cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3617378_d5.v1
title: Additional file 5: of Genome-wide analysis of LTR-retrotransposons in oil palm

description: Overview of LTR_STRUC results. For each full-length LTR retrotransposon, superfamily, putative lineage, overall length, identity percentage between both LTR sequences, target site duplication (TSD), polypurine tract (PPT) and tRNA binding site are provided, as well as the sequences of the element and of its LTRs. (XLSX 1543Â kb)
DOI: 10.6084/m9.figshare.c.3617390_d2.v1
title: Additional file 3: of RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways

description: High-confidence PHYB/PHYC-regulated genes. In different tabs, 2202 PHYB-regulated genes, 261 PHYC-regulated genes, 82 genes showing concerted regulation by PHYB and PHYC in the same direction and 22 genes showing concerted regulation by PHYB and PHYC in the opposite direction. Columns describe the genomic locus, the associated longest transcript which mapped to this locus, top BLAST hit and description and e-value, normalized counts from each library, fold-change (wild-type/phy-null mutant, genes highlighted green are upregulated in the phy-null mutant, genes highlighted red are downregulated in the phy-null mutant) and FDR-adjusted P values from DESeq and EdgeR (Padj &lt;0.01 highlighted in yellow). (XLSX 1200Â kb)
DOI: 10.6084/m9.figshare.c.3617363_d10.v1
title: Additional file 5: of Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus

description: Blast result to identify ASGV-associated contigs assembled from ASGV-infected sRNA data. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3617390_d4.v1
title: Additional file 4: of RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways

description: FDR-adj P &lt;0.01 PHYB/PHYC-regulated genes significant in just one experiment. In different tabs, 5320, PHYB-regulated genes, 1037 PHYC-regulated genes and 336 genes showing concerted regulation by PHYB and PHYC. Columns describe the genomic locus, the associated longest transcript which mapped to this locus, top BLAST hit and description and e-value, normalized counts from each library, fold-change (wild-type/phy-null mutant, genes highlighted green are upregulated in the phy-null mutant, genes highlighted red are downregulated in the phy-null mutant) and FDR-adjusted P values from DESeq and EdgeR (Padj &lt;0.01 highlighted in yellow). (XLSX 3100Â kb)
DOI: 10.6084/m9.figshare.c.3617378_d8.v1
title: Additional file 1: of Genome-wide analysis of LTR-retrotransposons in oil palm

description: De novo consensus TE databases. Contains the E. oleifera (E08_denovoLibTEs.txt) and E. guineensis (p5_denovoLibTEs.txt) databases. (ZIP 15,038Â kb)
DOI: 10.17863/cam.53867
title: Crystallographic diffraction data for structure of the VPS39 C-terminal domain

description: Crystallographic diffraction data used to solve the structure of the human VPS39 putative zinc finger domain as deposited with the PDB ID 6ZE9. For more information, see the README.txt file.
DOI: 10.6084/m9.figshare.c.3617408_d2.v1
title: Additional file 2: Table S1. of Sex-specific differences in fetal and infant growth patterns: a prospective population-based cohort study

description: Adjusted linear regression analyses on fetal growth. (XLSX 12 kb)
DOI: 10.17863/cam.81059
title: Research Data supporting PhD Thesis Submission: Evolutionary conservation of host responses to arbuscular mycorrhizal symbiosis in liverworts

description: This dataset supports the data presented in the following PhD thesis: "Evolutionary conservation of host responses to arbuscular mycorrhizal symbiosis in liverworts" submitted by Mara Sgroi for the Degree of Doctor in Philosophy in March 2021. The detailed methods used to generate each supplementary file are described in detail in the Methods Chapter of the associated thesis record. This dataset comprises of: (Supplementary Table 1) Results of differential expression analysis of RNA-seq data from M. paleacea thalli colonized by Rhizophagus irregularis after 5, 8, or 11 weeks post inoculation or after treatment with R. irregularis germinated spore exudates; (Supplementary Table 2) GO enrichment analysis of differentially expressed genes during M. paleacea arbuscular mycorrhizal symbiosis; (Supplementary Table 3) List of genomic resources used as input for orthology inference analysis of 20 land plant genomes and 2 green algae genomes with the Orthofinder analysis pipeline; (Supplementary Table 4) table of transcript IDs belonging to each orthogroup identified by the Orthofinder analysis pipeline; (Supplementary table 5) list of Medicago truncatula direct orthologs of M. paleacea transcripts identified with the Orthofinder analysis pipeline; (Supplementary table 6) M. paleacea and M. truncatula orthologs significantly differentially expressed (RNAseq) during arbuscular mycorrhizal symbiosis; (Supplementary table 7) Amino-acid sequences of candidate M. paleacea pathogenesis-related and gibberellic acid biosynthetic genes, with corresponding M. polymorpha orthologs; (Supplementary File 1) transcript sequences of the Marchantia paleacea transcriptome assembled for the RNAseq analysis of M. paleacea thalli colonized by the arbuscular mycorrhizal fungus Rhizophagus irregularis and in non-colonized conditions. The transcriptome was assembled by combining RNAseq reads from 3 time points for the inoculated and the non-inoculated condition which were collected respectively at 5, 8 and 11 weeks post-inoculation with the fungus and the combined RNAseq reads of M. paleacea thalli treated with germinated spore exudates of R. irregularis or mock-treated; (Supplementary File 2) the predicted peptide sequences of the M. paleacea transcriptome, which were predicted and translated in silico using TransDecoder; (Supplementary File 3) the resolved, unannotated, phylogenetic trees of each orthogroup identified by orthology inference (Orthofinder2) analysis across 20 land plant genomes and 2 green algae;
DOI: 10.23668/psycharchives.4716
title: Dataset for: A mighty tool not only in perception: figure-ground mechanisms control binding an retrieval alike

description: Dataset for: Schmalbrock, P. & Frings, C. A mighty tool not only in perception: figure-ground mechanisms control binding an retrieval alike.
DOI: 10.6084/m9.figshare.c.3617468_d5.v1
title: Additional file 11: of Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants

description: Genbank accession numbers of all taxa used in phylogenetic analyses. (XLS 26 kb)
DOI: 10.6084/m9.figshare.c.3617441_d13.v1
title: Additional file 9: Table S1. of Landscape-level movement patterns by lions in western Serengeti: comparing the influence of inter-specific competitors, habitat attributes and prey availability

description: Results of competition to determine best model for each hypothesis (INTER, LAND and PREY) for each Season (DRY and WET). Best models as determined by ΔAIC are highlighted using bold text. Where ΔAIC
DOI: 10.6084/m9.figshare.c.3617468_d6.v1
title: Additional file 8: of Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants

description: Primers used in this study. (XLS 29 kb)
DOI: 10.6084/m9.figshare.c.3617495_d2.v1
title: Additional file 2: of Rationing in the intensive care unit in case of full bed occupancy: a survey among intensive care unit physicians

description: Raw data set of questionnaire results. (SAV 40Â kb)
DOI: 10.6084/m9.figshare.c.3617468_d7.v1
title: Additional file 7: of Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants

description: Values for 16S rRNA stability and AT content, across freeÂ living and symbiotic bacteria shown in Fig.Â 3. (XLS 33 kb)
DOI: 10.23668/psycharchives.4718
title: Dataset for: Combining response times and response quality indicators to identify speeders with low response quality in web surveys

description: Data from a web survey conducted in 2016 on the askGfK - Online Panel in Slovenia. The questionnaire was designed to explore the relationship between response quality, paradata and multitasking Accordingly, it included a wide set of response quality indicators. Quotas involving region, gender and age insured that the sample was representative of the Slovenian population 15 to 55 years.
DOI: 10.6084/m9.figshare.c.3617468_d8.v1
title: Additional file 3: of Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants

description: Sampling structure of collected C. chromaiodes colonies. (XLS 39 kb)
DOI: 10.6084/m9.figshare.c.3617507_d1.v1
title: Additional file 2: Table S1. of Cytosolic sulfotransferase 1A1 regulates HIV-1 minus-strand DNA elongation in primary human monocyte-derived macrophages

description: Primer and siRNA sequences. DNA and RNA primer sequences used in the study are listed from 5′ to 3′. siRNAs are listed with the siRNA name, Qiagen ID, and sequences from 5′ to 3′. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.c.3617492_d6.v1
title: Additional file 1: of Effect of IKZF1 deletions on signal transduction pathways in Philadelphia chromosome negative pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL)

description: Table S1. Data file containing processed raw data values of the PepChip.
DOI: 10.17863/cam.17106
title: Research data supporting "High Circular Polarization of Electroluminescence Achieved via Self-Assembly of a Light-Emitting Chiral Conjugated Polymer into Multidomain Cholesteric Films"

description: Left and right-handed circularly polarized components of Electro-Luminescence and corresponding dissymmetry factors.
DOI: 10.17863/cam.78718
title: Research Data Supporting “Medium-Density Amorphous Ice”

description: See README file for a detailed description of this dataset. It contains the simulation inputs, data, and code that support the findings of the study, along with all data and code to generate the figures.
DOI: 10.17863/cam.7652
title: Research data supporting "Coherent Structures in Interacting Vortex Rings"

description: Data associated with figures 1 and 2 of Physical Review Fluids Publication by J. Deng, J. Xue, X. Mao and C. P. Caulfield.
DOI: 10.6084/m9.figshare.c.3617657_d3.v1
title: Additional file 9: of Identification of the BRD1 interaction network and its impact on mental disorder risk

description: Ingenuity pathway analysis of BRD1 interaction networks. This Excel file includes three spreadsheets containing enriched categories, sub-categories, and canonical pathways identified by Ingenuity pathway analysis on the BRD1 interaction network. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.c.3617675_d1.v1
title: MOESM10 of Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer

description: Additional file 10. Group Counting Script. Script was used to count the unique groups of proteins, as well as identifying unique or shared groups.
DOI: 10.6084/m9.figshare.c.3617663_d2.v1
title: Additional file 1 of An integrative analysis of gene expression and molecular interaction data to identify dys-regulated sub-networks in inflammatory bowel disease

description: Code.zip â   Folder including the C code used in our optimisation. (ZIP 727 kb)
DOI: 10.6084/m9.figshare.c.3617675_d2.v1
title: MOESM2 of Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer

description: Additional file 2. Protein Families (62). Lists OrthoMCL ortholog groups when using a BLOSUM62 matrix.
DOI: 10.17863/cam.89753
title: Source data in support of: Simultaneous identification of viruses and viral variants with programmable DNA nanobait

description: Source data for the main figures of the article "Simultaneous identification of viruses and viral variants with programmable DNA nanobait" in Nature Nanotechnology. This dataset includes data for single events, plotting bar charts, and statistic test details. Data were recorded with home-built LabVIEW codes. They represent ionic current measurements over time. From these ionic current measurements, single events that correspond to nanobaits were extracted and used for further analysis and bar charts. , nanobait events were filtered out of raw ionic current traces, then the detection region was determined, and information of the spike’s presence at each specific site was extracted. The plotted displacement efficiency was calculated as a displacement efficiency for a measurement subtracted to a no target control for each site (fifty nanobait events for each of three nanopore recordings) unless stated otherwise. 99.9% confidence intervals for the displacement efficiencies were calculated for all measurements. The statistical significance between two sites without and with the target was tested using a two-sided Student’s T-test.
DOI: 10.6084/m9.figshare.c.3617663_d3.v1
title: Additional file 3 of An integrative analysis of gene expression and molecular interaction data to identify dys-regulated sub-networks in inflammatory bowel disease

description: Supplementary_Workbook.xls — Excel workbook comprising the interaction networks described in the main text and in the Supporting Information. Legends of each workbook sheet are included in the workbook ‘Summary’ sheet. (XLSX 210 kb)
DOI: 10.6084/m9.figshare.c.3617675_d3.v1
title: MOESM3 of Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer

description: Additional file 3. Group Counting Results (62). Contains the group IDs of families classified. Protein groups were initially generated using a BLOSUM62 matrix.
DOI: 10.6084/m9.figshare.c.3617675_d4.v1
title: MOESM5 of Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer

description: Additional file 5. Group Counting Results (45). Contains the group IDs of families classified. Protein groups were initially generated using a BLOSUM45 matrix.
DOI: 10.6084/m9.figshare.c.3617684_d1.v1
title: Additional file 1: of Studentsâ   drinking behavior and perceptions towards introducing alcohol policies on university campus in Denmark: a focus group study

description: Appendix 1: Code book. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3617675_d5.v1
title: MOESM7 of Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer

description: Additional file 7. Protochlamydia amoebophila genome. The genome-wide protein set of Protochlamydia amoebophila.
DOI: 10.17863/cam.95098
title: CONCEPTT Metabolomics results 2023_03_17

description: Results of Metabolomics analysis of the CONCEPTT randomised controlled trial of real time continuous glucose monitoring in women with type 1 diabetes in pregnancy.
DOI: 10.6084/m9.figshare.c.3617675_d6.v1
title: MOESM8 of Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer

description: Additional file 8. Additional OrthoMCL output (62). Results based on pairwise alignment between the two species when using a BLOSUM62 matrix.
DOI: 10.6084/m9.figshare.c.3617723_d14.v1
title: MOESM3 of A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1

description: Additional file 3. P_phaeoclathratiforme.fa. The genome-wide protein set of Pelodictyon phaeoclathratiforme BU-1, downloaded from UniProt.
DOI: 10.6084/m9.figshare.c.3617723_d15.v1
title: MOESM12 of A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1

description: Additional file 12. ensembl_1_cp_ppb_x_cp_cct.pl. The Perl script used to identify the protein families containing 1 copy in P. phaeoclathratiforme and multiple copies in C. tepidum from Ensembl Genomes.
DOI: 10.17863/cam.61808
title: Research data supporting "ParaDox: Eliminating Voltage Margins via Heterogeneous Fault Tolerance"

description: Gem5 modifications to support performance evaluation of using heterogeneous cores to perform processor error correction when undervolting or overclocking (the ParaDox technique). See the README.md file for more detailed information and usage instructions.
DOI: 10.6084/m9.figshare.c.3617723_d16.v1
title: MOESM13 of A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1

description: Additional file 13. unique_cct.pl. Perl script used to identify the protein families unique to C. tepidum from UniProt.
DOI: 10.6084/m9.figshare.c.3617759_d6.v1
title: Additional file 8: Table S8. of Genetic analysis of phytoene synthase 1 (Psy1) gene function and regulation in common wheat

description: Major metabolic pathways and candidate genes associated with Psy1 down-regulation. (XLSX 10.1Â kb)
DOI: 10.6084/m9.figshare.c.3617777_d1.v1
title: Additional file 2: of Contact diaries versus wearable proximity sensors in measuring contact patterns at a conference: method comparison and participantsâ   attitudes

description: Codebook. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.c.3617723_d17.v1
title: MOESM7 of A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1

description: Additional file 7. ensembl_ unique_cct.pl. The Perl script used to identify the protein families unique to C. tepidum from Ensembl Genomes.
DOI: 10.6084/m9.figshare.c.3617723_d18.v1
title: MOESM14 of A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1

description: Additional file 14. uniqe_ppb.pl. Perl script used to identify the protein families unique to P. phaeoclathratiforme from UniProt.
DOI: 10.6084/m9.figshare.c.3617777_d2.v1
title: Additional file 3: of Contact diaries versus wearable proximity sensors in measuring contact patterns at a conference: method comparison and participantsâ   attitudes

description: Acceptance data. (CSV 6 kb)
DOI: 10.6084/m9.figshare.c.3617759_d8.v1
title: Additional file 9: Table S9. of Genetic analysis of phytoene synthase 1 (Psy1) gene function and regulation in common wheat

description: Summary of silent mutations in Psy1 identified by TILLING. (XLSX 11.7Â kb)
DOI: 10.6084/m9.figshare.c.3617762_d5.v1
title: MOESM1 of RNAseq reveals hydrophobins that are involved in the adaptation of Aspergillus nidulans to lignocellulose

description: Additional file 1: File S1. The A. nidulans genes transcriptionally modulated post transfer from fructose to SEB.
DOI: 10.17863/cam.11276
title: Research data supporting [Probing the topological surface state in Bi2Se3 thin films using temperature-dependent terahertz spectroscopy]

description: Strong spin-momentum coupling in topological insulators give rise to topological surface states, protected against disorder scattering by time reversal symmetry. The study of these exotic quantum states not only provides an opportunity to explore fundamental phenomenon in condensed matter physics such as the spin hall effect, but also lays the foundation for applications in quantum computing to spintronics. Conventional electrical measurements suffer from substantial bulk interference, making it difficult to clearly identify topological surface state from the bulk. We use terahertz time-domain spectroscopy to study the temperature-dependent optical behavior of a 23-quintuple-thick film of bismuth selenide (Bi2Se3) allowing the deconvolution of the surface state response from the bulk. The signatures of the topological surface state at low temperatures (&lt; 30 K) with the optical conductance of Bi2Se3 exhibiting a metallic behavior are observed. Measurement of carrier dynamics, obtain an optical mobility, exceeding 2000 cm2/V•s at 4 K, indicative of a surface-dominated response. A scattering lifetime of ~0.18 ps and a carrier density of 6×1012 cm-2 at 4 K were obtained from the terahertz time-domain spectroscopy measurement. The terahertz conductance spectra reveal characteristic features at ~1.9 THz, attributed to the optical phonon mode, which becomes less prominent with temperature. The electrical transport measurements reveal weak antilocalization behavior in our Bi2Se3 sample. We obtain the number of surface state modes, α as 0.5, and the coherence length, Lφ, as 380 nm at low temperatures &lt; 10 K, further confirming the presence of a single topological surface state mode.
DOI: 10.6084/m9.figshare.c.3617723_d19.v1
title: MOESM5 of A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1

description: Additional file 5. ensembl_ppb.fa. The Fasta file containing the genome-wide protein set of Pelodictyon phaeoclathratiforme BU-1 from Ensembl Genomes.
DOI: 10.6084/m9.figshare.c.3617777_d3.v1
title: Additional file 10: of Contact diaries versus wearable proximity sensors in measuring contact patterns at a conference: method comparison and participantsâ   attitudes

description: Demographic data. (CSV 4 kb)
DOI: 10.17863/cam.54503
title: Theoretical model of the VPS39 zinc finger domain

description: VPS39 C-terminal domain residues predicted to bind zinc were identified via generation of a homology model using I-TASSER version 5.142 with the structure of S. cerevisiae Pcf11 (PDB ID: 2NAX) as the template.
DOI: 10.6084/m9.figshare.c.3617777_d4.v1
title: Additional file 12: of Contact diaries versus wearable proximity sensors in measuring contact patterns at a conference: method comparison and participantsâ   attitudes

description: Questionnaire analysis. (DO 10 kb)
DOI: 10.6084/m9.figshare.c.3617783_d1.v1
title: Additional file 1: Table S1. of Differential diagnostic value of CD5 and CD117 expression in thoracic tumors: A large scale study of 1465 non-small cell lung cancer cases

description: Antibodies applied in this study. (XLSX 10Â kb)
DOI: 10.17863/cam.82322
title: Research data supporting the study titled 'Large Scale Discovery of Microbial Fibrillar Adhesins and Identification of Novel Members of Adhesive Domain Families'.

description: This repository includes the potential Fibrillar Adhesin-like (FA-like) proteins in Firmicutes and Actinobacteria, which where predicted within this study using a Random Forest classification approach. Next to the UniProt protein identifier, the calculated feature properties are given. Additionally, this repository contains the pdb files of the N-terminal clusters in Firmicutes, which were found in the predicted FA-like proteins with minimal 4 known stalk domains and no known adhesive domain. The structures were predicted using AlphaFold2.