Additional file 1. Table S1. Correlations between CNN and manual gold standard on the artifacts-free images. Table S2. Internal validation: correlations on images with artifacts for the proposed CNN and the commercial software (Circle) in respect to the manual gold standard (GT). Also, the results relevant to interobserver variability between O1 and O2 reported for comparison. Table S3. External validation: correlations between CNN and manual gold standard on images with artifacts. Figure S1. Encoder module....

Additional file 2. The ontological unpacking analysis of the original VCM to produce the resulting OntoVCM.

Seascape connectivity studies, informing the level of exchange of individuals between populations, can provide extremely valuable data for marine population biology and conservation strategy definition. Here we used a multidisciplinary approach to investigate the connectivity of the marbled crab (Pachygrapsus marmoratus), a high dispersal species, in the Adriatic and Ionian basins. A combination of genetic analyses (based on 15 microsatellites screened in 314 specimens), Lagrangian simulations (obtained with a biophysical model of larval dispersal) and...

Additional file 2. Example of transformed metadata: In this .xlsx (MS Excel) file, we list all the output metadata categories generated for each sample from the transformation of the 1KGP input datasets. The output metadata include information collected from all the four 1KGP metadata files considered. Some categories are not reported in the source metadata files—they are identified by the label manually_curated__...—and were added by the developed pipeline to store technical details (e.g., download date,...

Abstract Background Population variant analysis is of great importance for gathering insights into the links between human genotype and phenotype. The 1000 Genomes Project established a valuable reference for human genetic variation; however, the integrative use of the corresponding data with other datasets within existing repositories and pipelines is not fully supported. Particularly, there is a pressing need for flexible and fast selection of population partitions based on their variant and metadata-related characteristics. Results Here,...

Supplemental material, sj-docx-1-jci-10.1177_01968599231167939 for Risk Narratives on Immigration During the COVID-19 Crisis in Italy: A Comparative Analysis of Facebook Posts Published by Politicians and by News media by Luca Serafini, Anita Gottlob, Francesco Pierri, Francesca Ieva and Stefano Ceri in Journal of Communication Inquiry

Abstract Background Guanine crystals are organic biogenic crystals found in many organisms. Due to their exceptionally high refractive index, they contribute to structural color and are responsible for the reflective effect in the skin and visual organs in animals such as fish, reptiles, and spiders. Occurrence of these crystals in animals has been known for many years, and they have also been observed in eukaryotic microorganisms, but not in prokaryotes. Results In this work, we...

Additional file 8: Figure S1. Distribution of genes detected in scRNA-seq data of patient derived organoidswith a coverage of 1 to 5 reads for transcripts. Figure S2. Distribution of Pearson correlation values obtained by analysing unmatchedand matchedCRC PDO bulk / PDO pseudo-bulk pairs. Figure S3. CRIS classification of CRC single sample data from GSE132465, pseudo-bulk, and at scRNA-seq resolution. B) represents the distribution of CRIS distances evaluated on each single cell, grey points. Black points...

Additional file 10: Table S9. NTP-based multiCRIS classification in the bulk CRC organoids. NTP analysis has been performed on bulk PDO data identifying sample with Single-label CRIS classification, Multi-labels CRIS classification, and Not classification. For classassignmentby NTP, FDR < 0.2 was considered significant.

Additional file 10: Table S9. NTP-based multiCRIS classification in the bulk CRC organoids. NTP analysis has been performed on bulk PDO data identifying sample with Single-label CRIS classification, Multi-labels CRIS classification, and Not classification. For classassignmentby NTP, FDR < 0.2 was considered significant.

Additional file 11: Table S10a. NTP-based multiCRIS classification on scRNA-seq profiles of CRC organoids. NTP analysis has been performed on scRNA-seq PDO data identifying cell with single-label class CRIS, Multi-label classes CRIS, and not classification. For classassignmentby NTP, FDR < 0.2 was considered significant. Table S10b. NTP-based multiCRIS classification in the CRC organoids. Summary table of NTP results on total single-cell datasets and at sample levels with percentages of cells assigned, not classified, single-label CRIS...

Additional file 12: Table S11. NTP-based multiCRIS classification on pseudo-bulk CRC patients. NTP analysis has been performed on CRC patients data identifying sample with Single-label CRIS classification, Multi-labels CRIS classification, and Not classification. For classassignmentby NTP, FDR < 0.2 was considered significant.

Additional file 15: Table S14. Multi-label performance evaluations of the considered algorithm-adapted strategies on testing data, comparing their results with multi-label assignments obtained from the multiCRIS version of the NTP approach.

Additional file 14: Table S13. Single-label performance evaluations of the considered algorithms on testing data, comparing their results with the ones of the original NTP approach.

Additional file 3: Table S3. Numbers and percentage of CRIS call assignments with different BH.FDR thresholds.

Additional file 2. Example of transformed metadata: In this .xlsx (MS Excel) file, we list all the output metadata categories generated for each sample from the transformation of the 1KGP input datasets. The output metadata include information collected from all the four 1KGP metadata files considered. Some categories are not reported in the source metadata files—they are identified by the label manually_curated__...—and were added by the developed pipeline to store technical details (e.g., download date,...

Abstract Background Population variant analysis is of great importance for gathering insights into the links between human genotype and phenotype. The 1000 Genomes Project established a valuable reference for human genetic variation; however, the integrative use of the corresponding data with other datasets within existing repositories and pipelines is not fully supported. Particularly, there is a pressing need for flexible and fast selection of population partitions based on their variant and metadata-related characteristics. Results Here,...

Additional file 2. Supplementary Tables S1, S2, and S3.

In-stent restenosis in superficial femoral arteries (SFAs) is a complex, multi-factorial and multi-scale vascular adaptation process whose thorough understanding is still lacking. Multi-scale computational agent-based modelling has recently emerged as a promising approach to decipher mechanobiological mechanisms driving the arterial response to the endovascular intervention. However, the long-term arterial response has never been investigated with this approach, although being of fundamental relevance. In this context, this study investigates the 1-year post-operative arterial wall remodelling in...

Additional file 1: Figure S1. Crystalline aggregates in colonies from a month-old plate of A. salmonicida subsp. pectinolytica 34mel. Figure S2. Size distribution of the base of the prismatic crystals formed by 34mel grown in different conditions and by A. media.

This paper investigates the economic impact of the three tiers risk framework implemented in Italy against the COVID-19 pandemic during the Autumn of 2020. Exploiting a large-scale dataset encompassing daily credit card transactions mediated by a large Italian bank, we estimate a set of panel event study models to disentangle the impact of restrictions with low, medium and high stringency levels in terms of consumption reduction. We show that space-time differentiated policies tend to produce...

Supplemental Material for Novel cannulation strategy with a bidirectional cannula for distal limb perfusion during peripheral veno-arterial extracorporeal life support: A preliminary, single-centre study by Jorik Simons, Arne R Doddema, Erik PJ Körver, Michele di Mauro, Sandra Agricola, Jeroen Smets, Renske Metz, Silvia Mariani, Maria Elena De Piero, Matteo Matteucci, Jamie Romeo, Justine M Ravaux, Walther NKA Van Mook, Barend Mees and Roberto Lorusso in Perfusion

Additional file 1: Figure S1. Crystalline aggregates in colonies from a month-old plate of A. salmonicida subsp. pectinolytica 34mel. Figure S2. Size distribution of the base of the prismatic crystals formed by 34mel grown in different conditions and by A. media.

Additional file 2: Figure S3. ESI–MS experiment for guanine produced by 34mel. Figure S4. ESI–MS and MS/MS experiments for commercial guanine. Figure S5. 1H-NMR characterization of 34mel crystals. Figure S6. UV–vis spectra for commercial and 34mel guanine in acid solution. Additional data 1. Elemental analysis of crystals purified from 34mel.