cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9696263
title: EXTENDED DATA [The conjunctival transcriptome in Ethiopians after trichiasis surgery: associations with the development of eyelid contour abnormalities and the effect of oral doxycycline treatment]

description: Clusters of co-expressed genes in the raw read count matrix for all samples. Using a Pearson correlation cut-off of 0.88, 40 clusters were identified. Panel A shows the names of genes in each cluster. Panel B shows the ten most enriched pathways for the genes in each cluster. Panel C shows results of differential expression testing of the cluster-sum (summed read counts of all genes in the cluster for each individual), adjusting for baseline cluster-sum expression, age and sex. Each group was compared to the reference group of Placebo-Good outcome.
DOI: 10.6084/m9.figshare.9696143
title: The conjunctival transcriptome in Ethiopians after trichiasis surgery: associations with the development of eyelid contour abnormalities and the effect of oral doxycycline treatment

description: Data includes: study ID, timepoint (in months), age, sex, trial arm, eyelid contour abnormalities (ECA) binary outcome, chlamydia detection (binary), qPCR cycle threshold values and qPCR delta cycle threshold values.
DOI: 10.6084/m9.figshare.9696143.v1
title: The conjunctival transcriptome in Ethiopians after trichiasis surgery: associations with the development of eyelid contour abnormalities and the effect of oral doxycycline treatment

description: Data includes: study ID, timepoint (in months), age, sex, trial arm, eyelid contour abnormalities (ECA) binary outcome, chlamydia detection (binary), qPCR cycle threshold values and qPCR delta cycle threshold values.
DOI: 10.6084/m9.figshare.9696176
title: Strong effects of genetic and lifestyle factors on biomarker variation and use of personalized cutoffs

description: GWAS summary statistics for abundance levels of 14 plasma protein biomarkers with relevance in cancer. Abundance levels in plasma were measured in healthy individuals. <br><br>These proteins are included: <br>CCL19, CCL24, CD40 ligand, CXCL10, CXCL5, E-selectin, Ep-CAM, IL-12, IL17RB, IL6RA, Kallikrein-11, MIA, MIC-A and VEGF-D. <br><br><br>
DOI: 10.6084/m9.figshare.9696059
title: Income Inequality and the Size of Government: A Causal Analysis

description: Data sample for the replication of results published in the paper.
DOI: 10.6084/m9.figshare.9696059.v1
title: Income Inequality and the Size of Government: A Causal Analysis

description: Data sample for the replication of results published in the paper.
DOI: 10.6084/m9.figshare.9695102
title: Attitudes Towards Aggressive Driving Behaviors

description: This dataset contains the responses from an online survey. The survey asked respondents to give numerical and binary ratings for how aggressive they considered various short video clips depicting driving behaviors to be.<br>Each csv file contains data for a seperate set of driving behaviors. (Close car following, Illegal passing, Speeding, or collisions and near-collisions)<br><br>Descriptions for data columns are in data_description.yaml<br>
DOI: 10.6084/m9.figshare.9695102.v1
title: Attitudes Towards Aggressive Driving Behaviors

description: This dataset contains the responses from an online survey. The survey asked respondents to give numerical and binary ratings for how aggressive they considered various short video clips depicting driving behaviors to be.<br>Each csv file contains data for a seperate set of driving behaviors. (Close car following, Illegal passing, Speeding, or collisions and near-collisions)<br><br>Descriptions for data columns are in data_description.yaml<br>
DOI: 10.6084/m9.figshare.9693623
title: PFL-COA-STRUCTURE-2

description: PFL-COA-STRUCTURE-2Optimized geometries of intermediates I-J and transition state TS7 starting from structure 2 taken from MD trajectory of non-acetylated (PFL•) topology with CoA in the active site.
DOI: 10.6084/m9.figshare.9693617
title: PFL-COA-STRUCTURE-1

description: PFL-COA-STRUCTURE-1Optimized geometries of intermediates I-J and transition state TS7 starting from structure 1 taken from MD trajectory of non-acetylated (PFL•) topology with CoA in the active site.
DOI: 10.6084/m9.figshare.9693617.v1
title: PFL-COA-STRUCTURE-1

description: PFL-COA-STRUCTURE-1Optimized geometries of intermediates I-J and transition state TS7 starting from structure 1 taken from MD trajectory of non-acetylated (PFL•) topology with CoA in the active site.
DOI: 10.6084/m9.figshare.9693623.v1
title: PFL-COA-STRUCTURE-2

description: PFL-COA-STRUCTURE-2Optimized geometries of intermediates I-J and transition state TS7 starting from structure 2 taken from MD trajectory of non-acetylated (PFL•) topology with CoA in the active site.
DOI: 10.6084/m9.figshare.9693602
title: Metadata record for: Temporary dense seismic network during the 2016 Central Italy seismic emergency for microzonation studies

description: This dataset contains key characteristics about the data described in the Data Descriptor Temporary dense seismic network during the 2016 Central Italy seismic emergency for microzonation studies. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.9693587
title: ACPFLII-STRUCTURE-1

description: ACPFLII-STRUCTURE-1Optimized geometries of intermediates A-D and transition states TS1-3 starting from structure 1 taken from MD trajectory of acetylated (AcPFL II) topology without CoA in the active site.
DOI: 10.6084/m9.figshare.9693590
title: ACPFLII-STRUCTURE-2

description: ACPFLII-STRUCTURE-2Optimized geometries of intermediates A-D and transition states TS1-3 starting from structure 2 taken from MD trajectory of acetylated (AcPFL II) topology without CoA in the active site.
DOI: 10.6084/m9.figshare.9693587.v1
title: ACPFLII-STRUCTURE-1

description: ACPFLII-STRUCTURE-1Optimized geometries of intermediates A-D and transition states TS1-3 starting from structure 1 taken from MD trajectory of acetylated (AcPFL II) topology without CoA in the active site.
DOI: 10.6084/m9.figshare.9693602.v2
title: Metadata record for: Temporary dense seismic network during the 2016 Central Italy seismic emergency for microzonation studies

description: This dataset contains key characteristics about the data described in the Data Descriptor Temporary dense seismic network during the 2016 Central Italy seismic emergency for microzonation studies. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.9693602.v1
title: Metadata record for: Temporary dense seismic network during the 2016 Central Italy seismic emergency for microzonation studies

description: This dataset contains key characteristics about the data described in the Data Descriptor Temporary dense seismic network during the 2016 Central Italy seismic emergency for microzonation studies. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.9693329
title: Persistent vs transient alteration of folliculogenesis and estrous cycle after neonatal vs adult exposure to Bisphenol A. Supplementary material.

description: Supplementary material of the article "Persistent vs transient alteration of folliculogenesis and estrous cycle after neonatal vs adult exposure to Bisphenol A. Supplementary material."
DOI: 10.6084/m9.figshare.9693329.v1
title: Persistent vs transient alteration of folliculogenesis and estrous cycle after neonatal vs adult exposure to Bisphenol A. Supplementary material.

description: Supplementary material of the article "Persistent vs transient alteration of folliculogenesis and estrous cycle after neonatal vs adult exposure to Bisphenol A. Supplementary material."
DOI: 10.6084/m9.figshare.9693164.v1
title: Scalable Bayesian inference for coupled hidden Markov and semi-Markov models

description: Bayesian inference for coupled hidden Markov models frequently relies on data augmentation techniques for imputation of the hidden state processes. Considerable progress has been made on developing such techniques, mainly using Markov chain Monte Carlo (MCMC) methods. However, as the dimensionality and complexity of the hidden processes increase some of these methods become inefficient, either because they produce MCMC chains with high autocorrelation or because they become computationally intractable. Motivated by this fact we developed a novel MCMC algorithm, which is a modification of the forward filtering backward sampling algorithm, that achieves a good balance between computation and mixing properties, and thus can be used to analyse models with large numbers of hidden chains. Even though our approach is developed under the assumption of a Markovian model, we show how this assumption can be relaxed leading to minor modifications in the algorithm. Our approach is particularly well suited to epidemic models, where the hidden Markov chains represent the infection status of an individual through time. The performance of our method is assessed on simulated data on epidemic models for the spread of <i>Escherichia coli</i> O157:H7 in cattle.
DOI: 10.6084/m9.figshare.9692918
title: Truth table

description: The project contains the true differential state of each gene and transcript, as well as the simulation details, from simulated RNA-seq data for 12 paired-ended samples (i.e., biological replicates).<br>Column 'gene_ds_status' is 1 for differentially spliced genes, 0 otherwise.<br>Column 'gene_ds_status' is 1 for differentially expressed genes, 0 otherwise.Column 'transcript_ds_status' is 1 for differentially spliced transcripts, 0 otherwise.<br>With differentially splicing, we refer to differential transcript usage (DTU).<br><br>Samples belong to two groups: samples 1 to 6 constitute the first group, while samples 7 to 12 represent the second group.In each group 1,000 genes exhibit differential transcript usage (DTU) and further 1,000 genes (partially overlapping with the previous set) shows differential gene expression (DGE) between groups.<br>Genes showing DTU were simulated by randomly permuting the relative abundance of the four most expressed transcripts; for gene with two or three transcripts only, all transcripts relative abundances were permuted.<br>The dataset is used to benchmark DTU methods in the manuscript entitled "BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty".<br>The code for simulating the data is available on GitHub at https://github.com/SimoneTiberi/BANDITS_manuscript .<br>
DOI: 10.6084/m9.figshare.9692765
title: Two new pill millipedes (Diplopoda: Glomerida: Glomeridae) from high mountains of Vietnam

description: Two new pill millipede species, namely <i>Hyleoglomeris hoanglien</i> sp. nov. and <i>H. fanxipan</i> sp. nov., are described from high elevations (approximately 2,800–2,900 m) of the Hoang Lien National Park, northern Vietnam. A new species, <i>H. hoanglien</i> sp. nov. is clearly distinguished by the telopods being short, stout and incrassate, femora strongly condensed, tibia without modifications, syncoxital lobe bifid trapeziform, and syncoxital horns with an apical seta and a spine. <i>Hyleoglomeris fanxipan</i> sp. nov., is diagnosed by the telopods being long and robust, tibia without modifications, syncoxital lobe roundly trapeziform, and syncoxital horns truncated at tip. COI-based DNA barcodes of the two species are also provided for the first time in the genus <i>Hyleoglomeris</i>. The K2P genetic distance between the two new species is 0.148. In addition, an identification key to the Vietnamese <i>Hyleoglomeris</i> species is also provided. http://www.zoobank.org/urn:lsid:zoobank.org:pub:6DEFED42-0D65-4F50-9D24-A0923B9D1709
DOI: 10.6084/m9.figshare.9692765.v1
title: Two new pill millipedes (Diplopoda: Glomerida: Glomeridae) from high mountains of Vietnam

description: Two new pill millipede species, namely <i>Hyleoglomeris hoanglien</i> sp. nov. and <i>H. fanxipan</i> sp. nov., are described from high elevations (approximately 2,800–2,900 m) of the Hoang Lien National Park, northern Vietnam. A new species, <i>H. hoanglien</i> sp. nov. is clearly distinguished by the telopods being short, stout and incrassate, femora strongly condensed, tibia without modifications, syncoxital lobe bifid trapeziform, and syncoxital horns with an apical seta and a spine. <i>Hyleoglomeris fanxipan</i> sp. nov., is diagnosed by the telopods being long and robust, tibia without modifications, syncoxital lobe roundly trapeziform, and syncoxital horns truncated at tip. COI-based DNA barcodes of the two species are also provided for the first time in the genus <i>Hyleoglomeris</i>. The K2P genetic distance between the two new species is 0.148. In addition, an identification key to the Vietnamese <i>Hyleoglomeris</i> species is also provided. http://www.zoobank.org/urn:lsid:zoobank.org:pub:6DEFED42-0D65-4F50-9D24-A0923B9D1709
DOI: 10.15131/shef.data.9692753
title: Resistance evolution against phage combinations depends on the timing and order of exposure

description: Globally rising rates of antibiotic resistance have renewed interest in phage therapy where combinations of phages have been successfully used to treat multidrug resistant infections. To optimise phage therapy, we first need to understand how bacteria evolve resistance against combinations of multiple phages. Here we use simple laboratory experiments and genome sequencing to show that the timing and order of phage exposure determine the strength, cost and mutational basis of resistance evolution in the opportunistic pathogen Pseudomonas aeruginosa. These findings suggest that phage combinations can be optimised to limit the emergence and persistence of resistance, thereby promoting the long-term usefulness of phage therapy.
DOI: 10.6084/m9.figshare.9692744
title: Data package for SCB cohort and other

description: Data package with genome-wide expression data from SCB cohort, and other data sets from NCBI GEO.
DOI: 10.15131/shef.data.9692753.v1
title: Resistance evolution against phage combinations depends on the timing and order of exposure

description: Globally rising rates of antibiotic resistance have renewed interest in phage therapy where combinations of phages have been successfully used to treat multidrug resistant infections. To optimise phage therapy, we first need to understand how bacteria evolve resistance against combinations of multiple phages. Here we use simple laboratory experiments and genome sequencing to show that the timing and order of phage exposure determine the strength, cost and mutational basis of resistance evolution in the opportunistic pathogen Pseudomonas aeruginosa. These findings suggest that phage combinations can be optimised to limit the emergence and persistence of resistance, thereby promoting the long-term usefulness of phage therapy.
DOI: 10.6084/m9.figshare.9692918.v3
title: Truth table

description: The project contains the true differential state of each gene and transcript, as well as the simulation details, from simulated RNA-seq data for 12 paired-ended samples (i.e., biological replicates).<br>Column 'gene_ds_status' is 1 for differentially spliced genes, 0 otherwise.<br>Column 'gene_ds_status' is 1 for differentially expressed genes, 0 otherwise.Column 'transcript_ds_status' is 1 for differentially spliced transcripts, 0 otherwise.<br>With differentially splicing, we refer to differential transcript usage (DTU).<br><br>Samples belong to two groups: samples 1 to 6 constitute the first group, while samples 7 to 12 represent the second group.In each group 1,000 genes exhibit differential transcript usage (DTU) and further 1,000 genes (partially overlapping with the previous set) shows differential gene expression (DGE) between groups.<br>Genes showing DTU were simulated by randomly permuting the relative abundance of the four most expressed transcripts; for gene with two or three transcripts only, all transcripts relative abundances were permuted.<br>The dataset is used to benchmark DTU methods in the manuscript entitled "BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty".<br>The code for simulating the data is available on GitHub at https://github.com/SimoneTiberi/BANDITS_manuscript .<br>
DOI: 10.6084/m9.figshare.9692714
title: s16_ultrasound

description: Fine-wire intramuscular EMG Subject 14 Protocol: Long Residual Limb Needle positions within muscles
DOI: 10.6084/m9.figshare.9692744.v1
title: Data package for SCB cohort and other

description: Data package with genome-wide expression data from SCB cohort, and other data sets from NCBI GEO.
DOI: 10.6084/m9.figshare.9692711
title: s15_ultrasound

description: Fine-wire intramuscular EMG Subject 13 Protocol: Short Residual Limb Needle positions within muscles
DOI: 10.6084/m9.figshare.9692711.v1
title: s15_ultrasound

description: Fine-wire intramuscular EMG Subject 13 Protocol: Short Residual Limb Needle positions within muscles
DOI: 10.6084/m9.figshare.9692714.v1
title: s16_ultrasound

description: Fine-wire intramuscular EMG Subject 14 Protocol: Long Residual Limb Needle positions within muscles
DOI: 10.6084/m9.figshare.9692744.v2
title: Data package for SCB cohort and other

description: Data package with genome-wide expression data from SCB cohort, and other data sets from NCBI GEO.
DOI: 10.15468/6nrr7n
title: A revision of the Patagonian predaceous midges of the subgenus Acanthohelea of Stilobezzia excluding the S. (A.) edwardsi group (Diptera: Ceratopogonidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Cazorla, Carla G., Spinelli, Gustavo R. (2014): A revision of the Patagonian predaceous midges of the subgenus Acanthohelea of Stilobezzia excluding the S. (A.) edwardsi group (Diptera: Ceratopogonidae). Journal of Natural History 49 (3): 155-209, DOI: 10.1080/00222933.2014.939728
DOI: 10.6084/m9.figshare.9692429
title: Quantification and equivalence classes

description: The project contains the quantification output of Salmon (including equivalence classes) from simulated RNA-seq data for 12 paired-ended samples (i.e., biological replicates).<br>Reads were first aligned via splice-aware genome aligner STAR, then Salmon was used on the aligned reads to compute transcript-level estimated counts (quant.sf files) and equivalence classes (aux_info/eq_classes.txt files).<br>100 bootstrap replicates are computed from Salmon for each sample.<br><br>Samples belong to two groups: samples 1 to 6 constitute the first group, while samples 7 to 12 represent the second group.In each group 1,000 genes exhibit differential transcript usage (DTU) and further 1,000 genes (partially overlapping with the previous set) shows differential gene expression (DGE) between groups.<br>Genes showing DTU were simulated by randomly permuting the relative abundance of the four most expressed transcripts; for gene with two or three transcripts only, all transcripts relative abundances were permuted.<br>The dataset is used to benchmark DTU methods in the manuscript entitled "BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty".<br>The code for simulating the data is available on GitHub at https://github.com/SimoneTiberi/BANDITS_manuscript .<br>
DOI: 10.6084/m9.figshare.9692429.v1
title: Quantification and equivalence classes

description: The project contains the quantification output of Salmon (including equivalence classes) from simulated RNA-seq data for 12 paired-ended samples (i.e., biological replicates).<br>Reads were first aligned via splice-aware genome aligner STAR, then Salmon was used on the aligned reads to compute transcript-level estimated counts (quant.sf files) and equivalence classes (aux_info/eq_classes.txt files).<br>100 bootstrap replicates are computed from Salmon for each sample.<br><br>Samples belong to two groups: samples 1 to 6 constitute the first group, while samples 7 to 12 represent the second group.In each group 1,000 genes exhibit differential transcript usage (DTU) and further 1,000 genes (partially overlapping with the previous set) shows differential gene expression (DGE) between groups.<br>Genes showing DTU were simulated by randomly permuting the relative abundance of the four most expressed transcripts; for gene with two or three transcripts only, all transcripts relative abundances were permuted.<br>The dataset is used to benchmark DTU methods in the manuscript entitled "BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty".<br>The code for simulating the data is available on GitHub at https://github.com/SimoneTiberi/BANDITS_manuscript .<br>
DOI: 10.6084/m9.figshare.9692402
title: tbe_datasets.zip

description: Datasets used for the paper "A Fast and Memory-Efficient Implementation of the Transfer Bootstrap"
DOI: 10.6084/m9.figshare.9692381
title: Additional file 6: of Transcriptome profiling of brain myeloid cells revealed activation of Itgal, Trem1, and Spp1 in western diet-induced obesity

description: The top CD11b+CD45hi cell-related genes in WD-fed mice. The top DE genes enriched in CD11b+CD45hi cells were defined as those with expression levels above 100â cpm and at least 10-fold higher compared to CD11b+CD45lo cells. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.9692381.v1
title: Additional file 6: of Transcriptome profiling of brain myeloid cells revealed activation of Itgal, Trem1, and Spp1 in western diet-induced obesity

description: The top CD11b+CD45hi cell-related genes in WD-fed mice. The top DE genes enriched in CD11b+CD45hi cells were defined as those with expression levels above 100â cpm and at least 10-fold higher compared to CD11b+CD45lo cells. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.9692372
title: Additional file 5: of Transcriptome profiling of brain myeloid cells revealed activation of Itgal, Trem1, and Spp1 in western diet-induced obesity

description: The top CD11b+CD45lo cell-related genes in WD-fed mice. The top DE genes enriched in CD11b+CD45hi cells were defined as those with expression levels above 100â cpm and at least two-fold higher compared to CD11b+CD45lo cells. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.9692372.v1
title: Additional file 5: of Transcriptome profiling of brain myeloid cells revealed activation of Itgal, Trem1, and Spp1 in western diet-induced obesity

description: The top CD11b+CD45lo cell-related genes in WD-fed mice. The top DE genes enriched in CD11b+CD45hi cells were defined as those with expression levels above 100â cpm and at least two-fold higher compared to CD11b+CD45lo cells. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.9692363
title: Additional file 4: of Transcriptome profiling of brain myeloid cells revealed activation of Itgal, Trem1, and Spp1 in western diet-induced obesity

description: Gene list comparing the transcriptomes of CD11b+CD45hi from CD-fed mice and WD-fed mice. The positive FC value means the gene expression CD11b+CD45hi is larger in WD-fed mice than that in CD-fed mice and vice versa. DE genes were defined as FDRâ
DOI: 10.6084/m9.figshare.9692357
title: Additional file 3: of Transcriptome profiling of brain myeloid cells revealed activation of Itgal, Trem1, and Spp1 in western diet-induced obesity

description: Gene list comparing the transcriptomes of CD11b+CD45lo with CD11b+CD45hi cells in CD-fed mice. Pairwise comparison of transcriptomes between CD11b+CD45lo and CD11b+CD45hi cells in CD-fed mice. The positive FC value means the gene expression is larger in CD11b+CD45hi than in CD11b+CD45lo and vice versa. (XLSX 1700 kb)