cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5571802.v1
title: Dataset for: In-vitro characterization of gamma oscillations in the hippocampal formation of the domestic chick

description: Avian and mammalian brains have evolved independently from each other for about 300 million years. During that time, the hippocampal formation (HF) has diverged in morphology and cyto-architecture, but seems to have conserved much of its function. It is therefore an open question how seemingly different neural organizations can generate the same function. A prominent feature of the mammalian hippocampus is that it generates different neural oscillations, including the gamma rhythm, which plays an important role in memory processing. In this study, we investigate whether the avian hippocampus also generates gamma oscillations, and whether similar pharmacological mechanisms are involved in this function. We investigated the existence of gamma oscillations in avian HF using in vitro electrophysiology in P0-P12 domestic chick (Gallus gallus domesticus) HF brain slices. Persistent gamma frequency oscillations were induced by the bath application of the cholinergic agonist carbachol, but not by kainate, a glutamate receptor agonist. Similar to other species, carbachol-evoked gamma oscillations were sensitive to GABAA, AMPA/kainate, and muscarinic (M1) receptor antagonism. Therefore, similar to mammalian species, muscarinic receptor-activated avian HF gamma oscillations may arise via a pyramidal-interneuron gamma (PING) based mechanism. Gamma oscillations are most prominent in the ventromedial area of the hippocampal slices, and gamma power is reduced more laterally and dorsally in the HF. We conclude that similar micro-circuitry may exist in the avian and mammalian hippocampal formation, and this is likely to relate to the shared function of the two structures.
DOI: 10.6084/m9.figshare.5571679
title: DBC, DOC, and DBC:DOC ratios for natural waters across the freshwater-to-marine continuum

description: This table includes a list of dissolved black carbon (DBC) concentrations, dissolved organic carbon (DOC) concentrations, and DBC:DOC ratios in natural waters across the freshwater-to-marine continuum. This table is a compilation of pre-existing literature values.
DOI: 10.6084/m9.figshare.5571811.v1
title: IEEE TCDS SI Language Development n_v = 123 (autonomousl)

description: n_v = 123 (autonomousl)
DOI: 10.6084/m9.figshare.5570305
title: Rapid changes in Atlantic grey seal milk from birth to weaning – immune factors and indicators of metabolic strain

description: Datasets for proteomic and metabolomic analyses of grey seal milk associated with the paper "Rapid changes in Atlantic grey seal milk from birth to weaning – immune factors and indicators of metabolic strain" to be published in Scientific Reports by Amanda Lowe, Sami Bawazeer, David Watson, Suzanne McGill, Richard Burchmore, Paddy Pomeroy and Malcolm Kennedy.<br>
DOI: 10.6084/m9.figshare.5571523.v1
title: On the Multilevel Nature of Meta-Analysis: A Tutorial, Comparison of Software Programs, and Discussion of Analytic Choices

description: The term “multilevel meta-analysis” is encountered not only in applied research studies, but in multilevel resources comparing traditional meta-analysis to multilevel meta-analysis. In this tutorial, we argue that the term “multilevel meta-analysis” is redundant since all meta-analysis can be formulated as a special kind of multilevel model. To clarify the multilevel nature of meta-analysis the four standard meta-analytic models are presented using multilevel equations and fit to an example data set using four software programs: two specific to meta-analysis (metafor in R and SPSS macros) and two specific to multilevel modeling (PROC MIXED in SAS and HLM). The same parameter estimates are obtained across programs underscoring that all meta-analyses are multilevel in nature. Despite the equivalent results, not all software programs are alike and differences are noted in the output provided and estimators available. This tutorial also recasts distinctions made in the literature between traditional and multilevel meta-analysis as differences between meta-analytic <i>choices</i>, not between meta-analytic <i>models</i>, and provides guidance to inform choices in estimators, significance tests, moderator analyses, and modeling sequence. The extent to which the software programs allow flexibility with respect to these decisions is noted, with metafor emerging as the most favorable program reviewed.
DOI: 10.6084/m9.figshare.5570281
title: Monthly precipitation comparison during base and future periods at Stavely, Alberta, Canada

description: Precipitation Change at Stavely, Alberta, Canada
DOI: 10.6084/m9.figshare.5570284
title: Maximum Temperature Change at Stavely, Alberta, Canada

description: Maximum Temperature Change at Stavely, Alberta, Canada
DOI: 10.6084/m9.figshare.5571679.v1
title: Literature_DBC_DOC_values.xlsx

description: This table includes a list of dissolved black carbon and dissolved organic carbon measurements in natural waters across the freshwater-to-marine continuum. This table is a compilation of pre-existing literature values.
DOI: 10.6084/m9.figshare.5570260
title: Details of several soil, grazing and fertilizer related properties

description: Details of several soil, grazing and fertilizer related properties <br>
DOI: 10.6084/m9.figshare.5570281.v1
title: Monthly precipitation comparison during base and future periods at Stavely, Alberta, Canada

description: Precipitation Change at Stavely, Alberta, Canada
DOI: 10.6084/m9.figshare.5570260.v1
title: Details of several soil, grazing and fertilizer related properties

description: Details of several soil, grazing and fertilizer related properties <br>
DOI: 10.6084/m9.figshare.5570284.v1
title: Maximum Temperature Change at Stavely, Alberta, Canada

description: Maximum Temperature Change at Stavely, Alberta, Canada
DOI: 10.6084/m9.figshare.5571679.v2
title: Literature_DBC_DOC_values.xlsx

description: This table includes a list of dissolved black carbon (DBC) concentrations, dissolved organic carbon (DOC) concentrations, and DBC:DOC ratios in natural waters across the freshwater-to-marine continuum. This table is a compilation of pre-existing literature values.
DOI: 10.6084/m9.figshare.5570149
title: Phénologie des espèces steppiques

description: Nous présentons au niveau de cette base de données la phénologie de 114 espèces steppiques. Pour cela, nous avons choisi trois stations à armoise blanche (<i>Artemisia herba-alba </i>Asso.) de la région du Sud algérois (Djelfa) dans lesquelles nous avons installé 5 placettes permanentes servant à la réalisation des relevés phénologiques selon 9 compagnes d'échantillonnage. Les stations choisies sont Chabka 2, Oued Sdeur et Mankab Ben Hamed. La phénologie est identifiée en tenant compte de 4 phases phrénologiques, à savoir; la phase végétative (Vg), la phase de floraison (Fl), la phase de fructification (Fr) et la phase de dormance (Do). Nous avons également retenu la phase d'apparition des bourgeons floraux (Bg) de l'armoise blanche seulement. <br>
DOI: 10.6084/m9.figshare.5571679.v4
title: DBC, DOC, and DBC:DOC ratios for natural waters across the freshwater-to-marine continuum

description: This table includes a list of dissolved black carbon (DBC) concentrations, dissolved organic carbon (DOC) concentrations, and DBC:DOC ratios in natural waters across the freshwater-to-marine continuum. This table is a compilation of pre-existing literature values.
DOI: 10.6084/m9.figshare.5570155
title: Supporting InformationTablesSubmitted - GlobalBioCycle .docx

description: Supporting Information (Tables) for: Modelling nitrous oxide emissions from rough fescue grassland soils subjected to long term grazing of different intensities using the Soil and Water Assessment Tool (SWAT)
DOI: 10.6084/m9.figshare.5570155.v1
title: Supporting InformationTablesSubmitted - GlobalBioCycle .docx

description: Supporting Information (Tables) for: Modelling nitrous oxide emissions from rough fescue grassland soils subjected to long term grazing of different intensities using the Soil and Water Assessment Tool (SWAT)
DOI: 10.6084/m9.figshare.5571679.v3
title: DBC, DOC, and DBC:DOC ratios for natural waters across the freshwater-to-marine continuum

description: This table includes a list of dissolved black carbon (DBC) concentrations, dissolved organic carbon (DOC) concentrations, and DBC:DOC ratios in natural waters across the freshwater-to-marine continuum. This table is a compilation of pre-existing literature values.
DOI: 10.17028/rd.lboro.5570056
title: Supplementary information files for Leucine elicits myotube hypertrophy and enhances maximal contractile force in tissue engineered skeletal muscle in vitro

description: Supplementary information files for Leucine elicits myotube hypertrophy and enhances maximal contractile force in tissue engineered skeletal muscle in vitro.<br>The amino acid leucine is thought to be important for skeletal muscle growth by virtue of its ability to acutely activate mTORC1 and enhance muscle protein synthesis, yet little data exist regarding its impact on skeletal muscle size and its ability to produce force. We utilized a tissue engineering approach in order to test whether supplementing culture medium with leucine could enhance mTORC1 signaling, myotube growth, and muscle function. Phosphorylation of the mTORC1 target proteins 4EBP-1 and rpS6 and myotube hypertrophy appeared to occur in a dose dependent manner, with 5 and 20 mM of leucine inducing similar effects, which were greater than those seen with 1 mM. Maximal contractile force was also elevated with leucine supplementation; however, although this did not appear to be enhanced with increasing leucine doses, this effect was completely ablated by co-incubation with the mTOR inhibitor rapamycin, showing that the augmented force production in the presence of leucine was mTOR sensitive. Finally, by using electrical stimulation to induce chronic (24 hr) contraction of engineered skeletal muscle constructs, we were able to show that the effects of leucine and muscle contraction are additive, since the two stimuli had cumulative effects on maximal contractile force production. These results extend our current knowledge of the efficacy of leucine as an anabolic nutritional aid showing for the first time that leucine supplementation may augment skeletal muscle functional capacity, and furthermore validates the use of engineered skeletal muscle for highly-controlled investigations into nutritional regulation of muscle physiology.
DOI: 10.17028/rd.lboro.5570056.v1
title: Supplementary information files for Leucine elicits myotube hypertrophy and enhances maximal contractile force in tissue engineered skeletal muscle in vitro

description: Supplementary information files for Leucine elicits myotube hypertrophy and enhances maximal contractile force in tissue engineered skeletal muscle in vitro.<br>The amino acid leucine is thought to be important for skeletal muscle growth by virtue of its ability to acutely activate mTORC1 and enhance muscle protein synthesis, yet little data exist regarding its impact on skeletal muscle size and its ability to produce force. We utilized a tissue engineering approach in order to test whether supplementing culture medium with leucine could enhance mTORC1 signaling, myotube growth, and muscle function. Phosphorylation of the mTORC1 target proteins 4EBP-1 and rpS6 and myotube hypertrophy appeared to occur in a dose dependent manner, with 5 and 20 mM of leucine inducing similar effects, which were greater than those seen with 1 mM. Maximal contractile force was also elevated with leucine supplementation; however, although this did not appear to be enhanced with increasing leucine doses, this effect was completely ablated by co-incubation with the mTOR inhibitor rapamycin, showing that the augmented force production in the presence of leucine was mTOR sensitive. Finally, by using electrical stimulation to induce chronic (24 hr) contraction of engineered skeletal muscle constructs, we were able to show that the effects of leucine and muscle contraction are additive, since the two stimuli had cumulative effects on maximal contractile force production. These results extend our current knowledge of the efficacy of leucine as an anabolic nutritional aid showing for the first time that leucine supplementation may augment skeletal muscle functional capacity, and furthermore validates the use of engineered skeletal muscle for highly-controlled investigations into nutritional regulation of muscle physiology.
DOI: 10.6084/m9.figshare.5570038
title: Data from Bajanca & Vandel 2017.xlsx

description: Values behind statistics and graphs from:<br><b>Epigenetic regulators modulate muscle damage in Duchenne muscular dystrophy model</b><br>by Bajanca & Vandel, 2017
DOI: 10.6084/m9.figshare.5570038.v1
title: Data from Bajanca & Vandel 2017.xlsx

description: Values behind statistics and graphs from:<br><b>Epigenetic regulators modulate muscle damage in Duchenne muscular dystrophy model</b><br>by Bajanca & Vandel, 2017
DOI: 10.6084/m9.figshare.5570149.v1
title: Phénologie des espèces steppiques

description: Nous présentons au niveau de cette base de données la phénologie de 114 espèces steppiques. Pour cela, nous avons choisi trois stations à armoise blanche (<i>Artemisia herba-alba </i>Asso.) de la région du Sud algérois (Djelfa) dans lesquelles nous avons installé 5 placettes permanentes servant à la réalisation des relevés phénologiques selon 9 compagnes d'échantillonnage. Les stations choisies sont Chabka 2, Oued Sdeur et Mankab Ben Hamed. La phénologie est identifiée en tenant compte de 4 phases phrénologiques, à savoir; la phase végétative (Vg), la phase de floraison (Fl), la phase de fructification (Fr) et la phase de dormance (Do). Nous avons également retenu la phase d'apparition des bourgeons floraux (Bg) de l'armoise blanche seulement. <br>
DOI: 10.6084/m9.figshare.5570149.v2
title: Phénologie des espèces steppiques

description: Nous présentons au niveau de cette base de données la phénologie de 114 espèces steppiques. Pour cela, nous avons choisi trois stations à armoise blanche (<i>Artemisia herba-alba </i>Asso.) de la région du Sud algérois (Djelfa) dans lesquelles nous avons installé 5 placettes permanentes servant à la réalisation des relevés phénologiques selon 9 compagnes d'échantillonnage. Les stations choisies sont Chabka 2, Oued Sdeur et Mankab Ben Hamed. La phénologie est identifiée en tenant compte de 4 phases phrénologiques, à savoir; la phase végétative (Vg), la phase de floraison (Fl), la phase de fructification (Fr) et la phase de dormance (Do). Nous avons également retenu la phase d'apparition des bourgeons floraux (Bg) de l'armoise blanche seulement. <br>
DOI: 10.6084/m9.figshare.5568454
title: DinoREF: a curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene

description: Mordret, S., Piredda, R., Vaulot, D., Montresor, M., Kooistra, H. C. F. & Sarno, D. (under revision 2018). DinoREF: a curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene. <i>Molecular Ecology Resources.</i><br><b><br></b><b>Supplementary Material</b><b> 1 </b> List of 18S sequences included in DinoREF including annotations extracted from GenBank and literature sources (see “read-me” for details on metadata).<b>Supplementary Material 2</b>Fasta file (.fast) of sequences used to build DinoREF including the GenBank Accession number of each sequence.<b>Supplementary Material 3</b>DinoREF taxonomy file 1 (.taxonomy) with the taxonomy provided by GenBank for each sequence included in the database. <b>Supplementary Material 4</b>DinoREF taxonomy file 2 (.taxonomy) with the 8-level taxonomy for each sequence included in the database. <b>Supplementary Material 5</b>DinoREF taxonomy file 3 (.taxonomy) with the classification by Superclades for each sequence included in the database.<b>Supplementary Material 6</b>List of V4 unique sequences. When multiple 18S sequences share the same V4 region, the sequences IDs (GenBank # and species name) are reported, one after the other, in the same row.<b>Supplementary Material 7</b>List of OTUs_98%. When multiple V4 sequences cluster in the same OTU at 98%, the sequences IDs (GenBank # and species name) are reported, one after the other, in the same row.<b>Supplementary Material 8</b> Fasta file (.fasta) of sequences of early branching dinoflagellates.<br>
DOI: 10.6084/m9.figshare.5570149.v4
title: Phénologie des espèces steppiques

description: Nous présentons au niveau de cette base de données la phénologie de 114 espèces steppiques. Pour cela, nous avons choisi trois stations à armoise blanche (<i>Artemisia herba-alba </i>Asso.) de la région du Sud algérois (Djelfa) dans lesquelles nous avons installé 5 placettes permanentes servant à la réalisation des relevés phénologiques selon 9 compagnes d'échantillonnage. Les stations choisies sont Chabka 2, Oued Sdeur et Mankab Ben Hamed. La phénologie est identifiée en tenant compte de 4 phases phrénologiques, à savoir; la phase végétative (Vg), la phase de floraison (Fl), la phase de fructification (Fr) et la phase de dormance (Do). Nous avons également retenu la phase d'apparition des bourgeons floraux (Bg) de l'armoise blanche seulement. <br>
DOI: 10.6084/m9.figshare.5570149.v3
title: Phénologie des espèces steppiques

description: Nous présentons au niveau de cette base de données la phénologie de 114 espèces steppiques. Pour cela, nous avons choisi trois stations à armoise blanche (<i>Artemisia herba-alba </i>Asso.) de la région du Sud algérois (Djelfa) dans lesquelles nous avons installé 5 placettes permanentes servant à la réalisation des relevés phénologiques selon 9 compagnes d'échantillonnage. Les stations choisies sont Chabka 2, Oued Sdeur et Mankab Ben Hamed. La phénologie est identifiée en tenant compte de 4 phases phrénologiques, à savoir; la phase végétative (Vg), la phase de floraison (Fl), la phase de fructification (Fr) et la phase de dormance (Do). Nous avons également retenu la phase d'apparition des bourgeons floraux (Bg) de l'armoise blanche seulement. <br>
DOI: 10.6084/m9.figshare.5568454.v1
title: DinoREF: a curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene

description: Mordret, S., Piredda, R., Vaulot, D., Montresor, M., Kooistra, H. C. F. & Sarno, D. (under revision 2018). DinoREF: a curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene. <i>Molecular Ecology Resources.</i><br><b><br></b><b>Supplementary Material</b><b> 1 </b> List of 18S sequences included in DinoREF including annotations extracted from GenBank and literature sources (see “read-me” for details on metadata).<b>Supplementary Material 2</b>Fasta file (.fast) of sequences used to build DinoREF including the GenBank Accession number of each sequence.<b>Supplementary Material 3</b>DinoREF taxonomy file 1 (.taxonomy) with the taxonomy provided by GenBank for each sequence included in the database. <b>Supplementary Material 4</b>DinoREF taxonomy file 2 (.taxonomy) with the 8-level taxonomy for each sequence included in the database. <b>Supplementary Material 5</b>DinoREF taxonomy file 3 (.taxonomy) with the classification by Superclades for each sequence included in the database.<b>Supplementary Material 6</b>List of V4 unique sequences. When multiple 18S sequences share the same V4 region, the sequences IDs (GenBank # and species name) are reported, one after the other, in the same row.<b>Supplementary Material 7</b>List of OTUs_98%. When multiple V4 sequences cluster in the same OTU at 98%, the sequences IDs (GenBank # and species name) are reported, one after the other, in the same row.<b>Supplementary Material 8</b> Fasta file (.fasta) of sequences of early branching dinoflagellates.<br>
DOI: 10.6084/m9.figshare.5568409
title: DNA methylation and obesity traits: An epigenome-wide association study. The REGICOR study

description: Obesity is associated with increased risk of several diseases and has become epidemic. Obesity is highly heritable but the genetic variants identified by genome-wide association studies explain only limited variability. Epigenetics could contribute to explain the missing variability. The study aim was to discover differential methylation patterns related to obesity. We designed an epigenome-wide association study with a discovery phase in a subsample of 641 REGICOR study participants, validated by analysis of 2,515 participants in the Framingham Offspring Study. Blood DNA methylation was assessed using Illumina HumanMethylation450 BeadChip. Next, we meta-analyzed the data using the fixed effects method and performed a functional and pathway analysis using the Ingenuity Pathway Analysis software. We were able to validate 94 CpGs associated with body mass index (BMI) and 49 CpGs associated with waist circumference, located in 95 loci. In addition, we newly discovered 70 CpGs associated with BMI and 33 CpGs related to waist circumference. These CpGs explained 25.94% and 29.22% of the variability of BMI and waist circumference, respectively, in the REGICOR sample. We also evaluated 65 of the 95 validated loci in the GIANT genome-wide association data; 10 of them had Tag SNPs associated with BMI. The top-ranked diseases and functions identified in the functional and pathway analysis were neurologic, psychological, endocrine, and metabolic.
DOI: 10.6084/m9.figshare.5568412
title: Short versus long double-stranded RNA activation of a post-transcriptional gene knockdown pathway

description: RNA interference (RNAi) utilizes a conserved cellular autoimmune defense mechanism involving the internalization of dsRNA into cells and the activation of a set of RNAi related genes. Using RNAi, complete sex reversal is achievable in males of the prawn <i>Macrobrachium rosenbergii</i> by knocking down the transcript level of an insulin-like androgenic gland hormone (<i>Mr-IAG</i>) through injections of dsRNA of the entire <i>Mr-IAG</i> ORF sequence (ds<i>Mr-IAG</i> – 518bp). Interestingly, <i>in-vivo</i> knockdown success and ds<i>Mr-IAG</i> lengths seemed to correlate, with long dsRNA being the most effective and short dsRNA fragments showing no effect. However, little is known about the RNAi machinery in <i>M. rosenbergii</i>. We discovered the <i>Mr-Dicer</i> and <i>Mr-Argonaute</i> gene families, associated with the major knockdown pathways, in our <i>M. rosenbergii</i> transcriptomic library. In response to ds<i>Mr-IAG</i> administration, only post-transcriptional pathway-related gene transcript levels were upregulated. In addition, a passive dsRNA channel (a <i>SID1</i> gene ortholog) that allows external dsRNA to enter cells was found. Its function was validated by observing <i>Mr-SID1</i> specific upregulation dependent on dsRNA lengths, while attempted loss-of-function experiments were lethal. Our results, which suggest differential systemic responses to dsRNA lengths, provide evidence that the above RNAi-based manipulation occurs via the post-transcriptional pathway. The temporal nature of the latter pathway supports the safety of using such RNAi-based biotechnologies in aquaculture and environmental applications. Unlike reports of RNAi driven by the administration of small dsRNA fragments <i>in-vitro</i>, the case presented here demonstrates length dependency <i>in-vivo</i>, suggesting further complexity in the context of the entire organism.