cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1621235.v1
title: Effects of ABA and CaCl<sub>2</sub> on GABA accumulation in fava bean germinating under hypoxia-NaCl stress

description: Effects of exogenous abscisic acid (ABA) and CaCl<sub>2</sub> on γ-aminobutyric acid (GABA) accumulation of germinated fava bean under hypoxia-NaCl stress were investigated. Exogenous ABA resulted in the enhancement of glutamate decarboxylase (GAD) and diamine oxidase (DAO) activity as well as GABA content in cotyledon and shoot. CaCl<sub>2</sub> increased both enzyme activities in shoot and GABA content in cotyledon and shoot. ABA downregulated <i>GAD</i> expression in cotyledon and radicle, while upregulated that in shoot; it also upregulated <i>DAO</i> expression in each organ. CaCl<sub>2</sub> upregulated <i>GAD</i> expression in cotyledon, while downregulated that in radicle. However, it upregulated <i>DAO</i> expression in shoot, downregulated that in radicle. ABA inhibitor fluridon and ethylenediaminetetraacetic acid inhibited GAD and DAO activities significantly so that inhibited GABA accumulation through reducing ABA biosynthesis and chelating Ca<sup>2+</sup>, respectively. However, they upregulated <i>GAD</i> and <i>DAO</i> expression in varying degrees. These results indicate that ABA and Ca<sup>2+</sup> participate in GABA biosynthesis in fava bean during germination under hypoxia-NaCl stress.
DOI: 10.6084/m9.figshare.1620635
title: Molecular characterization of avian rotaviruses circulating in Italian poultry flocks

description: Avian rotaviruses are still largely undefined despite being widespread in several avian species and despite the economic impact of rotavirus (RV) enteritis in poultry flocks<i>.</i> In this study, the presence of different avian RV groups was investigated in commercial poultry flocks reared in Northern and Central Italy and with a history of enteric diseases. Faeces or intestinal contents from different avian species previously found to contain RV particles by electron microscopy (EM) were analysed by both RNA-polyacrylamide gel electrophoresis and reverse transcription-polymerase chain reaction specific for groups A, D, F and G RVs. Group D avian RV was detected in 107 of 117 samples tested (91.5%), whereas groups A, F and G avian RVs were present in 70 (59%), 61 (52.1%) and 31 (26.5%) samples, respectively. Multiple presence of different RV groups was detected in 83% of samples. This study provides novel data on the prevalence of genetically different avian RVs in Italian poultry flocks. This information is useful to elucidate the epidemiology of avian RVs circulating in Italy.
DOI: 10.6084/m9.figshare.1620635.v1
title: Molecular characterization of avian rotaviruses circulating in Italian poultry flocks

description: Avian rotaviruses are still largely undefined despite being widespread in several avian species and despite the economic impact of rotavirus (RV) enteritis in poultry flocks<i>.</i> In this study, the presence of different avian RV groups was investigated in commercial poultry flocks reared in Northern and Central Italy and with a history of enteric diseases. Faeces or intestinal contents from different avian species previously found to contain RV particles by electron microscopy (EM) were analysed by both RNA-polyacrylamide gel electrophoresis and reverse transcription-polymerase chain reaction specific for groups A, D, F and G RVs. Group D avian RV was detected in 107 of 117 samples tested (91.5%), whereas groups A, F and G avian RVs were present in 70 (59%), 61 (52.1%) and 31 (26.5%) samples, respectively. Multiple presence of different RV groups was detected in 83% of samples. This study provides novel data on the prevalence of genetically different avian RVs in Italian poultry flocks. This information is useful to elucidate the epidemiology of avian RVs circulating in Italy.
DOI: 10.6084/m9.figshare.1619957
title: Ovine rumen papillae biopsy via oral endoscopy; a rapid and repeatable method for serial sampling

description: AIMS: To explore and validate the utility of rumen endoscopy for collection of rumen papillae for gene expression measurement.METHODS: Four adult Coopworth ewes were fasted for either 4 or 24 hours. Animals were sedated, placed in a dorsally recumbent position at 45 degrees with the head upright, and an endoscope inserted via a tube inserted into the mouth. Biopsies of rumen papillae were taken from the ventral surface of the rumen atrium under visual guidance. Two biopsies were collected from one of the animals that had been fasted for 4 hours, and three from one of the animals that had been fasted for 24 hours. Video of the rumen atrium and reticulum was also collected. The animals recovered uneventfully. Biopsies were subsequently used for extraction and sequencing of mRNA.RESULTS: The ventral surface of the rumen atrium was accessible after 4 hours off pasture, but a larger region was accessible after 24 hours of fasting. Sedation allowed access for endoscope use for around 5 to 10 minutes after which increased saliva flow was noted. Rumen papillae biopsies were easily collected, with samples from a variety of sites collected in the ∼10 minute time window. High quality RNA was obtained for stranded mRNA sequencing. Of the resulting reads, 69–70% mapped uniquely to version 3.1 of the ovine genome, and 48–49% to a known gene. The rumen mRNA profiles were consistent with a previously reported study.CONCLUSIONS: This method for obtaining rumenal tissue was found to be rapid and resulted in no apparent short or long term effects on the animal. High quality RNA was successfully extracted and amplified from the rumen papillae biopsies, indicating that this technique could be used for future gene expression studies. The use of rumen endoscopy could be extended to collection of a variety of rumen and reticulum anatomical measurements and deposition and retrieval of small sensors from the rumen. Rumen endoscopy offers an attractive and cost effective approach to repeated rumen biopsies compared with serial slaughter or use of cannulated animals.McRae_Supp._Info_2.pdfMcRae_Supp._Info_1.mp4
DOI: 10.6084/m9.figshare.1619958
title: Zircon and Titanite U–Pb SHRIMP dating of unexposed basement units of the Buenos Aires region, southeastern Río de La Plata Craton, Argentina

description: ABSTRACTWe present U–Pb Sensitive High Mass Resolution Ion MicroProbe (SHRIMP) data of unexposed igneous-metamorphic basement rocks from two areas of the southeastern Río de la Plata craton (RPC; Buenos Aires city) located within the Buenos Aires–Piedra Alta (BAPA) terrane – and the Tapalqué area (Buenos Aires province) – located within the Tandilia terrane, and discuss the tectonic evolution of that portion of the craton based on both the new data and previous work. The newly obtained geochronological data of drill cores indicate that: (a) arc magmatism occurred at 2164–2186 Ma corresponding to early ‘Trans-Amazon’ (early Rhyacian) arc magmatism; (b) the age of collision between the BAPA and Tandilia terranes is inferred to have commenced at ca. 2110 Ma; (c) peak metamorphism occurred at ca. 2069 Ma; and (d) the presence of rocks related to the RPC is confirmed under Cenozoic sediments in a large area between Martin Garcia Island and Tandil. We envisage an early Rhyacian divergent double subduction scheme between the BAPA and Tandilia terranes – i.e. N-dipping towards BAPA and S-dipping towards Tandilia – prior to the late Rhyacian collision between these two terranes.
DOI: 10.6084/m9.figshare.1619960
title: nd2reader 2.0.0

description: Pure Python library for reading NIS Elements ND2 images and metadata
DOI: 10.6084/m9.figshare.1619957.v1
title: Ovine rumen papillae biopsy via oral endoscopy; a rapid and repeatable method for serial sampling

description: AIMS: To explore and validate the utility of rumen endoscopy for collection of rumen papillae for gene expression measurement.METHODS: Four adult Coopworth ewes were fasted for either 4 or 24 hours. Animals were sedated, placed in a dorsally recumbent position at 45 degrees with the head upright, and an endoscope inserted via a tube inserted into the mouth. Biopsies of rumen papillae were taken from the ventral surface of the rumen atrium under visual guidance. Two biopsies were collected from one of the animals that had been fasted for 4 hours, and three from one of the animals that had been fasted for 24 hours. Video of the rumen atrium and reticulum was also collected. The animals recovered uneventfully. Biopsies were subsequently used for extraction and sequencing of mRNA.RESULTS: The ventral surface of the rumen atrium was accessible after 4 hours off pasture, but a larger region was accessible after 24 hours of fasting. Sedation allowed access for endoscope use for around 5 to 10 minutes after which increased saliva flow was noted. Rumen papillae biopsies were easily collected, with samples from a variety of sites collected in the ∼10 minute time window. High quality RNA was obtained for stranded mRNA sequencing. Of the resulting reads, 69–70% mapped uniquely to version 3.1 of the ovine genome, and 48–49% to a known gene. The rumen mRNA profiles were consistent with a previously reported study.CONCLUSIONS: This method for obtaining rumenal tissue was found to be rapid and resulted in no apparent short or long term effects on the animal. High quality RNA was successfully extracted and amplified from the rumen papillae biopsies, indicating that this technique could be used for future gene expression studies. The use of rumen endoscopy could be extended to collection of a variety of rumen and reticulum anatomical measurements and deposition and retrieval of small sensors from the rumen. Rumen endoscopy offers an attractive and cost effective approach to repeated rumen biopsies compared with serial slaughter or use of cannulated animals.McRae_Supp._Info_2.pdfMcRae_Supp._Info_1.mp4
DOI: 10.6084/m9.figshare.1619958.v1
title: Zircon and Titanite U–Pb SHRIMP dating of unexposed basement units of the Buenos Aires region, southeastern Río de La Plata Craton, Argentina

description: ABSTRACTWe present U–Pb Sensitive High Mass Resolution Ion MicroProbe (SHRIMP) data of unexposed igneous-metamorphic basement rocks from two areas of the southeastern Río de la Plata craton (RPC; Buenos Aires city) located within the Buenos Aires–Piedra Alta (BAPA) terrane – and the Tapalqué area (Buenos Aires province) – located within the Tandilia terrane, and discuss the tectonic evolution of that portion of the craton based on both the new data and previous work. The newly obtained geochronological data of drill cores indicate that: (a) arc magmatism occurred at 2164–2186 Ma corresponding to early ‘Trans-Amazon’ (early Rhyacian) arc magmatism; (b) the age of collision between the BAPA and Tandilia terranes is inferred to have commenced at ca. 2110 Ma; (c) peak metamorphism occurred at ca. 2069 Ma; and (d) the presence of rocks related to the RPC is confirmed under Cenozoic sediments in a large area between Martin Garcia Island and Tandil. We envisage an early Rhyacian divergent double subduction scheme between the BAPA and Tandilia terranes – i.e. N-dipping towards BAPA and S-dipping towards Tandilia – prior to the late Rhyacian collision between these two terranes.
DOI: 10.6084/m9.figshare.1619909
title: Supplemental data for "Effect of tree-to-shrub type conversion in lower montane forests of the Sierra Nevada on streamflow"

description: This file contains data and parameter sets used for running the RHESSys ecohydrologic model.
DOI: 10.6084/m9.figshare.1619905
title: Schematic representation of human chromosome 21

description: Schematic representation of human chromosome 21 long-arm comprised of mouse chromosomal segments from chromosomes 16, 17, and 10. The portion of chromosome 16 that is found in trisomy in the Ts65Dn mouse expands from Mrpl39 (mitochondrial ribosomal protein, human MRPL39) to Zfp295 (zinc finger protein 295, human ZNF295) and harbors miR-155 and miR-802.
DOI: 10.6084/m9.figshare.1619909.v1
title: Supplemental data for "Effect of tree-to-shrub type conversion in lower montane forests of the Sierra Nevada on streamflow"

description: This file contains data and parameter sets used for running the RHESSys ecohydrologic model.
DOI: 10.6084/m9.figshare.1619905.v1
title: Schematic representation of human chromosome 21

description: Schematic representation of human chromosome 21 long-arm comprised of mouse chromosomal segments from chromosomes 16, 17, and 10. The portion of chromosome 16 that is found in trisomy in the Ts65Dn mouse expands from Mrpl39 (mitochondrial ribosomal protein, human MRPL39) to Zfp295 (zinc finger protein 295, human ZNF295) and harbors miR-155 and miR-802.
DOI: 10.6084/m9.figshare.1619908
title: FireintensitiesPLOSONE.csv

description: Historical (1994-2010) fire intensity data provided by SOPFEU who has agrred to share it for research purposes.The dataset contains fire intensity records by fire region and fuel type.The geographical coordinates as well as the final size of each fire event are also available. SupFin: Final size (ha)Comb: Fuel type (C-2, C-3)FIRE_CODE: fire regionINT: intensit
DOI: 10.6084/m9.figshare.1619908.v1
title: FireintensitiesPLOSONE.csv

description: Historical (1994-2010) fire intensity data provided by SOPFEU who has agrred to share it for research purposes.The dataset contains fire intensity records by fire region and fuel type.The geographical coordinates as well as the final size of each fire event are also available. SupFin: Final size (ha)Comb: Fuel type (C-2, C-3)FIRE_CODE: fire regionINT: intensit
DOI: 10.6084/m9.figshare.1619897
title: Figure 1/S1: Ribosomal protein alignment - Metagenomic Evidence for the Presence of Comammox Nitrospira-like bacteria in a Drinking Water System

description: Alignment used to construct RAxML (1) based maximum likelihood phylogenetic tree corresponding to the radial cladogram in Figure 1A in the main manuscript and annotated tree in the supplementary material Figure S1. 16 syntetic ribosomal proteins (2) were aligned separately with correponding sequence from the Nitrospira metagenome bin using muscle (3) . Each protein alignment was trimmed using trimal with the gappyout flag (4) and the trimmed alingments were concantenated to create a superalignment using FasconCAT (5). 1. Stamatakis A. 2014. RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Bioinformatics 30: 1312-1313. doi: 10.1093/bioinformatics/btu033. 2. Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. 2013. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun 4. doi: 10.1038/ncomms3120 3. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792-1797 4. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972-1973. doi: 10.1093/bioinformatics/btp348 5. Kück P, Meusemann K. 2010. FASconCAT: Convenient handling of data matrices. Molecular Phylogenetics and Evolution 56:1115-1118.
DOI: 10.6084/m9.figshare.1619899
title: Strong relationships in acid-base chemistry

description: Inputframe contains patient data - to be handled by PHCalc-all.R, an R script file to make the modeling and statistics. Theoretical exercise.r is an R scriptfile to show experiments with sodium lactate and sodium bicarbonare. kaplan boron.r is an R script file to make the fibroblast experiment described by Kaplan and Boron.
DOI: 10.6084/m9.figshare.1619896
title: Thesis_Everdingen

description: Materials for Eveline van Everdingen's Master Thesis: "Multitasking Behavior and Gaze-Following Technology for Workplace Video-Conferencing" for the Research Master Artificial Intelligence at VU University Amsterdam This fileset contains: - The final thesis - The data of the user experiments as decribed in the paper, including data analysis, distribution of participants and the conditions. - The code for the dual-webcam switching software as described in the paper
DOI: 10.6084/m9.figshare.1619897.v1
title: Figure 1/S1: Ribosomal protein alignment - Metagenomic Evidence for the Presence of Comammox Nitrospira-like bacteria in a Drinking Water System

description: Alignment used to construct RAxML (1) based maximum likelihood phylogenetic tree corresponding to the radial cladogram in Figure 1A in the main manuscript and annotated tree in the supplementary material Figure S1. 16 syntetic ribosomal proteins (2) were aligned separately with correponding sequence from the Nitrospira metagenome bin using muscle (3) . Each protein alignment was trimmed using trimal with the gappyout flag (4) and the trimmed alingments were concantenated to create a superalignment using FasconCAT (5). 1. Stamatakis A. 2014. RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Bioinformatics 30: 1312-1313. doi: 10.1093/bioinformatics/btu033. 2. Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. 2013. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun 4. doi: 10.1038/ncomms3120 3. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792-1797 4. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972-1973. doi: 10.1093/bioinformatics/btp348 5. Kück P, Meusemann K. 2010. FASconCAT: Convenient handling of data matrices. Molecular Phylogenetics and Evolution 56:1115-1118.
DOI: 10.6084/m9.figshare.1619899.v1
title: Strong relationships in acid-base chemistry

description: Inputframe contains patient data - to be handled by PHCalc-all.R, an R script file to make the modeling and statistics. Theoretical exercise.r is an R scriptfile to show experiments with sodium lactate and sodium bicarbonare. kaplan boron.r is an R script file to make the fibroblast experiment described by Kaplan and Boron.
DOI: 10.6084/m9.figshare.1619891
title: Figura 5.1. Distribución del número acumulado de respuestas de los participantes por etapa

description: Distribución del número acumulado de respuestas de los participantes por cada una de las tres etapas. Mientras que el grupo 4 solo necesita de la primera etapa para completar las tareas correctamente, los demás necesitan de las siguientes, en las cuales van acumulando progresivamente un mayor número de respuestas correctas.Acosta-Silva, D. A. (2016, April 18). <i>La sensitividad cognitiva: hacia un modelo de su funcionamiento</i>. Tesis doctoral para optar al título de Doctor en Ciencias Sociales, Niñez y Juventud. Centro de Estudios Avanzados en Niñez y Juventud (Cinde), Universidad de Manizales http://doi.org/10.17605/OSF.IO/TZPF6 <br>
DOI: 10.6084/m9.figshare.1619893
title: GAMES discovery data sets

description: GAMES Consortium endurance athlete GWAS discovery data sets (GENATHLETE and Japanese endurance runners in PLINK format).
DOI: 10.6084/m9.figshare.1619890
title: Tabla 5.1 Taxonomía para la transferencia lejana

description: Modelo para la taxonomía para la transferencia lejana propuesta por Barnett y Ceci (2002). Traducido y adaptado de <i>When and Where Do We Apply What We Learn? A Taxonomy for Far Transfer</i> por S. M. Barnett y S. J. Ceci, 2002, Psychological Bulletin, 128(4), p. 621. © 2002 American Psychological Association.
DOI: 10.6084/m9.figshare.1619891.v1
title: Figura 5.1. Distribución del número acumulado de respuestas de los participantes por etapa

description: Distribución del número acumulado de respuestas de los participantes por cada una de las tres etapas. Mientras que el grupo 4 solo necesita de la primera etapa para completar las tareas correctamente, los demás necesitan de las siguientes, en las cuales van acumulando progresivamente un mayor número de respuestas correctas.Acosta-Silva, D. A. (2016, April 18). <i>La sensitividad cognitiva: hacia un modelo de su funcionamiento</i>. Tesis doctoral para optar al título de Doctor en Ciencias Sociales, Niñez y Juventud. Centro de Estudios Avanzados en Niñez y Juventud (Cinde), Universidad de Manizales http://doi.org/10.17605/OSF.IO/TZPF6 <br>
DOI: 10.6084/m9.figshare.1619888
title: Effects of protection and sediment stress on coral reefs in Saint Lucia

description: data set used in Begin et al 2014. Effects of protection and sediment stress on coral reefs in Saint Lucia. PLOS One.
DOI: 10.6084/m9.figshare.1619889
title: Tabla 4.12 Frecuencias absolutas códigos grupo 4

description: Frecuencias absolutas códigos grupo 4Acosta-Silva, D. A. (2016, April 18). <i>La sensitividad cognitiva: hacia un modelo de su funcionamiento</i>. Tesis doctoral para optar al título de Doctor en Ciencias Sociales, Niñez y Juventud. Centro de Estudios Avanzados en Niñez y Juventud (Cinde), Universidad de Manizales http://doi.org/10.17605/OSF.IO/TZPF6
DOI: 10.6084/m9.figshare.1619902.v3
title: The benefits of open research: How sharing can help researchers succeed

description: <em>This is a working paper. Feedback is welcome!</em> <strong>Abstract</strong><br>Open access, open data, open source, and other open scholarship practices are growing in necessity and popularity, rapidly becoming part of the integral workflow of researchers. However, widespread adoption of many of these practices has not yet been achieved. Understandably, researchers have concerns as to how sharing their work will affect their careers. Some of these concerns stem from a lack of awareness about the career benefits associated with open research. Herein, we review literature on the open citation advantage, media attention for publicly available research, collaborative possibilities, and special funding opportunities to show how open practices can give researchers a competitive advantage.
DOI: 10.6084/m9.figshare.1619888.v1
title: Effects of protection and sediment stress on coral reefs in Saint Lucia

description: data set used in Begin et al 2014. Effects of protection and sediment stress on coral reefs in Saint Lucia. PLOS One.
DOI: 10.6084/m9.figshare.1619896.v2
title: Thesis_Everdingen

description: Materials for Eveline van Everdingen's Master Thesis: "Multitasking Behavior and Gaze-Following Technology for Workplace Video-Conferencing" for the Research Master Artificial Intelligence at VU University Amsterdam This fileset contains: - The final thesis - The data of the user experiments as decribed in the paper, including data analysis, distribution of participants and the conditions. - The code for the dual-webcam switching software as described in the paper
DOI: 10.6084/m9.figshare.1619883
title: Códigos con mayores frecuencias en el protocolo del participante 4.02

description: Códigos con mayores frecuencias en el protocolo del participante 4.02Acosta-Silva, D. A. (2016, April 18). <i>La sensitividad cognitiva: hacia un modelo de su funcionamiento</i>. Tesis doctoral para optar al título de Doctor en Ciencias Sociales, Niñez y Juventud. Centro de Estudios Avanzados en Niñez y Juventud (Cinde), Universidad de Manizales http://doi.org/10.17605/OSF.IO/TZPF6
DOI: 10.6084/m9.figshare.1619884
title: Códigos con mayores frecuencias en el protocolo del participante 4.03

description: Códigos con mayores frecuencias en el protocolo del participante 4.03Acosta-Silva, D. A. (2016, April 18). <i>La sensitividad cognitiva: hacia un modelo de su funcionamiento</i>. Tesis doctoral para optar al título de Doctor en Ciencias Sociales, Niñez y Juventud. Centro de Estudios Avanzados en Niñez y Juventud (Cinde), Universidad de Manizales http://doi.org/10.17605/OSF.IO/TZPF6
DOI: 10.6084/m9.figshare.1619889.v2
title: Tabla 4.12 Frecuencias absolutas códigos grupo 4

description: Frecuencias absolutas códigos grupo 4Acosta-Silva, D. A. (2016, April 18). <i>La sensitividad cognitiva: hacia un modelo de su funcionamiento</i>. Tesis doctoral para optar al título de Doctor en Ciencias Sociales, Niñez y Juventud. Centro de Estudios Avanzados en Niñez y Juventud (Cinde), Universidad de Manizales http://doi.org/10.17605/OSF.IO/TZPF6