cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28074407.v1
title: MJG2403_Mops Minimal Media

description: Time-lapse microscopy of MJG2403 grown on MOPS minimal media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28072376
title: 20240820_TEM

description: Transmission electron microscopy of cells were grown overnight and then sub-cultured into fresh LB, grown at 37°C shaking for 3 hours before being rinsed and then resuspended in TEM buffer and delivered for preparation.Wild-type MG1655 (MJG0001) and <i>ppk relA spoT </i>(MJG1282) were grown in LB at 37°C until exponential phase growth (approximately OD600 0.3–0.5). Cells were then spun down and collected. Remove media from pellet and fixin 1% Osmium tetroxide (148) in 0.1M Sodium Cacodylate BufferpH 7.4 at room temperature in the dark for 1 hour, then 3 times 0.1M Sodium Cacodylate BufferpH 7.4 rinse for 15 minutes each. 1% Low molecular weight tannic acid (Ted Pella Inc) for 20 minutes, 3 times 0.1M Sodium Cacodylate BufferpH 7.4 rinse for 15 minutes each.
DOI: 10.6084/m9.figshare.28072376.v1
title: 20240820_TEM

description: Transmission electron microscopy of cells were grown overnight and then sub-cultured into fresh LB, grown at 37°C shaking for 3 hours before being rinsed and then resuspended in TEM buffer and delivered for preparation.Wild-type MG1655 (MJG0001) and <i>ppk relA spoT </i>(MJG1282) were grown in LB at 37°C until exponential phase growth (approximately OD600 0.3–0.5). Cells were then spun down and collected. Remove media from pellet and fixin 1% Osmium tetroxide (148) in 0.1M Sodium Cacodylate BufferpH 7.4 at room temperature in the dark for 1 hour, then 3 times 0.1M Sodium Cacodylate BufferpH 7.4 rinse for 15 minutes each. 1% Low molecular weight tannic acid (Ted Pella Inc) for 20 minutes, 3 times 0.1M Sodium Cacodylate BufferpH 7.4 rinse for 15 minutes each.
DOI: 10.6084/m9.figshare.28072667.v1
title: MJG0001_MOPS Minimal Media

description: Time-lapse microscopy of MJG2403 grown on MOPS minimal media at 37°C. Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074245
title: MJG2402_MOPS minimal media

description: Time-lapse microscopy of MJG2402 grown on MOPS minimal media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074245.v1
title: MJG2402_MOPS minimal media

description: Time-lapse microscopy of MJG2402 grown on MOPS minimal media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074404
title: MJG2405_LB media

description: Time-lapse microscopy of MJG2405 <i>∆ppk ∆relA ∆spoT </i>grown on LB agarose pads at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28072370
title: Microscopy with no reporters

description: These strains were grown overnight in LB at 37°C, then sub-cultured into fresh LB, grown for 2-3 hours, then plated on LB agarose pads and imaged directly. MJG0001, MJG0224, MJG0226, MJG1090, MJG1116, MJG1282, MJG1287
DOI: 10.6084/m9.figshare.28072370.v1
title: Microscopy with no reporters

description: These strains were grown overnight in LB at 37°C, then sub-cultured into fresh LB, grown for 2-3 hours, then plated on LB agarose pads and imaged directly. MJG0001, MJG0224, MJG0226, MJG1090, MJG1116, MJG1282, MJG1287
DOI: 10.6084/m9.figshare.28074395
title: MJG2404_MOPS minimal media

description: Time-lapse microscopy of MJG2404 grown on MOPS minimal media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074395.v1
title: MJG2404_MOPS minimal media

description: Time-lapse microscopy of MJG2404 grown on MOPS minimal media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.15468/dl.wb9gke
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-84.57345 -37.54616,-26.95198 -37.54616,-26.95198 19.75258,-84.57345 19.75258,-84.57345 -37.54616))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Butis koilomatodon (Bleeker, 1849)"
 ]
}

 The dataset includes 15 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044602-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28071542
title: <i>∆ppk ∆relA ∆spoT RpoB3443</i>

description: Raw data of MJG1581 <i>∆ppk ∆relA ∆spoT RpoB3443 </i>grown on LB.
DOI: 10.6084/m9.figshare.28071542.v1
title: <i>∆ppk ∆relA ∆spoT RpoB3443</i>

description: Raw data of MJG1581 <i>∆ppk ∆relA ∆spoT RpoB3443 </i>grown on LB.
DOI: 10.25934/pr00010852
title: Development of an Artificial Intelligence/Machine Learning (AI/ML) model-based clinical trial simulation platform to better characterize Loss of Ambulation in Duchenne Muscular Dystrophy (DMD)

description: This project aims to develop a new technology to build tools that improve drug development for Duchenne Muscular Dystrophy (DMD). DMD is a rare genetic condition that affects about 1 in every 3,500 male births worldwide. It causes muscle weakness and progressive loss of muscle function, leading to severe disability and significantly shortened life expectancy.

Currently, developing treatments for DMD is challenging, time-consuming, and expensive. This research seeks to address these challenges by creating tools that better predict how DMD progresses over time. These tools will also help researchers understand how safe and effective potential treatments might be, speeding up the development of new therapies and reducing costs.

The research involves designing a computer-based platform using Artificial Intelligence (AI) and Machine Learning (ML). These advanced technologies will analyze existing data to simulate how DMD progresses and how patients might respond to treatments.

The outcomes of this research could transform how treatments for DMD are developed, ultimately improving the lives of individuals living with this condition
DOI: 10.6084/m9.figshare.26999425.v1
title: Hamm and Gray 2024 Figure 5

description: <b>FIG 5 Strains lacking polyP and (p)ppGpp have disrupted cell division.</b><b> </b>(<b>A</b>)<b> </b>Confocal fluorescence time-lapse microscopy of the mutant <i>ppk relA spoT</i><i> </i>FtsZ-GFP (MJG2405) on an LB agarose pad at 37°C. The triple mutant forms two Z-rings in the middle of the cell, releasing a mini cell (red arrows). There are also two Z-rings which form at either pole of a single cell, both functional and releasing a mini cell (white arrows). Example of mini-cell formation and release can be seen in CEM (S4). (<b>B</b>) Confocal fluorescence time-lapse microscopy of the mutant <i>ppk relA</i><i> </i>FtsZ-GFP (MJG2403) on an LB agarose pad at 37°C. This image shows a mutant forming three Z-rings at one pole, and at least 3 at the opposite pole as well, with no Z-rings forming in the middle of the cell, for a total of six Z-rings in a single cell. This cell continued to grow without lysing (<b>Supplemental Video SV5</b>).
DOI: 10.6084/m9.figshare.26999425
title: Hamm and Gray 2024 Figure 5

description: <b>FIG 5 Strains lacking polyP and (p)ppGpp have disrupted cell division.</b><b> </b>(<b>A</b>)<b> </b>Confocal fluorescence time-lapse microscopy of the mutant <i>ppk relA spoT</i><i> </i>FtsZ-GFP (MJG2405) on an LB agarose pad at 37°C. The triple mutant forms two Z-rings in the middle of the cell, releasing a mini cell (red arrows). There are also two Z-rings which form at either pole of a single cell, both functional and releasing a mini cell (white arrows). Example of mini-cell formation and release can be seen in CEM (S4). (<b>B</b>) Confocal fluorescence time-lapse microscopy of the mutant <i>ppk relA</i><i> </i>FtsZ-GFP (MJG2403) on an LB agarose pad at 37°C. This image shows a mutant forming three Z-rings at one pole, and at least 3 at the opposite pole as well, with no Z-rings forming in the middle of the cell, for a total of six Z-rings in a single cell. This cell continued to grow without lysing (<b>Supplemental Video SV5</b>).
DOI: 10.15468/dl.kf828n
title: Occurrence Download

description: A dataset containing 4539 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-87.05179 -34.83552,-25.7128 -34.83552,-25.7128 18.24227,-87.05179 18.24227,-87.05179 -34.83552))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Canis familiaris Linnaeus, 1758"
 ]
}

 The dataset includes 4539 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044603-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9nphvq
title: Occurrence Download

description: A dataset containing 3027 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-88.29096 -34.54101,-26.95198 -34.54101,-26.95198 17.99382,-88.29096 17.99382,-88.29096 -34.54101))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Capra hircus Linnaeus, 1758"
 ]
}

 The dataset includes 3027 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044605-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j2errp
title: Occurrence Download

description: A dataset containing 292155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (Observation.org, Nature data from around the World, Royal Botanic Gardens, Kew - Herbarium Specimens)",
 "Country is one of (Brazil)",
 "Repatriated is true"
 ]
}

 The dataset includes 292155 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044595-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15472/fyostd
title: Caracterización biótica del parque solar Helios Lanceros 19.9 MWac y parque solar Helios Guamo 19.9 MWac - Tolima

description: Este proyecto fue realizado por la empresa Joyco SAS BIC, para el muestreo de epifitas para la realización de la caracterización del Parque Solar Helios Lanceros 19.9 MWac - Tolima y Parque Solar Helios Guamo 19.9 MWac.
description: En este recurso se presentan 32 registros de especímenes de epifitas y mamíferos observados en los municipios de Espinal y Tolima correspondientes al departamento de Tolima durante el mes de abril del 2024. Los especímenes se encuentran agrupados en 11 ordenes y 16 familias de las clases Arthoniomycetes, Bryopsida, Jungermanniopsida, Lecanoromycetes y Mammalia.
DOI: 10.15468/dl.5cdyzk
title: Occurrence Download

description: A dataset containing 5545 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cavia aperea Erxleben, 1777"
 ]
}

 The dataset includes 5545 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044606-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b6neja
title: Occurrence Download

description: A dataset containing 259 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-87.67137 -40.43489,-26.95198 -40.43489,-26.95198 17.40358,-87.67137 17.40358,-87.67137 -40.43489))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cichla kelberi Kullander & Ferreira, 2006"
 ]
}

 The dataset includes 259 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044607-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6073/pasta/ec6e5c76c7ad4e0da0a8d1cec84fa3f5
title: Dissolved inorganic nutrients from NES-LTER Transect cruises, including 4 macro-nutrients from water column bottle samples, ongoing since 2017

description: Dissolved inorganic nutrients are measured from water column bottle samples taken on NES-LTER Transect cruises (ongoing since 2017) and include nitrate + nitrite, ammonium, silicate, and phosphate. Sampling frequency is approximately seasonal. Samples were filtered, frozen, then processed at the Woods Hole Oceanographic Institution’s Nutrient Analytical Facility. Each sample may have up to 2 replicates, indicated by a or b in the data table. These macro-nutrients are analyzed in seawater using a colorimetric assay in which light absorbance is measured versus known standards, and final concentrations are calculated in micromole per liter.
DOI: 10.7294/28024418
title: Data associated with "Early life exposure to the antibiotic tetracycline alters in-hive development of the adult honey bee gut microbiome"

description: These are bacterial 16S rRNA gene amplicon data and metadata from a honey bee experiment examining the impact of the antibiotic tetracycline on in-hive development of the gut microbiome. Honey bees were treated with tetracycline or control sucrose at emergence, marked by treatment, and then placed back in hives. Bees from treatment and control groups were then re-collected from hives at 7 and 14 days following treatment. The dataset includes bacterial 16S amplicon sequences, sequencing information necessary for demultiplexing and using the amplicon data, and total bacterial 16S qPCR data for a subset of the samples.
DOI: 10.7294/28024418.v1
title: Data associated with "Early life exposure to the antibiotic tetracycline alters in-hive development of the adult honey bee gut microbiome"

description: These are bacterial 16S rRNA gene amplicon data and metadata from a honey bee experiment examining the impact of the antibiotic tetracycline on in-hive development of the gut microbiome. Honey bees were treated with tetracycline or control sucrose at emergence, marked by treatment, and then placed back in hives. Bees from treatment and control groups were then re-collected from hives at 7 and 14 days following treatment. The dataset includes bacterial 16S amplicon sequences, sequencing information necessary for demultiplexing and using the amplicon data, and total bacterial 16S qPCR data for a subset of the samples.