cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10040138.v1
title: MOESM2 of Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters

description: Additional file 2. Overview of type, sequence location and open chromatin marks of TREs targeted by probe sets used in this study (fosmid pools 1 and 2; 6-kb probes 1 and 2). Data are based on [52]. For the segment covered by 6-kb probe 2, no TREs were identified in the used databases. Sequence coordinates represent the coordinates for hg38 after conversion of hg19 into hg38 by liftover. The used databases do not provide data on ‘open chromatin marks’ H3K9ac and H3K4me3 as additional indirect information for their state of activity at the respective loci in BJ1 cells. In the sheet ‘open chromatin marks,’ available data for IMR90 fibroblasts are shown instead. IMR90 cells show an almost identical DHS[+] profile to BJ1 cells ( www.roadmapepigenomics.org ); accordingly, similar epigenetic signatures between both cell lines can be assumed.
DOI: 10.6084/m9.figshare.10040129
title: MOESM20 of Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters

description: Additional file 20. Position and primer sequences used for amplification of ~1-kb subfragments for assembling of 6-kb probes 1 and 2. Data are based on hg19.
DOI: 10.6084/m9.figshare.10040129.v1
title: MOESM20 of Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters

description: Additional file 20. Position and primer sequences used for amplification of ~1-kb subfragments for assembling of 6-kb probes 1 and 2. Data are based on hg19.
DOI: 10.6084/m9.figshare.10040069
title: Additional file 6: of Musical patterns for comparative epigenomics

description: Prostate Tumor. (RAR 3 kb)
DOI: 10.6084/m9.figshare.10040072
title: of Musical patterns for comparative epigenomics

description: of Musical patterns for comparative epigenomics
DOI: 10.6084/m9.figshare.10040063
title: Additional file 5: of Musical patterns for comparative epigenomics

description: Premalignant Prostate. (MIDI 10 kb)
DOI: 10.6084/m9.figshare.10040066
title: of Musical patterns for comparative epigenomics

description: of Musical patterns for comparative epigenomics
DOI: 10.6084/m9.figshare.10040069.v1
title: Additional file 6: of Musical patterns for comparative epigenomics

description: Prostate Tumor. (RAR 3 kb)
DOI: 10.6084/m9.figshare.10040060
title: Additional file 4: of Musical patterns for comparative epigenomics

description: Normal Prostate. (MIDI 1 kb)
DOI: 10.6084/m9.figshare.10040072.v1
title: of Musical patterns for comparative epigenomics

description: of Musical patterns for comparative epigenomics
DOI: 10.6084/m9.figshare.10040054
title: Additional file 2: of Musical patterns for comparative epigenomics

description: Figure S2. Comparison of multiple tumor specimens from the same patient for the PCDHGA10 gene. (MIDI 1 kb)
DOI: 10.6084/m9.figshare.10040057
title: Additional file 3: of Musical patterns for comparative epigenomics

description: Embryonic Stem Cell Short. (MIDI 1 kb)
DOI: 10.6084/m9.figshare.10040066.v1
title: of Musical patterns for comparative epigenomics

description: of Musical patterns for comparative epigenomics
DOI: 10.6084/m9.figshare.10040057.v1
title: Additional file 3: of Musical patterns for comparative epigenomics

description: Embryonic Stem Cell Short. (MIDI 1 kb)
DOI: 10.6084/m9.figshare.10040051
title: Additional file 1: of Musical patterns for comparative epigenomics

description: Figure S1. Sheet music based on the single embryonic stem cell methylation levels of the first 2499 CpG sites on chromosome 1. (MIDI 2 kb)
DOI: 10.6084/m9.figshare.10040054.v1
title: Additional file 2: of Musical patterns for comparative epigenomics

description: Figure S2. Comparison of multiple tumor specimens from the same patient for the PCDHGA10 gene. (MIDI 1 kb)
DOI: 10.6084/m9.figshare.10040051.v1
title: Additional file 1: of Musical patterns for comparative epigenomics

description: Figure S1. Sheet music based on the single embryonic stem cell methylation levels of the first 2499 CpG sites on chromosome 1. (MIDI 2 kb)
DOI: 10.6084/m9.figshare.10039847
title: Additional file 5: Table S5. of The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

description: Results of the MEDUSA analysis for the sigmodontine radiation. MEDUSA analysis were conducted using 6000 trees randomly selected from the posterior distribution found in BEAST, pruned to a backbone tree representing only genera. Node numbers correspond to those in Fig. 3. Shifts are indicated as magnitudes of difference over the background rate estimated from the data. (XLS 6 kb)
DOI: 10.6084/m9.figshare.10039844
title: Additional file 4: Table S4. of The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

description: Results of fitting diversification models to the completed data sets for the sigmodontine radiation in Laser and TreePar. Table showing the diversification models fitted to the branching times derived from the 1000 completed data sets generated via CorSiM. For each simulation (#sim) AIC values and Delta AIC are given. AIC values for the best fitting models according AIC are highlighted in bold numbers. Models considered: pure-birth model -PB-, birth-death -BD-, two rate-variable models [logistic density-dependent model and the exponential density-dependent model (DDL and DDX respectively)] and BD2r and Y2r [variants of BD PB models with a rate shift at a certain time “st”]. In the Laser analysis, parameters are abbreviated as follows: λ = speciation rate; μ = extinction rate; r = net diversification rates (speciation-extinction), kd = k-parameter from the DDL model; xp = the x-parameter from the DDX model. In the TreePar analysis: r1 = initial rate and r2 = final rate; a = extinction fraction (extinction/speciation); st = shift time. Mean and standard deviation of AIC, delta AIC and parameters values are given for the entire data set. (XLS 775 kb)
DOI: 10.6084/m9.figshare.10039838
title: Additional file 2: Table S2. of The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

description: Taxonomic richness paired along the backbone tree employed in the MEDUSA analysis. (XLS 11 kb)
DOI: 10.6084/m9.figshare.10039841
title: Additional file 3: Table S3. of The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

description: Results of fitting diversification models to the empirical phylogeny of Sigmodontinae. Summary of diversification models fitted to the branching times derived from the empirical phylogeny of Sigmodontinae (MCC tree). Models considered: pure-birth model -PB-, birth-death -BD-, two rate-variable models [logistic density-dependent model and the exponential density-dependent model (DDL and DDX respectively)], three time-varying models [incorporating declining speciation rate , increasing extinction and a model where both rates can vary (SPVAR, EXVAR, BOTH respectively)], and BD2r and Y2r [variants of BD PB models with a rate shift at a certain time “st”]. Bold parameter values indicate the best fitting models according to AIC values. Parameters are abbreviated as follows: a = extinction fraction (extinction/speciation); k = parameter exponential change in speciation rate; kd = k-parameter from the DDL model; λ = speciation rate; μ = extinction rate; r = net diversification rates (speciation-extinction), r1 = initial rate and r2 = final rate; st = shift time; xp = the x-parameter from the DDX model and z = parameter exponential change in extinction rate. a time-varying model (XLS 7 kb)
DOI: 10.6084/m9.figshare.10039844.v1
title: Additional file 4: Table S4. of The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

description: Results of fitting diversification models to the completed data sets for the sigmodontine radiation in Laser and TreePar. Table showing the diversification models fitted to the branching times derived from the 1000 completed data sets generated via CorSiM. For each simulation (#sim) AIC values and Delta AIC are given. AIC values for the best fitting models according AIC are highlighted in bold numbers. Models considered: pure-birth model -PB-, birth-death -BD-, two rate-variable models [logistic density-dependent model and the exponential density-dependent model (DDL and DDX respectively)] and BD2r and Y2r [variants of BD PB models with a rate shift at a certain time “st”]. In the Laser analysis, parameters are abbreviated as follows: λ = speciation rate; μ = extinction rate; r = net diversification rates (speciation-extinction), kd = k-parameter from the DDL model; xp = the x-parameter from the DDX model. In the TreePar analysis: r1 = initial rate and r2 = final rate; a = extinction fraction (extinction/speciation); st = shift time. Mean and standard deviation of AIC, delta AIC and parameters values are given for the entire data set. (XLS 775 kb)
DOI: 10.6084/m9.figshare.10039847.v1
title: Additional file 5: Table S5. of The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

description: Results of the MEDUSA analysis for the sigmodontine radiation. MEDUSA analysis were conducted using 6000 trees randomly selected from the posterior distribution found in BEAST, pruned to a backbone tree representing only genera. Node numbers correspond to those in Fig. 3. Shifts are indicated as magnitudes of difference over the background rate estimated from the data. (XLS 6 kb)
DOI: 10.6084/m9.figshare.10039835
title: Additional file 1: Table S1. of The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

description: Detail of specimens examined in this study. GenBank accession numbers, trait values, and distributional range for the species included in this study. Traits were coded as detailed in the “Material and Methods” section. Vegetation: 1) open vegetation, 2) mixed, or 3) forest. Altitudinal range: 1) lowlands, 2) middle range, or 3) highland. Molar type was coded as 0) tetralophodont, or 1) pentalophodont. The distribution coded for the ClaSSE models is listed under the “Area” column 1) remainder of the distribution, 2) Andean, and 3) tropical lowlands. All GenBank accession numbers for analyzed sequences are given in the last two columns. “N” indicates missing data. (XLS 44 kb)
DOI: 10.6084/m9.figshare.10039835.v1
title: Additional file 1: Table S1. of The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

description: Detail of specimens examined in this study. GenBank accession numbers, trait values, and distributional range for the species included in this study. Traits were coded as detailed in the “Material and Methods” section. Vegetation: 1) open vegetation, 2) mixed, or 3) forest. Altitudinal range: 1) lowlands, 2) middle range, or 3) highland. Molar type was coded as 0) tetralophodont, or 1) pentalophodont. The distribution coded for the ClaSSE models is listed under the “Area” column 1) remainder of the distribution, 2) Andean, and 3) tropical lowlands. All GenBank accession numbers for analyzed sequences are given in the last two columns. “N” indicates missing data. (XLS 44 kb)
DOI: 10.6084/m9.figshare.10039838.v1
title: Additional file 2: Table S2. of The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

description: Taxonomic richness paired along the backbone tree employed in the MEDUSA analysis. (XLS 11 kb)
DOI: 10.6084/m9.figshare.10039841.v1
title: Additional file 3: Table S3. of The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

description: Results of fitting diversification models to the empirical phylogeny of Sigmodontinae. Summary of diversification models fitted to the branching times derived from the empirical phylogeny of Sigmodontinae (MCC tree). Models considered: pure-birth model -PB-, birth-death -BD-, two rate-variable models [logistic density-dependent model and the exponential density-dependent model (DDL and DDX respectively)], three time-varying models [incorporating declining speciation rate , increasing extinction and a model where both rates can vary (SPVAR, EXVAR, BOTH respectively)], and BD2r and Y2r [variants of BD PB models with a rate shift at a certain time “st”]. Bold parameter values indicate the best fitting models according to AIC values. Parameters are abbreviated as follows: a = extinction fraction (extinction/speciation); k = parameter exponential change in speciation rate; kd = k-parameter from the DDL model; λ = speciation rate; μ = extinction rate; r = net diversification rates (speciation-extinction), r1 = initial rate and r2 = final rate; st = shift time; xp = the x-parameter from the DDX model and z = parameter exponential change in extinction rate. a time-varying model (XLS 7 kb)
DOI: 10.6084/m9.figshare.10039826
title: Additional file 9: Figure S4. of The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

description: Ancestral state reconstruction for the vegetation type occupied for sigmodontine rodents. Habitats associated with vegetation are illustrated by colored bars on the tips of the branches. Pies at internal nodes represent ancestral probabilities of the traits recovered by simmap. (TIFF 766 kb)
DOI: 10.6084/m9.figshare.10039829
title: Additional file 10: Figure S5. of The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

description: Ancestral state reconstruction for the molar plan of sigmodontine rodents. Molar morphology is illustrated by colored bars on the tips of the branches. Pies at internal nodes represent ancestral probabilities of the traits recovered by simmap. (TIFF 725 kb)
DOI: 10.6084/m9.figshare.10039826.v1
title: Additional file 9: Figure S4. of The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

description: Ancestral state reconstruction for the vegetation type occupied for sigmodontine rodents. Habitats associated with vegetation are illustrated by colored bars on the tips of the branches. Pies at internal nodes represent ancestral probabilities of the traits recovered by simmap. (TIFF 766 kb)
DOI: 10.6084/m9.figshare.10039829.v1
title: Additional file 10: Figure S5. of The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

description: Ancestral state reconstruction for the molar plan of sigmodontine rodents. Molar morphology is illustrated by colored bars on the tips of the branches. Pies at internal nodes represent ancestral probabilities of the traits recovered by simmap. (TIFF 725 kb)
DOI: 10.6084/m9.figshare.10039799
title: Additional file 4: of Real-time diagnostic analysis of MinIONâ ˘-based metagenomic sequencing in clinical microbiology evaluation: a case report

description: List of identified bacteria. The file is deposited at https://doi.org/10.6084/m9.figshare.7380074 . (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.10039799.v1
title: Additional file 4: of Real-time diagnostic analysis of MinIONâ ˘-based metagenomic sequencing in clinical microbiology evaluation: a case report

description: List of identified bacteria. The file is deposited at https://doi.org/10.6084/m9.figshare.7380074 . (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.10039565
title: MOESM1 of EnRoot: a narrow-diameter, inexpensive and partially 3D-printable minirhizotron for imaging fine root production

description: Additional file 1. Bash script to correct image distortion with a how-to-use guide and Fig. S2.1.
DOI: 10.6084/m9.figshare.10039565.v1
title: MOESM1 of EnRoot: a narrow-diameter, inexpensive and partially 3D-printable minirhizotron for imaging fine root production

description: Additional file 1. Bash script to correct image distortion with a how-to-use guide and Fig. S2.1.
DOI: 10.6084/m9.figshare.10039508
title: of An auditory display tool for DNA sequence analysis

description: of An auditory display tool for DNA sequence analysis
DOI: 10.6084/m9.figshare.10039508.v1
title: of An auditory display tool for DNA sequence analysis

description: of An auditory display tool for DNA sequence analysis
DOI: 10.6084/m9.figshare.10039472
title: Additional file 1: of ARTAG in the basal forebrain: widening the constellation of astrocytic tau pathology

description: Additional information on case demographics and qualitative/semi-quantitative assessment of ARTAG pathology with summary of data. ARTAG pathology was semi-quantitatively rated 1-4 (low to high burden) under columns K-U. (XLSX 30Â kb)
DOI: 10.6084/m9.figshare.10039472.v1
title: Additional file 1: of ARTAG in the basal forebrain: widening the constellation of astrocytic tau pathology

description: Additional information on case demographics and qualitative/semi-quantitative assessment of ARTAG pathology with summary of data. ARTAG pathology was semi-quantitatively rated 1-4 (low to high burden) under columns K-U. (XLSX 30Â kb)
DOI: 10.6084/m9.figshare.10039391
title: Additional file 11: Table S1. of Cambrian suspension-feeding tubicolous hemichordates

description: Biogeographical distribution of the fossil Margaretia and index of specimens used in this study. Reference numbers can be found in the main text. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.10039391.v1
title: Additional file 11: Table S1. of Cambrian suspension-feeding tubicolous hemichordates

description: Biogeographical distribution of the fossil Margaretia and index of specimens used in this study. Reference numbers can be found in the main text. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.10039346
title: Additional file 1: of Technology-aided assessments of sensorimotor function: current use, barriers and future directions in the view of different stakeholders

description: Responses. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.10039346.v1
title: Additional file 1: of Technology-aided assessments of sensorimotor function: current use, barriers and future directions in the view of different stakeholders

description: Responses. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.10039316
title: Additional file 2: of Ultrasound plays a key role in imaging and management of genital angiomyofibroblastoma: a case report

description: Published case reports of AMFB up to the time of the writing of this report. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.10039322
title: MOESM1 of An Analysis of Waves Underlying Grid Cell Firing in the Medial Enthorinal Cortex

description: Code for 2D simulations. Code written in C++/CUDA programming language. Equipment requirements: Nvidia CUDA drivers and Nvidia graphics card with compute capability â Ľ3.5. The Armadillo C++ package must be installed. Run commands: $ cmake . $ make $./SpatialNavigationCUDA. (zip)
DOI: 10.6084/m9.figshare.10039316.v1
title: Additional file 2: of Ultrasound plays a key role in imaging and management of genital angiomyofibroblastoma: a case report

description: Published case reports of AMFB up to the time of the writing of this report. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.10039322.v1
title: MOESM1 of An Analysis of Waves Underlying Grid Cell Firing in the Medial Enthorinal Cortex

description: Code for 2D simulations. Code written in C++/CUDA programming language. Equipment requirements: Nvidia CUDA drivers and Nvidia graphics card with compute capability â Ľ3.5. The Armadillo C++ package must be installed. Run commands: $ cmake . $ make $./SpatialNavigationCUDA. (zip)
DOI: 10.6084/m9.figshare.10039301
title: Additional file 2: of A novel SPEG mutation causes non-compaction cardiomyopathy and neuropathy in a floppy infant with centronuclear myopathy

description: Enclosed video sequence 1 and 2 showing a four-chamber view and an isolated view of the left ventricle that depict restrictive cardiac malfunction in left-ventricular non-compaction cardiomyopathy. (ZIP 908 kb)
DOI: 10.6084/m9.figshare.10039301.v1
title: Additional file 2: of A novel SPEG mutation causes non-compaction cardiomyopathy and neuropathy in a floppy infant with centronuclear myopathy

description: Enclosed video sequence 1 and 2 showing a four-chamber view and an isolated view of the left ventricle that depict restrictive cardiac malfunction in left-ventricular non-compaction cardiomyopathy. (ZIP 908 kb)
DOI: 10.6084/m9.figshare.12860819
title: R0191_20170920a_videos

description: Rat 0191, skilled reaching data collected on 9/20/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.10039190
title: Additional file 8: of Correction to: Dual transcriptome of the immediate neutrophil and Candida albicans interplay

description: Table ST4 Aâ C Differential gene expression analysis of Candida. Comprehensive gene expression analysis table of neutrophil-or NET-treated Candida cells in yeast form (A) and in hyphae form (B). Respectively to the form, each condition was tested against the unchallenged, but adjusted fungal cell controls. Union of all 797 DEGs in Candida cells (C). (XLSX 4327 kb)
DOI: 10.6084/m9.figshare.10039175
title: Additional file 4: of Correction to: Dual transcriptome of the immediate neutrophil and Candida albicans interplay

description: Table ST2 A-C Differential gene expression analysis of neutrophils. Comprehensive gene expression analysis table of neutrophils infected with yeast (A) and hyphae (B). Each condition was tested against the uninfected PMN control. Union of all 318 protein-coding DEGs in neutrophils (C). (XLSX 19149 kb)
DOI: 10.6084/m9.figshare.10039190.v1
title: Additional file 8: of Correction to: Dual transcriptome of the immediate neutrophil and Candida albicans interplay

description: Table ST4 Aâ C Differential gene expression analysis of Candida. Comprehensive gene expression analysis table of neutrophil-or NET-treated Candida cells in yeast form (A) and in hyphae form (B). Respectively to the form, each condition was tested against the unchallenged, but adjusted fungal cell controls. Union of all 797 DEGs in Candida cells (C). (XLSX 4327 kb)
DOI: 10.6084/m9.figshare.10039175.v1
title: Additional file 4: of Correction to: Dual transcriptome of the immediate neutrophil and Candida albicans interplay

description: Table ST2 A-C Differential gene expression analysis of neutrophils. Comprehensive gene expression analysis table of neutrophils infected with yeast (A) and hyphae (B). Each condition was tested against the uninfected PMN control. Union of all 318 protein-coding DEGs in neutrophils (C). (XLSX 19149 kb)
DOI: 10.6084/m9.figshare.10039169
title: Additional file 2: of Correction to: Dual transcriptome of the immediate neutrophil and Candida albicans interplay

description: Table ST1 Mapping results. Mapping statistics of neutrophil and Candida reads using NextGenMap. (XLS 41 kb)
DOI: 10.6084/m9.figshare.10039160
title: Additional file 11: of Correction to: Dual transcriptome of the immediate neutrophil and Candida albicans interplay

description: Table ST6 Aâ D Quantification results. Comprehensive gene quantification table of neutrophil transcriptome in read counts (A) and in RPKM (B) as well as of Candida transcriptome in read counts (C) and in RPKM (D). (XLSX 18989 kb)
DOI: 10.6084/m9.figshare.10039169.v1
title: Additional file 2: of Correction to: Dual transcriptome of the immediate neutrophil and Candida albicans interplay

description: Table ST1 Mapping results. Mapping statistics of neutrophil and Candida reads using NextGenMap. (XLS 41 kb)
DOI: 10.6084/m9.figshare.10039160.v1
title: Additional file 11: of Correction to: Dual transcriptome of the immediate neutrophil and Candida albicans interplay

description: Table ST6 Aâ D Quantification results. Comprehensive gene quantification table of neutrophil transcriptome in read counts (A) and in RPKM (B) as well as of Candida transcriptome in read counts (C) and in RPKM (D). (XLSX 18989 kb)