cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5519550
title: Annotation results of two human retina organoids

description: Cell annotation was based on i) marker genes which were extracted from literature and expert knowledge, or (ii) via a transfer learning tool CaSTLe (Lieberman Y, Rokach L, Shay T, 2018) using the Cowan <em>et al</em>. (2020) organoid reference data set. Data preprocessing of both scRNA-seq data sets was done in scanpy (Wolf, F., Angerer, P. & Theis, 2018), and are included as h5ad-files. The annotation results are included in the .csv files
description: {"references": ["Cowan, C. S. et al. (2020). Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution. Cell , 182, 1623\u20131640.e34."]}
DOI: 10.5281/zenodo.4561751
title: Individual TE expression detection

description: This data set was used to study and compare tools with respect to detecting the expression of transposable elements at the level of individual instances.
DOI: 10.5281/zenodo.4561750
title: Individual TE expression detection

description: This data set was used to study and compare tools with respect to detecting the expression of transposable elements at the level of individual instances.
DOI: 10.5281/zenodo.5525816
title: RNA velocity analysis of human retinal organoids

description: The scVelo package (Bergen, V., Lange, M., Peidli, S. et al. , 2020) was used to derive RNA velocities from two human retinal organoid models. Using the PAGA tool (Wolf, F.A., Hamey, F.K., Plass, M. et al., 2019), abstracted graphs of the cell types and the pseudotime assessment were visualized
DOI: 10.5281/zenodo.5525815
title: RNA velocity analysis of human retinal organoids

description: The scVelo package (Bergen, V., Lange, M., Peidli, S. et al. , 2020) was used to derive RNA velocities from two human retinal organoid models. Using the PAGA tool (Wolf, F.A., Hamey, F.K., Plass, M. et al., 2019), abstracted graphs of the cell types and the pseudotime assessment were visualized
DOI: 10.6084/m9.figshare.16676653
title: traindata.zip

description: Training-validation dataset as part of article "Effect of the synergetic use of Sentinel-1, Sentinel-2, LiDAR and derived data in Land Cover Classification of a Semiarid Mediterranean Area", subbmited to the journal International Journal of Geographical Information Science
DOI: 10.6084/m9.figshare.16676653.v1
title: traindata.zip

description: Training-validation dataset as part of article "Effect of the synergetic use of Sentinel-1, Sentinel-2, LiDAR and derived data in Land Cover Classification of a Semiarid Mediterranean Area", subbmited to the journal International Journal of Geographical Information Science
DOI: 10.21335/nmdc-957527320
title: Sound velocity profiles

description: This dataset contains sound velocity profiles collected for the Mapping Authority since the 1980s. The profiles usually also have temperature and salinity. The measurements available have been quality controlled using standard CMEMS QC for near realtime data. Some of the profiles contains sound velocity measurements while other profiles have calculated value sound velocity or salinity. The sound velocity is calculated with DelGrosso 1974 equation and salinity is calculated with inverse use of DelGrosso 1974 equation. Depth is computed with Unesco 1983 equation for salinity=35 and temperature=0 deg C
DOI: 10.5281/zenodo.5526117
title: Pisa Database 2000

description: Pisa Database 2000
DOI: 10.5519/qd.8gqe0htr
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (8 records)
DOI: 10.5519/qd.1ut8nf4h
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (8 records)
DOI: 10.5519/qd.k2h8q6bb
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (4 records)
DOI: 10.5519/qd.dbbu0ig5
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (7 records)
DOI: 10.5519/qd.lszps2qd
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (6 records)
DOI: 10.5519/qd.i1um4zre
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (23 records)
DOI: 10.5519/qd.v3y55wvv
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (50 records)
DOI: 10.5519/qd.5asjmspz
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (3 records)
DOI: 10.5519/qd.7t3gf2zl
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (21 records)
DOI: 10.5519/qd.8swyadrd
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (22 records)
DOI: 10.5519/qd.cdxklzdm
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (120 records)
DOI: 10.5519/qd.eg06t6lg
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (17 records)
DOI: 10.5281/zenodo.5526124
title: Pisa Database 2000

description: Pisa Database 2000
DOI: 10.5281/zenodo.5526116
title: Pisa Database 2000

description: Pisa Database 2000
DOI: 10.15161/oar.it/74120
title: CovidStat project data

description: This record contains the daily updated data of the CovidStat project. CovidStat is a project carried out by the CovidStat Working Group at INFN, whose creation was promoted within the Italian National Institute of Nuclear Physics with the aim of making a statistical analysis of the data provided daily by the Civil Protection on the spread of the pandemic in Italy. CovidStat data can interactively be browsed at https://covid19.infn.it.
description: The software to process this Root TTree is in the related identifier. Be sure to use the right corresponding version, based on the data in which Root TTree was generated.
DOI: 10.25430/researchdata.cab.unipd.it.00000540
title: Testing trapping protocols for detecting the Citrus Longhorn Beetle, Anoplophora chinensis (Coleoptera: Cerambycidae)

description: Captures of traps during the CLB survey conducted in Lombardy Region in 2017
DOI: 10.5281/zenodo.5524171
title: Data from: An interactive key to Central European species of the Pteromalus albipennis species group and other species of the genus (Hymenoptera: Chalcidoidea: Pteromalidae), with the description of a new species

description: Here we provide the complete set of files used by Klimmek and Baur (2018, see References section below for the complete citation) for constructing the Xper3 key. In particular, we provide the following documents: - Pteromalus_albipennis_group-Xper3_key_CSV_file_C31EBC58D7853C45B9CEC06C6BEF7104.csv: Data matrix of morphologic characters in CSV file format. - Pteromalus_albipennis_group-Xper3_key_SDD_file_C31EBC58D7853C45B9CEC06C6BEF7104.xperience.sdd.xml: Data matrix of morphologic characters in SDD/XML file format. - Pteromalus_albipennis_group_Xper3_key_IMAGES.zip: Complete set of images, grouped according to the original folder structure as used by the Xper3 software. File names correspond to those used in the SDD/XML file. - Xper3_Image__File_name.jpg: All images are also listed individually. File names after the prefix "Xper3_Image__" correspond to those used in the SDD/XML file. NOTE: Even though file names include species names, the latter appear not in a very consistent format (sometimes they appear at the beginning of a file name, sometimes at the end, with genus name or without, etc.). For those looking for all images of a particular species, download and unpack the ZIP file and go to the folder "items". There, images are group together according to species names. <strong>Citation of this package</strong><br> Use the citation provided by Zenodo (on this webpage). <strong>Contact</strong><br> Hannes Baur, Natural History Museum Bern, Switzerland
description: {"references": ["Klimmek F, Baur H (2018) An interactive key to Central European species of the Pteromalus albipennis species group and other species of the genus (Hymenoptera: Chalcidoidea: Pteromalidae), with the description of a new species. Biodiversity Data Journal 6: e27722. https://doi.org/10.3897/BDJ.6.e27722"]}
DOI: 10.5281/zenodo.5524170
title: Data from: An interactive key to Central European species of the Pteromalus albipennis species group and other species of the genus (Hymenoptera: Chalcidoidea: Pteromalidae), with the description of a new species

description: Here we provide the complete set of files used by Klimmek and Baur (2018, see References section below for the complete citation) for constructing the Xper3 key. In particular, we provide the following documents: - Pteromalus_albipennis_group-Xper3_key_CSV_file_C31EBC58D7853C45B9CEC06C6BEF7104.csv: Data matrix of morphologic characters in CSV file format. - Pteromalus_albipennis_group-Xper3_key_SDD_file_C31EBC58D7853C45B9CEC06C6BEF7104.xperience.sdd.xml: Data matrix of morphologic characters in SDD/XML file format. - Pteromalus_albipennis_group_Xper3_key_IMAGES.zip: Complete set of images, grouped according to the original folder structure as used by the Xper3 software. File names correspond to those used in the SDD/XML file. - Xper3_Image__File_name.jpg: All images are also listed individually. File names after the prefix "Xper3_Image__" correspond to those used in the SDD/XML file. NOTE: Even though file names include species names, the latter appear not in a very consistent format (sometimes they appear at the beginning of a file name, sometimes at the end, with genus name or without, etc.). For those looking for all images of a particular species, download and unpack the ZIP file and go to the folder "items". There, images are group together according to species names. <strong>Citation of this package</strong><br> Use the citation provided by Zenodo (on this webpage). <strong>Contact</strong><br> Hannes Baur, Natural History Museum Bern, Switzerland
description: {"references": ["Klimmek F, Baur H (2018) An interactive key to Central European species of the Pteromalus albipennis species group and other species of the genus (Hymenoptera: Chalcidoidea: Pteromalidae), with the description of a new species. Biodiversity Data Journal 6: e27722. https://doi.org/10.3897/BDJ.6.e27722"]}
DOI: 10.6084/m9.figshare.16676740.v1
title: Human Data VI task

description: Human behavior in a VI task as described by paper "Choice history effects improve reward harvesting efficiency in mice and humans" in Figure 2.
DOI: 10.6084/m9.figshare.16676740
title: Human Data VI task

description: Human behavior in a VI task as described by paper "Choice history effects improve reward harvesting efficiency in mice and humans" in Figure 2.
DOI: 10.6084/m9.figshare.13794125
title: Simulation_measurement_14L

description: This folder contains the simulated surface measurements for breast model 14L with vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13795172
title: simulation_measurement_14L_background

description: This folder contains the simulated surface measurements for breast model 14L without vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13796324
title: simulation_measurement_08R

description: This folder contains the simulated surface measurements for breast model 08R with vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13836491
title: basic breast atlas

description: This folder contains the basic optical breast atlas for the five patients.
DOI: 10.6084/m9.figshare.13836506
title: natural-shape breast atlas

description: This folder contains the natural-shape breast 3D surfaces; the basic breast atlas with Frangi filter, and further with level set segmentation; the natural-shape vessel 3D surfaces; and the natural-shape optical breast atlas, for the five patients.
DOI: 10.6084/m9.figshare.13836563
title: deformed breast atlas

description: This folder contains the deformed breast 3D surfaces; and the deformed vessel 3D surfaces; and the deformed optical breast atlas; for the five patients.
DOI: 10.6084/m9.figshare.13836683
title: simulation_configuration

description: This folder contains the deformed breast models in the cuboid containers; and the COMSOL optical simulations; for the five breast models.
DOI: 10.6084/m9.figshare.13796324.v1
title: simulation_measurement_08R

description: This folder contains the simulated surface measurements for breast model 08R with vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13839167
title: simulation_measurement _08L_background

description: This folder contains the simulated surface measurements for breast model 08L without vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13836683.v1
title: simulation_configuration

description: This folder contains the deformed breast models in the cuboid containers; and the COMSOL optical simulations; for the five breast models.
DOI: 10.6084/m9.figshare.13836491.v1
title: basic breast atlas

description: This folder contains the basic optical breast atlas for the five patients.
DOI: 10.6084/m9.figshare.13843715
title: simulation_measurement_10R_background

description: This folder contains the simulated surface measurements for breast model 10R without vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13844750
title: simulation_measurement_06L

description: This folder contains the simulated surface measurements for breast model 06L with vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13839167.v1
title: simulation_measurement _08L_background

description: This folder contains the simulated surface measurements for breast model 08L without vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13849844
title: simulation_measurement_08L

description: This folder contains the simulated surface measurements for breast model 08L with vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13840436
title: simulation_measurement_10R

description: This folder contains the simulated surface measurements for breast model 10R with vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13840436.v1
title: simulation_measurement_10R

description: This folder contains the simulated surface measurements for breast model 10R with vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13843715.v1
title: simulation_measurement_10R_background

description: This folder contains the simulated surface measurements for breast model 10R without vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13795172.v1
title: simulation_measurement_14L_background

description: This folder contains the simulated surface measurements for breast model 14L without vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13850729
title: simulation_measurement_08R_background

description: This folder contains the simulated surface measurements for breast model 08R without vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13836506.v1
title: natural-shape breast atlas

description: This folder contains the natural-shape breast 3D surfaces; the basic breast atlas with Frangi filter, and further with level set segmentation; the natural-shape vessel 3D surfaces; and the natural-shape optical breast atlas, for the five patients.
DOI: 10.6084/m9.figshare.13852367
title: simulation_mua_ground truth

description: This folder contains the ground truth of absorption coefficients for the five breast models.
DOI: 10.6084/m9.figshare.13861865
title: simulation_measurement_06L_background

description: This folder contains the simulated surface measurements for breast model 06L without vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13849844.v1
title: simulation_measurement_08L

description: This folder contains the simulated surface measurements for breast model 08L with vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.14977947
title: simulation_mua_reconstructed

description: Reconstructed absorption coefficients map from the simulated measurement data by Tikhonov, compressive sensing with L1-norm, and compressive sensing with total variation methods, for the five breast models.
DOI: 10.6084/m9.figshare.13852367.v1
title: simulation_mua_ground truth

description: This folder contains the ground truth of absorption coefficients for the five breast models.
DOI: 10.6084/m9.figshare.13850729.v1
title: simulation_measurement_08R_background

description: This folder contains the simulated surface measurements for breast model 08R without vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.13861865.v1
title: simulation_measurement_06L_background

description: This folder contains the simulated surface measurements for breast model 06L without vessel inhomogeneity. The measurements include transmittance and reflectance images for every source location.
DOI: 10.6084/m9.figshare.16660762.v3
title: ICP raw data.zip

description: Studies on novel diagnostic and predictive biomarkers of Intrahepatic Cholestasis of Pregnancy through metabolomics and proteomics raw data
DOI: 10.5281/zenodo.5201852
title: TLS Dataset

description: Tertiary lymphoid structures (TLS) dataset. Histological cases were retrieved from the archive of the Norfolk and Norwich University Hospital histopathology department. Tumours were classified according to the 2015 WHO classification. For each patient, TLS assessment was based on a representative tissue block, with adequate tumour material and interface between normal and tumor tissue well represented. Annotation was performed on tumour tissue slides from 18 patients with primary lung cancer. There were 8 tumours, of which there were 14 adenocarcinoma (5 acinar predominant, 1, papillary, 2 solid predominant and 6 lepidic predominant), 3 squamous cell carcinomas and 2 sarcomatoid carcinomas. The age range of the patients was 54-82 years old, with an average of 69 ± 2.4 years. The tumour size was between 8 and 62 mm, with an average of 28 ± 6.4. TLS was defined as all dense lymphocytic aggregates and 144 TLS were annotated by 2 histopathologists (FK, MDC) with 100% concordance. To assess the generalizability of the model, this dataset was created for internal training-validation and further validation in independent populations. Please cite as: Barmpoutis P, Di Capite M, Kayhanian H, Waddingham W, Alexander DC, Jansen M, et al. (2021) Tertiary lymphoid structures (TLS) identification and density assessment on H&E-stained digital slides of lung cancer. PLoS ONE 16(9): e0256907. https://doi.org/10.1371/journal.pone.0256907
DOI: 10.5281/zenodo.5201851
title: TLS Dataset

description: Tertiary lymphoid structures (TLS) dataset. Histological cases were retrieved from the archive of the Norfolk and Norwich University Hospital histopathology department. Tumours were classified according to the 2015 WHO classification. For each patient, TLS assessment was based on a representative tissue block, with adequate tumour material and interface between normal and tumor tissue well represented. Annotation was performed on tumour tissue slides from 18 patients with primary lung cancer. There were 8 tumours, of which there were 14 adenocarcinoma (5 acinar predominant, 1, papillary, 2 solid predominant and 6 lepidic predominant), 3 squamous cell carcinomas and 2 sarcomatoid carcinomas. The age range of the patients was 54-82 years old, with an average of 69 ± 2.4 years. The tumour size was between 8 and 62 mm, with an average of 28 ± 6.4. TLS was defined as all dense lymphocytic aggregates and 144 TLS were annotated by 2 histopathologists (FK, MDC) with 100% concordance. To assess the generalizability of the model, this dataset was created for internal training-validation and further validation in independent populations. Please cite as: Barmpoutis P, Di Capite M, Kayhanian H, Waddingham W, Alexander DC, Jansen M, et al. (2021) Tertiary lymphoid structures (TLS) identification and density assessment on H&E-stained digital slides of lung cancer. PLoS ONE 16(9): e0256907. https://doi.org/10.1371/journal.pone.0256907
DOI: 10.25550/3-jvdw
title: Mks

description: This unpublished dataset is based on the [Cc2d2a](https://www.alliancegenome.org/gene/MGI:1924487) gene, which is: involved in cilium assembly and protein localization to ciliary transition zone. Acts upstream of or within several processes, including animal organ development; cilium assembly; and neural tube closure. Located in ciliary transition zone. Part of MKS complex. Used to study Meckel syndrome and visceral heterotaxy. Human ortholog(s) of this gene implicated in Joubert syndrome 9; Meckel syndrome 6; and intellectual disability. Orthologous to human CC2D2A. The Mks (Cc2d2a) data are closely related to the other ciliopathy datasets in MusMorph, including B9d, Ift, and Tctn.
DOI: 10.25550/3-jve0
title: Ift

description: This unpublished dataset is based on the [Ift88](https://www.alliancegenome.org/gene/MGI:98715) gene, which serves numerous ciliary functions: Enables kinesin binding activity. Involved in regulation of autophagosome assembly and regulation of cilium assembly. Acts upstream of or within several processes, including animal organ development; cell surface receptor signaling pathway; and spermatid development. Located in several cellular components, including axonemal basal plate; microtubule organizing center; and non-motile cilium. Part of intraciliary transport particle B. Is expressed in several structures, including alimentary system; brain; genitourinary system; heart; and respiratory system. Used to study autosomal recessive polycystic kidney disease. Orthologous to human IFT88. The Ift data are closely related to the other ciliopathy datasets in MusMorph, including Mks, Tctn, and B9d.
DOI: 10.25550/3-jve2
title: Tctn

description: This unpublished dataset is based on two genes: (1) [Tctn2](https://www.alliancegenome.org/gene/MGI:1915228), which is: Involved in cilium assembly; protein localization to ciliary transition zone; and smoothened signaling pathway. Located in ciliary transition zone. Part of MKS complex. Is expressed in several structures, including central nervous system; retina; and turbinate bone primordium. Human ortholog(s) of this gene implicated in Joubert syndrome 24 and Meckel syndrome 8. Orthologous to human TCTN2. (2) [Tmem231](https://www.alliancegenome.org/gene/MGI:2685024), which: Acts upstream of or within several processes, including embryonic digit morphogenesis; neuroepithelial cell differentiation; and smoothened signaling pathway. Located in ciliary membrane and ciliary transition zone. Part of MKS complex. Is expressed in embryo. Human ortholog(s) of this gene implicated in Joubert syndrome 20 and Meckel syndrome. Orthologous to human TMEM231. The Tctn data are closely related to the other ciliopathy datasets in MusMorph, including B9d, Ift, and Mks.