cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25002608
title: Supplementary Material for: Sertraline promotes health and longevity in Caenorhabditis elegans

description: Introduction: While several antidepressants have been identified as potential geroprotectors, the effect and mechanism of sertraline on healthspan remain to be elucidated. Here, we explored the role of sertraline in lifespan and healthspan of Caenorhabditis elegans (C. elegans).
Methods: The optimal effect concentration of sertraline was first screened in wild-type N2 worms under heat stress conditions. Then, we examined the effects of sertraline on lifespan, reproduction, lipofuscin accumulation, mobility, and stress resistance. Finally, the expression of the 5-HT signaling and aging-related genes was investigated to explore the underlying mechanism, and the lifespan assays were performed in ser-7 RNAi strain, daf-2, daf-16, and aak-2 mutants.
Results: Sertraline extended lifespan in C. elegans with concomitant extension of healthspan as indicated by increasing mobility and reducing fertility and lipofuscin accumulation, as well as enhanced resistance to different abiotic stresses. Mechanistically, ser-7 orchestrated sertraline-induced longevity via the regulation of insulin and AMPK pathways, and sertraline-induced lifespan extension in nematodes was abolished in ser-7 RNAi strain, daf-2, daf-16, and aak-2 mutants.
Conclusion: Sertraline promotes health and longevity in C. elegans through ser-7-insulin/AMPK pathways.
DOI: 10.6084/m9.figshare.25002608.v1
title: Supplementary Material for: Sertraline promotes health and longevity in Caenorhabditis elegans

description: Introduction: While several antidepressants have been identified as potential geroprotectors, the effect and mechanism of sertraline on healthspan remain to be elucidated. Here, we explored the role of sertraline in lifespan and healthspan of Caenorhabditis elegans (C. elegans).
Methods: The optimal effect concentration of sertraline was first screened in wild-type N2 worms under heat stress conditions. Then, we examined the effects of sertraline on lifespan, reproduction, lipofuscin accumulation, mobility, and stress resistance. Finally, the expression of the 5-HT signaling and aging-related genes was investigated to explore the underlying mechanism, and the lifespan assays were performed in ser-7 RNAi strain, daf-2, daf-16, and aak-2 mutants.
Results: Sertraline extended lifespan in C. elegans with concomitant extension of healthspan as indicated by increasing mobility and reducing fertility and lipofuscin accumulation, as well as enhanced resistance to different abiotic stresses. Mechanistically, ser-7 orchestrated sertraline-induced longevity via the regulation of insulin and AMPK pathways, and sertraline-induced lifespan extension in nematodes was abolished in ser-7 RNAi strain, daf-2, daf-16, and aak-2 mutants.
Conclusion: Sertraline promotes health and longevity in C. elegans through ser-7-insulin/AMPK pathways.
DOI: 10.25505/fiz.icsd.cc25w4dm
title: CSD 2022080: Experimental Crystal Structure Determination

description: Related Article: Tong Wu, Kotaro Fujii, Taito Murakami, Masatomo Yashima, Satoru Matsuishi|2020|Inorg.Chem.|59|15384|doi:10.1021/acs.inorgchem.0c02356
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc25w4fn
title: CSD 2022081: Experimental Crystal Structure Determination

description: Related Article: Tong Wu, Kotaro Fujii, Taito Murakami, Masatomo Yashima, Satoru Matsuishi|2020|Inorg.Chem.|59|15384|doi:10.1021/acs.inorgchem.0c02356
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc25w4gp
title: CSD 2022082: Experimental Crystal Structure Determination

description: Related Article: Tong Wu, Kotaro Fujii, Taito Murakami, Masatomo Yashima, Satoru Matsuishi|2020|Inorg.Chem.|59|15384|doi:10.1021/acs.inorgchem.0c02356
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc25w4bk
title: CCDC 2022078: Experimental Crystal Structure Determination

description: Related Article: Kouji Taniguchi, Masaki Nishio, Nobuyuki Abe, Po-Jung Huang, Shojiro Kimura, Taka-hisa Arima, Hitoshi Miyasaka|2021|Angew.Chem.,Int.Ed.|60|14350|doi:10.1002/anie.202103121
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dlbmz
title: CCDC 2222161: Experimental Crystal Structure Determination

description: Related Article: Indira S. Divya, Amit Mondal, Surojit Bhunia, Kiran S. R. N. Mangalampalli, Jubi John, C. Malla Reddy, Sunil Varughese|2023|Cryst.Growth Des.|23|2550|doi:10.1021/acs.cgd.2c01445
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gz3h2
title: CCDC 2293054: Experimental Crystal Structure Determination

description: Related Article: Jakoba Wacker, Jennifer R. Lynch, Sumanta Banerjee, Peter A. Macdonald, Alan R. Kennedy, Biprajit Sarkar, Robert E. Mulvey|2023|Chem.Commun.|60|91|doi:10.1039/D3CC05527B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.20387/bonares-67q1-90wr
title: RhizoWheat, rhizobox experiment, early growth, rhizosphere processes, rhizo2

description: Biochemical, microbial, enzymatic, plant growth data of three rotational positions of winter wheat grown in rhizotrons sampled on the beginning of stem elongation phase.This table contains the index of all tables forming this data collection.

Related datasets are listed in the metadata element 'Related Identifier'.
Dataset version 1.0
DOI: 10.5281/zenodo.10517750
title: Soil Microbiome Inoculation Studies: Microcosms and Agarose Mini-Bead Paired Studies

description: Readme file content

The files stored here contain the following material as supplementary and source data for the manuscript in submission

Niche Availability and Competitive Facilitation Control Proliferation of Bacterial Strains Intended for Soil Microbiome Interventions

Senka Čaušević 1, Manupriyam Dubey 1, Marian Morales 1, Guillem Salaza r2, Vladimir Sentchilo 1, Nicolas Carraro 1, Hans-Joachim Ruscheweyh 2, Shinichi Sunagawa 2, and Jan Roelof van der Meer 1

1) Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland

2) Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
DOI: 10.5281/zenodo.10517751
title: Soil Microbiome Inoculation Studies: Microcosms and Agarose Mini-Bead Paired Studies

description: Readme file content

The files stored here contain the following material as supplementary and source data for the manuscript in submission

Niche Availability and Competitive Facilitation Control Proliferation of Bacterial Strains Intended for Soil Microbiome Interventions

Senka Čaušević 1, Manupriyam Dubey 1, Marian Morales 1, Guillem Salaza r2, Vladimir Sentchilo 1, Nicolas Carraro 1, Hans-Joachim Ruscheweyh 2, Shinichi Sunagawa 2, and Jan Roelof van der Meer 1

1) Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland

2) Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
DOI: 10.5281/zenodo.10517970
title: CaliParticles: A Benchmark Standard for Experiments in Granular Materials

description: Granular materials are discrete particulate media that can flow like a liquid but also be rigid like a solid. This complex mechanical behavior originates in part from the particles shape. How particle shape affects mechanical behavior remains poorly understood. Understanding this micro-macro link would enable the rational design of potentially cheap, light weight or robust materials. To aid this development, we have produced a set of standard particle shapes that can be used as benchmarks for granular materials research. Here we describe the collection of benchmark shapes. Some part of the particles are modeled on superquadrics, others are custom designed. The particles used so far were made from polyoxymethylene (POM) and Thermoplastic elastomers (TPE) whose specifications are also listed. The benchmark shapes are available as molds in a plastics manufacturing company, whose contact information is also included. The company is capable of making other molds as well, giving access to more particle shapes. The same particle shapes can thus also be made in different types of (colored) plastic, and in amounts of 50.000 particles or more, larger than conveniently be produced with a 3D printer. We also provide the associated .step and .stl files in the repository in which this document is included.
DOI: 10.5281/zenodo.7147021
title: CaliParticles: A Benchmark Standard for Experiments in Granular Materials

description: Granular materials are discrete particulate media that can flow like a liquid but also be rigid like a solid. This complex mechanical behavior originates in part from the particles shape. How particle shape affects mechanical behavior remains poorly understood. Understanding this micro-macro link would enable the rational design of potentially cheap, light weight or robust materials. To aid this development, we have produced a set of standard particle shapes that can be used as benchmarks for granular materials research. Here we describe the collection of benchmark shapes. Some part of the particles are modeled on superquadrics, others are custom designed. The particles used so far were made from polyoxymethylene (POM) and Thermoplastic elastomers (TPE) whose specifications are also listed. The benchmark shapes are available as molds in a plastics manufacturing company, whose contact information is also included. The company is capable of making other molds as well, giving access to more particle shapes. The same particle shapes can thus also be made in different types of (colored) plastic, and in amounts of 50.000 particles or more, larger than conveniently be produced with a 3D printer. We also provide the associated .step and .stl files in the repository in which this document is included.
DOI: 10.48425/z9xxxk1d
title: V_rodents_cameratraps_annual_metadata_intensive_quadrats

description: Annual metadata of small mammal cameras on the Varanger peninsula, in heath and meadow habitats. The dataset contains information recorded during the annual camera check, such as the serial number of the camera, the condition of the camera and other relevant comments.

The dataset includes four different types of files and all data files are saved as ;-separated txt-files:
 
* One data file per year with metadata from the annual camera check (_YEAR.txt)
* One coordinate file with coordinates of all sites (_coordinates.txt)
* One auxiliary file with information about which sites are included in the study design (_aux.txt)
* One readme file with additional information (_readme.pdf)

Image metadata is available in the dataset 'V_rodents_cameratraps_image_metadata_heath_meadow'. Classification of all images is available in the datasets 'V_rodents_cameratraps_image_classification_heath_meadow'.
DOI: 10.5281/zenodo.10478744
title: Custom reference transcriptome for transgenic mouse genome based on mm10

description: Reads were aligned to this custom reference genome, which was created based on the mouse mm10 reference genome v1.2.0 provided by 10x Genomics. Firstly, sequences for transgenes Sgcb1a1 (3’ of ER + 130 bp linker + 3’ UTR of Scgb1a1), Sftpc (rtTA-M2 coding sequence) and DTA were added to the reference genome FASTA file. Subsequently, the endogenous Esr1 (genomic position Chr10:4611989-5005614) and 3’ UTR of Scgb1a1 (genomic position Chr19:9083642-9083739) were masked from the genome. Then, three lines corresponding to the newly-added transgene sequences were added to the reference genome GTF file. Lastly, Cell Ranger was used to create the reference genome package from the modified FASTA and GTF files.
DOI: 10.5281/zenodo.10478745
title: Custom reference transcriptome for transgenic mouse genome based on mm10

description: Reads were aligned to this custom reference genome, which was created based on the mouse mm10 reference genome v1.2.0 provided by 10x Genomics. Firstly, sequences for transgenes Sgcb1a1 (3’ of ER + 130 bp linker + 3’ UTR of Scgb1a1), Sftpc (rtTA-M2 coding sequence) and DTA were added to the reference genome FASTA file. Subsequently, the endogenous Esr1 (genomic position Chr10:4611989-5005614) and 3’ UTR of Scgb1a1 (genomic position Chr19:9083642-9083739) were masked from the genome. Then, three lines corresponding to the newly-added transgene sequences were added to the reference genome GTF file. Lastly, Cell Ranger was used to create the reference genome package from the modified FASTA and GTF files.
DOI: 10.57745/vmfujv
title: variables.txt

description: geochemical composition data of 146 marine sediments wastes collected before dredging operations between 2010 and 2021.Variables content in the dataset - Id_sample: Sample identification number; LAT_RGF93: Latitude of the sampling point; LONG_RGF93: Longitude of the sampling point; Sediment_type: harbor type; pH: hydrogen potential measurements; Cl: Chloride content (mg Cl kg-1 w.w.); F: Fluoride content (mg F kg-1 w.w.); SO4: Sulphate content (mg SO4 kg-1 w.w.); Cd: Cadmium content (mg Cd kg-1 w.w.); Cr: Chromium content (mg Cr kg-1 w.w.); Al: Aluminium content (mg Al kg-1 w.w.); As: Arsenic content (mg As kg-1 w.w.); Cu: Copper content (mg Cu kg-1 w.w.) ; Ni: Nickel content (mg Ni kg-1 w.w.) ; Pb: Lead content (mg Pb kg-1 w.w.); Zn: Zinc content (mg Zn kg-1 w.w.); Hg: Mercury content (mg Hg kg-1 w.w.); TBT: Tributyltin content (µg TBT kg-1 w.w.); HAP: Polycyclic aromatic hydrocarbons content (mg HAP kg-1 w.w.); PCB: Polychlorinated biphenyls content (mg PCB kg-1 w.w.); Sand: Gravel content (&gt; 2000µm) (%); Mud_2mm: Vase (fine fraction &lt;63 µm, over &lt;2mm) content (%); Density: Bulk density (g cm-3); Total_N: Total nitrogen content (g N kg −1 w.w.); Total_P: Total Phosphorus content (mg P2O5 kg-1 w.w.); DM: Dry matter content (%); OM: Organic Matter content (g kg −1 w.w.). (w.w.: wet weight).
DOI: 10.57745/rr9eqq
title: geochemical_analysis.tab

description: :unav
DOI: 10.5281/zenodo.10459749
title: Long-term field studies are critical for safeguarding biodiversity: a new concept and concern

description: The data file associated with Figure 1b provides population data from the Kattegat-Skagerack harbour seal (Phoca vitulina). Historical data are reconstructed based on bounty statistics (1). Data from 1970 are based on systematic annual surveys (2,3,4). Projections beyond 2023 are hypothetical illustrations of potential population developments inspired by a population projection model (3).

1 Heide-Jørgensen, M.-P., and Härkönen, T. J. (1988). Rebuilding seal stocks in the kattegat-skagerrak. Mar. Mammal Sci. 4, 231–246. doi: 10.1111/j.1748-7692.1988.tb00204.x.

2 Härkönen, T., Dietz, R., Reijnders, P., Teilmann, J., Harding, K., Hall, A., et al. (2006). The 1988 and 2002 phocine distemper virus epidemics in European harbour seals. Dis. Aquat. Organ. 68, 115–130. doi: 10.3354/dao068115.

3 Silva, W. T. A. F., Bottagisio, E., Härkönen, T., Galatius, A., Olsen, M. T., and Harding, K. C. (2021). Risk for overexploiting a seemingly stable seal population: influence of multiple stressors and hunting. Ecosphere 12. doi: 10.1002/ecs2.3343.

4 SMHI (2020). SharkWeb. Available at: https://sharkweb.smhi.se/hamta-data/ [Accessed March 6, 2023].
DOI: 10.5281/zenodo.10517927
title: Long-term field studies are critical for safeguarding biodiversity: a new concept and concern

description: The data file associated with Figure 1b provides population data from the Kattegat-Skagerack harbour seal (Phoca vitulina). Historical data are reconstructed based on bounty statistics (1). Data from 1970 are based on systematic annual surveys (2,3,4). Projections beyond 2023 are hypothetical illustrations of potential population developments inspired by a population projection model (3).

1 Heide-Jørgensen, M.-P., and Härkönen, T. J. (1988). Rebuilding seal stocks in the kattegat-skagerrak. Mar. Mammal Sci. 4, 231–246. doi: 10.1111/j.1748-7692.1988.tb00204.x.

2 Härkönen, T., Dietz, R., Reijnders, P., Teilmann, J., Harding, K., Hall, A., et al. (2006). The 1988 and 2002 phocine distemper virus epidemics in European harbour seals. Dis. Aquat. Organ. 68, 115–130. doi: 10.3354/dao068115.

3 Silva, W. T. A. F., Bottagisio, E., Härkönen, T., Galatius, A., Olsen, M. T., and Harding, K. C. (2021). Risk for overexploiting a seemingly stable seal population: influence of multiple stressors and hunting. Ecosphere 12. doi: 10.1002/ecs2.3343.

4 SMHI (2020). SharkWeb. Available at: https://sharkweb.smhi.se/hamta-data/ [Accessed March 6, 2023].
DOI: 10.5281/zenodo.10516341
title: SocialDrought: A Social and News Media Driven Dataset and Analytical Platform Towards Understanding Societal Impact of Drought

description: Drought poses significant challenges to sustainability across various sectors in our society, leading to substantial consequences on agriculture, environments, ecosystems, public health, and socioeconomic stability. While prior work has studied the impacts of drought using professionally measured data sources, the societal perspectives of drought impacts remain largely under-explored. In this work, we present SocialDrought, a novel and comprehensive dataset to facilitate research on the societal impacts of drought. In particular, SocialDrought consists of three major components: 1) over 1.5 million social media posts, 2) over 1,400 news articles collected and verified by domain experts, and 3) over 31,000 meteorological records from the U.S. Drought Monitor about drought severity. In addition, we also introduce an online platform for interactive and real-time data exploration for timely insights about the societal impacts of drought. Our interdisciplinary dataset integrates both conventional meteorological data and unconventional social and news media data to provide a  holistic understanding of drought impacts. SocialDrought enables new opportunities to study the societal impacts of drought through the lens of social and news media. This work represents an important step toward improving policy-making and mitigation strategies in response to the critical challenges posed by drought and other environmental issues.
DOI: 10.5281/zenodo.10516342
title: SocialDrought: A Social and News Media Driven Dataset and Analytical Platform Towards Understanding Societal Impact of Drought

description: Drought poses significant challenges to sustainability across various sectors in our society, leading to substantial consequences on agriculture, environments, ecosystems, public health, and socioeconomic stability. While prior work has studied the impacts of drought using professionally measured data sources, the societal perspectives of drought impacts remain largely under-explored. In this work, we present SocialDrought, a novel and comprehensive dataset to facilitate research on the societal impacts of drought. In particular, SocialDrought consists of three major components: 1) over 1.5 million social media posts, 2) over 1,400 news articles collected and verified by domain experts, and 3) over 31,000 meteorological records from the U.S. Drought Monitor about drought severity. In addition, we also introduce an online platform for interactive and real-time data exploration for timely insights about the societal impacts of drought. Our interdisciplinary dataset integrates both conventional meteorological data and unconventional social and news media data to provide a  holistic understanding of drought impacts. SocialDrought enables new opportunities to study the societal impacts of drought through the lens of social and news media. This work represents an important step toward improving policy-making and mitigation strategies in response to the critical challenges posed by drought and other environmental issues.
DOI: 10.5281/zenodo.10213384
title: emacs-gc-stats: Does garbage collection actually slow down Emacs?

description: This dataset contains raw data, reproducible analysis (Org file), and presentation sources (Org file) for "emacs-gc-stats: Does garbage collection actually slow down Emacs?" presented at EmacsConf 2023: https://emacsconf.org/2023/talks/gc/
The file structure (inside the compressed emacs-gc-stats.tar.gz):

analysis.org contains the Org sources to generate all the plots
presentation.org contains the Org source of the presentation
0.eld - 129.eld contain the raw submitted data
*.svg files are annotated graphs prepared for the presentation
gc-duration/ contains processed statistics of GC duration
gc-duration-evo/ contains statistics of GC evolution over time
gc-merged/ contains statistics of agglomerated GCs
gc-pause/ contains statistics of GC frequency
dat/ contains filtered raw data in tabulated format prepared for Gnuplot
DOI: 10.5281/zenodo.10213383
title: emacs-gc-stats: Does garbage collection actually slow down Emacs?

description: This dataset contains raw data, reproducible analysis (Org file), and presentation sources (Org file) for "emacs-gc-stats: Does garbage collection actually slow down Emacs?" presented at EmacsConf 2023: https://emacsconf.org/2023/talks/gc/
The file structure (inside the compressed emacs-gc-stats.tar.gz):

analysis.org contains the Org sources to generate all the plots
presentation.org contains the Org source of the presentation
0.eld - 129.eld contain the raw submitted data
*.svg files are annotated graphs prepared for the presentation
gc-duration/ contains processed statistics of GC duration
gc-duration-evo/ contains statistics of GC evolution over time
gc-merged/ contains statistics of agglomerated GCs
gc-pause/ contains statistics of GC frequency
dat/ contains filtered raw data in tabulated format prepared for Gnuplot