cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1613867
title: The transcription initiation sites of eggplant latent viroid strands map within distinct motifs in their <i>in vivo</i> RNA conformations

description: Eggplant latent viroid (ELVd), like other members of family <i>Avsunviroidae</i>, replicates in plastids through a symmetric rolling-circle mechanism in which elongation of RNA strands is most likely catalyzed by a nuclear-encoded polymerase (NEP) translocated to plastids. Here we have addressed where NEP initiates transcription of viroid strands. Because this step is presumably directed by sequence/structural motifs, we have previously determined the conformation of the monomeric linear (+) and (−) RNAs of ELVd resulting from hammerhead-mediated self-cleavage. <i>In silico</i> predictions with 3 softwares led to similar bifurcated conformations for both ELVd strands. <i>In vitro</i> examination by non-denaturing PAGE showed that they migrate as prominent single bands, with the ELVd (+) RNA displaying a more compact conformation as revealed by its faster electrophoretic mobility. <i>In vitro</i> SHAPE analysis corroborated the ELVd conformations derived from thermodynamics-based predictions <i>in silico</i>. Moreover, sequence analysis of 94 full-length natural ELVd variants disclosed co-variations, and mutations converting canonical into wobble pairs or vice versa, which confirmed <i>in vivo</i> most of the stems predicted <i>in silico</i> and <i>in vitro</i>, and additionally helped to introduce minor structural refinements. Therefore, results from the 3 experimental approaches were essentially consistent among themselves. Application to RNA preparations from ELVd-infected tissue of RNA ligase-mediated rapid amplification of cDNA ends, combined with pretreatments to modify the 5′ ends of viroid strands, mapped the transcription initiation sites of ELVd (+) and (−) strands <i>in vivo</i> at different sequence/structural motifs, in contrast with the situation previously observed in 2 other members of the family <i>Avsunviroidae</i>.
DOI: 10.6084/m9.figshare.1613867.v1
title: The transcription initiation sites of eggplant latent viroid strands map within distinct motifs in their <i>in vivo</i> RNA conformations

description: Eggplant latent viroid (ELVd), like other members of family <i>Avsunviroidae</i>, replicates in plastids through a symmetric rolling-circle mechanism in which elongation of RNA strands is most likely catalyzed by a nuclear-encoded polymerase (NEP) translocated to plastids. Here we have addressed where NEP initiates transcription of viroid strands. Because this step is presumably directed by sequence/structural motifs, we have previously determined the conformation of the monomeric linear (+) and (−) RNAs of ELVd resulting from hammerhead-mediated self-cleavage. <i>In silico</i> predictions with 3 softwares led to similar bifurcated conformations for both ELVd strands. <i>In vitro</i> examination by non-denaturing PAGE showed that they migrate as prominent single bands, with the ELVd (+) RNA displaying a more compact conformation as revealed by its faster electrophoretic mobility. <i>In vitro</i> SHAPE analysis corroborated the ELVd conformations derived from thermodynamics-based predictions <i>in silico</i>. Moreover, sequence analysis of 94 full-length natural ELVd variants disclosed co-variations, and mutations converting canonical into wobble pairs or vice versa, which confirmed <i>in vivo</i> most of the stems predicted <i>in silico</i> and <i>in vitro</i>, and additionally helped to introduce minor structural refinements. Therefore, results from the 3 experimental approaches were essentially consistent among themselves. Application to RNA preparations from ELVd-infected tissue of RNA ligase-mediated rapid amplification of cDNA ends, combined with pretreatments to modify the 5′ ends of viroid strands, mapped the transcription initiation sites of ELVd (+) and (−) strands <i>in vivo</i> at different sequence/structural motifs, in contrast with the situation previously observed in 2 other members of the family <i>Avsunviroidae</i>.
DOI: 10.6084/m9.figshare.1613879.v1
title: Disparate Metabolic Responses in Mice Fed a High-fat Diet Supplemented with Maize-derived Non-digestible Feruloylated Oligo- and Polysaccharides are Linked to Changes in the Gut Microbiota

description: Studies have suggested links between colonic fermentation of dietary fibers and improved metabolic health. The objectives of this study were to determine if non-digestible feruloylated oligo- and polysaccharides (FOPS), a maize-derived dietary fiber, could counteract the deleterious effects of high-fat (HF) feeding in mice and explore if metabolic benefits were linked to the gut microbiota. C57BL/6J mice (n=8/group) were fed a low-fat (LF; 10 kcal% fat), HF (62 kcal% fat), or HF diet supplemented with FOPS (5%, w/w). Pronounced differences in FOPS responsiveness were observed: four mice experienced cecal enlargement and enhanced short chain fatty acid production, indicating increased cecal fermentation (F-FOPS). Only these mice displayed improvements in glucose metabolism compared with HF-fed mice. Blooms in the gut microbial genera Blautia and Akkermansia were observed in three of the F-FOPS mice; these shifts were associated with reductions in body and adipose tissue weights compared with the HF-fed control mice. No improvements in metabolic markers or weights were detected in the four mice whose gut microbiota did not respond to FOPS. These findings demonstrate that FOPS-induced improvements in weight gain and metabolic health in mice depended on the ability of an individual’s microbiota to ferment FOPS.
DOI: 10.6084/m9.figshare.1613866
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - Supplemental-table-S3.csv

description: Comparison of ML bootstrap support and RF distances from all analyses<br>
DOI: 10.6084/m9.figshare.1613864
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - Supplemental-table-S1.xlsx

description: Detailed sample information<br>
DOI: 10.6084/m9.figshare.1613865
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - Supplemental-table-S2.csv

description: Pairwise RF distances between different trees<br>
DOI: 10.6084/m9.figshare.1613863
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - Fig-S7.pdf

description: Phylogentic informativeness<br>
DOI: 10.6084/m9.figshare.1613866.v2
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - Supplemental-table-S3.csv

description: Comparison of ML bootstrap support and RF distances from all analyses<br>
DOI: 10.6084/m9.figshare.1613862
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - FIG-S6-ASTRID.trees

description: ASTRID trees<br>
DOI: 10.6084/m9.figshare.1613866.v1
title: Supplemental-table-S3.csv

description: Comparison of ML bootstrap support and RF distances from all analyses<br>
DOI: 10.6084/m9.figshare.1613861
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - FIG-S5-ASTRAL.trees

description: ASTRAL trees<br>
DOI: 10.6084/m9.figshare.1613865.v1
title: Supplemental-table-S2.csv

description: Pairwise RF distances between different trees<br>
DOI: 10.6084/m9.figshare.1613860
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - FIG-S4-svdquartets-qmc.trees

description: SVDquartets trees reconciled with qmc<br>
DOI: 10.6084/m9.figshare.1613864.v1
title: Supplemental-table-S1.xlsx

description: Detailed sample information<br>
DOI: 10.6084/m9.figshare.1613862.v2
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - FIG-S6-ASTRID.trees

description: ASTRID trees<br>
DOI: 10.6084/m9.figshare.1613863.v2
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - Fig-S7.pdf

description: Phylogentic informativeness<br>
DOI: 10.6084/m9.figshare.1613859
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - FIG-S3-SMRT-ML-QMC.trees

description: SMRT-ML trees reconciled with QMC algorithm<br>
DOI: 10.6084/m9.figshare.1613861.v2
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - FIG-S5-ASTRAL.trees

description: ASTRAL trees<br>
DOI: 10.6084/m9.figshare.1613862.v1
title: FIG-S6-ASTRID.trees

description: ASTRID trees<br>
DOI: 10.6084/m9.figshare.1613863.v1
title: Fig-S7.pdf

description: Phylogentic informativeness<br>
DOI: 10.6084/m9.figshare.1613860.v2
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - FIG-S4-svdquartets-qmc.trees

description: SVDquartets trees reconciled with qmc<br>
DOI: 10.6084/m9.figshare.1613857
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - FIG-S1-RAxML.trees

description: RAxML trees<br>
DOI: 10.6084/m9.figshare.1613858
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - FIG-S2-SMRT-ML.trees

description: SMRT-ML trees<br>
DOI: 10.6084/m9.figshare.1613860.v1
title: FIG-S4-svdquartets-qmc.trees

description: SVDquartets trees reconciled with qmc<br>
DOI: 10.6084/m9.figshare.1613861.v1
title: FIG-S5-ASTRAL.trees

description: ASTRAL trees<br>
DOI: 10.6084/m9.figshare.1613859.v2
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - FIG-S3-SMRT-ML-QMC.trees

description: SMRT-ML trees reconciled with QMC algorithm<br>
DOI: 10.6084/m9.figshare.1613856
title: List of Angiosperms from Espírito Santo State, Brazil

description: This database is supplementary material of the article "Angiosperm Checklist of Espírito Santo: using electronic tools to improve the knowledge of an Atlantic Forest biodiversity hotspot" published in the Journal Rodriguésia in 2015 (<strong>DOI: 10.1590/2175-7860201566414</strong>).
DOI: 10.6084/m9.figshare.1613855
title: Additional datasets from 'A chemosynthetic weed: the tubeworm Sclerolinum contortum is a bipolar, cosmopolitan species' BMC Evolutionary Biology

description: Specimen occurrence in DarwinCore format Siboglinidae COI, 18S and 16S combined alignment in nexus format Sclerolinum COI alignment in nexus format
DOI: 10.6084/m9.figshare.1613857.v2
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - FIG-S1-RAxML.trees

description: RAxML trees<br>
DOI: 10.6084/m9.figshare.1613858.v2
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - FIG-S2-SMRT-ML.trees

description: SMRT-ML trees<br>
DOI: 10.6084/m9.figshare.1613857.v1
title: FIG-S1-RAxML.trees

description: RAxML trees<br>
DOI: 10.6084/m9.figshare.1613859.v1
title: FIG-S3-SMRT-ML-QMC.trees

description: SMRT-ML trees reconciled with QMC algorithm<br>
DOI: 10.6084/m9.figshare.1613855.v1
title: Additional datasets from 'A chemosynthetic weed: the tubeworm Sclerolinum contortum is a bipolar, cosmopolitan species' BMC Evolutionary Biology

description: Specimen occurrence in DarwinCore format Siboglinidae COI, 18S and 16S combined alignment in nexus format Sclerolinum COI alignment in nexus format
DOI: 10.6084/m9.figshare.1613858.v1
title: FIG-S2-SMRT-ML.trees

description: SMRT-ML trees<br>
DOI: 10.6084/m9.figshare.1613851
title: Streptococcus pyogenes - seer visualation

description: This is output from seer to be used in phandango. Drag and drop the files in to visualise a Manhattan plot along with a reference genome and metadata. jscandy-nocovar.plot shows elements associated with country of isolation jscandy-local.plot shows elements associated with invasivenessseer.pyogenes.hits.txt.gz is the raw output from seer
DOI: 10.6084/m9.figshare.1613843
title: Tabla 3.1 Distribución de las tareas de la etapa de detección

description: Descripción de las siete tareas, correspondiendo a cuatro tareas de detección y tres tareas para evitar el efecto de la administración de las pruebas. Todas presentaban la misma estructura argumentativa, las mismas instrucciones y seguían el mismo procedimiento, pero las tareas para evitar la familiarización no requerían de la deducción para ser completadas. Por su parte, las tareas de detección incluían tres de las cuatro formas de las deducciones condicionales: el modus ponens, el modus tollens y la negación del antecedente, recordando que, según la lógica formal, las dos primeras generan razonamientos válidos y la última inválidos. Estas formas podían presentar todos sus elementos (premisas y conclusión) o algunos de ellos.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
DOI: 10.6084/m9.figshare.1613851.v1
title: Streptococcus pyogenes - seer visualation

description: This is output from seer to be used in phandango. Drag and drop the files in to visualise a Manhattan plot along with a reference genome and metadata. jscandy-nocovar.plot shows elements associated with country of isolation jscandy-local.plot shows elements associated with invasiveness
DOI: 10.6084/m9.figshare.1613843.v1
title: 3.1 Distribución de las tareas de la etapa de detección

description: Descripción de las siete tareas, correspondiendo a cuatro tareas de detección y tres tareas para evitar el efecto de la administración de las pruebas. Todas presentaban la misma estructura argumentativa, las mismas instrucciones y seguían el mismo procedimiento, pero las tareas para evitar la familiarización no requerían de la deducción para ser completadas. Por su parte, las tareas de detección incluían tres de las cuatro formas de las deducciones condicionales: el modus ponens, el modus tollens y la negación del antecedente, recordando que, según la lógica formal, las dos primeras generan razonamientos válidos y la última inválidos. Estas formas podían presentar todos sus elementos (premisas y conclusión) o algunos de ellos.
DOI: 10.6084/m9.figshare.1613843.v3
title: Tabla 3.1 Distribución de las tareas de la etapa de detección

description: Descripción de las siete tareas, correspondiendo a cuatro tareas de detección y tres tareas para evitar el efecto de la administración de las pruebas. Todas presentaban la misma estructura argumentativa, las mismas instrucciones y seguían el mismo procedimiento, pero las tareas para evitar la familiarización no requerían de la deducción para ser completadas. Por su parte, las tareas de detección incluían tres de las cuatro formas de las deducciones condicionales: el modus ponens, el modus tollens y la negación del antecedente, recordando que, según la lógica formal, las dos primeras generan razonamientos válidos y la última inválidos. Estas formas podían presentar todos sus elementos (premisas y conclusión) o algunos de ellos.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
DOI: 10.6084/m9.figshare.1613832
title: Mephedrone annotations for Twitter

description: This file contains 5,000 manually double-annotated tweets on whether they represent a relevant or non-relevant mention to mephedrone, a novel psychoactive substance.
DOI: 10.6084/m9.figshare.1613843.v2
title: 3.1 Distribución de las tareas de la etapa de detección

description: Descripción de las siete tareas, correspondiendo a cuatro tareas de detección y tres tareas para evitar el efecto de la administración de las pruebas. Todas presentaban la misma estructura argumentativa, las mismas instrucciones y seguían el mismo procedimiento, pero las tareas para evitar la familiarización no requerían de la deducción para ser completadas. Por su parte, las tareas de detección incluían tres de las cuatro formas de las deducciones condicionales: el modus ponens, el modus tollens y la negación del antecedente, recordando que, según la lógica formal, las dos primeras generan razonamientos válidos y la última inválidos. Estas formas podían presentar todos sus elementos (premisas y conclusión) o algunos de ellos.
DOI: 10.6084/m9.figshare.1613793
title: The palynostratigraphy of the Upper Maiolica, Selli Level and the Lower Marne a Fucoidi units in the proposed Barremian/Aptian (Lower Cretaceous) GSSP stratotype at Gorgo a Cerbara, Umbria–Marche Basin, Italy

description: The section of Gorgo a Cerbara in Italy has been proposed as the Global Stratotype Section and Point (GSSP) for the Barremian/Aptian boundary (Lower Cretaceous). This section displays the transition between the white pelagic limestones of the Maiolica Formation (Tithonian–lowermost Aptian) and the polychrome marls of the Marne a Fucoidi Formation (Aptian–Albian). The Oceanic Anoxic Event 1a (OAE 1a) anoxic horizon (Selli Level) is located in the latter formation. Here, we report for the first time a palynostratigraphical assessment of this key section, with a very high resolution in the Selli Level. Palynomorph groups recorded include acritarchs, microforaminiferal test linings, 58 dinoflagellate cysts, 44 sporomorph taxa, and freshwater fungal and algal bodies. These include such biostratigraphical markers as <i>Rhynchodiniopsis aptiana</i> and <i>Odontochitina operculata</i> among the dinoflagellate cysts and <i>Afropollis</i> cf. <i>jardinus</i> among sporomorphs. Biostratigraphical events recognised allow comparisons with previously studied successions in other similar areas (e.g. Cismon apticore in the Southern Alps, Italy). The distribution of taxa recorded in the Gorgo a Cerbara section is generally consistent with published data, but several differences between the assemblages recorded in the Cismon apticore and in this study were noted. The best global markers for the Barremian/Aptian boundary are represented by the disappearance of <i>R. aptiana</i> and by the appearance of <i>O. operculata</i>, but in this section these occurred 0.65–1.35 Myr after the magnetostratigraphically defined boundary, within the Selli Level. The angiosperm pollen <i>A</i>. cf. <i>jardinus</i> is recorded only within the Selli Level (from 1.4 to 1.6 Myr after the Barremian/Aptian boundary), consistent with an Early Aptian age. A cluster of 10 extremely short-ranging dinoflagellate cyst excursion taxa appear in this section coincident with the Nannoconid Crisis event and its associated thermal peak, ca. 10–20 kyr before the onset of the OAE 1a. Several short-ranging <i>Pteridophyta</i> spore species are found only within the Selli Level itself.
DOI: 10.6084/m9.figshare.1613793.v1
title: The palynostratigraphy of the Upper Maiolica, Selli Level and the Lower Marne a Fucoidi units in the proposed Barremian/Aptian (Lower Cretaceous) GSSP stratotype at Gorgo a Cerbara, Umbria–Marche Basin, Italy

description: The section of Gorgo a Cerbara in Italy has been proposed as the Global Stratotype Section and Point (GSSP) for the Barremian/Aptian boundary (Lower Cretaceous). This section displays the transition between the white pelagic limestones of the Maiolica Formation (Tithonian–lowermost Aptian) and the polychrome marls of the Marne a Fucoidi Formation (Aptian–Albian). The Oceanic Anoxic Event 1a (OAE 1a) anoxic horizon (Selli Level) is located in the latter formation. Here, we report for the first time a palynostratigraphical assessment of this key section, with a very high resolution in the Selli Level. Palynomorph groups recorded include acritarchs, microforaminiferal test linings, 58 dinoflagellate cysts, 44 sporomorph taxa, and freshwater fungal and algal bodies. These include such biostratigraphical markers as <i>Rhynchodiniopsis aptiana</i> and <i>Odontochitina operculata</i> among the dinoflagellate cysts and <i>Afropollis</i> cf. <i>jardinus</i> among sporomorphs. Biostratigraphical events recognised allow comparisons with previously studied successions in other similar areas (e.g. Cismon apticore in the Southern Alps, Italy). The distribution of taxa recorded in the Gorgo a Cerbara section is generally consistent with published data, but several differences between the assemblages recorded in the Cismon apticore and in this study were noted. The best global markers for the Barremian/Aptian boundary are represented by the disappearance of <i>R. aptiana</i> and by the appearance of <i>O. operculata</i>, but in this section these occurred 0.65–1.35 Myr after the magnetostratigraphically defined boundary, within the Selli Level. The angiosperm pollen <i>A</i>. cf. <i>jardinus</i> is recorded only within the Selli Level (from 1.4 to 1.6 Myr after the Barremian/Aptian boundary), consistent with an Early Aptian age. A cluster of 10 extremely short-ranging dinoflagellate cyst excursion taxa appear in this section coincident with the Nannoconid Crisis event and its associated thermal peak, ca. 10–20 kyr before the onset of the OAE 1a. Several short-ranging <i>Pteridophyta</i> spore species are found only within the Selli Level itself.
DOI: 10.6084/m9.figshare.1613791
title: Zebra finch group calling zf4f

description: Calling patterns of four female zebra finches, recorded in an indoor aviary in London in 2015. Two CSV files are included: each one describes a one-hour session. The CSV columns are: time (seconds), duration (seconds), microphone number (0-3). Note that the order of birds is swapped between the two days, so microphone number 0,1,2,3 in session2 corresponds to the same birds as microphone number 3,2,1,0 in session3. (We refer to this dataset as "zf4f".)
DOI: 10.6084/m9.figshare.1613788
title: Calanus Euxinus size measurements

description: Prosome lenght, total length, lateral width and dorsal width of the C.euxinus specimens used in acoustic estimations. Each rar file contains measurements from different stations. Stations information is writtine in a text file within the rar file.
DOI: 10.6084/m9.figshare.1613791.v1
title: Zebra finch group calling zf4f

description: Calling patterns of four female zebra finches, recorded in an indoor aviary in London in 2015. Two CSV files are included: each one describes a one-hour session. The CSV columns are: time (seconds), duration (seconds), microphone number (0-3). Note that the order of birds is swapped between the two days, so microphone number 0,1,2,3 in session2 corresponds to the same birds as microphone number 3,2,1,0 in session3. (We refer to this dataset as "zf4f".)
DOI: 10.6084/m9.figshare.1613833.v3
title: Fig. 2.2 Relación facultades-tareas-habilidades

description: En esta gráfica podemos observar cómo grupos de capacidades son empleadas para la realización de una sola tarea. Por otra parte, que las mismas capacidades pueden ser necesarias para cumplir diferentes tareas, aunque esto generalmente ocurra dentro del mismo dominio. Además, que existen tareas y habilidades individuales que pueden ser compartidas por diferentes dominios, así como tareas que no generan habilidades; y, finalmente, cómo las habilidades son generadas en relación a las tareas, no a las capacidades. Tomado de <em>Habilidades, competencias y experticias: más allá del saber qué y del saber</em> cómo por D. A. Acosta Silva y C. E. Vasco, 2013. Bogotá: Corporación Universitaria Unitec-Cinde.