cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/x1mzp-x9w37
title: Hylemonella gracilis

description: Session notes:  Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2008-11-01</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Hylemonella gracilis</p>
<strong>Strain:</strong> ATCC 19624</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (0.0°, 0.0°), step: 1°, constant angular increment, dosage: 0.0 eV/Å²,  defocus: 0.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2008-11-01-4_slicer6174.jpg: Flagella motor
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2008-11-01-4/rawdata/</p>08nov01a_b17x1_034.st,  Tilt Series (Pixel Size 0.632 nm), 1.0 GB  
        
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        08nov01a_b17x1_034.rec,  Reconstruction (Pixel Size 1.288 nm), 28.1 MB  
        
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DOI: 10.22002/7pef5-syt54
title: Salmonella typhimurium

description: Session notes: FliL deletion (plus T3SS) Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2011-11-23</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Salmonella typhimurium</p>
<strong>Strain:</strong> serovar Typhimurium str. LT2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: -1.5°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: 5.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2011-11-23-27_slicer7366.jpg: Flagella motor
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2011-11-23-27/rawdata/</p>11nov23a_fliL_0020.st,  Tilt Series (Pixel Size 0.512 nm), 710.2 MB  
        
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        11nov23a_fliL_0020.rec,  Reconstruction (Pixel Size 1.036 nm), 412.9 MB  
        
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DOI: 10.22002/4wp1x-daj92
title: Vibrio fischeri

description: Session notes: Vibrio fischeri flgP-deletion flagella, binned 4x total then filtered 0.28 (= 4.6nm resolution cutoff) Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2011-12-18</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Vibrio fischeri</p>
<strong>Strain:</strong> ES114</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: 10.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2011-12-18-3_slicer6390.jpg: Unknown filament mba2011-12-18-3_slicer6391.jpg: Unknown filament
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2011-12-18-3/rawdata/</p>11dec18a_DflgPVFisheri_0020.st,  Tilt Series (Pixel Size 0.632 nm), 1.1 GB  
        
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        11dec18a_DflgPVFisheri_0020.rec,  Reconstruction (Pixel Size 0.644 nm), 204.2 MB  
        
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DOI: 10.15468/dl.k5wdad
title: Occurrence Download

description: A dataset containing 156 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantago lanceolata",
 "Country is Bolivia (Plurinational State of)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 156 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044070-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57830/2310846
title: White Tailed Deer Inventory at Vicksburg National Military Park 2023 - Open Format Dataset

description: White-tailed deer (WTD) can exert substantial impacts on the ecosystems in the Southeastern United States. WTD populations in Vicksburg National Military Park (VICK) have not been surveyed since 2010. This study aimed to develop a cost-effective visual count-density conversion method using WTD counts from spotlight surveys and density estimates from fecal-DNA spatially explicit capture-recapture (SECR) models. We conducted spotlight surveys of WTD in January, March, and May, 2023. Average visual counts of WTD were 96.0 in January, March, and May. Direct visual deer counts were greater than those of the 2009 VICK WTD spotlight surveys by 40%-220%. Average WTD relative abundances were 8.5 deer per mile in January, March, and May, respectively. Average density estimated by distance sampling models was 0.65 deer per ha. We used eight microsatellite markers to genotype WTD fecal samples, fecal DNA spatially explicit capture-recapture models estimated 778 WTD within VICK. The WTD densities were positively related to the proportions of forests and open fields in VICK. White-tailed deer appeared to be overabundant within VICK, causing concerns relative to WTD-human conflicts and exacerbating the risk of wildlife disease transmission. We proposed a method for estimating WTD densities with visual counts, which will allow park staff to convert WTD visual counts from spotlight surveys to WTD densities until substantial changes in VICK’s vegetation and/or habitat management occur. The timely, cost-effective monitoring of WTD populations can help park staff better manage natural resources within VICK, including the mitigation of the damages caused by overabundant WTD to natural resources.
DOI: 10.57830/2311166
title: Macroinvertebrate Inventory of High Elevation Springs in Shenandoah National Park 2023-2024 - Open Format Dataset

description: Shenandoah National Park contains hundreds of natural springs which help form the headwaters of three major watersheds that empty into Chesapeake Bay. Virginia Tech partnered with the National Park Service Inventory and Monitoring program to sample macroinvertebrates and environmental measures related to water quality, habitat availability, and human use at 63 springs within the park, of which, 59 could were assessed and analyzed. The goals of this inventory were to assess the distributions of macroinvertebrates across springs in the park. Additionally, we sought to determine whether macroinvertebrate diversity and the presence of rare taxa have been impacted by modifications made to springs and/or by visitor use. We identified 205 unique taxa across the 59 springs. Of those taxa, we identified 17 rare taxa using NatureServe’s Conservation Status Rank. Rare taxa were present in 32 springs, 19 of which were modified and 13 were unmodified. Class Insecta represented 90% of rare taxa that were mostly in orders Trichoptera, Plecoptera, Ephemeroptera and Odonata. There was no difference in total taxa richness or abundance between the spring types. Richness and abundance for all taxa and for rare taxa were greater, on average, in modified springs; however, these differences were not statistically significant. The diversity of spring types, locations and habitats appear to support a diversity of species that are not being negatively affected by visitor usage or spring box infrastructure. The springs provide a regional species pool at high density that are likely source populations for the headwater streams.
DOI: 10.57830/2312961
title: Freshwater Snail Inventory of Upper Delaware Scenic and Recreational River 2022-2023 - Open Format Dataset

description: The Upper Delaware Scenic and Recreational River (UPDE) unit of the National Park Service partnered with the Academy of Natural Sciences of Drexel University (ANS) to perform a freshwater snail inventory within the park. ANS and UPDE teams conducted field research in July and August of 2022 and 2023 using a combination of kick sampling and hand-picking methods to determine the abundance and diversity of freshwater snail populations. Fifty-four sites were surveyed along the 73 miles of the Delaware River within UPDE and included cold-water and warmwater fisheries zones. In 2022, field collections occurred at 30 sites along the river edge from Hancock, NY to the No. 2 railroad bridge near Mill Rift, PA. In 2023, field work occurred at 24 sites in relatively disturbed areas and within unique river features that were not sampled in 2022. Snails were identified using traditional morphological taxonomy and DNA barcoding of the CO1 (Cytochrome c oxidase I) gene. Additional environmental DNA (eDNA) was analyzed from water collected at ten eDNA Atlas Sites. Based on genetic analysis, 27 species of gastropods were identified, one of which is a non-native species, the Japanese Mystery Snail (Cipangopaludina japonica); previous studies found 18 species and identified the mystery snail as the Chinese (Cipangopaludina chinensis). There were more snails below the Cannonsville Reservoir influence in the warmwater zone. A better understanding of the snail community and the ecosystem has been gained with the results of this inventory which will inform effective and responsible river management plans.
DOI: 10.22002/6vx84-agw61
title: Salmonella typhimurium

description: Session notes: FliL deletion (plus T3SS) Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2011-11-23</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Salmonella typhimurium</p>
<strong>Strain:</strong> serovar Typhimurium str. LT2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: -1.5°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: 5.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2011-11-23-31_slicer7375.jpg: Filament
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2011-11-23-31/rawdata/</p>11nov23a_fliL_0015.st,  Tilt Series (Pixel Size 0.512 nm), 726.7 MB  
        
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        11nov23a_fliL_0015.rec,  Reconstruction (Pixel Size 1.036 nm), 412.9 MB  
        
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DOI: 10.57830/2313465
title: Appalachian Cottontail Inventory at Fort Necessity National Battlefield 2024 - Open Format Dataset

description: The aim of this project was to determine if Appalachian cottontail (Sylvilagus obscurus) is present within Fort Necessity National Battlefield (FONE) to inform natural resource management. Sylvilagus obscurus is listed by the Pennsylvania Game Commission (PAGC) as a species of greatest conservation need in the Pennsylvania Wildlife Action Plan (2015-2025), yet little is known about their current population distribution in the Laurel Highlands area of southwestern Pennsylvania, where FONE is located. To gain a preliminary understanding of S. obscurus presence in FONE, we surveyed 20 randomly located plots for fecal pellets two times in February 2024. We also collected fecal pellets that were found incidentally while conducting the surveys. Thirty-two samples were collected, documented, and taken to the Pennsylvania State University genetics lab at the completion of field work. Genetic analysis indicated that six samples belonged to S. obscurus, thereby confirming the presence of S. obscurus within FONE and providing park biologists with preliminary occurrence data on a species of concern to inform management decisions.
DOI: 10.57830/2313733
title: Bat Inventory at Petroglyph National Monument 2023 - Open Format Dataset

description: Petroglyph National Monument (PETR or Monument) is 7,212 acres and is located on the outskirts of the City of Albuquerque. Adjacent land is rapidly being developed leading to increased visitation with potential stress on natural resources. Among these resources are bats which geographically supports the highest species diversity in the United States. There is a current data gap with bat presence/absence in PETR and how visitor activities and establishing, maintaining, or closing trails could impact bat populations. Characterizing seasonal bat use will help support the Visitor Use Management Plan. We surveyed 10 sites with remote acoustic detectors for a total of 2,964 detector nights from October 2022- October 2023 within five focal resource management areas. Analytic data collecting and acoustic analysis followed established USFWS guidelines and protocols. We acoustically detected 21 species. We calculated nightly activity levels for each species (mean number of calls per night) and species diversity index at each sampling location. Overall bat annual temporal activity was highest in August. While acoustic surveys cannot determine number of individuals on the landscape or determine specific roosting locations, it demonstrated spatially what areas are being used by bats and how frequently in PETR. This data will prove to be a useful management tool for determining potential actions at each focal area of interest on the Monument. In general, to minimize potential negative impacts, avoid direct impacts to possible roosting areas or conduct visual survey prior to action and if possible, avoid times when bat use is highest.
DOI: 10.22002/tf4r2-9pm03
title: Campylobacter jejuni

description: Session notes: Titan Krios dataset Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2012-08-29</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (0.0°, 0.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 15.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2012-08-29-17_slicer4885.jpg: Granule .  Flagellar motor .  vesicle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2012-08-29-17/3dimage_23183/</p>CJejuni_Tomo_31.rec,  Reconstruction (Pixel Size 0.5797 nm), 295.8 MB  
        
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        CJejuni_Tomo_31.st,  Tilt Series (Pixel Size 0.512 nm), 1.1 GB  
        
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DOI: 10.22002/0af0r-pvp92
title: Salmonella typhimurium

description: Session notes: Salmonella fliL minicells with T3SS Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2012-09-19</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Salmonella typhimurium</p>
<strong>Strain:</strong> serovar Typhimurium str. LT2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: -1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 5.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2012-09-19-21_slicer4519.jpg: Chemoreceptors mba2012-09-19-21_slicer4523.jpg: Flagella
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2012-09-19-21/rawdata/</p>12sep19a_fliL_0032.st,  Tilt Series (Pixel Size 0.512 nm), 636.0 MB  
        
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        12sep19a_fliL_0032.rec,  Reconstruction (Pixel Size 1.12 nm), 353.3 MB  
        
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DOI: 10.22002/g3smd-4d283
title: JV9279

description: Raw data files of JV9279
description: <strong>Tilt Series Date:</strong> 2018-11-13</p>
<strong>Data Taken By:</strong> Jun Zhang</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-54.0°, 54.0°), step: 2°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -4.0 μm,  magnification: 41000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jza2018-11-13-5/rawdata/</p>tilt010.mrc,  Tilt Series (Pixel Size 0.2654 nm), 1.5 GB  
        
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        tilt010_part52_2.rec,  Reconstruction (Pixel Size 1.0616 nm), 534.5 MB  
        
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DOI: 10.22002/cbh26-r8x96
title: Bdellovibrio Continuous Tilting

description: Raw data. Gain-normalization and defects correction have not been applied. For each dataset, 2 separate tilt-series were collected bidirectionally using the continuous-tilting method: first:0 to -60 degrees, then: 0 to 60 degrees. The two stacks were then combined using IMOD's Newstack command.
description: <strong>Tilt Series Date:</strong> 2018-03-26</p>
<strong>Data Taken By:</strong> Georges Chreifi</p>
<strong>Species / Specimen:</strong> Bdellovibrio bacteriovorus</p>
<strong>Strain:</strong> HD100</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 0.12°, constant angular increment, dosage: 103.0 eV/Å²,  defocus: -2.5 μm,  magnification: 53000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2018-03-26-12/rawdata/</p>BD_53kx_12.mrc,  Tilt Series (Pixel Size 0.2743 nm), 14.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2018-03-26-12/rawdata/BD_53kx_12.mrc"
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        Mar26_Correction_Files.zip,  Gain and defects correction, 25.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2018-03-26-12/file_19844/Mar26_Correction_Files.zip"
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DOI: 10.22002/7m5ds-8mr87
title: Bdellovibrio Continuous Tilting

description: Raw data. Gain-normalization and defects correction have not been applied. For each dataset, 2 separate tilt-series were collected bidirectionally using the continuous-tilting method: first:0 to -60 degrees, then: 0 to 60 degrees. The two stacks were then combined using IMOD's Newstack command.
description: <strong>Tilt Series Date:</strong> 2018-03-26</p>
<strong>Data Taken By:</strong> Georges Chreifi</p>
<strong>Species / Specimen:</strong> Bdellovibrio bacteriovorus</p>
<strong>Strain:</strong> HD100</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 0.12°, constant angular increment, dosage: 103.0 eV/Å²,  defocus: -2.5 μm,  magnification: 53000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2018-03-26-28/rawdata/</p>BD_53kx_30.mrc,  Tilt Series (Pixel Size 0.2743 nm), 14.2 GB  
        
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        Mar26_Correction_Files.zip,  Gain and defects correction, 25.1 MB  
        
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