cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24843702.v1
title: When Grinnellian generalist species seem to be more sensitive to altered habitats than specialists: the case of Orthoptera communities settled in coastal dunes

description: Numerous examples documented that species generalists for habitats are less sensitive to altered environment than specialists. However, in arid environments, an example indicated an opposite trend due to special adaptive features of organisms. We tested this hypothesis in the case of grasshopper communities, settled in the coastal dunes of northeast Algeria, as several aspects of dunes constitute stressful conditions resembling those of deserts. To define the dune-specific grasshoppers (specialists) and the dune non-specific ones (generalists), we applied the indicator value index to monthly samplings conducted in four coastal dune sites and 12 other sites of grasslands, fallow lands and scrublands in the same area. The degree of disturbance of each coastal dune site was deduced from the alteration of plant cover and richness. We investigated the relation between the specialist and generalist richness and abundance with the degree of perturbation using linear regressions. Results showed contrasting patterns for specialist and generalist grasshoppers: both abundance and richness of the generalists significantly decrease with an increasing degree of perturbation, while specialists show little to no changes. The higher resistance of specialist grasshoppers over generalists toward disturbance was not linked to the plant dune-specialists or generalists. This study is one of very few illustrating the relative resistance of specialized species toward disturbance.
DOI: 10.6084/m9.figshare.24843663
title: Beyond MD17: The Reactive xxMD Dataset

description: The xxMD (Extended Excited-state Molecular Dynamics) dataset is a comprehensive collection of non-adiabatic trajectories encompassing several photo-sensitive molecules. This dataset challenges existing Neural Force Field (NFF) models with broader nuclear configuration spaces that span reactant, transition state, product, and conical intersection regions, making it more chemically representative than its contemporaries.Key Features:Based on non-adiabatic dynamics, involving larger nuclear configuration space compared to previous datasets.Contains trajectories from four photo-sensitive molecules, each starting from an electronic excited state.Energies and forces computed using both multireference wave function theory and density functional theory.Samples reactant, transition state, product, and conical intersection regions of potential energy surfaces.Content:<b>xxMD-CASSCF</b>: This subset contains potential energies and forces for the first three electronic states of four molecules: azobenzene, dithiopehene, malonaldehyde, and stilbene.<b>xxMD-DFT</b>: Ground-state energies and forces re-computed using the M06 exchange-correlation functional for the trajectories in the xxMD-CASSCF subset.GitHub Repo: https://github.com/zpengmei/xxMD
DOI: 10.6084/m9.figshare.24843663.v1
title: Beyond MD17: The Reactive xxMD Dataset

description: The xxMD (Extended Excited-state Molecular Dynamics) dataset is a comprehensive collection of non-adiabatic trajectories encompassing several photo-sensitive molecules. This dataset challenges existing Neural Force Field (NFF) models with broader nuclear configuration spaces that span reactant, transition state, product, and conical intersection regions, making it more chemically representative than its contemporaries.Key Features:Based on non-adiabatic dynamics, involving larger nuclear configuration space compared to previous datasets.Contains trajectories from four photo-sensitive molecules, each starting from an electronic excited state.Energies and forces computed using both multireference wave function theory and density functional theory.Samples reactant, transition state, product, and conical intersection regions of potential energy surfaces.Content:<b>xxMD-CASSCF</b>: This subset contains potential energies and forces for the first three electronic states of four molecules: azobenzene, dithiopehene, malonaldehyde, and stilbene.<b>xxMD-DFT</b>: Ground-state energies and forces re-computed using the M06 exchange-correlation functional for the trajectories in the xxMD-CASSCF subset.GitHub Repo: https://github.com/zpengmei/xxMD
DOI: 10.5281/zenodo.10250220
title: Synthetic IAM with latent diffusion models

description: SyntheticHTR: Handwritten Text Image Synthesis based on Latent Diffusion Models
DOI: 10.5281/zenodo.10250221
title: Synthetic IAM with latent diffusion models

description: Synthetic dataset of IAM for Handwritten text Generation, generated with latent diffusion models.
DOI: 10.5281/zenodo.10250439
title: Synthetic IAM with latent diffusion models

description: Synthetic dataset of IAM for Handwritten text Generation, generated with latent diffusion models.
DOI: 10.5281/zenodo.10392228
title: Synthetic IAM with latent diffusion models

description: SyntheticHTR: Handwritten Text Image Synthesis based on Latent Diffusion Models
DOI: 10.5281/zenodo.10392946
title: Synthetic IAM with latent diffusion models

description: SyntheticHTR: Handwritten Text Image Synthesis based on Latent Diffusion Models
DOI: 10.6073/pasta/4835fff2b96f16677ab1abb9c46db34b
title: Water quality data for Green Lakes Valley, 2000 - ongoing.

description: This dataset contains water quality measurements made on Green Lakes 1, 2, 3, 4, 5, and Lake Albion. Green Lake 4 was initially sampled in 2000 and is ongoing. Ongoing sampling of Green Lakes 1 was started in 2014 and ongoing sampling of Lake Albion was started in 2016. Water samples were collected for analysis of chlorophyll a and nutrient analysis (which is available in glvwatsolu.dm.data) and field measurements for pH, temperature, specific conductivity, dissolved oxygen (DO), % saturation, secchi depth, PAR. Secchi depth is recorded at the 0m row however it is a measurement of depth and so the units are meters. Most samples were collected between 0800 and 1200 MST. The first sampling date each summer occurs shortly after the ice had melted. Data are collected from an inflatable raft at the point of deepest depth or from the lake inlet and outlet when surface flow is present. The majority of chlorophyll-a the measurements were taken at the surface (0m), the metalimnion (3m), and the hypolimnion nine (usually 8-11m). However, additional measurements were taken for side projects of the long-term dataset during several of the years and are included in this dataset. Water samples from the metalimnion or hypolimnion were collected using a Van Dorne sampler, and surface samples were collected as grab samples from the water column surface, the inlet and outlet. Field measurements were conducted using a YSI either DO or multiple probe meter (2014-2017, YSI MPS 556)(2018-ongoing, YSI ProPlus) and a Li-Cor meter with a quantum sensor. Chlorophyll-a was extracted from filtered samples and absorbance was measured before and after acidification to quantify chlorophyll a concentration.
DOI: 10.6084/m9.figshare.24843732
title: Genetic relatedness can alter the strength of plant-soil feedbacks

description: <b>Premise: </b>Intraspecific variation may play a key role in understanding the relationships between plants and their interactions with soil microbial communities. The soil microbes of individual plants can generate intraspecific variation in responsiveness of offspring, yet remains much less studied. To address this need, we explored how seedling relatedness to established <i>Solidago altissima</i> clones altered the plant-soil feedbacks that they experienced.<b>Methods: </b>Seedlings of known parentage were generated from a series of 24 clones grown in a common garden. Seedlings from these crosses were inoculated with soils from maternal, paternal, or unrelated clones and their performance compared to sterilized control inocula.<b>Results: </b>We found that soil inocula generated from <i>S. altissima</i> clones had an overall negative effect on seedling biomass. Furthermore, seedlings inoculated with maternal or paternal soils tended to experience larger negative effects than seedlings inoculated with unrelated soils. However, there was much variation among individual crosses, with not all responding to relatedness.<b>Conclusions: </b>Our data argue that genetic relatedness to the plant generating the soil microbial community may cause differential impacts on establishing seedlings, encouraging the regeneration of non-kin adjacent to established clones. Such intraspecific variation represents a potentially important source of heterogeneity in plant-soil feedbacks with implications for maintaining population genetic diversity.
DOI: 10.6084/m9.figshare.24843732.v1
title: Genetic relatedness can alter the strength of plant-soil feedbacks

description: <b>Premise: </b>Intraspecific variation may play a key role in understanding the relationships between plants and their interactions with soil microbial communities. The soil microbes of individual plants can generate intraspecific variation in responsiveness of offspring, yet remains much less studied. To address this need, we explored how seedling relatedness to established <i>Solidago altissima</i> clones altered the plant-soil feedbacks that they experienced.<b>Methods: </b>Seedlings of known parentage were generated from a series of 24 clones grown in a common garden. Seedlings from these crosses were inoculated with soils from maternal, paternal, or unrelated clones and their performance compared to sterilized control inocula.<b>Results: </b>We found that soil inocula generated from <i>S. altissima</i> clones had an overall negative effect on seedling biomass. Furthermore, seedlings inoculated with maternal or paternal soils tended to experience larger negative effects than seedlings inoculated with unrelated soils. However, there was much variation among individual crosses, with not all responding to relatedness.<b>Conclusions: </b>Our data argue that genetic relatedness to the plant generating the soil microbial community may cause differential impacts on establishing seedlings, encouraging the regeneration of non-kin adjacent to established clones. Such intraspecific variation represents a potentially important source of heterogeneity in plant-soil feedbacks with implications for maintaining population genetic diversity.
DOI: 10.5281/zenodo.10250458
title: Synthetic IMGUR5k dataset with latent diffusion models

description: SyntheticHTR: Handwritten Text Image Synthesis based on Latent Diffusion Models
DOI: 10.5281/zenodo.10250459
title: Synthetic IMGUR5k dataset with latent diffusion models

description: Regenerated partial IMGUR5k dataset using Latent Diffusion Models
DOI: 10.5281/zenodo.10392963
title: Synthetic IMGUR5k dataset with latent diffusion models

description: SyntheticHTR: Handwritten Text Image Synthesis based on Latent Diffusion Models
DOI: 10.5281/zenodo.10392982
title: Synthetic GW dataset with latent diffusion models

description: SyntheticHTR: Handwritten Text Image Synthesis based on Latent Diffusion Models
DOI: 10.5281/zenodo.10250451
title: Synthetic GW dataset with latent diffusion models

description: SyntheticHTR: Handwritten Text Image Synthesis based on Latent Diffusion Models
DOI: 10.5281/zenodo.10250452
title: Synthetic GW dataset with latent diffusion models

description: Synthetic regenerated George Washington dataset using Latent Diffusion Models
DOI: 10.21227/7hnq-dc32
title: PdfRep

description: With the widespread use of the Portable Document Format (PDF), it’s increasingly becoming a target for malware, highlighting the need for effective detection solutions. In recent years, machine learning-based methods for PDF malware detection have grown in popularity. However, the effectiveness of ML models is closely related to the quality of the training datasets. In this research, we investigated two widely used PDF malware datasets: Contagio and CIC. We found biases and representativeness issues that could affect the reliability and applicability of models built on them. Our statistical analysis revealed marked difference between these datasets and PDF malware samples from VirusTotal, as well as benign PDFs from Govdocs, pointing to the necessity for more representative datasets in PDF malware research.. To address this gap, we introduce a novel dataset: PdfRep. Our findings demonstrate that PdfRep outperforms both CIC and Contagio across various evaluation metrics. The main contribution of this paper is the introduction of PdfRep, a new PDF malware dataset that overcomes the limitations of representativeness in existing datasets. This enhancement substantially increases the accuracy of PDF malware detection models and holds promise for advancing the field of PDF malware detection research.
DOI: 10.5281/zenodo.8062340
title: Reference transcriptome for the siphonophore Marrus sp.

description: Long read--PacBio IsoSeq--reference transcriptome for the siphonophore Marrus sp.
DOI: 10.5281/zenodo.10378755
title: Data and analysis code

description: Data and analysis code for the paper 'Neuronal tuning to threat exposure remains stable in the mouse prefrontal cortex over multiple days' (PLOS Biology).

This repository contains:



The full dataset: - dataset.py

 Main analysis code: fig1-fig4.py and supplemental1-supplemental7.py

Function code: glm_to_predict_speed_from_neuronal_activity.py, glm_tst_50_neurons_no_iterations.py, Graphs.py, manifold.py, prediction.py, rate_coding.py, statistics_test.py, time_functions.py, time_locked_functions.py, transient.py

Source data for figures: - source_data.xls


The function code is normally stored in a folder called function.

 

Structure of the dataset:

The dataset is a python dictionary with 3 levels. 

Level 1: Animal ID



'animal294', dict

'animal295', dict

'animal329', dict

'animal337', dict

'animal339', dict

'animal341', dict


Level 2: Recording day



'day1', dict

'day3', dict

'day9', dict


Level 3: Variables



'A', spatial coordinate of extracted neurons, csc_matrix

'assignments':  assignments id of multisession registration, Numpy array

'assignments_filts': assignments id of multisession registration containing only detected neurons, NumPy array

'background_time': boolean array of timepoints when the behavior could not be clearly assigned to either struggle or immobility behavior, NumPy array.

'baseline_speed_bodyparts': dict with multiple NumPy arrays of the animal's speed of various bodyparts during baseline, dict

'baseline_speed_dlc': speed of the animal during baseline averaged for all bodyparts, NumPy array

'fn_baseline': calcium activity during baseline, NumPy array

'fn_tst': calcium activity during tail suspesion, NumPy array

'hemis': The hemisphere of the recording was from, str

'immobility_time': boolean array of timepoints the animal is immobile, NumPy array

'sex': the sex of the animal, str 

'struggle_time': boolean array of timepoints the animal is struggling, Numpy array

'tst_speed_bodyparts': dict with multiple NumPy arrays of the animal's speed of various bodyparts during tail suspension, dict

'tst_speed_dlc': speed of the animal during tail suspension averaged for all bodyparts, NumPy array
DOI: 10.6073/pasta/114a90da00f909622d96175ecfc15378
title: Hubbard Brook Experimental Forest: 15-minute Precipitation Measurements, 2011 - present

description: Beginning in 2011, ten electronic weighing rain gauges were progressively implemented at the Hubbard Brook Experimental Forest to measure precipitation at 15-minute intervals. These data were gathered at the Hubbard Brook Experimental Forest in Woodstock, NH, which is operated and maintained by the USDA Forest Service, Northern Research Station.
DOI: 10.5281/zenodo.10378756
title: Data and analysis code

description: Data and analysis code for the paper 'Neuronal tuning to threat exposure remains stable in the mouse prefrontal cortex over multiple days' (PLOS Biology).

This repository contains:



The full dataset: - dataset.py

 Main analysis code: fig1-fig4.py and supplemental1-supplemental7.py

Function code: glm_to_predict_speed_from_neuronal_activity.py, glm_tst_50_neurons_no_iterations.py, Graphs.py, manifold.py, prediction.py, rate_coding.py, statistics_test.py, time_functions.py, time_locked_functions.py, transient.py

Source data for figures: - source_data.xls


The function code is normally stored in a folder called function.

 

Structure of the dataset:

The dataset is a python dictionary with 3 levels. 

Level 1: Animal ID



'animal294', dict

'animal295', dict

'animal329', dict

'animal337', dict

'animal339', dict

'animal341', dict


Level 2: Recording day



'day1', dict

'day3', dict

'day9', dict


Level 3: Variables



'A', spatial coordinate of extracted neurons, csc_matrix

'assignments':  assignments id of multisession registration, Numpy array

'assignments_filts': assignments id of multisession registration containing only detected neurons, NumPy array

'background_time': boolean array of timepoints when the behavior could not be clearly assigned to either struggle or immobility behavior, NumPy array.

'baseline_speed_bodyparts': dict with multiple NumPy arrays of the animal's speed of various bodyparts during baseline, dict

'baseline_speed_dlc': speed of the animal during baseline averaged for all bodyparts, NumPy array

'fn_baseline': calcium activity during baseline, NumPy array

'fn_tst': calcium activity during tail suspesion, NumPy array

'hemis': The hemisphere of the recording was from, str

'immobility_time': boolean array of timepoints the animal is immobile, NumPy array

'sex': the sex of the animal, str 

'struggle_time': boolean array of timepoints the animal is struggling, Numpy array

'tst_speed_bodyparts': dict with multiple NumPy arrays of the animal's speed of various bodyparts during tail suspension, dict

'tst_speed_dlc': speed of the animal during tail suspension averaged for all bodyparts, NumPy array
DOI: 10.5281/zenodo.10393018
title: Synthetic Out-Of-Vocabulary IAM dataset with Latent Diffusion Models

description: SyntheticHTR: Handwritten Text Image Synthesis based on Latent Diffusion Models
DOI: 10.5281/zenodo.10393019
title: Synthetic Out-Of-Vocabulary IAM dataset with Latent Diffusion Models

description: SyntheticHTR: Handwritten Text Image Synthesis based on Latent Diffusion Models
DOI: 10.6084/m9.figshare.24768921
title: Quantitative cell morphology reveals fate-coupled regulation of cell size in <i>C. elegans</i> embryo

description: These are the links for accessing the data, code, and software in the paper "Quantitative cell morphology reveals fate-coupled regulation of cell size in <i>C. elegans</i> embryo".1. The <i>ITK-SNAP-CVE</i> in Windows/Mac/Linux versions is deposited on figshare.2. The data of 8 uncompressed wild-type embryos, 4 uncompressed RNAi-treated embryos, and 17 compressed wild-type embryos for <i>ITK-SNAP-CVE</i> is deposited on https://portland-my.sharepoint.com/:f:/g/personal/zelinli6-c_my_cityu_edu_hk/EibhRok6qa9Mh7wLJN7AS90Bv-HZaQhKk9ZvJ6W8xd-5IQ?e=Ug55xP.3. The zipped code for <i>CMap</i> is deposited on: https://portland-my.sharepoint.com/:u:/g/personal/zelinli6-c_my_cityu_edu_hk/Ec3zXvxQnLBJrNLFWcSfaCMBME_JNPYhJWIUCgQfIYmPPA?e=Ma8ben.4. The online code for <i>CMap</i> is deposited on: https://colab.research.google.com/drive/13F2R7HzMra8_CWsaD3FYNnt-GdzD1Tpy?usp=sharing.5. The manually annotated ground truth for training is deposited on: https://portland-my.sharepoint.com/:u:/g/personal/zelinli6-c_my_cityu_edu_hk/EQiw8h6UaPVOkmGmHc3NkSoBTCTzJ73LHhDvCSbSPzuvPw.6. The manually annotated ground truth for evaluation is deposited on: https://portland-my.sharepoint.com/:f:/g/personal/zelinli6-c_my_cityu_edu_hk/EkQ7XeS_kEJBopUIyKhtw4YBX4bNfkneboK13ETN0nfukg?e=nBQGIo.7. The manually annotated ground truth for apoptotic cells is deposited on: https://portland-my.sharepoint.com/:f:/g/personal/zelinli6-c_my_cityu_edu_hk/Emm1F1EnAg1OuxwK0Os22n8B1OrwGT8Sbfs8oYtq46HirQ?e=2XQXeg.Please contact Guoye Guan (guanguoye@gmail.com), Zelin Li (zelinli6-c@my.cityu.edu.hk), and Yiming Ma (20482302@life.hkbu.edu.hk) if there are any questions.
DOI: 10.6084/m9.figshare.24768921.v1
title: Quantitative cell morphology reveals fate-coupled regulation of cell size in <i>C. elegans</i> embryo

description: This is the link for accessing the data, code, and software in the paper "Quantitative cell morphology reveals fate-coupled regulation of cell size in <i>C. elegans</i> embryo".Please contact Guoye Guan (guanguoye@gmail.com), Zelin Li (zelinli6-c@my.cityu.edu.hk), and Yiming Ma (20482302@life.hkbu.edu.hk) if there are any questions.
DOI: 10.5281/zenodo.10393110
title: data
DOI: 10.5281/zenodo.10393111
title: data
DOI: 10.34740/kaggle/dsv/7211609
title: websites_e-comerce
DOI: 10.5281/zenodo.7939137
title: ESIPFed/CRYO-Harmonization: Data for DSJ article

description: Trying to get the DOI thing with Zenodo to work...
DOI: 10.5281/zenodo.7939138
title: ESIPFed/CRYO-Harmonization: Data for DSJ article

description: Trying to get the DOI thing with Zenodo to work...
DOI: 10.6073/pasta/d1465d1fcf7956578b0fb213d025c440
title: Hubbard Brook Experimental Forest: Daily Precipitation Rain Gage Measurements, 1956 - present

description: Precipitation has been measured at the Hubbard Brook Experimental Forest using rain gauges located in or around each watershed since 1956. Three types of rain gauges have been used: standard, mechanical weight recording, and electronic weight recording. Between 1956 and 2014, precipitation was measured weekly at standard gages located at 24 stations in or near gauged watersheds and at the headquarters building. Weight-recording gauges were located at 7 of the 24 stations and capture a continuous strip-chart record. Weekly totals were prorated using daily totals from the nearest recording gauges. Beginning in 2011, electronic weighing rain gauges were implemented to measure 15-minute precipitation. The number of precipitation stations was reduced to 10, when each station was fully converted to an electronic gauge for measuring 15-minute and daily precipitation beginning in 2015. These data were gathered at the Hubbard Brook Experimental Forest in Woodstock, NH, which is operated and maintained by the USDA Forest Service, Northern Research Station.
DOI: 10.5281/zenodo.10393132
title: Supplementary materials for the article entitled 'Metaphor Forces Argument Overtness', published in Linguistics

description: see the publication for details
DOI: 10.5281/zenodo.10393131
title: Supplementary materials for the article entitled 'Metaphor Forces Argument Overtness', published in Linguistics

description: see the publication for details
DOI: 10.6084/m9.figshare.24843867.v1
title: Minakuchi_ephys.mat

description: Data used to generate F1 and F3 in Minakuchi et al
DOI: 10.6084/m9.figshare.24843867
title: Minakuchi_ephys.mat

description: Data used to generate F1 and F3 in Minakuchi et al
DOI: 10.6084/m9.figshare.24843840
title: Native versus non-native dominance after disturbance varies with environmental context

description: These are the data supporting the manuscript submitted to the Journal of Arid Environment with the title Native versus non-native dominance after disturbance varies with environmental context
DOI: 10.5519/qd.ttrhy8op
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (11 records)
DOI: 10.5281/zenodo.10392969
title: 2020-2022-glacier-elevation-change-data-in-Muztag-Ata-and-Western-Nyainqentanglha-from-Pleiades-DEMs

description: This data set provides outlier removed, gap filled elevation change values (in meters) of the glaciers in the Muztagh Ata and Western Nyainqentanglha massif in High Mountain Asia from 2020 to 2022.