cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6874928.v1
title: Tree of life (archaea and bacteria only) and MAGs isolated from two hot springs in the Uzon Caldera, Kamchatka, Russia (tre file)

description: Taxonomy of our MAGs was refined by placing MAGs in a phylogenetic context using PhyloSift v. 1.0.1 with the updated PhyloSift markers database (version 4; 2018-02-12; https://figshare.com/articles/PhyloSift_markers_database/5755404/4). For this purpose, MAGs, all taxa previously identified by Burgess et al. (2012) with complete genomes available on NCBI (downloaded 2017-09-06) and all archaeal and bacterial genomes previously used in Hug et al. (2016) were placed in a phylogenetic tree. All genomes used in this tree and a mapping file can be found on figshare (https://doi.org/10.6084/m9.figshare.6863594.v1; https://doi.org/10.6084/m9.figshare.6863744.v2; https://doi.org/10.6084/m9.figshare.6863798.v1; https://doi.org/10.6084/m9.figshare.6863813.v1). For more information about the available core marker gene sets see Darling et al. 2014 (updated last on 2018-02-12). We used 37 of these single-copy marker genes (ribosomal protein S2 rpsB, S10 rpsJ, L1 rplA, L22, L4/L1e rplD, L2 rplB, S9 rpsl, L3 rplC, L14b/L23e rplN, S5, S19 rpsS, S7, L16/L10E rplP, S13 rpsM, L15, L25/L23, L6 rplF, L11 rplK, L5 rplE, S12/S23, L29, S3 rpsC, S11 rpsK, L10, S8, L18P/L5E, S15P/S13e, S17, S13 rplM, L24; and translation initiation factor IF-2, metalloendopeptidase, phenylalanyl-tRNA synthetase beta subunit, phenylalanyl-tRNA synthetase alpha subunit, tRNA pseudouridine synthase B, Porphobilinogen deaminase, and ribonuclease HII; i.e., PhyloSift markers DNGNGWU00001 - DNGNGWU00040 without DNGNGWU00004, DNGNGWU00008 and DNGNGWU00038). The amino acid alignment of these 37 concatenated genes was trimmed using trimAl v.1.2. Columns with gaps in more than 5% of the sequences were removed, as well as taxa with with less than 75% of the concatenated sequences. MAGs from ARK and ZAV that did not meet this threshold were manually kept in the alignment. The final alignment comprised 3,240 taxa (make a supplementary table) and 5,459 amino acid positions. This alignment was then used to build a new phylogenetic tree in RAxML v. 8.2.10 on the CIPRES Science Gateway web server. First, we searched for the best protein substitution model of the alignment with its empirical base frequencies using the Bayesian Information Criterion (BIC) within RAxML. Then, this substitution model; i.e, LG plus CAT (after Le and Gascuel), was used to infer a phylogenetic tree. We chose the rapid bootstrapping algorithm (flag -f a) to find the best scoring maximum likelihood tree with 10 starting trees in one run with the number of bootstraps automatically determined (MRE-based bootstopping criterion). One hundred fifty bootstrap replicates were conducted. The full tree inference required 2,236 computational hours on the CIPRES supercomputer.
DOI: 10.6084/m9.figshare.6874934.v2
title: Table with taxa we used for the tree of life - archaea and bacteria from Hug et al.'s tree of life in 2016, and MAGs isolated from two hot springs in the Uzon Caldera, Kamchatka, Russia

description: Table with all the taxa names and NCBI IDs that can be found in this tree: https://doi.org/10.6084/m9.figshare.6874928.v1
DOI: 10.6084/m9.figshare.6874928.v2
title: Tree of life - archaea and bacteria from Hug et al.'s tree of life in 2016; MAGs isolated from two hot springs in the Uzon Caldera, Kamchatka, Russia; and all taxa from Burgess et al. (2012) with one representative genome on NCBI (.tre file)

description: Taxonomy of our MAGs was refined by placing MAGs in a phylogenetic context using PhyloSift v. 1.0.1 with the updated PhyloSift markers database (version 4; 2018-02-12; https://figshare.com/articles/PhyloSift_markers_database/5755404/4). For this purpose, MAGs, all taxa previously identified by Burgess et al. (2012) with complete genomes available on NCBI (downloaded 2017-09-06) and all archaeal and bacterial genomes previously used in Hug et al. (2016) were placed in a phylogenetic tree. All genomes used in this tree and a mapping file can be found on figshare (https://doi.org/10.6084/m9.figshare.6863594.v1; https://doi.org/10.6084/m9.figshare.6863744.v2; https://doi.org/10.6084/m9.figshare.6863798.v1; https://doi.org/10.6084/m9.figshare.6863813.v1). For more information about the available core marker gene sets see Darling et al. 2014 (updated last on 2018-02-12). We used 37 of these single-copy marker genes (ribosomal protein S2 rpsB, S10 rpsJ, L1 rplA, L22, L4/L1e rplD, L2 rplB, S9 rpsl, L3 rplC, L14b/L23e rplN, S5, S19 rpsS, S7, L16/L10E rplP, S13 rpsM, L15, L25/L23, L6 rplF, L11 rplK, L5 rplE, S12/S23, L29, S3 rpsC, S11 rpsK, L10, S8, L18P/L5E, S15P/S13e, S17, S13 rplM, L24; and translation initiation factor IF-2, metalloendopeptidase, phenylalanyl-tRNA synthetase beta subunit, phenylalanyl-tRNA synthetase alpha subunit, tRNA pseudouridine synthase B, Porphobilinogen deaminase, and ribonuclease HII; i.e., PhyloSift markers DNGNGWU00001 - DNGNGWU00040 without DNGNGWU00004, DNGNGWU00008 and DNGNGWU00038). The amino acid alignment of these 37 concatenated genes was trimmed using trimAl v.1.2. Columns with gaps in more than 5% of the sequences were removed, as well as taxa with with less than 75% of the concatenated sequences. MAGs from ARK and ZAV that did not meet this threshold were manually kept in the alignment. The final alignment comprised 3,240 taxa (make a supplementary table) and 5,459 amino acid positions. This alignment was then used to build a new phylogenetic tree in RAxML v. 8.2.10 on the CIPRES Science Gateway web server. First, we searched for the best protein substitution model of the alignment with its empirical base frequencies using the Bayesian Information Criterion (BIC) within RAxML. Then, this substitution model; i.e, LG plus CAT (after Le and Gascuel), was used to infer a phylogenetic tree. We chose the rapid bootstrapping algorithm (flag -f a) to find the best scoring maximum likelihood tree with 10 starting trees in one run with the number of bootstraps automatically determined (MRE-based bootstopping criterion). One hundred fifty bootstrap replicates were conducted. The full tree inference required 2,236 computational hours on the CIPRES supercomputer.
DOI: 10.6084/m9.figshare.6874928.v4
title: Tree in Fig.2 - Archaeal and bacterial genomes used by Hug et al. in 2016 to construct a microbial tree of life; MAGs isolated from two hot springs in the Uzon Caldera, Kamchatka, Russia; and all genomes of taxa analyzed in Burgess et al. (2012) with one representative genome on NCBI (Newick file)

description: Taxonomy of our MAGs was refined by placing MAGs in a phylogenetic context using PhyloSift v. 1.0.1 with the updated PhyloSift markers database (version 4; 2018-02-12; https://figshare.com/articles/PhyloSift_markers_database/5755404/4). For this purpose, MAGs, all taxa previously identified by Burgess et al. (2012) with complete genomes available on NCBI (downloaded 2017-09-06) and all archaeal and bacterial genomes previously used in Hug et al. (2016) were placed in a phylogenetic tree. All genomes used in this tree and a mapping file can be found on figshare (https://doi.org/10.6084/m9.figshare.6863594.v1; https://doi.org/10.6084/m9.figshare.6863744.v2; https://doi.org/10.6084/m9.figshare.6863798.v1; https://doi.org/10.6084/m9.figshare.6863813.v1). For more information about the available core marker gene sets see Darling et al. 2014 (updated last on 2018-02-12). We used 37 of these single-copy marker genes (ribosomal protein S2 rpsB, S10 rpsJ, L1 rplA, L22, L4/L1e rplD, L2 rplB, S9 rpsl, L3 rplC, L14b/L23e rplN, S5, S19 rpsS, S7, L16/L10E rplP, S13 rpsM, L15, L25/L23, L6 rplF, L11 rplK, L5 rplE, S12/S23, L29, S3 rpsC, S11 rpsK, L10, S8, L18P/L5E, S15P/S13e, S17, S13 rplM, L24; and translation initiation factor IF-2, metalloendopeptidase, phenylalanyl-tRNA synthetase beta subunit, phenylalanyl-tRNA synthetase alpha subunit, tRNA pseudouridine synthase B, Porphobilinogen deaminase, and ribonuclease HII; i.e., PhyloSift markers DNGNGWU00001 - DNGNGWU00040 without DNGNGWU00004, DNGNGWU00008 and DNGNGWU00038). The amino acid alignment of these 37 concatenated genes was trimmed using trimAl v.1.2. Columns with gaps in more than 5% of the sequences were removed, as well as taxa with with less than 75% of the concatenated sequences. MAGs from ARK and ZAV that did not meet this threshold were manually kept in the alignment. The final alignment comprised 3,240 taxa (make a supplementary table) and 5,459 amino acid positions. This alignment was then used to build a new phylogenetic tree in RAxML v. 8.2.10 on the CIPRES Science Gateway web server. First, we searched for the best protein substitution model of the alignment with its empirical base frequencies using the Bayesian Information Criterion (BIC) within RAxML. Then, this substitution model; i.e, LG plus CAT (after Le and Gascuel), was used to infer a phylogenetic tree. We chose the rapid bootstrapping algorithm (flag -f a) to find the best scoring maximum likelihood tree with 10 starting trees in one run with the number of bootstraps automatically determined (MRE-based bootstopping criterion). One hundred fifty bootstrap replicates were conducted. The full tree inference required 2,236 computational hours on the CIPRES supercomputer.<br>--&gt; I added bootstraps later (check latest version)!
DOI: 10.6084/m9.figshare.6874922
title: Appendix

description: Appendix for Thesis Document
DOI: 10.6084/m9.figshare.6874922.v1
title: Appendix

description: Appendix for Thesis Document
DOI: 10.6084/m9.figshare.6874928.v3
title: Tree of life - archaea and bacteria from Hug et al.'s tree of life in 2016; MAGs isolated from two hot springs in the Uzon Caldera, Kamchatka, Russia; and all taxa from Burgess et al. (2012) with one representative genome on NCBI (.tre file)

description: Taxonomy of our MAGs was refined by placing MAGs in a phylogenetic context using PhyloSift v. 1.0.1 with the updated PhyloSift markers database (version 4; 2018-02-12; https://figshare.com/articles/PhyloSift_markers_database/5755404/4). For this purpose, MAGs, all taxa previously identified by Burgess et al. (2012) with complete genomes available on NCBI (downloaded 2017-09-06) and all archaeal and bacterial genomes previously used in Hug et al. (2016) were placed in a phylogenetic tree. All genomes used in this tree and a mapping file can be found on figshare (https://doi.org/10.6084/m9.figshare.6863594.v1; https://doi.org/10.6084/m9.figshare.6863744.v2; https://doi.org/10.6084/m9.figshare.6863798.v1; https://doi.org/10.6084/m9.figshare.6863813.v1). For more information about the available core marker gene sets see Darling et al. 2014 (updated last on 2018-02-12). We used 37 of these single-copy marker genes (ribosomal protein S2 rpsB, S10 rpsJ, L1 rplA, L22, L4/L1e rplD, L2 rplB, S9 rpsl, L3 rplC, L14b/L23e rplN, S5, S19 rpsS, S7, L16/L10E rplP, S13 rpsM, L15, L25/L23, L6 rplF, L11 rplK, L5 rplE, S12/S23, L29, S3 rpsC, S11 rpsK, L10, S8, L18P/L5E, S15P/S13e, S17, S13 rplM, L24; and translation initiation factor IF-2, metalloendopeptidase, phenylalanyl-tRNA synthetase beta subunit, phenylalanyl-tRNA synthetase alpha subunit, tRNA pseudouridine synthase B, Porphobilinogen deaminase, and ribonuclease HII; i.e., PhyloSift markers DNGNGWU00001 - DNGNGWU00040 without DNGNGWU00004, DNGNGWU00008 and DNGNGWU00038). The amino acid alignment of these 37 concatenated genes was trimmed using trimAl v.1.2. Columns with gaps in more than 5% of the sequences were removed, as well as taxa with with less than 75% of the concatenated sequences. MAGs from ARK and ZAV that did not meet this threshold were manually kept in the alignment. The final alignment comprised 3,240 taxa (make a supplementary table) and 5,459 amino acid positions. This alignment was then used to build a new phylogenetic tree in RAxML v. 8.2.10 on the CIPRES Science Gateway web server. First, we searched for the best protein substitution model of the alignment with its empirical base frequencies using the Bayesian Information Criterion (BIC) within RAxML. Then, this substitution model; i.e, LG plus CAT (after Le and Gascuel), was used to infer a phylogenetic tree. We chose the rapid bootstrapping algorithm (flag -f a) to find the best scoring maximum likelihood tree with 10 starting trees in one run with the number of bootstraps automatically determined (MRE-based bootstopping criterion). One hundred fifty bootstrap replicates were conducted. The full tree inference required 2,236 computational hours on the CIPRES supercomputer.<br>--&gt; I added bootstraps later (check latest version)!
DOI: 10.6084/m9.figshare.6874916
title: Burkina Faso Survey

description: Questionnaire and Survey from Burkina Faso
DOI: 10.7910/dvn/1t8n3n/5starn
title: 0V

description: sigma=0volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6874901
title: Learning Support Program.xls

description: This study used a quasi-experimental design in which HVNs were assigned to groups that either received respiratory physical assessment training and subsequent support for workplace technique utilization for 8 weeks after the training (experimental group), or received respiratory physical assessment training but not the subsequent support (control group). The two groups were then compared. <br>Participant characteristicsPractical testRespiratory physical assessment implementation score<br>satisfaction with learning support program<br><br>
DOI: 10.7910/dvn/1t8n3n/y3mecu
title: 0V

description: sigma=0volts
DOI: 10.6084/m9.figshare.6874880
title: Tweets Collected per Company

description: This folder contains up to 3,200 Tweets collected per company
DOI: 10.6084/m9.figshare.6874901.v1
title: Learning Support Program.xls

description: This study used a quasi-experimental design in which HVNs were assigned to groups that either received respiratory physical assessment training and subsequent support for workplace technique utilization for 8 weeks after the training (experimental group), or received respiratory physical assessment training but not the subsequent support (control group). The two groups were then compared. <br>Participant characteristicsPractical testRespiratory physical assessment implementation score<br>satisfaction with learning support program<br><br>
DOI: 10.6084/m9.figshare.6874916.v1
title: Burkina Faso Survey

description: Questionnaire and Survey from Burkina Faso
DOI: 10.6084/m9.figshare.6874877
title: Followers Collected per Company

description: This folder contains one csv file for each company containing their 900 most recent followers.
DOI: 10.6084/m9.figshare.6874877.v1
title: Followers Collected per Company

description: This folder contains one csv file for each company containing their 900 most recent followers.
DOI: 10.6084/m9.figshare.6874880.v1
title: Tweets Collected per Company

description: This folder contains up to 3,200 Tweets collected per company
DOI: 10.7910/dvn/1t8n3n/dmynih
title: 0V

description: sigma=0volts
DOI: 10.7910/dvn/1t8n3n/tien41
title: 0V

description: sigma=0volts
DOI: 10.7910/dvn/1t8n3n/bm3qwb
title: 0V

description: sigma=0volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/1t8n3n/qszevi
title: 0V

description: sigma=0volts
DOI: 10.6084/m9.figshare.6874865.v1
title: source code.zip

description: This is the source code of this study
DOI: 10.6084/m9.figshare.6874871.v5
title: EEG anticipation of random high and low arousal faces and sounds

description: Materials related to the paper "EEG anticipation of random high and low arousal faces and sounds" available at https://f1000research.com/articles/8-1508/v2<br>Auditory stimuli must be requested to the corresponding author due to copyright restrictions.<br><br><br>
DOI: 10.7910/dvn/1t8n3n/reic3e
title: 0V

description: sigma=0volts
DOI: 10.7910/dvn/1t8n3n/ncakau
title: 0V

description: sigma=0volts
DOI: 10.6084/m9.figshare.6874871.v6
title: EEG anticipation of random high and low arousal faces and sounds

description: Materials related to the paper "EEG anticipation of random high and low arousal faces and sounds" available at https://f1000research.com/articles/8-1508/v2<br>Auditory stimuli must be requested to the corresponding author due to copyright restrictions.<br>It also includes the Extended data related to the paper "Applying machine learning EEG signal classification to emotion‑related brain anticipatory activity" <br><br>
DOI: 10.7910/dvn/1t8n3n/6xsfbh
title: 0V

description: sigma=0volts
DOI: 10.6084/m9.figshare.6874793
title: Code and data from Genetic constraints on microevolutionary divergence of sex-biased gene expression

description: The evolution of sex-specific phenotypes is an important dimension of diversification and local adaptation. The sex-dependent regulation of gene expression is considered a key genomic mechanism facilitating sex-dependent adaptation. In many species, genes with male-biased expression evolve faster in DNA sequence and expression level than genes with female-biased or sexually monomorphic expression. While positive selection may be responsible for rapid DNA sequence evolution, why expression of male-biased genes also evolves rapidly remains unclear. Beyond sex differences in selection, some aspects to the genetic architecture of gene expression could contribute to the rapid evolution of male-biased gene expression. First, male-biased genes might simply have greater standing genetic variance than female-biased genes. Second, male-biased genes could be less constrained by pleiotropy, either within or between sexes. Here, we evaluate these alternative explanations on an intraspecific scale using a series of quantitative genetic experiments conducted on natural variation in male and female gene expression in the fly <i>Drosophila serrata</i>. Male-biased genes had significantly higher genetic variance than female-biased genes and were generally more narrowly expressed across tissues, suggesting lower within individual pleiotropy. However, consistent with stronger constraints due to between-sex pleiotropy, their between-sex genetic correlations, <i>r</i><sub>MF,</sub> were higher than female-biased genes and more strongly negatively associated with sex bias. Using an extensive clinal dataset, we tested whether sex differences in gene expression divergence among populations have been shaped by pleiotropy<i>.</i> Here, too male-biased gene divergence was more strongly associated with between-sex pleiotropy than female-biased gene divergence. Systematic differences in genetic variance and pleiotropy may be important factors influencing sex-specific adaptation arising through changes in gene expression. This article is part of the theme issue ‘Linking local adaptation with the evolution of sex differences’.
DOI: 10.7910/dvn/1t8n3n/uwdetg
title: 0V

description: sigma=0volts
DOI: 10.7910/dvn/1t8n3n/d3ogvw
title: 0V

description: sigma=0volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6874787
title: NetLogo code from The geography of sex: sexual conflict, environmental gradients and local loss of sex in facultatively parthenogenetic animals

description: Custom-written code used to run the simulations in the freely-available application NetLogo.
DOI: 10.6084/m9.figshare.6874784
title: NetLogo code for low mutation rate simulations from The geography of sex: sexual conflict, environmental gradients and local loss of sex in facultatively parthenogenetic animals

description: Custom-written code used to run the simulations in the freely-available application NetLogo.
DOI: 10.6084/m9.figshare.6874787.v1
title: NetLogo code from The geography of sex: sexual conflict, environmental gradients and local loss of sex in facultatively parthenogenetic animals

description: Custom-written code used to run the simulations in the freely-available application NetLogo.
DOI: 10.7910/dvn/1t8n3n/1b9ike
title: 0V

description: sigma=0volts
DOI: 10.7910/dvn/1t8n3n/pvobyc
title: 0V

description: sigma=0volts
DOI: 10.6084/m9.figshare.6874784.v1
title: NetLogo code for low mutation rate simulations from The geography of sex: sexual conflict, environmental gradients and local loss of sex in facultatively parthenogenetic animals

description: Custom-written code used to run the simulations in the freely-available application NetLogo.
DOI: 10.7910/dvn/1t8n3n/qsglpw
title: 0V

description: sigma=0volts
DOI: 10.6084/m9.figshare.6874778
title: ProteomeTools - Prosit iRT - Data

description: data used for training of iRT model
DOI: 10.7910/dvn/1t8n3n/jpd1uy
title: 0V

description: sigma=0volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
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DOI: 10.7910/dvn/1t8n3n/modiwd
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DOI: 10.7910/dvn/1t8n3n/4xcbby
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DOI: 10.7910/dvn/1t8n3n/5qoryx
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DOI: 10.7910/dvn/1t8n3n/xhsmqr
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DOI: 10.7910/dvn/1t8n3n/w1hx3d
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DOI: 10.7910/dvn/1t8n3n/cplauk
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DOI: 10.7910/dvn/1t8n3n/0txf2e
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description: sigma=0volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/1t8n3n/dmigzv
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DOI: 10.7910/dvn/1t8n3n/i1ptmm
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DOI: 10.7910/dvn/1t8n3n/2cfnfp
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DOI: 10.7910/dvn/1t8n3n/equdz4
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DOI: 10.7910/dvn/1t8n3n/oyuxdb
title: 0V

description: sigma=0volts
DOI: 10.7910/dvn/1t8n3n/vwhyie
title: 0V

description: sigma=0volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/1t8n3n/eszq5x
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DOI: 10.7910/dvn/1t8n3n/8fefgc
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description: sigma=0volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/1t8n3n/j3jnjm
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description: sigma=0volts
DOI: 10.7910/dvn/1t8n3n/yw6crr
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description: sigma=0volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/1t8n3n/ekusxj
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title: 0V

description: sigma=0volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/1t8n3n/7poso1
title: 0V

description: sigma=0volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;