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opencc-by-4.0Jul 2024View details →

Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in African American and European American patients with TNBC (Spatial Transcriptomic 10X Visium portion)

Racial disparities in triple-negative breast cancer (TNBC) outcomes have been reported. However, the biological mechanisms underlying these disparities remain unclear. We integrated imaging mass cytometry and spatial transcriptomics, to characterize the tumor microenvironment (TME) of African American (AA) and European American (EA) patients with TNBC. The TME in AA patients was characterized by interactions between endothelial cells, macrophages, and mesenchymal-like cells, which were associated with poor patient survival. In contrast, the EA TNBC-associated niche is enriched in T-cells and neutrophils suggestive of an exhaustion and suppression of otherwise active T cell responses. Ligand-receptor and pathway analyses of race-associated niches found AA TNBC to be “immune cold” and hence immunotherapy resistant tumors, and EA TNBC as ‘inflamed’ tumors that evolved a distinctive immunosuppressive mechanism. Our study revealed the presence of racially distinct tumor-promoting and immunosuppressive microenvironments in AA and EA patients with TNBC, which may explain the poor clinical outcomes.   This dataset contains the 10X Visium Spatial Transcriptomic data of TNBC patients. There are two cohorts.   Baylor Scott and White (BSW) cohort: 10x.visium.tar.gz, containing 10 patients with TNBC from Baylor Scott and White affiliated Hospital.  Each sample is made of Space Ranger processed spot-separated gene expression data (processed to HDF5 AnnData file). There are also H&E images, and spot coordinate files available.    For Georgia validation cohort, 400 genes used for validation of ESG signatures (associated with BA-Community 1 and WA-Community-1) were obtained and provided by Ritu Aneja's lab. These 400 genes' spot-based expression data across Black and White TNBC patients are provided. See file georgia.validation.visium.tar.gz. Expression was normalized by total counts per spot, followed by log-normalization by Giotto.   As well in our paper, we integrated a published racial TNBC cohort for deriving some of initial results in the paper. This refers to the Bassiouni et al (Cancer Research) paper in Carpten's group. GSM_giotto_processed.tar.gz refers to this dataset, which we deposit here. The data were normalized by Giotto using standard procedure.

opencc-by-4.0Jul 2024View details →

High-Resolution Pan-European Forest Structure Maps: An Integration of Earth Observation and National Forest Inventory Data

We developed Pan-European maps of timber volume (V), above-ground biomass (AGB), and deciduous-coniferous proportion (DCP) with a pixel size of 10 x 10 m2 for the reference year 2020 using a combination of a Sentinel 2 mosaic, Copernicus layers, and National Forest Inventory (NFI) data. For mapping, we used the k-Nearest Neighbor (kNN, k=7) approach with a harmonized database of species-specific V and AGB from 14 NFIs across Europe. This database encompasses approximately 151,000 sample plots, which were intersected with the above-mentioned Earth observation data. The maps cover 40<a> European countries, </a>forming a continuous coverage of the western part of the European continent. A sample of 1/3 of NFI plots was left out for validation, whereas 2/3 of the plots were used for mapping. Maps were created independently for 13 multi-country processing areas. Root-mean-squared-errors (RMSEs) for AGB ranged from 53 % in the Nordic processing area to <a>73 % </a>the South-Eastern area. The created maps are the first of their kind as they are utilizing a huge amount of harmonized NFI observations and consistent remote sensing data for high-resolution forest attribute mapping. While the published maps can be useful for visualization and other purposes, they are primarily meant as auxiliary information in model-assisted estimation where model-related biases can be mitigated, and field-based estimates improved. Therefore, additional calibration procedures were not applied, and especially high V and AGB values tend to be underestimated. Summarizing map values (pixel counting) over large regions such as countries or whole Europe will consequently result in biased estimates that need to be interpreted with care. The author list is sorted by last name except for the first and last authors who also serve as corresponding authors. Corresponding authors: <a href="mailto:Jukka.Miettinen@vtt.fi">Jukka.Miettinen@vtt.fi</a>, <a href="mailto:Johannes.Breidenbach@nibio.no">Johannes.Breidenbach@nibio.no</a>

opencc-zeroJan 2024View details →

Linked collectors and determiners for: A revision of European species of the genus Tetrastichus Haliday (Hymenoptera: Eulophidae) using integrative taxonomy.

Natural history specimen data linked to collectors and determiners held within, "A revision of European species of the genus Tetrastichus Haliday (Hymenoptera: Eulophidae) using integrative taxonomy". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/3e8022de-bd6e-4368-8b9b-cb21a863a8f2">https://bionomia.net/dataset/3e8022de-bd6e-4368-8b9b-cb21a863a8f2</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/3e8022de-bd6e-4368-8b9b-cb21a863a8f2">https://gbif.org/dataset/3e8022de-bd6e-4368-8b9b-cb21a863a8f2</a>. Formatted as a Frictionless Data package.

Figure 5 in Genetic integrity of the European grayling (Thymallus thymallus) populations within the Vienne River drainage basin after five decades of stockings

Figure 5 - Results of the Structure analysis (Q-values) for 8 loci (A) and 10 loci (B). Colours represent the different "k" units chosen using the approach of Evanno et al. (2005). Population names are shown on the x-axis, and Q-values (contribution or assignment from each k partition) are shown on the Y-axis. For 8 loci, k = 8, and for 10 loci k = 11.

Figure 2 in Genetic integrity of the European grayling (Thymallus thymallus) populations within the Vienne River drainage basin after five decades of stockings

Figure 2. - Close-up of grayling distribution and four sampled sites (stars) within the upper Vienne district in 2012 (relief background from IGN-Geoportail).

Figure 4 in Genetic integrity of the European grayling (Thymallus thymallus) populations within the Vienne River drainage basin after five decades of stockings

Figure 4. - Factorial Correspondence Analyses (FCA) of individuals based on the presence and absence of microsatellite alleles. A: Bi-variate plot of the first two FCA factors (F1 & F2), graphically partitioned by population. B: Bi-variate plot of the third and fourth FCA factors (F3 & F4) partitioned by population. The percentage inertia for each factor is as follows: FC1 = 4.44%; FC2 = 4.03%; FC3 = 3.46%; FC4 = 2.82%.

Figure 1 in Genetic integrity of the European grayling (Thymallus thymallus) populations within the Vienne River drainage basin after five decades of stockings

Figure 1. - Distribution of grayling in Europe (green) and its former distribution in France around 1900 (red). Sample sites (white stars = wild populations, black stars = hatcheries) are numbered following table II.

Figure 3 in Genetic integrity of the European grayling (Thymallus thymallus) populations within the Vienne River drainage basin after five decades of stockings

Figure 3. - Median Joining network of haplotypes found in this study augmented by additional published haplotypes provided for reference. All new haplotypes use the simple abbreviation "Ht" with a serial number reflecting the order in which they were first found in our data. The small black dots indicate substitutional steps whereas the small red dots represent multifurcating nodes. The following haplotypes and corresponding clade names stem from Weiss et al. (2002). "Danube drainage (Northern Alps)": Da1, Da2, Da4, Da11; "Mixed Central Europe": Rh1, Rh4, Rh6 all first reported from the Rhone basin; "Mixed Central Europe": At14, At15 both frequent and widespread in the Rhine basin; "Scandinavia": At6 reported from Finland; and AT1 first reported from the Loire River.

opencc-by-4.0Jun 2024View details →

zenodo36/100

European funded projects related to integrated robotic sensing

This repository contains the metadata of 1371 projects in tabular form (combinedProjectData.xlsx). The data was extracted from the European Union’s COmmunity Research and Development Information Service (CORDIS) repository. The dataset was used to support a review of the latest advancements in integrated robotic sensing. CORDIS was interrogated using a Boolean search, combining multiple chosen search terms using precise logical relationships, such as AND and OR. This search approach was used to obtain precise and relevant search results by specifying the relationships among the search terms, saving time and effort while minimising the likelihood of encountering irrelevant or unrelated material. The following Boolean search string was used: “(‘robot’ OR ‘robotic’ OR ‘robotically’ OR ‘roboti?ed’) AND (‘non-destructive’ OR ‘inspection’ OR ‘evaluation’ OR ‘NDT’ OR ‘NDE’ OR ‘sensing’ OR ‘sensor’)”. This resulted in searching projects whose title and short description (teaser) contained at least one of the words in the first set of brackets and at least one in the second set. Note that the “?” in ‘roboti?ed’ allowed looking for the presence of both the British English word “robotised” and the respective American English version “robotized”. Additionally, the search results were filtered according to the funding schemes. For the sake of reviewing the recent landscape, only projects funded through the HORIZON 2020 and HORIZON EUROPE schemes were considered. The described filtered search returned 1371 projects. The resulting metadata was extracted from the CORDIS repository for each of the found projects: the project start date, the end date, the total cost, the total EU contribution, the fields of science related to the project, the coordinating institution, and the participating institutions. The fields of science of each project are given as a list of strings detailing the fields of science related to the project. Each string shows a variable-depth hierarchy from the broadest classification to specific fields (e.g., “engineering and technology/materials engineering/composites”), following the hierarchical framework adopted by the European Commission. Finally, whereas each project has one and only one coordinator, it can have none, one or multiple participants. For the coordinator and each participant (if present), the following information was extracted: country of the coordinating/participating institution, amount of EU contribution received, amount of other funds available to the institution and the project outcome in terms of peer-reviewed journal papers, conference contributions and filed patents. Thus, the project metadata extracted from CORDIS was thoroughly analysed. The "fieldsOfScience_SunburstPlot.xlsx" file contains a sunburst chart that offers a lucid overview of the diverse scientific disciplines of the selected projects. The analysis of the fields of science strings has revealed a hierarchical depth going up to the seventh classification level, showing great permeance of robotic NDT and robotic sensing into numerous and specific fields.

zenodo36/100

FIGURE 1 in The Integrated Plant Record (IPR) analysis: Methodological advances and new insights into the evolution of European Palaeogene/Neogene vegetation

FIGURE 1. Zelkova zelkovifolia is a representative of the broad-leaved deciduous component.

opencc-by-4.0Dec 2020View details →

FIGURES 51–52 in Integrative taxonomy reveals three new species of European Lepidocyrtus lignorum-group (Collembola, Entomobryidae)

FIGURES 51–52. Lepidocyrtus semicoloratus sp. nov. dorsal chaetotaxy (left side): 51, Abd.II; 52, Abd.III. Broad circles–broad ciliated macrochaetae, small circles––thin ciliated macrochaetae.

FIGURES 48–50 in Integrative taxonomy reveals three new species of European Lepidocyrtus lignorum-group (Collembola, Entomobryidae)

FIGURES 48–50. Lepidocyrtus semicoloratus sp. nov. dorsal chaetotaxy (left side): 48, Th.II, 49; Th.III; 50, Abd.I. Circles–ciliated chaetae.

FIGURE 47 in Integrative taxonomy reveals three new species of European Lepidocyrtus lignorum-group (Collembola, Entomobryidae)

FIGURE 47. Lepidocyrtus semicoloratus sp. nov.: Dorsal head chaetotaxy (left side). Broad circles––long ciliated macrochaetae, small circles––short ciliated macrochaetae.

FIGURES 38–40 in Integrative taxonomy reveals three new species of European Lepidocyrtus lignorum-group (Collembola, Entomobryidae)

FIGURES 38–40. Lepidocyrtus milagrosae sp. nov.: 38, Abd.V chaetotaxy (left side), broad black circles––long ciliated chatae, small black circles––short ciliated or smooth chaetae; 39, trochanteral organ; 40, third leg unguis and unguiculus with three different possibilities of unguiculus outer margin.

FIGURES 34–35 in Integrative taxonomy reveals three new species of European Lepidocyrtus lignorum-group (Collembola, Entomobryidae)

FIGURES 34–35. Lepidocyrtus milagrosae sp. nov. dorsal chaetotaxy (left side): 34, Abd.II; 35, Abd.III. Broad circles––broad ciliated macrochaetae, small circles––thin ciliated macrochaetae.

FIGURES 36–37 in Integrative taxonomy reveals three new species of European Lepidocyrtus lignorum-group (Collembola, Entomobryidae)

FIGURES 36–37. Lepidocyrtus milagrosae sp. nov.: 36, Abd.IV chaetotaxy (left side); 37, basal plate of Abd.IV. Broad black circles––broad ciliated macrochaetae, small black circles––thin ciliated macrochaetae, crossed circles––pseudoporus.

FIGURE 23 in Integrative taxonomy reveals three new species of European Lepidocyrtus lignorum-group (Collembola, Entomobryidae)

FIGURE 23. Lepidocyrtus fuscocephalus sp. nov, L. milagrosae sp. nov. and L. semicoloratus sp. nov.: Pseudopores distribution: a, dorsal pseudopores; b–c, ventral pesudopores.