cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6226874
title: Coda wave interferometry during the heating of deep geothermal reservoir rocks (accompanies Azzola et al. (2018)).

description: Data published in <i>Coda wave interferometry during the heating of deep geothermal reservoir rocks</i> (Azzola et al., 2018).
DOI: 10.6084/m9.figshare.6226874.v1
title: Coda wave interferometry during the heating of deep geothermal reservoir rocks (accompanies Azzola et al. (2018)).

description: Data published in <i>Coda wave interferometry during the heating of deep geothermal reservoir rocks</i> (Azzola et al., 2018).
DOI: 10.6084/m9.figshare.6226745
title: Supplementary Material for: A Systematic Review and Meta-Analysis of the Effectiveness of Acetylcholinesterase Inhibitors and Memantine in Treating the Cognitive Symptoms of Dementia

description: <b><i>Background:</i></b> Acetylcholinesterase inhibitors (AChEIs) and memantine are commonly used in the management of dementia. In routine clinical practice, dementia is often monitored via the Mini-Mental State Examination (MMSE). We conducted a systematic review and meta-analysis of the effects of these drugs on MMSE scores. <b><i>Summary:</i></b> Eighty trials were identified. Pooled effect estimates were in favour of both AChEIs and memantine at 6 months. Meta-regression indicated that dementia subtype was a moderator of AChEI treatment effect, with the effect of treatment versus control twice as high for patients with Parkinson disease dementia/ dementia with Lewy bodies (2.11 MMSE points at 6 months) as for patients with Alzheimer disease/vascular dementia (0.91 MMSE points at 6 months). <b><i>Key Messages:</i></b> AChEIs demonstrate a modest effect versus control on MMSE scores which is moderated by dementia subtype. For memantine the effect is smaller.
DOI: 10.6084/m9.figshare.6226742
title: Supplementary Material for: Long-Term Moderate Exercise Rescues Age-Related Decline in Hippocampal Neuronal Complexity and Memory

description: <b><i>Background:</i></b> Aging impairs hippocampal neuroplasticity and hippocampus-related learning and memory. In contrast, exercise training is known to improve hippocampal neuronal function. However, whether exercise is capable of restoring memory function in old animals is less clear. <b><i>Objective:</i></b> Here, we investigated the effects of exercise on the hippocampal neuroplasticity and memory functions during aging. <b><i>Methods:</i></b> Young (3 months), middle-aged (9–12 months), and old (18 months) mice underwent moderate-intensity treadmill running training for 6 weeks, and their hippocampus-related learning and memory, and the plasticity of their CA1 neurons was evaluated. <b><i>Results:</i></b> The memory performance (Morris water maze and novel object recognition tests), and dendritic complexity (branch and length) and spine density of their hippocampal CA1 neurons decreased as their age increased. The induction and maintenance of high-frequency stimulation-induced long-term potentiation in the CA1 area and the expressions of neuroplasticity-related proteins were not affected by age. Treadmill running increased CA1 neuron long-term potentiation and dendritic complexity in all three age groups, and it restored the learning and memory ability in middle-aged and old mice. Furthermore, treadmill running upregulated the hippocampal expressions of brain-derived neurotrophic factor and monocarboxylate transporter-4 in middle-aged mice, glutamine synthetase in old mice, and full-length TrkB in middle-aged and old mice. <b><i>Conclusion:</i></b> The hippocampus-related memory function declines from middle age, but long-term moderate-intensity running effectively increased hippocampal neuroplasticity and memory in mice of different ages, even when the memory impairment had progressed to an advanced stage. Thus, long-term, moderate intensity exercise training might be a way of delaying and treating aging-related memory decline.
DOI: 10.6084/m9.figshare.6226742.v1
title: Supplementary Material for: Long-Term Moderate Exercise Rescues Age-Related Decline in Hippocampal Neuronal Complexity and Memory

description: <b><i>Background:</i></b> Aging impairs hippocampal neuroplasticity and hippocampus-related learning and memory. In contrast, exercise training is known to improve hippocampal neuronal function. However, whether exercise is capable of restoring memory function in old animals is less clear. <b><i>Objective:</i></b> Here, we investigated the effects of exercise on the hippocampal neuroplasticity and memory functions during aging. <b><i>Methods:</i></b> Young (3 months), middle-aged (9–12 months), and old (18 months) mice underwent moderate-intensity treadmill running training for 6 weeks, and their hippocampus-related learning and memory, and the plasticity of their CA1 neurons was evaluated. <b><i>Results:</i></b> The memory performance (Morris water maze and novel object recognition tests), and dendritic complexity (branch and length) and spine density of their hippocampal CA1 neurons decreased as their age increased. The induction and maintenance of high-frequency stimulation-induced long-term potentiation in the CA1 area and the expressions of neuroplasticity-related proteins were not affected by age. Treadmill running increased CA1 neuron long-term potentiation and dendritic complexity in all three age groups, and it restored the learning and memory ability in middle-aged and old mice. Furthermore, treadmill running upregulated the hippocampal expressions of brain-derived neurotrophic factor and monocarboxylate transporter-4 in middle-aged mice, glutamine synthetase in old mice, and full-length TrkB in middle-aged and old mice. <b><i>Conclusion:</i></b> The hippocampus-related memory function declines from middle age, but long-term moderate-intensity running effectively increased hippocampal neuroplasticity and memory in mice of different ages, even when the memory impairment had progressed to an advanced stage. Thus, long-term, moderate intensity exercise training might be a way of delaying and treating aging-related memory decline.
DOI: 10.6084/m9.figshare.6226727
title: Reproducible research

description: Presentation for the Motivational & Cognitive Control lab on Reproducible Research. Covers an introduction to the topic, its components (organization, documentation, automation, dissemination), and a very brief introductions to tools (version control, interactive notebooks, workflows) and how to get started<br><br>HTML slides are best viewed with Google Chrome.<br>
DOI: 10.6084/m9.figshare.6226727.v1
title: Reproducible research

description: Presentation for the Motivational & Cognitive Control lab on Reproducible Research. Covers an introduction to the topic, its components (organization, documentation, automation, dissemination), and a very brief introductions to tools (version control, interactive notebooks, workflows) and how to get started<br><br>Best viewed with Google Chrome.<br>
DOI: 10.6084/m9.figshare.6226718
title: Study dataset

description: Compliance with NPG checklist items: data dictionary available in project space. In version 2, 7 errors from the previous version at database lock (publication date for PMID 25409825 changed from 1/1/2000 to 20/11/2014; publication date for PMID 22622570 changed from 1/1/2000 to 23/05/2014; publication date for PMID 24336168 changed from 1/1/2000 to 15/12/2013; publication date for PMID 25262495 changed from 1/1/2000 to 28/09/2014. PMID 22796663 and 24952910 were categorised as both in vitro and in vivo but are in fact in vitro only; and PMID 22581782 was categorised as both but in fact is in vivo only.
DOI: 10.6084/m9.figshare.6226718.v1
title: Study dataset

description: Compliance with NPG checklist items: data dictionary available in project space. In version 2, 7 errors from the previous version at database lock (publication date for PMID 25409825 changed from 1/1/2000 to 20/11/2014; publication date for PMID 22622570 changed from 1/1/2000 to 23/05/2014; publication date for PMID 24336168 changed from 1/1/2000 to 15/12/2013; publication date for PMID 25262495 changed from 1/1/2000 to 28/09/2014. PMID 22796663 and 24952910 were categorised as both in vitro and in vivo but are in fact in vitro only; and PMID 22581782 was categorised as both but in fact is in vivo only.
DOI: 10.6084/m9.figshare.6226646
title: sequence data for Kobresia and Blysmus

description: 2b-RAD sequence data for <i>Kobresia tibetica</i> and<i> Blysmus sinocompressus</i>
DOI: 10.6084/m9.figshare.6226475
title: Electronic NMR DATA from Synthesis of 4-substituted ethers of benzophenone and their antileishmanial activities

description: Leishmaniasis is a vector-borne protozoan disease, it is mainly originated from the bite of sandfly and initiated when parasite is transmitted to human at metacyclic flagellated promastigote form. In the current study, a synthesis of a series of 4-substituted benzophenone ethers <b>1–20</b> was carried out in good yields and their <i>in vitro</i> antileishmanial activities were also screened. Among synthetic derivatives, 15 compounds <b>1</b>, <b>3</b>, <b>5–12</b>, <b>15</b> and <b>17</b>–<b>20</b> showed antileishmanial activities against promastigotes of <i>Leishmania major</i> with IC<sub>50</sub> values in the range of 1.19–82.30 µg ml<sup>−1</sup>, and the values were compared with those of the standard pentamidine (IC<sub>50 </sub>= 5.09 ± 0.09 µg ml<sup>−1</sup>). Our study identified a series of new antileishmanial molecules as potential lead. Structures of these synthetic compounds were deduced by different spectroscopic techniques, such as <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, EI-MS, HREI-MS and IR.
DOI: 10.6084/m9.figshare.6226475.v1
title: Electronic NMR DATA from Synthesis of 4-substituted ethers of benzophenone and their antileishmanial activities

description: Leishmaniasis is a vector-borne protozoan disease, it is mainly originated from the bite of sandfly and initiated when parasite is transmitted to human at metacyclic flagellated promastigote form. In the current study, a synthesis of a series of 4-substituted benzophenone ethers <b>1–20</b> was carried out in good yields and their <i>in vitro</i> antileishmanial activities were also screened. Among synthetic derivatives, 15 compounds <b>1</b>, <b>3</b>, <b>5–12</b>, <b>15</b> and <b>17</b>–<b>20</b> showed antileishmanial activities against promastigotes of <i>Leishmania major</i> with IC<sub>50</sub> values in the range of 1.19–82.30 µg ml<sup>−1</sup>, and the values were compared with those of the standard pentamidine (IC<sub>50 </sub>= 5.09 ± 0.09 µg ml<sup>−1</sup>). Our study identified a series of new antileishmanial molecules as potential lead. Structures of these synthetic compounds were deduced by different spectroscopic techniques, such as <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, EI-MS, HREI-MS and IR.
DOI: 10.6084/m9.figshare.6226466
title: Metabolic and taxonomic insights into the Gram-negative natural rubber degrading bacterium Steroidobacter cummioxidans sp. nov., strain 35Y

description: It contains genome data (contigs, nucleotide sequences, protein sequences, rRNA gene sequences, tRNA gene sequences of Steroidobacter cummioxidans 35Y.
DOI: 10.6084/m9.figshare.6226466.v2
title: Metabolic and taxonomic insights into the Gram-negative natural rubber degrading bacterium Steroidobacter cummioxidans sp. nov., strain 35Y

description: It contains genome data (contigs, nucleotide sequences, protein sequences, rRNA gene sequences, tRNA gene sequences of Steroidobacter cummioxidans 35Y.
DOI: 10.6084/m9.figshare.6225968
title: motion-test-data

description: Test dataset for "Mitigating head motion artefact in functional connectivity MRI".
DOI: 10.6084/m9.figshare.6225968.v1
title: motion-test-data

description: Test dataset for "Mitigating head motion artefact in functional connectivity MRI".
DOI: 10.6084/m9.figshare.6225890
title: Additional file 8: of Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

description: Table S7. shRNA clone list. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6225890.v1
title: Additional file 8: of Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

description: Table S7. shRNA clone list. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6225887
title: Additional file 7: of Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

description: Table S6. Random Forest ranking for iTreg classification. (TXT 546 kb)
DOI: 10.6084/m9.figshare.6225887.v1
title: Additional file 7: of Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

description: Table S6. Random Forest ranking for iTreg classification. (TXT 546 kb)
DOI: 10.6084/m9.figshare.6225881
title: Additional file 6: of Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

description: Table S5. Functional and disease annotation iTreg subnetwork. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.6225881.v1
title: Additional file 6: of Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

description: Table S5. Functional and disease annotation iTreg subnetwork. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.6225872
title: Additional file 5: of Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

description: Table S4. Network nodes and edges. (XLSX 109 kb)
DOI: 10.6084/m9.figshare.6225872.v1
title: Additional file 5: of Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

description: Table S4. Network nodes and edges. (XLSX 109 kb)
DOI: 10.6084/m9.figshare.6225863
title: Additional file 4: of Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

description: Table S3. Clustering and functional annotation. (XLSX 214 kb)
DOI: 10.6084/m9.figshare.6225863.v1
title: Additional file 4: of Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

description: Table S3. Clustering and functional annotation. (XLSX 214 kb)
DOI: 10.6084/m9.figshare.6225854
title: Additional file 3: of Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

description: Table S2. Differentially expressed genes and proteins. (XLSX 6515 kb)
DOI: 10.6084/m9.figshare.6225854.v1
title: Additional file 3: of Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

description: Table S2. Differentially expressed genes and proteins. (XLSX 6515 kb)
DOI: 10.6084/m9.figshare.6225842
title: Additional file 2: of Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

description: Table S1. Signature scores. (XLS 30 kb)
DOI: 10.6084/m9.figshare.6225842.v1
title: Additional file 2: of Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

description: Table S1. Signature scores. (XLS 30 kb)
DOI: 10.6084/m9.figshare.6225833
title: MOESM1 of Impacts of selected Ecological Focus Area options in European farmed landscapes on climate regulation and pollination services: a systematic map protocol

description: Additional file 1. Scoping results for developing search strings.
DOI: 10.6084/m9.figshare.6225833.v1
title: MOESM1 of Impacts of selected Ecological Focus Area options in European farmed landscapes on climate regulation and pollination services: a systematic map protocol

description: Additional file 1. Scoping results for developing search strings.
DOI: 10.6084/m9.figshare.6225806
title: ZmbZIP4-ChIPseq Data

description: The construct pCAMBIA1302-35S::ZmbZIP4-GFP was used for transformation of Maize inbred Qi319 young embryo via a gene gun (Bio-Rad). Stable transgenetic maize and the monoclonal antibody of GFP were used for ChIP-seq assay. The details of ChIP were as described by Kaufmann et al. (Kaufmann and Al, 2010). Sequencing platform: Illumina Hiseq 4000. Aligner and parameter: Clean Parameter “soap_mm_gz -p 4 -v 5 -s 35 -m 0 -x 600”. Peak caller and parameter: Peak Calling Parameter “macs14 -g 411831487 -p 1e-5 -w --space 50 -m 10, 30”. <br>
DOI: 10.6084/m9.figshare.6225806.v1
title: ZmbZIP4-ChIPseq-input-1.wiggle.tar.gz

description: The construct pCAMBIA1302-35S::ZmbZIP4-GFP was used for transformation of Maize inbred Qi319 young embryo via a gene gun (Bio-Rad). Stable transgenetic maize and the monoclonal antibody of GFP were used for ChIP-seq assay. The production and confirmation of transgenic lines were accomplished as previously described. The details of ChIP were as described by Kaufmann et al. (Kaufmann and Al, 2010). Sequencing platform: Illumina Hiseq 4000. Aligner and parameter: Clean Parameter “soap_mm_gz -p 4 -v 5 -s 35 -m 0 -x 600”. Peak caller and parameter: Peak Calling Parameter “macs14 -g 411831487 -p 1e-5 -w --space 50 -m 10, 30”. <br>
DOI: 10.6084/m9.figshare.6225761
title: dada2_amplicon_ex_workflow.tar.gz

description: Data files for tutorial found at: https://astrobiomike.github.io/amplicon/dada2_workflow_ex
DOI: 10.6084/m9.figshare.6225761.v1
title: dada2_amplicon_ex_workflow.tar.gz

description: https://astrobiomike.github.io/amplicon/dada2_workflow_ex#16s-and-18s-mixed-together
DOI: 10.6084/m9.figshare.6225761.v2
title: dada2_amplicon_ex_workflow.tar.gz

description: https://astrobiomike.github.io/amplicon/dada2_workflow_ex
DOI: 10.6084/m9.figshare.6225761.v3
title: dada2_amplicon_ex_workflow.tar.gz

description: https://astrobiomike.github.io/amplicon/dada2_workflow_ex
DOI: 10.6084/m9.figshare.6225761.v4
title: dada2_amplicon_ex_workflow.tar.gz

description: https://astrobiomike.github.io/amplicon/dada2_workflow_ex
DOI: 10.6084/m9.figshare.6225761.v5
title: dada2_amplicon_ex_workflow.tar.gz

description: Data files for tutorial found at: https://astrobiomike.github.io/amplicon/dada2_workflow_ex
DOI: 10.6084/m9.figshare.6225761.v6
title: dada2_amplicon_ex_workflow.tar.gz

description: Data files for tutorial found at: https://astrobiomike.github.io/amplicon/dada2_workflow_ex
DOI: 10.6084/m9.figshare.6225761.v7
title: dada2_amplicon_ex_workflow.tar.gz

description: Data files for tutorial found at: https://astrobiomike.github.io/amplicon/dada2_workflow_ex
DOI: 10.6084/m9.figshare.6225752
title: dada2_16S_18S_ex.tar.gz

description: https://astrobiomike.github.io/amplicon/16S_and_18S_mixed
DOI: 10.6084/m9.figshare.6225752.v1
title: dada2_16S_18S_ex.tar.gz

description: https://astrobiomike.github.io/amplicon/dada2_workflow_ex#16s-and-18s-mixed-together
DOI: 10.6084/m9.figshare.6225752.v2
title: dada2_16S_18S_ex.tar.gz

description: https://astrobiomike.github.io/amplicon/dada2_workflow_ex#16s-and-18s-mixed-together
DOI: 10.6084/m9.figshare.6225752.v3
title: dada2_16S_18S_ex.tar.gz

description: https://astrobiomike.github.io/amplicon/dada2_workflow_ex#16s-and-18s-mixed-together
DOI: 10.6084/m9.figshare.6225752.v5
title: dada2_16S_18S_ex.tar.gz

description: https://astrobiomike.github.io/amplicon/16S_and_18S_mixed
DOI: 10.6084/m9.figshare.6225752.v4
title: dada2_16S_18S_ex.tar.gz

description: https://astrobiomike.github.io/amplicon/16S_and_18S_mixed
DOI: 10.6084/m9.figshare.6225689
title: Tree.tre

description: 16S tree generated from the Lotus run for this manuscript: "The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms."
DOI: 10.6084/m9.figshare.6225689.v1
title: Tree.tre

description: 16S tree generated from the Lotus run for this manuscript: "The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms."
DOI: 10.6084/m9.figshare.6225686
title: OTU.txt

description: OTU table generated from the Lotus run for this manuscript: "The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms."
DOI: 10.6084/m9.figshare.6225683
title: map_file.csv

description: Metadata used in the Lotus run for this manuscript: "The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms."
DOI: 10.6084/m9.figshare.6225683.v1
title: map_file.csv

description: Metadata used in the Lotus run for this manuscript: "The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms."
DOI: 10.6084/m9.figshare.6225680
title: ddPCR_data.csv

description: ddPCR data supporting this manuscript: "The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms."
DOI: 10.6084/m9.figshare.6225680.v1
title: ddPCR_data.csv

description: ddPCR data supporting this manuscript: "The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms."
DOI: 10.6084/m9.figshare.6225668
title: lotus_logs

description: Supporting logs from the Lotus run for this manuscript: "The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms."
DOI: 10.6084/m9.figshare.6225662
title: Mating preference in black capuchin females_dataset .xlsx

description: Daily proportion of solicitations and copulations directed and/or involving the highest ranking male in two groups of wild black capuchin monkeys.
DOI: 10.6084/m9.figshare.6225662.v1
title: Mating preference in black capuchin females_dataset .xlsx

description: Daily proportion of solicitations and copulations directed and/or involving the highest ranking male in two groups of wild black capuchin monkeys.
DOI: 10.6084/m9.figshare.6225647
title: Development of a systematic method to assess similarity between nanomaterials for human hazard evaluation purposes – lessons learnt

description: Within the EU FP-7 GUIDEnano project, a methodology was developed to systematically quantify the similarity between a nanomaterial (NM) that has been tested in toxicity studies and the NM for which risk needs to be evaluated, for the purpose of extrapolating toxicity data between the two materials. The methodology is a first attempt to use current knowledge on NM property–hazard relationships to develop a series of pragmatic and systematic rules for assessing NM similarity. Moreover, the methodology takes into account the practical feasibility, in that it is based on generally available NM characterization information. In addition to presenting this methodology, the lessons learnt and the challenges faced during its development are reported here. We conclude that there is a large gap between the information that is ideally needed and its application to real cases. The current database on property–hazard relationships is still very limited, which hinders the agreement on the key NM properties constituting the basis of the similarity assessment and the development of associated science-based and unequivocal rules. Currently, one of the most challenging NM properties to systematically assess in terms of similarity between two NMs is surface coating and functionalization, which lacks standardized parameters for description and characterization methodology. Standardization of characterization methods that lead to quantitative, unambiguous, and measurable parameters describing NM properties are necessary in order to build a sufficiently robust property–hazard database that allows for evidence-based refinement of our methodology, or any other attempt to systematically assess the similarity of NMs.