cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8868893.v1
title: Data from Impacts of Directed Species Loss on Community Productivity in a Subtropical Forest Biodiversity Experiment

description: Data supporting the paper: Impacts of Directed Species Loss on Community Productivity in a Subtropical Forest Biodiversity Experiment.1. main_data.xlsx: data of plot-level stand volume and species richness for different extinction scenarios.2. partitioning_data.xlsx: data of additive paritioning of net extinction effects.3. species_info.xlsx: Species names and attributes. 4. JAGS_code_1.r: JAGS code for assessing the effects of species loss on productivity, corresponding to the equations 1-3 in the maintext. 5. JAGS_code_2.r: JAGS code for assessing the temporal trends of net extinction effect or its additive components, corresponding to the equation 8 in the maintext.6. JAGS_code_3.r: JAGS code for comparing effects of species loss among different extinction steps and at different ages, corresponding to the equation 9 in the maintext.
DOI: 10.6084/m9.figshare.8868854
title: voxelGeneCoexpression_P28.mat

description: The dataset is the basis of our analysis of correlated gene expression (CGE) in the developing mouse brain.
DOI: 10.6084/m9.figshare.8868851
title: voxelGeneCoexpression_P14.mat

description: The dataset is the basis of our analysis of correlated gene expression (CGE) in the developing mouse brain.
DOI: 10.6084/m9.figshare.8868854.v1
title: voxelGeneCoexpression_P28.mat

description: The dataset is the basis of our analysis of correlated gene expression (CGE) in the developing mouse brain.
DOI: 10.6084/m9.figshare.8868845
title: voxelGeneCoexpression_P4.mat

description: The dataset is the basis of our analysis of correlated gene expression (CGE) in the developing mouse brain.
DOI: 10.6084/m9.figshare.8868851.v1
title: voxelGeneCoexpression_P14.mat

description: The dataset is the basis of our analysis of correlated gene expression (CGE) in the developing mouse brain.
DOI: 10.6084/m9.figshare.8868833
title: voxelGeneCoexpression_E13pt5.mat

description: The dataset is the basis of our analysis of correlated gene expression (CGE) in the developing mouse brain.
DOI: 10.6084/m9.figshare.8868836
title: voxelGeneCoexpression_E15pt5.mat

description: The dataset is the basis of our analysis of correlated gene expression (CGE) in the developing mouse brain.
DOI: 10.6084/m9.figshare.8868842
title: voxelGeneCoexpression_E18pt5.mat

description: The dataset is the basis of our analysis of correlated gene expression (CGE) in the developing mouse brain.
DOI: 10.6084/m9.figshare.8868845.v1
title: voxelGeneCoexpression_P4.mat

description: The dataset is the basis of our analysis of correlated gene expression (CGE) in the developing mouse brain.
DOI: 10.6084/m9.figshare.8868836.v1
title: voxelGeneCoexpression_E15pt5.mat

description: The dataset is the basis of our analysis of correlated gene expression (CGE) in the developing mouse brain.
DOI: 10.6084/m9.figshare.8868842.v1
title: voxelGeneCoexpression_E18pt5.mat

description: The dataset is the basis of our analysis of correlated gene expression (CGE) in the developing mouse brain.
DOI: 10.6084/m9.figshare.8868593
title: ChoanoV2

description: Genome assembled by recruiting to ChoanoV1 and then assembledd with spades as described in detail in Needham et al., SI Methods.
DOI: 10.6084/m9.figshare.8868596
title: 4 well Bicosta minor draft assembly

description: This draft genome of B. minor was assembled by co-assembly of four single cells, see detailed methods in manuscript. <br>rename.1k.4well.B.minor.coassembly.fasta is the full assembly of the combined four wells.<br>B.minor.tetranucleotide.filtered.Choano-contigs.fa is the draft B. minor genome, with likely co-sorted prokaryotic or phage sequences (from, possibly, degraded prey) removed based on divergent tetranucleotide frequency.
DOI: 10.6084/m9.figshare.8868587
title: Phylogenomics of NCLDV

description: 25 files, including single gene alignments raw and filtered, concatenated gene alignments raw and filtered, and phylogenomic tree files <br> Single-gene alignments (untrimmed) for phylogenomic analysisDataset by Elisabeth Hehenberger<br>Single-gene alignments for 10 proteins in fasta format. Alignments were manually curated (removal of highly divergent and/or paralogous sequences, merging of sequence fragments) based on single-gene phylogenies. Merged sequences are indicated in the sequence name. Final alignments were performed with the MAFFT L-INS-i algorithm.<br>File name convention:OG numbers stand for the orthogroups recovered in this studyNCVOG numbers stand for the orthogroups recovered in:<br>N. Yutin, Y. I. Wolf, D. Raoult, E. V Koonin, Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution. Virol J. 6, 223 (2009).<br>Sequence name convention:Virus name; GenBank accession(except for the ChoanoV sequences)<br><br>Single-gene alignments (trimmed) for phylogenomic analysisDatasetmodified on 21.07.2018, 15:20 by Elisabeth HehenbergerTrimmed single-gene alignments for 10 proteins as used for concatenation in fasta format. Trimming was performed with BMGE using the default gap threshold and the BLOSUM30 similarity matrix.<br>File name convention:OG numbers stand for the orthogroups recovered in this studyNCVOG numbers stand for the orthogroups recovered in:<br>N. Yutin, Y. I. Wolf, D. Raoult, E. V Koonin, Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution. Virol J. 6, 223 (2009).<br>Sequence name convention:Virus name; GenBank accession(except for the ChoanoV seqeunces)<br>Concatenated alignments for phylogenomic analysisDatasetmodified on 21.07.2018, 16:50 by Elisabeth HehenbergerConcatenated alignments underlying phylogenomic trees.A README file contains details concerning the individual files.<br><br> Phylogenomic trees in newick formatDataset by Elisabeth Hehenberger<br>Phylogenomic reconstructions in newick format. All phylogenomic trees described in the publication can be found in newick format in this file, including a detailed description for each tree.<br>
DOI: 10.6084/m9.figshare.8868584
title: Chitinase phylogeny files

description: <b>Phylogeny and alignments of Choanovirus chitinase.</b><br><br>Elisabeth Hehenberger<br><br>Chitinase_alignment_PF00704_rp75_plus6viralseqs_mafft.fasta= untrimmed alignment in fasta format.<br>For the alignment, the representative proteome alignment at 75% co-membership threshold from pfam for PF00704 (Glycosyl hydrolases family 18 domain) was realigned with the ChoanoV1 protein as well as all five other putative viral chitinases currently in nr (NP_048613.3, NP_054156.1, NP_613105.1, YP_001427261.1 and YP_004732803.1), using the –auto option of MAFFT. Sequence names are either UniProt idenitifiers (for the representative proteome data) or GenBank Accession numbers (for the viral sequences; except the ChoanoV sequence)<br><br>Chitinase_alignment_PF00704_rp75_plus6viralseqs_trimal.fasta= trimmed alignment in fasta format.<br>Ambiguously aligned positions were removed using trimAL v1.2, with a gap threshold of 40%, resulting in a 14,915 sequence matrix with 224 aa positions.<br>Chitinase_phylogeny.txt:= phylogenetic tree in newick format, including a detailed description
DOI: 10.6084/m9.figshare.8868575
title: CCDB_8139.jpg

description: Single computed slice through a tomographic volume of mitochondria at the Node of Ranvier in rat peripheral nerve root
DOI: 10.6084/m9.figshare.8868581
title: Rhodopsin phylogeny files

description: Alignment files and tree files for rhodopsin phylogenetics, see rhodopsin_directory_list.txt for more information. By Chang Jae Choi.
DOI: 10.6084/m9.figshare.8868581.v1
title: Rhodopsin phylogeny files

description: Alignment files and tree files for rhodopsin phylogenetics, see rhodopsin_directory_list.txt for more information. By Chang Jae Choi.
DOI: 10.6084/m9.figshare.8868575.v1
title: CCDB_8139.jpg

description: Single computed slice through a tomographic volume of mitochondria at the Node of Ranvier in rat peripheral nerve root
DOI: 10.6084/m9.figshare.8868533
title: Data for "How Well Do Bibliometric Indicators Correlate with Scientific Eminence? A Comment on Simonton (2016). "

description: Bibliometric indices of 69 eminent psychologists born between 1842 and 1912. <br><br>Reputation, number of works cited, and total citations were computed by Simonton (1992) using 1981-1985 citation records (data obtained from Dean K. Simonton, personal communication, June 17, 2018). <br><br>The h-index was computed in June 2018 using Google Scholar. The search was restricted to the years between each author’s first and last cited publication. Author searches were repeated using the first name (e.g., “Gordon Allport”), the first initial (e.g., “G Allport”), and all the initials when applicable (e.g., “GW Allport”). Duplicate entries were excluded but multiple editions of the same book were retained.<br><br>Reference: Simonton, D. K. (1992). Leaders of American psychology, 1879-1967: Career development, creative output, and professional achievement. Journal of Personality and Social Psychology, 62, 5–17. <br>
DOI: 10.6084/m9.figshare.8868533.v1
title: Data for "How Well Do Bibliometric Indicators Correlate with Scientific Eminence? A Comment on Simonton (2016). "

description: Bibliometric indices of 69 eminent psychologists born between 1842 and 1912. <br><br>Reputation, number of works cited, and total citations were computed by Simonton (1992) using 1981-1985 citation records (data obtained from Dean K. Simonton, personal communication, June 17, 2018). <br><br>The h-index was computed in June 2018 using Google Scholar. The search was restricted to the years between each author’s first and last cited publication. Author searches were repeated using the first name (e.g., “Gordon Allport”), the first initial (e.g., “G Allport”), and all the initials when applicable (e.g., “GW Allport”). Duplicate entries were excluded but multiple editions of the same book were retained.<br><br>Reference: Simonton, D. K. (1992). Leaders of American psychology, 1879-1967: Career development, creative output, and professional achievement. Journal of Personality and Social Psychology, 62, 5–17. <br>
DOI: 10.6084/m9.figshare.8868545.v2
title: constructed lactose-consuming S.cerevisiae strains

description: the original data during constructing three lactose-consuming strains. in addition, the relationship between trehalose and tolerance was studied.
DOI: 10.6084/m9.figshare.8868545.v1
title: constructed lactose-consuming S.cerevisiae strains

description: the original data during constructing three lactose-consuming strains. in addition, the relationship between trehalose and tolerance was studied.
DOI: 10.6084/m9.figshare.8868572.v1
title: data.xlsx

description: Numerical simulation of induced cutting in deep coal
DOI: 10.6084/m9.figshare.8868413
title: Donante vivo de riñon

description: Base de datos
DOI: 10.6084/m9.figshare.8868572.v2
title: data.xlsx

description: Numerical simulation of induced cutting in deep coal
DOI: 10.6084/m9.figshare.8868572.v3
title: data.xlsx

description: Numerical simulation of induced cutting in deep coal
DOI: 10.6084/m9.figshare.8868572.v4
title: Numerical simulation of induced cutting in deep coal

description: Numerical simulation of induced cutting in deep coal
DOI: 10.6084/m9.figshare.8868308
title: Soil Greenhouse Gas Fluxes From Maize Production Under Different Soil Fertility Management Practices in East Africa

description: In sub-Saharan Africa (SSA), few studies have quantified greenhouse gas (GHG) emissions following application of soil amendments, for development of accurate national GHG inventories. Therefore, this study quantified soil GHG emissions using static chambers for two maize cropping seasons (one full year) of four different soil amendments in the central highlands of Kenya. The four treatments were: (i) animal manure; (ii) inorganic fertiliser; (iii) combined animal manure and inorganic fertiliser; and (iv) a no N-control (no amendment) laid out in a randomised complete block design. Cumulative annual soil fluxes (February 2017 – February 2018) ranged from -1.03<i>±</i>0.19 kg CH<sub>4</sub>-C ha<sup>-1</sup> yr<sup>-1</sup> from the manure inorganic fertiliser treatment to -0.09<i>±</i>0.03 kg CH<sub>4</sub>-C ha<sup>-1</sup> yr<sup>-1</sup> from the<sup> </sup>manure treatment, 1391<i>±</i>74 kg CO<sub>2</sub>-C ha<sup>-1</sup> yr<sup>-1</sup> from the control treatment to 3574<i>±</i>113 kg CO<sub>2</sub>-C ha<sup>-1</sup> yr<sup>-1</sup> from the<sup> </sup>manure treatment and 0.13<i>±</i>0.08 to 1.22<i>±</i>0.12 kg N<sub>2</sub>O-N ha<sup>-1</sup> yr<sup>-1</sup> in the control and manure treatments, respectively. Animal manure amendment produced the highest cumulative CO<sub>2</sub> emissions (<i>P</i>&lt;0.001), N<sub>2</sub>O emissions (<i>P</i>&lt;0.001) and maize yields (<i>P</i>=0.002) but the lowest N<sub>2</sub>O yield-scaled emission (YSE) (0.5 g N<sub>2</sub>O–N kg<sup>-1</sup> grain yield). Manure combined with inorganic fertiliser had the highest cumulative CH<sub>4 </sub>uptake (<i>P</i>&lt;0.001) and N<sub>2</sub>O YSE (2.2 g N<sub>2</sub>O–N kg<sup>-1</sup> grain yield). Our results indicate that while the use of animal manure may increase total GHG emissions, the concurrent increase in maize yields results in reduced yield-scaled GHG emissions.
DOI: 10.6073/pasta/d338c48ec580c052a59aec02c847c2bc
title: SBC LTER: Reef: Long-term experiment: Taxon-specific seasonal net primary production (NPP) for macroalgae

description: This dataset provides estimates of seasonal net primary production (NPP) for all taxa of macroalgae sampled in fixed plots at SBC LTER's long-term kelp removal experiment sites. NPP of understory taxa are calculated using field measurements of irradiance and biomass (derived from abundance) and laboratory estimates of taxon-specific photosynthetic parameters. NPP for the giant kelp, Macrocystis pyrifera, is calculated using linear relationships between frond density in a given season and average NPP for that season. Importantly, estimates for understory species include production lost as dissolved exudates while estimates of NPP for giant kelp do not.
DOI: 10.6084/m9.figshare.8867987
title: Mathematica Notebook (.nb) from The ecological and epidemiological consequences of reproductive interference between the vectors <i>Aedes aegypti</i> and <i>Aedes albopictus</i>

description: Mathematica notebook containing the derivations referred to in the text.
DOI: 10.6084/m9.figshare.8867987.v1
title: Mathematica Notebook (.nb) from The ecological and epidemiological consequences of reproductive interference between the vectors <i>Aedes aegypti</i> and <i>Aedes albopictus</i>

description: Mathematica notebook containing the derivations referred to in the text.
DOI: 10.6084/m9.figshare.8867876
title: Comparative genomics identifies potential virulence factors in <i>Clostridium tertium</i> and <i>C. paraputrificum</i>

description: Some well-known Clostridiales species such as <i>Clostridium difficile</i> and <i>C. perfringens</i> are agents of high impact diseases worldwide. Nevertheless, other foreseen Clostridiales species have recently emerged such as <i>Clostridium tertium</i> and <i>C. paraputrificum</i>. Three fecal isolates were identified as <i>Clostridium tertium</i> (Gcol.A2 and Gcol.A43) and <i>C. paraputrificum</i> (Gcol.A11) during public health screening for <i>C. difficile</i> infections in Colombia. <i>C. paraputrificum</i> genomes were highly diverse and contained large numbers of accessory genes. Genetic diversity and accessory gene percentage were lower among the <i>C. tertium</i> genomes than in the <i>C. paraputrificum</i> genomes. <i>C. difficile tcdA</i> and <i>tcdB</i> toxins encoding homologous sequences and other potential virulence factors were also identified. <i>EndoA</i> interferase, a toxic component of the type II toxin-antitoxin system, was found among the <i>C. tertium</i> genomes. <i>toxA</i> was the only toxin encoding gene detected in Gcol.A43, the Colombian isolate with an experimentally-determined high cytotoxic effect. Gcol.A2 and Gcol.A43 had higher sporulation efficiencies than Gcol.A11 (84.5%, 83.8% and 57.0%, respectively), as supported by the greater number of proteins associated with sporulation pathways in the <i>C. tertium</i> genomes compared with the <i>C. paraputrificum</i> genomes (33.3 and 28.4 on average, respectively). This work allowed complete genome description of two clostridiales species revealing high levels of intra-taxa diversity, accessory genomes containing virulence-factors encoding genes (especially in <i>C. paraputrificum</i>), with proteins involved in sporulation processes more highly represented in <i>C. tertium</i>. These finding suggest the need to advance in the study of those species with potential importance at public health level.
DOI: 10.6084/m9.figshare.8867876.v2
title: Comparative genomics identifies potential virulence factors in <i>Clostridium tertium</i> and <i>C. paraputrificum</i>

description: Some well-known Clostridiales species such as <i>Clostridium difficile</i> and <i>C. perfringens</i> are agents of high impact diseases worldwide. Nevertheless, other foreseen Clostridiales species have recently emerged such as <i>Clostridium tertium</i> and <i>C. paraputrificum</i>. Three fecal isolates were identified as <i>Clostridium tertium</i> (Gcol.A2 and Gcol.A43) and <i>C. paraputrificum</i> (Gcol.A11) during public health screening for <i>C. difficile</i> infections in Colombia. <i>C. paraputrificum</i> genomes were highly diverse and contained large numbers of accessory genes. Genetic diversity and accessory gene percentage were lower among the <i>C. tertium</i> genomes than in the <i>C. paraputrificum</i> genomes. <i>C. difficile tcdA</i> and <i>tcdB</i> toxins encoding homologous sequences and other potential virulence factors were also identified. <i>EndoA</i> interferase, a toxic component of the type II toxin-antitoxin system, was found among the <i>C. tertium</i> genomes. <i>toxA</i> was the only toxin encoding gene detected in Gcol.A43, the Colombian isolate with an experimentally-determined high cytotoxic effect. Gcol.A2 and Gcol.A43 had higher sporulation efficiencies than Gcol.A11 (84.5%, 83.8% and 57.0%, respectively), as supported by the greater number of proteins associated with sporulation pathways in the <i>C. tertium</i> genomes compared with the <i>C. paraputrificum</i> genomes (33.3 and 28.4 on average, respectively). This work allowed complete genome description of two clostridiales species revealing high levels of intra-taxa diversity, accessory genomes containing virulence-factors encoding genes (especially in <i>C. paraputrificum</i>), with proteins involved in sporulation processes more highly represented in <i>C. tertium</i>. These finding suggest the need to advance in the study of those species with potential importance at public health level.
DOI: 10.6084/m9.figshare.8867876.v1
title: Comparative genomics identifies potential virulence factors in <i>Clostridium tertium</i> and <i>C. paraputrificum</i>

description: Some well-known Clostridiales species such as <i>Clostridium difficile</i> and <i>C. perfringens</i> are agents of high impact diseases worldwide. Nevertheless, other foreseen Clostridiales species have recently emerged such as <i>Clostridium tertium</i> and <i>C. paraputrificum</i>. Three fecal isolates were identified as <i>Clostridium tertium</i> (Gcol.A2 and Gcol.A43) and <i>C. paraputrificum</i> (Gcol.A11) during public health screening for <i>C. difficile</i> infections in Colombia. <i>C. paraputrificum</i> genomes were highly diverse and contained large numbers of accessory genes. Genetic diversity and accessory gene percentage were lower among the <i>C. tertium</i> genomes than in the <i>C. paraputrificum</i> genomes. <i>C. difficile tcdA</i> and <i>tcdB</i> toxins encoding homologous sequences and other potential virulence factors were also identified. <i>EndoA</i> interferase, a toxic component of the type II toxin-antitoxin system, was found among the <i>C. tertium</i> genomes. <i>toxA</i> was the only toxin encoding gene detected in Gcol.A43, the Colombian isolate with an experimentally-determined high cytotoxic effect. Gcol.A2 and Gcol.A43 had higher sporulation efficiencies than Gcol.A11 (84.5%, 83.8% and 57.0%, respectively), as supported by the greater number of proteins associated with sporulation pathways in the <i>C. tertium</i> genomes compared with the <i>C. paraputrificum</i> genomes (33.3 and 28.4 on average, respectively). This work allowed complete genome description of two clostridiales species revealing high levels of intra-taxa diversity, accessory genomes containing virulence-factors encoding genes (especially in <i>C. paraputrificum</i>), with proteins involved in sporulation processes more highly represented in <i>C. tertium</i>. These finding suggest the need to advance in the study of those species with potential importance at public health level.
DOI: 10.6084/m9.figshare.8867864
title: Identifying Mikania micrantha Kunth in the wild via MMNet

description: the convolutional neural networks training, testing, and relevant imagery data for <em>Mikania micrantha</em> Kunth identification
DOI: 10.6084/m9.figshare.8867864.v1
title: Identifying Mikania micrantha Kunth in the wild via MMNet

description: the convolutional neural networks training, testing, and relevant imagery data for <em>Mikania micrantha</em> Kunth identification
DOI: 10.6084/m9.figshare.8867789
title: Workbook 8. CNTNAP2 gene expression and correlation analysis for APOE4-positive and APOE4-negative females and males. Frontal white matter, Hippocampus, Parietal cortex, Temporal cortex.xlsx

description: CNTNAP2 gene expression and correlation analysis for APOE4-positive and APOE4-negative females and males. Frontal white matter, Hippocampus, Parietal cortex, Temporal cortex
DOI: 10.6084/m9.figshare.8867786
title: Workbook 11. PSEN1 gene expression and correlation analysis for APOE4-positive and APOE4-negative females and males. Frontal white matter, Hippocampus, Parietal cortex, Temporal cortex.xlsx

description: PSEN1 gene expression and correlation analysis in APOE4-positive and APOE4-negative females and males. Frontal white matter, Hippocampus, Parietal cortex, Temporal cortex<br>
DOI: 10.6084/m9.figshare.8867780
title: Workbook 12. APP gene expression and correlation analysis for APOE4-positive and APOE4-negative females and males. Frontal white matter, Hippocampus, Parietal cortex, Temporal cortex.xlsx

description: APP gene expression and correlation analysis in APOE4-positive and APOE4-negative females and males. Frontal white matter, Hippocampus, Parietal cortex, Temporal cortex<br>
DOI: 10.6084/m9.figshare.8867783
title: Workbook 13. ADAM 10 gene expression and correlation analysis for APOE4-positive and APOE4-negative females and males. Frontal white matter, Hippocampus, Parietal cortex, Temporal cortex.xlsx

description: ADAM10 gene expression and correlation analysis in APOE4-positive and APOE4-negative females and males. Frontal white matter, Hippocampus, Parietal cortex, Temporal cortex<br>
DOI: 10.6084/m9.figshare.8867786.v1
title: Workbook 11. PSEN1 gene expression and correlation analysis for APOE4-positive and APOE4-negative females and males. Frontal white matter, Hippocampus, Parietal cortex, Temporal cortex.xlsx

description: PSEN1 gene expression and correlation analysis in APOE4-positive and APOE4-negative females and males. Frontal white matter, Hippocampus, Parietal cortex, Temporal cortex<br>
DOI: 10.6084/m9.figshare.8867789.v1
title: Workbook 8. CNTNAP2 gene expression and correlation analysis for APOE4-positive and APOE4-negative females and males. Frontal white matter, Hippocampus, Parietal cortex, Temporal cortex.xlsx

description: CNTNAP2 gene expression and correlation analysis for APOE4-positive and APOE4-negative females and males. Frontal white matter, Hippocampus, Parietal cortex, Temporal cortex