cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3646253_d12.v1
title: Additional file 6: of Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries

description: Counts for spectra assigned at the species level by the MEGAN5 LCA. Each row lists spectral counts assigned to a NCBI species level taxon in at least one NS or WS sample. The columns are paired, so that each NS sample is matched with its WS counterpart. The rows are sorted in descending order by the number of samples in which that species was assigned (using column Z).
DOI: 10.6084/m9.figshare.c.3646358_d1.v1
title: Additional file 7: Table S6. of Structure and variation of the mitochondrial genome of fishes

description: Proportion of invariable amino acid sites in 13 protein-coding genes in the mt genomes of 250 fishes. (XLSX 41Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d4.v1
title: Additional file 13: Table S10. of Structure and variation of the mitochondrial genome of fishes

description: Potential base pairing properties of stem regions in the 16S rRNA gene in the mt genomes of 250 fishes. (XLSX 86Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d2.v1
title: Additional file 5: Table S5. of Structure and variation of the mitochondrial genome of fishes

description: Variation in overlap length between protein-coding genes in the mt genomes of 250 fishes. (XLSX 41Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d3.v1
title: Additional file 2: Table S2. of Structure and variation of the mitochondrial genome of fishes

description: Start codons in 13 protein-coding genes in the mt genomes of 250 fishes. (XLSX 64Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d5.v1
title: Additional file 3: Table S3. of Structure and variation of the mitochondrial genome of fishes

description: Stop codons in 13 protein-coding genes in the mt genomes of 250 fishes. (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d7.v1
title: Additional file 9: Table S8. of Structure and variation of the mitochondrial genome of fishes

description: Occurrence of nucleotide pair types in 21 pair sites common to all 22 tRNAs in the mt genomes of 250 fishes. (XLSX 107Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d6.v1
title: Additional file 4: Table S4. of Structure and variation of the mitochondrial genome of fishes

description: Length variation in 13 protein-coding genes in the mt genomes of 250 fishes. (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d11.v1
title: Additional file 14: Table S11. of Structure and variation of the mitochondrial genome of fishes

description: Differences between previous and present rRNA secondary structure models. (XLSX 59Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d9.v1
title: Additional file 6: Figure S1-a. of Structure and variation of the mitochondrial genome of fishes

description: Aligned amino acid sequences of the ATP8 gene in mt genomes of 250 fishes. Figure S1-b. Aligned amino acid sequences of the ATP6 gene in mt genomes of 250 fishes. Figure S1-c. Aligned amino acid sequences of the COI gene in mt genomes of 250 fishes. Figure S1-d. Aligned amino acid sequences of the COII gene in mt genomes of 250 fishes. Figure S1-e. Aligned amino acid sequences of the COIII gene in mt genomes of 250 fishes. Figure S1-f. Aligned amino acid sequences of the Cyt b gene in mt genomes of 250 fishes. Figure S1-g. Aligned amino acid sequences of the ND1 gene in mt genomes of 249 fishes. Figure S1-h. Aligned amino acid sequences of the ND2 gene in mt genomes of 250 fishes. Figure S1-i. Aligned amino acid sequences of the ND3 gene in mt genomes of 250 fishes. Figure S1-j. Aligned amino acid sequences of the ND4L gene in mt genomes of 250 fishes. Figure S1-k. Aligned amino acid sequences of the ND4 gene in mt genomes of 250 fishes. Figure S1-l. Aligned amino acid sequences of the ND5 gene in mt genomes of 250 fishes. Figure S1-m. Aligned amino acid sequences of the ND6 gene in mt genomes of 249 fishes. (ZIP 3250Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d12.v1
title: Additional file 15: Figure S4-a. of Structure and variation of the mitochondrial genome of fishes

description: Aligned nucleotide sequences of the conserved sequence blocks-D and -I in the control region (CR) in mt genomes of 182 fishes. Figure S4-b. Aligned nucleotide sequences of the conserved sequence blocks-II and -III in the control region (CR) in mt genomes of 182 fishes. (ZIP 87Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d13.v1
title: Additional file 12: Table S9. of Structure and variation of the mitochondrial genome of fishes

description: Potential base pairing properties of stem regions in the 12S rRNA gene in the mt genomes of 250 fishes. (XLSX 76Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d15.v1
title: Additional file 1: Table S1. of Structure and variation of the mitochondrial genome of fishes

description: List of species examined in this study with DDBJ/EMBL/GenBank accession numbers. (XLS 83Â kb)
DOI: 10.6084/m9.figshare.c.3646358_d16.v1
title: Additional file 8: Table S7. of Structure and variation of the mitochondrial genome of fishes

description: Base frequencies for 83 nucleotide positions of 22 tRNA genes in the mt genomes of 250 fishes. (XLS 13112Â kb)
DOI: 10.6084/m9.figshare.c.3646361_d1.v1
title: Additional file 1: of A method for assessing efficiency of bacterial cell disruption and DNA release

description: Spreadsheet for converting nanomoles or nanograms of adenine to nanograms of DNA. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3646445_d9.v1
title: MOESM8 of Multi-breed and multi-trait co-association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds

description: Additional file 8: Table S6. Description of the 23 common genes across the Brazilian, Australian and French datasets.
DOI: 10.6084/m9.figshare.c.3646565_d1.v1
title: Additional file 1: of Use of a web-based educational intervention to improve knowledge of healthy diet and lifestyle in women with Gestational Diabetes Mellitus compared to standard clinic-based education

description: Results of Random Numbers by using a Random Number Generator. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3646577_d4.v1
title: Additional file 12: of Spatial reorganization of telomeres in long-lived quiescent cells

description: Full resolution contact map binned at 10 RF of G0 sir3Î  population presented in Additional file 3 . (DAT 24.6 mb)
DOI: 10.6084/m9.figshare.28049867
title: Lipin Variants in Niemann-Pick type C patients.

description: This dataset contains all lipin variants identified in Niemann-Pick type C patients.
DOI: 10.6084/m9.figshare.28049867.v1
title: Lipin Variants in Niemann-Pick type C patients.

description: This dataset contains all lipin variants identified in Niemann-Pick type C patients.
DOI: 10.6084/m9.figshare.c.3646577_d6.v1
title: Additional file 9: of Spatial reorganization of telomeres in long-lived quiescent cells

description: Full resolution contact map binned at 10 RF of G1 population presented in Fig. 3 . (DAT 24.7 mb)
DOI: 10.6084/m9.figshare.c.3646592_d3.v1
title: Additional file 4: of Systems-level organization of yeast methylotrophic lifestyle

description: Proteomic identification and quantification of methanol metabolic enzymes and control proteins in peroxisomal fractions and homogenates of P. pastoris cells grown on methanol. Containing the following three sheets: Protein hits: contains all identified proteins that met the threshold in at least one sample, with their respective MASCOT scores, number of peptides, and percent sequence coverage. Peptide hits: list of all identified peptides, their MASCOT scores, mass and charge values, and intensities. Peptides used for quant + areas: lists all peptides of the proteins in Table 3 that were used for quantification, and their respective peak areas in the different samples. (XLSX 879 kb)
DOI: 10.6084/m9.figshare.c.3646670_d9.v1
title: Additional file 2: Table S1. of Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase diversity

description: Genome analyses of C. subterraneus subspecies and other bacteria. (XLSX 965Â kb)
DOI: 10.6084/m9.figshare.c.3646670_d10.v1
title: Additional file 10: Table S2. of Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase diversity

description: Glycohydrolases found in C. subterraneus genomes. (XLSX 7Â kb)
DOI: 10.6084/m9.figshare.c.3646679_d2.v1
title: Additional file 2: Table S1. of A comparison of the enzymatic properties of three recombinant isoforms of thrombolytic and antibacterial proteinâ  Destabilase-Lysozyme from medicinal leech

description: List of oligonucleotides used. (XLS 30Â kb)
DOI: 10.6084/m9.figshare.c.3649814_d2.v1
title: Additional file 5: Table S4. of Resilient microorganisms in dust samples of the International Space Station—survival of the adaptation specialists

description: DADA2 output (archaeal primer set; negative controls removed). (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3649814_d3.v1
title: Additional file 1: Table S1. of Resilient microorganisms in dust samples of the International Space Station—survival of the adaptation specialists

description: DADA2 output including negative controls (universal primer set); Highlighted RSVs were also found in the negative controls "RISS-LB-incubation-NC" and "RISS-protocol-NC" and were therefore removed from the dataset for further analysis. (XLSX 212 kb)
DOI: 10.6084/m9.figshare.c.3649829_d2.v1
title: Additional file 2 of Skeleton-based cerebrovascular quantitative analysis

description: Normal047-segmentation.obj. This file is the segmentation result of the NO.47 data based on the Additional file 1: Normal047-MRA.mha. (OBJ 2846.72 kb)
DOI: 10.6084/m9.figshare.c.3649817_d3.v1
title: MOESM7 of Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters

description: Additional file 7: Table S1. The transporter classification database (TCDB) hits identified in this study.
DOI: 10.6084/m9.figshare.c.3649796_d4.v1
title: MOESM1 of Janus kinase inhibition suppresses PKC-induced cytokine release without affecting HIV-1 latency reversal ex vivo

description: Additional file 1: Table 1. Compounds screened in the kinase inhibitor library. Compounds are listed by Chemical Abstracts Service (CAS) number in the order shown in Fig. 2 along with the compound’s common names, known functions, and if they were observed to reduce IC IL-6 levels by ≥fourfold.
DOI: 10.6084/m9.figshare.c.3649835_d1.v1
title: MOESM2 of Genetic evidence that the Makira region in northeastern Madagascar is a hotspot of malaria transmission

description: Additional file 2. Contains the allele calls for the samples analyzed.
DOI: 10.6084/m9.figshare.c.3649814_d4.v1
title: Additional file 6: Table S5. of Resilient microorganisms in dust samples of the International Space Station—survival of the adaptation specialists

description: DADA2 output (universal primer set; negative controls removed). (XLSX 192 kb)
DOI: 10.6084/m9.figshare.c.3649829_d3.v1
title: Additional file 3 of Skeleton-based cerebrovascular quantitative analysis

description: Normal047-mesh.obj. This file is the mesh data of the segmentation result and only contains the CoW. (OBJ 25702.1kb)
DOI: 10.6084/m9.figshare.c.3649817_d5.v1
title: MOESM5 of Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters

description: Additional file 5: Database 3. The assembled transcriptome for Piromyces finnis.
DOI: 10.6084/m9.figshare.c.3649814_d6.v1
title: Additional file 2: Table S2. of Resilient microorganisms in dust samples of the International Space Station—survival of the adaptation specialists

description: DADA2 output including negative control (archaeal primer set); After chimera filtering (see the “Bioinformatical analysis and data processing” section), no reads remained in the negative control (“RISSArch-protocol-NC”). (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3651758_d5.v1
title: Additional file 6: of Efficacy of therapeutic suggestions under general anesthesia: a systematic review and meta-analysis of randomized controlled trials

description: Data with descriptive and effect size related information. (XLSX 60.6 kb)
DOI: 10.6084/m9.figshare.c.3651788_d2.v1
title: Additional file 2: of An ensemble micro neural network approach for elucidating interactions between zinc finger proteins and their target DNA

description: Validation of ZifNN predictions by comparison with experimental helices. The Hamming distance between the catalogue of experimentally determined helices and the helices predicted by our tool are reported for different target DNA sequences. The average identity for these predictions is about 71%. (XLSX 79Â kb)
DOI: 10.6084/m9.figshare.c.3651788_d3.v1
title: Additional file 3: of An ensemble micro neural network approach for elucidating interactions between zinc finger proteins and their target DNA

description: Evaluation within our top predictions for any given target DNA sequence. Analysis for the top 10 predictions for each experimental DNA target and their comparison based on e-s score for each prediction. Further string identities have also been calculated to check the variation between the top 10 predictions for each DNA target. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3651797_d1.v1
title: Additional file 1: of Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation

description: Tax4Fun showing predicted relative abundance of KEGG ortholog groups. Abbreviations: AH frogs, artificially hibernating frogs; NH frogs, nonhibernating frogs. Values are means ± SD. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.c.3651800_d1.v1
title: Additional file 3 of Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri

description: List of copy number expanded and copy number reduced genes in A. halleri and A. lyrata, by comparison to A. thaliana. (XLSX 1331 kb)
DOI: 10.6084/m9.figshare.c.3651800_d2.v1
title: Additional file 6 of Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri

description: Numbers of genes predicted to exhibit copy number divergence in A. lyrata by comparison to A. thaliana. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.c.3653936_d1.v1
title: Additional file 3: Table S3. of Mosaic structure of Mycobacterium bovis BCG genomes as a representation of phage sequencesâ   mobility

description: Localization of specific genome elements in BCG Russia genome. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.c.3653942_d1.v1
title: Additional file 1: Table S1. of Differential expression of alternatively spliced transcripts related to energy metabolism in colorectal cancer

description: Differential expression profiles of genes and transcripts in colon adenocarcinomas compared to matched normal tissues (TCGA data analyzed by CrossHub). (XLSX 43 MB)
DOI: 10.6084/m9.figshare.c.3653933_d2.v1
title: Additional file 3: of Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group

description: Bordor.325.Cent40.tgz. Phylogenomic alignment files and single gene trees for each gene included in the phylogeomic supermatrix. (TGZ 8396 kb)
DOI: 10.6084/m9.figshare.c.3653936_d2.v1
title: Additional file 1: Table S1. of Mosaic structure of Mycobacterium bovis BCG genomes as a representation of phage sequencesâ   mobility

description: Primers used for BCG Russia 368 genome gaps closure by PCR and Sanger sequencing. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3653924_d3.v1
title: Additional file 8: of Comprehensive analysis of draft genomes of two closely related pseudomonas syringae phylogroup 2b strains infecting mono- and dicotyledon host plants

description: Pan-genome for the strains of phylogroup 2. Summary table (XLSX 349 kb)
DOI: 10.6084/m9.figshare.28001450.v18
title: GBM-Reservoir: Dataset and Segmentations

description: In this repository, we present a brain tumor database collection comprising 23,049 samples, with each sample including four different types of MRI brain scans: FLAIR, T1, T1ce, and T2. Additionally, two segmentation masks (ground truth) are provided for each sample. The first mask is the raw output from the registration process, while the second is a post-processed version of the first, designed to simplify interpretation and optimize it for network training. These samples have been acquired via registration process of 438 samples available at the moment of registration from the original dataset provided by the BraTS 2022 Challenge. Registering each pair of existing brain scans results in two additional scans that retain a similar brain shape while featuring varying tumor locations. Consequently, by registering all possible pairs, a dataset originally consisting of n samples can be expanded to n<sup>2</sup> samples. The original dataset was collected from different institutions under standard clinical conditions, but with different equipment and imaging protocols. As a result, the image quality is heterogeneous, reflecting the diversity of clinical practices across institutions. This dataset can be utilized for various tasks, such as developing fully automated segmentation algorithms for new, unseen brain tumor cases, particularly through deep learning-based approaches, since ground truth is provided for each sample.
DOI: 10.6084/m9.figshare.c.3653924_d4.v1
title: Additional file 10: of Comprehensive analysis of draft genomes of two closely related pseudomonas syringae phylogroup 2b strains infecting mono- and dicotyledon host plants

description: Results of the COG-class enrichment analysis for the pan- and core genomes of groups M and D (XLSX 50 kb)
DOI: 10.6084/m9.figshare.c.3653936_d3.v1
title: Additional file 2: Table S2. of Mosaic structure of Mycobacterium bovis BCG genomes as a representation of phage sequencesâ   mobility

description: Localization and description of mutation in BCG Russia 368 genome vs. BCG Tokyo 172. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3653933_d4.v1
title: Additional file 2: of Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group

description: Bordor.325.refdat.dat. Reference protein dataset used as queries for homology searching in subject databases. (DAT 154 kb)
DOI: 10.6084/m9.figshare.c.3653954_d1.v1
title: Additional file 1: of Gene regulatory network inference using PLS-based methods

description: Code of PLSNET. The Matlab code of our proposed method (ZIP 4 kb)
DOI: 10.6084/m9.figshare.c.3653924_d6.v1
title: Additional file 11: of Comprehensive analysis of draft genomes of two closely related pseudomonas syringae phylogroup 2b strains infecting mono- and dicotyledon host plants

description: Distribution of effectors of the type III secretory system among the strains of phylogroup 2 (XLSX 274 kb)
DOI: 10.6084/m9.figshare.c.3653960_d1.v1
title: Additional file 3: Table S3 of Analysis of molecular networks and targets mining of Chinese herbal medicines on anti-aging

description: Part of the enrichment data of targets of Radix Morindae officinalis. (XLS 16 kb)
DOI: 10.6084/m9.figshare.c.3654722_d9.v1
title: Additional file 11: Table S2. of Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

description: Full demographics per patient. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.c.3655349_d1.v1
title: Additional file 2: Table S1. of Comparison of a teratogenic transcriptome-based predictive test based on human embryonic versus inducible pluripotent stem cells

description: “Developmental probe sets” significantly deregulated on day 14 with respect to day 0 for foreskin, IMR90 and H9 cell lines (absolute fold change ≥ 2, false discovery rate-corrected p value
DOI: 10.6084/m9.figshare.c.3655364_d2.v1
title: Additional file 2: Figure S2. of The developing hypopharyngeal microbiota in early life

description: Relative abundance of hypopharyngeal microbiota taxa over time. Krona plot showing the overall composition of the hypopharyngeal microbiota in all samples or at each time-point separately. This figure is interactive, and in the upper left corner the settings can be chosen; “Select dataset” to show data for 1 week, 1 month, 3 months, or all samples. “Max depth” sets to which taxonomic level the data is aggregated, 1 phylum, 2 class, 3 order, 4 family, 5 genus, 6 OTU. “Collapse” simplifies the chart by collapsing “redundant” wedges that are entirely composed of another wedge. “Snapshot” creates an svg image of the current display, and “Link” creates a link, including the current customized view. (HTML 403 kb)
DOI: 10.6084/m9.figshare.c.3656915_d2
title: Additional file 4 of Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation

description: Predicted transcription factos for each co-expression module. Comma-seperated values file Top 10 predicted transcription factors for each co-expression module. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.c.3656915_d3.v1
title: Additional file 2 of Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation

description: Co-expression module gene lists. Comma-seperated values file. This file contains the lists of all the genes in each co-expresion module. (XLSX 85 kb)
DOI: 10.6084/m9.figshare.c.3656915_d3
title: Additional file 2 of Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation

description: Co-expression module gene lists. Comma-seperated values file. This file contains the lists of all the genes in each co-expresion module. (XLSX 85 kb)
DOI: 10.6084/m9.figshare.c.3656945_d1.v1
title: Additional file 3 of ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data

description: ENCODE read-through and intra-chromosomal chimeras (TSV 102kb)
DOI: 10.6084/m9.figshare.c.3656948_d1.v1
title: Additional file 1: Table S1. of Horizontal gene transfer drives the evolution of Rh50 permeases in prokaryotes

description: Phyletic pattern of RH50 homologs in bacterial and archaeal genomes. Table S2. Taxonomic distribution of RH50 and AMT homologs in euryarchaeal methanogens. Table S3. Taxonomic distribution of RH50 and AMT homologs in Planctomycetes and Geobacter Genus. Table S4. The dataset of 121 RH50 chromosomal neighbours. (XLSX 127Â kb)
DOI: 10.6084/m9.figshare.c.3656954_d1.v1
title: Additional file 2: of The transcriptome of the mosquito Aedes fluviatilis (Diptera: Culicidae), and transcriptional changes associated with its native Wolbachia infection

description: Contigs of Wolbachia origin. List of contigs identified as being from Wolbachia pipientis. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.c.3656945_d1
title: Additional file 3 of ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data

description: ENCODE read-through and intra-chromosomal chimeras (TSV 102kb)
DOI: 10.6084/m9.figshare.c.3656951_d1.v1
title: Additional file 2: of Secure and scalable deduplication of horizontally partitioned health data for privacy-preserving distributed statistical computation

description: It is a Bash script that implements the algorithm we used to generate the simulated microbiology datasets. The script is discussed in Additional file 1. (SH 9Â kb)
DOI: 10.6084/m9.figshare.c.3656951_d1
title: Additional file 2: of Secure and scalable deduplication of horizontally partitioned health data for privacy-preserving distributed statistical computation

description: It is a Bash script that implements the algorithm we used to generate the simulated microbiology datasets. The script is discussed in Additional file 1. (SH 9Â kb)
DOI: 10.6084/m9.figshare.28049939
title: Lilium pomponium raw GC-MS files

description: Metabolite extraction from Lilium pomponium leaf tissue