cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5951107.v1
title: Additional file 1: of RNAseq analysis of bronchial epithelial cells to identify COPD-associated genes and SNPs

description: Tables S1, S2, S3, S4, S5 and S6. Table S1. This table provides: a) Gene-specific assay information including SNP sites, primer and internal standard sequences, b) Subject-specific demographic information, and c) assay- and subject-specific transcript abundance values (target gene molecules/106 ACTB molecules). Table S2. Population used for allele specific expression analysis: Summary demographic characteristics of the study population of allele specific expression (subject total n = 180). Table S3. Transcription factor-target inter-gene correlation in Control, COPD, or All subjects (p-value 0.95) and with p
DOI: 10.6084/m9.figshare.5951065
title: Innovation and employee injury risk in automotive disassembly operations

description: Engineering innovations in car disassembly systems are studied for affects on system operators’ risk of repetitive strain injury (RSI). Objective instrumented measures of injury risk factors with synchronised video-based task analyses were used to examine changes in operators’ RSI risk during two cases of engineering innovation: (1) a shift in industrial model from traditional extracting saleable parts to line-based full material recovery, and (2) the prospective effects of a simulated ‘Lean’-inspired process improvement in the line system. Both cases of innovation showed significantly increased movement speeds and reduced muscular recovery opportunities, implying increased RSI risk. This case study reveals a mechanism by which innovation may increase RSI risks for operators. Managers responsible for engineering innovation should ensure their teams have the tools and mandate necessary to control injury hazards as part of the development and design process. These cases suggest how failure to manage RSI hazards in the innovation process may allow increases of injury risks that can compromise operational performance. This ‘innovation pitfall’ has implications for operator health and organisational sustainability. Alternative pathways are discussed.
DOI: 10.6084/m9.figshare.5951065.v1
title: Innovation and employee injury risk in automotive disassembly operations

description: Engineering innovations in car disassembly systems are studied for affects on system operators’ risk of repetitive strain injury (RSI). Objective instrumented measures of injury risk factors with synchronised video-based task analyses were used to examine changes in operators’ RSI risk during two cases of engineering innovation: (1) a shift in industrial model from traditional extracting saleable parts to line-based full material recovery, and (2) the prospective effects of a simulated ‘Lean’-inspired process improvement in the line system. Both cases of innovation showed significantly increased movement speeds and reduced muscular recovery opportunities, implying increased RSI risk. This case study reveals a mechanism by which innovation may increase RSI risks for operators. Managers responsible for engineering innovation should ensure their teams have the tools and mandate necessary to control injury hazards as part of the development and design process. These cases suggest how failure to manage RSI hazards in the innovation process may allow increases of injury risks that can compromise operational performance. This ‘innovation pitfall’ has implications for operator health and organisational sustainability. Alternative pathways are discussed.
DOI: 10.6084/m9.figshare.5951062.v1
title: R script for General Mixed Yule Coalescent approach

description: This is the R script used for the GMYC analysis.
DOI: 10.6084/m9.figshare.5951059
title: Aligned datasets (ITS, LSU, SSU+ITS+LSU)

description: These are the multiple alignments of the ITS region, LSU region, and 3-gene dataset (SSU+ITS+LSU).
DOI: 10.6084/m9.figshare.5951059.v1
title: Aligned datasets (ITS, LSU, SSU+ITS+LSU)

description: These are the multiple alignments of the ITS region, LSU region, and 3-gene dataset (SSU+ITS+LSU).
DOI: 10.6084/m9.figshare.5951053
title: 6-gene aligned NEXUS

description: This is the aligned six-gene dataset, which was used as input for the molecular clock analysis.
DOI: 10.6084/m9.figshare.5951053.v1
title: 6-gene aligned NEXUS

description: This is the aligned six-gene dataset, which was used as input for the molecular clock analysis.
DOI: 10.6084/m9.figshare.5951038
title: Towards transformational creation of novel songs

description: We study transformational computational creativity in the context of writing songs and describe an implemented system that is able to modify its own goals and operation. With this, we contribute to three aspects of computational creativity and song generation: (1) <i>Application-wise</i>, songs are an interesting and challenging target for creativity, as they require the production of complementary music and lyrics. (2) <i>Technically</i>, we approach the problem of creativity and song generation using constraint programming. We show how constraints can be used declaratively to define a search space of songs so that a standard constraint solver can then be used to generate songs. (3) <i>Conceptually</i>, we describe a concrete architecture for transformational creativity where the creative (song writing) system has some responsibility for setting its own search space and goals. In the proposed architecture, a meta-level control component does this transparently by manipulating the constraints at runtime based on self-reflection of the system. Empirical experiments suggest the system is able to create songs according to its own taste.
DOI: 10.6084/m9.figshare.5951038.v2
title: Towards transformational creation of novel songs

description: We study transformational computational creativity in the context of writing songs and describe an implemented system that is able to modify its own goals and operation. With this, we contribute to three aspects of computational creativity and song generation: (1) <i>Application-wise</i>, songs are an interesting and challenging target for creativity, as they require the production of complementary music and lyrics. (2) <i>Technically</i>, we approach the problem of creativity and song generation using constraint programming. We show how constraints can be used declaratively to define a search space of songs so that a standard constraint solver can then be used to generate songs. (3) <i>Conceptually</i>, we describe a concrete architecture for transformational creativity where the creative (song writing) system has some responsibility for setting its own search space and goals. In the proposed architecture, a meta-level control component does this transparently by manipulating the constraints at runtime based on self-reflection of the system. Empirical experiments suggest the system is able to create songs according to its own taste.
DOI: 10.6084/m9.figshare.5951032
title: Hesperomyces virescens log files 6 gene clock analysis

description: Output log files BEAST molecular clock analysis (4 independent runs).
DOI: 10.6084/m9.figshare.5951032.v1
title: Hesperomyces virescens log files 6 gene clock analysis

description: Output log files BEAST molecular clock analysis (4 independent runs).
DOI: 10.6084/m9.figshare.5951029
title: High-throughput tool to discriminate effects of NMs (Cu-NPs, Cu-nanowires, CuNO<sub>3</sub>, and Cu salt aged): transcriptomics in <i>Enchytraeus crypticus</i>

description: The current testing of nanomaterials (NMs) via standard toxicity tests does not cover many of the NMs specificities. One of the recommendations lays on understanding the mechanisms of action, as these can help predicting long-term effects and safe-by-design production. In the present study, we used the high-throughput gene expression tool, developed for <i>Enchytraeus crypticus</i> (4 × 44k Agilent microarray), to study the effects of exposure to several copper (Cu) forms. The Cu treatments included two NMs (spherical and wires) and two copper-salt treatments (CuNO<sub>3</sub> spiked and Cu salt field historical contamination). To relate gene expression with higher effect level, testing was done with reproduction effect concentrations (EC<sub>20</sub>, EC<sub>50</sub>), using 3 and 7 days as exposure periods. Results showed that time plays a major role in the transcriptomic response, most of it occurring after 3 days. Analysis of gene expression profiles showed that Cu-salt-aged and Cu-nanowires (Nwires) differed from CuNO<sub>3</sub> and Cu-nanoparticles (NPs). Functional analysis revealed specific mechanisms: Cu-NPs uniquely affected senescence and cuticle pattern formation, which can result from the contact of the NPs with the worms’ tegument. Cu-Nwires affected reproduction via male gamete generation and hermaphrodite genitalia development. CuNO<sub>3</sub> affected neurotransmission and locomotory behavior, both of which can be related with avoidance response. Cu salt-aged uniquely affected phagocytosis and reproductive system development (via different mechanisms than Cu-Nwires). For the first time for Cu (nano)materials, the adverse outcome pathways (AOPs) drafted here provide an overview for common and unique effects per material and linkage with apical effects.
DOI: 10.6084/m9.figshare.5951029.v1
title: High-throughput tool to discriminate effects of NMs (Cu-NPs, Cu-nanowires, CuNO<sub>3</sub>, and Cu salt aged): transcriptomics in <i>Enchytraeus crypticus</i>

description: The current testing of nanomaterials (NMs) via standard toxicity tests does not cover many of the NMs specificities. One of the recommendations lays on understanding the mechanisms of action, as these can help predicting long-term effects and safe-by-design production. In the present study, we used the high-throughput gene expression tool, developed for <i>Enchytraeus crypticus</i> (4 × 44k Agilent microarray), to study the effects of exposure to several copper (Cu) forms. The Cu treatments included two NMs (spherical and wires) and two copper-salt treatments (CuNO<sub>3</sub> spiked and Cu salt field historical contamination). To relate gene expression with higher effect level, testing was done with reproduction effect concentrations (EC<sub>20</sub>, EC<sub>50</sub>), using 3 and 7 days as exposure periods. Results showed that time plays a major role in the transcriptomic response, most of it occurring after 3 days. Analysis of gene expression profiles showed that Cu-salt-aged and Cu-nanowires (Nwires) differed from CuNO<sub>3</sub> and Cu-nanoparticles (NPs). Functional analysis revealed specific mechanisms: Cu-NPs uniquely affected senescence and cuticle pattern formation, which can result from the contact of the NPs with the worms’ tegument. Cu-Nwires affected reproduction via male gamete generation and hermaphrodite genitalia development. CuNO<sub>3</sub> affected neurotransmission and locomotory behavior, both of which can be related with avoidance response. Cu salt-aged uniquely affected phagocytosis and reproductive system development (via different mechanisms than Cu-Nwires). For the first time for Cu (nano)materials, the adverse outcome pathways (AOPs) drafted here provide an overview for common and unique effects per material and linkage with apical effects.
DOI: 10.6084/m9.figshare.5950369
title: Data used in Lai et al. (2018). Nitrogen fixer abundance has no effect on biomass recovery during tropical secondary forest succession. Journal of Ecology.

description: <b>Data from: </b>Lai, H.R., J.S. Hall, S.A. Batterman, B.L. Turner & M. van Breugel (2018). Nitrogen fixer abundance has no effect on biomass recovery during tropical secondary forest succession. Journal of Ecology<br><b>Methods and materials;</b>See 'Methods & Materials' section in Lai et al. 2018 for details <br><b>Summary</b>:1) Nitrogen-fixing trees (N2 fixers) provide new nitrogen critical for rapid biomass accumulation of tropical forests during early secondary succession, but it remains unclear how the abundance of N2 fixers in the forest community affects the growth of non-fixers or the primary productivity of the whole forest. 2) On the one hand, N2 fixers may enhance forest productivity by providing a facilitative effect through the provision of plant-available nitrogen to non-fixing trees. On the other hand, N2 fixers may suppress the growth of non-fixers by growing faster and competing more vigorously for light and other resources. A third alternative is that the growth of N2 fixers themselves accumulate biomass rapidly, while having a neutral effect on non-fixers, leading to an overall increase in forest biomass.3) We examine these alternative hypotheses using five-year tree census data from 88 plots in 44 seasonal tropical moist secondary forests (3–32 years old) across a human-modified landscape in central Panama. We examined whether N2 fixers accumulated biomass more rapidly than non-fixers, and how relative biomass of N2 fixers as a functional group and as individual species influenced the growth of non-fixer and whole stand primary productivity.4) Surprisingly, we found no evidence for either a net competitive or a facilitative effect of N2 fixers as a functional group or individual species on the biomass recovery in these young forests. N2 fixers did not grow faster than non-fixers. Individual mortality rates were lower among N2 fixers, but biomass losses due to mortality were similar between the two groups. Overall, we found no relationship between the relative abundance of N2 fixers and stand primary productivity during succession. 5) Synthesis: N2-fixing trees may be critical for reducing nitrogen limitation and accelerating biomass growth during tropical secondary forest succession, thereby impacting the global carbon cycle. However, our findings indicate that, in early successional seasonal tropical moist forests, N2 fixers provide neither a net competitive nor a facilitative effect on non-fixing trees or the whole forest stand, likely because tropical N2 fixers utilize facultative fixation and hence abundance poorly approximates the ecosystem function of fixation. Our results indicate that models should not simply scale symbiotic fixation and its effects from N2-fixing tree abundance.<br>
DOI: 10.6084/m9.figshare.5950369.v2
title: Data used in Lai et al. (2018). Nitrogen fixer abundance has no effect on biomass recovery during tropical secondary forest succession. Journal of Ecology.

description: <b>Data from: </b>Lai, H.R., J.S. Hall, S.A. Batterman, B.L. Turner & M. van Breugel (2018). Nitrogen fixer abundance has no effect on biomass recovery during tropical secondary forest succession. Journal of Ecology<br><b>Methods and materials;</b>See 'Methods & Materials' section in Lai et al. 2018 for details <br><b>Summary</b>:1) Nitrogen-fixing trees (N2 fixers) provide new nitrogen critical for rapid biomass accumulation of tropical forests during early secondary succession, but it remains unclear how the abundance of N2 fixers in the forest community affects the growth of non-fixers or the primary productivity of the whole forest. 2) On the one hand, N2 fixers may enhance forest productivity by providing a facilitative effect through the provision of plant-available nitrogen to non-fixing trees. On the other hand, N2 fixers may suppress the growth of non-fixers by growing faster and competing more vigorously for light and other resources. A third alternative is that the growth of N2 fixers themselves accumulate biomass rapidly, while having a neutral effect on non-fixers, leading to an overall increase in forest biomass.3) We examine these alternative hypotheses using five-year tree census data from 88 plots in 44 seasonal tropical moist secondary forests (3–32 years old) across a human-modified landscape in central Panama. We examined whether N2 fixers accumulated biomass more rapidly than non-fixers, and how relative biomass of N2 fixers as a functional group and as individual species influenced the growth of non-fixer and whole stand primary productivity.4) Surprisingly, we found no evidence for either a net competitive or a facilitative effect of N2 fixers as a functional group or individual species on the biomass recovery in these young forests. N2 fixers did not grow faster than non-fixers. Individual mortality rates were lower among N2 fixers, but biomass losses due to mortality were similar between the two groups. Overall, we found no relationship between the relative abundance of N2 fixers and stand primary productivity during succession. 5) Synthesis: N2-fixing trees may be critical for reducing nitrogen limitation and accelerating biomass growth during tropical secondary forest succession, thereby impacting the global carbon cycle. However, our findings indicate that, in early successional seasonal tropical moist forests, N2 fixers provide neither a net competitive nor a facilitative effect on non-fixing trees or the whole forest stand, likely because tropical N2 fixers utilize facultative fixation and hence abundance poorly approximates the ecosystem function of fixation. Our results indicate that models should not simply scale symbiotic fixation and its effects from N2-fixing tree abundance.<br>
DOI: 10.6084/m9.figshare.5950369.v1
title: Data used for: Hao Ran Lai, Jefferson S. Hall, Sarah A. Batterman, Benjamin L. Turner & Michiel van Breugel (2018). Nitrogen fixer abundance has no effect on biomass recovery during tropical secondary forest succession. Journal of Ecology

description: <b>Data from: </b>Lai, H.R., J.S. Hall, S.A. Batterman, B.L. Turner & M. van Breugel (2018). Nitrogen fixer abundance has no effect on biomass recovery during tropical secondary forest succession. Journal of Ecology<br><b>Methods and materials;</b>See 'Methods & Materials' section in Lai et al. 2018 for details <br><b>Summary</b>:1) Nitrogen-fixing trees (N2 fixers) provide new nitrogen critical for rapid biomass accumulation of tropical forests during early secondary succession, but it remains unclear how the abundance of N2 fixers in the forest community affects the growth of non-fixers or the primary productivity of the whole forest. 2) On the one hand, N2 fixers may enhance forest productivity by providing a facilitative effect through the provision of plant-available nitrogen to non-fixing trees. On the other hand, N2 fixers may suppress the growth of non-fixers by growing faster and competing more vigorously for light and other resources. A third alternative is that the growth of N2 fixers themselves accumulate biomass rapidly, while having a neutral effect on non-fixers, leading to an overall increase in forest biomass.3) We examine these alternative hypotheses using five-year tree census data from 88 plots in 44 seasonal tropical moist secondary forests (3–32 years old) across a human-modified landscape in central Panama. We examined whether N2 fixers accumulated biomass more rapidly than non-fixers, and how relative biomass of N2 fixers as a functional group and as individual species influenced the growth of non-fixer and whole stand primary productivity.4) Surprisingly, we found no evidence for either a net competitive or a facilitative effect of N2 fixers as a functional group or individual species on the biomass recovery in these young forests. N2 fixers did not grow faster than non-fixers. Individual mortality rates were lower among N2 fixers, but biomass losses due to mortality were similar between the two groups. Overall, we found no relationship between the relative abundance of N2 fixers and stand primary productivity during succession. 5) Synthesis: N2-fixing trees may be critical for reducing nitrogen limitation and accelerating biomass growth during tropical secondary forest succession, thereby impacting the global carbon cycle. However, our findings indicate that, in early successional seasonal tropical moist forests, N2 fixers provide neither a net competitive nor a facilitative effect on non-fixing trees or the whole forest stand, likely because tropical N2 fixers utilize facultative fixation and hence abundance poorly approximates the ecosystem function of fixation. Our results indicate that models should not simply scale symbiotic fixation and its effects from N2-fixing tree abundance.<br>
DOI: 10.6084/m9.figshare.5950366
title: PONE-D-17-28414.dta

description: 1753 men and 1781 women participating in the 1982 Pelotas (Brazil) birth cohort study had measurements of anthropometry, body composition, lipids, glucose, blood pressure, and other cardiometabolic traits at age 30 years.
DOI: 10.6084/m9.figshare.5950360
title: Magnetic Seismology of Interstellar Gas Clouds: Unveiling a Hidden Dimension

description: Simulation outputs for filament and sheet like geometry and the setup scripts for FLASH code<br>
DOI: 10.6084/m9.figshare.5950360.v1
title: Magnetic Seismology of Interstellar Gas Clouds: Unveiling a Hidden Dimension

description: Simulation outputs for filament and sheet like geometry and the setup scripts for FLASH code<br>
DOI: 10.6084/m9.figshare.5950339
title: AmpliconArchitect_reconstructions

description: This dataset contains the AmpliconArchitect (https://github.com/virajbdeshpande/AmpliconArchitect) output for reconstruction of amplicons from the following samples:<br>1) 117 samples in "sample set 1" https://www.ncbi.nlm.nih.gov/bioproject/PRJNA338012/<br>2) 18 samples which replicates of samples in sample set 1<br>3) 67 cervical samples from TCGA with HPV infection<br>4) Amplicons from sample set 1 organized by various tags including: a) MultCluster, b) MultiChrom c) simple_cycles and d) BFB<br>5) 7 samples reported by L'abbate et al 2014<br>6) 3 samples reported by Sanborn et al 2013 + 1 sample reported by Oesper et al 2012<br>7) 9 samples reported by Akagi et al 2013.<br>1 summary file for each sample:_summary.txt - Summary of all amplicons reported in the sample.<br>4 files per amplicon:graph.txt file: Breakpoint graph and copy numberscycles.txt file: Simple cycles in amplicon.png and .pdf: SV view of reconstruction.<br>For viral amplicons from (3) and (7), 2 additional files (png and pdf) for each human interval connected to the viral genome.<br>.png and .cycles.txt files may be uploaded to http://genomequery.ucsd.edu:8800 for visualization and merging of cycles
DOI: 10.6084/m9.figshare.5950339.v1
title: AmpliconArchitect_reconstructions

description: This dataset contains the AmpliconArchitect (https://github.com/virajbdeshpande/AmpliconArchitect) output for reconstruction of amplicons from the following samples:<br>1) 117 samples in "sample set 1" https://www.ncbi.nlm.nih.gov/bioproject/PRJNA338012/<br>2) 18 samples which replicates of samples in sample set 1<br>3) Amplicons from sample set 1 organized by various tags including: a) MultCluster, b) MultiChrom c) simple_cycles and d) BFB.<br>4) 7 samples reported by L'abbate et al 2014<br>5) 3 samples reported by Sanborn et al 2013, Oesper et al 2012<br>6) 9 samples reported by Akagi et al 2013.<br>1 summary file for each sample:_summary.txt - Summary of all amplicons reported in the sample.<br>4 files per amplicon:graph.txt file: Breakpoint graph and copy numberscycles.txt file: Simple cycles in amplicon.png and .pdf: SV view of reconstruction.<br>For viral amplicons from Akagi et al, 2 additional files for each connected component of human intervals.<br>.png and .cycles.txt files may be uploaded to http://genomequery.ucsd.edu:8800 for visualization and merging of cyles
DOI: 10.6084/m9.figshare.5950315
title: LaplaceSoapBubblesQuestions.zip

description: LaPlace Soap Bubbles and Questions, a lesson in the Law of LaPlace surface tension and how it applies to the lungs
DOI: 10.6084/m9.figshare.5950315.v1
title: LaplaceSoapBubblesQuestions.zip

description: LaPlace Soap Bubbles and Questions, a lesson in the Law of LaPlace surface tension and how it applies to the lungs