Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
932
datasets available to search
ShareScore release 0.9.0
Dataset results
932 results for “Long term data”
Skogaryd data used for the paper: Evaluation of long-term carbon dynamics in a drained forested peatland using the ForSAFE-Peat Model.
<p>Dataset of abiotic and carbon exchange variables for Skogaryd drained afforested peatland. The dataset include measurements of soil temperature, ground water level, and carbon exhange as well as modelled carbon fluxes performed with the model ForSAFE-Peat </p>
Supplementary data for: Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome
<p><strong><em>Myzus persicae </em>clone O v2 frozen release</strong></p> <p>Genome assembly: Myzus_persicae_O_v2.0.scaffolds.fa.gz</p> <p>BRAKER2 gene models: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3</p> <p>List of gene models containing internal stop codons (removed from the protein and cds fasta files): Myzus_persicae_O_v2.0.scaffolds.braker2.bad_genes.lst</p> <p>BRAKER2 protein sequences: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.cds.fa</p> <p>BRAKER2 coding sequences (longest transcript per gene only): Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.cds.LTPG.fa</p> <p><em>De novo </em>repeat library (ReapeatModeler merged with repbase insecta): Myzus_persicae_O_v2.0_repeat_lib.repeatmodeler_merged_repbase_insecta.fa</p> <p>RepeatMasker transposable element annotation using the <em>M. persicae de novo</em> repeat library: Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff.out</p> <p>RepeatMasker transposable element annotation using the <em>M. persicae</em> <em>de novo r</em>epeat library (gff format): Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff</p> <p><strong><em>Acyrthosiphon pisum</em> clone JIC1 v1 frozen release</strong></p> <p>Genome assembly: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.fa.gz</p> <p>BRAKER2 gene models: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff</p> <p>List of gene models containing internal stop codons (removed from the protein and cds fasta files): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.bad_genes.lst</p> <p>BRAKER2 protein sequences: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.cds.fa</p> <p>BRAKER2 coding sequences (longest transcript per gene only): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.cds.LTPG.fa</p> <p><em>De novo </em>repeat library (ReapeatModeler merged with repbase insecta): Acyrthosiphon_pisum_JIC1_repeat_lib.repeatmodeler_merged_repbase_insecta.fa</p> <p>RepeatMasker transposable element annotation using the <em>A. pisum</em> <em>de novo</em> repeat library: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.out</p> <p>RepeatMasker transposable element annotation using the <em>A. pisum de novo</em> repeat library (gff format): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff</p> <p><strong><em>Rhodnius prolixus</em> DNA zoo chromosome-scale genome assembly annotation</strong></p> <p><em>R. prolixus </em>chromosome-scale genome assembly was obtained here: <a href="https://www.dnazoo.org/assemblies/Rhodnius_prolixus">https://www.dnazoo.org/assemblies/Rhodnius_prolixus</a>.</p> <p>Genome assembly: Rhodnius_prolixus-3.0.3_HiC.fasta</p> <p>BRAKER2 gene models: Rhodnius_prolixus-3.0.3_HiC.braker2.gff</p> <p>BRAKER2 protein sequences: Rhodnius_prolixus-3.0.3_HiC.braker2.gff.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): Rhodnius_prolixus-3.0.3_HiC.braker2.gff.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: Rhodnius_prolixus-3.0.3_HiC.braker2.gff.cds.fa</p> <p><strong><em>Triatoma rubrofasciata</em> chromosome-scale genome assembly annotation</strong></p> <p><em>T. rubrofasciata </em>chromosome-scale genome assembly was obtained here: <a href="http://dx.doi.org/10.5524/100614">http://dx.doi.org/10.5524/100614</a></p> <p>Genome assembly: zhuichun_assembly.fasta</p> <p>BRAKER2 gene models: zhuichun_assembly.braker2.gff</p> <p>BRAKER2 protein sequences: zhuichun_assembly.braker2.gff.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): zhuichun_assembly.braker2.gff.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: zhuichun_assembly.braker2.gff.cds.fa</p> <p><strong>Hemiptera orthogroups and species tree</strong></p> <p>OrthoFinder was used to cluster proteomes of 14 Hemiptera into orthogroups for phylogenomic analysis. All proteomes were reduced to the longest transcript per gene. See here for full details:</p> <p>Species included, taxon IDs and data source:</p> <p>Mcer = Myzus cerasi v1.1 (<a href="https://bipaa.genouest.org/sp/myzus_cerasi/">https://bipaa.genouest.org/sp/myzus_cerasi/</a>)</p> <p>MperO = Myzus persicae clone O v2 (This study)</p> <p>Dnox = Diuraphis noxia Thorpe et. al. gene predictions (<a href="https://bipaa.genouest.org/sp/diuraphis_noxia/">https://bipaa.genouest.org/sp/diuraphis_noxia/</a>)</p> <p>Apis = Acyrthosiphon pisum JIC1 v1 (This study)</p> <p>Pnig = Pentalonia nigronervosa (This study)</p> <p>Rmai = Rhopalosiphum maidis v0.1 (<a href="http://gigadb.org/dataset/100572">http://gigadb.org/dataset/100572</a>)</p> <p>Rpad = Rhopalosiphum padi v1.0 (<a href="https://bipaa.genouest.org/sp/rhopalosiphum_padi/">https://bipaa.genouest.org/sp/rhopalosiphum_padi/</a>)</p> <p>Agly = Aphis glycines biotype 4 v2.1 (<a href="https://zenodo.org/record/3453468#.XnpL5JOgLRY">https://zenodo.org/record/3453468#.XnpL5JOgLRY</a>)</p> <p>BtabMEAM1 = Bemissia tabacci MEAM1 v1.2 (<a href="http://www.whiteflygenomics.org/cgi-bin/bta/index.cgi">http://www.whiteflygenomics.org/cgi-bin/bta/index.cgi</a>)</p> <p>Trub = Triatoma rubrofasciata (This study)</p> <p>Rpro = Rhodnius prolixus (This study)</p> <p>Ofas = Oncopeltus fasciatus OGS v1.0 (<a href="https://i5k.nal.usda.gov/Oncopeltus_fasciatus">https://i5k.nal.usda.gov/Oncopeltus_fasciatus</a>)</p> <p>Sfuc = Sogatella furcifera v1 (<a href="http://dx.doi.org/10.5524/100255">http://dx.doi.org/10.5524/100255</a>)</p> <p>Nlug = Nilaparvata lugens (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0521-0#Sec42">https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0521-0#Sec42</a>)</p> <p>Files:</p> <p>Proteomes included in the analysis: proteomes.tar.gz</p> <p>Orthogroups: Orthogroups.txt</p> <p>Gene counts per orthogroup, per species: Orthogroups.GeneCount.csv</p> <p>Single copy conserved orthogroups used for species tree: SingleCopyOrthogroups.txt</p> <p>Species tree alignment: SpeciesTreeAlignment.fa</p> <p>r8s configuration file (includes time calibrations and OrthoFinder ML species tree with branch lengths): species_tree_rooted.r8s.nex</p> <p>r8s time calibrated species tree: r8s_tree.nwk</p>
Long-term litter fall data series from 34 boreal forest stands in Finland
<p><strong>Introduction</strong></p> <p>Litter fall data were collected on a network of 34 forest sampling plots in Finland from late 1950s to 2010s. The data collection spanned different time periods in different sampling plots. The data have been used for studies on the flowering and seed crop of forest trees, air quality, and insect damage (see list of publications in the end of this document). They have been used to develop seed production and needle litter fall models for Scots pine (<em>Pinus sylvestris</em>) and Norway spruce (<em>Picea abies</em>), a branch litter model for pine, and total litter fall models used in greenhouse gas inventories.</p> <p><strong>Data collection</strong></p> <p>The litter fall collection was set up in mature, single species stands. The focal tree species include Scots pine (<em>Pinus sylvestris</em>), Norway spruce (<em>Picea abies</em>), Silver birch (<em>Betula pendula</em>), Downy birch (<em>Betula pubescens</em>), Grey alder (<em>Alnus</em> <em>incana</em>), European rowan (<em>Sorbus aucuparia</em>), European larch (<em>Larix decidua</em>), and Siberian larch (<em>Larix sibirica</em>). The sampling plots varied in shape and in size with a typical area of 0.1-0.25 ha. Between 6 and 30 litter collecting funnels were used per plot. The funnels were made of galvanized sheet metal and attached to cloth bags to collect the falling litter. The sampling sites were monitored for changes in conditions, such as natural disturbances, tree harvesting, forestry operations, or construction on the plot or in its immediate proximity (none observed).</p> <p>The litter samples were collected from the sampling plots, usually four to six times per year in spring to autumn. The samples were dried in room temperature (except male flowers in 1960s – 1970s, see note in Table 1) and stored in paper bags. The dried samples were sorted into litter fractions (Table 1). These fractions varied between tree species and between years to some extent. Cones and seeds were counted, and all other litter fractions were weighed to the nearest milligram.</p> <table> <caption>Table 1. Litter fractions and their codes. The code of the litter fraction is used in the data files.</caption> <thead> <tr> <th scope="col">Code</th> <th scope="col">Litter fraction</th> <th scope="col">Description / note</th> </tr> </thead> <tbody> <tr> <td>1</td> <td>Male flowers</td> <td>In the 1960s – 1970s male flowers were dried in 105°C for 24 hours (Sarvas 1962, 1968).</td> </tr> <tr> <td>2</td> <td>Seeds</td> <td>Seed wings and seeds from species other than the focal one were included into the “other litter” fraction.</td> </tr> <tr> <td>3</td> <td>Female flowers</td> <td> </td> </tr> <tr> <td>4</td> <td>Needles</td> <td> </td> </tr> <tr> <td>5</td> <td>Insects and their faeces</td> <td> </td> </tr> <tr> <td>6</td> <td>Other litter</td> <td> </td> </tr> <tr> <td>7</td> <td>Lichens, branches, and tree bark</td> <td>In some years lichens, branches, and bark were combined in the same fraction, and in some they were separated in their own fractions (numbers 12-14 below).</td> </tr> <tr> <td>8</td> <td>Small cones (1 year)</td> <td>For pine stands, cones were separated into one-year old small cones and large cones. Cones were counted.</td> </tr> <tr> <td>9</td> <td>Cones</td> <td> </td> </tr> <tr> <td>10</td> <td>Cones and loose scales</td> <td>In some years loose scales were included in the same fraction as cones, and in some they were included into the “other litter” fraction.</td> </tr> <tr> <td>11</td> <td>Shifting dust</td> <td> </td> </tr> <tr> <td>12</td> <td>Branches</td> <td> </td> </tr> <tr> <td>13</td> <td>Lichens</td> <td> </td> </tr> <tr> <td>14</td> <td>Tree bark</td> <td> </td> </tr> <tr> <td>15</td> <td>Leaves</td> <td>For deciduous stands, leaves were separated into small (diameter < 1 cm) and large leaves (diameter > 1 cm), while for conifer stands all leaves were included into the “other litter” fraction.</td> </tr> <tr> <td>16</td> <td>Berries</td> <td> </td> </tr> </tbody> </table> <p>In addition to litter fall data, tree stand data were collected on most of the plots in some years. In the tree stand inventories, all trees in the sampling plot with diameter at breast height ≥ 7 cm were mapped, and all trees were counted and measured for diameter (at breast height and at 6 meters), total height, and height to first living branches. Stand basal area and dominant diameter and height were calculated. Stand age was estimated based on core samples from five trees outside but representative of the sample plot. Crown coverage was estimated with a Cajanus tube.</p> <p><strong>Description of the data files</strong></p> <p>The litter fall data is in eight csv-files, one per tree species. The files are named “Litter_Tree_species.csv”, for example “Litter_Betula_pendula.csv”.</p> <p>Variables (in columns) are consistent across the files (explained in Table 2), but note that there are varying numbers of columns between the tables in the files, as each litter collecting funnel has its own column and different maximum numbers of funnels were used in different sampling sites and tree species (see row “S1 – S30” in Table 2 for more details).</p> <table> <caption>Table 2. Variables included in the litter fall data files.</caption> <thead> <tr> <th scope="col">Variable name</th> <th scope="col">Description</th> </tr> </thead> <tbody> <tr> <td>PlotName</td> <td>Name of sampling plot.</td> </tr> <tr> <td>PlotAbbr</td> <td>Abbreviation of sampling plot name.</td> </tr> <tr> <td>Form</td> <td>Number identifying the original paper form.</td> </tr> <tr> <td>Year</td> <td>Year of data collection.</td> </tr> <tr> <td>TreeSpecies</td> <td>Tree species code: 1 = Scots pine, 2 = Norway spruce, 3 = Silver birch, 4 = Downy birch, 5 = Grey alder, 6 = Siberian larch, 7 = European larch, 8 = European rowan.</td> </tr> <tr> <td>LitterFraction</td> <td>Code for the litter fraction (1-16), explained in Table 1.</td> </tr> <tr> <td>Coefficient</td> <td>Coefficient used to transform the weight of the litter (g) to weight per square meter (g m<sup>-2</sup>). The coefficient is based on the number and area of the collection funnels.</td> </tr> <tr> <td>Date</td> <td>Date of sample collection.</td> </tr> <tr> <td>Period</td> <td>Variable used to define the time of data collection as calendar year or phenological year. The variable is based on the schedule of data collection in different years and on the focal tree species so that it corresponds to the species-specific litter fall schedule. For spruce, the peak needle fall is in the spring, so the calendar year is appropriate for describing the temporal variation in litter fall. For pine, the peak needle fall is in August–September, so a phenological year defined as July 1<sup>st</sup> – June 30<sup>th</sup> is appropriate for describing the temporal variation in litter fall. Period = -1 means the values in the row are allocated to the previous calendar year; period = 0 means the values are allocated to the current calendar year; and period = 1 means the values are allocated to the next calendar year.</td> </tr> <tr> <td>S1 – S30</td> <td>Columns S1 – S30 refer to litter collection funnels 1 – 30. The maximum number of funnels varies between tree species: for <em>silver birch</em> up to 30 funnels were used per plot, for downy birch up to 20 funnels, for spruce up to 10 funnels, for pine up to 15 funnels, for rowan 10 funnels, and for both larch species and alder 8 funnels. Missing values (NA) mean that the funnel was not used in the plot. Value -1 means that the funnel was used but the sample was missing. The values give the dry weight of the litter in mg.</td> </tr> <tr> <td>Combined</td> <td>For some samples, litter collected by different funnels has been combined and the total weight is shown in column S1. In this column, 0 = values have not been combined, and 1 = values have been combined.</td> </tr> <tr> <td>TotalWeight</td> <td>Total weight of the litter (mg).</td> </tr> <tr> <td>TotalWeightArea</td> <td>Total weight of the litter per area (mg m<sup>-2</sup>). Value is same as TotalWeight × Coefficient.</td> </tr> <tr> <td>Note</td> <td>Note</td> </tr> </tbody> </table> <p>Tree stand data is in one csv-file, named “Tree_stand_data.csv”, and can be combined with the litter fall data based on the sample plot abbreviations (variable “PlotAbbr” in both litter fall data files and the tree stand data file). Note that there is no tree stand data available for all the same years as litter fall data. There is no tree stand data available at all for one downy birch site (abbreviation HEI568), one spruce site (NOO85), one pine site (HEI566), and the alder, rowan, and larch sites. Tree stand data variables are explained in Table 3.</p> <table> <caption>Table 3. Variables included in the tree stand data file.</caption> <tbody> <tr> <td>Variable name</td> <td>Description</td> </tr> <tr> <td>PlotName</td> <td>Name of sampling plot.</td> </tr> <tr> <td>PlotAbbr</td> <td>Abbreviation of sampling plot name.</td> </tr> <tr> <td>Year</td> <td>Year of data collection.</td> </tr> <tr> <td>TreeSpecies</td> <td>Dominant tree species. 1 = Scots pine, 2 = Norway spruce, 3 = Silver birch, 4 = Downy birch.</td> </tr> <tr> <td>Age</td> <td>Stand age (years).</td> </tr> <tr> <td>SiteType</td> <td>Forest site type describing site productivity. 2 = xeric heath forest, 3 = sub-xeric heath forest, 4 = mesic heath forest, 5 = herb-rich heath forest. </td> </tr> <tr> <td>North</td> <td>North coordinate (m), coordinate system ETRS-TM35FIN.</td> </tr> <tr> <td>East</td> <td>East coordinate (m), coordinate system ETRS-TM35FIN.</td> </tr> <tr> <td>Elevation</td> <td>Elevation (m above sea level).</td> </tr> <tr> <td>N</td> <td>Stem number (ha<sup>-1</sup>).</td> </tr> <tr> <td>BA</td> <td>Basal area (m<sup>2</sup> ha<sup>-1</sup>).</td> </tr> <tr> <td>DomD</td> <td>Diameter (cm) of dominant trees.</td> </tr> <tr> <td>DomH</td> <td>Height (m) of dominant trees.</td> </tr> <tr> <td>CrownLength</td> <td>Crown length (m).</td> </tr> <tr> <td>V</td> <td>Stem volume (m<sup>3</sup> ha<sup>-1</sup>).</td> </tr> <tr> <td>CrownCover</td> <td>Crown coverage (%).</td> </tr> </tbody> </table> <p> </p> <p><strong>List of publications </strong></p> <p>Hilli, A., Hokkanen, T., Hyvönen, J. & Sutinen, M.-L. 2008. Long-term variation in Scots pine seed crop size and quality in northern Finland. Scandinavian Journal of Forest Research 23(5): 395-403. </p> <p>Koski, V. & Tallqvist, R. (1978). Results of long-time measurements of the quantity of flowering and seed crop of forest trees (in Finnish with English summary). Folia Forestalia, 364, 1-60. </p> <p>Kouki, J. & Hokkanen, T. 1992. Long-term needle litterfall of a Scots pine Pinus sylvestris stand: relation to temperature factors. Oecologia 89: 176-181. </p> <p>Lehtonen, A., Lindholm, M., Hokkanen, T., Salminen, H. & Jalkanen, R. 2008. Testing dependence between growth and needle litterfall in Scots pine - a case study in northern Finland. Tree Physiology 28(11): 1741-1749. </p> <p>Lehtonen, A., Sievänen, R., Mäkelä, A., Mäkipää, R., Korhonen, K.T. & Hokkanen, T. 2004. Potential litterfall of Scots pine branches in southern Finland. Ecological Modelling 180(2-3): 305-315. </p> <p>Leikola, M., Raulo, J. & Pukkala, T. (1982). Prediction of the variations of the seed crop of Scots pine and Norway spruce (in Finnish with English summary). Folia Forestalia, 537, 1-43. </p> <p>Niemistö, P., Hokkanen T. & Varama, M. 2004. Karikemäärän muutokset 1982–2001 ja puiden kunto lumi- ja hallamittariesiintymän vaivaamissa koivikoissa Noormarkussa. Metsätieteen aikakauskirja 1/2004: 21–41. </p> <p>Poikolainen, J. & Kuusinen, M. 2000. Abundance of epiphytic lichens in litterfall during 1967-1994. In: Forest condition in a changing environment - the Finnish case. Forestry Sciences, Vol. 65. Kluwer Academic Publishers / Ed. Mälkönen, E. Sivut: 171-172. </p> <p>Pukkala, T. 1987a. A model for predicting the seed crop of Picea abies and Pinus sylvestris (in Finnish with English abstract). Silva Fennica 21(2): 135-144. </p> <p>Pukkala, T. 1987b. Effect of seed production on the annual growth of Picea abies and Pinus sylvestris (in Finnish with English abstract). Silva Fennica 21(2): 145-158. </p> <p>Pukkala, T., Hokkanen, T. & Nikkanen, T. 2010. Prediction models for the annual seed crop of Norway spruce and Scots pine in Finland. Silva Fennica 44(4): 629-642. </p> <p>Ranta, E., Lindström, J., Kaitala, V., Crone, E., Lundberg, P., Hokkanen, T. & Kubin, E. 2010. Life history mediated responses to weather, phenology and large-scale population patterns. In: Hudson, I. L & Keatley, M. R. (eds.). Phenological Research. Springer, Dordrecht Heidelberg London New York, Netherlands. p. 321-338. </p> <p>Raulo, J. & Hokkanen, T. 1989. Litter fall of Alnus incana and Alnus glutinosa (in Finnish with English summary). Folia Forestalia 738. 25 s.</p> <p>Saarsalmi, A., Starr, M., Hokkanen, T., Ukonmaanaho, L., Kukkola, M., Nöjd, P. & Sievänen, R. 2007. Predicting annual canopy litterfall production for Norway spruce (Picea abies (L.) Karst.) stands. Forest Ecology and Management 242(2-3): 578-586. </p> <p>Sarvas, R. (1962). Investigations on the flowering and seed crop of Pinus Silvestris. Communicationes Instituti Forestalis Fenniae, 53, 1-198. </p> <p>Sarvas, R. 1968. Investigation on the flowering and seed crop of Picea abies. Communicationes Instituti Forestalis Fenniae 67.5. 84 pp. </p> <p>Starr, M., Saarsalmi, A., Hokkanen, T., Merilä, P. & Helmisaari, H.-S. 2005. Models of litterfall production for Scots pine (Pinus sylvestris L.) in Finland using stand, site and climate factors. Forest Ecology and Management 205: 215-225. </p> <p>Ťupek, B., Mäkipää, R., Heikkinen J., Peltoniemi, M., Ukonmaanaho, L., Hokkanen, T., Nöjd, P., Nevalainen, S., Lindgren, M. & Lehtonen, A. 2015: Foliar turnover rates in Finland — comparing estimates from needle-cohort and litterfall-biomass methods. Boreal Environment Research 20: 283–304</p>
Data from: The impact of long-term azithromycin on antibiotic resistance in HIV-associated chronic lung disease
<p><b>Background</b>: Selection for resistance to azithromycin (AZM) and other antibiotics such as tetracyclines and lincosamides remains a concern with long-term AZM use for treatment of chronic lung diseases (CLD). We investigated the impact of 48 weeks of AZM on the carriage and antibiotic resistance of common respiratory bacteria among children with HIV-associated CLD.</p> <p><b>Methods</b>: Nasopharyngeal (NP) swabs and sputa were collected at baseline, 48 and 72 weeks from participants with HIV-associated CLD randomised to receive weekly AZM or placebo for 48 weeks and followed post-intervention until 72 weeks. The primary outcomes were prevalence and antibiotic resistance of <i>Streptococcus pneumoniae</i> (SP), <i>Staphylococcus aureus </i>(SA), <i>Haemophilus influenzae </i>(HI), and <i>Moraxella catarrhalis </i>(MC) at these timepoints. Mixed-effects logistic regression and Fisher's exact test were used to compare carriage and resistance respectively.</p> <p><b>Results</b>: Of 347 (174 AZM, 173 placebo) participants (median age 15 years [IQR =13–18], females 49%),NP carriage was significantly lower in the AZM (n=159) compared to placebo (n=153) arm for SP (18% vs 41%, <i>p</i><0.001)<i>, </i>HI (7% vs 16%, p=0.01)<i>, </i>and MC (4% vs 11%, <i>p</i>=0.02); SP resistance to AZM (62% [18/29] vs 13%[8/63], <i>p</i><0.0001) or tetracycline (60%[18/29] vs 21%[13/63], <i>p</i><0.0001) were higher in the AZM arm. Carriage of SA resistant to AZM (91% [31/34] vs 3% [1/31],<i> p</i><0.0001), tetracycline (35% [12/34] vs 13% [4/31],<i> p</i>= 0.05) and clindamycin (79% [27/34] vs 3% [1/31],<i> p</i><0.0001) was also significantly higher in the AZM arm and persisted at 72 weeks. Similar findings were observed for sputa.</p> <p><b>Conclusions</b>: The persistence of antibiotic resistance and its clinical relevance for future infectious episodes requiring treatment needs further investigation.</p>
Data for Ecology Letters paper: Jack-of-all-trades paradigm meets long-term data: generalist herbivores are more widespread and locally less abundant.
<p>Data, R-code, and meta-data document for a 2022 paper in Ecology Letters that examines assumptions about associations between local abundance and dietary specialization using an 18-year dataset of caterpillar-plant interactions in Ecuador. </p>
Revisiting the cumulative effects of drought on global gross primary productivity based on new long-term series data (1982-2018)
<p><strong>Aim:</strong> Drought has broad and deep impacts on vegetation. Studies on the effects of drought on vegetation have been conducted over years. However, global-scale and long-term (>30 years) studies on the cumulative<strong> </strong>effect of drought are still lacking. Thus, combining a new satellite based gross primary productivity (GPP) and multi-timescale Standardized Precipitation Evapotranspiration Index datasets, we investigated the cumulative effect of drought on global vegetation GPP.</p> <p><strong>Location: </strong>Global.</p> <p><strong>Time period: </strong>1982 – 2018 (37 years).</p> <p><strong>Major taxa studied: </strong>Forests and grasslands.</p> <p><strong>Method: </strong>Based on correlation analysis framework, we investigated the cumulative effect duration of drought on global vegetation GPP. Meanwhile, the variability of this cumulative effect across different elevation gradients and climatic zones was analyzed using variance analysis.</p>
Data for Horowitz et al. (2022). The Energy System Transformation Needed to Achieve the U.S. Long-Term Strategy
<p>Data repository for Horowitz, et al. 2022, "The Energy System Transformation Needed to Achieve the U.S. Long-Term Strategy"</p> <p>All data shown in the paper is included here. Data includes results from:</p> <p>1. U.S. LTS GCAM scenarios (labeled "GCAM")<br> 2. U.S. LTS NEMS scenarios (labeled "NEMS")<br> 3. Princeton's Net-Zero America scenarios (labeled "NZA")<sup>a</sup><br> 4. Williams et al. (2020) scenarios (labeled "Williams")<sup>b</sup></p> <p><br> Results are included in the following files:</p> <p>1. waterfall.csv - Figure 1. Emissions decomposition by scenario. GCAM only.<br> 2. clean_fuels.csv - Figure 2. Clean fuel (bioliquids, biogas, and blue/green hydrogen) consumption. All models.<br> 3. coal.csv - Figure 2. Primary energy consumption of coal without CCS. All models.<br> 4. ZEV_stock.csv - Figure 2. Zero-emission vehicle percentage of light-duty vehicle stock. All models.<br> 5. ghg_by_type.csv - Figure 3. Greenhouse gas emissions by gas/source. GCAM only.</p> <p> </p> <p>Reference:</p> <p>a) Larson, E., Greig, C., Jenkins, J.,Mayfield, E., Pascale, A., Zhang, C., Drossman, J., Williams, R., Pacala, S., Socolow, R., et al. (2021). Net-zero America: Potential pathways, infrastructure, and impacts. (Princeton University).</p> <p>b) Williams, J. H., Jones, R. A., Haley, B., Kwok, G., Hargreaves, J., Farbes, J., & Torn, M. S. (2021). Carbon-Neutral Pathways for the United States. AGU Advances, 2, e2020AV000284. <a href="https://doi.org/https://doi.org/10.1029/2020AV000284">https://doi.org/https://doi.org/10.1029/2020AV000284</a>.</p>
Data from: Long-term and year-to-year stability and its drivers in a Mediterranean grassland
<p><span>Understanding the mechanisms underlying community stability has become an urgent need in order to protect ecosystems from global change and resulting biodiversity loss. While community stability can be influenced by richness, synchrony in annual fluctuations of species, species stability and functional traits, the relative contributions of these drivers to stability are still unclear. In semi-natural grasslands, land-use changes such as fertilization might affect stability by decreasing richness and influencing year-to-year fluctuations. In addition, they can promote long-term directional trends, shifting community composition and influencing grassland maintenance. Thus, it is important to consider how species and community stability vary year-to-year but also in the long term. </span></p> <p><span>Using a 14-year vegetation time series of a species-rich semi-natural Mediterranean grassland, we studied the relative importance of richness, synchrony, species stability and functional traits on community stability. To assess land-use change effects on stability, we applied a fertilization treatment. To distinguish stability patterns produced by year-to-year fluctuations from those caused by long-term trends, we compared the results obtained using a detrending approach from those without detrending. </span></p> <p><span>Stability is influenced by richness, synchrony and functional traits. Fertilization decreases species and community stability by promoting long-term trends in species composition, favouring competitive species and decreasing richness. Studying stability at the community and species level, and accounting for the effect of trends is essential to understand stability and its drivers more comprehensively.</span></p>
Data from: Long-term cattle grazing shifts the ecological state of forest soils
<p><span>Cattle grazing profoundly affects abiotic and biotic characteristics of ecosystems. While most research has been performed on grasslands, the effect of large managed ungulates on forest ecosystems has largely been neglected.</span></p> <p><span>Compared to a baseline semi-natural state, we investigated how long-term cattle grazing of birch forest patches affected the abiotic state and the ecological community (microbes and invertebrates) of the soil subsystem.</span></p> <p><span>Grazing strongly modified the soil abiotic environment by increasing phosphorus content, pH and bulk density, while reducing the C:N ratio. The reduced C:N-ratio was strongly associated with a lower microbial biomass, mainly caused by a reduction of fungal biomass. This was linked to a decrease in fungivorous nematode abundance and the nematode channel index, indicating </span><span>a relative </span><span>uplift in the importance of the bacterial energy-channel in the nematode assemblages. </span></p> <p><span>Cattle grazing highly modified invertebrate community composition producing distinct assemblages from the semi-natural situation. Richness and abundance of microarthropods was consistently reduced by grazing (excepting collembolan richness) and grazing-associated changes in soil pH, Olsen P and reduced soil pore volume (bulk density) limiting niche space and refuge from physical disturbance. Anecic earthworm species predominated in grazed patches, but were absent from ungrazed forest, and may benefit from manure inputs, while their deep vertical burrowing behaviour protects them from physical disturbance.</span></p> <p><span>Perturbation of birch forest habitat by long-term ungulate grazing profoundly modified soil biodiversity, either </span><span>directly through increased physical disturbance and manure input or indirectly by modifying soil abiotic conditions.</span><span> Comparative analyses revealed the ecosystem engineering potential of large ungulate grazers in forest systems through major shifts in the composition and structure of microbial and invertebrate assemblages, including the potential for reduced energy flow through the fungal decomposition pathway. The precise consequences for species trophic interactions and biodiversity-ecosystem function relationships remains to be established, however. </span></p>
Enzymatic digestion method development for long-term stored chitinaceous planktonic samples - Data
<table> <tbody> <tr> <td>Data for Carrillo-Barragán, Priscilla, Heather Sugden, Catherine Scott, and Clare Fitzsimmons. 2022.<br> “Enzymatic Digestion Method Development for Long-Term Stored Chitinaceous Planktonic Samples.”<br> Marine Pollution Bulletin. </td> </tr> </tbody> </table>
Data set from long-term wind and acceleration monitoring of the Gjemnessund Bridge
<p>The Gjemnessund Bridge has been monitored by accelerometers and anemometers for almost ten years. The data collected between 2013 and 2018 are now available in this open-access research entry, for free access and download. The data is collected in two h5-files (hierachical data format), with sampling rates 2 Hz and 10 Hz, downsampled from the raw sampling rate of 200 Hz. Some minimal signal processing is applied to the data in line with that applied to the Hardanger Bridge data described in Fenerci et al. (2021) and the Bergsøysund Bridge data described in Kvåle et al. (2022). The structure of the data is identical to that of the latter reference, which is described in a preprint appended to that research entry. The Python package opyndata available on GitHub contains useful tools compatible with the format of the dataset, for data import, processing and visualization.</p>
Data for: Red foxes enhance long-term tree growth near the Arctic treeline
<p>Recent climate warming is expected to increase tree growth and productivity, substantially altering ecological function and boundaries in northern ecosystems. Temperature and precipitation largely determine the range and growth of trees in any biome, yet variations in microsite conditions can also influence tree growth on a finer scale. By altering essential resources and habitat conditions, terrestrial organisms could modify Subarctic tree growth. Red foxes (<em>Vulpes vulpes</em>) are found in most terrestrial ecosystems and are considered ecosystem engineers by enriching soil nutrients and plant composition through denning. Added soil nutrients from prey remains, feces, and urine could benefit tree growth in Subarctic regions by alleviating soil nutrient limitations. We examined growth in white spruce (<em>Picea glauca</em>) trees growing on eight red fox dens and paired control sites near Churchill, Manitoba, Canada, at the Arctic treeline. Radial growth was 55% higher for trees on dens than on control sites between 1897 and 2017, despite similarities in tree ages, densities, and regional climate across all sites. By promoting tree growth near the treeline, red foxes may influence the position of the Arctic treeline. Although the impacts on tree growth largely depend on the spatial distribution of dens and predator activity in the boreal forest, predators can create distinct microhabitats across the landscape via ecosystem engineering processes, leading to increased vegetation productivity, persisting over many decades.</p>
Data from: AgMate: an optimal mating software versus other mate pair designing methods on long-term breeding of Pinus taeda L
<p>Breeding objectives aim to optimize two crucial but contrasting goals of maximizing genetic gain while managing genetic diversity. In advanced generations, this becomes a challenge in monoecious conifer tree species breeding programs because they suffer from inbreeding. Developing an algorithm that maximizes genetic gain while maintaining genetic diversity for monoecious species is imperative. While methods and algorithms for animal breeding are well-established, an efficient algorithm suited to monoecious species remains elusive. Towards this goal, we have adopted an evolutionary genetic algorithm, the Differential Evolution algorithm, to optimize mate pair designing in <em>Pinus taeda</em> (loblolly pine), a widely planted pine species in the southern USA. AgMate, an optimal mating for monoecious species software, is a multi-functional, completely automated optimization software. It utilizes genetic relationships and breeding values as input to create an optimal mating list. AgMate maximizes the genetic gain and minimizes the increase in average coancestry and inbreeding in the proposed progeny. AgMate was more effective in optimizing mating lists than positive assortative mating and random mating in short-term and long-term settings. AgMate mating list resulted in an average 93% genetic gain each cycle for ten cycles while simultaneously minimizing the increase in coancestry to 0.086. The framework and methods adapted for Pinus taeda are also relevant to the breeding of other monoecious species.</p>
Data and R code for long-term study of fire and climate effects on water quality in Clear Lake, California
<p>Long-term relationships between water quality, fire and climate for Clear Lake, California. Although the watershed has historically experienced frequent fire, the 2018 Mendocino Complex, which was the largest wildfire complex in state history, burned approximately 40% of the watershed, sparking concerns about drinking water quality and lake ecosystem health. This analysis spans approximately 1968-2021.</p>
Code and Data associated with "Idiosyncratic purifying selection on metabolic enzymes in the long-term evolution experiment with Escherichia coli"
<p>Code and data sufficient to reproduce analyses in "Idiosyncratic purifying selection on metabolic enzymes in the long-term evolution experiment with <em>Escherichia coli</em>".</p>
Code and data used in "A Tool for Air Pollution Scenarios (TAPS v1.0) to enable global, long-term, and flexible study of climate and air quality policies"
<p>Data and code for Tool for Air Pollution Scenarios (TAPS v1.0) as submitted to Geoscientific Model Development for publication. See the enclosed README and full user manual (https://github.com/watkin-mit/TAPS/wiki) for more information. </p>
data sets of "Dynamic Linear Modeling estimates of long-term ozone trends from homogenized Dobson Umkehr profiles at Arosa, Switzerland"
<p>data sets from "Dynamic Linear Modeling estimates of long-term ozone trends from homogenized Dobson Umkehr profiles at Arosa, Switzerland"</p> <p>Monthly means ozone profiles data sets of MCH homogenized Dobson D051 and of Brewer B040 used in the article entitled: "Dynamic Linear Modeling estimates of long-term ozone trends from homogenized Dobson Umkehr profiles at Arosa, Switzerland" by Eliane Maillard Barras, Alexander Haefele, René Stübi, Achille Jouberton, Herbert Schill, Irina Petropavlovskikh, Koji Miyagawa, Martin Stanek, and Lucien Froidevaux.</p> <p><a href="https://doi.org/10.5194/acp-2022-344">https://doi.org/10.5194/acp-2022-344</a></p>
Data for manuscript "Long-term variation in the quasi-five-day wave in the top layer of Venus clouds"
<p>The dataset contain the derived cloud motions from Akatsuki LIR level3c and the corrected LIR level3c brightness temperature. The data of each figure used for drawing are also contained.</p>
Data from: Local environment and coral composition affect recovery and determine long-term coral responses to recurrent mass mortalities in the Lakshadweep Archipelago
<p>A quarter century after the first global coral bleaching event in 1998, reports differ on the relative importance of anthropogenic influences, local environment and bleaching recurrence in determining the resilience of coral reefs. While life history traits largely determine how corals respond to temperature anomalies, it is unclear if these traits also determine how corals fare over time. From 1998 to 2022, we tracked compositional changes in reefs across the Lakshadweep Archipelago to explore how global El Niño events, and local environment (wave climate and depth) influenced coral responses to repeated mass bleaching. From the 1998 to the 2016 bleaching event, the magnitude of coral mortality reduced overall, particularly at deeper reefs (shallow: -38% to -3%; deep: -18% to -0.45%). Post-bleaching recovery correlated positively with higher wave exposure, linked to the creation of stable structures for coral settlement and survival. Across bleaching phases, recovery was initially slow (6-7 years post-mortality), but, given time, showed a much steeper increase, led by space-occupying genera like <em>Acropora</em>. However, recurring mass bleaching maintained coral cover low (~15% across all sites). These broad trends mask dynamic compositional patterns. Genera such as <em>Porites</em>, <em>Pocillopora</em>, and <em>Favia</em> declined less through time compared to <em>Acanthastrea</em>, <em>Turbinaria</em>, <em>Psammocora</em> and <em>Plesiastrea </em>among others. We identified six community clusters that describe contrasting long-term responses to local and global factors, mediated by depth and wave exposure. Interestingly, genera with different functional traits cluster together indicating that bleaching susceptibility interacts with depth and exposure, creating a spatial mosaic of coral assemblages. These clusters serve as a predictive, site-specific framework to understand the dynamically shifting but declining assemblage of Lakshadweep reefs. While local management could help maintain this changing composition, urgent global action is needed to secure the long-term ecological integrity of tropical reefs.</p>
Data and code from: Long-term climate impacts of large stratospheric water vapor perturbations
<p>The amount of water vapor injected into the stratosphere after the eruption of Hunga Tonga-Hunga Ha'apai (HTHH) was unprecedented, and it is therefore unclear what it might mean for surface climate. We use chemistry climate model simulations to assess the long-term surface impacts of stratospheric water vapor (SWV) anomalies similar to those caused by HTHH, but neglect the relatively minor aerosol loading from the eruption. The simulations show that the SWV anomalies lead to strong and persistent warming of Northern Hemisphere landmasses in boreal winter, and austral winter cooling over Australia, years after eruption, demonstrating that large SWV forcing can have surface impacts on a decadal timescale. We also emphasize that the surface response to SWV anomalies is more complex than simple warming due to greenhouse forcing and is influenced by factors such as regional circulation patterns and cloud feedbacks. Further research is needed to fully understand the multi-year effects of SWV anomalies and their relationship with climate phenomena like El Nino Southern Oscillation.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.