cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13181538.v1
title: Additional file 11 of A phylogenomic study of Steganinae fruit flies (Diptera: Drosophilidae): strong gene tree heterogeneity and evidence for monophyly

description: Additional file 4: BUSCO_cleaning_pipeline.txt: shell pipeline for curating BUSCO results.
DOI: 10.6084/m9.figshare.13181526.v1
title: Additional file 13 of A phylogenomic study of Steganinae fruit flies (Diptera: Drosophilidae): strong gene tree heterogeneity and evidence for monophyly

description: Additional file 13: supermatrix2.txt: awk script that concatenates alignments in MEGA format, preparing the data for a supermatrix analysis.
DOI: 10.6084/m9.figshare.13181574
title: Additional file 1 of Influence of socio-economic, demographic and climate factors on the regional distribution of dengue in the United States and Mexico

description: Additional file 1. Species distribution methods and results to estimate receptivity + model diagnostics (all models).
DOI: 10.6084/m9.figshare.13181574.v1
title: Additional file 1 of Influence of socio-economic, demographic and climate factors on the regional distribution of dengue in the United States and Mexico

description: Additional file 1. Species distribution methods and results to estimate receptivity + model diagnostics (all models).
DOI: 10.6084/m9.figshare.13181599
title: Additional file 4 of Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

description: Additional file 4.
DOI: 10.6084/m9.figshare.13181599.v1
title: Additional file 4 of Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

description: Additional file 4.
DOI: 10.6084/m9.figshare.13181605
title: Additional file 6 of Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

description: Additional file 6.
DOI: 10.6084/m9.figshare.13181605.v1
title: Additional file 6 of Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

description: Additional file 6.
DOI: 10.6084/m9.figshare.13181584.v1
title: Additional file 10 of Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

description: Additional file 10.
DOI: 10.6084/m9.figshare.13181590.v1
title: Additional file 1 of Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

description: Additional file 1.
DOI: 10.6084/m9.figshare.13181590
title: Additional file 1 of Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

description: Additional file 1.
DOI: 10.6084/m9.figshare.13181587.v1
title: Additional file 11 of Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

description: Additional file 11.
DOI: 10.6084/m9.figshare.13181587
title: Additional file 11 of Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

description: Additional file 11.
DOI: 10.6084/m9.figshare.13181611
title: Additional file 8 of Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

description: Additional file 8.
DOI: 10.6084/m9.figshare.13181611.v1
title: Additional file 8 of Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

description: Additional file 8.
DOI: 10.6084/m9.figshare.13181584
title: Additional file 10 of Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

description: Additional file 10.
DOI: 10.6084/m9.figshare.13181596
title: Additional file 3 of Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

description: Additional file 3.
DOI: 10.6084/m9.figshare.13181596.v1
title: Additional file 3 of Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa

description: Additional file 3.
DOI: 10.6084/m9.figshare.13181653
title: Additional file 6 of A simple, cost-effective high-throughput image analysis pipeline improves genomic prediction accuracy for days to maturity in wheat

description: Additional file 6: Table S3. provides information about the members of each subpopulation.
DOI: 10.6084/m9.figshare.13181653.v1
title: Additional file 6 of A simple, cost-effective high-throughput image analysis pipeline improves genomic prediction accuracy for days to maturity in wheat

description: Additional file 6: Table S3. provides information about the members of each subpopulation.
DOI: 10.6084/m9.figshare.13181638.v1
title: Additional file 1 of A simple, cost-effective high-throughput image analysis pipeline improves genomic prediction accuracy for days to maturity in wheat

description: Additional file 1: Tables S1. and S2 are lists of the 199 landraces and 87 cultivars from Iran bread wheat germplasm used in the present study.
DOI: 10.6084/m9.figshare.13181644.v1
title: Additional file 3 of A simple, cost-effective high-throughput image analysis pipeline improves genomic prediction accuracy for days to maturity in wheat

description: Additional file 3: Scripts S1. and S2 are defined function and written code in MATLAB.
DOI: 10.6084/m9.figshare.13181638
title: Additional file 1 of A simple, cost-effective high-throughput image analysis pipeline improves genomic prediction accuracy for days to maturity in wheat

description: Additional file 1: Tables S1. and S2 are lists of the 199 landraces and 87 cultivars from Iran bread wheat germplasm used in the present study.
DOI: 10.6084/m9.figshare.13181661.v1
title: Additional file 2 of “Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”

description: Additional file 2 Supplementary Table S1. Description of the genomic regions sequenced in T. harzianum IOC3844.
DOI: 10.6084/m9.figshare.13181661
title: Additional file 2 of “Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”

description: Additional file 2 Supplementary Table S1. Description of the genomic regions sequenced in T. harzianum IOC3844.
DOI: 10.6084/m9.figshare.13181664
title: Additional file 3 of “Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”

description: Additional file 3 Supplementary Table S4. Annotation of all genes predicted in T. harzianum IOC3844.
DOI: 10.6084/m9.figshare.13181667.v1
title: Additional file 4 of “Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”

description: Additional file 4 Supplementary Table S5. Description of the EC codes for T. harzianum IOC3844 genes.
DOI: 10.6084/m9.figshare.13181667
title: Additional file 4 of “Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”

description: Additional file 4 Supplementary Table S5. Description of the EC codes for T. harzianum IOC3844 genes.
DOI: 10.6084/m9.figshare.13181676.v1
title: Additional file 7 of “Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”

description: Additional file 7 FASTA sequences of proteins secreted in T. harzianum IOC3844 under cellulose conditions developed in the work of Horta et al., 2018.
DOI: 10.6084/m9.figshare.13181644
title: Additional file 3 of A simple, cost-effective high-throughput image analysis pipeline improves genomic prediction accuracy for days to maturity in wheat

description: Additional file 3: Scripts S1. and S2 are defined function and written code in MATLAB.
DOI: 10.6084/m9.figshare.13181673
title: Additional file 6 of “Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”

description: Additional file 6 Supplementary Table S7. Expression levels of the genes annotated in T. harzianum IOC3844 by means of RNA-Seq.
DOI: 10.6084/m9.figshare.13181664.v1
title: Additional file 3 of “Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”

description: Additional file 3 Supplementary Table S4. Annotation of all genes predicted in T. harzianum IOC3844.
DOI: 10.6084/m9.figshare.13181670
title: Additional file 5 of “Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”

description: Additional file 5 Supplementary Table S6. Description of the CAZyme genes in T. harzianum IOC3844.
DOI: 10.6084/m9.figshare.13181670.v1
title: Additional file 5 of “Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”

description: Additional file 5 Supplementary Table S6. Description of the CAZyme genes in T. harzianum IOC3844.
DOI: 10.6084/m9.figshare.13181676
title: Additional file 7 of “Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”

description: Additional file 7 FASTA sequences of proteins secreted in T. harzianum IOC3844 under cellulose conditions developed in the work of Horta et al., 2018.
DOI: 10.6084/m9.figshare.13181673.v1
title: Additional file 6 of “Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”

description: Additional file 6 Supplementary Table S7. Expression levels of the genes annotated in T. harzianum IOC3844 by means of RNA-Seq.
DOI: 10.6084/m9.figshare.13181712.v1
title: Additional file 1 of Report on planning comparison of VMAT, IMRT and helical tomotherapy for the ESCALOX-trial pre-study

description: Additional file 1. Raw data from DVH for analysis of plan comparison parameter.
DOI: 10.6084/m9.figshare.13181712
title: Additional file 1 of Report on planning comparison of VMAT, IMRT and helical tomotherapy for the ESCALOX-trial pre-study

description: Additional file 1. Raw data from DVH for analysis of plan comparison parameter.
DOI: 10.14768/2ddaba56-cf61-4d5b-83b7-e4a079ed836b
title: A study of daytime convective vortices and turbulence in the martian Planetary Boundary Layer based on half-a-year of InSight atmospheric measurements and Large-Eddy Simulations

description: The data archive contains all data and codes supporting the analysis in the paper A study of daytime convective vortices and turbulence in the martian Planetary Boundary Layer based on half-a-year of InSight atmospheric measurements and Large-Eddy Simulations, A. Spiga et al., Journal of Geophysical Research – Planets. This paper is also available on arxiv https://arxiv.org/abs/2005.01134. All InSight calibrated data used to produce this dataset are publicly available in the Planetary Data System. Data from the APSS pressure sensor and the temperature and wind (TWINS) sensor referenced in this paper is publicly available from the PDS (Planetary Data System) Atmospheres node. The direct link to the InSight data archive at the PDS Atmospheres node is: https://atmos.nmsu.edu/data_and_services/atmospheres_data/INSIGHT/insight.html. Surface brightness temperature measured by the HP3 radiometer is publicly available from the PDS Geosciences node: https://pds-geosciences.wustl.edu/missions/insight/hp3rad.htm (DOI reference https://doi.org/10.17189/1517568).
DOI: 10.5281/zenodo.3878435
title: Three-channel surface electrogastrogram (EGG) dataset recorded during fasting and post-prandial states in 20 healthy individuals

description: This repository contains Electrogastrography signals termed Electrogastrograms (EGG) recorded with surface Ag/AgCl electrodes placed over stomach and pre-processed in 20 healthy individuals (8 Females and 12 Males). The method for EGG recording and pre-processing together with subjects' data can be found in Popović et al. 2019. For each subject, EGG was recorded from three locations before (fasting state) and after (postprandial state) a commercial oat meal (274 kcal). Two 20 minutes recordings (files) are obtained for each subject - fasting and postprandial. Naming convention for files: <strong>subjects ID _ type of recording (fasting / postprandial)</strong>. Sample rate was set at 2 Hz and A/D card had 16 bits resolution. Gain of the amplifier was set at 1000. Overall, file size is 7200 samples (2400 samples for each channel). All signals were filtered with 3<sup>rd</sup> order band-pass Butterworth filter with cut-off frequencies of 0.03 Hz and 0.25 Hz. In order to avoid phase distortion, zero-phase digital filtering was performed in Matlab R2013a by filtfilt() function. GNU Octave code for analysis of EGG signals with statistical calculations presented in Popović et al. 2019 is also provided (eggAnalysis.m). For convenient test download and appropriate preview, we provided all signals in .zip and sample signal for ID1 in .txt form. <strong>Dataset contents</strong> EGG-database.zip, data files, text format eggAnalysis.m, GNU Octave code README.txt, metadata for data files, text format ID1_fasting.txt and ID1_postprandial.txt, sample data files for subject ID1, text format <strong>Data files contain numerical values with decimal point according to the following structure</strong> column - CH1* (recorded samples from channel 1) column - CH2* (recorded samples from channel 2) column - CH3* (recorded samples from channel 3) * For exact anatomical locations for EGG channels CH1, CH2, and CH3, please refer to Popović et al. 2019. If you find these signals useful for your own research or teaching class, please cite both relevant paper and dataset as: Popović, N.B., Miljković, N. and Popović, M.B., 2019. Simple gastric motility assessment method with a single-channel electrogastrogram. <em>Biomedical Engineering/Biomedizinische Technik</em>, <em>64</em>(2), pp.177-185, doi: 10.1515/bmt-2017-0218. Popović, N.B., Miljković, N. and Popović, M.B., 2020. Three-channel surface electrogastrogram (EGG) dataset recorded during fasting and post-prandial states in 20 healthy individuals [Data set]. <em>Zenodo</em>, doi: 10.5281/zenodo.3730617. DISCLAIMER: The GNU Octave code is provided without any guarantee and it is not intended for medical purposes.
description: The third version contains additional GNU Octave file for signal analysis.
DOI: 10.5281/zenodo.3730617
title: Three-channel surface electrogastrogram (EGG) dataset recorded during fasting and post-prandial states in 20 healthy individuals

description: This repository contains Electrogastrography signals termed Electrogastrograms (EGG) recorded with surface Ag/AgCl electrodes placed over stomach and pre-processed in 20 healthy individuals (8 Females and 12 Males). The method for EGG recording and pre-processing together with subjects' data can be found in Popović et al. 2019. For each subject, EGG was recorded from three locations before (fasting state) and after (postprandial state) a commercial oat meal (274 kcal). Two 20 minutes recordings (files) are obtained for each subject - fasting and postprandial. Naming convention for files: <strong>subjects ID _ type of recording (fasting / postprandial)</strong>. Sample rate was set at 2 Hz and A/D card had 16 bits resolution. Gain of the amplifier was set at 1000. Overall, file size is 7200 samples (2400 samples for each channel). All signals were filtered with 3<sup>rd</sup> order band-pass Butterworth filter with cut-off frequencies of 0.03 Hz and 0.25 Hz. In order to avoid phase distortion, zero-phase digital filtering was performed in Matlab R2013a by filtfilt() function. GNU Octave code for analysis of EGG signals with statistical calculations presented in Popović et al. 2019 is also provided (eggAnalysis.m). For convenient test download and appropriate preview, we provided all signals in .zip and sample signal for ID1 in .txt form. <strong>Dataset contents</strong> EGG-database.zip, data files, text format eggAnalysis.m, GNU Octave code README.txt, metadata for data files, text format ID1_fasting.txt and ID1_postprandial.txt, sample data files for subject ID1, text format <strong>Data files contain numerical values with decimal point according to the following structure</strong> column - CH1* (recorded samples from channel 1) column - CH2* (recorded samples from channel 2) column - CH3* (recorded samples from channel 3) * For exact anatomical locations for EGG channels CH1, CH2, and CH3, please refer to Popović et al. 2019. If you find these signals useful for your own research or teaching class, please cite both relevant paper and dataset as: Popović, N.B., Miljković, N. and Popović, M.B., 2019. Simple gastric motility assessment method with a single-channel electrogastrogram. <em>Biomedical Engineering/Biomedizinische Technik</em>, <em>64</em>(2), pp.177-185, doi: 10.1515/bmt-2017-0218. Popović, N.B., Miljković, N. and Popović, M.B., 2020. Three-channel surface electrogastrogram (EGG) dataset recorded during fasting and post-prandial states in 20 healthy individuals [Data set]. <em>Zenodo</em>, doi: 10.5281/zenodo.3730617. DISCLAIMER: The GNU Octave code is provided without any guarantee and it is not intended for medical purposes.
description: The third version contains additional GNU Octave file for signal analysis.
DOI: 10.6084/m9.figshare.1319442.v2
title: Decadal sustainability of spatial distribution of soil properties in a paddy field as a fingerprint reflecting soil-forming factors and field management

description: Spatiotemporal variations of soil properties were measured in a Japanese paddy field in order to evaluate how they were created and sustained through various field managements. The field was subjected to land consolidation during 1960s, heterogeneous application of manure in the late 1970s and land leveling in 1986, 1987 and 2003. Surface soils were collected from throughout the field in 2002 and 2012, and the physicochemical properties were analyzed. Additional analyses were carried out for relative altitude in 1986, 1999 and 2012, and soil hardness in 2012. In the field examined, the distribution of field attributes reflected past field managements. The heterogeneous distribution of relative altitude was partly explained by the passage of agricultural machinery, whereas the heterogeneous distribution of soil organic matter was partly explained by both past and recent applications of animal dung manure. In general, the measured soil properties were maintained from 2002 to 2012, and the pattern of spatial distribution did not change significantly for many of the properties. The correlation coefficient of the distribution patterns between 2002 and 2012 was highest for yellowness (0.95), followed by sand (0.90), acid-oxalate extractable iron (Fe; 0.88), available phosphorus (P; 0.87), redness (0.82), lightness (0.77), sand-size organic matter (0.74) and total nitrogen (N; 0.72). Land leveling carried out in 2003 barely influenced the distribution of these properties. Among these properties, soil color parameters and sand content can be measured rapidly without reagents and will be useful for characterizing paddy fields according to the distribution of stable soil properties. The analysis of the natural abundance of <sup>15</sup>N in soil was also effective to suggest the contribution of the application of animal dung manure to the accumulation of soil organic matter at a within-field scale. It can be concluded, as a general rule, that each paddy field has its own fingerprint which is unveiled by precise soil sampling and analyses of stable properties.
DOI: 10.6084/m9.figshare.1287664
title: Peribacteroid solution of soybean root nodules partly induces genomic loci for differentiation into bacteroids of free-living <i>Bradyrhizobium japonicum</i> cells

description: In leguminous root nodules, rhizobia differentiate into morphology specific to symbiosis, called bacteroids. As bacteroids are surrounded with peribacteroid membranes filled with peribacteroid solution (PBS), it is considered that PBS contains substances inducing differentiation of rhizobia into bacteroids. In this study, genome-wide expression profiles of <i>Bradyrhizobium japonicum</i> cells cultured in PBS purified from root nodule of soybean (<i>Glycine max</i> L.) were compared with those of bacteroids using macroarray. PBS treatment preferentially induced regions in a large symbiosis island including various symbiosis relevant genes such as <i>nod, fix, nol</i> and <i>noe</i>, in which 75% of regions were commonly induced in bacteroids, while general repressions outside of the symbiosis island seen in bacteroids were not observed in PBS treated cells. The present results suggest that PBS contained some, but not all, substances inducing expression of the genes which are involved in differentiation into bacteroids.
DOI: 10.6084/m9.figshare.1287664.v2
title: Peribacteroid solution of soybean root nodules partly induces genomic loci for differentiation into bacteroids of free-living <i>Bradyrhizobium japonicum</i> cells

description: In leguminous root nodules, rhizobia differentiate into morphology specific to symbiosis, called bacteroids. As bacteroids are surrounded with peribacteroid membranes filled with peribacteroid solution (PBS), it is considered that PBS contains substances inducing differentiation of rhizobia into bacteroids. In this study, genome-wide expression profiles of <i>Bradyrhizobium japonicum</i> cells cultured in PBS purified from root nodule of soybean (<i>Glycine max</i> L.) were compared with those of bacteroids using macroarray. PBS treatment preferentially induced regions in a large symbiosis island including various symbiosis relevant genes such as <i>nod, fix, nol</i> and <i>noe</i>, in which 75% of regions were commonly induced in bacteroids, while general repressions outside of the symbiosis island seen in bacteroids were not observed in PBS treated cells. The present results suggest that PBS contained some, but not all, substances inducing expression of the genes which are involved in differentiation into bacteroids.