cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13376044
title: Data for: Detection of oomycete pathogens in UK peat-free growing media and implications for plant health

description: This dataset on Zenodo accompanies the manuscript Frederickson-Matika et al. (2024), Detection of oomycete pathogens in UK peat-free growing media and implications for plant health.

There are two files:



metadata.tsv - plain text table as tab-separated variables

raw_data.tar.gz - compressed archive of 43 paired raw FASTQ files


This represents a subset of two complete Illumina MiSeq plates (in two dated folderes) run at the James Hutton Institute containing other environmental samples using the same protocol. Only the synthetic controls and peat-free samples are provided here.To repeat the analysis described in the paper, first install THAPBI PICT. See https://github.com/peterjc/thapbi-pict/ for instructions. At the time of the paper, v1.0.14 was the current release.

Next, decompress the raw data into a folder of paired gzipped FASTQ files. There is no need to decompress those:

    $ tar -zxvf raw_data.tar.gz    $ ls -1 plate_20220505/ plate_20230608/

If you wish, verify the checksums to confirm the data integrity:

    $ cd plate_20220505/
    $ md5sum -c MD5SUM.txt    $ cd ../plate_20230608/
    $ md5sum -c MD5SUM.txt    $ cd ..

Setup output directories:

   $ mkdir -p intermediate/ summary/

Run the THAPBI PICT pipeline:

   $ thapbi_pict pipeline -m 1s3g \          -i plate_*/ -o summary/peat-free \          -y plate_*/GBL*.fastq.gz \          -n plate_*/GBL*.fastq.gz \          -s intermediate/ \          -t metadata.tsv -u \          -x 9 -c 1,2,3,4,5,6,7,8

The options here are as follows:



-i - two input directories of paired raw FASTQ files.

-n - negative controls used to increase the absolute abundance threshold

-y - synthetic controls used to increase the fractional abundance threshold

-s - optional location to store intermediate files

-o - output stem for reports

-t - filename for tab-separated-variable metadata

-u - show unsequenced samples defined in the metadata

-x - which metadata column contains Illumina FASTQ filename stems

-c - which metadata columns to include in the report.


This assumes the following key default settings:



-a 100 (default absolite abundance threshold)

-f 0.001 (default fractional abundance threshold)

-d -(default provided ITS1 database).


With these settings, only synthetic sequences were found in the controls, and therefore the thresholds were not automatically increased any further.

Opening the output file summary/peat-free.ITS1.samples.1s3g.xlsx in Excel or similar should show you a table resembling Table 1 in the paper, but one row per sequencing sample, and additional columns with per-sample per-species read counts etc.
DOI: 10.6084/m9.figshare.27203226
title: Table of KEGG module reversibility for 33 IBD-enriched modules

description: This table describes the number of reversible and irreversible reactions in 33 KEGG modules that were found to be enriched in the gut metagenomes of individuals with Inflammatory Bowel Disease. The full story about these modules can be found in https://doi.org/10.7554/eLife.89862.1 and https://merenlab.org/data/ibd-gut-metabolism/. Reaction reversibility was determined using KEGG Pathway Maps (in which reversible reactions are represented by double-sided arrows) associated with a given module.
DOI: 10.6084/m9.figshare.27203226.v1
title: Table of KEGG module reversibility for 33 IBD-enriched modules

description: This table describes the number of reversible and irreversible reactions in 33 KEGG modules that were found to be enriched in the gut metagenomes of individuals with Inflammatory Bowel Disease. The full story about these modules can be found in https://doi.org/10.7554/eLife.89862.1 and https://merenlab.org/data/ibd-gut-metabolism/. Reaction reversibility was determined using KEGG Pathway Maps (in which reversible reactions are represented by double-sided arrows) associated with a given module.
DOI: 10.6084/m9.figshare.24581393
title: The process of value setting through co-design: the case of <i>La Borda</i>, Barcelona

description: Against the increasing commodification of housing, a new kind of housing cooperatives has emerged in Catalonia in the last decade. These cooperatives fall within the wider concept of collaborative housing (CH), i.e. they are collectively self-organised projects based on a collaborative design process, or ‘co-design’. In such a process, residents need to adjust their individual expectations and demands in order to reach a collective set of values to realise their housing project. The aim of this paper is to assess how values are set through co-design and translated into a housing project. To do so, we develop an analytical framework to conduct a longitudinal single case-study that traces back the co-design process of the resident-led housing cooperative <i>La Borda</i>, in Barcelona. Our findings shed light on how co-design unfolds and uncover trade-offs carried out to overcome tensions mostly between individual and collective demands and between building costs and quality.
DOI: 10.6084/m9.figshare.24581393.v1
title: The process of value setting through co-design: the case of <i>La Borda</i>, Barcelona

description: Against the increasing commodification of housing, a new kind of housing cooperatives has emerged in Catalonia in the last decade. These cooperatives fall within the wider concept of collaborative housing (CH), i.e. they are collectively self-organised projects based on a collaborative design process, or ‘co-design’. In such a process, residents need to adjust their individual expectations and demands in order to reach a collective set of values to realise their housing project. The aim of this paper is to assess how values are set through co-design and translated into a housing project. To do so, we develop an analytical framework to conduct a longitudinal single case-study that traces back the co-design process of the resident-led housing cooperative <i>La Borda</i>, in Barcelona. Our findings shed light on how co-design unfolds and uncover trade-offs carried out to overcome tensions mostly between individual and collective demands and between building costs and quality.
DOI: 10.21227/acwj-8098
title: A Mechanoluminescent Elastic Resistance Band for Quantitative Resistance Training

description: Resistance training with elastic bands has been proven to effectively enhance muscle performance, making it an important component of strength and fitness training. However, assessing the intensity of resistance training typically requires large equipment such as isokinetic dynamometers or complex methods like muscle electromyography. These approaches are highly dependent on professional assistance and cannot be conducted synchronously during training.  To solve these problems, we propose a mechanoluminescent elastic resistance band, which just utilizes one monocular vision system to record the deformation of mechanoluminescent elastic resistance, and calculate the force and work people do during training. We first selected a cubic fitting method for the stress-strain mapping relationship taking fitting performance and computing complexity into consideration. The coefficient of determination (R2) and root mean square error (RMSE) of fitting performances were more than 0.999 and about 0.05, respectively. Second, we designed one monocular vision system to detect the dimensions of elastic resistance band which acquired improvements (from 3.66% to 13.92%) to binocular vision system. Third, the mechanoluminescent elastic resistance could generate light when in dynamic stretching or releasing, which could compensate the band detection in different light intensity environment with more than 86.67% detection accuracy. Finally, this quantitative resistance training evaluation system was applied to evaluate different movements, and it could output the force and work trainers did to the band during training. Our study has provided a convenient and effective method for evaluating trainers' resistance training, which is a new way of quantitative resistance training evaluation
DOI: 10.5281/zenodo.13912857
title: Soil properties in agricultural systems affect microbial genomic traits

description: Code and supplementary table
DOI: 10.5281/zenodo.13912858
title: Soil properties in agricultural systems affect microbial genomic traits

description: Code and supplementary table
DOI: 10.15468/dl.b64tr5
title: Occurrence Download

description: A dataset containing 180921 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-106.24801 25.13752,-101.90853 25.13752,-101.90853 26.87446,-106.24801 26.87446,-106.24801 25.13752))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 180921 records from 500 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006034-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fvp7ah
title: Occurrence Download

description: A dataset containing 592 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-12.78821 29.33712,-13.36682 30.26289,-15.19907 29.52999,-18.11138 29.5107,-19.13358 27.36986,-16.74202 26.71411,-14.06115 27.21557,-12.78821 29.33712))",
 "TaxonKey is Testudines"
 ]
}

 The dataset includes 592 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006044-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.htqrta
title: Occurrence Download

description: A dataset containing 12081 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Number of sick and dead birds of Anseriformes and Charadriiformes by day submitted to Observation.org in The Netherlands and Belgium between 2016 and 2021"
 ]
}

 The dataset includes 12081 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006046-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/icpsr39190
title: Panel Study of Income Dynamics (PSID): Main Interview, 2021
title: Archival Version

description: The PSID is the world's longest-running nationally representative household panel survey. With over 50 years of data on the same families and their descendants, the PSID is a cornerstone of the data infrastructure for empirically based social science research in the U.S. PSID gathers data on the family as a whole and on individuals residing within the family, emphasizing the dynamic and interactive aspects of family economics, demography, and health. PSID data were collected annually from 1968-1997 and biennially after 1997.
In the Main Interview, one person per family is interviewed on a regular basis. Information about each family member is collected, but much greater detail is obtained about the reference person and, if married/cohabitating, the spouse or long-term cohabitor. Survey content changes to reflect evolving scientific and policy priorities, although many content areas have been consistently measured since 1968. Information includes employment, income, wealth, expenditures, time use, health, dementia screener, insurance, education, marriage, childbearing, philanthropy, and numerous other topics. Additional types of PSID data are available only under a restricted contract. These include but are not limited to: geospatial data below the level of state; mortality data; Medicare claims; and educational characteristics from the National Center for Education Statistics.
With low attrition and high success in following young adults as they form their own families, the sample size has grown from roughly 5,000 families in 1968 to more than 9,000 families and 24,000 individuals by 2021. Over the course of the study, the PSID has distributed data on more than 84,000 individuals. The long panel, genealogical design, and broad content of the data offer unique opportunities to conduct generational and life-course research.
The PSID now contains thousands of inter- and intragenerational relationships over 50 years of data, including (as of the 2021 wave):


"Paired" generational relationships, with each family in the pair providing independent interviews

Parent-Adult Child pairs: ~4,300
Sibling pairs: ~5,200
Cousin pairs: ~5,400


"Tripled" generational relationships, with all three generations providing independent interviews

Grandparent-Parent-Adult Child triplets: ~1,000




For information about earlier data collections, see Panel Study of Income Dynamics (PSID): Main Interview, 1968-2015.
In 2021, the main interview was updated to include questions about the impacts of the COVID-19 pandemic, including: loss of earnings, US government stimulus payments, charitable giving, participants' exposure to COVID-19, and vaccination status.
description: Datasets: 
DS0: Study-Level Files
DS1: Individual File, 2021
DS2: Family File, 2021
description: U.S. households.
description: computer-assisted telephone interview (CATI); web-based surveyThe data for this collection are available on the PSID Web site.
DOI: 10.3886/icpsr39190.v1
title: Panel Study of Income Dynamics (PSID): Main Interview, 2021
title: Version 1

description: The PSID is the world's longest-running nationally representative household panel survey. With over 50 years of data on the same families and their descendants, the PSID is a cornerstone of the data infrastructure for empirically based social science research in the U.S. PSID gathers data on the family as a whole and on individuals residing within the family, emphasizing the dynamic and interactive aspects of family economics, demography, and health. PSID data were collected annually from 1968-1997 and biennially after 1997.
In the Main Interview, one person per family is interviewed on a regular basis. Information about each family member is collected, but much greater detail is obtained about the reference person and, if married/cohabitating, the spouse or long-term cohabitor. Survey content changes to reflect evolving scientific and policy priorities, although many content areas have been consistently measured since 1968. Information includes employment, income, wealth, expenditures, time use, health, dementia screener, insurance, education, marriage, childbearing, philanthropy, and numerous other topics. Additional types of PSID data are available only under a restricted contract. These include but are not limited to: geospatial data below the level of state; mortality data; Medicare claims; and educational characteristics from the National Center for Education Statistics.
With low attrition and high success in following young adults as they form their own families, the sample size has grown from roughly 5,000 families in 1968 to more than 9,000 families and 24,000 individuals by 2021. Over the course of the study, the PSID has distributed data on more than 84,000 individuals. The long panel, genealogical design, and broad content of the data offer unique opportunities to conduct generational and life-course research.
The PSID now contains thousands of inter- and intragenerational relationships over 50 years of data, including (as of the 2021 wave):


"Paired" generational relationships, with each family in the pair providing independent interviews

Parent-Adult Child pairs: ~4,300
Sibling pairs: ~5,200
Cousin pairs: ~5,400


"Tripled" generational relationships, with all three generations providing independent interviews

Grandparent-Parent-Adult Child triplets: ~1,000




For information about earlier data collections, see Panel Study of Income Dynamics (PSID): Main Interview, 1968-2015.
In 2021, the main interview was updated to include questions about the impacts of the COVID-19 pandemic, including: loss of earnings, US government stimulus payments, charitable giving, participants' exposure to COVID-19, and vaccination status.
description: Datasets: 
DS0: Study-Level Files
DS1: Individual File, 2021
DS2: Family File, 2021
description: U.S. households.
description: computer-assisted telephone interview (CATI); web-based surveyThe data for this collection are available on the PSID Web site.
DOI: 10.5281/zenodo.13165226
title: Electric-Field Catalysis on Carbon Nanotubes in Electromicrofluidic Reactors:  Monoterpene Cyclizations: Original Data

description: Original data underlying the publication. Data are assembled according to the supporting information.
DOI: 10.5281/zenodo.13165225
title: Electric-Field Catalysis on Carbon Nanotubes in Electromicrofluidic Reactors:  Monoterpene Cyclizations: Original Data

description: Original data underlying the publication. Data are assembled according to the supporting information.
DOI: 10.5281/zenodo.13912895
title: Electric-Field Catalysis on Carbon Nanotubes in Electromicrofluidic Reactors:  Monoterpene Cyclizations: Original Data

description: Original data underlying the publication. Data are assembled according to the supporting information.
DOI: 10.3886/e198945v1
title: Data and Code for "Spending and Job Finding Impacts of Expanded Unemployment Benefits: Evidence from Administrative Micro Data"

description: We show that the largest increase in unemployment benefits in U.S. history had large spending impacts and small job-finding impacts. This finding has three implications. First, increased bene- fits were important for explaining aggregate spending dynamics—but not employment dynamics—during the pandemic. Second, benefit expansions allow us to study the MPC of normally low- liquidity households in a high-liquidity state. These households still have high MPCs. This suggests a role for permanent behavioral characteristics, rather than just current liquidity, in driving spending behavior. Third, the mechanisms driving our results imply that temporary benefit supplements are a promising countercyclical tool.
DOI: 10.15468/dl.5x9re5
title: Occurrence Download

description: A dataset containing 1166 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-12.78821 29.33712,-13.36682 30.26289,-15.19907 29.52999,-18.11138 29.5107,-19.13358 27.36986,-16.74202 26.71411,-14.06115 27.21557,-12.78821 29.33712))",
 "TaxonKey is Amphibia"
 ]
}

 The dataset includes 1166 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006051-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wfsd4c
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Reynoutria japonica Houtt.",
 "Geometry POLYGON((16.12 48.11, 16.62 48.11, 16.62 48.5, 16.12 48.5, 16.12 48.11))",
 "Year is 2020"
 ]
}

 The dataset includes 21 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006050-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.25273717
title: Test datasets of TSTA.

description: TSTA 是一种基于线程和 SIMD 的梯形成对/多序列比对方法。该数据集用于测试TSTA算法在真实和模拟数据上的速度。
DOI: 10.6084/m9.figshare.25273717.v1
title: Test datasets of TSTA.

description: TSTA 是一种基于线程和 SIMD 的梯形成对/多序列比对方法。该数据集用于测试TSTA算法在真实和模拟数据上的速度。
DOI: 10.15468/dl.hvgxcg
title: Occurrence Download

description: A dataset containing 38699 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Bombus terrestris (Linnaeus, 1758)",
 "PhylumKey is Arthropoda",
 "Year is greater than or equal to 1992",
 "Year is less than or equal to 2012",
 "Geometry POLYGON((-26 30, 46 30, 46 68, -26 68, -26 30))"
 ]
}

 The dataset includes 38699 records from 479 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006048-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13739050
title: Object color knowledge representation occurs in the macaque brain despite the absence of a developed language system
DOI: 10.5281/zenodo.13739051
title: Object color knowledge representation occurs in the macaque brain despite the absence of a developed language system
DOI: 10.15468/dl.bj78w4
title: Occurrence Download

description: A dataset containing 241723 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ornithogalum L."
 ]
}

 The dataset includes 241723 records from 1713 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006020-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-46103
title: Redemption tidings, vol. 16, nos. 1-26, 1 Jan. - 13 Dec. 1940

description: [description english/roman)] Issued fortnightly (every two weeks). "A full gospel magazine for all believers" -- subtitle. Includes Tidings from our missionaries in each issue (1 Jan. - 13 Dec. 1940).
DOI: 10.15468/dl.rrvuw6
title: Occurrence Download

description: A dataset containing 113 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Fossil, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Passiflora tetrandra Banks & Sol. ex DC."
 ]
}

 The dataset includes 113 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067451-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wyggbc
title: Occurrence Download

description: A dataset containing 6222 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((30.79581 50.88134,30.94958 51.10451,31.07018 51.27879,30.67968 51.29351,30.55782 51.16476,30.59982 51.10769,30.56666 51.00608,30.57993 50.8467,30.72915 50.81214,30.79581 50.88134))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6222 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0172652-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4vewpk
title: Occurrence Download

description: A dataset listing the 15077 species recorded in GBIF matching the query:
{
 "CollectionCode" : [
 "is BC"
 ]
}

 The dataset's 15077 records were derived from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0193157-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.