cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9kd51c5r6
title: Soil properties shape the heterogeneity of denitrification and N2O emissions across large-scale flooded paddy soils

description: The dataset's contents include the relative abundance of different
 denitrifier types at the genus level across eight different flooded paddy
 soils. This dataset categorizes denitrifier types in its first column
 labeled 'Type.' The second column, 'Genus,' associates
 each type with various species at the genus level. Subsequent columns
 present the relative abundance of these species in diverse sampling
 locations. Researchers can leverage this dataset to derive more patterns
 regarding the differences within specific dominant denitrifier species. No
 ethical considerations are pertinent to the utilization of this dataset.
description: # Soil properties shape the heterogeneity of denitrification and N2O
 emissions across large-scale flooded paddy soils
 Lists of the relative
 abundance of different denitrifying types at the genus level used in the
 analysis across the eight flooded paddy fields in southern China. The
 dataset's contents include the relative abundance of different
 denitrifier types at the genus level across eight different flooded paddy
 soils. This dataset categorizes denitrifier types in its first column
 labeled "Type," featuring names including *nirS*, *nirK*,
 *FnirK* and *nosZ*. The second column, "Genus," associates each
 type with various species at the genus level. Subsequent columns present
 the relative abundance of these species in the eight sampling locations.
 Researchers can leverage this dataset to derive more patterns regarding
 the differences within specific dominant denitrifier species. ##
 Description of the data and file structure This Microsoft Excel file
 includes the following information: * Type: *nirS*, *nirK*, *nosZ* and
 *FnirK* denitrifying communities * Genus: the corresponding taxa at genus
 level * GZ: Guizhou * FJ: Fujian * YN: Yunnan * GD: Guangdong * AH: Anhui
 * HN: Hunan * JX: Jiangxi * ZJ: Zhejiang
DOI: 10.25625/h16sz6
title: ESRF_2024 postprocessed data

description: The set of post-processed data from the ESRF measurements 2024 about bubbles close to objects
DOI: 10.5061/dryad.dz08kps4w
title: Microbe-induced plant resistance against insect pests depends on timing of inoculation, but is consistent across climatic conditions

description: To cope with abiotic and biotic stressors, plants have developed
 mutualistic associations with beneficial soil microbes, but little is
 known about how extreme abiotic conditions impact microbe-induce
 resistance to insect herbivores. Extreme temperatures are often
 accompanied by extremes in plant water availability, which together reduce
 plant growth and change plant physiology. There are potential consequences
 for increasing plant susceptibility to biotic stresses, and this poses a
 real challenge for plant productivity. We evaluated how the effects of
 beneficial soil bacteria (Acidovorax radicis N35e) on barley plant growth
 and resultant resistance against aphid infestation (Sitobion avenae) were
 impacted by a single heatwave event across a plant water availability
 gradient. We also tested if timing of bacterial inoculation (before or
 after the temperature treatment) affected bacteria-plant interactions on
 aphids. We found that heatwaves affected plant biomass allocation from
 aboveground to belowground tissues. Inoculation with A. radicis led to
 reduction of aphid numbers, but depended on timing of inoculation, and led
 to stronger resistance when inoculations occurred closer to aphid
 infestation. Remarkably, microbe-induced resistance against aphids was
 consistent across heatwave and water availability treatments. This study
 provides evidence that beneficial plant-bacteria interactions may
 represent a potential solution for sustainable agricultural practices to
 enhance plant growth and response to insect pests under climate change.
 Future field trials should investigate the consistency of beneficial
 effects reported here for a better understanding of multispecies
 interactions in the context of global change.
description: This study describes a pot experiment performed in climate
 chambers, using barley plants. Presented data represent values measured
 from individual plants (in rows). For detailed descriptions, we refer to
 the materials and methods of the paper.
description: # Microbe-induced plant resistance against insect pests depends on timing
 of inoculation, but is consistent across climatic conditions
 ## Description of the data
 and file structure The data is presented in an Excel table. The first tab
 'Metadata description' describes the metadata in the required
 detail. The second tab 'Raw data' provides all raw data
 measurements, with a series of explanatory variables (columns A-J),
 followed by a series of response variables (columns K-V).
DOI: 10.5061/dryad.4xgxd25hk
title: Palaearctic origin and repeated dispersal over the world shaped the biogeographic history of the saprophytic genus Coprinopsis (Psathyrellaceae, Basidiomycota)

description: Aim: The biogeographic history of most fungi is still poorly known, as
 well as the patterns and processes responsible for their diversification.
 Recent studies uncovered that most fungi have originated and present
 higher diversification rates in the temperate zone. The distributional
 pattern known for fungi is also different from many plants, animals and
 microbes. Using the most comprehensive phylogeny of the saprotrophic genus
 Coprinopsis, we aim to infer the biogeographic history and test
 evolutionary hypotheses in the genus. Location: Worldwide Taxon: Fungi,
 Basidiomycota, Psathyrellaceae, Coprinopsis Methods: We used a four-gene
 alignment with 100 species to estimate divergence times using two fossil
 calibrations within Agaricales. The chronograms were used to estimate
 diversification rates and geographic state-dependent models were applied.
 We further reconstructed the ancestral range history of the genus.
 Results: Molecular dating estimated that the genus has diverged ca. 41 Ma
 (Eocene) and originated in the Palaearctic region. Diversification rates
 showed a decreasing pattern towards the present across Coprinopsis,
 especially after the Miocene (ca. 14 Ma). The diversification models
 dependent on distribution showed cosmopolitan lineages with higher
 net-diversification rates. When we compared temperate and tropical
 regions, we found that temperate lineages have higher net-diversification
 rates. The biogeographic history of Coprinopsis estimated different routes
 of dispersal. The most common dispersal route was from the Palaearctic to
 the Nearctic (15 times), followed by the Palaeartic to the Neotropics (14
 times). Main Conclusions: The study is the first to estimate the
 diversification rates and the historical biogeography of the coprinoid
 genus Coprinopsis. The diversification dynamics estimates in Coprinopsis
 are in agreement with the “generalized diversification rates model”, where
 we found higher diversification rates in temperate regions compared to
 tropical regions. In general, the ancestral area and major dispersal
 routes recovered in the genus are similar to findings in other groups of
 fungi. 
description: # Palaearctic origin and repeated dispersal over the world shaped the
 biogeographic history of the saprophytic genus Coprinopsis
 (Psathyrellaceae, Basidiomycota)
 We include the materials
 used in the article, along with the images and tables containing taxonomic
 and geographic information utilized in the analyses. ## Description of the
 data and file structure We provide Figures 1 and 2 in .tiff format
 containing the results of the biogeographical analyses and a .csv file
 with geographic data for the species. The geographic regions in this file
 are coded as "0" for Nearctic, "1" for Neotropical,
 "2" for Palaearctic, "3" for Afrotropical,
 "4" for Oriental, and "5" for Australian.
 Additionally, a .doc file contains the supplementary information.
DOI: 10.5061/dryad.76hdr7t3b
title: SquamBase 1.0 – a dataset of squamate species traits

description: Motivation: I present a database that contains information on multiple key
 traits for all 11,744 recognized species of squamates worldwide. The
 database encompasses key traits and hopefully a reasonably comprehensive
 picture of available public knowledge. I present a comprehensive
 description of the sources and rationale leading to the assignment of each
 particular trait state for each species. Hopefully, the dataset can serve
 the scientific community and promote research and understanding of the
 group, comparisons with other taxa, and assessment of conservation needs.
 Furthermore, gaps in our knowledge of squamate traits become readily
 apparent and will hopefully lead to further study and even better
 knowledge. Main types of variables contained: morphological, ecological,
 life history, geographic and conservation-related traits Spatial location:
 Global Time period: Late Holocene to recent Major taxa and level of
 measurement: Squamata, species Software format: .xlsx
description: Data were manually collected over 18 years.
description: # SquamBase 1.0 – a dataset of squamate species traits
 The dataset contains data
 on multiple traits for all squamate species recognized as of January 2024
 ## Description of the data and file structure Each data field is
 accompanied by a metadata field, and a general sources field appears for
 each species. 'NA' cells across all files refer to data that are
 not available. ## Sharing/Access information Data were derived from
 ~10,285 sources (mostly literature sources).
DOI: 10.7910/dvn/ode0nm
title: Replication Data for "Teaching and Learning in Multi-grade Rural Schools: Experimental Evidence from Colombia"

description: This package replicates the randomization for the paper "Teaching and Learning in Multi-grade Rural Schools: Experimental Evidence from Colombia"
DOI: 10.7910/dvn/d6gqse
title: Replication Data for: The Two-Track Labor Market: Gender, Class, and Formal Employment in Bangladesh

description: Replication data and code for "The Two-Track Labor Market: Gender, Class, and Formal Employment in Bangladesh" by Tanvir Thamid (Bates College).

This package contains the Bangladesh Labor Force Survey 2024 (all four quarters) and Stata code to replicate all analyses, including: (1) two-track labor market structure, (2) Oaxaca-Blinder decomposition of the gender gap in formal employment, (3) wealth quintile analysis, (4) earnings quintile analysis, and (5) education gradients.


See README.md for detailed instructions.
DOI: 10.5281/zenodo.18405620
title: Dataset for the Systematic Literature Review on Blockchain-AI-based Software Engineering Tools

description:  



This dataset supports a systematic literature review (SLR) on the use of blockchain technology to enhance trustworthiness in AI-based software engineering tools and techniques.

The dataset includes structured information extracted from primary studies, including publication metadata, research focus, methodological characteristics, and thematic classifications.

The dataset is intended to improve transparency, reproducibility, and reuse of the review process and is provided to support the accompanying journal article.
DOI: 10.5281/zenodo.18405619
title: Dataset for the Systematic Literature Review on Blockchain-AI-based Software Engineering Tools

description:  



This dataset supports a systematic literature review (SLR) on the use of blockchain technology to enhance trustworthiness in AI-based software engineering tools and techniques.

The dataset includes structured information extracted from primary studies, including publication metadata, research focus, methodological characteristics, and thematic classifications.

The dataset is intended to improve transparency, reproducibility, and reuse of the review process and is provided to support the accompanying journal article.
DOI: 10.5061/dryad.c866t1gdw
title: Calculating functional diversity metrics using neighbor-joining trees

description: The study of functional diversity (FD) provides ways to understand
 phenomena as complex as community assembly or the dynamics of biodiversity
 change under multiple pressures. Different frameworks are used to quantify
 FD, either based on dissimilarity matrices (e.g., Rao entropy, functional
 dendrograms) or multidimensional spaces (e.g., convex hulls,
 kernel-density hypervolumes), each with their own strengths and limits.
 Frameworks based on dissimilarity matrices either do not enable the
 measurement of all components of FD (i.e., richness, divergence, and
 regularity), or result in the distortion of the functional space.
 Frameworks based on multidimensional spaces do not allow for comparisons
 with phylogenetic diversity (PD) measures and can be sensitive to
 outliers. We propose the use of neighbor-joining trees (NJ) to represent
 and quantify FD in a way that combines the strengths of current frameworks
 without many of their weaknesses. Importantly, our approach is uniquely
 suited for studies that compare FD with PD, as both share the use of trees
 (NJ or others) and the same mathematical principles. We test the ability
 of this novel framework to represent the initial functional distances
 between species with minimal functional space distortion and sensitivity
 to outliers. The results using NJ are compared with conventional
 functional dendrograms, convex hulls, and kernel-density hypervolumes
 using both simulated and empirical datasets. Using NJ, we demonstrate that
 it is possible to combine much of the flexibility provided by
 multidimensional spaces with the simplicity of tree-based representations.
 Moreover, the method is directly comparable with taxonomic diversity (TD)
 and PD measures, and enables quantification of the richness, divergence
 and regularity of the functional space.
description: # Calculating functional diversity metrics using neighbor-joining trees
 [Access this dataset on Dryad] https://doi.org/10.5061/dryad.c866t1gdw
 This includes R code and data used in the production of the paper by
 Cardoso et al. (subm.) Calculating functional diversity metrics using
 neighbor-joining trees. All code and data needed to reproduce the analyses
 and create the graphics is included. Also included is the AVONET data to
 reproduce the empirical example and the related Fig. 3. ## Description of
 the data and file structure Data is a RDS file for use in R. ##
 Sharing/Access information Data was derived from the following sources: -
 Tobias et al (2022) https://doi.org/10.1111/ele.13898. ## Code/Software
 Code was run in R version 4.3.2 and R Studio 2023.12.0 build 369
DOI: 10.5061/dryad.zcrjdfnkz
title: Data from: Automated cell lineage reconstruction using label-free 4D microscopy

description: Here we describe embGAN, a deep learning pipeline that addresses the
 challenge of automated cell detection and tracking in label-free 3D
 time-lapse imaging. The embGAN requires no manual data annotation for
 training, learns robust detections that exhibits a high degree of scale
 invariance and generalizes well to images acquired in multiple labs on
 multiple instruments.
description: Images were acquired using an Olympus IX83 inverted frame
 equipped with a UPLSAPO60xs2 objective, a Visitech iSIM multipoint
 confocal scanner, ASI MX2000XYZ stage, and a Hamamatsu Orca Fusion camera.
 The mCherry channel of JIM113 was acquired using 594 nm excitation and a
 605 nm long-pass emission filter using 150 ms exposures and a laser power
 that was empirically tuned to not cause any qualitative developmental
 delays versus un-imaged control embryos and maintain a ~100% hatch rate
 for imaged embryos. Embryos were imaged every 60 seconds with a 750 nm z
 spacing. DIC images were acquired with the Visitech scanner in brightfield
 bypass mode, a 50 ms camera exposure and the LED light source tuned to not
 generate any saturated pixels in the image. DIC illumination was generated
 using an Olympus UCD8 manual condenser equipped with a U525 oil immersion
 1.4 NA top lens and a DICTHR tilt-shift slider. Images were acquired using
 a micro-manager and cropped and converted to individual tiff volumes using
 Fiji.
description: # Data from: Automated cell lineage reconstruction using label-free 4D
 microscopy
 [https://doi.org/10.5061/dryad.zcrjdfnkz](https://doi.org/10.5061/dryad.zcrjdfnkz) The dataset contains training data for developing and evaluating deep learning approaches to automated cell detection and tracking in 3D DIC images. ## Description of the data and file structure Data is split into folders containing test and training data. Each folder contains 2D 8-bit images in TIF format with matching pairs of images acquired using DIC or fluorescence microscopy where cell nuclei are labeled with mCherry fluorescence. For training embGAN using our codebase, labels for the training and test sets must first be generated using the provided stardist.py script ([https://github.com/shahlab-ucla/embGAN)](https://github.com/shahlab-ucla/embGAN) ## Code/Software This data was acquired for use with our embGAN codebase ([https://github.com/shahlab-ucla/embGAN)](https://github.com/shahlab-ucla/embGAN) but can easily be used to train other deep learning based pipelines.
DOI: 10.5061/dryad.vmcvdnd0t
title: Data from: Human wildlife conflict in bardia banke complex data

description: The data is about the human-wildlife conflict in Bardia - Banke Complex,
 Nepal. This research was undertaken to investigate the patterns and
 conflict-causing factors of human killing and injury by large mammals
 especially by Asian elephant (Elephas maximus), Common leopard (Panthera
 pardus), and Bengal tiger (Panthera tigris) in the Bardia-Banke Complex of
 western Nepal. We collected human death records and injuries caused by
 wildlife between 2019 and (March) 2023, from the regular monitoring record
 database.
description: # HWC\_BBC\_Data has been uploaded which contains the data about the HWC.
 ## The file has 10 columns 1. Year - In which year the conflict happened.
 2. Season - In which season the conflict happened. 3. Month - In which
 month the conflict happened. 4. Time - Time when the conflict happened. 5.
 Gender - Who was killed male or female (Categorical) 6. AgeGroup -
 Categorical data (Categorized into 4; &lt;14, 16-30, 31-55, Above 55) 7.
 Species - (Species; Elephant, Leopard, Tiger) 8. Impact- What happened,
 killed or injured? 9. Activity - What were they doing while the animal was
 attacked? 10. Distance to the forest edge
 [https://doi.org/10.5061/dryad.vmcvdnd0t](https://doi.org/10.5061/dryad.vmcvdnd0t)
DOI: 10.18739/a2599z305
title: Seasonal soil active layer measurements from a Circumpolar Active Layer monitoring (CALM) grid, R56, Oktyabrskyy, West Siberia 2013-2020. Arctic Data Center.

description: The Circumpolar Active Layer Monitoring (CALM) program represents the only coordinated program providing collection, standardization, open access, and dissemination of active-layer data world-wide. Widespread, systematic changes in the thickness of the active layer could have profound effects on the flux of greenhouse gases, on the human infrastructure in cold regions, and on landscape and hydrologic processes. It is therefore critical that observational and analytical procedures continue over decadal periods to assess trends and detect cumulative, long-term changes. This dataset contains active-layer observations conducted by the CALM program since the 1990s, supported by a series of National Science Foundation (NSF) awards. CALM program is an integral part of the Global Terrestrial Network for Permafrost.
 CALM 2020 data are significantly reduced due to pandemic-related travel restrictions. Available 2020 data are limited in terms of extent, and observations were not as controlled as previous years in terms of measurement timing or method, and therefore should be treated with caution.
DOI: 10.18739/a2930nw3z
title: Seasonal soil active layer measurements from a Circumpolar Active Layer monitoring (CALM) grid, R29b, Bykovsky (Lena delta) (alas), Central Siberia 2004-2020. Arctic Data Center

description: The Circumpolar Active Layer Monitoring (CALM) program represents the only coordinated program providing collection, standardization, open access, and dissemination of active-layer data world-wide. Widespread, systematic changes in the thickness of the active layer could have profound effects on the flux of greenhouse gases, on the human infrastructure in cold regions, and on landscape and hydrologic processes. It is therefore critical that observational and analytical procedures continue over decadal periods to assess trends and detect cumulative, long-term changes. This dataset contains active-layer observations conducted by the CALM program since the 1990s, supported by a series of National Science Foundation (NSF) awards. CALM program is an integral part of the Global Terrestrial Network for Permafrost.
 CALM 2020 data are significantly reduced due to pandemic-related travel restrictions. Available 2020 data are limited in terms of extent, and observations were not as controlled as previous years in terms of measurement timing or method, and therefore should be treated with caution.
DOI: 10.18739/a2dv1cp7s
title: Seasonal soil active layer measurements from a Circumpolar Active Layer monitoring (CALM) grid, R57, Labytnangy, West Siberia 2013-2020. Arctic Data Center.

description: The Circumpolar Active Layer Monitoring (CALM) program represents the only coordinated program providing collection, standardization, open access, and dissemination of active-layer data world-wide. Widespread, systematic changes in the thickness of the active layer could have profound effects on the flux of greenhouse gases, on the human infrastructure in cold regions, and on landscape and hydrologic processes. It is therefore critical that observational and analytical procedures continue over decadal periods to assess trends and detect cumulative, long-term changes. This dataset contains active-layer observations conducted by the CALM program since the 1990s, supported by a series of National Science Foundation (NSF) awards. CALM program is an integral part of the Global Terrestrial Network for Permafrost.
 CALM 2020 data are significantly reduced due to pandemic-related travel restrictions. Available 2020 data are limited in terms of extent, and observations were not as controlled as previous years in terms of measurement timing or method, and therefore should be treated with caution.
DOI: 10.18739/a2jm23h21
title: Seasonal soil active layer measurements from a Circumpolar Active Layer monitoring (CALM) grid, R58 Erkuta, West Siberia 2017-2020. Arctic Data Center

description: The Circumpolar Active Layer Monitoring (CALM) program represents the only coordinated program providing collection, standardization, open access, and dissemination of active-layer data world-wide. Widespread, systematic changes in the thickness of the active layer could have profound effects on the flux of greenhouse gases, on the human infrastructure in cold regions, and on landscape and hydrologic processes. It is therefore critical that observational and analytical procedures continue over decadal periods to assess trends and detect cumulative, long-term changes. This dataset contains active-layer observations conducted by the CALM program since the 1990s, supported by a series of National Science Foundation (NSF) awards. CALM program is an integral part of the Global Terrestrial Network for Permafrost.
 CALM 2020 data are significantly reduced due to pandemic-related travel restrictions. Available 2020 data are limited in terms of extent, and observations were not as controlled as previous years in terms of measurement timing or method, and therefore should be treated with caution.