cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.97100.v1
title: Human SOD1 overexpressed in motoneurons confers resistance to BMAA treatment.

description: Shown are survival rates of 5 day-old male <em>sod1</em> transgenic flies under 3 mM BMAA treatment (10 flies per vial). Panels A, B, and C represent the survival rate of flies expressing mutant human A4V, G85R, wild type SOD1 proteins and control flies (D42&gt;CS and D42&gt;UAS-<em>dsod1</em>) in motoneurons using the D42-Gal4 driver. Flies expressing the human SOD1s (both the hSOD1WT, and mutants, hSOD1A4V and hSOD1G85R) survived longer compared to the control flies. At the 50% survival rate, the longevity is increased by 33%, 41% and 66 % for A4V, G85R, wt SOD1, respectively, when compared to D42&gt;<em>dsod1</em> and D42&gt;CS flies. Differences were considered statistically significant if pCS and D42&gt;A4V, respectively; n=50 for the rest of genotypes.
DOI: 10.6084/m9.figshare.97101
title: Survival curve of wild type (Canton S) Drosophila under various dosages of BMAA.

description: Five day-old male flies were reared in 1, 3, 5, and 10 mM BMAA diluted in 3% sucrose for up to 30 days (10 flies per vial). The 50% survival time for 1, 3, 5, and 10 mM BMAA was 19, 14, 10, and 4 days, respectively. The sham (0 mM BMAA) treated flies did not show any toxicity during the observation period. The statistics was performed using One-way ANOVA analysis of variance in Prizm software, p
DOI: 10.6084/m9.figshare.97101.v1
title: Survival curve of wild type (Canton S) Drosophila under various dosages of BMAA.

description: Five day-old male flies were reared in 1, 3, 5, and 10 mM BMAA diluted in 3% sucrose for up to 30 days (10 flies per vial). The 50% survival time for 1, 3, 5, and 10 mM BMAA was 19, 14, 10, and 4 days, respectively. The sham (0 mM BMAA) treated flies did not show any toxicity during the observation period. The statistics was performed using One-way ANOVA analysis of variance in Prizm software, p
DOI: 10.6084/m9.figshare.97102
title: Climbing behavior of 60 day-old flies.

description: Healthy looking 60 day-old male flies were selected for this assay. Ten flies were placed in a 100 ml glass cylinder. Following a brief and gentle tapping, the distribution of flies was then counted in 3 bins at different heights (above or at 35 mm height, between 7.5 mm and 35 mm, and 7.5 mm or lower). Climbing pattern of flies expressing SOD1 in motoneurons (A), glial cells (B), and co-expressing SOD1 in both motoneurons and glial cells (C) are shown. Flies expressing human SOD1 proteins in glial cells show a significant shift of distribution to the bottom of the cylinder compared to M1B&gt;UAS-<em>dsod1</em> (the control fly) and in comparison with their expression in motoneurons (A) or dual expression in MNs + glia (C). These observations suggest a significant impairment of climbing activities at 60 days in flies expressing human SOD1s in glia. The statistical significances were calculated using Prizm software, Two-way ANOVA and * p
DOI: 10.6084/m9.figshare.97102.v1
title: Climbing behavior of 60 day-old flies.

description: Healthy looking 60 day-old male flies were selected for this assay. Ten flies were placed in a 100 ml glass cylinder. Following a brief and gentle tapping, the distribution of flies was then counted in 3 bins at different heights (above or at 35 mm height, between 7.5 mm and 35 mm, and 7.5 mm or lower). Climbing pattern of flies expressing SOD1 in motoneurons (A), glial cells (B), and co-expressing SOD1 in both motoneurons and glial cells (C) are shown. Flies expressing human SOD1 proteins in glial cells show a significant shift of distribution to the bottom of the cylinder compared to M1B&gt;UAS-<em>dsod1</em> (the control fly) and in comparison with their expression in motoneurons (A) or dual expression in MNs + glia (C). These observations suggest a significant impairment of climbing activities at 60 days in flies expressing human SOD1s in glia. The statistical significances were calculated using Prizm software, Two-way ANOVA and * p
DOI: 10.6084/m9.figshare.384505
title: Autolysis data

description: To monitor autolysis, six flasks containing 50 mL of minimal medium, 10 mM ammonium tartrate and vitamin supplements were each inoculated with 3 x 10<sup>8</sup> conidia and placed on an orbital shaker. Flasks were removed at 24 or 48 h intervals, the submerged mycelia harvested using Miracloth (Calbiochem/Merck). The dry weights of the mycelia are recorded in this file.
DOI: 10.6084/m9.figshare.384505.v1
title: Autolysis data

description: To monitor autolysis, six flasks containing 50 mL of minimal medium, 10 mM ammonium tartrate and vitamin supplements were each inoculated with 3 x 10<sup>8</sup> conidia and placed on an orbital shaker. Flasks were removed at 24 or 48 h intervals, the submerged mycelia harvested using Miracloth (Calbiochem/Merck). The dry weights of the mycelia are recorded in this file.
DOI: 10.6084/m9.figshare.384509
title: Glucose uptake raw data

description: The uptake of D-[U-<sup>14</sup>C] glucose (10.6 GBq/mmol, Amersham) was measured in germinating conidia of A. <em>nidulans</em> strains MH2 (<em>xpr</em>G<sup>+</sup>), MK422 (<em>xpr</em>GΔ) and MK85 (<em>xpr</em>G1) as described previously by McCabe <em>et al</em>. (2003). Glucose uptake was measured in aliquots of 2.5 x 10<sup>7</sup> germinating conidia after transfer to media containing 0.025, 0.125, 0.5 or 2 mM glucose.
DOI: 10.6084/m9.figshare.384509.v1
title: Glucose uptake raw data

description: The uptake of D-[U-<sup>14</sup>C] glucose (10.6 GBq/mmol, Amersham) was measured in germinating conidia of A. <em>nidulans</em> strains MH2 (<em>xpr</em>G<sup>+</sup>), MK422 (<em>xpr</em>GΔ) and MK85 (<em>xpr</em>G1) as described previously by McCabe <em>et al</em>. (2003). Glucose uptake was measured in aliquots of 2.5 x 10<sup>7</sup> germinating conidia after transfer to media containing 0.025, 0.125, 0.5 or 2 mM glucose.
DOI: 10.6084/m9.figshare.384512
title: Conidiophore length data

description: To measure conidiophore length, strains inoculated into 1 cm<sup>2</sup> blocks of complete medium on microscope slides as described by Larone (1995). Conidiophores were photographed at 400 x magnification after growth at 37<sup>o</sup>C on microscope slides. Measurements were carried out using the ImageJ program (http://rsbweb.nih.gov/ij/).
DOI: 10.6084/m9.figshare.384512.v1
title: Conidiophore length data

description: To measure conidiophore length, strains inoculated into 1 cm<sup>2</sup> blocks of complete medium on microscope slides as described by Larone (1995). Conidiophores were photographed at 400 x magnification after growth at 37<sup>o</sup>C on microscope slides. Measurements were carried out using the ImageJ program (http://rsbweb.nih.gov/ij/).
DOI: 10.6084/m9.figshare.384520
title: Conidial number data

description: The number of asexual spores (conidia) per mm<sup>2</sup> produced by A. <em>nidulans</em> strains MH2 (<em>xpr</em>G<sup>+</sup>), MK422 (<em>xpr</em>GΔ) and MK85 (<em>xpr</em>G1) was determined by removing three plugs from colonies on complete medium containing 2.2% agar. The conidia from each plug were suspended in a solution of 0.01% TWEEN80 and counted in a haemocytometer. The experiment was repeated a total of four times using different batches of medium.
DOI: 10.6084/m9.figshare.384520.v1
title: Conidial number data

description: The number of asexual spores (conidia) per mm<sup>2</sup> produced by A. <em>nidulans</em> strains MH2 (<em>xpr</em>G<sup>+</sup>), MK422 (<em>xpr</em>GΔ) and MK85 (<em>xpr</em>G1) was determined by removing three plugs from colonies on complete medium containing 2.2% agar. The conidia from each plug were suspended in a solution of 0.01% TWEEN80 and counted in a haemocytometer. The experiment was repeated a total of four times using different batches of medium.
DOI: 10.6084/m9.figshare.670617
title: Chorophyll fluorescence data

description: Chlorophyll fluorescence characteristics of the dominant tree species at Daxiagu and Tianlongshan were measured in the summer seasons of 2007, 2008, and 2009.
DOI: 10.6084/m9.figshare.670617.v1
title: Fluorescence data

description: Demo description
DOI: 10.6084/m9.figshare.670617.v2
title: Chorophyll fluorescence data

description: Chlorophyll fluorescence characteristics of the dominant tree species at Daxiagu and Tianlongshan were measured in the summer seasons of 2007, 2008, and 2009.
DOI: 10.6084/m9.figshare.670617.v3
title: Chorophyll fluorescence data

description: Chlorophyll fluorescence characteristics of the dominant tree species at Daxiagu and Tianlongshan were measured in the summer seasons of 2007, 2008, and 2009.
DOI: 10.6084/m9.figshare.670620
title: Photosynthesis data

description: Photosynthetic traits of the dominant tree species as well as the environmental factors at Daxiagu Tianlongshan were measured in the summer seasons of 2007, 2008 and 2009.
DOI: 10.6084/m9.figshare.670620.v1
title: Photosynthesis data

description: Demo description
DOI: 10.6084/m9.figshare.670620.v2
title: Photosynthesis data

description: Photosynthetic traits of the dominant tree species as well as the environmental factors at Daxiagu Tianlongshan were measured in the summer seasons of 2007, 2008 and 2009.
DOI: 10.6084/m9.figshare.670620.v4
title: Photosynthesis data

description: Photosynthetic traits of the dominant tree species as well as the environmental factors at Daxiagu Tianlongshan were measured in the summer seasons of 2007, 2008 and 2009.
DOI: 10.6084/m9.figshare.670621
title: Water potential data

description: Leaf water potential of the dominant tree species at Daxiagu and Tianlongshan was measured in the summer season of 2009.
DOI: 10.6084/m9.figshare.670621.v1
title: Water potential

description: Demo description
DOI: 10.6084/m9.figshare.670621.v2
title: Water potential data

description: Leaf water potential of the dominant tree species at Daxiagu and Tianlongshan was measured in the summer season of 2009.
DOI: 10.6084/m9.figshare.670621.v3
title: Water potential data

description: Leaf water potential of the dominant tree species at Daxiagu and Tianlongshan was measured in the summer season of 2009.
DOI: 10.6084/m9.figshare.670621.v4
title: Water potential data

description: Leaf water potential of the dominant tree species at Daxiagu and Tianlongshan was measured in the summer season of 2009.
DOI: 10.6084/m9.figshare.670621.v5
title: Water potential data

description: Leaf water potential of the dominant tree species at Daxiagu and Tianlongshan was measured in the summer season of 2009.
DOI: 10.6084/m9.figshare.670621.v6
title: Water potential data

description: Leaf water potential of the dominant tree species at Daxiagu and Tianlongshan was measured in the summer season of 2009.
DOI: 10.6084/m9.figshare.670621.v7
title: Water potential data

description: Leaf water potential of the dominant tree species at Daxiagu and Tianlongshan was measured in the summer season of 2009.
DOI: 10.6084/m9.figshare.670623
title: Leaf nutrient and specific leaf area data

description: Mass- and area-based nitrogen and phosphorus content, and specific leaf area of the dominant tree species at Daxiagu and Tianlongshan.
DOI: 10.6084/m9.figshare.670623.v1
title: Misc.

description: Demo description
DOI: 10.6084/m9.figshare.670623.v2
title: Leaf nutrient and specific leaf area data

description: Mass- and area-based nitrogen and phosphorus content, and specific leaf area of the dominant tree species at Daxiagu and Tianlongshan.
DOI: 10.6084/m9.figshare.670623.v3
title: Leaf nutrient and specific leaf area data

description: Mass- and area-based nitrogen and phosphorus content, and specific leaf area of the dominant tree species at Daxiagu and Tianlongshan.
DOI: 10.6084/m9.figshare.678213
title: Genes with significant modulation at 2 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2

description: Genes listed in the first sheet were significantly modulated (J5 score &gt; 20 or &lt; -20) at 2 hours after CD3/CD28 stimulation, but not significantly modulated (J5 score &lt; 20 or &gt; -20) after stimulation in the presence of Akti1/2. Genes listed in the middle sheet were significantly modulated by 2 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2, but were nonetheless affected by the inhibitor. Genes listed on the last sheet were significantly modulated by 2 hours of CD3/CD28 stimulation only in the presence of Akti1/2.
DOI: 10.6084/m9.figshare.678213.v1
title: Genes with significant modulation at 2 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2

description: Genes listed in the first sheet were significantly modulated (J5 score &gt; 20 or &lt; -20) at 2 hours after CD3/CD28 stimulation, but not significantly modulated (J5 score &lt; 20 or &gt; -20) after stimulation in the presence of Akti1/2. Genes listed in the middle sheet were significantly modulated by 2 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2, but were nonetheless affected by the inhibitor. Genes listed on the last sheet were significantly modulated by 2 hours of CD3/CD28 stimulation only in the presence of Akti1/2.
DOI: 10.6084/m9.figshare.678214
title: Genes with significant modulation at 6 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2

description: Genes listed in the first sheet were significantly modulated at 6 hours after CD3/CD28 stimulation, but not significantly modulated after stimulation in the presence of Akti1/2. Genes listed in the middle sheet were significantly modulated by 6 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2, but were nonetheless affected by the inhibitor. Genes listed in the last sheet were significantly modulated by 6 hours of CD3/CD28 stimulation only in the presence of Akti1/2.
DOI: 10.6084/m9.figshare.678214.v2
title: Genes with significant modulation at 6 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2

description: Genes listed in the first sheet were significantly modulated at 6 hours after CD3/CD28 stimulation, but not significantly modulated after stimulation in the presence of Akti1/2. Genes listed in the middle sheet were significantly modulated by 6 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2, but were nonetheless affected by the inhibitor. Genes listed in the last sheet were significantly modulated by 6 hours of CD3/CD28 stimulation only in the presence of Akti1/2.
DOI: 10.6084/m9.figshare.678214.v1
title: Genes with significant modulation at 6 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2

description: Genes listed in the first sheet were significantly modulated at 6 hours after CD3/CD28 stimulation, but not significantly modulated after stimulation in the presence of Akti1/2. Genes listed in the middle sheet were significantly modulated by 6 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2, but were nonetheless affected by the inhibitor. Genes listed in the last sheet were significantly modulated by 6 hours of CD3/CD28 stimulation only in the presence of Akti1/2.
DOI: 10.6084/m9.figshare.678215
title: Genes with significant modulation at 12 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2

description: Genes listed in the first sheet were significantly modulated at 12 hours after CD3/CD28 stimulation, but not significantly modulated after stimulation in the presence of Akti1/2. Genes listed in the middle sheet were significantly modulated by 12 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2, but were nonetheless affected by the inhibitor. Genes listed in the last sheet were significantly modulated by 12 hours of CD3/CD28 stimulation only in the presence of Akti1/2.
DOI: 10.6084/m9.figshare.678215.v1
title: Genes with significant modulation at 12 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2

description: Genes listed in the first sheet were significantly modulated at 12 hours after CD3/CD28 stimulation, but not significantly modulated after stimulation in the presence of Akti1/2. Genes listed in the middle sheet were significantly modulated by 12 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2, but were nonetheless affected by the inhibitor. Genes listed in the last sheet were significantly modulated by 12 hours of CD3/CD28 stimulation only in the presence of Akti1/2.
DOI: 10.6084/m9.figshare.678215.v2
title: Genes with significant modulation at 12 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2

description: Genes listed in the first sheet were significantly modulated at 12 hours after CD3/CD28 stimulation, but not significantly modulated after stimulation in the presence of Akti1/2. Genes listed in the middle sheet were significantly modulated by 12 hours of CD3/CD28 stimulation in the presence or absence of Akti1/2, but were nonetheless affected by the inhibitor. Genes listed in the last sheet were significantly modulated by 12 hours of CD3/CD28 stimulation only in the presence of Akti1/2.
DOI: 10.6084/m9.figshare.683885.v2
title: Appendix for "Are Happy Developers more Productive? The Correlation of Affective States of Software Developers and their self-assessed Productivity"

description: This file contains the guidelines, which were employed to administer the Self-Assessment Manikin (SAM) [1] and the productivity questionnaire to the participants of the experiment reported in [2]. The guidelines have been written by following the technical manual by Lang et al. [3].
This document will be updated while preparing the camera-ready version of the paper. The camera-ready version of the paper will be made available on Figshare as well (the publisher permits that)
 
[1] Bradley, L.: Measuring emotion: the self-assessment semantic differential. Journal of Behavior Therapy and Experimental Psychiatry. 25, 1, 49–59 (1994).<br>[2] Graziotin, D., Wang, X., & Abrahamsson, P.. Are Happy Developers more Productive? The Correlation of Affective States of Software Developers and their self-assessed Productivity. In Product-Focused Software Process Improvement,. Paphos, Cyprus. Springer Verlag. In Press (2013).<br>[3] Lang, P.J. et al.: International affective picture system (IAPS): Technical manual and affective ratings. Gainesville FL NIMH Center for the study of emotion and attention University of Florida. Technical Report A–6 (1999).
DOI: 10.6084/m9.figshare.713512.v3
title: GigaGalaxy: A GigaSolution for reproducible and sustainable genomic data publication and analysis

description: Today's next generation sequencing (NGS) experiments generate substantially more data and are more broadly applicable to previous high-throughput genomic assays. Despite the plummeting costs of sequencing, downstream data processing and analysis create financial and bioinformatics challenges for many biomedical scientists. It is therefore important to make NGS data interpretation as accessible as data generation. GigaGalaxy (http://galaxy.cbiit.cuhk.edu.hk) represents a NGS data interpretation solution towards the big sequencing data challenge. We have ported the popular Short Oligonucleotide Analysis Package (http://soap.genomics.org.cn) as well as supporting tools such as Contiguator2 (http://contiguator.sourceforge.net) into the Galaxy framework, to provide seamless NGS mapping, de novo assembly, NGS data format conversion and sequence alignment visualization. Our vision is to create an open publication, review and analysis environment by integrating GigaGalaxy into the publication platform at GigaScience and its GigaDB database that links to more than 20 TBs of genomic data. We have begun this effort by re-implementing the data procedures described by Luo et al., (GigaScience 1: 18, 2012) as Galaxy workflows so that they can be shared in a manner which can be visualized and executed in GigaGalaxy. We hope to revolutionize the publication model with the aim of executable publications, where data analyses can be reproduced and reused.
DOI: 10.6084/m9.figshare.732736
title: Vitamin D levels in a pediatric population with mental disorders at two residential psychiatric treatment programs in Oregon

description: Hypovitaminosis file: 25(OH)D levels (ng/ml) of children with various mental disorders at two residential psychiatric treatment programs in Oregon, USA. Some children had multiple 25(OH)D levels taken. See Table 1 in the main article for disorders that fall under the ‘Other Disorders’. NOS – not otherwise specified.
Vitamin D by diagnostic category file: Some children in the study had multiple mental disorders so here we have arranged vitamin D level (ng/ml) by diagnostic category. See Table 1 in the main article for disorders that fall under the ‘Other’ category. ASD – autistic spectrum disorder.
DOI: 10.6084/m9.figshare.732736.v1
title: Vitamin D levels in a pediatric population with mental disorders at two residential psychiatric treatment programs in Oregon

description: Hypovitaminosis file: 25(OH)D levels (ng/ml) of children with various mental disorders at two residential psychiatric treatment programs in Oregon, USA. Some children had multiple 25(OH)D levels taken. See Table 1 in the main article for disorders that fall under the ‘Other Disorders’. NOS – not otherwise specified.
Vitamin D by diagnostic category file: Some children in the study had multiple mental disorders so here we have arranged vitamin D level (ng/ml) by diagnostic category. See Table 1 in the main article for disorders that fall under the ‘Other’ category. ASD – autistic spectrum disorder.
DOI: 10.6084/m9.figshare.776878
title: Drug Binding site file

description: The drug binding site list used to execute the TB- Drugome workflow.
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/
DOI: 10.6084/m9.figshare.776878.v1
title: Drug Binding site file

description: The drug binding site list used to execute the TB- Drugome workflow.
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/
DOI: 10.6084/m9.figshare.776879
title: Drug key file

description: A drug key file with the ids for the drugs used in the workflow.
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/
DOI: 10.6084/m9.figshare.776879.v1
title: Drug key file

description: A drug key file with the ids for the drugs used in the workflow.
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/
DOI: 10.6084/m9.figshare.776880
title: Homology Model list

description: The homology list file with the ids of the homology models associated to the proteins to be compared to the drug binding sites.
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/
DOI: 10.6084/m9.figshare.776880.v1
title: Homology Model list

description: The homology list file with the ids of the homology models associated to the proteins to be compared to the drug binding sites.
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/
DOI: 10.6084/m9.figshare.776882
title: SMAP configuration file

description: The configuration file for the SMAP tool (used for ligand binding sites comparison).
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/
DOI: 10.6084/m9.figshare.776883
title: Homology model file

description: Homology model information file to filter up homology models.
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/