cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5549149.v1
title: Panopticon As Corporation

description: This figure features in the IEEE SSSIT opinion piece that will be published in 2017 titled " Pervasive Technology: Aboriginal Communities and Oppression." The figure suggests that all online systems due to data retention laws in Australia are now subject to interception and interrogation by those who conduct surveillance of personal data and related service agencies.
DOI: 10.6084/m9.figshare.5548645
title: Additional Supplementary Figures and Tables

description: Additional supplementary data, tables, figures and code relating to doi: 10.1101/165787<br>
DOI: 10.6084/m9.figshare.5549065
title: Alignment used for reconstruction of Maximum likelihood tree showing phylogenetic placement of S. hawaiiensis based on concatenated rpoB-trpB-recA-atpD partial sequences

description: Alignment used for reconstruction of Maximum likelihood tree showing phylogenetic placement of S. hawaiiensis based on concatenated rpoB-trpB-recA-atpD
DOI: 10.6084/m9.figshare.5548636
title: Figure 3

description: <b>Figure</b><b> 3: </b><b>Mechanisms generating cell-specific gene expression in</b><b> </b><b>C</b><b><sub>4</sub></b><b> </b><b>Bundle</b><b> </b><b>Sheath</b><b>.</b> Schematic of co-linear genes from <i>S</i><i>. </i><i>bicolor,</i> depicting three classes of alterations to DNA accessibility and transcription factor binding to genes that are differentially expressed between whole leaf and bundle sheath cells. Whole leaf (blue) and bundle sheath (orange) DHS, DGF and differentially (DE) expressed DGF are depicted. Regions where a DHS was identified in one sample but not another are indicated by dashed boxes. Created using IGV genome browser and Inkscape
DOI: 10.6084/m9.figshare.5548645.v1
title: Additional Supplementary Figures and Tables

description: Additional supplementary data, tables, figures and code relating to doi: 10.1101/165787<br>
DOI: 10.6084/m9.figshare.5549065.v1
title: Alignment used for reconstruction of Maximum likelihood tree showing phylogenetic placement of S. hawaiiensis based on concatenated rpoB-trpB-recA-atpD

description: Alignment used for reconstruction of Maximum likelihood tree showing phylogenetic placement of S. hawaiiensis based on concatenated rpoB-trpB-recA-atpD
DOI: 10.6084/m9.figshare.5548627
title: Tweets on Super-typhoon Haiyan that hit the Philippines

description: This provides historical tweets (raw) on super-typhoon Haiyan (local name: Yolanda) and the creation dates of the tweets. This dataset was used in the following paper:<br>David CC, Ong JC, Legara EFT (2016) Tweeting Supertyphoon Haiyan: Evolving Functions of Twitter during and after a Disaster Event. PLoS ONE11(3): e0150190. https://doi.org/10.1371/journal.pone.0150190<br>Fields: tweet, created_at
DOI: 10.6084/m9.figshare.5548636.v1
title: Figure 3

description: <b>Figure</b><b> 3: </b><b>Mechanisms generating cell-specific gene expression in</b><b> </b><b>C</b><b><sub>4</sub></b><b> </b><b>Bundle</b><b> </b><b>Sheath</b><b>.</b> Schematic of co-linear genes from <i>S</i><i>. </i><i>bicolor,</i> depicting three classes of alterations to DNA accessibility and transcription factor binding to genes that are differentially expressed between whole leaf and bundle sheath cells. Whole leaf (blue) and bundle sheath (orange) DHS, DGF and differentially (DE) expressed DGF are depicted. Regions where a DHS was identified in one sample but not another are indicated by dashed boxes. Created using IGV genome browser and Inkscape
DOI: 10.6084/m9.figshare.5548594
title: Capacitated Competitive Facility Location Problem

description: Data set for Capacitated Competitive Facility Location Problem including seven problem instances with different sizes
DOI: 10.6084/m9.figshare.5548582
title: SNP based strain tree

description: SNP-based strain phylogeny for all A. fumigatus strains. Accompanies Figure 1.
DOI: 10.6084/m9.figshare.5548585
title: Idiomorph flanking locus tree

description: Maximum likelihood phylogeny of the conserved downstream flanking region of the idiomorph locus. Accompanies Figure 4.
DOI: 10.6084/m9.figshare.5548594.v1
title: Capacitated Competitive Facility Location Problem

description: Data set for Capacitated Competitive Facility Location Problem including seven problem instances with different sizes
DOI: 10.6084/m9.figshare.5548582.v1
title: SNP based strain tree

description: SNP-based strain phylogeny for all A. fumigatus strains. Accompanies Figure 1.
DOI: 10.6084/m9.figshare.5548579
title: AmcilCP_DsBox.pdb

description: We chose the chromoprotein AmilCP, a natural compound found in Acropora millepora, as a reporter protein to see if our BioBrick works. In order to enhance the translation of the AmilCP RNA during the cold shock response, we decided to add what is called the DS Box (or DB). Indeed, several studies have reported that this small RBS sequence have a high affinity for the ribosome when coupled with the AmilCP at low temperature. What lead us to use bioinformatic tools is that this DB’s RNA sequence must be located into the target protein RNA sequence. Although, as it has been said, AmilCP is a chromoprotein that owes it color to its 3D structure.
DOI: 10.6084/m9.figshare.5548576
title: idiomorph flanking region alignment

description: Nucleotide alignment of the downstream conserved region of the idiomorphic locus. Accompanies Figure 4.
DOI: 10.6084/m9.figshare.5548579.v1
title: AmcilCP_DsBox.pdb

description: We chose the chromoprotein AmilCP, a natural compound found in Acropora millepora, as a reporter protein to see if our BioBrick works. In order to enhance the translation of the AmilCP RNA during the cold shock response, we decided to add what is called the DS Box (or DB). Indeed, several studies have reported that this small RBS sequence have a high affinity for the ribosome when coupled with the AmilCP at low temperature. What lead us to use bioinformatic tools is that this DB’s RNA sequence must be located into the target protein RNA sequence. Although, as it has been said, AmilCP is a chromoprotein that owes it color to its 3D structure.
DOI: 10.6084/m9.figshare.5548585.v1
title: Idiomorph flanking locus tree

description: Maximum likelihood phylogeny of the conserved downstream flanking region of the idiomorph locus. Accompanies Figure 4.
DOI: 10.6084/m9.figshare.5548573
title: fusarielin nucleotide alignment

description: Nucleotide alignment of the fusarielin-like Cluster 4.
DOI: 10.6084/m9.figshare.5548570
title: Fusarielin locus phylogeny

description: Maximum likelihood phylogeny of the fusarielin-like Cluster 4. Shown in Figure 3.
DOI: 10.6084/m9.figshare.5548576.v1
title: idiomorph flanking region alignment

description: Nucleotide alignment of the downstream conserved region of the idiomorphic locus. Accompanies Figure 4.
DOI: 10.6084/m9.figshare.5548558
title: Alignments for Cluster 35

description: Alignments for genes in Cluster 35
DOI: 10.6084/m9.figshare.5548570.v1
title: Fusarielin locus phylogeny

description: Maximum likelihood phylogeny of the fusarielin-like Cluster 4. Shown in Figure 3.
DOI: 10.6084/m9.figshare.5548573.v1
title: fusarielin nucleotide alignment

description: Nucleotide alignment of the fusarielin-like Cluster 4.
DOI: 10.6084/m9.figshare.5548555
title: Cluster 4 alignments

description: Alignments for the genes in the fusarielin like cluster 4.
DOI: 10.6084/m9.figshare.5548558.v1
title: Alignments for Cluster 35

description: Alignments for genes in Cluster 35
DOI: 10.6084/m9.figshare.5548546
title: Fusarielin-like cluster 4 trees

description: Maximum likelihood phylogeny for cluster 4. Accompanies Figure 3.
DOI: 10.6084/m9.figshare.5548549
title: Cluster 35 trees

description: Maximum likelihood trees for genes in Cluster 35. Accompanies S4 Figure and S5 Figure.
DOI: 10.6084/m9.figshare.5548552
title: Alignments for Cluster 1

description: Alignments for genes in Cluster 1
DOI: 10.6084/m9.figshare.5548531
title: Beta tubulin tree

description: Beta tubulin maximum likelihood phylogeny. From S10 figure.
DOI: 10.6084/m9.figshare.5548537
title: Cluster 1 trees

description: Maximum likelihood trees for cluster 1. Accompanies Figure 5.
DOI: 10.6084/m9.figshare.5548552.v1
title: Alignments for Cluster 1

description: Alignments for genes in Cluster 1
DOI: 10.6084/m9.figshare.5548519
title: Supplemental Material for Klim et al., 2018

description: p { margin-bottom: 0.21cm; direction: ltr; color: rgb(0, 0, 10); line-height: 115%; text-align: left; }p.western { font-family: "Calibri", serif; font-size: 11pt; }p.cjk { font-family: "Calibri"; font-size: 11pt; }p.ctl { font-family: "Arial"; font-size: 11pt; }a:link { color: rgb(0, 0, 255); text-decoration: none; } <b>Additional file 1.</b> Final alignments (files with .aln.fasta extension) and phylogenetic trees (files with fastree.newick extension) for all the protein families analyzed in the study. Additionally, in case of three protein families: AIF, OMI and caspase/metacaspase the subfolders were created, containing the key subtrees (files in nexml format generated with Dendroscope). <br> <b>Additional file 2</b><b>.</b> Additional BLASTP results and taxonomy reports conducted to confirm the key results in case of the three protein families: AIF, caspase/metacaspase and htra. BLASTP results and taxonomy reports were obtained with NCBI WWW with two strategies: by selecting only a few eukaryotic proteomes (for the species from Table S2 in Supplementary Methods) as a search database (see file eukaryotic_strategy.pdf) and by extending selected proteomes from the first search strategy with all bacterial and archeal proteomes (see file extended_strategy.pdf). Please see README.md for more details regarding information for given specific file. <br> <b>Additional file 3. </b>Mega sessions for consensus phylogenetic trees calculated for arbitrarily chosen metacaspases and caspases, OMI/HTRA proteases and AIFs. Separate sessions files are available for calculations based on MLE (maximum likelihood estimation), NJ (neighbor-joining) and ME (minimal evolution). <br> <b>Additional Figure S1.</b> Competition assay between <i>ndi1</i><i>Δ </i>and wild-type Saccharomyces cerevisiae BY4741 strains under anaerobic conditions. <br> <b>Additional Figure S2.</b> Growth curves for all tested in this study yeast strains cultivated in prolonged cultures in aerobic (A) or anaerobic (B) conditions. The values of mean and standard deviation from duplicate experiments are shown for each time point. <br> <b>Additional Figure S3. </b>Yeast strains used in the experimental evolution are unable to grow on medium supplemented with non-fermentable carbon source. Cells grown on glucose-containing (A) and glycerol-containing (B) solid medium. Single colonies were streaked on the appropriate plate and incubated at 28⁰C for 3 days. Wild-type strain shows robust growth on both media, whereas mutant strains grow only on glucose-containing plate.<br> <br>
DOI: 10.6084/m9.figshare.5548534
title: Calmodulin tree.txt

description: Calmodulin maximum likelihood phylogeny. From S10 figure.
DOI: 10.6084/m9.figshare.5548534.v1
title: Calmodulin tree.txt

description: Calmodulin maximum likelihood phylogeny. From S10 figure.
DOI: 10.6084/m9.figshare.5548519.v2
title: Supplemental Material for Klim et al., 2018

description: p { margin-bottom: 0.21cm; direction: ltr; color: rgb(0, 0, 10); line-height: 115%; text-align: left; }p.western { font-family: "Calibri", serif; font-size: 11pt; }p.cjk { font-family: "Calibri"; font-size: 11pt; }p.ctl { font-family: "Arial"; font-size: 11pt; }a:link { color: rgb(0, 0, 255); text-decoration: none; } <b>Additional file 1.</b> Final alignments (files with .aln.fasta extension) and phylogenetic trees (files with fastree.newick extension) for all the protein families analyzed in the study. Additionally, in case of three protein families: AIF, OMI and caspase/metacaspase the subfolders were created, containing the key subtrees (files in nexml format generated with Dendroscope). <br> <b>Additional file 2</b><b>.</b> Additional BLASTP results and taxonomy reports conducted to confirm the key results in case of the three protein families: AIF, caspase/metacaspase and htra. BLASTP results and taxonomy reports were obtained with NCBI WWW with two strategies: by selecting only a few eukaryotic proteomes (for the species from Table S2 in Supplementary Methods) as a search database (see file eukaryotic_strategy.pdf) and by extending selected proteomes from the first search strategy with all bacterial and archeal proteomes (see file extended_strategy.pdf). Please see README.md for more details regarding information for given specific file. <br> <b>Additional file 3. </b>Mega sessions for consensus phylogenetic trees calculated for arbitrarily chosen metacaspases and caspases, OMI/HTRA proteases and AIFs. Separate sessions files are available for calculations based on MLE (maximum likelihood estimation), NJ (neighbor-joining) and ME (minimal evolution). <br> <b>Additional Figure S1.</b> Competition assay between <i>ndi1</i><i>Δ </i>and wild-type Saccharomyces cerevisiae BY4741 strains under anaerobic conditions. <br> <b>Additional Figure S2.</b> Growth curves for all tested in this study yeast strains cultivated in prolonged cultures in aerobic (A) or anaerobic (B) conditions. The values of mean and standard deviation from duplicate experiments are shown for each time point. <br> <b>Additional Figure S3. </b>Yeast strains used in the experimental evolution are unable to grow on medium supplemented with non-fermentable carbon source. Cells grown on glucose-containing (A) and glycerol-containing (B) solid medium. Single colonies were streaked on the appropriate plate and incubated at 28⁰C for 3 days. Wild-type strain shows robust growth on both media, whereas mutant strains grow only on glucose-containing plate.<br> <br>
DOI: 10.6084/m9.figshare.5548519.v1
title: Ancestral State Reconstruction of the Apoptosis Machinery in the Common Ancestor of Eukaryotes

description: p { margin-bottom: 0.21cm; direction: ltr; color: rgb(0, 0, 10); line-height: 115%; text-align: left; }p.western { font-family: "Calibri", serif; font-size: 11pt; }p.cjk { font-family: "Calibri"; font-size: 11pt; }p.ctl { font-family: "Arial"; font-size: 11pt; }a:link { color: rgb(0, 0, 255); text-decoration: none; } <b>Additional file 1.</b> Final alignments (files with .aln.fasta extension) and phylogenetic trees (files with fastree.newick extension) for all the protein families analyzed in the study. Additionally, in case of three protein families: AIF, OMI and caspase/metacaspase the subfolders were created, containing the key subtrees (files in nexml format generated with Dendroscope). <br> <b>Additional file 2</b><b>.</b> Additional BLASTP results and taxonomy reports conducted to confirm the key results in case of the three protein families: AIF, caspase/metacaspase and htra. BLASTP results and taxonomy reports were obtained with NCBI WWW with two strategies: by selecting only a few eukaryotic proteomes (for the species from Table S2 in Supplementary Methods) as a search database (see file eukaryotic_strategy.pdf) and by extending selected proteomes from the first search strategy with all bacterial and archeal proteomes (see file extended_strategy.pdf). Please see README.md for more details regarding information for given specific file. <br> <b>Additional file 3. </b>Mega sessions for consensus phylogenetic trees calculated for arbitrarily chosen metacaspases and caspases, OMI/HTRA proteases and AIFs. Separate sessions files are available for calculations based on MLE (maximum likelihood estimation), NJ (neighbor-joining) and ME (minimal evolution). <br> <b>Additional Figure S1.</b> Competition assay between <i>ndi1</i><i>Δ </i>and wild-type Saccharomyces cerevisiae BY4741 strains under anaerobic conditions. <br> <b>Additional Figure S2.</b> Growth curves for all tested in this study yeast strains cultivated in prolonged cultures in aerobic (A) or anaerobic (B) conditions. The values of mean and standard deviation from duplicate experiments are shown for each time point. <br> <b>Additional Figure S3. </b>Yeast strains used in the experimental evolution are unable to grow on medium supplemented with non-fermentable carbon source. Cells grown on glucose-containing (A) and glycerol-containing (B) solid medium. Single colonies were streaked on the appropriate plate and incubated at 28⁰C for 3 days. Wild-type strain shows robust growth on both media, whereas mutant strains grow only on glucose-containing plate.<br> <br>
DOI: 10.6084/m9.figshare.5548531.v1
title: Beta tubulin tree

description: Beta tubulin maximum likelihood phylogeny. From S10 figure.
DOI: 10.6084/m9.figshare.5548459
title: TraRECo: Flux simulator workshop

description: Flux simulator workshop to generate simulated read data used in performance evaluation of TraRECo, a de novo transcriptome assembler developed by S. Yoon
DOI: 10.6084/m9.figshare.5548492
title: Notch1 expression after Yhhu4952 treatment

description: Notch1 expression after various concentration of Yhhu4952 treatment on OPCs.
DOI: 10.6084/m9.figshare.5548492.v1
title: Notch1 expression after Yhhu4952 treatment

description: Notch1 expression after various concentration of Yhhu4952 treatment on OPCs.
DOI: 10.6084/m9.figshare.5548459.v1
title: TraRECo: Flux simulator workshop

description: Flux simulator workshop to generate simulated read data used in performance evaluation of TraRECo, a de novo transcriptome assembler developed by S. Yoon
DOI: 10.6084/m9.figshare.5548315
title: Wide field SBP mosaics

description: Subbasal nerve plexus Mosaic images acquired in vivo using laser-scanning confocal microscopy of the cornea in healthy subjects and type 2 diabetes mellitus subjects of the same age. Mosaics represent wide-field images of the plexus incorporating 3D nerve path data projected onto a 2D plane.
DOI: 10.6084/m9.figshare.5547985
title: Key to Mosaic Dataset

description: This Excel file contains detailed information relating to the Mosaic images, including subject ID number, Eye, Mosaic filename, Mosaic area, subbasal nerve fiber length density in the entire mosaic by manual and automated nerve tracing methods, subbasal nerve fiber length density in the whorl region of the mosaic by manual and automated nerve tracing methods, diabetes status of each subject (normal gluocose tolerance, impaired glucose tolerance, and duration since diagnosis of type 2 diabetes mellitus.The following Clinical/demographic parameters have also been included: age, sex, smoking status, blood HbA1c level, body mass index, average fasting plasma glucose and average 2-hour plasma glucose.
DOI: 10.6084/m9.figshare.5547970
title: Temporal and spatial distribution of isotopes in river water in Central Europe: 50 years experience with the Austrian network of isotopes in rivers

description: The Austrian network of isotopes in rivers comprises about 15 sampling locations and has been operated since 1976. The Danube isotope time series goes back to 1963. The isotopic composition of river water in Central Europe is mainly governed by the isotopic composition of precipitation in the catchment area; evaporation effects play only a minor role. Short-term and long-term isotope signals in precipitation are thus transmitted through the whole catchment. The influence of climatic changes has become observable in the long-term stable isotope time series of precipitation and surface waters. Environmental <sup>3</sup>H values were around 8 TU in 2015, short-term <sup>3</sup>H pulses up to about 80 TU in the rivers Danube and March were a consequence of releases from nuclear power plants. The complete isotope data series of this network will be included in the Global Network of Isotopes in Rivers database of the International Atomic Energy Agency (IAEA) in 2017. This article comprises a review of 50 years isotope monitoring on rivers and is also intended to provide base information on the (isotope-)hydrological conditions in Central Europe specifically for the end-users of these data, e.g. for modelling hydrological processes. Furthermore, this paper includes the 2006–2015 supplement adding to the Danube isotope set published earlier.
DOI: 10.6084/m9.figshare.5547985.v1
title: Key to Mosaic Dataset

description: This Excel file contains detailed information relating to the Mosaic images, including subject ID number, Eye, Mosaic filename, Mosaic area, subbasal nerve fiber length density in the entire mosaic by manual and automated nerve tracing methods, subbasal nerve fiber length density in the whorl region of the mosaic by manual and automated nerve tracing methods, diabetes status of each subject (normal gluocose tolerance, impaired glucose tolerance, and duration since diagnosis of type 2 diabetes mellitus.The following Clinical/demographic parameters have also been included: age, sex, smoking status, blood HbA1c level, body mass index, average fasting plasma glucose and average 2-hour plasma glucose.
DOI: 10.6084/m9.figshare.5547970.v1
title: Temporal and spatial distribution of isotopes in river water in Central Europe: 50 years experience with the Austrian network of isotopes in rivers

description: The Austrian network of isotopes in rivers comprises about 15 sampling locations and has been operated since 1976. The Danube isotope time series goes back to 1963. The isotopic composition of river water in Central Europe is mainly governed by the isotopic composition of precipitation in the catchment area; evaporation effects play only a minor role. Short-term and long-term isotope signals in precipitation are thus transmitted through the whole catchment. The influence of climatic changes has become observable in the long-term stable isotope time series of precipitation and surface waters. Environmental <sup>3</sup>H values were around 8 TU in 2015, short-term <sup>3</sup>H pulses up to about 80 TU in the rivers Danube and March were a consequence of releases from nuclear power plants. The complete isotope data series of this network will be included in the Global Network of Isotopes in Rivers database of the International Atomic Energy Agency (IAEA) in 2017. This article comprises a review of 50 years isotope monitoring on rivers and is also intended to provide base information on the (isotope-)hydrological conditions in Central Europe specifically for the end-users of these data, e.g. for modelling hydrological processes. Furthermore, this paper includes the 2006–2015 supplement adding to the Danube isotope set published earlier.
DOI: 10.6084/m9.figshare.5547829
title: Gene annotations for ExcisionFinder

description: Gene annotations used for excision finder, originally from RefSeq.
DOI: 10.6084/m9.figshare.5547847
title: LUSC.mRNAseq.txt

description: mRNA expression of LUSC patients
DOI: 10.6084/m9.figshare.5547829.v1
title: Gene annotations for ExcisionFinder

description: Gene annotations used for excision finder, originally from RefSeq.
DOI: 10.6084/m9.figshare.5547817
title: hg19 PAM sites

description: This contains the PAM sites found in hg19 (GrCh37) as described on the ExcisionFinder wiki and manuscript.
DOI: 10.6084/m9.figshare.5547820
title: GrCh37 (hg19) fasta

description: Fasta required for parts of preprocessing in ExcisionFinder.