cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4909532.v1
title: The response of mesophyll conductance and Rubisco activity to water stress vary with the rice supplied nitrogen nutrition

description: <b>Figure 1</b> Rice xylem sap amount (A), root secretion rate (B) and water use efficiency (C) under different N forms and water conditions. The data refer to the mean ±SE (<i>n</i>=4). N, NP, A, AP, NA and NAP represent the nitrate (NO<sub>3</sub><sup>-</sup>), NO<sub>3</sub><sup>-</sup>+PEG6000, ammonium (NH<sub>4</sub><sup>+</sup>), NH<sub>4</sub><sup>+</sup>+PEG6000, mixture of ammonium and nitrate (NO<sub>3</sub><sup>-</sup>+NH<sub>4</sub><sup>+</sup>) and NO<sub>3</sub><sup>-</sup>+NH<sub>4</sub><sup>+</sup>+PEG6000 treatments, respectively. Significant differences (<i>p</i>&lt;5%) between treatments of rice are indicated by different letters. The same as below. <b>Figure 2</b> Rice leaf Chl (A), total N (B) and Rubisco (C) contents under the different N forms and water conditions. <b>Figure 3</b> The relationships of net photosynthesis (<i>A</i>) and water use efficiency (WUE) to the mesophyll conductance (<i>g<sub>m</sub></i>), stomatal conductance (<i>g<sub>s</sub></i>) and ratio of g<sub>m</sub>/g<sub>s</sub> in rice leaves.
DOI: 10.6084/m9.figshare.4909499
title: Scores for mastoidectomy performances

description: <b>Data description</b><br>Attending surgeons and residents performed mastoidectomies using a virtual temporal bone surgery simulator developed at the Ohio Supercomputer Center. Those mastoidectomy performances were evaluated by attending surgeons using a instrument consisting of several binary questions. The mastoidectomy performance was played back for the raters using the software. Raters were blinded to the identity of the person who performed the surgery. There were two sets of ratings, trial 1 and trial 2. The text of the binary questions is in 'metric_instructions.csv'. The rating data is in 'mastoid_test.csv'.<br>This data was acquired under work supported by NIDCD, R01DC011321.<br>For questions, contact Thomas Kerwin, kerwin@osc.edu.<br><b>Column definitions</b><br>These are the descriptions for the columns in 'mastoid_test.csv'. I refer to the person who performed the virtual surgery as the 'surgeon' and the person rating the performance as the 'grader'.<br>* site: the institution where the surgeon resides* Duration: time in seconds that it took the grader to evaluate the performance* grader: id of the grader* drillingID: an id that is unique for each surgery* PGY: This gives the post graduate year of the surgeon. "PGY1" means a person in their first year of residency. Attending surgeons have a value of "Expert". "MS" is a medical student not yet graduated. "Fellow" refers to a fellow.* rating: a subjective rating given by the graders for the overall quality of the surgery. Three values: Novice, Intermediate, Expert* value: binary rating given for the specified rating item* questionNum: rating item number* userid: unique id for each surgeon* trial: specifies if the grading was done using the first or second set of binary rating questions
DOI: 10.6084/m9.figshare.4909499.v1
title: Scores for mastoidectomy performances

description: <b>Data description</b><br>Attending surgeons and residents performed mastoidectomies using a virtual temporal bone surgery simulator developed at the Ohio Supercomputer Center. Those mastoidectomy performances were evaluated by attending surgeons using a instrument consisting of several binary questions. The mastoidectomy performance was played back for the raters using the software. Raters were blinded to the identity of the person who performed the surgery. There were two sets of ratings, trial 1 and trial 2. The text of the binary questions is in 'metric_instructions.csv'. The rating data is in 'mastoid_test.csv'.<br>This data was acquired under work supported by NIDCD, R01DC011321.<br>For questions, contact Thomas Kerwin, kerwin@osc.edu.<br><b>Column definitions</b><br>These are the descriptions for the columns in 'mastoid_test.csv'. I refer to the person who performed the virtual surgery as the 'surgeon' and the person rating the performance as the 'grader'.<br>* site: the institution where the surgeon resides* Duration: time in seconds that it took the grader to evaluate the performance* grader: id of the grader* drillingID: an id that is unique for each surgery* PGY: This gives the post graduate year of the surgeon. "PGY1" means a person in their first year of residency. Attending surgeons have a value of "Expert". "MS" is a medical student not yet graduated. "Fellow" refers to a fellow.* rating: a subjective rating given by the graders for the overall quality of the surgery. Three values: Novice, Intermediate, Expert* value: binary rating given for the specified rating item* questionNum: rating item number* userid: unique id for each surgeon* trial: specifies if the grading was done using the first or second set of binary rating questions
DOI: 10.6084/m9.figshare.4909346
title: Application of GC/MS Soft Ionization for Isomeric Biological Compound Analysis

description: Isomers are compounds with the same molecular formula. Many different types of isomers are ubiquitous and play important roles in living organisms. Despite their early discovery, the actual analysis of isomers has been tricky and has confounded researchers. Using mass spectrometry (MS) to distinguish or identify isomers is an emergent topic and challenge for analytical chemists. We review some techniques for analyzing isomers with emphasis on MS, e.g., the roles of ion reaction, hydrogen–deuterium exchange, ion mobility mass spectrometry, ion spectroscopy, and energy change in producing isomer-specific fragments. In particular, soft ionization for gas chromatography–mass spectrometry (GC–MS) is a focus in this review. Awareness of the advantages and technical problems of these techniques would inspire innovation in future approaches.
DOI: 10.6084/m9.figshare.4909346.v1
title: Application of GC/MS Soft Ionization for Isomeric Biological Compound Analysis

description: Isomers are compounds with the same molecular formula. Many different types of isomers are ubiquitous and play important roles in living organisms. Despite their early discovery, the actual analysis of isomers has been tricky and has confounded researchers. Using mass spectrometry (MS) to distinguish or identify isomers is an emergent topic and challenge for analytical chemists. We review some techniques for analyzing isomers with emphasis on MS, e.g., the roles of ion reaction, hydrogen–deuterium exchange, ion mobility mass spectrometry, ion spectroscopy, and energy change in producing isomer-specific fragments. In particular, soft ionization for gas chromatography–mass spectrometry (GC–MS) is a focus in this review. Awareness of the advantages and technical problems of these techniques would inspire innovation in future approaches.
DOI: 10.6084/m9.figshare.4907381
title: II.2 - Agrogenom intermediary result files: detection of potential paralogous lineages

description: File set as generated by find_ancestral_duplications.py program:modified_trees/:<br>Gene trees are modified where branch supports were low and SPR moves allowed to decrease the amount of duplication and loss events; saved as Newick trees.normed_trees/:the same trees saved in custom phyloXML format including the reconciliation information.<br>treeshelves/:<br>the same annotated tree as serialized Python objects.subfams/:lists of (posibly overlapping) unicopy leaf sets extracted from gene families<br>subtrees/:unicopy_subtrees extracted from the (modified) gene trees, the leaf labels only bear the species label; saved as Newick trees.subtree2leaves/:dictionary of subfamily leaf sets to the corresponding subtree files.
DOI: 10.6084/m9.figshare.4907429
title: Data set BMC HiB

description: "<i>Haemophilus influenzae</i> as a common etiologic agent in infants hospitalized for community-acquired pneumonia"<br><b>Objetive: </b>Determinate the prevalence, epidemiological and clinical characteristics of <i>Haemophilus influenzae</i> type B and the Non-typeable <i>Haemophilus influenzae</i> in infants under 1 year old hospitalized with community acquired pneumonia in Peru from 2010 to 2012. <b>Results:</b> Among the 339 infants with CAP, <i>Haemophilus influenzae spp</i>. was detected in 26.84% of samples via PCR. A total of 22 cases of Hib positives samples were observed being paroxysm of cough the only associated symptom (p&lt;0.001) in this group. Low vaccination coverage was observed across all patients with Hib positive samples<br>
DOI: 10.6084/m9.figshare.4907378
title: II.0 - Agrogenom database gene annotation table

description: Annotation table including gene positions on replicons and their function.
DOI: 10.6084/m9.figshare.4907381.v2
title: II.2 - Agrogenom intermediary result files: detection of potential paralogous lineages

description: File set as generated by find_ancestral_duplications.py program:modified_trees/:<br>Gene trees are modified where branch supports were low and SPR moves allowed to decrease the amount of duplication and loss events; saved as Newick trees.normed_trees/:the same trees saved in custom phyloXML format including the reconciliation information.<br>treeshelves/:<br>the same annotated tree as serialized Python objects.subfams/:lists of (posibly overlapping) unicopy leaf sets extracted from gene families<br>subtrees/:unicopy_subtrees extracted from the (modified) gene trees, the leaf labels only bear the species label; saved as Newick trees.subtree2leaves/:dictionary of subfamily leaf sets to the corresponding subtree files.
DOI: 10.6084/m9.figshare.4907378.v2
title: II.0 - Agrogenom database gene annotation table

description: Annotation table including gene positions on replicons and their function.
DOI: 10.6084/m9.figshare.4907381.v1
title: II.2 Agrogenom intermediary result files: detection of potential paralogous lineages

description: File set as generated by find_ancestral_duplications.py program:modified_trees/:<br>Gene trees are modified where branch supports were low and SPR moves allowed to decrease the amount of duplication and loss events; saved as Newick trees.normed_trees/:the same trees saved in custom phyloXML format including the reconciliation information.<br>treeshelves/:<br>the same annotated tree as serialized Python objects.subfams/:lists of (posibly overlapping) unicopy leaf sets extracted from gene families<br>subtrees/:unicopy_subtrees extracted from the (modified) gene trees, the leaf labels only bear the species label; saved as Newick trees.subtree2leaves/:dictionary of subfamily leaf sets to the corresponding subtree files.
DOI: 10.6084/m9.figshare.4907378.v1
title: II.0 Agrogenom database gene annotation table

description: Annotation table including gene positions on replicons and their function.
DOI: 10.6084/m9.figshare.4907351
title: I.1 - Agrogenom homologous sequence clustering

description: Clustering of protein sequences extracted from genomes (see item #I.0) using BLAST similarity search and SiLiX (single-linkage clustering) followed by HiFiX (alignment-based refinement of clustering; splits clusters into subclusters with more homogeneous domain structures)<br><br>families/49RHIZOB.blastout file is intentionally missing because too bulky (11Gb); please re-compute it yourself or contact the author for sharing.
DOI: 10.6084/m9.figshare.4907429.v1
title: Data set BMC HiB

description: "<i>Haemophilus influenzae</i> as a common etiologic agent in infants hospitalized for community-acquired pneumonia"
DOI: 10.6084/m9.figshare.4907306
title: Dispersal syndromes in freshwater fishes

description: Data from Comte & Olden (accepted, PRSL-B) containing dispersal metrics and trait values for 116 freshwater fish species from a global review. <br>
DOI: 10.6084/m9.figshare.4907285
title: Beam electrons as a source of H-alpha flare ribbons

description: Data for the paperDruett, M. et al. Beam electrons as a source of H-a flare ribbons. Nat. Commun. 8, 15905 doi: 10.1038/ncomms15905 (2017).
DOI: 10.6084/m9.figshare.4907270
title: Field- and Lab-Based Potentiometric Titrations of Microbial Mats from the Fairmont Hot Spring, Canada

description: Potentiometric titrations are an effective tool to constrain the protonation constants and site concentrations for microbial surface ligands. Protonation models developed from these experiments are often coupled with data from metal adsorption experiments to calculate microbial ligand-metal binding constants. Ultimately, the resulting surface complexation models can be used to predict metal immobilization behavior across diverse chemical conditions. However, most protonation and metal-ligand thermodynamic constants have been generated in laboratory experiments that use cultured microbes which may differ in their chemical reactivity from environmental samples. In this study, we investigate the use of <i>in situ</i> field potentiometric titrations of microbial mats at a carbonate hot spring located at Fairmont Hot Springs, British Columbia, with the aim to study microbial reactivities in a natural field system. We found that authigenic carbonate minerals complicated the potentiometric titration process due to a “carbonate spike” introduced by the contribution of inorganic carbonate mineral dissolution and subsequent carbonate speciation changes during the transition from low to high pH. This inhibits the determination of microbial surface ligand variety and concentrations. Our preliminary study also highlights the need for developing novel probes to quantify <i>in situ</i> microbial mat reactivity in future field investigations.
DOI: 10.6084/m9.figshare.4907306.v1
title: Dispersal syndromes in freshwater fishes

description: Data from Comte & Olden (accepted, PRSL-B) containing dispersal metrics and trait values for 116 freshwater fish species from a global review. <br>
DOI: 10.6084/m9.figshare.4907351.v1
title: I.1 Agrogenom homologous sequence clustering

description: Clustering of protein sequences extracted from genomes (see item #I.0) using BLAST similarity search and SiLiX (single-linkage clustering) followed by HiFiX (alignment-based refinement of clustering; splits clusters into subclusters with more homogeneous domain structures)<br><br>families/49RHIZOB.blastout file is intentionally missing because too bulky (11Gb); please re-compute it yourself or contact the author for sharing.
DOI: 10.6084/m9.figshare.4907270.v1
title: Field- and Lab-Based Potentiometric Titrations of Microbial Mats from the Fairmont Hot Spring, Canada

description: Potentiometric titrations are an effective tool to constrain the protonation constants and site concentrations for microbial surface ligands. Protonation models developed from these experiments are often coupled with data from metal adsorption experiments to calculate microbial ligand-metal binding constants. Ultimately, the resulting surface complexation models can be used to predict metal immobilization behavior across diverse chemical conditions. However, most protonation and metal-ligand thermodynamic constants have been generated in laboratory experiments that use cultured microbes which may differ in their chemical reactivity from environmental samples. In this study, we investigate the use of <i>in situ</i> field potentiometric titrations of microbial mats at a carbonate hot spring located at Fairmont Hot Springs, British Columbia, with the aim to study microbial reactivities in a natural field system. We found that authigenic carbonate minerals complicated the potentiometric titration process due to a “carbonate spike” introduced by the contribution of inorganic carbonate mineral dissolution and subsequent carbonate speciation changes during the transition from low to high pH. This inhibits the determination of microbial surface ligand variety and concentrations. Our preliminary study also highlights the need for developing novel probes to quantify <i>in situ</i> microbial mat reactivity in future field investigations.
DOI: 10.6084/m9.figshare.4907285.v1
title: Beam electrons as a source of H-alpha flare ribbons

description: Data for the paperDruett, M. et al. Beam electrons as a source of H-a flare ribbons. Nat. Commun. 8, 15905 doi: 10.1038/ncomms15905 (2017).
DOI: 10.6084/m9.figshare.4907165
title: RNA-seq raw data of PS-N_2_1

description: File 1 of RNA-seq raw data of N48-2 biological replicate 2 spikelets at pollen mother cell stage. Paired-end sequencing strategy was applied on the Illumina HiSeq 4000 sequencing platform.
DOI: 10.6084/m9.figshare.4907165.v1
title: RNA-seq raw data of PS-N_2_1

description: File 1 of RNA-seq raw data of N48-2 biological replicate 2 spikelets at pollen mother cell stage. Paired-end sequencing strategy was applied on the Illumina HiSeq 4000 sequencing platform.
DOI: 10.6084/m9.figshare.4907141
title: metal ions

description: 5 types of metal ions
DOI: 10.6084/m9.figshare.4907147
title: plosone_db.rar

description: The datsets that we used for mining high utility-probability sequential patterns
DOI: 10.6084/m9.figshare.4907141.v1
title: metal ions

description: 5 types of metal ions
DOI: 10.6084/m9.figshare.4907087
title: I.4 - Agrogenom species phylogeny

description: Different methods were attempted to estimate the species tree:a) concatenating gene alignements and using RAxML (under a GTRCAT model, 50 rate categories) to infer the tree from the single concatenate: 1) of 455 core unicopy gene families present in all 47 genomes; 2) of 49 unicopy ribosomal gene families present in at least 45/47 genomes;b) using multiple concatenate of a random jackknife sample of genes and inferring a tree with PhyML (under a GTR+G8+I model) for each of them, and then generate the MRE consensus and use split frequency from the sample's trees to infer branch support: 3) from 500 samples of 25 gene families out of the 455 unicopy core families.<br><br>The reftree/ folder contains the chosen phylogeny, which is based on strategy (3) and further tree annotations such as internal node names.
DOI: 10.6084/m9.figshare.4907147.v1
title: plosone_db.rar

description: The datsets that we used for mining high utility-probability sequential patterns
DOI: 10.6084/m9.figshare.4907051
title: I.3 - Agrogenom gene phylogenies

description: 10774 gene family trees.Obtained with PhyML, GTR+G8+I model and SH-like branch supports from codon alignments (see project item #1) of all families with &gt;=3 sequences.
DOI: 10.6084/m9.figshare.4907066
title: II.1 - Agrogenom rooted gene phylogenies

description: 10774 rooted gene family trees.Obtained from unrooted gene trees (see project item #2) by two different means:- if the gene trees were multicopy, i.e. had several tips assigned to the same species: using TPMS combo rooting criterion minimizing species multiplicity (gene copy number) of clades and taxonomic depth of the anccesral node;<br>- if the gene tree was unicopy, i.e. had tips assigned at most one species: using Prunier reconciliation and rooting according to the most parsimonious transfer scenario.
DOI: 10.6084/m9.figshare.4907087.v2
title: I.4 - Agrogenom species phylogeny

description: Different methods were attempted to estimate the species tree:a) concatenating gene alignements and using RAxML (under a GTRCAT model, 50 rate categories) to infer the tree from the single concatenate: 1) of 455 core unicopy gene families present in all 47 genomes; 2) of 49 unicopy ribosomal gene families present in at least 45/47 genomes;b) using multiple concatenate of a random jackknife sample of genes and inferring a tree with PhyML (under a GTR+G8+I model) for each of them, and then generate the MRE consensus and use split frequency from the sample's trees to infer branch support: 3) from 500 samples of 25 gene families out of the 455 unicopy core families.<br><br>The reftree/ folder contains the chosen phylogeny, which is based on strategy (3) and further tree annotations such as internal node names.
DOI: 10.6084/m9.figshare.4907051.v2
title: I.3 - Agrogenom gene phylogenies

description: 10774 gene family trees.Obtained with PhyML, GTR+G8+I model and SH-like branch supports from codon alignments (see project item #1) of all families with &gt;=3 sequences.
DOI: 10.6084/m9.figshare.4907087.v1
title: 4 - Agrogenom species phylogeny

description: Different methods were attempted to estimate the species tree:a) concatenating gene alignements and using RAxML (under a GTRCAT model, 50 rate categories) to infer the tree from the single concatenate: 1) of 455 core unicopy gene families present in all 47 genomes; 2) of 49 unicopy ribosomal gene families present in at least 45/47 genomes;b) using multiple concatenate of a random jackknife sample of genes and inferring a tree with PhyML (under a GTR+G8+I model) for each of them, and then generate the MRE consensus and use split frequency from the sample's trees to infer branch support: 3) from 500 samples of 25 gene families out of the 455 unicopy core families.<br><br>The reftree/ folder contains the chosen phylogeny, which is based on strategy (3) and further tree annotations such as internal node names.
DOI: 10.6084/m9.figshare.4907024
title: I.2 - Agrogenom homologous gene family alignments

description: 6662 gene families nucleic sequence aligned at the codon level.<br>Obtained with MUSCLE on corresponding protein alignments and then pal2nal to reverse-translate in CDS alignments.
DOI: 10.6084/m9.figshare.4907051.v1
title: 2 - Agrogenom gene phylogenies

description: 10774 gene family trees.Obtained with PhyML, GTR+G8+I model and SH-like branch supports from codon alignments (see project item #1) of all families with &gt;=3 sequences.
DOI: 10.6084/m9.figshare.4907066.v1
title: Agrogenom rooted gene phylogenies

description: 10774 rooted gene family trees.Obtained by two different means:- if the gene trees were multicopy, i.e. had several tips assigned to the same species: using TPMS combo rooting criterion minimizing species multiplicity (gene copy number) of clades and taxonomic depth of the anccesral node;<br>- if the gene tree was unicopy, i.e. had tips assigned at most one species: using Prunier reconciliation and rooting according to the most parsimonious transfer scenario.
DOI: 10.6084/m9.figshare.4907024.v2
title: I.2 - Agrogenom homologous gene family alignments

description: 6662 gene families nucleic sequence aligned at the codon level.<br>Obtained with MUSCLE on corresponding protein alignments and then pal2nal to reverse-translate in CDS alignments.
DOI: 10.6084/m9.figshare.4907009.v1
title: Ex vivo turtle cortex with visual stimulation [Shew Lab & Wessel Lab]

description: This data set was generated and analyzed for our paper, titled, "Adaptation towards scale-free dynamics improves cortical stimulus discrimination at the cost of reduced detection", published in PLOS Computational Biology.
DOI: 10.6084/m9.figshare.4907024.v1
title: 1 - Agrogenom homologous gene family alignments

description: 6662 gene families nucleic sequence aligned at the codon level.<br>Used MUSCLE on corresponding protein alignments and then pal2nal to reverse-translate in CDS alignments.
DOI: 10.6084/m9.figshare.4906976
title: 5 types of nucleotides(ADP,ATP,AMP,GDP,GTP), DNA and HEME

description: 5 types pf nucleotide (ADP,ATP,AMP,GDP,GTP), DNA and HEME
DOI: 10.6084/m9.figshare.4907066.v2
title: 3- Agrogenom rooted gene phylogenies

description: 10774 rooted gene family trees.Obtained from unrooted gene trees (see project item #2) by two different means:- if the gene trees were multicopy, i.e. had several tips assigned to the same species: using TPMS combo rooting criterion minimizing species multiplicity (gene copy number) of clades and taxonomic depth of the anccesral node;<br>- if the gene tree was unicopy, i.e. had tips assigned at most one species: using Prunier reconciliation and rooting according to the most parsimonious transfer scenario.
DOI: 10.6084/m9.figshare.4907009.v2
title: Ex vivo turtle cortex with visual stimulation [Shew Lab & Wessel Lab]

description: This data set was generated and analyzed for our paper, titled, "Adaptation towards scale-free dynamics improves cortical stimulus discrimination at the cost of reduced detection", published in PLOS Computational Biology.