cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25573/data.10068062.v1
title: SST_Naos, STRI Pier

description: Sea Surface temperature monitoring at the STRI dock, Naos Island.<br>Location: 8.91749 -79.53284<br>Depth: 2.4m<br>Status: Inactive<br>
DOI: 10.25573/data.10068095.v1
title: ST_Galeta Channel

description: Sea Surface temperature monitoring in the outflow channel in front of the Galeta Station pier<br>Location (more exact coordinates available on request): 9.40 -79.85<br>Depth: 3m<br>Status: Active<br>
DOI: 10.25573/data.10068104
title: SST_Gulf of Chiriqui, Isla Canal Afuera

description: Sea Surface temperature monitoring at Isla Canal Afuera, in the Gulf of Chiriqui.<br>Location: 7.69633 -81.61603<br>Depth: 2.4m<br>Status: Inactive<br>
DOI: 10.25386/genetics.10006487
title: Supplemental Material for Corbett-Detig et al., 2019

description: Figure S1. Distance between mapping positions of read pairs in each sample. <br>Figure S2. Error in breakpoint position estimates at subsampled lower read depths. <br>Figure S3. Polytene chromosomal arm 2R of Anopheles gambiae.<br>Table S1. Library properties for Hi-C data collected in this work. <br>Table S2. Minimum observed ratio of total distance spanned in simulated “inverted”:unmodified proximity ligation data.<br>Table S3. Predicted mapping positions of inversions studied in this work. <br>Table S4. Breakpoint adjacent contigs obtained from a recent An. coluzzii genome assembly<br>Table S5. The ratio of normalized proportions of read pair mapping to quadrants two and four for each arrangement. <br>
DOI: 10.25386/genetics.10006487.v1
title: Supplemental Material for Corbett-Detig et al., 2019

description: Figure S1. Distance between mapping positions of read pairs in each sample. <br>Figure S2. Error in breakpoint position estimates at subsampled lower read depths. <br>Figure S3. Polytene chromosomal arm 2R of Anopheles gambiae.<br>Table S1. Library properties for Hi-C data collected in this work. <br>Table S2. Minimum observed ratio of total distance spanned in simulated “inverted”:unmodified proximity ligation data.<br>Table S3. Predicted mapping positions of inversions studied in this work. <br>Table S4. Breakpoint adjacent contigs obtained from a recent An. coluzzii genome assembly<br>Table S5. The ratio of normalized proportions of read pair mapping to quadrants two and four for each arrangement. <br>
DOI: 10.25387/g3.10010408.v2
title: Supplemental Material for Laffafian and Tepass, 2019

description: Table S1, Figures S1, S2, S3 and S4<br>
DOI: 10.6084/m9.figshare.10094936.v1
title: Yearly Rainfall - For Journal.xls

description: Dataset in Excel version 2016 format
DOI: 10.25387/g3.9905279.v1
title: Supplemental Material for Pallares, Picard, and Ayroles, 2020

description: File S1 contains step-by-step instructions for the TM3’seq library preparation protocol. File S2 contains step-by-step instructions for the mRNA extraction protocol. File S3 describes how to implement UMIs in the TM3’seq standard protocol. Table S1 contains the sequences of the oligos used in the TM3’seq protocol. Figure S1 describes general mapping parameters of the RNA samples used in this manuscript. Figure S2 shows the effect of sequencing depth and amplification cycles for TM3’seq libraries. Figure S3 summarized the results of ERCC analysis of NEB and TM3’seq libraries. Figure S4 and S5 show the raw ERCC-Dashboard output of the ERCC analysis for TM3'seq and NEB, respectively.
DOI: 10.25387/g3.9905279
title: Supplemental Material for Pallares, Picard, and Ayroles, 2020

description: File S1 contains step-by-step instructions for the TM3’seq library preparation protocol. File S2 contains step-by-step instructions for the mRNA extraction protocol. File S3 describes how to implement UMIs in the TM3’seq standard protocol. Table S1 contains the sequences of the oligos used in the TM3’seq protocol. Figure S1 describes general mapping parameters of the RNA samples used in this manuscript. Figure S2 shows the effect of sequencing depth and amplification cycles for TM3’seq libraries. Figure S3 summarized the results of ERCC analysis of NEB and TM3’seq libraries. Figure S4 and S5 show the raw ERCC-Dashboard output of the ERCC analysis for TM3'seq and NEB, respectively.
DOI: 10.25573/data.10005215.v1
title: Dataset: Factors influencing blue carbon accumulation across a 32‐year chronosequence of created coastal marshes

description: Saline coastal marshes are blue carbon ecosystems with relatively high soil carbon (C) stocks and high rates of soil C accumulation. Loss of saline wetlands due to relative sea‐level rise, land‐use change, and hydrologic alterations liberates previously stored C and reduces the capacity for future C sequestration. Widespread wetland loss has prompted marsh restoration and creation projects around the world; however, little is known about the timescale and capacity for created marshes to function as blue C sinks and the role of environmental conditions in mediating soil C accumulation in restoration sites. Using a chronosequence of five created saline marshes ranging in age from 5 to 32 yr and two adjacent natural reference marshes in southwest Louisiana, USA, short‐ and longer‐term C accumulation rates (SCAR and LCAR, respectively) were determined using feldspar marker horizons and peat depth in cores at six locations in each marsh. Created marshes ranged in elevation from −12 to 41 cm (NAVD88) and supported assorted plant community compositions driven by local environmental conditions. SCAR ranged from 75 to 430 g C·m<sup>−2</sup>·yr<sup>−1</sup>, which were comparable in the two youngest and two oldest marshes. Longer‐term CAR ranged from 18 to 99 g C·m<sup>−2</sup>·yr<sup>−1</sup> but did not significantly differ among marshes of different ages. Our findings indicate that LCAR in these created marshes were influenced by site‐specific environmental conditions (i.e., stem density and mineral sediment) rather than marsh age. Results suggest that conditions appropriate for the establishment of vegetation with high stem densities, such as Distichlis spicata and Spartina patens, may facilitate higher LCAR in created marshes, which may be useful for restoration project planning and mitigation of climate change.<br>
DOI: 10.25573/data.9856769.v1
title: Dataset: Modeling organic carbon accumulation rates and residence times in coastal vegetated ecosystems

description: Coastal vegetated 'blue carbon' ecosystems can store large quantities of organic carbon (OC) within their soils; however, the importance of these sinks for climate change mitigation depends on the OC accumulation rate (CAR) and residence time. Here we evaluate how two modeling approaches, a Bayesian age-depth model alone or in combination with a two-pool OC model, aid in our understanding of the timelines of OC within seagrass soils. Fitting these models to data from Posidonia oceanica soil cores, we show that age-depth models provided reasonable CAR estimates but resulted in a 22% higher estimation of OC burial rates when ephemeral rhizosphere OC was not subtracted. This illustrates the need to standardize CAR estimation to match the research target and time frames under consideration. Using a two-pool model in tandem with an age-depth model also yielded reasonable, albeit lower, CAR estimates with lower estimate uncertainty, which increased our ability to detect among-site differences and seascape-level trends. Moreover, the two-pool model provided several other useful soil OC diagnostics, including OC inputs, decay rates, and transit times. At our sites, soil OC decayed quite slowly both within fast-cycling (0.028 +/- 0.014 yr<sup>-1</sup>) and slow-cycling (0.0007 +/- 0.0003 yr<sup>-1</sup>) soil pools, resulting in OC taking between 146 and 825 yrs to transit the soil system. Further, an estimated 85% to 93% of OC inputs enter slow-cycling soil pools, with transit times ranging from 891 to 3115 yrs, substantiating the importance of P. oceanica soils as natural, long-term OC sinks.<br>
DOI: 10.6084/m9.figshare.3761562.v1281
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.8194175.v2
title: Supplemental_DATA.tar.gz

description: This data is unpublished. please contact Frank Aylward before using for any other projects (faylward@vt.edu).<br><br>
DOI: 10.6084/m9.figshare.3761562.v1282
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.25386/genetics.10162688.v1
title: Supplemental Material for Daskalov et al., 2019

description: Eleven supplementary figures, two supplementary tables and one video file for the article 'Programmed cell death in <i>Neurospora crassa</i> is controlled by the allorecognition determinant <i>rcd-1</i>' by Daskalov et al.
DOI: 10.6084/m9.figshare.3761562.v1283
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.10251056.v1
title: All collection Data (Sara & Ashir)

description: all the data collection for all the buildings/faculties across the 4 weeks of observation by Sara and Ashir.
DOI: 10.6084/m9.figshare.3761562.v1284
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.10261019.v1
title: date for figures of“Initial cost barrier of ammonia control in central China”in GRL.docx

description: <b><i>This is the date corresponding to figures of “Initial cost barrier of ammonia control in central China” in Geophysical Research Letters. </i></b>
DOI: 10.6084/m9.figshare.9092045.v8
title: Microarray data trained deep auto-encoder with three hidden layer having 512 nodes

description: <br>3 layer deep auto-encoder trained on 20K micro-array data samples: MicroarrayDeep512_512_512_AE20K.h5<br>3 layer sparsified deep auto-encoder trained on 20K micro-array data samples: MicroarrayDeep512_512_512_AE_Regularised20K.h53 layer denoised deep auto-encoder trained on 20K micro-array data samples:MicroarrayDeep512_512_512_AE_Denoised20K.h5<br>5 layer funnel shaped deep auto-encoder trained on 20K micro-array data samples: MicroarrayDeep512_256_128_256_512_AE20K.h53 layer funnel shaped deep auto-encoder trained on 20K micro-array data samples:MicroarrayDeep512_128_512_AE20K.h5<br>
DOI: 10.25387/g3.10248929
title: Supplemental Material for Schoonmaker et al., 2019

description: Figure S1 gives the distribution of Ka values for the three MIG genomesTen core data files are broken down as:1-3: Gene order files:· Meloidogyne_arenaria_POInT_geneorders.txt · Meloidogyne_incognita_POInT_geneorders.txt· Meloidogyne_javanica_POInT_geneorders.txt4: The inferred ancestral gene order: Nematode_WGT_OptOrder.txt5-8: 4 models of gene loss after triplication:· WGT_Null_model.txt· WGT_1Frac_model.txt· WGT_1FracS_model.txt· WGT_1FracS2_model.txt9: The optimized phylogenetic topology, Nematode_WGT_OptTopo.tre and 10: The set of orthology predictions from POInT: ThreeSpp_WGT_1Frac_SingF_DSep_Top2_m2Opt2_postprobs.txt.
DOI: 10.25387/g3.10248929.v1
title: Supplemental Material for Schoonmaker et al., 2019

description: Figure S1 gives the distribution of Ka values for the three MIG genomesTen core data files are broken down as:1-3: Gene order files:· Meloidogyne_arenaria_POInT_geneorders.txt · Meloidogyne_incognita_POInT_geneorders.txt· Meloidogyne_javanica_POInT_geneorders.txt4: The inferred ancestral gene order: Nematode_WGT_OptOrder.txt5-8: 4 models of gene loss after triplication:· WGT_Null_model.txt· WGT_1Frac_model.txt· WGT_1FracS_model.txt· WGT_1FracS2_model.txt9: The optimized phylogenetic topology, Nematode_WGT_OptTopo.tre and 10: The set of orthology predictions from POInT: ThreeSpp_WGT_1Frac_SingF_DSep_Top2_m2Opt2_postprobs.txt.
DOI: 10.6084/m9.figshare.10261019.v2
title: data for figures of“Initial cost barrier of ammonia control in central China”in GRL

description: <b><i>This is the data corresponding to figures of “Initial cost barrier of ammonia control in central China” in Geophysical Research Letters. </i></b>
DOI: 10.6084/m9.figshare.3761562.v1285
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.6808853.v8
title: Young adults make rational sexual decisions

description: The ZIP file contains all necessary codes (Matlab and R) and data for reproducing the results from the paper (Hatz, Park, McCarty, McCarthy, & Davis-Stober, submitted). It also includes the instruction and stimuli we used for the monetary gamble task from the paper.<br>The pdf file "readme.pdf" provides a step-by-step instruction for readers to reproduce the results.
DOI: 10.25405/data.ncl.10099439
title: EMPoWER Report: Supplementary File 1 (mapping outcomes and papers)

description: This is an Excel table consisting of: a list of all the studies included in the HTA EMPoWER mixed methods evidence synthesis (author, year); the verbatim outcomes reported in those papers that were included in the EMPoWER evidence synthesis; the outcome measures reported in the papers as having been used for data collection; and the mapping of the verbatim outcome and measure onto the 12 concepts reported in the HTA EMPoWER report.
DOI: 10.25573/data.10046189.v1
title: Dataset: Accretion rates of low intertidal salt marshes in the Pacific Northwest

description: Salt-marsh accretion rate was investigated at sites that spanned a gradient in relative rate of sea-level rise in Washington and Oregon. Mean accretion rate over all sites was 3.6 mm yr<sup>-1</sup> (95% CI = 2.4 to 4.8 mm yr<sup>-1</sup>), which exceeded present mean sea-level-rise rate (1.3 mm yr<sup>-1</sup>; sd = 0.6). However, a mean rise rate of 5.5 mm yr<sup>-1</sup> (sd = 1.9) predicted by a moderate sea-level-change scenario to occur by the year 2050 exceeds mean accretion rate. Marshes with adequate sediment input seemed to have the capacity to keep pace with an increased sea-level-rise rate. Lowest accretion rates were recorded at sites with the least sediment supply. Accretion rate showed a weak negative correlation with sediment organic matter (measured as volatile solids) and marsh standing stock. The data suggest that moderate and high rise-rate scenarios would threaten the existence of salt marshes in the region in the absence of increased sediment supply. A better understanding is required of marsh accretion and predicted rate of sea-level rise to refine predictions of the effects of sea-level rise on Pacific Northwest salt marshes.<br>
DOI: 10.25387/g3.10265867
title: Supplemental Material for Lynch et al., 2019

description: Supplemental Material<br>
DOI: 10.25387/g3.10265867.v1
title: Supplemental Material for Lynch et al., 2019

description: Supplemental Material<br>
DOI: 10.6084/m9.figshare.3761562.v1286
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.25405/data.ncl.10099439.v1
title: EMPoWER Report: Supplementary File 1 (mapping outcomes and papers)

description: This is an Excel table consisting of: a list of all the studies included in the HTA EMPoWER mixed methods evidence synthesis (author, year); the verbatim outcomes reported in those papers that were included in the EMPoWER evidence synthesis; the outcome measures reported in the papers as having been used for data collection; and the mapping of the verbatim outcome and measure onto the 12 concepts reported in the HTA EMPoWER report.
DOI: 10.6084/m9.figshare.3761562.v1287
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.7756808.v2
title: Trypanosoma brucei EATRO1125 AnTat1.1 assembled and annotated minicircle genome

description: additional data associated with Nucleic Acids Research submission by Cooper et al.<br><br>
DOI: 10.6084/m9.figshare.3761562.v1288
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.3761562.v1289
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.25387/g3.10269809
title: Supplemental Material for Neve, et al., 2019

description: <b>Metabolomics analysis</b> <i>E. coli</i> metabolite profiling was performed at Metabolon, Inc (Durham, NC) with 5 biological replicates of each test bacterial strain (MG1655, OP50, HB101). <i>E. coli</i> colonies were inoculated in LB, grown overnight, and then plated on Nematode Growth Medium (NGM) Agar plates to form lawns for three days at 20°C. Lawns were then scraped off of the surface of the agar and collected in distilled deionized water. Samples were then washed 3 times. Each sample contained approximately 0.1mg of pooled bacterial pellet which was then flash frozen using liquid nitrogen. Metabolomics profiling was performed in the method described previously (Evans <i>et al.</i> 2009). Statistical analysis was performed using Welch’s two-sample t-test to identify compounds that differed significantly between bacterial strains.<br><br><b>Methodology for performing Reproductive Lifespans with Betaine supplementation </b> Reproductive lifespans (RLS) were performed at 20°C on animals that were developmentally synchronized using a variation of the “egg prep” methodology described in (Porta-de-la-Riva <i>et al.</i> 2012). Well-fed animals were raised for two generations on standard NGM plates seeded with OP50. The third generation of animals were plated on antibiotic free NGM plates seeded with the test bacteria, and if necessary, an inducible agent (IPTG) or supplement (Betaine at 20mM during development, and 100mM after L4, based upon plate volume). Upon development to the L4 stage, worms were singled to individual plates containing their specified food source. The animals were then transferred to fresh plates every day at the same time until reproduction cessation, determined as the point when no progeny were produced for three consecutive days. Two days after the individual worms were transferred, plates were checked, and double checked for progeny. Animals that bag or die were noted as censors. Reproductive span curves were calculated using Kaplan-Meier survival analysis and compared using the log-rank test. At least two independent trials were conducted.<br>PCR of stated loci was conducted with primers listed<br>
DOI: 10.25387/g3.10269809.v1
title: Supplemental Material for Neve, et al., 2019

description: <b>Metabolomics analysis</b> <i>E. coli</i> metabolite profiling was performed at Metabolon, Inc (Durham, NC) with 5 biological replicates of each test bacterial strain (MG1655, OP50, HB101). <i>E. coli</i> colonies were inoculated in LB, grown overnight, and then plated on Nematode Growth Medium (NGM) Agar plates to form lawns for three days at 20°C. Lawns were then scraped off of the surface of the agar and collected in distilled deionized water. Samples were then washed 3 times. Each sample contained approximately 0.1mg of pooled bacterial pellet which was then flash frozen using liquid nitrogen. Metabolomics profiling was performed in the method described previously (Evans <i>et al.</i> 2009). Statistical analysis was performed using Welch’s two-sample t-test to identify compounds that differed significantly between bacterial strains.<br><br><b>Methodology for performing Reproductive Lifespans with Betaine supplementation </b> Reproductive lifespans (RLS) were performed at 20°C on animals that were developmentally synchronized using a variation of the “egg prep” methodology described in (Porta-de-la-Riva <i>et al.</i> 2012). Well-fed animals were raised for two generations on standard NGM plates seeded with OP50. The third generation of animals were plated on antibiotic free NGM plates seeded with the test bacteria, and if necessary, an inducible agent (IPTG) or supplement (Betaine at 20mM during development, and 100mM after L4, based upon plate volume). Upon development to the L4 stage, worms were singled to individual plates containing their specified food source. The animals were then transferred to fresh plates every day at the same time until reproduction cessation, determined as the point when no progeny were produced for three consecutive days. Two days after the individual worms were transferred, plates were checked, and double checked for progeny. Animals that bag or die were noted as censors. Reproductive span curves were calculated using Kaplan-Meier survival analysis and compared using the log-rank test. At least two independent trials were conducted.<br>PCR of stated loci was conducted with primers listed<br>
DOI: 10.25387/g3.9994643
title: Supplemental Material for Busche et al., 2019

description: <b>File S1.</b> Per chromosome read coverage distribution of Dwarf Cavendish reads. <b>File S2</b>. Comparison of SNVs in the duplicated segment on the long arm of chromosome 2 to all other SNVs in the genome. The higher read coverage at variants indicates a duplication of this region. <b>File S3</b>. List of public genomic banana sequence read samples used for comparison against Dwarf Cavendish based on the DH Pahang reference. <b>File S4</b>. Coverage plots of public genomic banana sequence read samples (File S1) for comparison against Dwarf Cavendish based on the DH Pahang reference. Samples are: <i>Musa acuminata</i>, <i>Musa acuminata</i> AYP_BOSN_r1, <i>Musa acuminata </i>ssp. banksii, <i>Musa acuminata </i>ssp.<i> </i>burmannica, <i>Musa acuminata</i> Cavendish BaXiJiao, <i>Musa acuminata </i>Gros Michel, <i>Musa acuminata </i>ssp. malaccensis, <i>Musa acuminata</i> Sucrier (Pisang Mas), <i>Musa acuminata</i> Sucrier (Pisang Mas 1998-2307), <i>Musa </i><i>acuminata</i> ssp. zebrina (blood banana), <i>Musa balbisiana</i> Pisang Klutuk Wulung, <i>Musa itinerans</i>, <i>Musa schizocarpa.</i><b><br></b> <b>File S5</b>. List of selected high impact variants between Dwarf Cavendish and DH Pahang with resulting effects predicted by SnpEff.<br><b></b>