cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3886/e112564v1-117460
title: Replication data for: The Colonial Origins of Comparative Development: An Empirical Investigation: Reply

description: Acemoglu, Johnson, and Robinson (2001) established that economic institutions today are correlated with expected mortality of European colonialists. David Albouy argues this relationship is not robust. He drops all data from Latin America and much of the data from Africa, making up almost 60 percent of our sample, despite much information on the mortality of Europeans in those places during the colonial period. He also includes a "campaign" dummy that is coded inconsistently; even modest corrections undermine his claims. We also show that limiting the effect of outliers strengthens our results, making them robust to even extreme versions of Albouy's critiques. (JEL D02, E23, F54, I12, N40, O43, P14)
DOI: 10.6073/pasta/beb6635175cbce79c9f83ddf657075ee
title: Eight Mile Lake Research Watershed, Thaw Gradient: Seasonal thaw depth 2004-2020

description: In this larger study, we are asking the question: Is old carbon that comprises the bulk of the soil organic matter pool released in response to thawing of permafrost? We are answering this question by using a combination of field and laboratory experiments to measure radiocarbon isotope ratios in soil organic matter, soil respiration, and dissolved organic carbon, in tundra ecosystems. The objective of these proposed measurements is to develop a mechanistic understanding of the SOM sources contributing to C losses following permafrost thawing. We are making these measurements at an established tundra field site near Healy, Alaska in the foothills of the Alaska Range. Field measurements center on a natural experiment where permafrost has been observed to warm and thaw over the past several decades. This area represents a gradient of sites each with a different degree of change due to permafrost thawing. As such, this area is unique for addressing questions at the time and spatial scales relevant for change in arctic ecosystems.
DOI: 10.6073/pasta/6cd8d60e00b384d718715c9882da74ae
title: Review of ecological research approaches for the study of extreme events in aquatic ecosystems

description: Extreme climatic events have increased in frequency globally, with a simultaneous surge in scientific interest about their ecological consequences, particularly in sensitive freshwater, coastal, and marine ecosystems. In this context, it is imperative that ecologists apply their expertise to understand and predict the ecological impacts of extreme events, and to collaborate across disciplines and sectors to improve socio-ecological resilience to extreme events. However, ecological research on extreme events is often opportunistic and hampered by lack of coordination, among ecologists and among interdisciplinary collaborators. We conducted a literature search to investigate the research approaches that ecologists use to study extreme events in aquatic ecosystems (including freshwater, coastal, and marine ecosystems), that is, to understand how, when, and where ecologists study these events, and to identify areas to improve research practices. We used keywords related to ecology, aquatic ecosystems, and types of extreme events to identify 215 relevant papers in the literature and we examined these papers to identify 49 studies that met our inclusion criteria of including observations of ecological responses to an extreme event occurring in an aquatic ecosystem. We then extracted information from the 49 included papers, including information on the ecosystem, the extreme event, the spatial and temporal approaches to sampling, the types of response variables sampled, and the magnitude of responses measured. This dataset collates research approaches to the study of extreme events in aquatic ecosystems at a broad scale. Based on this literature review, we identified key areas where aquatic ecologists can improve research practices, including prioritizing pre- and post-event data collection, leveraging long-term and cross-site monitoring networks, and adopting novel approaches to analysis, synthesis, and collaboration.
DOI: 10.6084/m9.figshare.19709917.v3
title: TABLE S6

description: Information for pangenome analyses of <em>Bifidobacterium</em> species used in this study.
DOI: 10.6084/m9.figshare.19709917
title: TABLE S6, PANGENOME

description: Information for pangenome analyses of <em>Bifidobacterium</em> species used in this study. <strong>A</strong>) 107 published <em>B. breve </em>genomes used in the analyses; <strong>B</strong>) 310 published genomes <em>B. longum</em> genomes used in the analyses; <strong>C</strong>) homologous gene clusters (HGCs) of <em>B. breve</em> generated in metapangenome analyses using 26 <em>in-house</em> MAGs and 107 published genomes; <strong>D</strong>) HGCs of <em>B. longum</em> generated using 26 <em>in-house</em> MAGs and 107 published genomes; <strong>E</strong>) statistics of metapangenome analyses of <em>B. breve </em>and <em>B. longum</em> genomes; <strong>F</strong>) strains-specific HGCs that was only observed in <em>B. breve </em>in this cohort; <strong>G</strong>) enriched<em> B. breve </em>HGCs; <strong>H</strong>) COG functions in <em>B. breve</em> genomes enriched in this study comparing the other genomes of genBank; <strong>I</strong>) PFAM functions in <em>B. breve</em> genomes enriched in this study comparing the other genomes of genBank; <strong>J</strong>) ANI (Average Nucleotide Identity) score of the <em>B. breve</em> genomes used in this study.
DOI: 10.6084/m9.figshare.19709917.v4
title: TABLE S6

description: Information for pangenome analyses of <em>Bifidobacterium</em> species used in this study. <strong>A</strong>) 107 published <em>B. breve </em>genomes used in the analyses; <strong>B</strong>) 310 published genomes <em>B. longum</em> genomes used in the analyses; <strong>C</strong>) homologous gene clusters (HGCs) of <em>B. breve</em> generated in metapangenome analyses using 26 <em>in-house</em> MAGs and 107 published genomes; <strong>D</strong>) HGCs of <em>B. longum</em> generated using 26 <em>in-house</em> MAGs and 107 published genomes; <strong>E</strong>) statistics of metapangenome analyses of <em>B. breve </em>and <em>B. longum</em> genomes; <strong>F</strong>) strains-specific HGCs that was only observed in <em>B. breve </em>in this cohort; <strong>G</strong>) enriched<em> B. breve </em>HGCs; <strong>H</strong>) COG functions in <em>B. breve</em> genomes enriched in this study comparing the other genomes of genBank; <strong>I</strong>) PFAM functions in <em>B. breve</em> genomes enriched in this study comparing the other genomes of genBank; <strong>J</strong>) ANI (Average Nucleotide Identity) score of the <em>B. breve</em> genomes used in this study.
DOI: 10.6084/m9.figshare.19723252
title: TABLE S3 ASV

description: Amplicon sequence variant (ASV) of the intestinal microbiota. ASVs were generated using the software package DADA2 v1.14 (Callahan et al., 2016). The SILVA database (Quast et al., 2013) release 132 was used to assigned taxonomy. <strong>A</strong>) Species count table of short-read sequencing of the V3V4 region of 16S rRNA gene on Illumina HiSeq platform. <strong>B</strong>) ASV count table of the short-read sequencing. <strong>C</strong>) Taxonomic information of the each of the ASVs of short-read sequencing. <strong>D</strong>) ASV count table of the long-read sequencing of the full-length 16S rRNA gene on PacBio Sequel II platform. <strong>E</strong>) Taxonomic information of the each of the ASVs of long-read sequencing.
DOI: 10.6084/m9.figshare.19723252.v4
title: TABLE S3 ASV

description: Amplicon sequence variant (ASV) of the intestinal microbiota. ASVs were generated using the software package DADA2 v1.14 (Callahan et al., 2016). The SILVA database (Quast et al., 2013) release 132 was used to assigned taxonomy. <strong>A</strong>) Species count table of short-read sequencing of the V3V4 region of 16S rRNA gene on Illumina HiSeq platform. <strong>B</strong>) ASV count table of the short-read sequencing. <strong>C</strong>) Taxonomic information of the each of the ASVs of short-read sequencing. <strong>D</strong>) ASV count table of the long-read sequencing of the full-length 16S rRNA gene on PacBio Sequel II platform. <strong>E</strong>) Taxonomic information of the each of the ASVs of long-read sequencing.
DOI: 10.6084/m9.figshare.19723252.v3
title: TABLE S3

description: <strong>Table S3</strong>. Amplicon sequence variant (ASV) of the intestinal microbiota. ASVs were generated using the software package DADA2 v1.14 (Callahan et al., 2016). The SILVA database (Quast et al., 2013) release 132 was used to assigned taxonomy. <strong>A</strong>) Species count table of short-read sequencing of the V3V4 region of 16S rRNA gene on Illumina HiSeq platform. <strong>B</strong>) ASV count table of the short-read sequencing. <strong>C</strong>) Taxonomic information of the each of the ASVs of short-read sequencing. <strong>D</strong>) ASV count table of the long-read sequencing of the full-length 16S rRNA gene on PacBio Sequel II platform. <strong>E</strong>) Taxonomic information of the each of the ASVs of long-read sequencing.
DOI: 10.6084/m9.figshare.19723255
title: TABLE S5 GENOME

description: Information of the metagenomes sequencing of <em>Bifidobacterium</em> abundant samples. <strong>A</strong>) Statistics of metagenomic sequencing of 30 samples with &gt;10% <em>Bifidobacterium </em>abundance using short-read sequencing on Illumina NovaSeq platform; <strong>B</strong>) Statistics of the metagenome-assembled genomes (MAGs) of <em>Bifidobacterium</em> species in this cohort, including 26 <em>B. breve</em> and 4 <em>B. longum</em>; <strong>C</strong>) Statistics of Pacific Biosciences Sequel II sequencing reads and assembly. Assembly was performed using Canu-1.8 (Koren et al., 2017).
DOI: 10.6084/m9.figshare.19723255.v3
title: TABLE S5 GENOME

description: Information of the metagenomes sequencing of <em>Bifidobacterium</em> abundant samples. <strong>A</strong>) Statistics of metagenomic sequencing of 30 samples with &gt;10% <em>Bifidobacterium </em>abundance using short-read sequencing on Illumina NovaSeq platform; <strong>B</strong>) Statistics of the metagenome-assembled genomes (MAGs) of <em>Bifidobacterium</em> species in this cohort, including 26 <em>B. breve</em> and 4 <em>B. longum</em>; <strong>C</strong>) Statistics of Pacific Biosciences Sequel II sequencing reads and assembly. Assembly was performed using Canu-1.8 (Koren et al., 2017).
DOI: 10.6084/m9.figshare.19723255.v2
title: TABLE S5

description: Information of the metagenomes sequencing of <em>Bifidobacterium</em> abundant samples. <strong>A</strong>) Statistics of metagenomic sequencing of 30 samples with &gt;10% <em>Bifidobacterium </em>abundance using short-read sequencing on Illumina NovaSeq platform; <strong>B</strong>) Statistics of the metagenome-assembled genomes (MAGs) of <em>Bifidobacterium</em> species in this cohort, including 26 <em>B. breve</em> and 4 <em>B. longum</em>; <strong>C</strong>) Statistics of Pacific Biosciences Sequel II sequencing reads and assembly. Assembly was performed using Canu-1.8 (Koren et al., 2017).
DOI: 10.5281/zenodo.6525718
title: zaplotnik/Metrics-of-Hadley-circulation-strength

description: Hadley cell strength This is a collection of open data sources related to the study of the sensitivity of the trend of Hadley cell (HC) strength to the applied HC strength measure. The applied metrics are described in manuscript: Pikovnik, Zaplotnik, Boljka, Žagar, 2021. Metrics of the Hadley circulation strength and associated circulation trends (under review at EGU Weather and Climate Dynamics). The HC strength is commonly evaluated by metrics derived from the mass-weighted zonal-mean stream function in isobaric coordinates. Other metrics include the velocity potential and the vertical velocity. These metrics of the HC strength are here complemented by a measure of the average HC strength, obtained by averaging the stream function in the latitude-pressure ($\varphi$-$p$) plane, and by the total energy of unbalanced zonal-mean circulation in the normal-mode function decomposition. The two new measures alleviate the vertical and meridional inhomogeneities of the trends in the HC strength. The data is organised into the following folder: <code>HC_strength_timeseries</code> <code>HC_strength_normalized_timeseries</code>: timeseries normalized by the climatological mean value <code>HC_strength_psi_trends</code>: trends of stream-function-based metrics <code>HC_strength_relative_trends</code>: trends of normalized timeseries <code>HC_strength_maxmin_pressure_levels</code>: pressure levels of maximum and minimum values in the annual-mean streamfunction fields <code>animation</code>: animation of the changes of annual-mean, january and july Hadley cell, desribed by the zonal-mean streamfunction in the latitude-pressure plane <code>correlations_AHC</code>: correlation of the average HC strength measure with other streamfunction based measures; for Northern Hadley cell (NHC) and Southern Hadley cell (SHC)
DOI: 10.5281/zenodo.6519181
title: zaplotnik/Metrics-of-Hadley-circulation-strength

description: Hadley cell strength This is a collection of open data sources related to the study of the sensitivity of the trend of Hadley cell (HC) strength to the applied HC strength measure. The applied metrics are described in manuscript: Pikovnik, Zaplotnik, Boljka, Žagar, 2021. Metrics of the Hadley circulation strength and associated circulation trends (under review at EGU Weather and Climate Dynamics). The HC strength is commonly evaluated by metrics derived from the mass-weighted zonal-mean stream function in isobaric coordinates. Other metrics include the velocity potential and the vertical velocity. These metrics of the HC strength are here complemented by a measure of the average HC strength, obtained by averaging the stream function in the latitude-pressure ($\varphi$-$p$) plane, and by the total energy of unbalanced zonal-mean circulation in the normal-mode function decomposition. The two new measures alleviate the vertical and meridional inhomogeneities of the trends in the HC strength. The data is organised into the following folder: <code>HC_strength_timeseries</code> <code>HC_strength_normalized_timeseries</code>: timeseries normalized by the climatological mean value <code>HC_strength_psi_trends</code>: trends of stream-function-based metrics <code>HC_strength_relative_trends</code>: trends of normalized timeseries <code>HC_strength_maxmin_pressure_levels</code>: pressure levels of maximum and minimum values in the annual-mean streamfunction fields <code>animation</code>: animation of the changes of annual-mean, january and july Hadley cell, desribed by the zonal-mean streamfunction in the latitude-pressure plane <code>correlations_AHC</code>: correlation of the average HC strength measure with other streamfunction based measures; for Northern Hadley cell (NHC) and Southern Hadley cell (SHC)
DOI: 10.6073/pasta/6b0570b9f16b69f725a63a3fe24859dd
title: Eight Mile Lake Research Watershed, Carbon in Permafrost Experimental Heating and Drying Research (DryPEHR): Half-hourly soil moisture and temperature data, 2010-2021

description: This drying and warming experiment addresses the following questions: 1) Does ecosystem drying, warming and permafrost thaw cause a net release or uptake of C from the ecosystem to the atmosphere?, 2) Does the decomposition of old C that comprises the bulk of the soil C pool influence ecosystem C loss? 3) How do drying and warmign affect plant communities and ecosystem properties? We are answering these questions using a combined warming and drying experiment (DryPEHR), which is situated with the Carbon in Permafrost Experimental Heating Research (CiPEHR) project and located in an upland tundra field site near Healy, Alaska in the foothills of the Alaska Range. Warming treatment here refers to growing season air temperature warming (~1C) using open top chambers (OTC) combined with soil 'warming' using snow fences during the snow covered months. Drying is achieve using an automated pumping system that lowers the water table in the dry plots. Soil warming began in 2008; OTCs and drying in 2011.This data set includes half-hourly values of surface moisture content (gravimetric, 0-5cm), depth-integrated soil moisture (volumetric, 0-20 cm), and soil temperature in winter warming and summer warming, drying, and control treatment plots at DryPEHR.
DOI: 10.34943/758573dc-1202-42f4-8d95-d3e799bf96ff
title: Tsawwassen - Duke Point Ferry Route Carbon Dioxide Sensor Deployed 2022-02-04

description: The Pro-Oceanus CO2-Pro FT (SN 36-325-81) was deployed on 2022-02-04 on Tsawwassen - Duke Point Ferry Route. This ferry route goes between Tsawwassen terminal in Vancouver, BC and the Duke Point terminal, Nanaimo BC. This device is a Carbon Dioxide Sensor. Carbon Dioxide sensors monitor CO2 levels in the ocean. CO2 sensors measure the partial pressure, or the concentration of dissolved CO2 in seawater by a variety of techniques. It was deployed on a mobile platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.34943/1ba187b1-937b-46f1-840b-04a15b306788
title: Tsawwassen - Duke Point Ferry Route Carbon Dioxide Sensor Deployed 2022-02-04

description: The Pro-Oceanus CO2-Pro FT (SN 36-325-81) was deployed on 2022-02-04 on Tsawwassen - Duke Point Ferry Route. This ferry route goes between Tsawwassen terminal in Vancouver, BC and the Duke Point terminal, Nanaimo BC. This device is a Carbon Dioxide Sensor. Carbon Dioxide sensors monitor CO2 levels in the ocean. CO2 sensors measure the partial pressure, or the concentration of dissolved CO2 in seawater by a variety of techniques. It was deployed on a mobile platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.6073/pasta/47eff2bd7dda816f077eb871ab6fadb7
title: Eight Mile Lake Research Watershed, Thaw Gradient: half-hourly soil temperature 2004-2021

description: In this larger study, we are asking the question: Is old carbon that comprises the bulk of the soil organic matter pool released in response to thawing of permafrost? We are answering this question by using a combination of field and laboratory experiments to measure radiocarbon isotope ratios in soil organic matter, soil respiration, and dissolved organic carbon, in tundra ecosystems. The objective of these proposed measurements is to develop a mechanistic understanding of the SOM sources contributing to C losses following permafrost thawing. We are making these measurements at an established tundra field site near Healy, Alaska in the foothills of the Alaska Range. Field measurements center on a natural experiment where permafrost has been observed to warm and thaw over the past several decades. This area represents a gradient of sites each with a different degree of change due to permafrost thawing. As such, this area is unique for addressing questions at the time and spatial scales relevant for change in arctic ecosystems. This data set includes soil temperature at multiple depths in the profile at different locations within gradient of sites described.
DOI: 10.25345/c5tt4fx5n
title: MassIVE MSV000089434 - Mallassezia furfur conditioned media WT v KO - MSP-MS
title: Mallassezia furfur conditioned media WT v KO - MSP-MS
DOI: 10.6073/pasta/b0c2df23060d1e78ce4bd8facc353f29
title: Eight Mile Lake Research Watershed, Thaw Gradient: half-hourly soil moisture 2010-2021

description: In this larger study, we are asking the question: Is old carbon that comprises the bulk of the soil organic matter pool released in response to thawing of permafrost? We are answering this question by using a combination of field and laboratory experiments to measure radiocarbon isotope ratios in soil organic matter, soil respiration, and dissolved organic carbon, in tundra ecosystems. The objective of these proposed measurements is to develop a mechanistic understanding of the SOM sources contributing to C losses following permafrost thawing. We are making these measurements at an established tundra field site near Healy, Alaska in the foothills of the Alaska Range. Field measurements center on a natural experiment where permafrost has been observed to warm and thaw over the past several decades. This area represents a gradient of sites each with a different degree of change due to permafrost thawing. As such, this area is unique for addressing questions at the time and spatial scales relevant for change in arctic ecosystems. This data set includes soil moisture intergrate over a 20cm soil profile at different locations within gradient of sites described.
DOI: 10.6073/pasta/d2968d6a2de7deb2ad012c1b0cf21a12
title: Jornada Basin LTER: Wireless meteorological station at NPP T-EAST site: 5-minute summary wind and air temperature data: 2013 - ongoing

description: 5-minute summary data at NPP T-EAST met station. Average air temperature, wind speed and wind direction are measured and calculated based on 1-second scan rate of all sensors located at an automated meteorological station installed at Jornada LTER NPP T-EAST site. Wind speed is measured at 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature at approximate 2.5m. This climate station is operated by the Jornada LTER Program. This is an ONGOING dataset.
DOI: 10.25345/c5q23r417
title: MassIVE MSV000089435 - Dermal Thirdhand Smoke Exposure Induces Oxidative Damage, Initiates Skin Inflammatory Markers, and Adversely Alters the Human Plasma Proteome
title: Plasma proteomics data from the human dermal exposure to thirdhand smoke clinical investigation.
DOI: 10.5066/p9ha1c08
title: Argon data for HD-B1 intercalibration

description: This data release includes 40Ar/39Ar intercalibration data from the U.S. Geological Survey for neutron fluence monitors HD-B1 (Heidelberg biotite) and FCs (Fish Canyon sanidine). Potassium-bearing mineral grains were analyzed by argon geochronology at the U.S. Geological Survey Argon Geochronology Laboratory in Denver, Colorado. These data provide intercalibration information between the two fluence monitors.
DOI: 10.15468/n3gagq
title: Global Register of Introduced and Invasive Species - Bikar Atoll, Marshall Islands

description: The Global Register of Introduced and Invasive Species (GRIIS) presents validated and verified national checklists of introduced (alien) and invasive alien species at the country, territory, and associated island level. Checklists are living entities, especially for biological invasions given the growing nature of the problem. GRIIS checklists are based on a published methodology and supported by the Integrated Publishing Tool that jointly enable ongoing improvements and updates to expand their taxonomic coverage and completeness. All kingdoms of organisms occurring in all environments and systems are covered. Checklists are reviewed and verified by networks of country or species experts. Verified checklists/ species records, as well as those under review, are presented on the online GRIIS website (www.griis.org) in addition to being published through the GBIF Integrated Publishing Tool.