cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.157349
title: Bacteria cladogram

description: This cladogram is a simplified version of figure 2 in Wu & Eisen ("A simple fast and accurate method of phylogenomic inference, 2008, Genome Biology 2008, 9:R151, doi:10.1186/gb-2008-9-10-r151). Also indicated in the tree are the expected possitions of eukaryote sequences with an endosymbiotic origin (indicated as CYANOBACTERIA and MITOCHONDRIA).
DOI: 10.6084/m9.figshare.177719.v2
title: File S1. Gene data from V. cholera and V. mimicus.

description: Gene data of SI region from seven V. cholerae and one V. mimicus genomes used in this study.
DOI: 10.6084/m9.figshare.159692.v2
title: Raw data for figures 1-7: Anacardic acid, a histone acetyltransferase inhibitor, modulates LPS-induced IL-8 expression in a human alveolar epithelial cell line A549.

description: Figure 1: The dose- and time- dependent IL-8 release from A549 cells in vitro. Figure 2: Time course analysis of LPS-mediated IL-8 gene expression in A549 cells in vitro. Figure 3: Time course analysis of LPS-induced histone H4 acetylation at the promoter region of the IL-8 gene in A549 cells in vitro . Figure 4: Effect of TSA on LPS-stimulated IL-8 release from A549 cells in vitro. Figure 5: Time course analysis of TSA on LPS-stimulated IL-8 gene activation from A549 cells in vitro. Figure 6: Effect of anacardic acid on LPS-stimulated IL-8 release from A549 cells in vitro. Figure 7: Time course analysis of anacardic acid on LPS-stimulated IL-8 gene activation in A549 cells in vitro.
DOI: 10.6084/m9.figshare.177719.v1
title: File S1

description: Gene data of SI region from seven V. cholerae and one V. mimicus genomes used in this study.
DOI: 10.6084/m9.figshare.157346
title: Bacteria cladogram

description: This cladogram is a simplified version of figure 2 in Wu & Eisen ("A simple fast and accurate method of phylogenomic inference, 2008, Genome Biology 2008, 9:R151, doi:10.1186/gb-2008-9-10-r151). Also indicated in the tree are the expected possitions of eukaryote sequences with an endosymbiotic origin (indicated as CYANOBACTERIA and MITOCHONDRIA).
DOI: 10.6084/m9.figshare.159692.v1
title: Raw data for figures 1 - 7.

description: Figure 1: The dose- and time- dependent IL-8 release from A549 cells in vitro. Figure 2: Time course analysis of LPS-mediated IL-8 gene expression in A549 cells in vitro. Figure 3: Time course analysis of LPS-induced histone H4 acetylation at the promoter region of the IL-8 gene in A549 cells in vitro . Figure 4: Effect of TSA on LPS-stimulated IL-8 release from A549 cells in vitro. Figure 5: Time course analysis of TSA on LPS-stimulated IL-8 gene activation from A549 cells in vitro. Figure 6: Effect of anacardic acid on LPS-stimulated IL-8 release from A549 cells in vitro. Figure 7: Time course analysis of anacardic acid on LPS-stimulated IL-8 gene activation in A549 cells in vitro.
DOI: 10.6084/m9.figshare.157335
title: Solar Orbiter Data Analysis Working Group update

description: Update on activities of Solar Orbiter Data Analysis Working Group (SODAWG).
DOI: 10.6084/m9.figshare.157265
title: Atomic fragment-based descriptor test data

description: Test data set and its corresponding descriptor values for the atomic descriptors described in the paper "Enrichment of True Positives from Structural Alerts Through the Use of Novel Atomic Fragment Based Descriptors" by Anthony Long and Patrik Rydberg. The molecules in test.smi have been used with the java-code published and output printed to a csv file. The atom numbering are consecutive according to the SMILES strings.
DOI: 10.6084/m9.figshare.157323
title: Program script

description: Script used for the detection of synaptic events written for the scientific/engineering program Igor Pro that allows users to define their own event detection parameters.
DOI: 10.6084/m9.figshare.157335.v1
title: Solar Orbiter Data Analysis Working Group update

description: Update on activities of Solar Orbiter Data Analysis Working Group (SODAWG).
DOI: 10.6084/m9.figshare.157262
title: Raw data: genomic signatures

description: Genomic dissimilarity [δ(f,g)] values between Streptococcus strains.
DOI: 10.6084/m9.figshare.157265.v1
title: Atomic fragment-based descriptor test data

description: Test data set and its corresponding descriptor values for the atomic descriptors described in the paper "Enrichment of True Positives from Structural Alerts Through the Use of Novel Atomic Fragment Based Descriptors" by Anthony Long and Patrik Rydberg. The molecules in test.smi have been used with the java-code published and output printed to a csv file. The atom numbering are consecutive according to the SMILES strings.
DOI: 10.6084/m9.figshare.157261
title: Raw data: average amino acid identiy

description: Percentage of average amino acid identity (AAI) between Streptococcus strains.
DOI: 10.6084/m9.figshare.157323.v2
title: Program script

description: Script used for the detection of synaptic events written for the scientific/engineering program Igor Pro that allows users to define their own event detection parameters.
DOI: 10.6084/m9.figshare.157260
title: Raw data: MLSA nucleotide sequences

description: Similarity values for the MLSA nucleotide sequences (lower left) and 16S rRNA gene sequences (upper right) for the Streptococcus strains.
DOI: 10.6084/m9.figshare.157323.v1
title: Program script

description: Script used for the detection of synaptic events written for the scientific/engineering program Igor Pro that allows users to define their own event detection parameters.
DOI: 10.6084/m9.figshare.157262.v1
title: Table 5 raw data

description: Genomic dissimilarity [δ(f,g)] values between Streptococcus strains.
DOI: 10.6084/m9.figshare.157260.v1
title: Table 2 raw data

description: Similarity values for the MLSA nucleotide sequences (lower left) and 16S rRNA gene sequences (upper right) for the Streptococcus strains.
DOI: 10.6084/m9.figshare.157261.v1
title: Table 4 raw data

description: Percentage of average amino acid identity (AAI) between Streptococcus strains.
DOI: 10.6084/m9.figshare.157262.v2
title: Table 5 raw data

description: Genomic dissimilarity [δ(f,g)] values between Streptococcus strains.
DOI: 10.6084/m9.figshare.157261.v2
title: Table 4 raw data

description: Percentage of average amino acid identity (AAI) between Streptococcus strains.
DOI: 10.6084/m9.figshare.157258.v1
title: Research proposal: Integrating computational science with biology to study collective animal behavior

description: This is a three-page research proposal that we wrote for funding requests. In this document, we propose an integration of our digital swarm evolution platform with a biological system to study the evolution of simulated prey behavior in response to predation. Particularly, we are looking to establish whether the predator confusion effect exists, and whether it can select for swarming behavior in groups of evolving prey that initially move randomly.
DOI: 10.6084/m9.figshare.157260.v2
title: Table 2 raw data

description: Similarity values for the MLSA nucleotide sequences (lower left) and 16S rRNA gene sequences (upper right) for the Streptococcus strains.
DOI: 10.6084/m9.figshare.157262.v3
title: Table 5 raw data

description: Genomic dissimilarity [δ(f,g)] values between Streptococcus strains.
DOI: 10.6084/m9.figshare.157260.v3
title: Table 2 raw data

description: Similarity values for the MLSA nucleotide sequences (lower left) and 16S rRNA gene sequences (upper right) for the Streptococcus strains.
DOI: 10.6084/m9.figshare.157261.v3
title: Table 4 raw data

description: Percentage of average amino acid identity (AAI) between Streptococcus strains.
DOI: 10.6084/m9.figshare.157262.v4
title: Table 5 raw data

description: Genomic dissimilarity [δ(f,g)] values between Streptococcus strains.
DOI: 10.6084/m9.figshare.157262.v6
title: Raw data: genomic signatures

description: Genomic dissimilarity [δ(f,g)] values between Streptococcus strains.
DOI: 10.6084/m9.figshare.157256.v2
title: Lesson Plan for One Hour Undergraduate Discussion Session on Noninvasive Prenatal Diagnostics using Next Generation Sequencing.

description: This document provides an example lesson plan for a 1-hour discussion session at the undergraduate level on noninvasive prenatal diagnostics using next generation sequencing. The goals of this discussion session are to: 1) introduce students to concept of noninvasive prenatal genetic testing using next generation sequencing; 2) provide students with ability to evaluate evidence for the technology underlying new genetic testing methods; and 3) Provide students with the background to interpret results of a diagnostic test for trisomy 21.
DOI: 10.6084/m9.figshare.157260.v4
title: Table 2 raw data

description: Similarity values for the MLSA nucleotide sequences (lower left) and 16S rRNA gene sequences (upper right) for the Streptococcus strains.
DOI: 10.6084/m9.figshare.157261.v4
title: Table 4 raw data

description: Percentage of average amino acid identity (AAI) between Streptococcus strains.
DOI: 10.6084/m9.figshare.157262.v5
title: Table 5 raw data

description: Genomic dissimilarity [δ(f,g)] values between Streptococcus strains.
DOI: 10.6084/m9.figshare.157246
title: Simulation scripts

description: Scripts used to simulate and analyze the hypothetical pharmacokinetic model data
DOI: 10.6084/m9.figshare.157256.v3
title: Lesson Plan for One Hour Undergraduate Discussion Session on Noninvasive Prenatal Diagnostics using Next Generation Sequencing.

description: This document provides an example lesson plan for a 1-hour discussion session at the undergraduate level on noninvasive prenatal diagnostics using next generation sequencing. The goals of this discussion session are to: 1) introduce students to concept of noninvasive prenatal genetic testing using next generation sequencing; 2) provide students with ability to evaluate evidence for the technology underlying new genetic testing methods; and 3) Provide students with the background to interpret results of a diagnostic test for trisomy 21.
DOI: 10.6084/m9.figshare.157260.v6
title: Raw data: MLSA nucleotide sequences

description: Similarity values for the MLSA nucleotide sequences (lower left) and 16S rRNA gene sequences (upper right) for the Streptococcus strains.
DOI: 10.6084/m9.figshare.157260.v5
title: Table 2 raw data

description: Similarity values for the MLSA nucleotide sequences (lower left) and 16S rRNA gene sequences (upper right) for the Streptococcus strains.
DOI: 10.6084/m9.figshare.157211
title: Number of microglia in the nTS three days post chorda tympani transection in mice treated with naloxone

description: The number of microglia in the rostral (RC) subnucleus of the nTS at three days post CTx in mice treated with naloxone (NLX). Three animals from each treatment group (0mg, 5mg, 10mg) were analyzed. From each animal, six microglial counts were taken throughout the rostral levels on both intact (Int) and transected (Tx) sides. The cell counts were analyzed using SPSS software with appropriate ANOVAs and Tukey’s post-hoc analysis. Significance was defined as p&lt;0.05.
DOI: 10.6084/m9.figshare.157210
title: Two-bottle preference experiments with water and 200mM sucrose before and after treatment with naloxone

description: Two-bottle preference experiments with water and 200mM sucrose before and after treatment with naloxone. In the first set of experiments in Figure 7A, three mice had continual access to water and sugar solution. The animals were trained for three days before receiving naloxone treatment. For each day, the total amounts of each liquid consumed were used to calculate the preference score [sucrose (mL)/total fluid (mL)] such that the higher the score indicates the greater the sweet preference with 0.5 representing no preference. In the second set of experiments in Figure 7B, four mice were placed on a 22.5 hour water deprivation schedule where they had access to bottles of water and sugar solution the remaining 1.5 hours per day.
DOI: 10.6084/m9.figshare.157256.v4
title: Lesson Plan for One Hour Undergraduate Discussion Session on Noninvasive Prenatal Diagnostics using Next Generation Sequencing

description: This document provides an example lesson plan for a 1-hour discussion session at the undergraduate level on noninvasive prenatal diagnostics using next generation sequencing. The goals of this discussion session are to: 1) introduce students to concept of noninvasive prenatal genetic testing using next generation sequencing; 2) provide students with ability to evaluate evidence for the technology underlying new genetic testing methods; and 3) provide students with the background to interpret results of a diagnostic test for trisomy 21.
DOI: 10.6084/m9.figshare.157246.v1
title: Simulation scripts

description: Scripts used to simulate and analyze the hypothetical pharmacokinetic model data
DOI: 10.6084/m9.figshare.157209
title: Two-bottle preference experiments with water and 300mM sucrose before and after chorda tympani transection and treatment with naloxone

description: Two-bottle preference experiments with water and 300mM sucrose before and after chorda tympani transection (CTx) and treatment with naloxone (NLX). In the first set of experiments in Figure 6A, four mice had continual access to the two bottles (water and sugar solution). The animals were trained for three days before undergoing CTx and receiving naloxone or saline treatment (post). For each day, the total amounts of each liquid consumed were used to calculate the preference score [sucrose (mL)/total fluid (mL)]. The higher the score indicates the greater the sweet preference with 0.5 representing no preference. In the second set of experiments in Figure 6B, another four mice were placed on a 22.5 hour water deprivation schedule where they had access to bottles of water and sugar solution the remaining 1.5 hours per day. The animals were trained for four days before undergoing CTx and receiving naloxone or saline treatment.
DOI: 10.6084/m9.figshare.157210.v1
title: Figure 7 raw data

description: Two-bottle preference experiments with water and 200mM sucrose before and after treatment with naloxone. In the first set of experiments in Figure 7A, three mice had continual access to water and sugar solution. The animals were trained for three days before receiving naloxone treatment. For each day, the total amounts of each liquid consumed were used to calculate the preference score [sucrose (mL)/total fluid (mL)] such that the higher the score indicates the greater the sweet preference with 0.5 representing no preference. In the second set of experiments in Figure 7B, four mice were placed on a 22.5 hour water deprivation schedule where they had access to bottles of water and sugar solution the remaining 1.5 hours per day.
DOI: 10.6084/m9.figshare.157210.v2
title: Two-bottle preference experiments with water and 200mM sucrose before and after treatment with naloxone

description: Two-bottle preference experiments with water and 200mM sucrose before and after treatment with naloxone. In the first set of experiments in Figure 7A, three mice had continual access to water and sugar solution. The animals were trained for three days before receiving naloxone treatment. For each day, the total amounts of each liquid consumed were used to calculate the preference score [sucrose (mL)/total fluid (mL)] such that the higher the score indicates the greater the sweet preference with 0.5 representing no preference. In the second set of experiments in Figure 7B, four mice were placed on a 22.5 hour water deprivation schedule where they had access to bottles of water and sugar solution the remaining 1.5 hours per day.
DOI: 10.6084/m9.figshare.157211.v2
title: Number of microglia in the nTS three days post chorda tympani transection in mice treated with naloxone

description: The number of microglia in the rostral (RC) subnucleus of the nTS at three days post CTx in mice treated with naloxone (NLX). Three animals from each treatment group (0mg, 5mg, 10mg) were analyzed. From each animal, six microglial counts were taken throughout the rostral levels on both intact (Int) and transected (Tx) sides. The cell counts were analyzed using SPSS software with appropriate ANOVAs and Tukey’s post-hoc analysis. Significance was defined as p&lt;0.05.
DOI: 10.6084/m9.figshare.157208
title: Number of microglia in the nTS three days post chorda tympani transection in C57BL6/J, C3HeB and C3H mice

description: The number of microglia in the rostral central (RC) subnucleus of the nTS at three days post chorda tympani transection (CTx) in C57BL6/J (wild-type), C3HeB (TLR4 wild-type) and C3H (TLR4 mutant) animals. Three animals from each genotype were analyzed. From each animal, six microglial counts were taken throughout the rostral levels on both intact (Int) and transected (Tx) sides. The cell counts were analyzed using SPSS software with appropriate ANOVAs and Tukey’s post-hoc analysis. Significance was defined as p&lt;0.05.
DOI: 10.6084/m9.figshare.157209.v2
title: Two-bottle preference experiments with water and 300mM sucrose before and after chorda tympani transection and treatment with naloxone

description: Two-bottle preference experiments with water and 300mM sucrose before and after chorda tympani transection (CTx) and treatment with naloxone (NLX). In the first set of experiments in Figure 6A, four mice had continual access to the two bottles (water and sugar solution). The animals were trained for three days before undergoing CTx and receiving naloxone or saline treatment (post). For each day, the total amounts of each liquid consumed were used to calculate the preference score [sucrose (mL)/total fluid (mL)]. The higher the score indicates the greater the sweet preference with 0.5 representing no preference. In the second set of experiments in Figure 6B, another four mice were placed on a 22.5 hour water deprivation schedule where they had access to bottles of water and sugar solution the remaining 1.5 hours per day. The animals were trained for four days before undergoing CTx and receiving naloxone or saline treatment.
DOI: 10.6084/m9.figshare.157211.v1
title: Figure 8 raw data

description: The number of microglia in the rostral (RC) subnucleus of the nTS at three days post CTx in mice treated with naloxone (NLX). Three animals from each treatment group (0mg, 5mg, 10mg) were analyzed. From each animal, six microglial counts were taken throughout the rostral levels on both intact (Int) and transected (Tx) sides. The cell counts were analyzed using SPSS software with appropriate ANOVAs and Tukey’s post-hoc analysis. Significance was defined as p&lt;0.05.
DOI: 10.6084/m9.figshare.157207
title: Iba1 and cd11b fluorescence levels three days post chorda tympani transection in mice treated with minocycline or not treated

description: Fluorescence levels of Iba1 and cd11b at three days post chorda tympani transection (CTx) in animals that were treated with minocycline (Mino) and animals that were not treated (No Mino). Three animals for each treatment, Mino and No Mino, were analyzed. The fluorescent intensity of Iba1 and cd11b were measured within a defined circular region of interest (ROI=1,596 40 µm2) in ImageJ. For each animal, two ROI measurements were taken at levels R2 (sheet 1) and R3 (sheet 2) on the intact (Int) and transected (Tx) sides in the following regions: rostral central (RC) subnucleus of the nTS, ventral (V) subnucleus of the nTS and the spinal vestibular nucleus (SpVe). The fluorescent levels on the transected sides were normalized by subtracting the fluorescent levels from the intact sides. These normalized values, which were used to generate the graphs shown in Figure 4, were then analyzed using SPSS software with the appropriate 2-way ANOVAs and Tukey’s post-hoc analysis where significant differences were defined as p&lt;0.05.
DOI: 10.6084/m9.figshare.157208.v2
title: Number of microglia in the nTS three days post chorda tympani transection in C57BL6/J, C3HeB and C3H mice

description: The number of microglia in the rostral central (RC) subnucleus of the nTS at three days post chorda tympani transection (CTx) in C57BL6/J (wild-type), C3HeB (TLR4 wild-type) and C3H (TLR4 mutant) animals. Three animals from each genotype were analyzed. From each animal, six microglial counts were taken throughout the rostral levels on both intact (Int) and transected (Tx) sides. The cell counts were analyzed using SPSS software with appropriate ANOVAs and Tukey’s post-hoc analysis. Significance was defined as p&lt;0.05.
DOI: 10.6084/m9.figshare.157209.v1
title: Figure 6 raw data

description: Two-bottle preference experiments with water and 300mM sucrose before and after chorda tympani transection (CTx) and treatment with naloxone (NLX). In the first set of experiments in Figure 6A, four mice had continual access to the two bottles (water and sugar solution). The animals were trained for three days before undergoing CTx and receiving naloxone or saline treatment (post). For each day, the total amounts of each liquid consumed were used to calculate the preference score [sucrose (mL)/total fluid (mL)]. The higher the score indicates the greater the sweet preference with 0.5 representing no preference. In the second set of experiments in Figure 6B, another four mice were placed on a 22.5 hour water deprivation schedule where they had access to bottles of water and sugar solution the remaining 1.5 hours per day. The animals were trained for four days before undergoing CTx and receiving naloxone or saline treatment.
DOI: 10.6084/m9.figshare.157206
title: Number of microglia in the nTS three days post chorda tympani transection in mice treated with minocycline, saline or no treatment

description: The number of microglia in the rostral central (RC) subnucleus of the nTS at three days post chorda tympani transection (CTx) in mice treated with minocycline (Mino), saline or no treatment. Three animals from each treatment were analyzed. From each animal, six microglial counts were taken throughout the rostral levels on both intact (Int) and transected (Tx) sides. The cell counts were analyzed using SPSS software with appropriate ANOVAs and Tukey’s post-hoc analysis. Significance was defined as p&lt;0.05.
DOI: 10.6084/m9.figshare.157207.v2
title: Iba1 and cd11b fluorescence levels three days post chorda tympani transection in mice treated with minocycline or not treated

description: Fluorescence levels of Iba1 and cd11b at three days post chorda tympani transection (CTx) in animals that were treated with minocycline (Mino) and animals that were not treated (No Mino). Three animals for each treatment, Mino and No Mino, were analyzed. The fluorescent intensity of Iba1 and cd11b were measured within a defined circular region of interest (ROI=1,596 40 µm2) in ImageJ. For each animal, two ROI measurements were taken at levels R2 (sheet 1) and R3 (sheet 2) on the intact (Int) and transected (Tx) sides in the following regions: rostral central (RC) subnucleus of the nTS, ventral (V) subnucleus of the nTS and the spinal vestibular nucleus (SpVe). The fluorescent levels on the transected sides were normalized by subtracting the fluorescent levels from the intact sides. These normalized values, which were used to generate the graphs shown in Figure 4, were then analyzed using SPSS software with the appropriate 2-way ANOVAs and Tukey’s post-hoc analysis where significant differences were defined as p&lt;0.05.
DOI: 10.6084/m9.figshare.157208.v1
title: Figure 5 raw data

description: The number of microglia in the rostral central (RC) subnucleus of the nTS at three days post chorda tympani transection (CTx) in C57BL6/J (wild-type), C3HeB (TLR4 wild-type) and C3H (TLR4 mutant) animals. Three animals from each genotype were analyzed. From each animal, six microglial counts were taken throughout the rostral levels on both intact (Int) and transected (Tx) sides. The cell counts were analyzed using SPSS software with appropriate ANOVAs and Tukey’s post-hoc analysis. Significance was defined as p&lt;0.05.