Find research datasets worth reusing

opencc-by-4.0Mar 2024View details →

SUAG Single-Use Assembly Graph-Structured Dataset

The SUAG (Single-Use Assembly Graph) dataset is a comprehensive collection designed to advance research in the domain of single-use assembly systems and graph-based representations. This dataset encompasses a rich repository of structured information, bringing together detailed insights into pharmaceutical Single-Use Assemblies (SUAs) and their corresponding graph structures. Key Features: <ul> <li>Single-Use Assembly Data: Detailed records of diverse SUAs, including bioreactors, tubing sets, and related components, providing a holistic view of assembly configurations.</li> <li>Graph Representations: Graph structures capture the interconnectivity and relationships among components within each SUA, offering a unique perspective on their functional and spatial arrangements.</li> <li>Variety of Applications: The dataset caters to a wide range of applications, from biopharmaceutical production to system optimization, facilitating diverse research endeavors.</li> </ul>   Dataset Structure:  <ul> <li>The dataset containes three classes of SUA graphs, named: Bioreactor, Mixer, and conection.</li> <li>Classes containe 236,196 Graphs,  1,088 Graphs, 300,327 Graphs respectively. </li> <li>Items named sequentially in each class and saved in their row nature in npy format.</li> <li>Each graph file consists of a list of an edges list showing nodes' names and nodes' connectivity.</li> </ul> graph structure example, file m_0.npy in Mixer class:  <code>[['M' 'L1S1'], ['L1S1' 'L1P1'], ['M' 'L2S1'], ['L2S1' 'L2A2'], ['M' 'L5A1'], ['M' 'L3T1']]</code> The 'L' letter when followed by a number such as the case in L1, indicates the components level. components/nodes in different levels are not the same component/nodes.  The node attribute/component is what follows for example in L1S1, the node/component is S. digit 1 indicates that the component S1 is not the same node as S2.  We decided on this numerical way to reduce ambiguity when two nodes of the same components appear in the graph but they are different items in the pipeline.    Component list:    'B' -> 'bioreactorBag'    'H' -> 'hydrophobicFilter'    'F' -> 'hydrophilicFilter'    'Q' -> 'quickCoupler'    'Y' -> 'yConnector'    'X' -> 'xConnector'    'P' -> 'plug'    'A' -> 'asepticConnector'    'D' -> 'asepticDisconnector'    'S' -> 'straightFitting'    'M' -> 'mixerBag'    'R' -> 'couplerReducer'    'T' -> 'triclampConnector'    'N' -> 'tConnector'    'G' -> 'twoDimensionalBag'    'I' -> 'threeDimensionalBag'    'E' -> 'triclampConnector'    'O' -> 'sipConnector'    'J' -> 'bottle'    'C' -> 'mechanicDisconnector'    'Z' -> 'lConnector'     Researchers, practitioners, and educators can leverage the SUAG dataset to explore innovative solutions, develop algorithms for graph-based analyses, and enhance understanding of the evolving landscape of single-use assembly systems.

opencc-by-4.0Mar 2024View details →

Processed datasets used in Almet et al. (2024), "Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics"

These are the processed anndata objects used in Almet et al. (2024), "Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics". These datasets are stored as .h5ad files and are intended to be used with the <a href="https://scanpy.readthedocs.io/en/stable/api.html">Scanpy</a> package in Python. They contain all relevant cell type annotation, unnormalized and transformed gene expression counts, as well as the inferred intercellular fow networks inferred by FlowSig.

opencc-by-4.0Apr 2024View details →

Automated cell type annotation and exploration of single cell signalling dynamics using mass cytometry and machine learning

In this repository we share processed data that were generated using the bioinformatics framework we developed in publication "Automated cell type annotation and exploration of single cell signalling dynamics using mass cytometry and machine learning". These datasets accompany the source codes provided in our GitHub page https://github.com/dkleftogi/singleCellClassification.  The datasets are as follows: <ol> <li>cofactors_v2.RDa : antibody-specific co-factors used to harmonise fcs files from different batches</li> <li>ctrl_annotated.RDa : the annotated cohort of seven healthy donors</li> <li>data_umap.RDa : UMAP representation of the data used to generate the figures in our paper</li> <li>DREMI_feature_matrix.RDa : the DREMI feature matrix used for ML-based modelling presented in our paper</li> <li>median_feature_matrix.RDa : the baseline feature matrix based on medians used for ML-bases modelling in the paper</li> <li>patient_annotated.RDa : the annotated cohort of leukemia patients (n=43)</li> </ol> We note that the raw files of the leukemia cohort can be found in http://flowrepository.org/id/RvFr0LLv9McDJ89jgK50G4lwnfDFRTrcMelxYgnSIcE2Cymrpf2qh2NaWybtWDNH

Single-cell RNA sequencing of CNS-infiltrating HSC-derived phagocytes of Ms4a3Ai14, BM chimeric mice (CD45.2 Csf2rb-/-: CD45.1 Csf2rb+/+ and CD45.2 Ifngr1-/-: CD45.1 Ifngr1+/+) using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.

Single-cell RNA sequencing of CNS-infiltrating HSC-derived phagocytes of Ms4a3Ai14 at onset and peak EAE,  BM chimeric mice (CD45.2 Csf2rb-/-: CD45.1 Csf2rb+/+ and CD45.2 Ifngr1-/-: CD45.1 Ifngr1+/+) using 10X Genomics platform. The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell. Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from Ms4a3Ai14 mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger's in-built cell calling algorithms, we proceeded with Seurat v4 workflow.

Single-cell RNA sequencing of Lymph node-infiltrating HSC-derived phagocytes of Ms4a3Ai14 using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.

Single-cell RNA sequencing of Lymph node-infiltrating HSC-derived phagocytes of Ms4a3Ai14 at onset and peak EAE using 10X Genomics platform. The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell. Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from Ms4a3Ai14 mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger's in-built cell calling algorithms, we proceeded with Seurat v4 workflow.

Single-cell RNA sequencing of Bone Marrow-infiltrating HSC-derived phagocytes of Ms4a3Ai14 using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.

Single-cell RNA sequencing of Bone Marrow-infiltrating HSC-derived phagocytes of Ms4a3Ai14 at onset and peak EAE using 10X Genomics platform. The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell. Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from Ms4a3Ai14 mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger's in-built cell calling algorithms, we proceeded with Seurat v4 workflow.

Single-cell RNA sequencing of Blood-infiltrating HSC-derived phagocytes of Ms4a3Ai14 using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.

Single-cell RNA sequencing of Blood-infiltrating HSC-derived phagocytes of Ms4a3Ai14 at onset and peak EAE using 10X Genomics platform. The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell. Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from Ms4a3Ai14 mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger's in-built cell calling algorithms, we proceeded with Seurat v4 workflow.

opencc-by-4.0Feb 2022View details →

Absolute measurement of cellular activities using photochromic single-fluorophore biosensors and intermittent quantification: data and code example

Minimal code example, raw and derived data for the publication on 'Absolute measurement of cellular activities using photochromic single-fluorophore biosensors and intermittent quantification'.

opennotspecifiedAug 2011View details →

The upper canines of the male Sulawesi Babirusa grow upwards through the snout and continue to grow in a backward-curving spiral. They are too brittle and shallow rooted to be used in fighting and theirfunction, if any, is unknown. Until recently, all babirusas were classified as a single species. The genus has now been split into at least three species, based on features of their skulls and teeth and the amount of hair on their bodies. The Sulawest Babirusa has nearly naked skin. The name Babyrousa celebensis specifically refers to animals from north Sulawesi and the taxonomic identity of babirusas onthe rest of the island remains undecided. Unlike other pig species, babirusas do not have noses adapted for rooting. Babyrousa celebensis Lore Lindu National Park, Sulawesi. Photo: Berndt Fischer/ photolibrary.com in Suidae

The upper canines of the male Sulawesi Babirusa grow upwards through the snout and continue to grow in a backward-curving spiral. They are too brittle and shallow rooted to be used in fighting and theirfunction, if any, is unknown. Until recently, all babirusas were classified as a single species. The genus has now been split into at least three species, based on features of their skulls and teeth and the amount of hair on their bodies. The Sulawest Babirusa has nearly naked skin. The name Babyrousa celebensis specifically refers to animals from north Sulawesi and the taxonomic identity of babirusas onthe rest of the island remains undecided. Unlike other pig species, babirusas do not have noses adapted for rooting. Babyrousa celebensis Lore Lindu National Park, Sulawesi. Photo: Berndt Fischer/ photolibrary.com

opencc-by-4.0Jul 2022View details →

Animal Recognition Using Methods Of Fine-Grained Visual Analysis - Kashtanka Pets (400 Hand-labelled Images - Cats & Dogs, Single Folder)

400 images (200 cats, 200 dogs) hand-labelled by Maria E. with head and body bounding box labels in YOLOv5 format.  Images are in a single folder, no separate folders for cats and dogs.

opennotspecifiedNov 2017View details →

Distribution. Now restricted to the Channel Country of SW Queensland and the Lake Eyre Basin in NE South Australia. Descriptive notes. Head-body 95-120 mm, tail 105-160 mm, ear 23-29 mm, hindfoot 32-37 mm; weight 30-50 g. The Fawn Hopping Mouse has body form typical of hopping mice, with very long hindfeet, long tail with distal brush of longer hairs, very long ears, and large protruberant eyes. Dorsal fur is of variable color, from pale pinkish fawn to gray; ventral fur white. Unlike most other hopping mice, it has no throat pouch, but males have a glandular area of naked skin on the chest. Habitat. Occurs in low shrublands and tussock grasslands on stony ("gibber") plains and claypans. Shows marked habitat segregation from the Dusky Hopping Mouse (N. fuscus), which is closely associated with sandy substrates. Food and Feeding. The Fawn Hopping Mouse is mostly granivorous, but also eats other plant material (stems, leaves) and occasionally invertebrates. It uses succulent, salt-adapted plants around edges of claypans as a source of water. Breeding. Reproduction is probably largely opportunistic and aseasonal, with high reproductive output from near-continuous breeding after periods of high rainfall; reported littersize is 1-5, most commonly three; gestation period 38-43 days for nonlactating females. Females may mature later than other hopping mice, with reproductive maturity reached at about six months. Activity patterns. Terrestrial and nocturnal. Fawn Hopping Mice shelter during day in burrow systems that are typically simpler and shallower than those of other hopping mice. Movements, Home range and Social organization. Fawn Hopping Mice generally live singly or in small groups; typically uncommon within range, but population density may increase by an order of magnitude following periods of high rainfall. Status and Conservation. Classified as Near Threatened on The IUCN Red List. The Fawn Hopping Mouse has shown marked decline in range (estimated at greater than 50%), and presumably population size, since European settlement of Australia. This is mostlikely due to predation by the introduced house cat and Red Fox (Vulpes vulpes), and to habitat degradation associated with pastoralism. Bibliography. Brazenor (1934), Burbidge et al. (2008), Finlayson (1939), Gould (1853), Jackson & Groves (2015), Murray et al. (1999), Ogilby (1892), Thomas (1921h), Van Dyck & Strahan (2008), Waite (1898), Watts & Aslin (1981), Woinarski et al. (2014), Wood Jones (1925). in Muridae

Distribution. Now restricted to the Channel Country of SW Queensland and the Lake Eyre Basin in NE South Australia. Descriptive notes. Head-body 95-120 mm, tail 105-160 mm, ear 23-29 mm, hindfoot 32-37 mm; weight 30-50 g. The Fawn Hopping Mouse has body form typical of hopping mice, with very long hindfeet, long tail with distal brush of longer hairs, very long ears, and large protruberant eyes. Dorsal fur is of variable color, from pale pinkish fawn to gray; ventral fur white. Unlike most other hopping mice, it has no throat pouch, but males have a glandular area of naked skin on the chest. Habitat. Occurs in low shrublands and tussock grasslands on stony ("gibber") plains and claypans. Shows marked habitat segregation from the Dusky Hopping Mouse (N. fuscus), which is closely associated with sandy substrates. Food and Feeding. The Fawn Hopping Mouse is mostly granivorous, but also eats other plant material (stems, leaves) and occasionally invertebrates. It uses succulent, salt-adapted plants around edges of claypans as a source of water. Breeding. Reproduction is probably largely opportunistic and aseasonal, with high reproductive output from near-continuous breeding after periods of high rainfall; reported littersize is 1-5, most commonly three; gestation period 38-43 days for nonlactating females. Females may mature later than other hopping mice, with reproductive maturity reached at about six months. Activity patterns. Terrestrial and nocturnal. Fawn Hopping Mice shelter during day in burrow systems that are typically simpler and shallower than those of other hopping mice. Movements, Home range and Social organization. Fawn Hopping Mice generally live singly or in small groups; typically uncommon within range, but population density may increase by an order of magnitude following periods of high rainfall. Status and Conservation. Classified as Near Threatened on The IUCN Red List. The Fawn Hopping Mouse has shown marked decline in range (estimated at greater than 50%), and presumably population size, since European settlement of Australia. This is mostlikely due to predation by the introduced house cat and Red Fox (Vulpes vulpes), and to habitat degradation associated with pastoralism. Bibliography. Brazenor (1934), Burbidge et al. (2008), Finlayson (1939), Gould (1853), Jackson & Groves (2015), Murray et al. (1999), Ogilby (1892), Thomas (1921h), Van Dyck & Strahan (2008), Waite (1898), Watts & Aslin (1981), Woinarski et al. (2014), Wood Jones (1925).

Figure 15 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 15. Molecular phylogeny of y-larvae (Facetotecta) based on 18S data combining sequences of nine specimens of Hansenocaris demodex sp. nov. and 13 other specimens from Sesoko Island with sequences of Hansenocaris itoi and other limited information from GenBank. For more information on specimens and types, see Table 6 and Figure 14.

Figure 11 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 11. Hansenocaris demodex sp. nov., nauplii from Sesoko Island photographed alive (A–J) or as slide-mounted exuvium (K, L). A–E, different naupliar instars; F, penultimate naupliar instar with exuviae from two prior moults still attached posteriorly; G, cyprid with exuviae from three prior naupliar moults still attached posteriorly; H, last-stage nauplius in lateral view; I, posterior end of cyprid with three prior naupliar moults still attached; J, posterior end of cyprid with three prior naupliar moults still attached; K, L, exuvium of last-stage nauplius, ventral and lateral views. Abbreviations: a1, first antenna; a2, second antenna; ce, cypris eye; md, mandible; ne, nauplius eye; LSN, last-stage nauplius; thx, thorax. Squares with dotted outlines: dish numbers, sample numbers and museum numbers; some larvae died before preservation and are only referred to by their dish

Figure 13 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 13. Hansenocaris demodex sp. nov., paratypes from Sesoko Island in SEM:, an early nauplius (LSN − 3?) (A–C) and a later nauplius (LSN − 2) with unmoulted later larval stages still inside. A, ventral view; B, lateral view; C, cephalic shield, frontal view; D, ventrolateral view; E, lateral view; F, cephalic shield, frontal view; G, cephalic shield, dorsal view. Abbreviations: a1, first antennae; a2, second antennae; dc sp, dorsocaudal spine; ex, exopod; fur sp, furcal spine; la, labrum; md, mandible. Small Arabic numerals, many annotated with l or r for left and right, respectively, refer to those surface structures that could be matched with those of the LSN (see Table 4). Green overlay, LSN; purple overlay, LSN − 1; red overlay, anterior field of facets. Squares with dotted outline: sample numbers, museum numbers and type status.

Figure 12 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 12. Hansenocaris demodex sp. nov., early nauplius (LSN − 5 or LSN − 6?) from Sesoko Island in SEM. A, ventrolateral view; B, lateral view; C, dorsal view; D, frontal view; E, labrum and naupliar appendages, right side; F, naupliar appendages, right side, median view; G, first and second antennae, right side, lateral view, asterisk indicating rudimentary segment of a2 exopod; H, dorsocaudal spine and furcal spines, terminal view. Abbreviations: a1, first antenna; a2, second antenna; ba, basis; co, coxa; dc sp, dorsocaudal spine; en, endopod; ex, exopod; fur sp, furcal spine; F-1 to F-3, frontal plates 1–3; la, labrum complex; md, mandible; rud, rudimentary; W, window plate. Small Arabic numerals, many annotated with l or r for left and right, respectively, refer to those cuticular structures that could be matched with those of the LSN (see Table 4). Yellow overlay, cephalic shield; blue overlay, faciotrunk; red overlay, anterior field of facets. Square with dotted outline: museum number.

Figure 10 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 10. Hansenocaris demodex sp. nov., cyprid from Green Island in SEM. A, lateral view; B, cephalic shield, frontal view; C, putative lattice organ, close-up; D, thoracic limbs 1–6; E, thorax, abdomen and telson, dorsal view. Abbreviations: ba, basis; co, coxa; en, endopod; ex, exopod; la, labrum; pro scle, proximal sclerites of thoracopods; thp 1, thoracopod 1; thp 6, thoracopod 6. Small Arabic numerals, many annotated with l or r for left and right, respectively, refer to cuticular structures (see Table 5). Square with dotted outline: sample number and museum numbers. Dotted arrows in D point to long medial setae of thoracopodal endopods.

Figure 9 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 9. Hansenocaris demodex sp. nov., holotype (A, B, D, E) and paratype (C) cyprid from Sesoko Island in SEM. A, posterior thoracic segments and anterior abdominal segments, lateral view; B, thoracopods, ventral view; C, telson, dorsall view; D, telson, terminal view; E, right furcal ramus, posterior view. Abbreviations: fur ram, furcal ramus; ba, basis; co, coxa; en, endopod; ex, exopod; pro scle, proximal sclerites of thoracopods; thp 1, thoracopod 1. Roman numerals I–VI – thoracic segments. Large Arabic numerals 1–3 – abdominal segments 1–3. Small Arabic numerals, many annotated with l or r for left and right, respectively, refer to cuticular structures (see Table 5). Square with dotted outlines: sample numbers, museum numbers and type status.

Figure 14 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 14. Morphology of four types of y-larvae from Sesoko Island used for molecular analyses (see overview in Table 6), all photographed in life. A, Hansenocaris demodex sp. nov., lecithotrophic LSN (last-stage nauplius) with cyprid inside. B, 'Bumblebee' type, lecithotrophic LSN with cyprid inside. C, 'Big brown' type, lecithotrophic LSN with cyprid inside. D, planktotrophic nauplius, identified as Itô's (1986a) Pacific type I. Squares with dotted outline: sample numbers.

Figure 6 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 6. Hansenocaris demodex sp. nov., last-stage nauplius (LSN) from Green Island in SEM. A, lateral view; B, dorsal view. C, ventral view; D, frontal view. Abbreviations: a1, first antenna; a2, second antenna; dc sp, dorsocaudal spine; fur sp, furcal spine; la, labrum; md, mandible. Arabic numerals, many annotated with l or r for left and right, respectively, refer to cuticular structures (see Table 4). Square with dotted outline: sample number and museum number.

Figure 8 in Integrative taxonomy of crustacean y-larvae (Thecostraca: Facetotecta) using laboratory-rearing and molecular analyses of single specimens, with the description of a new vermiform species

Figure 8. Hansenocaris demodex sp. nov., holotype (B, C) and paratypes (A, D), cyprids from Sesoko Island in SEM. A, live specimen in four different positions; B, cephalic shield, frontal view; C, cephalic shield, dorsal view; D, cephalic shield, oblique posterior view. Abbreviations: par occ pro, paraocular process. Small Arabic numerals, many annotated with l or r for left and right, respectively, refer to cuticular structures of the cyprid (see Table 5). Squares with dotted outlines: sample numbers, museum numbers and type status.