cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0438289
title: Replication data for: Redefining dominance calculation: Increased competition flattens the dominance hierarchy in dairy cows

description: Dominance hierarchies are known for mitigating conflicts and guiding priority of access to limited resources in gregarious animals. The dominance hierarchy of dairy cows is typically constructed using agonistic interactions, usually monitored at the feed bunk right after fresh feed delivery when competition is high resulting in numerous interactions. Yet, the outcome of agonistic interactions under time of high competition time may be more influenced by cows’ high valuation of fresh feed than their intrinsic dominance attributes. Thus, the dominance hierarchy constructed using agonistic interactions under high versus low competition times might differ. The aim of this study was to test how the structure of the dominance hierarchy changes in relation to different levels of competition. We monitored a dynamically changing group of 48 lactating dairy cows over 10 mo with 6 cows exchanged every 16 d, totally 159 cows. We used a validated algorithm to continuously detect the actor and reactor of replacement behaviors as cows competed for feed. We calculated feeder occupancy, the percentage of occupied feed bins, to characterize competition at the moment of each replacement, and created 25 corresponding dominance hierarchies using Elo ratings for occupancy levels ranging from 13% to 100%. With each 10% rise in feeder occupancy, hierarchy steepness fell by 0.02 (R2 = 0.96) and two-way dyads rose by 1.3% (R2 = 0.84). The win rate of the dominant cow within dyads declined with increased feeder occupancy (y = -0.11x -0.21, P &lt; 0.001). Our findings provide evidence that there is noticeable variation in inferred hierarchies based on the competition context, with high competition flattening the hierarchy as subordinate animals succeed more in replacing others in order to gain feed access. This finding underscores that during heightened competition, the valuation of resources impacts agonistic behaviors and the subsequently constructed dominance hierarchy more than the individual's intrinsic dominance attributes. We recommend that researchers avoid using agonistic interactions occurring immediately after fresh feed delivery to establish dominance hierarchies. We also urge researchers to differentiate agonistic interactions based on context when constructing dominance hierarchies to draw inferences on animal behavior, cognition and health.
DOI: 10.14288/1.0434220
title: Data from: A test of the green wave hypothesis in omnivorous brown bears across North America

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Herbivorous animals tend to seek out plants at intermediate phenological states to improve energy intake while minimizing consumption of fibrous material. In some ecosystems, the timing of green-up is heterogeneous and propagates across space in a wave-like pattern, known as the green wave. Tracking the green wave allows individuals to prolong access to higher-quality forage. While there is a plethora of empirical support for such behavior in herbivorous taxa, the green wave hypothesis (GWH) is nuanced based on factors such as body morphometrics and digestive capacity. Furthermore, little is known about whether other taxa, such as omnivores, track the green wave. Our objective was to assess whether the GWH can be extended to explain the movements of omnivores. Using GPS collar data from seven populations (n = 127 individuals) of brown bears (&lt;em&gt;Ursus&lt;/em&gt; &lt;em&gt;arctos&lt;/em&gt;) across their entire North American range, we first tested whether bears tracked the green wave. Using conditional resource selection functions, we found that variation in proxies of vegetative forage quality better-explained movement and habitat selection than proxies of forage biomass in over half of the bears in our study, providing evidence of green wave tracking. Second, we assess factors that explained variation in green wave tracking using linear mixed-effects models. Green wave tracking in brown bears was explained by the variation in availability of green-up within spring home ranges, and how green-up transitioned across those home ranges. Our results demonstrate that the GWH can partially explain movement of a non-migratory omnivorous species, extending the generality of the GWH as a broad predictor of animal space use. The green wave is another resource wave brown bears track, and our findings help predict brown bear space use, which can be used to guide conservation and habitat restoration efforts.&lt;/p&gt;
DOI: 10.14288/1.0434628
title: Can a social partner alleviate conditioned place aversion caused by isolation and pain in dairy calves?

description: Social buffering occurs when the presence of a partner mitigates the stress response of an individual. In two experiments, we assessed the effects of social buffering in dairy calves, with and without a known conspecific, when either subjected to isolation from the larger group (Experiment 1; n = 12) or to recovery from the painful procedure of hot-iron disbudding (Experiment 2; n = 25). In Experiment 2, we also tested whether the level of fearfulness of each calf and the frequency of interactions between the two calves affected the degree of buffering. In both experiments the effects of buffering were assessed using a conditioned place aversion paradigm, with the prediction that calves would find experiences less aversive when exposed to the stressor with a conspecific. All calves were exposed to two conditioning treatments (i.e., exposed alone or with a ‘support’ partner), each session lasted 6 h each and were 48 h apart. Conditioned place aversion tests (with calves tested alone) occurred at 48, 72, 96 h after the second treatment. We found no evidence of social buffering for responses to either isolation from the group or the recovery from the painful experience. The number of physical interactions between the calves during treatment and the fearfulness of the calves also did not account for the individual variation observed.
DOI: 10.6073/pasta/09bc8775516293fc3bb1c4df2ba55c71
title: Monitoring juvenile Chinook salmon outmigration using rotary screw traps on Feather River

description: California Department of Water Resources (DWR) currently operates
 multiple eight-foot rotary screw traps (RSTs) in both the Low Flow
 Channel (LFC) and High Flow Channel (HFC) of the upper 21.5 river
 miles of the Lower Feather River. The LFC extends from the Fish
 Barrier Dam at river mile (RM) 67.2 to the Thermalito Outlet (RM
 59). The HFC extends from the Thermalito Outlet to the confluence
 with the Sacramento River. This survey has been ongoing since 1997
 with the objective of documenting general salmonid emigration
 attributes, such as timing, abundance and composition of salmon and
 investigating the influence of environmental factors thought to
 initiate emigration, such as flow, turbidity and water temperature.
 Data from this monitoring will also be used to inform the
 development of a juvenile production estimate (JPE) for spring-run
 Chinook salmon in the Sacramento River Watershed as required by
 Incidental Take Permit No. 2081-2019-006-00 issued by CA Department
 of Fish and Wildlife (CDFW) to DWR for the long-term operation of
 the State Water Project. Data within the current year’s monitoring
 season are considered provisional.
DOI: 10.14288/1.0434659
title: Data for: The benefits of climate change mitigation to retaining rainbow trout habitat in British Columbia, Canada

description: Excel files with all input data used to analyze climate change effects on the suitability of rainbow trout habitat in British Columbia, Canada.
DOI: 10.14288/1.0434251
title: Data from: Parallel shifts in trout feeding morphology suggest rapid adaptation to alpine lake environments

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Eco-evolutionary interactions following ecosystem change provide critical insight into the ability of organisms to adapt to shifting resource landscapes. Here we explore evidence for the rapid parallel evolution of trout feeding morphology following eco-evolutionary interactions with zooplankton in alpine lakes stocked at different points in time in the Wind River Range (Wyoming, USA). In this system, trout predation has altered the zooplankton species community and driven a decrease in average zooplankton size. In some lakes that were stocked decades ago, we find shifts in gill raker traits consistent with the hypothesis that trout have rapidly adapted to exploit available smaller-bodied zooplankton more effectively. We explore this morphological response in multiple lake populations across two species of trout (cutthroat trout, Oncorhynchus clarkii, and golden trout Oncorhynchus aguabonita) and examine the impact of resource availability on morphological variation in gill raker number among lakes. Furthermore, we present genetic data to provide evidence that historically stocked cutthroat trout populations likely derive from multiple population sources, and incorporate variation from genomic relatedness in our exploration of environmental predictors of feeding morphology. These findings describe rapid adaptation and eco-evolutionary interactions in trout and document an evolutionary response to novel, contemporary ecosystem change.&lt;/p&gt;
DOI: 10.14288/1.0439804
title: Data for: Emergence of the Loa mantle component in the Hawaiian Islands based on the geochemistry of Kaua‘i shield-stage basalts

description: This is a supporting table for the associated paper in Geochemistry, Geophysics, Geosystems. This table is a compilation of major element, recalculated major element (at 16 wt% MgO), trace element, and radiogenic (Pb-Sr-Nd-Hf) isotopic data for shield-stage Hawaiian and Northwest Hawaiian Ridge basaltic samples. All isotopic data has been renormalized to the same standard values and all references for each data type is included.
DOI: 10.57967/hf/5225
title: EYE-lit
DOI: 10.22002/24fa2-ef346
title: Coxiella burnetii_wt_D15

description: Nine Mile phase II clone 4 (NMIIC4) strain. Wild-type cells day-15  culture.
description: <strong>Tilt Series Date:</strong> 2016-11-04</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Coxiella burnetii</p>
<strong>Strain:</strong> Nine Mile phase II clone 4</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Robert Heinzen. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in Robert Heinzen's lab @NIAID and ~50 ul cells were sent to us.</p>
<strong>Sample Preparation:</strong> Refer to Heinzen lab</p>
  dga2016-11-04-89_slicer17265.jpg: membrane vesicle chain
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-89/rawdata/</p>15D_Pos4_atlas20060.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-89/rawdata/15D_Pos4_atlas20060.mrc"
        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20060_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-89/3dimage_108198/15D_Pos4_atlas20060_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20060.ali,  577.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20060.tlt,  648.0 B  
        
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        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20060_fid.tlt,  648.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-89/file_24724/15D_Pos4_atlas20060_fid.tlt"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/3w5r5-dm154
title: Coxiella burnetii_wt_D15

description: Nine Mile phase II clone 4 (NMIIC4) strain. Wild-type cells day-15  culture.
description: <strong>Tilt Series Date:</strong> 2016-11-04</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Coxiella burnetii</p>
<strong>Strain:</strong> Nine Mile phase II clone 4</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Robert Heinzen. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in Robert Heinzen's lab @NIAID and ~50 ul cells were sent to us.</p>
<strong>Sample Preparation:</strong> Refer to Heinzen lab</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-66/rawdata/</p>15D_Pos4_atlas20037.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-66/rawdata/15D_Pos4_atlas20037.mrc"
        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20037_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20037.ali,  292.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20037.tlt,  328.0 B  
        
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        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20037_fid.tlt,  328.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/d7y26-49k91
title: Shewanella WT OMV

description: Shewanella outer membrane vesicles, WT, high resolution
description: <strong>Tilt Series Date:</strong> 2018-07-25</p>
<strong>Data Taken By:</strong> LaurenAnn Metskas</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: 0.0 μm,  magnification: 82000x. </p>
<strong>Microscope:</strong> None</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> IMOD, ctffind4, custom scripts</p>
<strong>Collaborators and Roles:</strong> purified by Lori Zacharoff in the El Naggar lab at USC; data collected by Lauren Ann Metskas; data processed by Lauren Ann Metskas</p>
<strong>Sample Preparation:</strong> quantifoil finder grid, 10nm BSA-gold, 100% humidity, double blotted, -1.5 to -5 micron defocus</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-07-25-14/rawdata/</p>19_dose-filt.st,  Tilt Series (Pixel Size 0.1778 nm), 2.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-07-25-14/rawdata/19_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        19_dose-filt.rec,  Reconstruction (Pixel Size 0.7112 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        TS_19.mrc.mdoc,  24.8 kB  
        
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        > <i class="download icon"></i> Download </a></p>

        frames.tar.bz2,  zipped raw frames, 2.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-07-25-14/file_20179/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 9.1 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-07-25-14/file_20180/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qtqbj-97n09
title: H. Neapolitanus Carboxysomes

description: Carboxysomes purified from H. Neapolitanus, WT, high resolution
description: <strong>Tilt Series Date:</strong> 2019-08-21</p>
<strong>Data Taken By:</strong> LaurenAnn Metskas</p>
<strong>Species / Specimen:</strong> Halothiobacillus neapolitanus</p>
<strong>Strain:</strong> c2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: 0.0 μm,  magnification: 81000x. </p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> IMOD, ctffind4, novaCTF, custom bash and Matlab scripts</p>
<strong>Collaborators and Roles:</strong> purified by Tom Laughlin in the Savage lab at Berkeley; data collected by Lauren Ann Metskas; data processed by Lauren Ann Metskas</p>
<strong>Purification / Growth Conditions / Treatment:</strong> purified by the Savage lab</p>
<strong>Sample Preparation:</strong> protochip C-flat 2/2-300 grid, 10nm BSA-gold, 100% humidity, defocus varying -1 to -5.5 microns</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-44/rawdata/</p>44_dose-filt.st,  Tilt Series (Pixel Size 0.1104 nm), 4.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-44/rawdata/44_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        44_dose-filt.rec,  Reconstruction (Pixel Size 0.8832 nm), 281.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-44/3dimage_113099/44_dose-filt.rec"
        > <i class="download icon"></i> Download </a></p>

        TS_44.mrc.mdoc,  30.2 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-44/rawdata/TS_44.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>

        frames.tar.bz2,  zipped raw frames, 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-44/file_26689/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 15.7 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-44/file_26690/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.tpmr82
title: Occurrence Download

description: A dataset containing 3699 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Echium rosulatum"
 ]
}

 The dataset includes 3699 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036427-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/g5dcx-s9j83
title: Mega gas vesicles

description: Mega gas vesicles, purified from E. coli, -1 to -5 micron defocus. Reconstruct with included scripts for ctf-corrected bin1 tomogram.
description: <strong>Tilt Series Date:</strong> 2019-09-25</p>
<strong>Data Taken By:</strong> LaurenAnn Metskas</p>
<strong>Species / Specimen:</strong> Bacillus megaterium</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-48.0°, 51.0°), step: 3°, constant angular increment, dosage: 70.0 eV/Å²,  defocus: 0.0 μm,  magnification: 81000x. </p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> IMOD 4.9.8, ctffind4, custom scripts</p>
<strong>Collaborators and Roles:</strong> purified by Rob Hurt and George Lu from the Shapiro lab at Caltech; data collected by Lauren Ann Metskas; data processed by Lauren Ann Metskas with assistance from Przemek Dutka</p>
<strong>Purification / Growth Conditions / Treatment:</strong> purified Mega gas vesicles in 10 mM HEPES</p>
<strong>Sample Preparation:</strong> protochips C-flat 2/2-300 grid, 10nm BSA-gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-43/rawdata/</p>43_dose-filt.st,  Tilt Series (Pixel Size 0.1104 nm), 3.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-43/rawdata/43_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        43_dose-filt.rec,  Reconstruction (Pixel Size 0.8832 nm), 405.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        TS_43.mrc.mdoc,  28.2 kB  
        
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        > <i class="download icon"></i> Download </a></p>

        frames.tar.bz2,  zipped raw frames, 1.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-43/file_27807/frames.tar.bz2"
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        scripts.tar.bz2,  zipped processing scripts, 26.0 kB  
        
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