH. The research work of A.M.P, M.L.D., and J.P.-T. was funded by the European Commission-NextGenerationEU (Regulation EU 2020/2094), through CSIC's Global Health Platform (PTI Salud Global). I.M. is a senior clinical investigator at FWO Vlaanderen supported by a VIB GC PID grant, by FWO grants G0B5120N (DADA2) and G0E8420N, and by the Jeffrey Modell Foundation. I.M. holds an ERC-StG MORE2ADA2 grant and is also supported by ERN-RITA. A.Y. is supported by fellowships from the European Academy of Dermatology and Venereology and the Swiss National Science Foundation and by an Early Career Award from the Thrasher Research Fund. Y.-H.C. is supported by an A*STAR International Fellowship (AIF). M.O. was supported by the David Rockefeller Graduate Program, the New York Hideyo Noguchi Memorial Society (HNMS), the Funai Foundation for Information Technology (FFIT), the Honjo International Scholarship Foundation (HISF), and the National Cancer Institute (NCI) F99 Award (F99CA274708). A.A.A. was supported by Ministerio de Ciencia Tecnología e Innovación MINCIENCIAS, Colombia (111584467551/CT 415-2020). D.L. is supported by a fellowship from the FRM for medical residents and fellows. E.H. received funding from the Bank of Montreal Chair of Pediatric Immunology, Foundation of CHU Sainte-Justine, CIHR grants PCC-466901 and MM1-181123, and a Canadian Pediatric Society IMPACT study. Q.P.-H. received funding from the European Union's Horizon 2020 research and innovation program (ATAC, 101003650), the Swedish Research Council, and the Knut and Alice Wallenberg Foundation. Work in the Laboratory of Virology and Infectious Disease was supported by NIH grants P01AI138398-S1, 2U19AI111825, R01AI091707-10S1, and R01AI161444; a George Mason University Fast Grant; the G. Harold and Leila Y. Mathers Charitable Foundation; the Meyer Foundation; and the Bawd Foundation. R.P.L. is on the board of directors of both Roche and the Roche subsidiary Genentech. J.L.P. was supported by a Francois Wallace Monahan Postdoctoral Fellowship at the Rockefeller University and by a European Molecular Biology Organization Long-Term Fellowship (ALTF 380-2018). Publisher Copyright: © 2023 American Association for the Advancement of Science. All rights reserved.Multisystem inflammatory syndrome in children (MIS-C) is a rare and severe condition that follows benign COVID-19. We report autosomal recessive deficiencies of OAS1, OAS2, or RNASEL in five unrelated children with MIS-C. The cytosolic double-stranded RNA (dsRNA)-sensing OAS1 and OAS2 generate 2'-5'-linked oligoadenylates (2-5A) that activate the single-stranded RNA-degrading ribonuclease L (RNase L). Monocytic cell lines and primary myeloid cells with OAS1, OAS2, or RNase L deficiencies produce excessive amounts of inflammatory cytokines upon dsRNA or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stimulation. Exogenous 2-5A suppresses cytokine production in OAS1-deficient but not RNase L-deficient cells. Cytokine production in RNase L-deficient cells is impaired by MDA5 or RIG-I deficiency and abolished by mitochondrial antiviral-signaling protein (MAVS) deficiency. Recessive OAS-RNase L deficiencies in these patients unleash the production of SARS-CoV-2-triggered, MAVS-mediated inflammatory cytokines by mononuclear phagocytes, thereby underlying MIS-C.publishersversionpublishe