cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21227/4hx3-0217
title: Deep-Depth

description: Nonlinear distortion is critical for optical communication systems with a high baud rate and a high-order modulation format. Thus, a simple and accurate method to measure the nonlinear distortion is highly desired. Although simple notch, which directly removes the certain frequency components of nonlinear system input and then measures the re-growth components of nonlinear system output, is straightforward to measure nonlinear distortion, it is only applicable to the Gaussian input. However, pulse amplitude modulation (PAM) and quadrature amplitude modulation (QAM), which are widely used in communication systems, are not Gaussian signals. In this study, we propose a deep-depth probability-maintained notch generation method for the PAM to accurately characterize the nonlinear distortion based on the signal spectrum measurement. Employing the proposed time order perturbation, the notch depth for PAM2/4/8 achieves 20/24/28 dB, which allows for a large dynamic range nonlinear distortion measurement for various modulation formats. The experiment demonstrates that the nonlinear noise power ratio could be measured within a root mean square error of 0.6 dB for the uniform PAM2/4/8 as well as the probabilistic shaped PAM4/8. The proposed method is also applicable to square QAM modulation formats because a square QAM is composed of two independent PAMs.
DOI: 10.6084/m9.figshare.c.3639251_d2
title: MOESM2 of Inoculation insensitive promoters for cell type enriched gene expression in legume roots and nodules

description: Additional file 2: Table S1. L. japonicus roots showing GUS staining when transformed with the tested promoter:GUS constructs. Table S2. Oligonucleotide primers used for amplification and cloning of promoter fragments presented in this manuscript.
DOI: 10.6084/m9.figshare.c.3639254_d1
title: MOESM2 of An engineered cryptic Hxt11 sugar transporter facilitates glucoseâ  xylose co-consumption in Saccharomyces cerevisiae

description: Additional file 2. Supplementary tables. Table S1. SNPs identified in the DS68625-evo strain by genome sequencing. Table S2. Fermentation profiles by the selected S. cerevisiae strain expressing Hxt11 and the Hxt11 N366M and N366T mutants during anaerobic batch cultivation. Table S3. Oligonucleotides used in hexose transporter strain construction. Table S4. Oligonucleotides used for construction hexokinase deletion strain. Table S5. Oligonucleotides used in qPCR. Table S6. Primers used for saturation mutagenesis of HXT11.
DOI: 10.6084/m9.figshare.c.3639281_d1
title: Additional file 1: of TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data

description: Source code for TagDigger version 1.0. (GZ 29Â kb)
DOI: 10.21227/d0e7-zm60
title: test

description: Nonlinear distortion is critical for optical communication systems with a high baud rate and a high-order modulation format. Thus, a simple and accurate method to measure the nonlinear distortion is highly desired. Although simple notch, which directly removes the certain frequency components of nonlinear system input and then measures the re-growth components of nonlinear system output, is straightforward to measure nonlinear distortion, it is only applicable to the Gaussian input. However, pulse amplitude modulation (PAM) and quadrature amplitude modulation (QAM), which are widely used in communication systems, are not Gaussian signals. In this study, we propose a deep-depth probability-maintained notch generation method for the PAM to accurately characterize the nonlinear distortion based on the signal spectrum measurement. Employing the proposed time order perturbation, the notch depth for PAM2/4/8 achieves 20/24/28 dB, which allows for a large dynamic range nonlinear distortion measurement for various modulation formats. The experiment demonstrates that the nonlinear noise power ratio could be measured within a root mean square error of 0.6 dB for the uniform PAM2/4/8 as well as the probabilistic shaped PAM4/8. The proposed method is also applicable to square QAM modulation formats because a square QAM is composed of two independent PAMs.
DOI: 10.15468/dl.pksvyp
title: Occurrence Download

description: A dataset containing 1954 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Colombia, Ecuador)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Weinmannia rollottii Killip"
 ]
}

 The dataset includes 1954 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034133-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tqvu6d
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is North America",
 "CoordinateUncertaintyInMeters 0.0-10000.0",
 "Geometry POLYGON((-85.11676 36.55768,-70.98046 36.55768,-70.98046 42.63883,-85.11676 42.63883,-85.11676 36.55768))",
 "TaxonKey is Haemaphysalis longicornis Neumann, 1901"
 ]
}

 The dataset includes 27 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034134-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f7s3fv
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "TaxonKey is Quercus pedunculata Ehrh."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034135-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3639527_d13
title: Additional file 3: of 
                     HOTAIR and its surrogate DNA methylation signature indicate carboplatin resistance in ovarian cancer

description: Normalised beta-value DNAme data matrix that was used to identify the 67 HOTAIR -associated CpGs. This data matrix has dimensions 5000 CpGs (the 5000 most variable positions) by 134 samples; samples are annotated according to whether they are HOTAIRâ  +â  ve/-ve and type of chemotherapy received. (XLSX 9331 kb)
DOI: 10.6084/m9.figshare.c.3639536_d2
title: MOESM2 of Identification of potential protein biomarkers for early detection of pregnancy in cow urine using 2D DIGE and label free quantitation

description: Additional file 2: Table S1. List of identified proteins revealed by Max Quant Softawre.
DOI: 10.6084/m9.figshare.c.3639854_d1
title: Additional file 1: of modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks

description: All Supplementary tables are merged into single Excel file. Table S1. ROC- and PR-AUC values for 14 Human PDZ domains with artificial negative interaction data. Approximately equal number of binder and nonbinder were considered in small sets and average AUC is calculated for each domain. For SCRIBBLE1_LAP4_3, PSCDBP and NHERF2_2, equal number of non-binder peptides were randomly selected and AUC is calculated. This is repeated twice to get average AUC. Table S2. List of 43 PDZ domains included in modPDzpep testset. PDZ domains which cannot be predicted by POW are marked as ‘N’, while those used in the training are marked ‘T’. The list of test set peptides for these 43 PDZ domains is available under Benchmark link of modPDZpep server. Table S3. List of phage display peptides which showed exact match in human C-terminal proteome Table S4. Amino acid variants present on human PDZ domains. (XLS 55 kb)
DOI: 10.6084/m9.figshare.c.3639860_d2
title: Additional file 10: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Detailed GRADE assessment results. (XLS 31Â kb)
DOI: 10.6084/m9.figshare.c.3639860_d3
title: Additional file 8: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Detailed within-study risk-of-bias assessment results. (XLS 92Â kb)
DOI: 10.6084/m9.figshare.c.3639860_d4
title: Additional file 7: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Summary table of PICO characteristics for each relevant article. (XLS 65Â kb)
DOI: 10.6084/m9.figshare.c.3639860_d6
title: Additional file 6: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Citation list of all 77 relevant articles. (XLS 44Â kb)
DOI: 10.6084/m9.figshare.c.3639860_d9
title: Additional file 4: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Correlation values from previous studies. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3639860_d12
title: Additional file 11: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Sensitivity analysis of imputing different correlations for combining multiple outcome measures within a study. (XLS 29Â kb)
DOI: 10.6084/m9.figshare.c.3639860_d13
title: Additional file 12: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Sensitivity analysis of imputing different pre-post correlations for paired meta-analyses. (XLS 27Â kb)
DOI: 10.6084/m9.figshare.c.3639860_d11
title: Additional file 13: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Sensitivity analysis of comparing meta-analysis estimates for pre-post vs. pre-follow-up measurements. (XLS 26Â kb)
DOI: 10.6084/m9.figshare.c.3639863_d1
title: Additional file 6: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

description: List of probes in pathways significantly enriched based on early nutritional history in the liver. The list of differentially expressed mRNA probes comprising the pathways intermediary metabolism; oxidation-reduction; zymogens; peptidyl-prolyl-isomerases; cytoskeleton; and cell cycle that are significantly enriched based on early nutritional history in the liver are outlined in separate worksheets. Probe names highlighted in yellow were selected for RT-PCR confirmation. (XLSX 28Â kb)
DOI: 10.6084/m9.figshare.c.3639863_d5
title: Additional file 5: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

description: List of probes in pathways significantly enriched based on early nutritional history in the brain. The list of differentially expressed mRNA probes comprising the pathways neurological system process; homocysteine and methionine metabolism; and neuroendocrine peptides that are significantly enriched based on early nutritional history in the brain are outlined in separate worksheets. Probe names highlighted in yellow were selected for RT-PCR confirmation. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3639863_d6
title: Additional file 1: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

description: List of mRNA probes differentially expressed based on nutritional history in the brain and liver. The lists of 1787 (3-week + Brain) and of 924 (3-week + Liver) differentially expressed mRNA probes (fold change ≥ 1.5 and p [nutritional history] ≤ 0.05), both at the end of the early exposure (Fig. 1; 3-week, diet V vs. diet M) and in the brain or liver of juvenile trout at the end of the V-challenge (Fig. 1; V-his vs. M-his). The list of 159 probes with overlapping significant expression profiles in both brain and liver comparisons is shown in a separate worksheet. Probe names highlighted in yellow were selected for RT-PCR confirmation. (XLSX 216 kb)
DOI: 10.6084/m9.figshare.c.3640139_d10
title: Additional file 27: of Ascertainment bias from imputation methods evaluation in wheat

description: Best linear unbiased predictors (BLUPs) for each genotype for days to heading. (txt 8 kb)
DOI: 10.6084/m9.figshare.c.3640139_d11
title: Additional file 19: of Ascertainment bias from imputation methods evaluation in wheat

description: Barley SNP marker map. Markers, chromosome and position (cM) are presented as columns. (txt 18 kb)
DOI: 10.6084/m9.figshare.c.3640139_d13
title: Additional file 24: of Ascertainment bias from imputation methods evaluation in wheat

description: Wheat GBS dataset with 35 % missing information. Genotypes are presented as rows and SNPs as columns. (txt 16.3 Mb)
DOI: 10.6084/m9.figshare.c.3640139_d14
title: Additional file 18: of Ascertainment bias from imputation methods evaluation in wheat

description: Barley SNP marker score array. Genotypes are presented as rows and SNPs as columns. (txt 278 kb)
DOI: 10.6084/m9.figshare.c.3640139_d16
title: Additional file 25: of Ascertainment bias from imputation methods evaluation in wheat

description: Wheat GBS bin map for 35 % coverage. Markers, chromosome and position (bins) are presented as columns. (txt 287 kb)
DOI: 10.6084/m9.figshare.c.3640139_d20
title: Additional file 28: of Ascertainment bias from imputation methods evaluation in wheat

description: Best linear unbiased predictors (BLUPs) for each genotype for thousands kernel weight. (txt 9 kb)
DOI: 10.6084/m9.figshare.c.3640139_d23
title: Additional file 20: of Ascertainment bias from imputation methods evaluation in wheat

description: Wheat GBS dataset with 50 % missing information. Genotypes are presented as rows and SNPs as columns. (txt 16.3 Mb)
DOI: 10.6084/m9.figshare.c.3640139_d24
title: Additional file 21: of Ascertainment bias from imputation methods evaluation in wheat

description: Wheat GBS bin map for 50 % coverage. Markers, chromosome and position (bins) are presented as columns. (txt 287 kb)
DOI: 10.6084/m9.figshare.c.3640139_d25
title: Additional file 22: of Ascertainment bias from imputation methods evaluation in wheat

description: Wheat GBS dataset with 25 % missing information. Genotypes are presented as rows and SNPs as columns. (txt 16.3 Mb)
DOI: 10.6084/m9.figshare.c.3640139_d29
title: Additional file 23: of Ascertainment bias from imputation methods evaluation in wheat

description: Wheat GBS bin map for 25 % coverage. Markers, chromosome and position (bins) are presented as columns. (txt 287 kb)
DOI: 10.6084/m9.figshare.c.3640142_d1
title: Additional file 2: of Ex vivo immunosuppressive effects of mesenchymal stem cells on Crohn’s disease mucosal T cells are largely dependent on indoleamine 2,3-dioxygenase activity and cell-cell contact

description: Mesenchymal stem cells with T cells from non-inflamed Crohn’s mucosa. Representative time-lapse imaging of a co-culture with bone marrow-derived mesenchymal stem cells of a healthy donor and T cells isolated from non-inflamed mucosa of a patient with Crohn’s disease. A slow and continuous interaction is evident, and a few cells with morphological features of apoptosis (those with nuclear fragmentation and cellular swelling) and apoptotic bodies become evident at the end of the period of registration. The images were serially recorded every 30 min for 12 h. Magnification: 100×. (ZIP 6800 kb)
DOI: 10.6084/m9.figshare.c.3640367_d3
title: Additional file 6: Figure S4. of CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation

description: Relationship between the p value threshold for SNP inclusion and trait clustering. a Similar clusters for obesity (I), autoimmunity (II), and atherosclerosis (III) are observed with the different p value thresholds. Therefore, the detection of informative clusters is robust to varying the number of SNPs in the analysis, although traits are lost as the p value threshold is made more stringent. In all cases, the number of clusters (k) in the analysis was set to 20. The locations of the three clusters were also marked in the entire dendrogram and heat map of pairwise human traits for the p value threshold of 10â  5 (b), 10â  7 (c) and 10â  10 (d). (ZIP 3188 kb)
DOI: 10.6084/m9.figshare.c.3640367_d8
title: Additional file 3: Table S2. of CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation

description: CPAG results based on NHGRI GWAS Catalog (last visit on 4 September 2013). Listed are associated diseaseâ  trait pairs and counts of overlap based on the SNP, SNP_LD, and gene-based methods. Based on these counts, a series of statistical tests were done to test the significance of the similarity, including Fisherâ  s exact test, an empirical permutations test (10,000 permutations), hypergeometric test and binomial test. The last three columns list the overlapping genes, SNPs and SNPs in LD. (XLSX 1076 kb)
DOI: 10.6084/m9.figshare.c.3640571_d1
title: Additional file 2 of Parameterizing sequence alignment with an explicit evolutionary model

description: Tarball that contains the source code for the programs introduced in this manuscript, as well as the Perl scripts used to generate the experiments in this work and the results of the experiments. (ZIP 42,496 kb)
DOI: 10.6084/m9.figshare.c.3640580_d1
title: Additional file 1: of The cervix as a natural tamponade in postpartum hemorrhage caused by placenta previa and placenta previa accreta: a prospective study

description: Cervical Inversion_placenta accreta. This is a movie file showing detailed steps of the technique of cervical inversion. (XML 7 kb)
DOI: 10.6084/m9.figshare.c.3640583_d4
title: Additional file 13: Table S7. of New genes drive the evolution of gene interaction networks in the human and mouse genomes

description: Gene age datasets used in this study. (XLS 5395 kb)
DOI: 10.6084/m9.figshare.c.3640595_d1
title: Additional file 12: Table S10. of Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research

description: BLASTn results of the putative sex chromosome contigs (chromosome X and Y) queried against the arthropoda database in GenBank. (XLSX 729Â kb)
DOI: 10.6084/m9.figshare.c.3640805_d4
title: Additional file 14: of Coordinated inhibition of C/EBP by Tribbles in multiple tissues is essential for Caenorhabditis elegans development

description: Primary data for Figs.Â 3b, c, k and 5b and Figures S4a and S6b. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3640805_d6
title: Additional file 8: Table S1. of Coordinated inhibition of C/EBP by Tribbles in multiple tissues is essential for Caenorhabditis elegans development

description: List of CEBP-1 target genes and hierarchical clustering of genes and functional classes (XLSX 64Â kb)
DOI: 10.6084/m9.figshare.c.3640805_d9
title: Additional file 11: Table S2. of Coordinated inhibition of C/EBP by Tribbles in multiple tissues is essential for Caenorhabditis elegans development

description: List of strains and alleles. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3640805_d10
title: Additional file 12: Table S3. of Coordinated inhibition of C/EBP by Tribbles in multiple tissues is essential for Caenorhabditis elegans development

description: List of plasmids and primers used for qRT-PCR. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3640811_d4
title: Additional file 7: Table S2. of Molecular analysis of the Sydney rock oyster (Saccostrea glomerata) CO2 stress response

description: S. glomerata DE transcripts. List of 1626 DE transcripts determined with Bowtie-RSEM-EBSeq, using a FDR threshold of 0.05. Sequence descriptions are based on blast homology searches against the NCBI nr database (e-value cut-off: 10-5, hit number threshold: 25), and on InterProScan domain/family information. Posterior fold change (FC) was based on the normalised data, whereas real FC was based on the raw data. C1 stands for control, C2 for treatment condition. (XLSX 124 kb)
DOI: 10.6084/m9.figshare.c.3640817_d1
title: MOESM3 of Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

description: Additional file 3. Results of genotype accuracy analyses. Genotype accuracy analyses were performed by comparing sequence-derived genotypes and those obtained using the high-density SNP bead chip for 152 samples (39 Holstein, 49 Montbéliarde, 41 Normande and 23 Blonde d’Aquitaine).
DOI: 10.6084/m9.figshare.c.3640817_d2
title: MOESM4 of Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

description: Additional file 4. List of LoF and deleterious missense variants for which no homozygous individual for the alternative allele was observed in our samples. For each variant, overall and per breed genotype (0/0, 0/1 and 1/1) distribution as well as the frequency for the alternative allele are indicated. The functional annotation results and SIFT predictions are also indicated.
DOI: 10.6084/m9.figshare.c.3640817_d4
title: MOESM1 of Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

description: Additional file 1. Summary of sequence coverage and sequence alignment to the reference genome. Total and mapped reads, as well as total and percent of correctly mapped reads are indicated for each sample. The estimated sequence coverage was also obtained for each sample.
DOI: 10.6084/m9.figshare.c.3641021_d3
title: Additional file 12: of De novo assembly and transcriptome analysis of Plasmodium gallinaceum identifies the Rh5 interacting protein (ripr), and reveals a lack of EBL and RH gene family diversification

description: Annotation file for the assembly with quality trimming.
DOI: 10.6084/m9.figshare.c.3641021_d5
title: Additional file 8: of De novo assembly and transcriptome analysis of Plasmodium gallinaceum identifies the Rh5 interacting protein (ripr), and reveals a lack of EBL and RH gene family diversification

description: Mapping file for the assembly without quality trimming.
DOI: 10.6084/m9.figshare.c.3641021_d6
title: Additional file 13: of De novo assembly and transcriptome analysis of Plasmodium gallinaceum identifies the Rh5 interacting protein (ripr), and reveals a lack of EBL and RH gene family diversification

description: Mapping file for the assembly with quality trimming.
DOI: 10.6084/m9.figshare.c.3641021_d8
title: Additional file 14: of De novo assembly and transcriptome analysis of Plasmodium gallinaceum identifies the Rh5 interacting protein (ripr), and reveals a lack of EBL and RH gene family diversification

description: Sequence table file for the assembly with quality trimming.
DOI: 10.6084/m9.figshare.c.3641021_d12
title: Additional file 15: of De novo assembly and transcriptome analysis of Plasmodium gallinaceum identifies the Rh5 interacting protein (ripr), and reveals a lack of EBL and RH gene family diversification

description: KEGG pathway file for the assembly with quality trimming.
DOI: 10.6084/m9.figshare.c.3641021_d11
title: Additional file 10: of De novo assembly and transcriptome analysis of Plasmodium gallinaceum identifies the Rh5 interacting protein (ripr), and reveals a lack of EBL and RH gene family diversification

description: KEGG pathway file for the assembly without quality trimming.
DOI: 10.6084/m9.figshare.c.3641021_d14
title: Additional file 9: of De novo assembly and transcriptome analysis of Plasmodium gallinaceum identifies the Rh5 interacting protein (ripr), and reveals a lack of EBL and RH gene family diversification

description: Sequence table file for the assembly without quality trimming.