cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8003771
title: Macadamia Transcriptome Assembly

description: Macadamia transcriptome assemblies from pooled leaf, stem, bud, root, floral and nut tissue. Using normalized cDNA libraries, we generated comprehensive RNA-Seq datasets using the Illumina NextSeq 500 platform. 78871 of macadamia unigenes respectively were generated and functionally annotated using a combination of de novo transcriptome assembly, redundancy reduction and Basic Local Alignment Search Tool (BLAST) searches to the Universal Protein Resource UniProtKB/Swiss-Prot database.
DOI: 10.6084/m9.figshare.8003777.v1
title: Mango Transcriptome Assembly

description: This mango transcriptome assembly was derived from pooled leaf, stem, bud, root, floral and fruit tissue. Using normalized cDNA libraries, we generated comprehensive RNA-Seq datasets using the Illumina NextSeq 500 platform. 82198 of mango unigenes were generated and functionally annotated using a combination of <i>de novo</i> transcriptome assembly, redundancy reduction and Basic Local Alignment Search Tool (BLAST) searches to the Universal Protein Resource UniProtKB/Swiss-Prot database.
DOI: 10.6084/m9.figshare.8003762.v1
title: Avocado Transcriptome Assembly

description: Avocado transcriptome assembly from pooled leaf, stem, bud, root, floral and fruit tissue. Using normalized cDNA libraries, we generated comprehensive RNA-Seq datasets using the Illumina NextSeq 500 platform. 63420 of avocado unigenes respectively were generated and functionally annotated using a combination of de novo transcriptome assembly, redundancy reduction and Basic Local Alignment Search Tool (BLAST) searches to the Universal Protein Resource UniProtKB/Swiss-Prot database.
DOI: 10.6084/m9.figshare.8003771.v1
title: Macadamia Transcriptome Assembly

description: Macadamia transcriptome assemblies from pooled leaf, stem, bud, root, floral and nut tissue. Using normalized cDNA libraries, we generated comprehensive RNA-Seq datasets using the Illumina NextSeq 500 platform. 78871 of macadamia unigenes respectively were generated and functionally annotated using a combination of de novo transcriptome assembly, redundancy reduction and Basic Local Alignment Search Tool (BLAST) searches to the Universal Protein Resource UniProtKB/Swiss-Prot database.
DOI: 10.6084/m9.figshare.8003705
title: RNA-seq coverage IGV track, 3dpf larvae

description: IGV viewer-compatible 25 bp sliding window RNA-seq coverage tracks file for 3dpf RNA-seq library.
DOI: 10.6084/m9.figshare.8003708
title: Annotation track for IGV viewer

description: Gene annotation track for viewing in the genomic browser software. Contains extracted 3/5'-UTRs and CDSs, as well as mRNA/tRNA and gene features.
DOI: 10.6084/m9.figshare.8003783.v4
title: EGU_Khadka_20190408.pdfRoads and Landslides

description: This is my EGU abstract and PICO presentation on "Roads, landslides, and local social-ecological resilience in Far Western Nepal".
DOI: 10.6084/m9.figshare.8003705.v1
title: RNA-seq coverage IGV track, 3dpf larvae

description: IGV viewer-compatible 25 bp sliding window RNA-seq coverage tracks file for 3dpf RNA-seq library.
DOI: 10.6084/m9.figshare.8003702
title: Nanopore RNA-seq mapped to genome, index file

description: BAM alignment index file with Nanopore RNA-seq mapping to the DT genome.
DOI: 10.6084/m9.figshare.8003708.v1
title: Annotation track for IGV viewer

description: Gene annotation track for viewing in the genomic browser software. Contains extracted 3/5'-UTRs and CDSs, as well as mRNA/tRNA and gene features.
DOI: 10.6084/m9.figshare.8003696
title: RNA-seq coverage IGV track, adult fish

description: IGV viewer-compatible 25 bp sliding window RNA-seq coverage tracks file for adult RNA-seq library.
DOI: 10.6084/m9.figshare.8003699
title: Nanopore RNA-seq mapped.to genome, BAM file

description: BAM alignment file with Nanopore RNA-seq mapping to the DT genome.
DOI: 10.6084/m9.figshare.8003783.v3
title: EGU_Khadka_20190408.pdf

description: This is my EGU abstract and PICO presentation on "Roads, landslides, and local social-ecological resilience in Far Western Nepal".
DOI: 10.6084/m9.figshare.8003693
title: Genome assembly file

description: FASTA sequence file with the Danionella translucida (DT) assembly scaffolds.
DOI: 10.6084/m9.figshare.8003702.v1
title: Nanopore RNA-seq mapped to genome, index file

description: BAM alignment index file with Nanopore RNA-seq mapping to the DT genome.
DOI: 10.6084/m9.figshare.8003696.v1
title: RNA-seq coverage IGV track, adult fish

description: IGV viewer-compatible 25 bp sliding window RNA-seq coverage tracks file for adult RNA-seq library.
DOI: 10.6084/m9.figshare.8003693.v1
title: Genome assembly file

description: FASTA sequence file with the Danionella translucida (DT) assembly scaffolds.
DOI: 10.6084/m9.figshare.8003525
title: Mitochondrial DNA diversity and gene flow in Southeast Asian populations of the synchronously flashing firefly, <i>Pteroptyx tener</i> Olivier (Coleoptera: Lampyridae)

description: Populations of the iconic, synchronously flashing firefly, <i>Pteroptyx tener</i> (Coleoptera: Lampyridae), are increasingly being threatened by habitat destruction and land conversion activities in Malaysia. Concerns on how this may have impacted the species led us to undertake an analysis of <i>P. tener</i> genetic diversity here. We also investigated how <i>P. tener</i> arrived at its present distribution along the west coast of Peninsular Malaysia using maps of Pleistocene sea levels in Southeast Asia and information on its mitochondrial DNA haplotype distribution. We detected three genetically-distinct populations in Malaysia, one each on the east and west coasts of Peninsular Malaysia and the other in Sarawak/Borneo. We found strong support for a scenario where an ancestral <i>P. tener</i> population diverged to form the Sepetang and Selangor River firefly populations when it became disconnected from the Malacca River system as sea levels rose during the late Pleistocene. An introduction event subsequently occurred when the Selangor and Sepetang River populations contributed to the formation of the Linggi River population. Lastly, the admixture event leading to the founding of the Linggi River population most likely occurred when it was connected to the Malacca River system during periods of changing sea levels in the late Pleistocene.
DOI: 10.6084/m9.figshare.8003318
title: Mid-upper arm circumference predicts death in adult patients admitted to a TB ward in the Philippines: a prospective cohort study

description: Dataset and data dictionary for the published paper.<br>
DOI: 10.6084/m9.figshare.8003333
title: Table S1.xls

description: Small RNA sequencing reveals a novel tsRNA-26576 mediating tumorigenesis of breast cancer
DOI: 10.6084/m9.figshare.8003525.v1
title: Mitochondrial DNA diversity and gene flow in Southeast Asian populations of the synchronously flashing firefly, <i>Pteroptyx tener</i> Olivier (Coleoptera: Lampyridae)

description: Populations of the iconic, synchronously flashing firefly, <i>Pteroptyx tener</i> (Coleoptera: Lampyridae), are increasingly being threatened by habitat destruction and land conversion activities in Malaysia. Concerns on how this may have impacted the species led us to undertake an analysis of <i>P. tener</i> genetic diversity here. We also investigated how <i>P. tener</i> arrived at its present distribution along the west coast of Peninsular Malaysia using maps of Pleistocene sea levels in Southeast Asia and information on its mitochondrial DNA haplotype distribution. We detected three genetically-distinct populations in Malaysia, one each on the east and west coasts of Peninsular Malaysia and the other in Sarawak/Borneo. We found strong support for a scenario where an ancestral <i>P. tener</i> population diverged to form the Sepetang and Selangor River firefly populations when it became disconnected from the Malacca River system as sea levels rose during the late Pleistocene. An introduction event subsequently occurred when the Selangor and Sepetang River populations contributed to the formation of the Linggi River population. Lastly, the admixture event leading to the founding of the Linggi River population most likely occurred when it was connected to the Malacca River system during periods of changing sea levels in the late Pleistocene.
DOI: 10.6084/m9.figshare.8003120
title: Performance of alternative measures to Body Mass Index in the assessment of moderate and severe under-nutrition among acutely unwell patients hospitalized in a TB ward in the Philippines: A cross-sectional study.

description: Complete dataset and data dictionary for published paper.<br>
DOI: 10.6084/m9.figshare.8003306
title: MA-CA-SP molecular dynamics trajectory for HIV-1 Gag protein

description: <b>MA-CA-SP1_trajectory.tar.gz </b>is a compressed folder containing files md_0_1.gro and md_0_1.xtc that correspond to a molecular dynamics trajectory of 50 ns for MA-CA-SP1. This model includes amino acids 2 to 377 of protein GAG-HIV1 (UNIPROT code P12497) in a compact conformation.<br><b>md.mdp</b> is a text file with the conditions to generate the molecular dynamics run.<br> <br> The simulation was performed using the GROMACS package version 2018.1 (Abraham et al., 2015) in conjunction with the GROMOS 53A6 force field (Oostenbrink et al., 2004). Water was represented explicitly using the SPC/E model (Berendsen et al.,1987). The system was simulated under periodic conditions in a dodecahedron box. The temperature was maintained throughout the simulation by independently coupling the protein and the solvent to an external temperature bath at 310 K with a coupling constant tau_t= 0.1 ps using a modified Berendsen thermostat (Bussi et al., 2007). The pressure was maintained at 1 bar by weakly coupling the system to an isotropic pressure bath (Parrinello & Rahman., 1981) using an isothermal compressibility of 4.5 x 10<sup>-5</sup> bar<sup>-1 </sup>and a coupling constant of tau_p= 2.0 ps. During the simulations, the length of all bonds within the protein was constrained using the LINear Constraint Solver (LINCS) algorithm (Hess et al. 1997). All bonds, even heavy atom-H bonds were constrained. The time step for integrating the equations of motion was 2 fs. The algorithm used for computing long range electrostatic interactions was Particle-Mesh-Ewald (PME) (Petersen et al. 1995). <br> Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., Lindahl, E. (2015) SoftwareX 1–2:19–25. <br> Berendsen, H. J. C., Postma, J. P .M., and van Gunsteren, W. F., DiNola, A., Haak, J. R. (1984). J. Chem. pHYS. 81, 3684-3690. <br> Bussi, G., Donadio, D., Parrinello, M., (2007). J. Chem. Phys. 126, 014101-7. <br> Hess, B., Bekker, H.,Berendsen, H.J.C., and Fraaijc, J. G.E.M. (1997). J. Comput. Chem. 18, 1463-1472. <br> Oostenbrink B.C., Pitera J.W., Lipzig M.M.H., Meerman J.H.N., Gunsteren W.F. van (2000) J. Comput. Chem. 25:1656-1676. <br> Parrinello, M. and Rahman, A. (1981). J. Appl. Phys. 52, 7182-7190. <br> Petersen H. G. (1995) J. Chem. Phys. 103, 3668-3679.<br>
DOI: 10.6084/m9.figshare.8003120.v2
title: Performance of alternative measures to Body Mass Index in the assessment of moderate and severe under-nutrition among acutely unwell patients hospitalized in a TB ward in the Philippines: A cross-sectional study.

description: Complete dataset and data dictionary for published paper.<br>
DOI: 10.6084/m9.figshare.8003306.v1
title: MA-CA-SP molecular dynamics trajectory for HIV-1 Gag protein

description: <b>MA-CA-SP1_trajectory.tar.gz </b>is a compressed folder containing files md_0_1.gro and md_0_1.xtc that correspond to a molecular dynamics trajectory of 50 ns for MA-CA-SP1. This model includes amino acids 2 to 377 of protein GAG-HIV1 (UNIPROT code P12497) in a compact conformation.<br><b>md.mdp</b> is a text file with the conditions to generate the molecular dynamics run.<br> <br> The simulation was performed using the GROMACS package version 2018.1 (Abraham et al., 2015) in conjunction with the GROMOS 53A6 force field (Oostenbrink et al., 2004). Water was represented explicitly using the SPC/E model (Berendsen et al.,1987). The system was simulated under periodic conditions in a dodecahedron box. The temperature was maintained throughout the simulation by independently coupling the protein and the solvent to an external temperature bath at 310 K with a coupling constant tau_t= 0.1 ps using a modified Berendsen thermostat (Bussi et al., 2007). The pressure was maintained at 1 bar by weakly coupling the system to an isotropic pressure bath (Parrinello & Rahman., 1981) using an isothermal compressibility of 4.5 x 10<sup>-5</sup> bar<sup>-1 </sup>and a coupling constant of tau_p= 2.0 ps. During the simulations, the length of all bonds within the protein was constrained using the LINear Constraint Solver (LINCS) algorithm (Hess et al. 1997). All bonds, even heavy atom-H bonds were constrained. The time step for integrating the equations of motion was 2 fs. The algorithm used for computing long range electrostatic interactions was Particle-Mesh-Ewald (PME) (Petersen et al. 1995). <br> Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., Lindahl, E. (2015) SoftwareX 1–2:19–25. <br> Berendsen, H. J. C., Postma, J. P .M., and van Gunsteren, W. F., DiNola, A., Haak, J. R. (1984). J. Chem. pHYS. 81, 3684-3690. <br> Bussi, G., Donadio, D., Parrinello, M., (2007). J. Chem. Phys. 126, 014101-7. <br> Hess, B., Bekker, H.,Berendsen, H.J.C., and Fraaijc, J. G.E.M. (1997). J. Comput. Chem. 18, 1463-1472. <br> Oostenbrink B.C., Pitera J.W., Lipzig M.M.H., Meerman J.H.N., Gunsteren W.F. van (2000) J. Comput. Chem. 25:1656-1676. <br> Parrinello, M. and Rahman, A. (1981). J. Appl. Phys. 52, 7182-7190. <br> Petersen H. G. (1995) J. Chem. Phys. 103, 3668-3679.<br>
DOI: 10.6084/m9.figshare.8003120.v1
title: Performance of alternative measures to Body Mass Index in the assessment of moderate and severe under-nutrition among acutely unwell patients hospitalized in a TB ward in the Philippines: A cross-sectional study.

description: Complete dataset and data dictionary for published paper.<br>
DOI: 10.6084/m9.figshare.8003333.v1
title: Table S1.xls

description: Small RNA sequencing reveals a novel tsRNA-26576 mediating tumorigenesis of breast cancer
DOI: 10.6084/m9.figshare.8002862
title: MOESM2 of The NuA4 acetyltransferase and histone H4 acetylation promote replication recovery after topoisomerase I-poisoning

description: Additional file 2: Table S1. S. pombe strains used in this study.
DOI: 10.6084/m9.figshare.8002862.v1
title: MOESM2 of The NuA4 acetyltransferase and histone H4 acetylation promote replication recovery after topoisomerase I-poisoning

description: Additional file 2: Table S1. S. pombe strains used in this study.
DOI: 10.6084/m9.figshare.8002823
title: Additional file 4: of Three-dimensional greyscale transrectal ultrasound-guidance and biopsy core preembedding for detection of prostate cancer: Dutch clinical cohort study

description: Biopsy Gleason score among patients with positive biopsies. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8002820
title: Additional file 3: of Three-dimensional greyscale transrectal ultrasound-guidance and biopsy core preembedding for detection of prostate cancer: Dutch clinical cohort study

description: Tumour biopsy characteristics among patients with positive biopsies. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8002823.v1
title: Additional file 4: of Three-dimensional greyscale transrectal ultrasound-guidance and biopsy core preembedding for detection of prostate cancer: Dutch clinical cohort study

description: Biopsy Gleason score among patients with positive biopsies. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8002820.v1
title: Additional file 3: of Three-dimensional greyscale transrectal ultrasound-guidance and biopsy core preembedding for detection of prostate cancer: Dutch clinical cohort study

description: Tumour biopsy characteristics among patients with positive biopsies. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8002727
title: Additional file 3: of Phylogenetic mapping of scale nanostructure diversity in snakes

description: (Tonini_SnakesCommon.nwk) â The Newick tree file containing the 340 species analysed for models of character evolution, phylogenetic mapping and correlation among characters. The file was built by pruning the time-calibrated tree among 9754 species of squamates [20], keeping the 353 species for which we have obtained nanomorphological data, followed by removal of redundant subspecies. (NWK 14 kb)
DOI: 10.6084/m9.figshare.8002727.v1
title: Additional file 3: of Phylogenetic mapping of scale nanostructure diversity in snakes

description: (Tonini_SnakesCommon.nwk) â The Newick tree file containing the 340 species analysed for models of character evolution, phylogenetic mapping and correlation among characters. The file was built by pruning the time-calibrated tree among 9754 species of squamates [20], keeping the 353 species for which we have obtained nanomorphological data, followed by removal of redundant subspecies. (NWK 14 kb)
DOI: 10.6084/m9.figshare.8002703
title: Additional file 16: of Phylogenetic mapping of scale nanostructure diversity in snakes

description: Summary statistics for the phylogenetic generalised least squares regression (PGLS). (TXT 8 kb)
DOI: 10.6084/m9.figshare.8002706
title: Additional file 17: of Phylogenetic mapping of scale nanostructure diversity in snakes

description: Summary statistics for the phylogenetic generalised linear mixed models (PGLMM). (TXT 22 kb)
DOI: 10.6084/m9.figshare.8002706.v1
title: Additional file 17: of Phylogenetic mapping of scale nanostructure diversity in snakes

description: Summary statistics for the phylogenetic generalised linear mixed models (PGLMM). (TXT 22 kb)
DOI: 10.6084/m9.figshare.8002703.v1
title: Additional file 16: of Phylogenetic mapping of scale nanostructure diversity in snakes

description: Summary statistics for the phylogenetic generalised least squares regression (PGLS). (TXT 8 kb)
DOI: 10.6084/m9.figshare.8002649
title: Additional file 3: of Proteome and transcriptome analyses reveal key molecular differences between quality parameters of commercial-ripe and tree-ripe fig (Ficus carica L.)

description: Table S3. All identified proteins annotated in Moraceae and local RNA-Seq assembly dataset databases. (XLSX 146 kb)
DOI: 10.6084/m9.figshare.8002649.v1
title: Additional file 3: of Proteome and transcriptome analyses reveal key molecular differences between quality parameters of commercial-ripe and tree-ripe fig (Ficus carica L.)

description: Table S3. All identified proteins annotated in Moraceae and local RNA-Seq assembly dataset databases. (XLSX 146 kb)
DOI: 10.6084/m9.figshare.8002598
title: Additional file 7: of The different tolerance to magnesiumÂ deficiency of two grapevine rootstocks relies on the ability to cope with oxidative stress

description: Table S7. List of transcripts differentially expressed in roots at 14 days between 1103P and SO4 depending on the growth condition. Transcripts specifically modulated at 14 days in presence (+Mg) and absence (-Mg) of Mg and modulated between the two genotypes in both nutritional conditions. Probe ID, adjusted p-value, Log2(ratio), Functional annotation and Gene Ontology term were reported for each transcript. (XLSX 85 kb)
DOI: 10.6084/m9.figshare.8002595
title: Additional file 6: of The different tolerance to magnesiumÂ deficiency of two grapevine rootstocks relies on the ability to cope with oxidative stress

description: Table S6. List of transcripts differentially expressed in roots at 4 days between 1103P and SO4 depending on the growth condition. Transcripts specifically modulated at 4 days in presence (+Mg) and absence (-Mg) of Mg and modulated between the two genotypes in both nutritional conditions. Probe ID, adjusted p-value, Log2(ratio), Functional annotation and Gene Ontology term were reported for each transcript. (XLSX 87 kb)
DOI: 10.6084/m9.figshare.8002589
title: Additional file 5: of The different tolerance to magnesiumÂ deficiency of two grapevine rootstocks relies on the ability to cope with oxidative stress

description: Table S5. Differentially expressed transcripts identified by each comparison of transcriptional profiles. Probe ID, adjusted p-value, Log2(ratio) and Functional annotation were reported for each transcript. (XLSX 163 kb)
DOI: 10.6084/m9.figshare.8002595.v1
title: Additional file 6: of The different tolerance to magnesiumÂ deficiency of two grapevine rootstocks relies on the ability to cope with oxidative stress

description: Table S6. List of transcripts differentially expressed in roots at 4 days between 1103P and SO4 depending on the growth condition. Transcripts specifically modulated at 4 days in presence (+Mg) and absence (-Mg) of Mg and modulated between the two genotypes in both nutritional conditions. Probe ID, adjusted p-value, Log2(ratio), Functional annotation and Gene Ontology term were reported for each transcript. (XLSX 87 kb)
DOI: 10.6084/m9.figshare.8002598.v1
title: Additional file 7: of The different tolerance to magnesiumÂ deficiency of two grapevine rootstocks relies on the ability to cope with oxidative stress

description: Table S7. List of transcripts differentially expressed in roots at 14 days between 1103P and SO4 depending on the growth condition. Transcripts specifically modulated at 14 days in presence (+Mg) and absence (-Mg) of Mg and modulated between the two genotypes in both nutritional conditions. Probe ID, adjusted p-value, Log2(ratio), Functional annotation and Gene Ontology term were reported for each transcript. (XLSX 85 kb)
DOI: 10.6084/m9.figshare.8002580
title: Additional file 3: of The different tolerance to magnesiumÂ deficiency of two grapevine rootstocks relies on the ability to cope with oxidative stress

description: Table S3. List of metabolites differentially abundant in roots at 14 days between 1103P and SO4 depending on the growth condition. Metabolites specifically modulated at 14 days in presence (+Mg) and absence (-Mg) of Mg and modulated between the two genotypes in both nutritional conditions. Identity of compound, p(Corr) and FC were reported. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.8002589.v1
title: Additional file 5: of The different tolerance to magnesiumÂ deficiency of two grapevine rootstocks relies on the ability to cope with oxidative stress

description: Table S5. Differentially expressed transcripts identified by each comparison of transcriptional profiles. Probe ID, adjusted p-value, Log2(ratio) and Functional annotation were reported for each transcript. (XLSX 163 kb)
DOI: 10.6084/m9.figshare.8002580.v1
title: Additional file 3: of The different tolerance to magnesiumÂ deficiency of two grapevine rootstocks relies on the ability to cope with oxidative stress

description: Table S3. List of metabolites differentially abundant in roots at 14 days between 1103P and SO4 depending on the growth condition. Metabolites specifically modulated at 14 days in presence (+Mg) and absence (-Mg) of Mg and modulated between the two genotypes in both nutritional conditions. Identity of compound, p(Corr) and FC were reported. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.8002568
title: Additional file 1: of The different tolerance to magnesiumÂ deficiency of two grapevine rootstocks relies on the ability to cope with oxidative stress

description: Table S1. Metabolites differentially abundant in roots between 1103P and SO4 at 4 and 14 days of growth in presence (+Mg) and absence (-Mg) of Mg identified by the comparison of profile obtained by QTOF and GC-MS analyses. Description, p(Corr) and fold change (FC) were reported. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.8002574
title: Additional file 4: of Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes

description: Orthologs of Crl regulon in Bacteria and Archaea genomes. (GZ 1446 kb)
DOI: 10.6084/m9.figshare.8002565
title: Additional file 3: of Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes

description: Homologs of Crl in Bacteria and Archaea genomes. (TXT 64 kb)