cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3637499_d7.v1
title: Additional file 5: Table S4. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

description: Binning results in P21-Nrl-WT vs. P21-Nrl-KO, P0 vs. P21-Nrl-WT and P0 vs. P21-Nrl-KO comparisons. Custom bioinformatics pipeline and binning of P21-Nrl-WT vs. P21-Nrl-KO (S4.1), P0 (P0CE + P0NE) vs. P21WTcomparison (S4.2) and P0 (P0CE + P0NE) vs. P21KO comparison (S4.3). (XLSX 4018 kb)
DOI: 10.6084/m9.figshare.c.3637502_d4.v1
title: Additional file 1: of 
                     Wolbachia pseudogenes and low prevalence infections in tropical but not temperate Australian tephritid fruit flies: manifestations of lateral gene transfer and endosymbiont spillover?

description: Collection data for field-caught fruit flies from this study. Information for collection location, climate group and year, specimen specific ID number, sex, result for wsp and 16S rDNA screening and GenBank accession number of COI partial gene are included. (CSV 61Â kb)
DOI: 10.5519/qd.vh66hkmh
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (63 records)
DOI: 10.6084/m9.figshare.c.3637616_d1.v1
title: Additional file 1: of Gross and histopathological evaluation of human inflicted bruises in Danish slaughter pigs

description: Histological evaluation of bruises. Presence/absence (1/0) of: hyper-leukocytosis, leukocytes and hemorrhage in the dermis; neutrophils, hyper-leukocytosis, macrophages and hemorrhage in the subcutis; necrosis, neutrophils, macrophages, leukocytes in the interstitial space, leukocytes present intramuscularly, hyper-leukocytosis and hemorrhage in the muscle tissue. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3637622_d1.v1
title: Additional file 3: of The cell surface mucin podocalyxin regulates collective breast tumor budding

description: Is Movie S3 showing collective invasion of control 4T1 cells that express considerable endogenous podocalyxin in 3-D culture, and Movie S4 showing decreased collective invasion of 4T1 cells in 3-D culture when endogenous podocalyxin is stably knocked down. (ZIP 1243 kb)
DOI: 10.6084/m9.figshare.c.3637622_d2.v1
title: Additional file 1: of The cell surface mucin podocalyxin regulates collective breast tumor budding

description: Is Figure S1 showing podocalyxin has little effect on subcutaneous tumor size a or proliferation in monolayer culture b, Figure S2 showing podocalyxin overexpression promotes local invasion of MCF-7 tumor cell xenografts,. Figure S3 showing that the ezrin inhibitor NSC668394 disrupts apical podocalyxin localization in monolayer culture, Figure S4 showing normal mammary epithelial cells continue to form spheres and form single, polarized lumens in 3-D culture, and Figure S5 showing podocalyxin expression increases EGF-mediated signaling. (ZIP 1056 kb)
DOI: 10.6084/m9.figshare.c.3637640_d1.v1
title: Additional file 1: of Comparison of clinical outcomes between luminal invasive ductal carcinoma and luminal invasive lobular carcinoma

description: Dataset supporting the conclusions of this article. (XLSX 94Â kb)
DOI: 10.6084/m9.figshare.c.3637712_d3.v1
title: Additional file 5: of Inferring microbial interaction network from microbiome data using RMN algorithm

description: List of the reliable OTU-triplets ranking by I ( O m , O c , O t ) values in the ascending order. These OTU-triplets were selected when the threshold was set at 0≦L d(O m, O c, O t) ≦3.8 and D(O m, O c, O t)
DOI: 10.6084/m9.figshare.c.3637712_d4.v1
title: Additional file 6: of Inferring microbial interaction network from microbiome data using RMN algorithm

description: The nonlinear correlation coefficient of OTU pairs predicted by RMN algorithm. (XLS 20 kb)
DOI: 10.6084/m9.figshare.c.3637712_d6.v1
title: Additional file 4: of Inferring microbial interaction network from microbiome data using RMN algorithm

description: List of top 100 possible OTU-triplets ranking by I ( O m , O c , O t ) values in the ascending order. These OTU-triplets were selected without using the threshold set at 0≦L d(O m, O c, O t) ≦3.8 and D(O m, O c, O t)
DOI: 10.6084/m9.figshare.c.3637712_d5.v1
title: Additional file 3: of Inferring microbial interaction network from microbiome data using RMN algorithm

description: The table of OTUs for all the samples at the genus level with data standardization. (XLS 26 kb)
DOI: 10.6084/m9.figshare.c.3637736_d2.v1
title: MOESM4 of Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus

description: Additional file 4. Proteomics complementary information. For each condition (Maltose, Pine and Aspen), data are given regarding identified proteins (e.g. number of identified spectra, number of unique peptides, number of specific peptides) and data regarding each identified peptide (e.g. sequence, e value, charge).
DOI: 10.6084/m9.figshare.c.3637745_d1.v1
title: Additional file 1: of A proficient cost reduction framework for de-duplication of records in data integration

description: Dataset-A with one duplicate against an original record and one modification per duplicate record. (CSV 92 kb)
DOI: 10.6084/m9.figshare.c.3637745_d2.v1
title: Additional file 2: of A proficient cost reduction framework for de-duplication of records in data integration

description: Dataset-C with up to 9 duplicates against an original record. (CSV 90 kb)
DOI: 10.6084/m9.figshare.c.3637868_d2.v1
title: Additional file 1: of The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes

description: A text file in BED format containing domain subRVIS sub-region boundaries. Each sub-region name contains three fields separated by a colon - the gene name; the domain type, which is either the CDD PSSM-Id of the aligned domain or a â  -â   denoting that no CDD domain was aligned to this region; the domain type again followed by an underscore, followed by the occurrence number of this domain type. (TXT 10178 kb)
DOI: 10.6084/m9.figshare.c.3637868_d3.v1
title: Additional file 3: of The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes

description: A text file of the FDR adjusted P values per-gene for the domain subRVIS gene-specific tests across the subset of genes for which we have at least two regions and at least one reported pathogenic variant. (TXT 35 kb)
DOI: 10.6084/m9.figshare.c.3637868_d7.v1
title: Additional file 11: of The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes

description: A text file of exonic: subRVIS scores, subGERP scores, genic RVIS scores, pathogenic counts, mutation rates, and coverage percentages. (TXT 15950 kb)
DOI: 10.6084/m9.figshare.c.3637868_d11.v1
title: Additional file 9: of The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes

description: A text file with the standard deviation of the domain subRVIS scores, per gene, across genes with at least three regions. (TXT 671 kb)
DOI: 10.6084/m9.figshare.c.3637868_d9.v1
title: Additional file 4: of The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes

description: A text file of the FDR adjusted P values per-gene for the exon subRVIS gene-specific tests across the subset of genes for which we have at least two regions and at least one reported pathogenic variant. (TXT 35 kb)
DOI: 10.6084/m9.figshare.c.3638078_d10.v1
title: Additional file 7: Figure S3. of Karyotype differentiation in 19 species of river loach fishes (Nemacheilidae, Teleostei): extensive variability associated with rDNA and heterochromatin distribution and its phylogenetic and ecological interpretation

description: Karyotypes arranged from Giemsa-stained chromosomes and dual-colour FISH showing 5S and 45S rDNA sites. Giemsa-stained karyotypes (left column) and dual-colour FISH (right column) with 45S rDNA (red, arrows) and 5S rDNA (green, arrowheads) probes on (A,B) L. costata, (C,D) M. guentheri, (E,F) N. binotatus, (G,H) P. pictilis, (I,J) P. brevis, (K.L) P. lucidorsum, (M,N) S. bolavenensis, (O,P) S. corica, (Q,R) S. hypsiura, (S,T) S. pridii, (U,V) S. lendlii, (W) S. savona. The FISH chromosomes were counterstained with DAPI and the images were converted to grayscale. Inset (D) – chromosome pair 18 from M. guentheri female showing absence of heterochromatic p-arm in contrast to a single homologue in the male karyotype. Inset (V) depicts the absence of a 45S rDNA site on one homologue in female (pair 3). In P. brevis (J), note the syntenical association of both rDNAs on pair 13. Note also the intense size polymorphism in S. bolavenensis (pair 1) (N) and S. corica (pair 7) (P). Additional polymorphic rDNA sites from the other specimen are boxed for S. corica (pairs 7 and 17) (P) and S. hypsiura (pair 18) (R). Bar = 10 μm. (ZIP 2482 kb)
DOI: 10.6084/m9.figshare.c.3638078_d8.v1
title: Additional file 2: Figure S1. of Karyotype differentiation in 19 species of river loach fishes (Nemacheilidae, Teleostei): extensive variability associated with rDNA and heterochromatin distribution and its phylogenetic and ecological interpretation

description: Mitotic metaphases of selected nemacheilid species after C-banding or DAPI-staining. (A,D,C,F.G,H,I,J,M,O,P,Q) DAPI staining; (D,E,K,L,N) C-banding improved with DAPI counterstaining. Metaphases from both methods are converted to inverted pictures. (A) B. barbatula, (B) L. costata, (C,D) M. guentheri (E) N. binotatus, (F) P. pictilis, (G) P. zonalternans, (H) P. brevis, (I) P. sp., (J) P. elongata, (K) P. lucidorsum, (L) S. bolavenensis, (M) S. corica, (N) S. hypsiura, (O) S. pridii, (P) S. savona, (Q) S. lendlii. Arrows depicts whole-armed heterochromatin, arrowheads denote interstitial heterochromatin, the asterisk indicates C-positive NORs (as rare feature among species under study). For comparison of banding patterns between both methods, see pics. C and D. Note that several species share marked interstitial heterochromatic sites indicating the remnants of putative chromosomal rearrangements (e.g., pericentric inversion) (A,E,L,M,Q). Of particular interest are the completely heterochromatic arms in m-sm chromosomes occuring in a subset of species (C,D,L,M,P,Q). Note also heterochromaic p-arms in some st-a chromosomes (C,D,E,O,P). Bar = 10 μm. (ZIP 4276 kb)
DOI: 10.6084/m9.figshare.c.3638078_d11.v1
title: Additional file 5: Table S3. of Karyotype differentiation in 19 species of river loach fishes (Nemacheilidae, Teleostei): extensive variability associated with rDNA and heterochromatin distribution and its phylogenetic and ecological interpretation

description: GenBank accession numbers of 5S and 28S rRNA sequences of four nemacheilids (P. elongata, S. bolavenensis, S. corica, S. fasciolata) and one botiid species (B. almorhae). (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3638078_d12.v1
title: Additional file 9: Table S4. of Karyotype differentiation in 19 species of river loach fishes (Nemacheilidae, Teleostei): extensive variability associated with rDNA and heterochromatin distribution and its phylogenetic and ecological interpretation

description: Distribution of AT- and GC-rich sites and its relation to constitutive heterochromatin and rDNA regions in nemacheilid genomes as inferred from C-banding, DAPI- and CMA3-stainings. Species order reflects their phylogenetic relationships. (XLSX 13 kb)
DOI: 10.5281/zenodo.14382085
title: Spatial Profiling Reveals Equivalence-Derived Molecular Signatures of Brain Mimicry and Adaptation in Breast Cancer Brain Metastases

description: This collection of data accompanies the study: Umeh Garcia et al. Spatial Profiling Reveals Equivalence-Derived Molecular Signatures of Brain Mimicry and Adaptation in Breast Cancer Brain Metastases. (2024). 

Data collected and processed as a part of this study of breast cancer brain metastases (BCBM) include: 



Nanostring GeoMx Digitial Spatial Profiling collected from 149 unique patients, across 235 tissue tissue cores, generating 473 Area Of Interest (AOI) transcriptome profiles (reduced to 450 after quality control filtering), including technical replicates.

Tissue cores from BCBM (including adjacent normal brain), primary invasive breast cancers, and normal (non-cancer) brain

Analysis of 18,677 RNAs (whole transcriptome atlas probe set) in 450 areas of interest (AOIs)

Introduction the “Equivalent Expression Index” a highly specific and accurate algorithm that identifies statistically significant "Equivalently-Expressed Genes" (EEGs)


Uploaded data include: 



DCC count files

LabWorksheet / Annotation file including biospecimen metadata information

Probe Kit Configuration (PKC) file

Count Matrices



Processed raw data frame (AOI x gene matrix)

Processed Q3 normalized data frame (AOI x gene matrix)



GeoMx DSP Scan Images: high resolution PNGs of DSP slides (w/ AOIs)



PNG file names correspond to "scan name" column in Lab Worksheet / Annotation file



Equivalence Expression Index (EEI) Folder containing: 



LICENSE

EEI README.md

Equivalent_Expression_Index.Rmd

Inputs - example files for demo

Outputs - example files for demo
DOI: 10.5281/zenodo.14382086
title: Spatial Profiling Reveals Equivalence-Derived Molecular Signatures of Brain Mimicry and Adaptation in Breast Cancer Brain Metastases

description: This collection of data accompanies the study: Umeh Garcia et al. Spatial Profiling Reveals Equivalence-Derived Molecular Signatures of Brain Mimicry and Adaptation in Breast Cancer Brain Metastases. (2024). 

Data collected and processed as a part of this study of breast cancer brain metastases (BCBM) include: 



Nanostring GeoMx Digitial Spatial Profiling collected from 149 unique patients, across 235 tissue tissue cores, generating 473 Area Of Interest (AOI) transcriptome profiles (reduced to 450 after quality control filtering), including technical replicates.

Tissue cores from BCBM (including adjacent normal brain), primary invasive breast cancers, and normal (non-cancer) brain

Analysis of 18,677 RNAs (whole transcriptome atlas probe set) in 450 areas of interest (AOIs)

Introduction the “Equivalent Expression Index” a highly specific and accurate algorithm that identifies statistically significant "Equivalently-Expressed Genes" (EEGs)


Uploaded data include: 



DCC count files

LabWorksheet / Annotation file including biospecimen metadata information

Probe Kit Configuration (PKC) file

Processed raw gene x AOI matrix

Processed Q3 normalized gene x AOI matrix


Link to Equivalence Expression Index code on Github
DOI: 10.5281/zenodo.14397703
title: Spatial Profiling Reveals Equivalence-Derived Molecular Signatures of Brain Mimicry and Adaptation in Breast Cancer Brain Metastases

description: This collection of data accompanies the study: Umeh Garcia et al. Spatial Profiling Reveals Equivalence-Derived Molecular Signatures of Brain Mimicry and Adaptation in Breast Cancer Brain Metastases. (2024). 

Data collected and processed as a part of this study of breast cancer brain metastases (BCBM) include: 



Nanostring GeoMx Digitial Spatial Profiling collected from 149 unique patients, across 235 tissue tissue cores, generating 473 Area Of Interest (AOI) transcriptome profiles (reduced to 450 after quality control filtering), including technical replicates.

Tissue cores from BCBM (including adjacent normal brain), primary invasive breast cancers, and normal (non-cancer) brain

Analysis of 18,677 RNAs (whole transcriptome atlas probe set) in 450 areas of interest (AOIs)

Introduction the “Equivalent Expression Index” a highly specific and accurate algorithm that identifies statistically significant "Equivalently-Expressed Genes" (EEGs)


Uploaded data include: 



DCC count files

LabWorksheet / Annotation file including biospecimen metadata information

Probe Kit Configuration (PKC) file

Processed raw data frame (AOI x gene matrix)

Processed Q3 normalized data frame (AOI x gene matrix)

Equivalence Expression Index (EEI) Folder containing:



LICENSE

EEI README.md

Equivalent_Expression_Index.Rmd

Inputs - example files for demo

Outputs - example files for demo




Link to Equivalence Expression Index code on Github - currently private
DOI: 10.5281/zenodo.14398080
title: Spatial Profiling Reveals Equivalence-Derived Molecular Signatures of Brain Mimicry and Adaptation in Breast Cancer Brain Metastases

description: This collection of data accompanies the study: Umeh Garcia et al. Spatial Profiling Reveals Equivalence-Derived Molecular Signatures of Brain Mimicry and Adaptation in Breast Cancer Brain Metastases. (2024). 

Data collected and processed as a part of this study of breast cancer brain metastases (BCBM) include: 



Nanostring GeoMx Digitial Spatial Profiling collected from 149 unique patients, across 235 tissue tissue cores, generating 473 Area Of Interest (AOI) transcriptome profiles (reduced to 450 after quality control filtering), including technical replicates.

Tissue cores from BCBM (including adjacent normal brain), primary invasive breast cancers, and normal (non-cancer) brain

Analysis of 18,677 RNAs (whole transcriptome atlas probe set) in 450 areas of interest (AOIs)

Introduction the “Equivalent Expression Index” a highly specific and accurate algorithm that identifies statistically significant "Equivalently-Expressed Genes" (EEGs)


Uploaded data include: 



DCC count files

LabWorksheet / Annotation file including biospecimen metadata information

Probe Kit Configuration (PKC) file

Processed raw data frame (AOI x gene matrix)

Processed Q3 normalized data frame (AOI x gene matrix)

Equivalence Expression Index (EEI) Folder containing:



LICENSE

EEI README.md

Equivalent_Expression_Index.Rmd

Inputs - example files for demo

Outputs - example files for demo




Link to Equivalence Expression Index code on Github - currently private
DOI: 10.5281/zenodo.14425487
title: Spatial Profiling Reveals Equivalence-Derived Molecular Signatures of Brain Mimicry and Adaptation in Breast Cancer Brain Metastases

description: This collection of data accompanies the study: Umeh Garcia et al. Spatial Profiling Reveals Equivalence-Derived Molecular Signatures of Brain Mimicry and Adaptation in Breast Cancer Brain Metastases. (2024). 

Data collected and processed as a part of this study of breast cancer brain metastases (BCBM) include: 



Nanostring GeoMx Digitial Spatial Profiling collected from 149 unique patients, across 235 tissue tissue cores, generating 473 Area Of Interest (AOI) transcriptome profiles (reduced to 450 after quality control filtering), including technical replicates.

Tissue cores from BCBM (including adjacent normal brain), primary invasive breast cancers, and normal (non-cancer) brain

Analysis of 18,677 RNAs (whole transcriptome atlas probe set) in 450 areas of interest (AOIs)

Introduction the “Equivalent Expression Index” a highly specific and accurate algorithm that identifies statistically significant "Equivalently-Expressed Genes" (EEGs)


Uploaded data include: 



DCC count files

LabWorksheet / Annotation file including biospecimen metadata information

Probe Kit Configuration (PKC) file

Count Matrices



Processed raw data frame (AOI x gene matrix)

Processed Q3 normalized data frame (AOI x gene matrix)



GeoMx DSP Scan Images: high resolution PNGs of DSP slides (w/ AOIs)



PNG file names correspond to "scan name" column in Lab Worksheet / Annotation file



Equivalence Expression Index (EEI) Folder containing: 



LICENSE

EEI README.md

Equivalent_Expression_Index.Rmd

Inputs - example files for demo

Outputs - example files for demo
DOI: 10.6084/m9.figshare.c.3638099_d5.v1
title: Additional file 5: of A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B

description: Integrated data for the RH map and BAC contigs of chromosome 6B. The markers, distance between markers and cumulative distance are provided for the 6B RH map. The marker location on the deletion bin is also indicated. The ordered contig data mapped on the RH map with each of the markers provide the contig name, contig size, number of BAC clones, number of MTP clones and names of the markers anchored in the same contig. The physical position of each contig is denoted by the cumulative contig size starting from the contig ‘6BS_CTG219’ located on the end of 6BS. (XLSX 189 kb)
DOI: 10.5281/zenodo.14510579
title: Supporting data for 'A spinless spin qubit'
DOI: 10.6084/m9.figshare.c.3638135_d1.v1
title: MOESM1 of Low tuberculosis case detection: a community and health facility based study of contributory factors in the Nkwanta South district of Ghana

description: Additional file 1. Data file 1: OPD record review for 2012 at Nkwanta south district hospital; Data file 2: TB clients 2012; Nkwanta south district: SSM test; Data file 3: TB clients 2012; Nkwanta south district; Data file 4: Nkwanta south district TB programme; records from TB register.
DOI: 10.6084/m9.figshare.c.3638357_d1.v1
title: Additional file 2: of Surprisingly rich repertoire of Wnt genes in the demosponge Halisarca dujardini

description: wnt.tree.nwk.txt: Newick format Bayesian inference gene tree of Wnt ligands. Species: Amq, Amphimedon queenslandica, Ate, Achaearanea (Parasteatoda) tepidariorum, Bf, Branchiostoma floridae, Cte, Capitella teleta, Hdu, Halisarca dujardini, Hs, Homo sapiens, Lgi, Lottia gigantea, Ml, Mnemiopsis leidyi, Nv, Nematostella vectensis, Oca, Oscarella carmela, Olo, Oscarella lobularis, Sci, Sycon ciliatum, Sko, Saccoglossus kowalewski, Spu, Strongylocentrotus purpuratus, Tc, Tribolium castaneum. (TXT 3Â kb)
DOI: 10.6084/m9.figshare.c.3638357_d2.v1
title: Additional file 1: of Surprisingly rich repertoire of Wnt genes in the demosponge Halisarca dujardini

description: wnt.alignment.nex.txt: trimmed alignment of Wnt protein sequences used to generate Bayesian inference trees shown in Additional file 1 and Fig.Â 1. Species: Amq, Amphimedon queenslandica, Ate, Achaearanea (Parasteatoda) tepidariorum, Bf, Branchiostoma floridae, Cte, Capitella teleta, Hdu, Halisarca dujardini, Hs, Homo sapiens, Lgi, Lottia gigantea, Ml, Mnemiopsis leidyi, Nv, Nematostella vectensis, Oca, Oscarella carmela, Olo, Oscarella lobularis, Sci, Sycon ciliatum, Sko, Saccoglossus kowalewski, Spu, Strongylocentrotus purpuratus, Tc, Tribolium castaneum. (TXT 39Â kb)
DOI: 10.6084/m9.figshare.c.3638393_d1.v1
title: Additional file 3: of Wide prevalence of hybridization in two sympatric grasshopper species may be shaped by their relative abundances

description: Hybrid detection (conservative and relaxed), hybridization rate and assignment to the different hybrid classes (F1, F2, backcrosses with ach parental species) in the 16 sampled populations using the three programs adegenet, NewHybrids and STRUCTURE (q value: 0.2–0.8 and 0.09–0.91). (XLSX 162 kb)
DOI: 10.6084/m9.figshare.c.3638393_d2.v1
title: Additional file 6: of Wide prevalence of hybridization in two sympatric grasshopper species may be shaped by their relative abundances

description: Deviations from Hardy-Weinberg-Equilibrium and inbreeding coefficient for both species and each population and locus. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.c.3638393_d3.v1
title: Additional file 2: of Wide prevalence of hybridization in two sympatric grasshopper species may be shaped by their relative abundances

description: Performance test of the three programs adegenet, NewHybrids and STRUCTURE (q-values 0.2–0.8 and 0.09–0.91). Assignment of 238 purebred species and 800 simulated hybrids by each program and correct assignment to the different hybrid classes (F1, F2 and backcrosses with each parental species) by the programs adegenet and NewHybrids. (XLSX 173 kb)
DOI: 10.6084/m9.figshare.c.3638393_d4.v1
title: Additional file 7: of Wide prevalence of hybridization in two sympatric grasshopper species may be shaped by their relative abundances

description: Fixation indices for genetic differentiation (F ST ) between the populations within one species and between the species in syntopic and allotopic populations. (XLSX 19Â kb)