cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25378/janelia.13114352.v2
title: Isotropic 3D electron microscopy reference data of wild-type, immortalized breast cancer cell, SUM159 (jrc_sum159-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Sample</b>: Wild-type SUM-159 cell<b>Sample description</b>: Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structure with nanometer resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations inasmuch as they only visualize a single slice or a relatively small volume of the cell, respectively. Here, we overcome these limitations by long-term imaging whole cells and tissues via the enhanced Focus Ion Beam Scanning Electron Microscopy (FIB-SEM) platform in high resolution mode with month-long acquisition duration. We use this approach to generate reference 3D image data sets at 4-nm isotropic voxels. Together with subsequent segmentation, we hope to create a reference library to explore comprehensive quantification of whole cells and all their constituents, thus addressing questions related to cell identities, cell morphologies, cell-cell interactions, as well as intracellular organelle organization and structure.<b>Protocol</b>: High pressure freezing, freeze-substitution resin embedding with 2% OsO4 0.1% UA 3% H2O in Acetone, resin embedding in Eponate 12.<b>Contributions</b>: Sample provided by Jeeyun Chung, Tobias Walther and Bob Farese (Harvard U.), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).<b>Acquisition ID</b>: jrc_sum159-1<b>Final voxel size (nm)</b>: 4.00 x 4.00 x 4.56 (X, Y, Z)<b>Dimensions (µm)</b>: 64 x 11 x 35 (X, Y, Z)<b>Imaging start date:</b> 2017-11-21<b>Imaging duration (days)</b>: 17<b>Primary energy (eV)</b>: 1200<b>Imaging current (nA)</b>: .25<b>Scanning speed (MHz)</b>: .2<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-1<br><b>Publication:</b> Xu et al., 2021
DOI: 10.15468/dl.4w98w2
title: Occurrence Download

description: A dataset containing 36448 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Streptomyces Waksman & Henrici, 1943"
 ]
}

 The dataset includes 36448 records from 425 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015592-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xnw8x8
title: Occurrence Download

description: A dataset containing 7027 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-76.01295 6.83174,-76.27973 6.26851,-76.67992 4.47567,-76.34643 2.54517,-75.14588 1.8787,-72.94487 2.74505,-71.44418 3.77717,-71.64428 5.90375,-72.87818 7.09655,-74.6123 7.75793,-76.01295 6.83174))",
 "HasGeospatialIssue is false",
 "TaxonKey is Porphyriops melanops",
 "Year 2000-2025"
 ]
}

 The dataset includes 7027 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003030-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f4nkr5
title: Occurrence Download

description: A dataset containing 739070 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Ecuador",
 "Geometry POLYGON((-78.66245 -3.4636,-77.36031 -2.52974,-76.95257 -1.58273,-78.04427 -0.88562,-79.53055 -1.13553,-78.66245 -3.4636))"
 ]
}

 The dataset includes 739070 records from 655 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003025-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zcdefx
title: Occurrence Download

description: A dataset containing 24178 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Ecuador",
 "Geometry POLYGON((-78.5231 -1.19519,-79.18556 -1.54369,-79.15266 -2.60459,-78.42894 -2.92739,-77.48317 -2.59843,-76.96505 -2.26124,-77.18632 -1.59314,-77.84707 -1.20375,-78.5231 -1.19519))",
 "TaxonKey is Amphibia"
 ]
}

 The dataset includes 24178 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003032-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4kp49c
title: Occurrence Download

description: A dataset containing 33080789 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 1910-1955"
 ]
}

 The dataset includes 33080789 records from 5938 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003028-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j3c58j
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Syrmaticus ellioti",
 "Country is Chinese Taipei",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049101-250811113504898/datasets/export for details.
DOI: 10.15468/dl.nzgfk3
title: Occurrence Download

description: A dataset containing 14061 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Vaccinium vitis-idaea)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is North America"
 ]
}

 The dataset includes 14061 records from 127 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002158-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9wjfqq
title: Occurrence Download

description: A dataset containing 6348 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Abrodictyum obscurum, Abrophyllum ornans, Abrotanella forsteroides, Abrotanella scapigera, Acacia acanthoclada acanthoclada, Acacia acuminata, Acacia aemula muricata, Acacia alata, Acacia assimilis atroviridis)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6348 records from 113 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002159-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/rw8bpx9drv
title: Data for: Effect of toluene on siloxane biodegradation and microbial communities in biofilters

description: This repository contains the raw and processed experimental data associated with the research article "Effect of toluene on siloxane biodegradation and microbial communities in biofilters".
The study investigates the biological removal of volatile methyl siloxanes (VMS), specifically octamethyltrisiloxane (L3) and octamethylcyclotetrasiloxane (D4), from a gas stream mimicking landfill biogas. The data compares the performance of two biofilters (BFs) packed with different materials: a mixture of wood chips and compost (WC) versus expanded perlite (PER). Furthermore, the dataset covers the effect of co-treating an aromatic compound (Toluene) on VMS biodegradation efficiency and the resulting shifts in microbial communities.
DOI: 10.17632/rw8bpx9drv.1
title: Data for: Effect of toluene on siloxane biodegradation and microbial communities in biofilters

description: This repository contains the raw and processed experimental data associated with the research article "Effect of toluene on siloxane biodegradation and microbial communities in biofilters".
The study investigates the biological removal of volatile methyl siloxanes (VMS), specifically octamethyltrisiloxane (L3) and octamethylcyclotetrasiloxane (D4), from a gas stream mimicking landfill biogas. The data compares the performance of two biofilters (BFs) packed with different materials: a mixture of wood chips and compost (WC) versus expanded perlite (PER). Furthermore, the dataset covers the effect of co-treating an aromatic compound (Toluene) on VMS biodegradation efficiency and the resulting shifts in microbial communities.
DOI: 10.57760/sciencedb.35998
title: Genotype data from 200 sequencing samples
title: Genotype data from 200 sequencing samples

description: The SNP genotype data of 200 soybean varieties includes positions, variant information, and the genotypes of each sample
description: The SNP genotype data of 200 soybean varieties includes positions, variant information, and the genotypes of each sample
DOI: 10.17632/z7ych8wmg5
title: Dry–wet cycles induce metal cation leaching to govern soil aggregate stability via altering soil internal forces

description: Research hypothesis
We hypothesised that metal cation leaching induced by dry-wet cycles can affect soil internal force, thereby reducing aggregate stability, and specific ion effects playing critical roles throughout.

In this study, both drainage and non-drainage conditions were employed to elucidate the mechanisms of metal cation leaching on soil aggregate stability via altering soil internal forces during dry-wet cycles. Overall, our findings indicate that soil aggregate stability decreased as the metal cation are leached during dry-wet cycles. Specifically, metal cation leaching reduces the quantity of metal cations adsorbed onto soil colloid surfaces, thereby enhancing the net force between soil particles and consequently decreasing aggregate stability during dry-wet cycles. Repeated dry-wet cycles lead to the stabilization of metal cation leaching and the net forces of soil internal forces, which directly govern soil aggregate stability. Additionally, significant specific ion effects on soil aggregate stability were observed during dry-wet cycles, mediated by cationic non-classical polarization that alters soil internal forces. In summary, metal cation leaching affects soil internal force, thereby reducing aggregate stability during dry-wet cycles, with specific ion effects playing critical roles throughout.
DOI: 10.17632/z7ych8wmg5.1
title: Dry–wet cycles induce metal cation leaching to govern soil aggregate stability via altering soil internal forces

description: Research hypothesis
We hypothesised that metal cation leaching induced by dry-wet cycles can affect soil internal force, thereby reducing aggregate stability, and specific ion effects playing critical roles throughout.

In this study, both drainage and non-drainage conditions were employed to elucidate the mechanisms of metal cation leaching on soil aggregate stability via altering soil internal forces during dry-wet cycles. Overall, our findings indicate that soil aggregate stability decreased as the metal cation are leached during dry-wet cycles. Specifically, metal cation leaching reduces the quantity of metal cations adsorbed onto soil colloid surfaces, thereby enhancing the net force between soil particles and consequently decreasing aggregate stability during dry-wet cycles. Repeated dry-wet cycles lead to the stabilization of metal cation leaching and the net forces of soil internal forces, which directly govern soil aggregate stability. Additionally, significant specific ion effects on soil aggregate stability were observed during dry-wet cycles, mediated by cationic non-classical polarization that alters soil internal forces. In summary, metal cation leaching affects soil internal force, thereby reducing aggregate stability during dry-wet cycles, with specific ion effects playing critical roles throughout.
DOI: 10.3886/e244530
title: College of Nursing Sciences, Ikot-Ekpene, Akwa Ibom State, 2026/2027 ADMISSION FORM is out call 09031383306 DR MR JAMES (+249031383306) for TRANSCRIPT Collection School Admin Line 09031383306 To apply Also 2026/2027 Nursing form

description: College of Nursing Sciences, Ikot-Ekpene, Akwa Ibom State, 2026/2027 ADMISSION FORM is out call 09031383306 DR MR JAMES (+249031383306) for TRANSCRIPT Collection School Admin Line 09031383306 To apply Also 2026/2027 Nursing form
DOI: 10.5281/zenodo.18323764
title: PDBBind_PLIP
DOI: 10.5281/zenodo.18323765
title: PDBBind_PLIP
DOI: 10.5281/zenodo.18324414
title: Multi-species detection results by FastSTR
DOI: 10.5281/zenodo.18324415
title: Multi-species detection results by FastSTR
DOI: 10.17632/f6vszhy5rn
title: amine dehydrogenase

description: Amine dehydrogenases (AmDHs) catalyze the reductive amination of ketones with inorganic ammonia as the amino donor, offering an attractive method for the synthesis of chiral amines. Because the wild-type AmDHs show low activity and limited substrate scope, most synthetic applications involve the engineered AmDHs from L-amino acid dehydrogenases. However, they continue the stereoselectivity of L-amino acid dehydrogenases. In this study, using 4-phenylbutan-2-one (1a) as the model substrate, a (R)-enantiospecific AmDH (M0) derived from L-amino acid dehydrogenase was converted to (S)-enantioselective enzymes (M2-M7) through several rounds of semi-rational iterative mutations. Among the variants, M7 achieved 98% conversion and 95% ee (S) for 1a, and its catalytic efficiency (kcat/Km) is 20 times that of M0. Variant M6-1 exhibits excellent stereoselectivity (&gt;99% ee) towards para-substituted aralkylamines. The substrate spectra of these variants involve 49 aryl alkyl ketones. Molecular docking and dynamics simulations provided insights into the role of mutations in substrate recognition and stereoselective control, revealing that the mutations resulted in movement of the benzene ring and methyl group of 1c, that facilitated the Re-face of iminium intermediate toward the coenzyme, thus achieving the enantioselectivity inversion. This study is the first to create a highly active engineered AmDH using L-amino acid dehydrogenases as the template for the direct synthesis of (S)-amines and (R)-β-amino alcohols.
DOI: 10.17632/f6vszhy5rn.1
title: amine dehydrogenase

description: Amine dehydrogenases (AmDHs) catalyze the reductive amination of ketones with inorganic ammonia as the amino donor, offering an attractive method for the synthesis of chiral amines. Because the wild-type AmDHs show low activity and limited substrate scope, most synthetic applications involve the engineered AmDHs from L-amino acid dehydrogenases. However, they continue the stereoselectivity of L-amino acid dehydrogenases. In this study, using 4-phenylbutan-2-one (1a) as the model substrate, a (R)-enantiospecific AmDH (M0) derived from L-amino acid dehydrogenase was converted to (S)-enantioselective enzymes (M2-M7) through several rounds of semi-rational iterative mutations. Among the variants, M7 achieved 98% conversion and 95% ee (S) for 1a, and its catalytic efficiency (kcat/Km) is 20 times that of M0. Variant M6-1 exhibits excellent stereoselectivity (&gt;99% ee) towards para-substituted aralkylamines. The substrate spectra of these variants involve 49 aryl alkyl ketones. Molecular docking and dynamics simulations provided insights into the role of mutations in substrate recognition and stereoselective control, revealing that the mutations resulted in movement of the benzene ring and methyl group of 1c, that facilitated the Re-face of iminium intermediate toward the coenzyme, thus achieving the enantioselectivity inversion. This study is the first to create a highly active engineered AmDH using L-amino acid dehydrogenases as the template for the direct synthesis of (S)-amines and (R)-β-amino alcohols.
DOI: 10.17632/wsn3zcdvdg
title: Wind-Preconditioned Water Erosion on Typical Aeolian Sandy Soil

description: The data is derived from simulated wind-water erosion experiments conducted on typical aeolian sandy soil. The experimental design incorporates three key variables: preceding wind speed (0, 7, 9, 11 m/s), rainfall intensity (60, 90, 120 mm/h), and slope (10°, 15°). Based on experimental observations, hydrodynamic parameters including unit runoff power and shear force were calculated, alongside the enrichment ratio and mean weight diameter to characterize sediment sorting and transport. These metrics are utilized to reveal soil loss mechanisms under varying erosive dynamic conditions.
DOI: 10.17632/wsn3zcdvdg.1
title: Wind-Preconditioned Water Erosion on Typical Aeolian Sandy Soil

description: The data is derived from simulated wind-water erosion experiments conducted on typical aeolian sandy soil. The experimental design incorporates three key variables: preceding wind speed (0, 7, 9, 11 m/s), rainfall intensity (60, 90, 120 mm/h), and slope (10°, 15°). Based on experimental observations, hydrodynamic parameters including unit runoff power and shear force were calculated, alongside the enrichment ratio and mean weight diameter to characterize sediment sorting and transport. These metrics are utilized to reveal soil loss mechanisms under varying erosive dynamic conditions.
DOI: 10.17632/snzb5g6ddy
title: APCEM-Enhanced Cervical Cytology Image Dataset

description: A meticulously determined compilation of 4,253 cytology of cervical Pap smear images, representing multiple phases of epithelial abnormalities along with normal cellular conditions, makes up the APCEM-Enhanced Cervical Cytology Image dataset. The dataset is intended to assist studies in cytological image analysis, medical image modification, and cervical cancer screening. In order to enhance image quality while preserving cytological structure fidelity and diagnostic significance, all images have been manipulated using the approach recommended APCEM (Adaptive Parameterized Cytology Enhancement Model).

Research Hypothesis

Pap smear images visual quality and structural clarity can be significantly improved by carefully constructed traditional image enhancement techniques that adjust to cytological image properties without sacrificing diagnostic morphology. Improved interpretability and higher-quality inputs for subsequent analytical and computational studies in cervical cancer research are made possible by such upgrading.

What the Data Shows

There are 4,253 cervical cytology images in the collection that were obtained under standard laboratory imaging circumstances. It comprises six cytological broad categories that are clinically significant: ASCH (119 images), ASCUS (340 images), HSIL (1,300 images), LSIL (1,241 images), NILM (779 images), and SCC (474 images). Realistic variations in staining intensity, cellular density, overlap, background artifacts, and disease severity are displayed in the images, which mirror the features of actual cytology slides.

Notable Features

• Standardized magnitude of cytology sights after APCEM preprocessing.
• Six cytological classes brought about with the Bethesda System.
• Modern adaptive restructuring pipeline without optimization based on learning.
• Medical imaging applications such as contrast enhancement and noise mitigation.
• Preservation of cytoplasmic equipment, cellular structure, and the edges of cells.

How to Interpret and Use the Data

The APCEM classical adaptive image enhancement pipeline, which involves resolution normalization, luminance-based contrast enhancement in LAB color space, edge-preserving non-local means denoising, and rough masking for structural refinement, was employing to improve the images in the APCEM-Enhanced Cervical Cytology Image dataset. While avoiding artificial feature amplification, the augmentation optimizes cellular visibility and contrast-to-noise ratio. The dataset can be deployed as a standardized preprocessing resource for cervical cytology research, as well as for statistical image analysis, enhancement benchmarking, and visual clarity evaluation.

Potential Applications

• Evaluation of cervical cytology image quality and augmentation.
• Comparing traditional methods for improving medical images.
• Foundational preprocessing for cervical cancer screening research.
• Academic studies in computer vision, medical imaging, and cytopathology.
DOI: 10.17632/snzb5g6ddy.2
title: APCEM-Enhanced Cervical Cytology Image Dataset

description: A meticulously determined compilation of 4,253 cytology of cervical Pap smear images, representing multiple phases of epithelial abnormalities along with normal cellular conditions, makes up the APCEM-Enhanced Cervical Cytology Image dataset. The dataset is intended to assist studies in cytological image analysis, medical image modification, and cervical cancer screening. In order to enhance image quality while preserving cytological structure fidelity and diagnostic significance, all images have been manipulated using the approach recommended APCEM (Adaptive Parameterized Cytology Enhancement Model).

Research Hypothesis

Pap smear images visual quality and structural clarity can be significantly improved by carefully constructed traditional image enhancement techniques that adjust to cytological image properties without sacrificing diagnostic morphology. Improved interpretability and higher-quality inputs for subsequent analytical and computational studies in cervical cancer research are made possible by such upgrading.

What the Data Shows

There are 4,253 cervical cytology images in the collection that were obtained under standard laboratory imaging circumstances. It comprises six cytological broad categories that are clinically significant: ASCH (119 images), ASCUS (340 images), HSIL (1,300 images), LSIL (1,241 images), NILM (779 images), and SCC (474 images). Realistic variations in staining intensity, cellular density, overlap, background artifacts, and disease severity are displayed in the images, which mirror the features of actual cytology slides.

Notable Features

• Standardized magnitude of cytology sights after APCEM preprocessing.
• Six cytological classes brought about with the Bethesda System.
• Modern adaptive restructuring pipeline without optimization based on learning.
• Medical imaging applications such as contrast enhancement and noise mitigation.
• Preservation of cytoplasmic equipment, cellular structure, and the edges of cells.

How to Interpret and Use the Data

The APCEM classical adaptive image enhancement pipeline, which involves resolution normalization, luminance-based contrast enhancement in LAB color space, edge-preserving non-local means denoising, and rough masking for structural refinement, was employing to improve the images in the APCEM-Enhanced Cervical Cytology Image dataset. While avoiding artificial feature amplification, the augmentation optimizes cellular visibility and contrast-to-noise ratio. The dataset can be deployed as a standardized preprocessing resource for cervical cytology research, as well as for statistical image analysis, enhancement benchmarking, and visual clarity evaluation.

Potential Applications

• Evaluation of cervical cytology image quality and augmentation.
• Comparing traditional methods for improving medical images.
• Foundational preprocessing for cervical cancer screening research.
• Academic studies in computer vision, medical imaging, and cytopathology.