cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4624573
title: Longitudinal assessment of the Edinburgh Cognitive and Behavioural Amyotrophic Lateral Sclerosis Screen (ECAS): lack of practice effect in ALS patients?

description: <i>Objective</i>: The study objective was to assess whether controls and ALS patients show a practice effect in the Edinburgh Cognitive and Behavioural ALS Screen (ECAS) on repeated longitudinal testing and if the ECAS detects progression of cognitive or behavioural changes over time. <i>Methods</i>: The ECAS was administered serially to ALS patients (<i>n</i> = 24 after six months, <i>n</i> = 10 after 12–18 months) and controls (<i>n</i> = 21 after six months). The ECAS was fully performed by all participants. For comparison purposes the Frontal Assessment Battery (FAB) was administered to a subgroup of 14 patients and 14 controls. <i>Results</i>: After six months controls showed a significantly higher overall score (<i>p</i> Conclusions: In conclusion, in contrast to healthy controls, ALS patients show no practice effects. This could reflect ‘pre-symptomatic’ cognitive decline and progressive behavioural symptoms.
DOI: 10.6084/m9.figshare.4622611
title: Performance of the Vectrino Profiler at the sediment–water interface

description: The Vectrino Profiler is increasingly recognized as a promising instrument for characterizing near-bed velocities and turbulence due to its high spatio-temporal resolution and velocity profiling range. However, its measurement performance in the vicinity of the bed (&lt;10 mm) is not well documented. This study reports on the comparisons of mean velocity, turbulent kinetic energy, and power spectral density above various bed materials between the Vectrino Profiler and particle image velocimetry in a laboratory flume. Our analyses demonstrate that the bed interference adversely influences the measurements as close as 1.7–5 mm above the bed, depending on the bed material. We provide a criterion to identify the vertical extent of the interference region. Outside of the interference region, best agreement between the Vectrino Profiler and particle image velocimetry was found around the sweet-spot of the profiler where the observed differences were &lt;6% for mean velocities and &lt;10% for turbulent kinetic energy.
DOI: 10.6084/m9.figshare.4624573.v1
title: Longitudinal assessment of the Edinburgh Cognitive and Behavioural Amyotrophic Lateral Sclerosis Screen (ECAS): lack of practice effect in ALS patients?

description: <i>Objective</i>: The study objective was to assess whether controls and ALS patients show a practice effect in the Edinburgh Cognitive and Behavioural ALS Screen (ECAS) on repeated longitudinal testing and if the ECAS detects progression of cognitive or behavioural changes over time. <i>Methods</i>: The ECAS was administered serially to ALS patients (<i>n</i> = 24 after six months, <i>n</i> = 10 after 12–18 months) and controls (<i>n</i> = 21 after six months). The ECAS was fully performed by all participants. For comparison purposes the Frontal Assessment Battery (FAB) was administered to a subgroup of 14 patients and 14 controls. <i>Results</i>: After six months controls showed a significantly higher overall score (<i>p</i> Conclusions: In conclusion, in contrast to healthy controls, ALS patients show no practice effects. This could reflect ‘pre-symptomatic’ cognitive decline and progressive behavioural symptoms.
DOI: 10.6084/m9.figshare.4622494
title: New draft item

description: The mesh and data files of paper entitled "The Effect of Tumour Size on Drug Transport and Uptake in 3-D Tumour models Reconstructed from Magnetic Resonance Images"<br>
DOI: 10.6084/m9.figshare.4622530
title: 2015-09-04_T-NTD-3new_66pM-100mW-LP-BP-Dich532-635_7.hdf5
DOI: 10.6084/m9.figshare.4622530.v1
title: 16-ch TCSPC single-molecule measurement of dsDNA using line-excitation

description: Data files in Photon-HDF5 format for freely-diffusing single-molecule measurements of a 80-base-pair dsDNA labeled with ATTO550.
DOI: 10.6084/m9.figshare.4622470
title: Discovering How Trending Article Types Change Over Time in Different Countries

description: For our Big Data Project we spent a lot of time learning about Altmetrics and its data before concluding on a topic to Analyze. We researched about the company, Altmetric itself and looked in depth at the data sets provided to us. We used python tools to open the files and physically read through them to get a comprehensive understanding of what the Altmetrics dataset was. Having no prior knowledge of any type of Big Data or data analysis it took some time to really understand what the data was and how we would be able to analyze it. With all of our team members having a lot of experience programming we decided to use R for data analysis. Coming from a Java, R was a bit of a learning curve due to all of the packages, however we quickly realized these packages were R’s main strength as it made the tools needed to analyze Altmetric data readily and easily available. In doing this research our team began to realize the importance of Altmetric. The data collected was extremely relevant, organized and easy to analyze on both a macro and micro level. This allows us to be able to see where science is going and see what people in general are interested in and which people are interested in specific topics. Prior to learning about Altmetrics are team would have never known data like this was available. The fact that Altmetrics has this information and is allowing people to study these important trends. Once we familiarized ourselves with the basics of what we needed to get started, it was time to choose a topic. Something that originally peaked our interest was the demographics section of the Altmetric dataset. We chose to focus on the locations in the demographics section. For our final question that we came up with, How did trending article types change over time in different countries?. This would determine how significant new research is and contrast the differences between different countries’ preferences towards research papers.
DOI: 10.6084/m9.figshare.4622494.v1
title: New draft item

description: The mesh and data files of paper entitled "The Effect of Tumour Size on Drug Transport and Uptake in 3-D Tumour models Reconstructed from Magnetic Resonance Images"<br>
DOI: 10.6084/m9.figshare.4622470.v1
title: Discovering How Trending Article Types Change Over Time in Different Countries

description: For our Big Data Project we spent a lot of time learning about Altmetrics and its data before concluding on a topic to Analyze. We researched about the company, Altmetric itself and looked in depth at the data sets provided to us. We used python tools to open the files and physically read through them to get a comprehensive understanding of what the Altmetrics dataset was. Having no prior knowledge of any type of Big Data or data analysis it took some time to really understand what the data was and how we would be able to analyze it. With all of our team members having a lot of experience programming we decided to use R for data analysis. Coming from a Java, R was a bit of a learning curve due to all of the packages, however we quickly realized these packages were R’s main strength as it made the tools needed to analyze Altmetric data readily and easily available. In doing this research our team began to realize the importance of Altmetric. The data collected was extremely relevant, organized and easy to analyze on both a macro and micro level. This allows us to be able to see where science is going and see what people in general are interested in and which people are interested in specific topics. Prior to learning about Altmetrics are team would have never known data like this was available. The fact that Altmetrics has this information and is allowing people to study these important trends. Once we familiarized ourselves with the basics of what we needed to get started, it was time to choose a topic. Something that originally peaked our interest was the demographics section of the Altmetric dataset. We chose to focus on the locations in the demographics section. For our final question that we came up with, How did trending article types change over time in different countries?. This would determine how significant new research is and contrast the differences between different countries’ preferences towards research papers.
DOI: 10.6084/m9.figshare.4622293
title: Zebrafish Developmental Stages transcriptome gene correlation network

description: Processed layout file for use with BioLayout Express 3D. Produced with BioLayout by setting the pearson correlation threshold to 0.94 and clustering using MCL. Reported in White et al. 2017<br>
DOI: 10.6084/m9.figshare.4622311
title: Zebrafish Developmental Stages DeTCT count data

description: Count data generated by DeTCT 3' end profiling, from zebrafish embryos from 18 developmental stages from 1-cell to 5 dpf (White et al. 2017)<br>
DOI: 10.6084/m9.figshare.4622221
title: Edge effect on the spatial distribution of trees in an Araucaria Rainforest fragment in Brazil

description: These files are complementary data from the paper " Edge effect on the spatial distribution of trees in an Araucaria Rainforest fragment in Brazil”. The paper was published in Rodriguesia journal in 2018. The files are:<br> <b>Data1_Pine and Data2_Agriculture:</b> These files contain the lists of individuals measured in Pine and Agriculture plots during the field inventories from 1995 and 2013. They contain the name of the specie of each individual, the coordinates X and Y, the DBH (diameter at breast height) from 1995 and 2013 (if the individual was live in this two years), and the defined category (Living, Recruitment and/or Mortality). The data is collected as part of the Brazilian Long Term Ecological Research Program (PELD) Site 9, for what there are performed annul inventories since 1995. In these inventories all the trees with DBH ≥ 10cm are measured (at DBH), classified according to its specie, and geographically positioned. During the years of the inventories, many individuals are recruited, as well many individuals are found dead. Considering this, we classified each one in these categories, but it is possible for a same individual to be part of two categories at the same time. The coordinates are in UTM, and the datum utilized was SAD69, fuse 22 south.<br> <b>Figure1_Pine and Figure2_Agriculture:</b> These figures shown the special distribution, the Kernel density map, and the GAM (Generalized Additive Model) model of all analyzed species in Pine and Agriculture plots, considering also the categories of Living, Recruitment and Mortality. The GAM model was calculated to evaluate the relationship between number o individuals of each specie and edge distance (considering categories at each 10 meters). The Kernel density model was created using ArcMap 10.4.1, and it represents the occurrence density of each specie (for each category) in both plots.<br> <b>Table1_Pine and Table2_Agriculture: </b> In these tables are presented the values of the Spearman’s Correlation Coefficients (ρ) and the GAM statistical results, calculated to evaluate the relationship between number of individuals of each species and the edge distance in Pine and Agriculture plot. This was calculated considering the categories Living, Recruitment and Mortality of individuals.<br> <b> </b> <b>Table3_EGroup:</b> This table presents the values of the Spearman’s Correlation Coefficients (ρ) and the GAM statistical results, calculated to evaluate the relationship between number of individuals by ecological group and edge distance in Pine and Agriculture plots. These values are calculated considering the categories Living, Recruitment and Mortality of individuals. The groups are divided in LS/C (Late Secondary or climax), and P and ES (Pioneer and Early Secondary).<br>
DOI: 10.6084/m9.figshare.4622059
title: RW_EW_LW_NESPAIN

description: Here you can find the tree-ring width, latewood width and earlywood width raw series of the Prynees and the Iberian Range (northeast of Spain).
DOI: 10.6084/m9.figshare.4622221.v2
title: Edge effect on the spatial distribution of trees in an Araucaria Rainforest fragment in Brazil

description: These files are complementary data from the paper " Edge effect on the spatial distribution of trees in an Araucaria Rainforest fragment in Brazil”. The paper was published in Rodriguesia journal in 2018. The files are:<br> <b>Data1_Pine and Data2_Agriculture:</b> These files contain the lists of individuals measured in Pine and Agriculture plots during the field inventories from 1995 and 2013. They contain the name of the specie of each individual, the coordinates X and Y, the DBH (diameter at breast height) from 1995 and 2013 (if the individual was live in this two years), and the defined category (Living, Recruitment and/or Mortality). The data is collected as part of the Brazilian Long Term Ecological Research Program (PELD) Site 9, for what there are performed annul inventories since 1995. In these inventories all the trees with DBH ≥ 10cm are measured (at DBH), classified according to its specie, and geographically positioned. During the years of the inventories, many individuals are recruited, as well many individuals are found dead. Considering this, we classified each one in these categories, but it is possible for a same individual to be part of two categories at the same time. The coordinates are in UTM, and the datum utilized was SAD69, fuse 22 south.<br> <b>Figure1_Pine and Figure2_Agriculture:</b> These figures shown the special distribution, the Kernel density map, and the GAM (Generalized Additive Model) model of all analyzed species in Pine and Agriculture plots, considering also the categories of Living, Recruitment and Mortality. The GAM model was calculated to evaluate the relationship between number o individuals of each specie and edge distance (considering categories at each 10 meters). The Kernel density model was created using ArcMap 10.4.1, and it represents the occurrence density of each specie (for each category) in both plots.<br> <b>Table1_Pine and Table2_Agriculture: </b> In these tables are presented the values of the Spearman’s Correlation Coefficients (ρ) and the GAM statistical results, calculated to evaluate the relationship between number of individuals of each species and the edge distance in Pine and Agriculture plot. This was calculated considering the categories Living, Recruitment and Mortality of individuals.<br> <b> </b> <b>Table3_EGroup:</b> This table presents the values of the Spearman’s Correlation Coefficients (ρ) and the GAM statistical results, calculated to evaluate the relationship between number of individuals by ecological group and edge distance in Pine and Agriculture plots. These values are calculated considering the categories Living, Recruitment and Mortality of individuals. The groups are divided in LS/C (Late Secondary or climax), and P and ES (Pioneer and Early Secondary).<br>
DOI: 10.6084/m9.figshare.4622050
title: Transcriptomic characterization of gall tissue of Japanese elm tree (<i>Ulmus davidiana</i> var. japonica) induced by the aphid <i>Tetraneura nigriabdominalis</i>

description: Insect galls are abnormal plant tissues induced by parasitic insect(s) for use as their habitat. In previous work, we suggested that gall tissues induced by the aphid <i>Tetraneura nigriabdominalis</i> on Japanese elm trees are less responsive than leaf tissues to jasmonic acid (JA), which is involved in the production of volatile organic compounds as a typical defensive reaction of plants against attack by insect pests. A comprehensive analysis of gene expression by RNA sequencing indicated that the number of JA responsive genes was markedly lower in gall tissues than in leaf tissues. This suggests that gall tissues are mostly defective in JA signaling, although JA signaling is not entirely compromised in gall tissue. Gene ontology analysis sheds light on some stress-related unigenes with higher expression levels in gall tissues, suggesting that host plants sense aphids as a biotic stress but are defective in the JA-mediated defense response in gall tissues. The aphid-induced gall tissues on Japanese elm trees are less responsive than leaf tissues to jasmonic acid, which may provide the aphid with beneficial environments.
DOI: 10.6084/m9.figshare.4622221.v1
title: Edge effect on the spatial distribution of trees in an Araucari Rainforest fragment in Brazil

description: These files are complementary data from the paper " Edge effect on the spatial distribution of trees in an Araucaria Rainforest fragment in Brazil”. The paper was published in Rodriguesia journal in 2018. The files are:<br> <b>Data1_Pine and Data2_Agriculture:</b> These files contain the lists of individuals measured in Pine and Agriculture plots during the field inventories from 1995 and 2013. They contain the name of the specie of each individual, the coordinates X and Y, the DBH (diameter at breast height) from 1995 and 2013 (if the individual was live in this two years), and the defined category (Living, Recruitment and/or Mortality). The data is collected as part of the Brazilian Long Term Ecological Research Program (PELD) Site 9, for what there are performed annul inventories since 1995. In these inventories all the trees with DBH ≥ 10cm are measured (at DBH), classified according to its specie, and geographically positioned. During the years of the inventories, many individuals are recruited, as well many individuals are found dead. Considering this, we classified each one in these categories, but it is possible for a same individual to be part of two categories at the same time. The coordinates are in UTM, and the datum utilized was SAD69, fuse 22 south.<br> <b>Figure1_Pine and Figure2_Agriculture:</b> These figures shown the special distribution, the Kernel density map, and the GAM (Generalized Additive Model) model of all analyzed species in Pine and Agriculture plots, considering also the categories of Living, Recruitment and Mortality. The GAM model was calculated to evaluate the relationship between number o individuals of each specie and edge distance (considering categories at each 10 meters). The Kernel density model was created using ArcMap 10.4.1, and it represents the occurrence density of each specie (for each category) in both plots.<br> <b>Table1_Pine and Table2_Agriculture: </b> In these tables are presented the values of the Spearman’s Correlation Coefficients (ρ) and the GAM statistical results, calculated to evaluate the relationship between number of individuals of each species and the edge distance in Pine and Agriculture plot. This was calculated considering the categories Living, Recruitment and Mortality of individuals.<br> <b> </b> <b>Table3_EGroup:</b> This table presents the values of the Spearman’s Correlation Coefficients (ρ) and the GAM statistical results, calculated to evaluate the relationship between number of individuals by ecological group and edge distance in Pine and Agriculture plots. These values are calculated considering the categories Living, Recruitment and Mortality of individuals. The groups are divided in LS/C (Late Secondary or climax), and P and ES (Pioneer and Early Secondary).<br>
DOI: 10.6084/m9.figshare.4622059.v2
title: RW_EW_LW_NESPAIN

description: Here you can find the tree-ring width, latewood width and earlywood width raw series of the Prynees and the Iberian Range (northeast of Spain).
DOI: 10.6084/m9.figshare.4622050.v1
title: Transcriptomic characterization of gall tissue of Japanese elm tree (<i>Ulmus davidiana</i> var. japonica) induced by the aphid <i>Tetraneura nigriabdominalis</i>

description: Insect galls are abnormal plant tissues induced by parasitic insect(s) for use as their habitat. In previous work, we suggested that gall tissues induced by the aphid <i>Tetraneura nigriabdominalis</i> on Japanese elm trees are less responsive than leaf tissues to jasmonic acid (JA), which is involved in the production of volatile organic compounds as a typical defensive reaction of plants against attack by insect pests. A comprehensive analysis of gene expression by RNA sequencing indicated that the number of JA responsive genes was markedly lower in gall tissues than in leaf tissues. This suggests that gall tissues are mostly defective in JA signaling, although JA signaling is not entirely compromised in gall tissue. Gene ontology analysis sheds light on some stress-related unigenes with higher expression levels in gall tissues, suggesting that host plants sense aphids as a biotic stress but are defective in the JA-mediated defense response in gall tissues. The aphid-induced gall tissues on Japanese elm trees are less responsive than leaf tissues to jasmonic acid, which may provide the aphid with beneficial environments.
DOI: 10.6084/m9.figshare.4622059.v1
title: RW_EW_LW_NESPAIN.zip

description: Here you can find the tree-ring width, latewood width and earlywood width raw series of the Prynees and the Iberian Range (northeast of Spain).
DOI: 10.6084/m9.figshare.4622035
title: Data_Qu&Stewart.xlsx

description: Supplementary Data (qPCR assays) for Qu & Stewart
DOI: 10.6084/m9.figshare.4622032
title: <i>n</i>-Hexanal and (<i>Z</i>)-3-hexenal are generated from arachidonic acid and linolenic acid by a lipoxygenase in <i>Marchantia polymorpha</i> L.

description: Most terrestrial plants form green leaf volatiles (GLVs), which are mainly composed of six-carbon (C6) compounds. In our effort to study the distribution of the ability of lipoxygenase (LOX) to form GLVs, we found that a liverwort, <i>Marchantia polymorpha</i>, formed <i>n</i>-hexanal and (<i>Z</i>)-3-hexenal. Some LOXs execute a secondary reaction to form short chain volatiles. One of the LOXs from <i>M. polymorpha</i> (MpLOX7) oxygenized arachidonic and α-linolenic acids at almost equivalent efficiency and formed C6-aldehydes during its catalysis; these are likely formed from hydroperoxides of arachidonic and α-linolenic acids, with a cleavage of the bond between carbon at the base of the hydroperoxy group and carbon of double bond, which is energetically unfavorable. These lines of evidence suggest that one of the LOXs in liverwort employs an unprecedented reaction to form C6 aldehydes as by-products of its reaction with fatty acid substrates. One of <i>Marchantia polymorpha</i> lipoxygenases forms six-carbon aldehydes as by-products.
DOI: 10.6084/m9.figshare.4622029
title: Biochemical synthesis of uniformly <sup>13</sup>C-labeled diterpene hydrocarbons and their bioconversion to diterpenoid phytoalexins <i>in planta</i>

description: Phytocassanes and momilactones are the major diterpenoid phytoalexins inductively produced in rice as bioactive substances. Regardless of extensive studies on the biosynthetic pathways of these phytoalexins, bioconversion of diterpene hydrocarbons is not shown <i>in planta</i>. To elucidate the entire biosynthetic pathways of these phytoalexins, uniformly <sup>13</sup>C-labeled <i>ent</i>-cassadiene and <i>syn</i>-pimaradiene were enzymatically synthesized with structural verification by GC–MS and <sup>13</sup>C-NMR. Application of the <sup>13</sup>C-labeled substrates on rice leaves led to the detection of <sup>13</sup>C-labeled metabolites using LC-MS/MS. Further application of this method in the moss <i>Hypnum plumaeforme</i> and the nearest out-group of <i>Oryza</i> species <i>Leersia perrieri</i>, respectively, resulted in successful bioconversion of these labeled substrates into phytoalexins in these plants. These results demonstrate that genuine biosynthetic pathways from these diterpene hydrocarbons to the end product phytoalexins occur in these plants and that enzymatically synthesized [U-<sup>13</sup>C<sub>20</sub>] diterpene substrates are a powerful tool for chasing endogenous metabolites without dilution with naturally abundant unlabeled compounds. Uniformly labeled <sup>13</sup>C-diterpene: A powerful tool for tracing endogenous metabolites without dilution with naturally abundant unlabeled compounds
DOI: 10.6084/m9.figshare.4622035.v1
title: Data_Qu&Stewart.xlsx

description: Supplementary Data (qPCR assays) for Qu & Stewart