BUSCADOR RECOLECTA

Innate myeloid cell (IMC) populations form an essential part of innate immunity. Flow cytometric (FCM) monitoring of IMCs in peripheral blood (PB) has great clinical potential for disease monitoring due to their role in maintenance of tissue homeostasis and ability to sense micro-environmental changes, such as inflammatory processes and tissue damage. However, the lack of standardized and validated approaches has hampered broad clinical implementation. For accurate identification and separation of IMC populations, 62 antibodies against 44 different proteins were evaluated. In multiple rounds of EuroFlow-based design-testing-evaluation-redesign, finally 16 antibodies were selected for their non-redundancy and separation power. Accordingly, two antibody combinations were designed for fast, sensitive, and reproducible FCM monitoring of IMC populations in PB in clinical settings (11-color; 13 antibodies) and translational research (14-color; 16 antibodies). Performance of pre-analytical and analytical variables among different instruments, together with optimized post-analytical data analysis and reference values were assessed. Overall, 265 blood samples were used for design and validation of the antibody combinations and in vitro functional assays, as well as for assessing the impact of sample preparation procedures and conditions. The two (11- and 14-color) antibody combinations allowed for robust and sensitive detection of 19 and 23 IMC populations, respectively. Highly reproducible identification and enumeration of IMC populations was achieved, independently of anticoagulant, type of FCM instrument and center, particularly when database/software-guided automated (vs. manual “expert-based”) gating was used. Whereas no significant changes were observed in identification of IMC populations for up to 24h delayed sample processing, a significant impact was observed in their absolute counts after >12h delay. Therefore, accurate identification and quantitation of IMC populations requires sample processing on the same day. Significantly different counts were observed in PB for multiple IMC populations according to age and sex. Consequently, PB samples from 116 healthy donors (8-69 years) were used for collecting age and sex related reference values for all IMC populations. In summary, the two antibody combinations and FCM approach allow for rapid, standardized, automated and reproducible identification of 19 and 23 IMC populations in PB, suited for monitoring of innate immune responses in clinical and translational research settings., Peer reviewed

[Usage notes] The dataset of the Atlas of mitochondrial genetic diversity for Western Palearctic butterflies (COI sequences and metadata) is available in the iodatabase R package available at https://github.com/leondap/iodatabase. Here the R script with a few supplementaty files is available in order to replicate the figures composing the Atlas, [Motivation] Butterflies represent a model in biology and a flagship group for invertebrate conservation. We provide four new resources for the Western-Palearctic butterflies: 1) An updated checklist comprising 552 species; 2) a curated dataset of 32,129 mitochondrial COI sequences for 532 species, including a de novo reference library for the Maghreb (Morocco and northern Algeria and Tunisia) and Macaronesia (Azores, Madeira and Canary Islands); 3) seven indexes of intraspecific genetic variation (IGV): observed and expected number of haplotypes, haplotype and nucleotide diversity, two fixation indexes, and maximum p-distance; 4) species-level maps illustrating the distribution of COI variability and haplotype networks. The updated checklist will be fundamental for any application dealing with butterfly diversity in Western Palearctic. IGV indexes provide measures for genetic polymorphism and spatial structure and represent proxies for dispersal capacity. These resources will facilitate comparative studies of macrogenetics, will foster integrative taxonomy, and will aid conservation strategies., [Main types of variables contained] A complete species checklist in table format, 32,129 mitochondrial DNA-barcodes provided with metadata (species membership, WGS84 coordinates, sequence length), and a book in PDF format including the IGV atlas and indexes., [Spatial location and grain] The checklist encompasses Europe up to Urals in the east, north Macaronesia (Azores, Madeira and Canary Islands), as well as the Maghreb (Morocco and northern Algeria and Tunisia). DNA-barcodes have been retained in the geographic interval of -31.3–67.5 degrees of longitude and 27.5–71.2 degrees of latitude., [Time period and grain] DNA-barcodes originate from studies published between 1998-2022 and from de novo sequencing of 2,608 specimens done between 2007-2022., [Major taxa and level of measurement] Butterflies (Lepidoptera, Papilionoidea), analysed from individual to species level., [Software format] Data and functions to manage the dataset are provided in the iodatabase R package (https://github.com/leondap/iodatabase) and in Dryad., Università degli Studi di Firenze ., Peer reviewed

The dataset of the Atlas of mitochondrial genetic diversity for Western Palearctic butterflies (COI sequences and metadata) is available in the iodatabase R package available at https://github.com/leondap/iodatabase.-- Here the R script with a few supplementaty files is available in order to replicate the figures composing the Atlas., [Motivation] Butterflies represent a model in biology and a flagship group for invertebrate conservation. We provide four new resources for the Western-Palearctic butterflies: 1) An updated checklist comprising 552 species; 2) a curated dataset of 32,129 mitochondrial COI sequences for 532 species, including a de novo reference library for the Maghreb (Morocco and northern Algeria and Tunisia) and Macaronesia (Azores, Madeira and Canary Islands); 3) seven indexes of intraspecific genetic variation (IGV): observed and expected number of haplotypes, haplotype and nucleotide diversity, two fixation indexes, and maximum p-distance; 4) species-level maps illustrating the distribution of COI variability and haplotype networks. The updated checklist will be fundamental for any application dealing with butterfly diversity in Western Palearctic. IGV indexes provide measures for genetic polymorphism and spatial structure and represent proxies for dispersal capacity. These resources will facilitate comparative studies of macrogenetics, will foster integrative taxonomy, and will aid conservation strategies., [Main types of variables contained] A complete species checklist in table format, 32,129 mitochondrial DNA-barcodes provided with metadata (species membership, WGS84 coordinates, sequence length), and a book in PDF format including the IGV atlas and indexes., [Spatial location and grain] The checklist encompasses Europe up to Urals in the east, north Macaronesia (Azores, Madeira and Canary Islands), as well as the Maghreb (Morocco and northern Algeria and Tunisia). DNA-barcodes have been retained in the geographic interval of -31.3–67.5 degrees of longitude and 27.5–71.2 degrees of latitude., [Time period and grain] DNA-barcodes originate from studies published between 1998-2022 and from de novo sequencing of 2,608 specimens done between 2007-2022., [Major taxa and level of measurement] Butterflies (Lepidoptera, Papilionoidea), analysed from individual to species level., [Software format] Data and functions to manage the dataset are provided in the iodatabase R package (https://github.com/leondap/iodatabase) and in Dryad., Funding provided by: Università degli Studi di Firenze. Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100004434, Peer reviewed

Material For modeling AlphaFold2_multimer was used. AlphaFold2 was downloaded from https://github.com/deepmind/alphafold/releases. Full length amino acid sequences of human PHF14 and HMG20A were used: >NP_001291433.1 high mobility group protein 20A isoform a [Homo sapiens] >NP_001007158.1 PHD finger protein 14 isoform 1 [Homo sapiens] To perform PHF14-HMG20A complex models we used Alphafold_multimers (v2.1.1) with --db_preset=reduced_dbs, --model_preset=multimer --max_template_date=2021-11-01, and default parameters. Computation was performed in the CESGA Supercomputing Center. RCSB PDB (https://www.rcsb.org/3d-view) or Swiss PDB viewer (DeepView) were used for structure viewing. Procedure Full lenth amino-acid protein sequences were obtained form NCBI Protein. Then, to perform PHF14-HMG20A complex models we used Alphafold_multimers (v2.1.1) with --db_preset=reduced_dbs, --model_preset=multimer --max_template_date=2021-11-01, and default parameters. A PAE plot (Predicted Aligned Error Plot) is uploaded. PAE plot "reports AlphaFold’s expected position error at residue x, when the predicted and true structures are aligned on residue y. This is useful for assessing confidence in global features, especially domain packing. For residues x and y drawn from two different domains, a consistently low PAE at (x, y) suggests AlphaFold is confident about the relative domain positions" (https://deepmind.com/research/publications/2021/enabling-high-accuracy-protein-structure-prediction-at-the-proteome-scale). A distogram (Matrix of distances between different parts of the proteins) is also uploaded., Structural modeling by using the AlphaFold2_multimer software, indicated that HMG20A forms a complex with PHF14 through the establishment of a two-stranded alpha-helical coiled-coil structure, Peer reviewed

Cumulative cultural evolution (CCE) occurs among humans who may be presented with many similar options from which to choose, as well as many social influences and diverse environments. It is unknown what general principles underlie the wide range of CCE dynamics and whether they can all be explained by the same unified paradigm. Here, we present a scalable evolutionary model of discrete choice with social learning, based on a few behavioural science assumptions. This paradigm connects the degree of transparency in social learning to the human tendency to imitate others. Computer simulations and quantitative analysis show the interaction of three primary factors—information transparency, popularity bias and population size—drives the pace of CCE. The model predicts a stable rate of evolutionary change for modest degrees of popularity bias. As popularity bias grows, the transition from gradual to punctuated change occurs, with maladaptive sub-populations arising on their own. When the popularity bias gets too severe, CCE stops. This provides a consistent framework for explaining the rich and complex adaptive dynamics taking place in the real-world, such as modern digital media., Peer reviewed

This is the database used in the script 'information_density_whitepapers'., Peer reviewed

This dataset includes the publication date of all the collected articles in the field of optics, as well as their file name and DOI., AGAUR 2019 BP 00206. Grant PID2020-117822GB-I00 funded by MCIN/AEI/10.13039/501100011033 and, as appropriate, by “ERDF A way of making Europe”, by the “European Union” or by the “European Union NextGenerationEU/PRTR”., Peer reviewed

This dataset includes the release date of all the collected cryptocurrency whitepapers, as well as their file name, size and compressed size., AGAUR 2019 BP 00206. Grant PID2020-117822GB-I00 funded by MCIN/AEI/10.13039/501100011033 and, as appropriate, by “ERDF A way of making Europe”, by the “European Union” or by the “European Union NextGenerationEU/PRTR”., Peer reviewed

These are example scripts for processing data for the publication "Dilution of expertise in the rise and fall of collective innovation". Requires Pyhton 3.8 and XCODE for macOS 11.3. Dependence on open-sorce library glfw 3.3.3 and OpenGL., AGAUR 2019 BP 00206. Grant PID2020-117822GB-I00 funded by MCIN/AEI/10.13039/501100011033 and, as appropriate, by “ERDF A way of making Europe”, by the “European Union” or by the “European Union NextGenerationEU/PRTR”., Peer reviewed

This zip file contains the processed bipartite networks of word-sentence associations for all compiled cryptocurrency whitepapers until 2020., AGAUR BP 2019 00206. Grant PID2020-117822GB-I00 funded by MCIN/AEI/10.13039/501100011033 and, as appropriate, by “ERDF A way of making Europe”, by the “European Union” or by the “European Union NextGenerationEU/PRTR”., Peer reviewed