cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/240542d4d29c9b1bb61ce22ad0eccb57
title: Mechanisms driving the soil organic matter decomposition response to nutrient enrichment:Nutrient Network. A cross-site investigation of bottom-up control over herbaceous plant community dynamics and ecosystem function.

description: This experiment is one implementation of a globally distributed experiment, known as the Nutrient Network. At Cedar Creek, as in over 70 other sites in grasslands around the world, the experiment aims to describe impacts of increased nutrients (nitrogen, phosphorus, potassium, sulfur and other metals) and decreased herbivory (removal of mammals by fencing). Two overarching questions are being explored with these manipulations: 1. To what extent are plant production and diversity co-limited by multiple nutrients in herbaceous-dominated communities? 2. Under what conditions do grazers or fertilization control plant biomass, diversity, and composition? By utilizing identical protocols at diverse grassland sites around the world, NutNet aims to uncover both the generalities in ecosystem functioning, and the contingencies or differences which can obscure those common mechanisms. In addition to the standard NutNet protocol, e247 includes an additional low Nitrogen gradient (1 gram Nitrogen per meter squared per year and 5 grams Nitrogen per meter squared per year in addition to the standard 10 grams Nitrogen per meter squared per year).
DOI: 10.21227/eagc-ta82
title: Mouse brain lightfield-confocal stack dataset

description: Dataset of fluorescent mice brain vessels Confocal 3D volumes aligned to Light-Field images.Confocal:Single volume dimension: 1287x1287x64.Number of samples: 362Voxel size: 0.086x0.086x0.9 um.Objective: 40x/1.3 Oil.Stain: tomato lectin (DyLight594 conjugated, DL-1177, Vector Laboratories).LightField:Image dimensions 1287x1287.PixelSize: 3.45 um.Pixels per lenslet: 33x33.Lenslet Pitch: 112 um.MLA2Sensor distance: 2500um.Tube-lens focal length: 165mm.Objective: 40x/0.9 Air.H5 containing:volData: confocal volumes 1287x1287x64 voxels.LFData: LF 4D tensor 33x33x39x39 (Angular coord x, angular coord y, spatial coord x, spatial coord y).gridCoords: image grid positions.
DOI: 10.21227/nbqj-bb76
title: Mouse brain lightfield-confocal stack dataset

description: Dataset of fluorescent mice brain vessels Confocal 3D volumes aligned to Light-Field images.Confocal:Single volume dimension: 1287x1287x64.Number of samples: 362Voxel size: 0.086x0.086x0.9 um.Objective: 40x/1.3 Oil.Stain: tomato lectin (DyLight594 conjugated, DL-1177, Vector Laboratories).LightField:Image dimensions 1287x1287.PixelSize: 3.45 um.Pixels per lenslet: 33x33.Lenslet Pitch: 112 um.MLA2Sensor distance: 2500um.Tube-lens focal length: 165mm.Objective: 40x/0.9 Air.H5 containing:volData: confocal volumes 1287x1287x64 voxels.LFData: LF 4D tensor 33x33x39x39 (Angular coord x, angular coord y, spatial coord x, spatial coord y).gridCoords: image grid positions.
DOI: 10.5281/zenodo.4147737
title: Database of the ODYM-RECC v2.4 model, used for the Germany case study on material efficiency and climate change mitigation

description: Database of the ODYM-RECC v2.4 model, used for the Germany case study on material efficiency and climate change mitigation. For the model code, see https://github.com/YaleCIE/RECC-ODYM. The model results archived here were calculated by running the ODYM-RECC scripts of commit no. cb3a388 with the data in this archive.
DOI: 10.5281/zenodo.4147736
title: Database of the ODYM-RECC v2.4 model, used for the Germany case study on material efficiency and climate change mitigation

description: Database of the ODYM-RECC v2.4 model, used for the Germany case study on material efficiency and climate change mitigation. For the model code, see https://github.com/YaleCIE/RECC-ODYM. The model results archived here were calculated by running the ODYM-RECC scripts of commit no. cb3a388 with the data in this archive.
DOI: 10.5066/p94eklpp
title: SPARROW model inputs and simulated streamflow, nutrient and suspended-sediment loads in streams of the Southwestern United States, 2012 Base Year (ver. 2.0, October 2020)

description: The U.S. Geological Survey's (USGS) SPAtially Referenced Regression On Watershed attributes (SPARROW) model was used to aid in the interpretation of monitoring data and simulate streamflow and water-quality conditions in streams across the Southwestern Region of the Unites States. SPARROW is a hybrid empirical/process-based mass balance model that can be used to estimate the major sources and environmental factors that affect the long-term supply, transport, and fate of contaminants in streams. The spatially explicit model structure is defined by a river reach network coupled with contributing catchments. The model is calibrated by statistically relating watershed sources and transport-related properties to monitoring-based water-quality load estimates. This USGS data release includes input and output files associated with 2012 SPARROW simulations of streamflow, total nitrogen, total phosphorus and suspended-sediment load in streams of the Southwestern region. This dataset was revised in October 2020. Variables were added to the sw_sparrow_model_input.txt file that had previously been calculated in SW SPARROW model control files. A coding error was fixed in the suspended sediment model control files, resulting in updates to sw_sparrow_model_output_SS.txt. Duplicated COMIDs were removed from all output files. Suspended sediment values were reported in metric tons per year. Model construction, calibration and results are described in Wise, Anning, and Miller (2019, https://doi.org/10.3133/sir20195106). First posted - January 6, 2020 (available from author) Reivsed - October 26,2020 (version 2.0)
DOI: 10.6084/m9.figshare.12971780
title: Isomer-specific molecular interaction of cationic glucosamine with benzoate and phthalates: individual stabilities of unresolvable-isomer complexes detected by NMR titration

description: Some biogenic compounds undergo conformational isomerism, and the isomers may interact distinctively with other substances to form molecular complexes individually with different stabilities. In the present work, such molecular interaction specific to isomers was confirmed for the complexation of cationic glucosamine anomers with benzoate and phthalate anions. The individual stability constants of the anomer complexes were determined by tracing <sup>1</sup>H NMR shifts of each anomer in titration with the appropriate carboxylate. In the complexes of benzoate, phthalate and terephthalate, the binding forces in the β-anomer complexes are two to five times as strong as those of the corresponding α-anomer complexes. The formulae of titration curves for determining individual stabilities have been developed in a generalised form to be applicable to the complexation of other unresolvable isomers with different compositions.
DOI: 10.21227/awm0-g750
title: Brazilian Flights Dataset

description: This webpage provides information about the Brazilian Flight Dataset (BFD). The description includes the data sources from regular flights (VRA) and weather data. The VRA is provided by ANAC (Agência Nacional de Aviação Civil) and contains all Brazilian flights. The weather data is provided by ASOS (Automated Surface Observing Systems). ASOS is managed by IOWA University (USA). It contains weather data collected by sensors installed at airports around the world.
DOI: 10.21227/97w2-pv88
title: Brazilian Flights Dataset

description: This webpage provides information about the Brazilian Flight Dataset (BFD). The description includes the data sources from regular flights (VRA) and weather data. The VRA is provided by ANAC (Agência Nacional de Aviação Civil) and contains all Brazilian flights. The weather data is provided by ASOS (Automated Surface Observing Systems). ASOS is managed by IOWA University (USA). It contains weather data collected by sensors installed at airports around the world.
DOI: 10.5066/p9gflbg8
title: SPARROW model inputs and simulated streamflow, nutrient and suspended-sediment loads in streams of the Southwestern United States, 2012 Base Year

description: The U.S. Geological Survey's (USGS) SPAtially Referenced Regression On Watershed attributes (SPARROW) model was used to aid in the interpretation of monitoring data and simulate streamflow and water-quality conditions in streams across the Southwestern Region of the Unites States. SPARROW is a hybrid empirical/process-based mass balance model that can be used to estimate the major sources and environmental factors that affect the long-term supply, transport, and fate of contaminants in streams. The spatially explicit model structure is defined by a river reach network coupled with contributing catchments. The model is calibrated by statistically relating watershed sources and transport-related properties to monitoring-based water-quality load estimates. This USGS data release includes input and output files associated with 2012 SPARROW simulations of streamflow, total nitrogen, total phosphorus and suspended-sediment load in streams of the Southwestern region. Model construction, calibration and results are described in Wise, Anning, and Miller (2019, https://doi.org/10.3133/sir20195106).
DOI: 10.21227/74z8-hs97
title: Brazilian Flights Dataset

description: This webpage provides information about the Brazilian Flight Dataset (BFD). The description includes the data sources from regular flights (VRA) and weather data. The VRA is provided by ANAC (Agência Nacional de Aviação Civil) and contains all Brazilian flights. The weather data is provided by ASOS (Automated Surface Observing Systems). ASOS is managed by IOWA University (USA). It contains weather data collected by sensors installed at airports around the world.
DOI: 10.6084/m9.figshare.13154378
title: Motility analysis dataset for Vickermania

description: This is a collection of videos with tracked cells, the table data with tracking results and further processing (estimation of displacement, velocity etc.).
DOI: 10.6084/m9.figshare.13157594
title: personality and cognition_data.xlsx

description: Personality and cognition data - Morris water maze, Active allothetic place avoidance, Open field test, Elevated plus maze test, T-maze test
DOI: 10.6084/m9.figshare.13154483
title: Cell cycle analysis dataset for Vickermania

description: This are fluorescent images of two species of Vickermania used to analyze the cell cycle and the organelle counts on this images.
DOI: 10.6084/m9.figshare.13154483.v2
title: Cell cycle analysis dataset for Vickermania

description: This are fluorescent images of two species of Vickermania used to analyze the cell cycle and the organelle counts on this images.
DOI: 10.6084/m9.figshare.13154483.v1
title: Cell cycle analysis dataset for Vickermania

description: This are fluorescent images of two species of Vickermania used to analyze the cell cycle and the organelle counts on this images.
DOI: 10.17632/vvgcgs65x3.5
title: Data for: Aeolian additions of Podzolic soils on the high-altitude mountains in central Taiwan

description: The data used in the article.
DOI: 10.5281/zenodo.4148473
title: On the (Un-)Adoption of JavaScript Front-end Frameworks

description: DBR
DOI: 10.5281/zenodo.4021476
title: Ooh Na Na Alternative Identifiers

description: A dump of the alternative identifiers extracted from the OBO Foundry as a three column TSV - prefixes, primary identifiers, and alt identifiers. Generated with the following code: <pre><code class="language-bash">pip install pyobo pyobo database alts</code></pre>
DOI: 10.5281/zenodo.4021477
title: Inspector Javert's Xref Database

description: It would have been really useful for Inspector Javert to find Jean Valjean if he had the cross-references between the identifies of all of the people he met in Montreuil-sur-Mer to the prisoner database (all he needed was 24601!). Since this dataset has a long name, you can feel free to abbreviate it as IJXD. We have the same problem in bioinformatics, so this is a database of cross-references extracted from OBO Foundry and other sources by PyOBO. It is a gzipped five-column TSV file that has source namespace, source identifier, target namespace, target identifier, and provenance. Each has been normalized so cross-references from different sources can be integrated and traversed. It was generated with the following code in the shell: <pre>pip install pyobo pyobo obo xrefs</pre> More information on this blog post: https://cthoyt.com/2020/04/19/inspector-javerts-xref-database.html.
DOI: 10.5281/zenodo.4021482
title: Ooh Na Na Synonyms

description: This is a gzipped three-column TSV file that has prefixes, identifiers, and synonyms for lots of biomedical entities drawn from the terminologies and ontologies in PyOBO. It was generated with the following code in the shell: <pre><code class="language-bash">pip install pyobo pyobo database synonyms</code></pre> <pre>Any silly name suggestions that include literary references are welcome :) </pre>
DOI: 10.17632/cy5gcfvzxy.1
title: Data for: Schizotypal traits are not related to multisensory integration or audiovisual speech perception

description: Data for: Schizotypal traits are not related to multisensory integration or audiovisual speech perception
DOI: 10.6084/m9.figshare.13157873
title: Data - Field Experiment - Year 1

description: Dataset recording plant lifetime fitness data in year 1 of the field experiment.
DOI: 10.6084/m9.figshare.13157873.v1
title: Data - Field Experiment - Year 1

description: Dataset recording plant lifetime fitness data in year 1 of the field experiment.
DOI: 10.6084/m9.figshare.13157726
title: Postnatal SMG Integrated.rds

description: Redy-to-use Seurat objects associated with GSE150327 dataset (Salivary gland scRNAseq)The analysis code is available as supplementary material in the manuscript and in github repository: https://github.com/chiblyaa/Salivary-Gland-DevelopmentPlease cite the associated manuscript when using this resource: http://dx.doi.org/10.2139/ssrn.3651506<br>
DOI: 10.6084/m9.figshare.13157867
title: Supplement, data and code "Evaluating water- and health-related development projects: A cross-project and micro-based approach"

description: This fileset contains the supplement, the data and the replication code for the paper "Evaluating water- and health-related development projects: A cross-project and micro-based approach".<br><br>Abstract: We present a micro-based approach to evaluate the effect of water- and health-related development projects which complements established evaluation methods. We collect information from 1.8 million individuals from DHS clusters (Demographic and Health Surveys) in 38 developing economies between 1986 and 2017. By geocodes, we combine cluster information with over 14,000 sub-national projects from the World Bank. We then investigate the impact of the projects employing fixed effects estimation techniques. Our findings indicate that the time to gather water and child mortality tend to decrease when projects are realized. The quality of drinking water and sanitation facilities are also positively affected by projects. Our data allows us to account for cluster heterogeneity, which is an important extension to the cross-country literature. Various robustness checks support our findings.<br>
DOI: 10.6084/m9.figshare.13157726.v1
title: Postnatal SMG Integrated.rds

description: Redy-to-use Seurat objects associated with GSE150327 dataset (Salivary gland scRNAseq)The analysis code is available as supplementary material in the manuscript and in github repository: https://github.com/chiblyaa/Salivary-Gland-DevelopmentPlease cite the associated manuscript when using this resource: http://dx.doi.org/10.2139/ssrn.3651506<br>
DOI: 10.6084/m9.figshare.13157687
title: Embryonic SMG Integrated.rds

description: Redy-to-use Seurat objects associated with GSE150327 dataset (Salivary gland scRNAseq) The analysis code is available as supplementary material in the manuscript and in github repository: https://github.com/chiblyaa/Salivary-Gland-DevelopmentPlease cite the associated manuscript when using this resource: http://dx.doi.org/10.2139/ssrn.3651506<br> Direct questions to chiblyaa@nih.gov
DOI: 10.6084/m9.figshare.13157687.v1
title: Embryonic SMG Integrated.rds

description: Redy-to-use Seurat objects associated with GSE150327 dataset (Salivary gland scRNAseq) published in manuscript ISCIENCE-D-20-01304The analysis code is available as supplementary material in the manuscript and in github repository: https://github.com/chiblyaa/Salivary-Gland-Development<br> Direct questions to chiblyaa@nih.gov
DOI: 10.5281/zenodo.4148570
title: On the (Un-)Adoption of JavaScript Front-end Frameworks

description: DBR
DOI: 10.5281/zenodo.4148472
title: On the (Un-)Adoption of JavaScript Front-end Frameworks

description: DBR
DOI: 10.5281/zenodo.4141383
title: ATHENA: A Framework based on Diverse Weak Defenses for Building Adversarial Defense

description: This is the dataset associated with ATHENA, a framework based on Diverse Weak Defenses for building Adversarial Defense.
DOI: 10.5281/zenodo.4141382
title: ATHENA: A Framework based on Diverse Weak Defenses for Building Adversarial Defense

description: This is the dataset associated with ATHENA, a framework based on Diverse Weak Defenses for building Adversarial Defense.
DOI: 10.5281/zenodo.4148592
title: On the (Un-)Adoption of JavaScript Front-end Frameworks

description: DBR
DOI: 10.5281/zenodo.4148591
title: On the (Un-)Adoption of JavaScript Front-end Frameworks

description: DBR
DOI: 10.6084/m9.figshare.13133270
title: Prokka annotation for the genomes of Streptomyces sp. G11C, CHD11 and Vc74B-19

description: Prokka annotation for the genomes of Streptomyces sp. G11C, CHD11 and Vc74B-19, as described in referenced article<br>
DOI: 10.6084/m9.figshare.13133270.v1
title: Prokka annotation for the genomes of Streptomyces sp. G11C, CHD11 and Vc74B-19

description: Prokka annotation for the genomes of Streptomyces sp. G11C, CHD11 and Vc74B-19, as described in referenced article<br>
DOI: 10.18430/m35v8t
title: X-ray diffraction data for the crystal structure of SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with SF354 (5V8T)
DOI: 10.18430/m37kff
title: X-ray diffraction data for the crystal structure of TrmD tRNA (guanine-N1)-methyltransferase from Corynebacterium diphtheriae in complex with SAH (7KFF)
DOI: 10.5281/zenodo.4148005
title: GM12878 200kb resolution full diploid genome structures

description: Population of 10000 full diploid genome structures of human lymphoblastoid GM12878 cell line, 200kb resolution, generated using the Integrated Genome Modeling (IGM) software developed in the Alber lab at UCLA HiC input file: GM_HiC_input.hcs Structure file: GM12878_HiC_10kstructures.dcd mmCIF format deposition file: GM12878_HiC_IGM_model.cif
DOI: 10.5281/zenodo.4148004
title: GM12878 200kb resolution full diploid genome structures

description: Population of 10000 full diploid genome structures of human lymphoblastoid GM12878 cell line, 200kb resolution, generated using the Integrated Genome Modeling (IGM) software developed in the Alber lab at UCLA HiC input file: GM_HiC_input.hcs Structure file: GM12878_HiC_10kstructures.dcd mmCIF format deposition file: GM12878_HiC_IGM_model.cif
DOI: 10.6084/m9.figshare.12851840.v1
title: A novel microRNA boosts hyper-β-oxidation of fatty acids in liver by impeding CEP350-mediated sequestration of PPARα and thus restricts chronic hepatitis C

description: Imbalance in lipid metabolism induces steatosis in liver during Chronic hepatitis C (CHC). Contribution of microRNAs in regulating lipid homoeostasis and liver disease progression is well established using small RNA-transcriptome data. Owing to the complexity in the development of liver diseases, the existence and functional importance of yet undiscovered regulatory miRNAs in disease pathogenesis was explored in this study using the unmapped sequences of the transcriptome data of HCV-HCC liver tissues following miRDeep2.pl pipeline. MicroRNA-c12 derived from the first intron of LGR5 of chromosome 12 was identified as one of the miRNA like sequences retrieved in this analysis that showed human specific origin. Northern blot hybridization has proved its existence in the hepatic cell line. Enrichment of premiR-c12 in dicer-deficient cells and miR-c12 in Ago2-RISC complex clearly suggested that it followed canonical miRNA biogenesis pathway and accomplished its regulatory function. Expression of this miRNA was quite low in CHC tissues than normal liver implying HCV-proteins might be regulating its biogenesis. Promoter scanning and ChIP analysis further revealed that under expression of p53 and hyper-methylation of STAT3 binding site upon HCV infection restricted its expression in CHC tissues. Centrosomal protein 350 (CEP350), which sequestered PPARα, was identified as one of the targets of miR-c12 using Miranda and validated by luciferase assay/western blot analysis. Furthermore, reduced triglyceride accumulation and enhanced PPARα mediated transcription of β-oxidation genes upon restoration of miR-c12 in liver cells suggested its role in lipid catabolism. Thus this study is reporting miR-c12 for the first time and showed its’ protective role during chronic HCV infection.
DOI: 10.6084/m9.figshare.12851813
title: Diversification of piRNAs expressed in PGCs and somatic cells during embryonic gonadal development

description: piRNAs are small non-coding RNAs known to play a main role in defence against transposable elements in germ cells. However, other potential functions, such as biogenesis and differences in somatic and germline expression of these regulatory elements, are not yet fully unravelled. Here, we analysed a variety of piRNA sequences detected in mouse male and female primordial germ cells (PGCs) and gonadal somatic cells at crucial stages during embryonic differentiation of germ cells (11.5–13.5 days post-coitum). NGS of sncRNA and bioinformatic characterization of piRNAs from PGCs and somatic cells, in addition to piRNAs associated with TEs, indicated functional diversification in both cell types. Differences in the proportion of the diverse types of piRNAs are detected between somatic and germline during development. However, the global diversified patterns of piRNA expression are mainly shared between germ and somatic cells, we identified piRNAs related with molecules involved in ribosome components and translation pathway, including piRNAs derived from rRNA (34%), tRNA (10%) and snoRNA (8%). piRNAs from both tRNA and snoRNA are mainly derived from 3ʹ and 5ʹ end regions. These connections between piRNAs and rRNAs, tRNAs or snoRNAs suggest important functions of specialized piRNAs in translation regulation during this window of gonadal development.
DOI: 10.6084/m9.figshare.12851819
title: An extension to: Systematic assessment of commercially available low-input miRNA library preparation kits

description: High-throughput sequencing has emerged as the favoured method to study microRNA (miRNA) expression, but biases introduced during library preparation have been reported. We recently compared the performance (sensitivity, reliability, titration response and differential expression) of six commercially-available kits on synthetic miRNAs and human RNA, where library preparation was performed by the vendors. We hereby supplement this study with data from two further commonly used kits (NEBNext, NEXTflex) whose manufacturers initially declined to participate. NEXTflex demonstrated the highest sensitivity, which may reflect its use of partially-randomized adapter sequences, but overall performance was lower than the QIAseq and TailorMix kits. NEBNext showed intermediate performance. We reaffirm that biases are kit specific, complicating the comparison of miRNA datasets generated using different kits.