cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5678431.v1
title: Additional file 1 of On the impact of relatedness on SNP association analysis

description: R script for simulation. This R script supports simulation of synthetic genotypes for a family study. Instead of genotype simulation, genotypes can also be loaded from a CSV file. Allele frequencies are calculated, monomorphic SNPs are filtered and pairwise relatedness is estimated. Given SNP genotypes and a value for the heritability, variance inflation λis calculated. Additionally, the expected λ ′ is estimated. Finally, the script simulates phenotypes under the null and alternative hypothesis and provides results regarding the T statistic. The R library “mvtnorm” is required for sampling multivariate normally distributed phenotypes. Parameters can be modified to simulate different scenarios. However, the number of samples, the number of SNPs and the number of phenotype realisations per SNP should be limited to reduce the computational burden. For example, running the script on an Intel Xeon X5560 CPU (2.80 GHz) for synthetic family study 3 (SFS3) with parameter set f=111, m=2, c=3 (n=999), 100000 SNPs, 1000 phenotype realisations per SNP and 1000 SNPs required 8.3 GB RAM and took
DOI: 10.6084/m9.figshare.5678428
title: Additional file 6 of Dorsal spine evolution in threespine sticklebacks via a splicing change in MSX2A

description: Allele-specific expression measurements. Pyrosequencing data used for calculating MSX2A and CPEB4A allele-specific expression ratios. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.5678428.v1
title: Additional file 6 of Dorsal spine evolution in threespine sticklebacks via a splicing change in MSX2A

description: Allele-specific expression measurements. Pyrosequencing data used for calculating MSX2A and CPEB4A allele-specific expression ratios. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.5678419
title: Additional file 5 of Dorsal spine evolution in threespine sticklebacks via a splicing change in MSX2A

description: QTL mapping data and scripts. Genotype and phenotype data used for mapping spine length QTL in the JAMA Ă PAXB cross. (ZIP 5024 kb)
DOI: 10.6084/m9.figshare.5678419.v1
title: Additional file 5 of Dorsal spine evolution in threespine sticklebacks via a splicing change in MSX2A

description: QTL mapping data and scripts. Genotype and phenotype data used for mapping spine length QTL in the JAMA Ă PAXB cross. (ZIP 5024 kb)
DOI: 10.6084/m9.figshare.5678386
title: Additional file 4 of Dorsal spine evolution in threespine sticklebacks via a splicing change in MSX2A

description: Transgenic analysis. Dorsal spine measurements of PAXB sticklebacks carrying different MSX2A transgenes. (ZIP 22 kb)
DOI: 10.6084/m9.figshare.5678371
title: Additional file 3 of Dorsal spine evolution in threespine sticklebacks via a splicing change in MSX2A

description: Sequence information. Exon sequencing results, alignments of MSX2A protein sequences, and sequences of plasmids used for transgenesis. (ZIP 42 kb)
DOI: 10.6084/m9.figshare.5678371.v1
title: Additional file 3 of Dorsal spine evolution in threespine sticklebacks via a splicing change in MSX2A

description: Sequence information. Exon sequencing results, alignments of MSX2A protein sequences, and sequences of plasmids used for transgenesis. (ZIP 42 kb)
DOI: 10.6084/m9.figshare.5678368
title: Additional file 2: Table S1. of Maternal variant in the upstream of FOXP3 gene on the X chromosome is associated with recurrent infertility in Japanese Black cattle

description: Detailed features among SNPs in QTL_2 and QTL_5 for infertility in repeat-breeding Japanese Black heifers that failed to conceive by ET Positions are based on the UMD3.1 assembly of the bovine genome. a QTL_No. are shown in Table 1. Table S2. Neighboring Ensembl genes in QTLs on the X chromosome associated with infertility in repeat-breeding Japanese Black heifers that failed to conceive by ET. Positions are based on the UMD3.1 assembly of the bovine genome. a QTL_No. are shown in Table 1. Table S3. PANTHER gene ontology analyses of genes in the QTLs. Positions are based on the UMD3.1 assembly of the bovine genome. a QTL_No. are shown in Table 1. Table S4. Cattle QTLdb hits within and near QTL_2 and QTL_5. Positions are based on the UMD3.1 assembly of the bovine genome. a QTL No. are shown in Table 1. b QTL_ID and Trait_ID were assigned using Cattle QTLdb. c PUBMED_ID were assigned using Cattle QTLdb. Table S5. The risk-haplotype in the QTL_2 for infertility in repeat-breeding Japanese Black heifers that failed to conceive by ET. Positions are based on the UMD3.1 assembly of the bovine genome. Table S6. Sequence ontology in QTL_2. a Sequence ontology was assigned to an allele by Ensembl variant effect predictor (VEP). Table S7. Detailed features of FOXP3 (ENSBTAT00000017660) transcript and the exon positions. Positions are based on the UMD3.1 assembly of the bovine genome. Table S8. Primer information for FOXP3 (ENSBTAT00000017660). Table S9. Detailed features of RUNX binding site in FOXP3 reporter construct (92375252â 92,377,691Â bp). Positions are based on the UMD3.1 assembly of the bovine genome. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.5678368.v1
title: Additional file 2: Table S1. of Maternal variant in the upstream of FOXP3 gene on the X chromosome is associated with recurrent infertility in Japanese Black cattle

description: Detailed features among SNPs in QTL_2 and QTL_5 for infertility in repeat-breeding Japanese Black heifers that failed to conceive by ET Positions are based on the UMD3.1 assembly of the bovine genome. a QTL_No. are shown in Table 1. Table S2. Neighboring Ensembl genes in QTLs on the X chromosome associated with infertility in repeat-breeding Japanese Black heifers that failed to conceive by ET. Positions are based on the UMD3.1 assembly of the bovine genome. a QTL_No. are shown in Table 1. Table S3. PANTHER gene ontology analyses of genes in the QTLs. Positions are based on the UMD3.1 assembly of the bovine genome. a QTL_No. are shown in Table 1. Table S4. Cattle QTLdb hits within and near QTL_2 and QTL_5. Positions are based on the UMD3.1 assembly of the bovine genome. a QTL No. are shown in Table 1. b QTL_ID and Trait_ID were assigned using Cattle QTLdb. c PUBMED_ID were assigned using Cattle QTLdb. Table S5. The risk-haplotype in the QTL_2 for infertility in repeat-breeding Japanese Black heifers that failed to conceive by ET. Positions are based on the UMD3.1 assembly of the bovine genome. Table S6. Sequence ontology in QTL_2. a Sequence ontology was assigned to an allele by Ensembl variant effect predictor (VEP). Table S7. Detailed features of FOXP3 (ENSBTAT00000017660) transcript and the exon positions. Positions are based on the UMD3.1 assembly of the bovine genome. Table S8. Primer information for FOXP3 (ENSBTAT00000017660). Table S9. Detailed features of RUNX binding site in FOXP3 reporter construct (92375252â 92,377,691Â bp). Positions are based on the UMD3.1 assembly of the bovine genome. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.5678329
title: Additional file 1 of Dorsal spine evolution in threespine sticklebacks via a splicing change in MSX2A

description: Table S1. Markers used for fine mapping on chromosome 4. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.5678329.v1
title: Additional file 1 of Dorsal spine evolution in threespine sticklebacks via a splicing change in MSX2A

description: Table S1. Markers used for fine mapping on chromosome 4. (XLSX 10 kb)
DOI: 10.5281/zenodo.4008883
title: Pre-processed data for kmspd

description: This is the pre-processed SAR data used for the paper k-means on Positive Definite Matrices, and an Application to Clustering in Radar Image Sequences Code for reproducing results in the paper is available at github.com/frycast/kmspd Any use of this data should attribute the author Pascal Catellazzi for his work in pre-processing.
DOI: 10.5281/zenodo.4008882
title: Pre-processed data for kmspd

description: This is the pre-processed SAR data used for the paper k-means on Positive Definite Matrices, and an Application to Clustering in Radar Image Sequences Code for reproducing results in the paper is available at github.com/frycast/kmspd Any use of this data should attribute the author Pascal Catellazzi for his work in pre-processing.
DOI: 10.6084/m9.figshare.5678257
title: Additional file 5: Table S1. of CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences

description: Distribution of identically classified, uniquely classified, and unidentified OTUs across all taxonomic ranks for data presented in Additional file 4: Figure S1 (Benucci et al., unpublished). (XLSX 47Â kb)
DOI: 10.6084/m9.figshare.5678257.v1
title: Additional file 5: Table S1. of CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences

description: Distribution of identically classified, uniquely classified, and unidentified OTUs across all taxonomic ranks for data presented in Additional file 4: Figure S1 (Benucci et al., unpublished). (XLSX 47Â kb)
DOI: 10.6084/m9.figshare.5678197
title: Additional file 3: of CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences

description: otu_processing.sh pipeline. Contains code for sequence quality control and OTU-picking. (SH 2Â kb)
DOI: 10.6084/m9.figshare.5678197.v1
title: Additional file 3: of CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences

description: otu_processing.sh pipeline. Contains code for sequence quality control and OTU-picking. (SH 2Â kb)
DOI: 10.6084/m9.figshare.5678179
title: Additional file 2: of CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences

description: CONSTAX.tar.gz compressed directory. Contains test datasets, Python, Shell, and R scripts to use the tool. (GZ 175Â kb)
DOI: 10.6084/m9.figshare.5678179.v1
title: Additional file 2: of CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences

description: CONSTAX.tar.gz compressed directory. Contains test datasets, Python, Shell, and R scripts to use the tool. (GZ 175Â kb)
DOI: 10.6084/m9.figshare.5678032
title: MOESM4 of Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning

description: Additional file 4. Genes included in the different categories analyzed in this work.
DOI: 10.6084/m9.figshare.5678032.v1
title: MOESM4 of Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning

description: Additional file 4. Genes included in the different categories analyzed in this work.
DOI: 10.6084/m9.figshare.5678014
title: Additional file 1: Table S1. of Comparative gene co-expression network analysis of epithelial to mesenchymal transition reveals lung cancer progression stages

description: Genes and gene co-expression modules by WGCNA in H358 EMT. Table S2. Genes and gene co-expression modules by WGCNA in A549 EMT. Table S3. 254 EMT-dynamic genes (XLSX 612Â kb)
DOI: 10.6084/m9.figshare.5678014.v1
title: Additional file 1: Table S1. of Comparative gene co-expression network analysis of epithelial to mesenchymal transition reveals lung cancer progression stages

description: Genes and gene co-expression modules by WGCNA in H358 EMT. Table S2. Genes and gene co-expression modules by WGCNA in A549 EMT. Table S3. 254 EMT-dynamic genes (XLSX 612Â kb)
DOI: 10.6084/m9.figshare.5677993
title: Additional file 2: Table S2. of Chromosome 9p copy number gains involving PD-L1 are associated with a specific proliferation and immune-modulating gene expression program active across major cancer types

description: Enrichment analysis of GO categories in the 75-gene list. (XLSX 240 kb)
DOI: 10.6084/m9.figshare.5677993.v1
title: Additional file 2: Table S2. of Chromosome 9p copy number gains involving PD-L1 are associated with a specific proliferation and immune-modulating gene expression program active across major cancer types

description: Enrichment analysis of GO categories in the 75-gene list. (XLSX 240 kb)
DOI: 10.6084/m9.figshare.5677969
title: Additional file 1: Table S1. of Chromosome 9p copy number gains involving PD-L1 are associated with a specific proliferation and immune-modulating gene expression program active across major cancer types

description: Gene list of 75 top up-regulated genes identified in a genome-wide transcriptome analysis across 22 cancer types. The list was obtained by filtering for genes harboring significant and at least 1.5-fold enhanced mRNA expression in tumors with PD-L1 gains across at least 6 cancer types. Pan-cancer p-values were calculated using Fisher’s method (* = significant, ** = significant after Bonferroni correction for 22,849 genes). The set of 75 genes was enriched for the chromosomal regions 9p13 to 9p24 (36 genes) as well as the biological processes ‘cell cycle’ (22 genes) and ‘immune system process’ (16 genes). (XLSX 34 kb)
DOI: 10.6084/m9.figshare.5677969.v1
title: Additional file 1: Table S1. of Chromosome 9p copy number gains involving PD-L1 are associated with a specific proliferation and immune-modulating gene expression program active across major cancer types

description: Gene list of 75 top up-regulated genes identified in a genome-wide transcriptome analysis across 22 cancer types. The list was obtained by filtering for genes harboring significant and at least 1.5-fold enhanced mRNA expression in tumors with PD-L1 gains across at least 6 cancer types. Pan-cancer p-values were calculated using Fisher’s method (* = significant, ** = significant after Bonferroni correction for 22,849 genes). The set of 75 genes was enriched for the chromosomal regions 9p13 to 9p24 (36 genes) as well as the biological processes ‘cell cycle’ (22 genes) and ‘immune system process’ (16 genes). (XLSX 34 kb)
DOI: 10.6084/m9.figshare.5677861
title: S1 Dataset.zip

description: Algorithm in the paper is applicable to point clouds. More point-cloud models with the computed SDFs are in S1 Dataset.zip.
DOI: 10.6084/m9.figshare.5677750
title: Movielens DataSet

description: Movielens is a movie recommendation dataset widely used for benchmarking process. 385There are nearly 100,000 hard ratings on 19 different types of movies (Action, Comedy 386and so on).
DOI: 10.6084/m9.figshare.5677741
title: Flixster-dataset.zip

description: Flixster19 is a classical recommendation dataset which nearly contains 535013 hard 418 ratings on 19 different types of movies (Drama, Comedy and so on).
DOI: 10.6084/m9.figshare.5677705
title: Tree of Life based on a comparison of whole-genome protein

description: This file is related object of "DOI: 10.1038/s41598-018-25090-8".This file contain distance matrixes (.dat) and tree files (.tree). The former is Phylip and BioNJ compatible format, and the latter is FigTree format. In tree files, each species possess taxonomy information, so you can change branch color by the information in FigTree. PDF version of these trees will be published soon in Scientific Reports. You can download Applications from following links.<br>http://tree.bio.ed.ac.uk/software/figtree/http://www.atgc-montpellier.fr/bionj/<br>http://evolution.genetics.washington.edu/phylip.html<br><br>
DOI: 10.6084/m9.figshare.5677705.v1
title: Tree of Life based on a comparison of whole-genome protein

description: This file is related object of "DOI: 10.1038/s41598-018-25090-8".This file contain distance matrixes (.dat) and tree files (.tree). The former is Phylip and BioNJ compatible format, and the latter is FigTree format. In tree files, each species possess taxonomy information, so you can change branch color by the information in FigTree. PDF version of these trees will be published soon in Scientific Reports. You can download Applications from following links.<br>http://tree.bio.ed.ac.uk/software/figtree/http://www.atgc-montpellier.fr/bionj/<br>http://evolution.genetics.washington.edu/phylip.html<br><br>
DOI: 10.1285/i22390359v37
title: La riscrittura al femminile del mito nel panorama letterario slavo del XX-XXI secolo

description: Questo numero speciale della rivista Lingue e Linguaggi è un volume monografico dal titolo La riscrittura al femminile del mito nel panorama letterario slavo del XX-XXI secolo. I saggi in esso contenuti, ad opera di insigni autori del panorama nazionale e internazionale, scaturiscono dal Progetto di Rilevante Interesse Nazionale (De)costruzione del mito nella letteratura femminile contemporanea in Russia e in Polonia. Uno studio comparato (P.R.I.N. 2015), che ha messo in evidenza come le scrittrici di area slava partecipino dell'attuale scenario letterario nazionale esercitando una forte influenza a partire dagli assunti filosofici specifici delle loro opere per giungere ad una forma estetica caratterizzata da un'eterogeneità di stili. Gli autori qui pubblicati evidenziano come le scrittrici contemporanee, russe e polacche in particolare, ma anche serbo-croate, ricorrendo frequentemente al gioco letterario di "demitologizzazione" e "remitologizzazione", realizzino nelle loro opere un vero e proprio "bricolage multimitico" oppure scelgano il genere fiabesco, il fantasy, se non addirittura il gotico-horror per l'affermazione di una nuova visione del mondo. Gli undici saggi, che costituiscono la struttura compositiva di questa monografia, individuano nelle nuove mitopoiesi il luogo di scontro ideologico, di emancipazione e di affermazione identitaria dove i temi trattati dell'amore, della morte, dell'arte rivelano tutto il loro potenziale assumendo il valore di "integrazione" simbolica della donna.
DOI: 10.6084/m9.figshare.5677696
title: MistRep_Oecologia_Data.xlsx

description: Data for different aspects of the study are provided on different sheets: Nectar Sugars, Morphology, Pollen Production, Pollinator Visitation, Pollen Deposition, Fruit Success, Parasite Phenology data. Metadata sheet defines the meaning of column names and data values for across all sheets, except "Parasite phenology data" sheet. "Parasite phenology metadata" sheet provides column explanations for that sheet.
DOI: 10.6084/m9.figshare.5677696.v1
title: MistRep_Oecologia_Data.xlsx

description: Data for different aspects of the study are provided on different sheets: Nectar Sugars, Morphology, Pollen Production, Pollinator Visitation, Pollen Deposition, Fruit Success, Parasite Phenology data. Metadata sheet defines the meaning of column names and data values for across all sheets, except "Parasite phenology data" sheet. "Parasite phenology metadata" sheet provides column explanations for that sheet.
DOI: 10.6084/m9.figshare.5677690
title: Automating Ebook Metadata Evaluation

description: Talk given at Minitex Technical Services Symposium, St. Paul, MN, December 6, 2017.
DOI: 10.6084/m9.figshare.5677690.v1
title: Automating Ebook Metadata Evaluation

description: Talk given at Minitex Technical Services Symposium, St. Paul, MN, December 6, 2017.
DOI: 10.1285/i22390359v37p1
title: Frontespizio
DOI: 10.6084/m9.figshare.5677585
title: A Transcatheter Valve for all Cardiac Positions

description: A Transcatheter Valve for all Cardiac Positions
DOI: 10.6084/m9.figshare.5677573
title: Acoustophoretic purification of platelets: feasibility and impact on platelet activation and function

description: Purity, limited platelet activation, and preservation of platelet function are important stakes of preparation of platelet concentrates (PC) for clinical use. In fact, contaminating red blood cells and leukocytes, as well as activated and/or poorly functional platelets in PC, represents a risk of poor efficiency and adverse side effects during platelet transfusion. Therefore, optimization of preparation and storage of PC is still an active field of research. Shear-induced platelet activation is an unwanted side effect of the hard-spin (up to 5000<i>g</i>) step of centrifugation-based methods currently used in blood banks to prepare PC from whole blood samples. Here, we evaluated the effectiveness of an acoustic-based fractionation device for the isolation of human platelets from whole blood bags. The purity, activation status, and functionality of platelets isolated by acoustopheresis were compared with those of platelets isolated using a reference protocol known to produce limited platelet activation and consisting of two consecutive soft-spin centrifugations (120<i>g</i> and 1200<i>g</i>). Platelet concentration and purity were determined using an automated hematology analyzer. Platelet activation status and platelet reactivity to collagen and thrombin were assessed in flow cytometry by measurement of surface expression of P-selectin and activated integrin αIIbβ3. The ability of isolated platelets to incorporate into a thrombus when transfused to NOD/SCID mice was investigated by intravital microscopy using the ferric chloride-induced thrombosis model. Blood fractionation by acoustophoresis led to the elimination of more than 80% of red blood cells and leukocytes from the platelet fraction, whose mean purity was of 92.8 ± 12.8%. The activation status and reactivity to collagen and thrombin of acoustophoresis-isolated platelets were similar to those of platelets isolated by soft-spin centrifugation. Finally, acoustophoresis-isolated platelets were tethered, adhered to the vessel wall, and incorporated into a growing thrombus following ferric chloride-induced vascular injury. Together, our results indicate that acoustophoresis is a suitable method for the isolation of human platelets with minimal platelet activation and preservation of platelet function.
DOI: 10.6084/m9.figshare.5677573.v2
title: Acoustophoretic purification of platelets: feasibility and impact on platelet activation and function

description: Purity, limited platelet activation, and preservation of platelet function are important stakes of preparation of platelet concentrates (PC) for clinical use. In fact, contaminating red blood cells and leukocytes, as well as activated and/or poorly functional platelets in PC, represents a risk of poor efficiency and adverse side effects during platelet transfusion. Therefore, optimization of preparation and storage of PC is still an active field of research. Shear-induced platelet activation is an unwanted side effect of the hard-spin (up to 5000<i>g</i>) step of centrifugation-based methods currently used in blood banks to prepare PC from whole blood samples. Here, we evaluated the effectiveness of an acoustic-based fractionation device for the isolation of human platelets from whole blood bags. The purity, activation status, and functionality of platelets isolated by acoustopheresis were compared with those of platelets isolated using a reference protocol known to produce limited platelet activation and consisting of two consecutive soft-spin centrifugations (120<i>g</i> and 1200<i>g</i>). Platelet concentration and purity were determined using an automated hematology analyzer. Platelet activation status and platelet reactivity to collagen and thrombin were assessed in flow cytometry by measurement of surface expression of P-selectin and activated integrin αIIbβ3. The ability of isolated platelets to incorporate into a thrombus when transfused to NOD/SCID mice was investigated by intravital microscopy using the ferric chloride-induced thrombosis model. Blood fractionation by acoustophoresis led to the elimination of more than 80% of red blood cells and leukocytes from the platelet fraction, whose mean purity was of 92.8 ± 12.8%. The activation status and reactivity to collagen and thrombin of acoustophoresis-isolated platelets were similar to those of platelets isolated by soft-spin centrifugation. Finally, acoustophoresis-isolated platelets were tethered, adhered to the vessel wall, and incorporated into a growing thrombus following ferric chloride-induced vascular injury. Together, our results indicate that acoustophoresis is a suitable method for the isolation of human platelets with minimal platelet activation and preservation of platelet function.