cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20250442
title: Additional file 2 of Genome of the hoverfly Eupeodes corollae provides insights into the evolution of predation and pollination in insects

description: Additional file 2: Table S5. GO enrichment analysis of Syrphidae-specific genes (Fisher’s exact test, p &lt; 0.05). Table S6. GO enrichment analysis of species-specific genes of Eupeodes corollae (Fisher’s exact test, p &lt; 0.05). Table S7. GO enrichment analysis of the homologous genes shared between Eupeodes corollae and Scaeva pyrastri (Fisher’s exact test, p &lt; 0.05). Table S8. GO enrichment analysis of the homologous genes shared between Eupeodes corollae and ladybugs (Fisher’s exact test, p &lt; 0.05). Table S9. GO enrichment analysis of the homologous genes shared between Eupeodes corollae and honeybees (Fisher’s exact test, p &lt; 0.05). Table S10. Differentially expressed genes in adults compared to larvae stage in Eupeodes corollae.
DOI: 10.6084/m9.figshare.20250442.v1
title: Additional file 2 of Genome of the hoverfly Eupeodes corollae provides insights into the evolution of predation and pollination in insects

description: Additional file 2: Table S5. GO enrichment analysis of Syrphidae-specific genes (Fisher’s exact test, p &lt; 0.05). Table S6. GO enrichment analysis of species-specific genes of Eupeodes corollae (Fisher’s exact test, p &lt; 0.05). Table S7. GO enrichment analysis of the homologous genes shared between Eupeodes corollae and Scaeva pyrastri (Fisher’s exact test, p &lt; 0.05). Table S8. GO enrichment analysis of the homologous genes shared between Eupeodes corollae and ladybugs (Fisher’s exact test, p &lt; 0.05). Table S9. GO enrichment analysis of the homologous genes shared between Eupeodes corollae and honeybees (Fisher’s exact test, p &lt; 0.05). Table S10. Differentially expressed genes in adults compared to larvae stage in Eupeodes corollae.
DOI: 10.6084/m9.figshare.20250444
title: Additional file 1 of Extracellular vesicle miR-32 derived from macrophage promotes arterial calcification in mice with type 2 diabetes via inhibiting VSMC autophagy

description: Additional file 1. MS analyze the interaction protein of Mef2d.
DOI: 10.6084/m9.figshare.20250444.v1
title: Additional file 1 of Extracellular vesicle miR-32 derived from macrophage promotes arterial calcification in mice with type 2 diabetes via inhibiting VSMC autophagy

description: Additional file 1. MS analyze the interaction protein of Mef2d.
DOI: 10.6084/m9.figshare.20250447
title: Additional file 2 of Extracellular vesicle miR-32 derived from macrophage promotes arterial calcification in mice with type 2 diabetes via inhibiting VSMC autophagy

description: Additional file 2. Transcriptome sequencing analyze the influence of macrophage for genes expression in VSMC.
DOI: 10.6084/m9.figshare.20250447.v1
title: Additional file 2 of Extracellular vesicle miR-32 derived from macrophage promotes arterial calcification in mice with type 2 diabetes via inhibiting VSMC autophagy

description: Additional file 2. Transcriptome sequencing analyze the influence of macrophage for genes expression in VSMC.
DOI: 10.6084/m9.figshare.21299026
title: Additional file 4 of Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

description: Additional file 4: Table S1. Detailed information of all 138 TaRING zinc finger genes identified in tomato genome.
DOI: 10.6084/m9.figshare.21299026.v1
title: Additional file 4 of Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

description: Additional file 4: Table S1. Detailed information of all 138 TaRING zinc finger genes identified in tomato genome.
DOI: 10.6084/m9.figshare.12910410
title: Additional file 13 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 13: Figure S2. The intron sequence deletion of rpoC1 gene of Avena atlantica (2049 bp; GWHAOPC01000000) and Triticum urartu (2052 bp; NC021762.1) compared to Taraxacum amplum (2746 bp; KX499525.1). a The 688 bp intron deletion marked by two black arrows in alignment sequences. b-n The rpoC1 sequence alignment 1–2746 bp of A. atlantica, Triticum urartu and Taraxacum amplum.
DOI: 10.6084/m9.figshare.12910410.v1
title: Additional file 13 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 13: Figure S2. The intron sequence deletion of rpoC1 gene of Avena atlantica (2049 bp; GWHAOPC01000000) and Triticum urartu (2052 bp; NC021762.1) compared to Taraxacum amplum (2746 bp; KX499525.1). a The 688 bp intron deletion marked by two black arrows in alignment sequences. b-n The rpoC1 sequence alignment 1–2746 bp of A. atlantica, Triticum urartu and Taraxacum amplum.
DOI: 10.6084/m9.figshare.21299029
title: Additional file 5 of Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

description: Additional file 5: Table S2. One-to-one orthologous relationships among T.aestivum and T.aestivum, A.thaliana, A. tauschii, B. distachyon, H. vulgare, rice, S.italica and Zea mays, respectively.
DOI: 10.6084/m9.figshare.21299029.v1
title: Additional file 5 of Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

description: Additional file 5: Table S2. One-to-one orthologous relationships among T.aestivum and T.aestivum, A.thaliana, A. tauschii, B. distachyon, H. vulgare, rice, S.italica and Zea mays, respectively.
DOI: 10.6084/m9.figshare.12910416
title: Additional file 15 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 15: Figure S4. Comparison of border distance between adjacent genes and junctions of the LSC, SSC and two IR regions among (a) eleven Avena species and Triticum aestivum plastomes, and (b) fourteen Avena species plastomes available in NCBI. The adjacent border genes are denoted by colored boxes. The gaps between genes and the borders are denoted by the base pair (bp) lengths. The figure is not to scale with respect to sequence length and only shows relative changes near the IR/SC borders
DOI: 10.6084/m9.figshare.12910416.v1
title: Additional file 15 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 15: Figure S4. Comparison of border distance between adjacent genes and junctions of the LSC, SSC and two IR regions among (a) eleven Avena species and Triticum aestivum plastomes, and (b) fourteen Avena species plastomes available in NCBI. The adjacent border genes are denoted by colored boxes. The gaps between genes and the borders are denoted by the base pair (bp) lengths. The figure is not to scale with respect to sequence length and only shows relative changes near the IR/SC borders
DOI: 10.6084/m9.figshare.21299032
title: Additional file 6 of Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

description: Additional file 6: Table S3. The information of cis-acting elements on the promoters of T. aestivum RING-zf genes.
DOI: 10.6084/m9.figshare.21299032.v1
title: Additional file 6 of Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

description: Additional file 6: Table S3. The information of cis-acting elements on the promoters of T. aestivum RING-zf genes.
DOI: 10.6084/m9.figshare.21299035
title: Additional file 7 of Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

description: Additional file 7: Table S4. The information of transcriptome data of T. aestivum RING-zf genes.
DOI: 10.6084/m9.figshare.21299035.v1
title: Additional file 7 of Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

description: Additional file 7: Table S4. The information of transcriptome data of T. aestivum RING-zf genes.
DOI: 10.6084/m9.figshare.21299038
title: Additional file 8 of Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

description: Additional file 8: Table S5. The list of primers.
DOI: 10.6084/m9.figshare.21299038.v1
title: Additional file 8 of Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

description: Additional file 8: Table S5. The list of primers.
DOI: 10.6084/m9.figshare.12910443
title: Additional file 3 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 3: Table S3. Nucleotide diversity (Pi) analyses of 13 Avena species (two congeneric species download from NCBI) and Triticum aestivum_NC002762.1 plastomes computed by DnaSP v.6 [29]. a Pi values of 131 plastid genes. The rps12 is treated as three parts as the second gene divided into two independent transcription units. b Pi values of 130 intergenic regions.
DOI: 10.6084/m9.figshare.12910443.v1
title: Additional file 3 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 3: Table S3. Nucleotide diversity (Pi) analyses of 13 Avena species (two congeneric species download from NCBI) and Triticum aestivum_NC002762.1 plastomes computed by DnaSP v.6 [29]. a Pi values of 131 plastid genes. The rps12 is treated as three parts as the second gene divided into two independent transcription units. b Pi values of 130 intergenic regions.
DOI: 10.6084/m9.figshare.20250477
title: Additional file 1 of Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome

description: Additional file 1: Table S1. Detailed information on all infant antibiotic exposures.
DOI: 10.6084/m9.figshare.12910446
title: Additional file 4 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 4: Table S4. Repetitive motif abundance in eleven Avena species and dandelion (Taraxacum amplum) plastomes computed by REPuter [30] and Phobos [31]. a Repetitive motif abundance computed by REPuter. F, P, R and C indicate the repeat types forward, palindrome, reverse and complement repeat, respectively. b Repeat type statistic analysis computed by REPuter. F, P, R and C indicate the repeat types forward, palindrome, reverse and complement, respectively. c Repeat distribution statistic analysis. LSC, SSC, IR, IGS and CDS indicate large single-copy, small single-copy, inverted repeat regions, intergenic and protein-coding sequences, respectively. d Tandem repeat abundance computed by Phobos. e Tandem repeat distribution statistic analysis.
DOI: 10.6084/m9.figshare.20250477.v1
title: Additional file 1 of Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome

description: Additional file 1: Table S1. Detailed information on all infant antibiotic exposures.
DOI: 10.6084/m9.figshare.12910446.v1
title: Additional file 4 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 4: Table S4. Repetitive motif abundance in eleven Avena species and dandelion (Taraxacum amplum) plastomes computed by REPuter [30] and Phobos [31]. a Repetitive motif abundance computed by REPuter. F, P, R and C indicate the repeat types forward, palindrome, reverse and complement repeat, respectively. b Repeat type statistic analysis computed by REPuter. F, P, R and C indicate the repeat types forward, palindrome, reverse and complement, respectively. c Repeat distribution statistic analysis. LSC, SSC, IR, IGS and CDS indicate large single-copy, small single-copy, inverted repeat regions, intergenic and protein-coding sequences, respectively. d Tandem repeat abundance computed by Phobos. e Tandem repeat distribution statistic analysis.
DOI: 10.6084/m9.figshare.20250480
title: Additional file 2 of Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome

description: Additional file 2: Table S2. Summary sample size by body sites, postnatal ages, gestational ages, antibiotic treatment groups, and collection times.
DOI: 10.6084/m9.figshare.20250480.v1
title: Additional file 2 of Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome

description: Additional file 2: Table S2. Summary sample size by body sites, postnatal ages, gestational ages, antibiotic treatment groups, and collection times.
DOI: 10.6084/m9.figshare.12910449
title: Additional file 5 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 5: Table S5. Simple sequence repeat (SSR) sequences in eleven Avena species plastomes computed by Perlscript MicroSAtellite (MISA) [32]. a SSR sequence abundance. b SSR sequence distribution. IGS: intergenic sequences; CDS: protein-coding sequences; p1: mononucleotide repeat; p2: dinucleotide repeat; p3: trinucleotide repeat; p4: tetranucleotide repeat; c: composite SSR
DOI: 10.6084/m9.figshare.12910449.v1
title: Additional file 5 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 5: Table S5. Simple sequence repeat (SSR) sequences in eleven Avena species plastomes computed by Perlscript MicroSAtellite (MISA) [32]. a SSR sequence abundance. b SSR sequence distribution. IGS: intergenic sequences; CDS: protein-coding sequences; p1: mononucleotide repeat; p2: dinucleotide repeat; p3: trinucleotide repeat; p4: tetranucleotide repeat; c: composite SSR
DOI: 10.6084/m9.figshare.20774771
title: Testing Stability in Functional Event Observations with an Application to IPO Performance

description: Many sequentially observed functional data objects are available only at the times of certain events. For example, the trajectory of stock prices of companies after their initial public offering (IPO) can be observed when the offering occurs, and the resulting data may be affected by changing circumstances. It is of interest to investigate whether the mean behavior of such functions is stable over time, and if not, to estimate the times at which apparent changes occur. Since the frequency of events may fluctuates over time, we propose a change point analysis that has two steps. In the first step, we segment the series into segments in which the frequency of events is approximately homogeneous using a new binary segmentation procedure for event frequencies. After adjusting the observed curves in each segment based on the frequency of events, we proceed in the second step by developing a method to test for and estimate change points in the mean of the observed functional data objects. We establish the consistency and asymptotic distribution of the change point detector and estimator in both steps, and study their performance using Monte Carlo simulations. An application to IPO performance data illustrates the proposed methods.
DOI: 10.6084/m9.figshare.20774771.v2
title: Testing Stability in Functional Event Observations with an Application to IPO Performance

description: Many sequentially observed functional data objects are available only at the times of certain events. For example, the trajectory of stock prices of companies after their initial public offering (IPO) can be observed when the offering occurs, and the resulting data may be affected by changing circumstances. It is of interest to investigate whether the mean behavior of such functions is stable over time, and if not, to estimate the times at which apparent changes occur. Since the frequency of events may fluctuates over time, we propose a change point analysis that has two steps. In the first step, we segment the series into segments in which the frequency of events is approximately homogeneous using a new binary segmentation procedure for event frequencies. After adjusting the observed curves in each segment based on the frequency of events, we proceed in the second step by developing a method to test for and estimate change points in the mean of the observed functional data objects. We establish the consistency and asymptotic distribution of the change point detector and estimator in both steps, and study their performance using Monte Carlo simulations. An application to IPO performance data illustrates the proposed methods.
DOI: 10.6084/m9.figshare.12910452
title: Additional file 6 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 6: Table S6. Statistics between tandem repeats, indels and SNPs of plastome alignments between eleven Avena species presented here available in Genome Warehouse database and two Avena species available in NCBI (NC031650.1 and NC027468.1) with A. sativa_Liu312 as a reference. (a) Tandem repeats detected in Avena sativa_312 chloroplast genome using Phobos [31]. (b) Information of indels and SNPs in the complete chloroplast genome alignments.
DOI: 10.6084/m9.figshare.20774771.v1
title: Testing Stability in Functional Event Observations with an Application to IPO Performance

description: Many sequentially observed functional data objects are available only at the times of certain events. For example, the trajectory of stock prices of companies after their initial public offering (IPO) can be observed when the offering occurs, and the resulting data may be affected by changing circumstances. It is of interest to investigate whether the mean behaviour of such functions is stable over time, and if not, to estimate the times at which apparent changes occur. Since the frequency of events may fluctuates over time, we propose a change point analysis that has two steps. In the first step, we segment the series into segments in which the frequency of events is approximately homogeneous using a new binary segmentation procedure for event frequencies. After adjusting the observed curves in each segment based on the frequency of events, we proceed in the second step by developing a method to test for and estimate change points in the mean of the observed functional data objects. We establish the consistency and asymptotic distribution of the change point detector and estimator in both steps, and study their performance using Monte Carlo simulations. An application to IPO performance data illustrates the proposed methods.
DOI: 10.6084/m9.figshare.12910452.v1
title: Additional file 6 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 6: Table S6. Statistics between tandem repeats, indels and SNPs of plastome alignments between eleven Avena species presented here available in Genome Warehouse database and two Avena species available in NCBI (NC031650.1 and NC027468.1) with A. sativa_Liu312 as a reference. (a) Tandem repeats detected in Avena sativa_312 chloroplast genome using Phobos [31]. (b) Information of indels and SNPs in the complete chloroplast genome alignments.
DOI: 10.6084/m9.figshare.20250483
title: Additional file 3 of Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome

description: Additional file 3: Table S3. Raw genus count data.
DOI: 10.6084/m9.figshare.20250483.v1
title: Additional file 3 of Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome

description: Additional file 3: Table S3. Raw genus count data.
DOI: 10.6084/m9.figshare.12910455
title: Additional file 7 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 7: Table S7. The number and presence statistics of tandem repeats, indels and SNPs of plastome alignments between eleven Avena species presented here and two Avena species available in NCBI (NC031650.1 and NC027468.1) with A. sativa_Liu312 as a reference within each 150 bp window.
DOI: 10.6084/m9.figshare.12910455.v1
title: Additional file 7 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 7: Table S7. The number and presence statistics of tandem repeats, indels and SNPs of plastome alignments between eleven Avena species presented here and two Avena species available in NCBI (NC031650.1 and NC027468.1) with A. sativa_Liu312 as a reference within each 150 bp window.
DOI: 10.6084/m9.figshare.20250486
title: Additional file 4 of Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome

description: Additional file 4: Table S4. Raw species count data.
DOI: 10.6084/m9.figshare.20250486.v1
title: Additional file 4 of Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome

description: Additional file 4: Table S4. Raw species count data.
DOI: 10.6084/m9.figshare.20250489
title: Additional file 5 of Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome

description: Additional file 5: Table S5. Microbial pathway abundance data.
DOI: 10.6084/m9.figshare.20250489.v1
title: Additional file 5 of Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome

description: Additional file 5: Table S5. Microbial pathway abundance data.
DOI: 10.6084/m9.figshare.12910458
title: Additional file 8 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 8: Table S8. Maximum likelihood parameter estimates and substitutions for the 27 plastid genes (atpA, atpE, atpF, atpI, ccsA, infA, matK, ndhA, ndhB, ndhD, ndhF, ndhH, ndhI, petA, psbA, rbcL, rpl2, rpl32, rpl33, rpoA, rpoB, rpoC1, rpoC2, rps2, rps3, rps11, and ycf4).
DOI: 10.6084/m9.figshare.12910458.v1
title: Additional file 8 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 8: Table S8. Maximum likelihood parameter estimates and substitutions for the 27 plastid genes (atpA, atpE, atpF, atpI, ccsA, infA, matK, ndhA, ndhB, ndhD, ndhF, ndhH, ndhI, petA, psbA, rbcL, rpl2, rpl32, rpl33, rpoA, rpoB, rpoC1, rpoC2, rps2, rps3, rps11, and ycf4).
DOI: 10.6084/m9.figshare.12910461
title: Additional file 9 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 9: Table S9. GC percent and codon usage for Avena plastomes computed by CodonW v.1.4.2 [38]. a Genomic GC percent and codon usage statistic analysis. b The third codon usage statistic analysis.