cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.2650101
title: Precursor dataset PDkhi

description: Dataset for TotalControl flow database precursor simulation of a pressure-driven high Reynolds number boundary layer flow (Casename PDkhi).

Further information, including description of the case and dataset can be found in the deliverable report at: 

Andersen SJ, Meyers J, Munters W, Sood I, Troldborg N. "Flow Database for reference wind farms part 1: precursor simulations"
DOI: 10.6073/pasta/52ceb4a7e7821d89e44f5fbbab966211
title: Fluxes of Carbonyl Sulfide at Harvard Forest EMS Tower since 2010

description: Carbonyl sulfide (OCS), the most abundant sulfur compound in the atmosphere, controls the
     sulfur budget and aerosol loading of the stratosphere in times of low volcanic activity. OCS is
     also closely tied to the vegetative carbon cycle and may provide an independent measure of the
     photosynthetic uptake of carbon. However, the detailed nature of the biogeochemical cycling of
     OCS throughout the seasons in terrestrial ecosystems has not been thoroughly explored. We
     measured the seasonal response of the ecosystem flux of OCS above a deciduous temperate forest
     using an infrared laser absorption spectrometer at Harvard Forest (MA, USA) in 2011. Fluxes
     were calculated using two complementary approaches: gradient – flux (also known as flux –
     gradient; January – July, 2011) and eddy covariance flux (August – December, 2011), which
     agreed within the combined error for a period with both measurements. Strong uptake of OCS by
     the forest was observed during most of the growing season, but significant uptake also occurred
     when the deciduous leaves were not present. A strong diel cycle of mid-day OCS uptake was
     observed in May/June and August/September, consistent with OCS uptake by processes parallel to
     CO2 photosynthetic uptake, at the ecosystem scale, for these months. The results show that
     while overall OCS and CO2 both show evidence of vegetative uptake, the OCS flux cannot be
     explained by this process alone and the relationship between OCS and CO2 changes throughout the
     year above this mixed deciduous forest. The data imply that terrestrial uptake of OCS, and
     hence the stratospheric sulfur cycle, are potentially quite sensitive to extremes in
     temperature and soil moisture.
DOI: 10.14469/hpc/5586
title: Houk TS1 6-31G(d) chloroform IRC

description: Gaussian Calculation
DOI: 10.6073/pasta/f11f9e70318538519fba71aa2ce59c6f
title: Climate Change Impacts on Forest Biodiversity at Harvard Forest since 2011

description: Climate change is rapidly transforming forests over much of the globe in ways that are not anticipated by current science.  Large-scale forest diebacks, apparently linked to interactions involving drought, warm winters, and other species, are becoming alarmingly frequent.  Models of biodiversity and climate have not provided guidance on if/where/when such responses will occur.  Instead models often predict potential numbers of extinctions, but these forecasts not are linked in any mechanistic way to the processes that could cause them.  Both modeling and field studies rely on aggregate metrics of species presence/absence or relative abundance at regional scales, but climate affects individuals.  Aggregation of individual data to the species level, hides or even qualitatively changes climate effects.  By sampling and analysis at the individual scale across continental variation in climate, this study can link the individual scale processes to regional responses.  This study will exploit existing research sites and the new NEON platform of sites for synthesis of models and data to determine when and where predicting climate impacts on biodiversity is a plausible goal, understand where surprises are likely to occur, and attribute those predictions back to individual tree health and vulnerability to climate risk factors.
        The study will provide climate vulnerability forecasts for forest biodiversity that are directly linked to the process scale.  Our goal is provide probabilistic forecasts for the joint distribution of forest responses to climate change, including growth, reproduction, and mortality risk.  For scientists, US Forest Service researchers, and policy makers predictions will anticipate combined risks of increasing drought and longer growing seasons.  Methods developed under this project will be disseminated through training workshops for postdoctoral associates at other universities and resource managers.
DOI: 10.18716/nmrshiftdb2/20253146
title: NMR data for Campher
DOI: 10.21227/fj4r-8p14
title: By-example data query for AutomationML using tree patterns

description: This data set contains explementary data to demonstrate the utility of By-example data query in AutomationML
DOI: 10.21227/zcv3-xp33
title: By-example data query for AutomationML using tree patterns

description: This data set contains explementary data to demonstrate the utility of By-example data query in AutomationML
DOI: 10.5281/zenodo.2653738
title: Low Frequency Radio Pulses Produced by Terrestrial Gamma-ray Flashes

description: The data supports the manuscript entitled “Low Frequency Radio Pulses Produced by Terrestrial Gamma-ray Flashes<br>
” that is under review in GRL. These files can be opened by MATLAB. The data can be used freely for scientific purposes with appropriate citation.
DOI: 10.5281/zenodo.2653739
title: Low Frequency Radio Pulses Produced by Terrestrial Gamma-ray Flashes

description: The data supports the manuscript entitled “Low Frequency Radio Pulses Produced by Terrestrial Gamma-ray Flashes<br>
” that is under review in GRL. These files can be opened by MATLAB. The data can be used freely for scientific purposes with appropriate citation.
DOI: 10.5281/zenodo.2653840
title: Coarse-grained simulations of cholesterol in symmetric lipid bilayers with restraints on cholesterol positions

description: Membranes consisting of 520 phospholipids varying levels of chain unsaturation together with 56 (10 mol%) cholesterol molecules were simulated at 298 K. The phospholipids had either 2 (DLiPC) or 4 (DAPC) double bonds in both of their chains. The Martini force field [1] was used and the membranes were generated using insane [2]. In the simulations, a flat-bottom potential was applied to the cholesterol molecules to either prevent them from partitioning to the membrane core, or from performing complete flip–flops.

The simulations were run for 10 microsecond using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file (note that the temperature varies between simulations).

The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data:


	Topology files (top) and molecular definitions (itp)
	Index files (ndx)
	Run parameter files (mdp)
	A run input file (tpr)
	Trajectory file (xtc) written every 1 ns
	Energy file (edr) written every 100 ps
	Log file (log)
	Final structure file (gro)
	Continue point file (cpt)


The files are named LLLL_CG_CHOLXX_RR_TTT.FFF, where


	LLLL is the type of phospholipid
	CG stands for coarse-grained (All atom data in a separate upload)
	CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)
	TTT is the temperature
	RR is the width of the flat-bottom potential
	FFF is the tile type (see above)


Note that topologies/index files are the same regardless of temperature, and hence their file names do not have the TTT section. Moreover, md_RR.mdp is common for both lipid types yet activates a different flat-bottom potential based on RR.

[1] <strong>DOI: </strong>10.1021/jp071097f

[2] <strong>DOI: </strong>10.1021/acs.jctc.5b00209

[3] <strong>DOI: </strong>10.1016/j.softx.2015.06.001
DOI: 10.5281/zenodo.2653841
title: Coarse-grained simulations of cholesterol in symmetric lipid bilayers with restraints on cholesterol positions

description: Membranes consisting of 520 phospholipids varying levels of chain unsaturation together with 56 (10 mol%) cholesterol molecules were simulated at 298 K. The phospholipids had either 2 (DLiPC) or 4 (DAPC) double bonds in both of their chains. The Martini force field [1] was used and the membranes were generated using insane [2]. In the simulations, a flat-bottom potential was applied to the cholesterol molecules to either prevent them from partitioning to the membrane core, or from performing complete flip–flops.

The simulations were run for 10 microsecond using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file (note that the temperature varies between simulations).

The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data:


	Topology files (top) and molecular definitions (itp)
	Index files (ndx)
	Run parameter files (mdp)
	A run input file (tpr)
	Trajectory file (xtc) written every 1 ns
	Energy file (edr) written every 100 ps
	Log file (log)
	Final structure file (gro)
	Continue point file (cpt)


The files are named LLLL_CG_CHOLXX_RR_TTT.FFF, where


	LLLL is the type of phospholipid
	CG stands for coarse-grained (All atom data in a separate upload)
	CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)
	TTT is the temperature
	RR is the width of the flat-bottom potential
	FFF is the tile type (see above)


Note that topologies/index files are the same regardless of temperature, and hence their file names do not have the TTT section. Moreover, md_RR.mdp is common for both lipid types yet activates a different flat-bottom potential based on RR.

[1] <strong>DOI: </strong>10.1021/jp071097f

[2] <strong>DOI: </strong>10.1021/acs.jctc.5b00209

[3] <strong>DOI: </strong>10.1016/j.softx.2015.06.001
DOI: 10.5286/isis.e.rb1910485
title: Determination of experimental compositions of half-Heusler thermoelectrics prepared via arc-melting

description: Half-Heusler intermetallics are promising for application in thermoelectric waste heat recovery. In this experiment we want to use neutron powder diffraction to investigate the experimental compositions of a series of Ti1-xZr0.5xHf0.5xNiCuySn and ZrNi1+ySn half-Heuslers. This information is needed to link the measured thermoelectric properties to the experimental compositions of these samples. This knowledge will then feedback into our synthesis programme.
DOI: 10.5286/isis.e.rb1910485-1
title: Determination of experimental compositions of half-Heusler thermoelectrics prepared via arc-melting

description: Half-Heusler intermetallics are promising for application in thermoelectric waste heat recovery. In this experiment we want to use neutron powder diffraction to investigate the experimental compositions of a series of Ti1-xZr0.5xHf0.5xNiCuySn and ZrNi1+ySn half-Heuslers. This information is needed to link the measured thermoelectric properties to the experimental compositions of these samples. This knowledge will then feedback into our synthesis programme.
DOI: 10.5286/isis.e.rb1910485-2
title: Determination of experimental compositions of half-Heusler thermoelectrics prepared via arc-melting

description: Half-Heusler intermetallics are promising for application in thermoelectric waste heat recovery. In this experiment we want to use neutron powder diffraction to investigate the experimental compositions of a series of Ti1-xZr0.5xHf0.5xNiCuySn and ZrNi1+ySn half-Heuslers. This information is needed to link the measured thermoelectric properties to the experimental compositions of these samples. This knowledge will then feedback into our synthesis programme.
DOI: 10.14469/hpc/5587
title: Houk TS1 6-31G(d) benzene

description: Gaussian Calculation
DOI: 10.6073/pasta/0f3bb178808f25d688d3d1a1cb02ead5
title: Soil moisture and snowdepth measurements in the Black Sand experiment for East Knoll, Audubon, Lefty, Soddie and Trough in 2018

description: The purpose of the Black Sand experiment is to measure treatment
  effects on date of snowmelt on Niwot Ridge. Five sites with paired
  plots (treatment and control) were implemented across Niwot as part of
  the extended summer research program in order to understand the
  effects of earlier snowmelt.
DOI: 10.5281/zenodo.1221163
title: Synthetic Data for Neutrophil Analysis: Sets one large neutrophil shape and Poisson noise

description: <strong>Synthetic Datasets with  one large irregular shape and Poisson noise.</strong>

<strong>Part of the PhagoSight neutrophil tracking and analysis package (Henry, et al., PLOS ONE, 2013):</strong>

 

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636

http://www.phagosight.org

https://github.com/phagosight/phagosight

 

A series of synthetic data sets that reproduce different behaviour characteristics of migrating neutrophils were generated in MATLAB. The data sets consisted of one artificial neutrophil that travelled along a path that presented different conditions of tortuosity, times to activation during 98 time frames.

Numerous data sets of neutrophils in zebrafish were carefully observed before setting the characteristics. One trajectory was manually determined by setting the row, column positions of the centroid at every time point for 98 time frames. The trajectory was designed so that it would represent different neutrophil behaviours: some moments were very oriented and had movements with uniform distance between time frames, whilst others were less uniform and would move at different velocities, some were tortuous whilst others were straight.

Each time frame consisted of 11 slices of z-stack each with 275 x 275 pixels, where the neutrophil was formed by Gaussian distributions of higher intensities than the background and <strong>Poisson noise </strong>(check the corresponding sets with <strong>smaller </strong>regular shapes with Gaussian noise and irregular shapes with Poisson noise).

 

Files corresponding to the sets with irregular shapes and Poisson noise (noise increases from 1 to 5):


	<strong>    Ground Truth       syntheticData_L_mat_La </strong>
	<strong>    First data set         syntheticData_L1_mat_Re</strong>
	<strong>    Second data set     syntheticData_L2_mat_Re</strong>
	<strong>    Third data set       syntheticData_L3_mat_Re</strong>
	<strong>    Fourth data set     syntheticData_L4_mat_Re</strong>
	<strong>    Fifth data set        syntheticData_L5_mat_Re</strong>


 

Corresponding GIF files are also included as illustrations of the cells in motion.

 

Main Reference:

<strong><em>PhagoSight</em>: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model</strong> <br>
Henry KM, Pase L, Ramos-Lopez CF, Lieschke GJ, Renshaw SA, Reyes-Aldasoro CC. (2013) <em>PhagoSight</em>: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model. PLOS ONE 8(8): e72636. https://doi.org/10.1371/journal.pone.0072636
DOI: 10.5281/zenodo.1221164
title: Synthetic Data for Neutrophil Analysis: Sets one large neutrophil shape and Poisson noise

description: <strong>Synthetic Datasets with  one large irregular shape and Poisson noise.</strong>

<strong>Part of the PhagoSight neutrophil tracking and analysis package (Henry, et al., PLOS ONE, 2013):</strong>

 

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636

http://www.phagosight.org

https://github.com/phagosight/phagosight

 

A series of synthetic data sets that reproduce different behaviour characteristics of migrating neutrophils were generated in MATLAB. The data sets consisted of one artificial neutrophil that travelled along a path that presented different conditions of tortuosity, times to activation during 98 time frames.

Numerous data sets of neutrophils in zebrafish were carefully observed before setting the characteristics. One trajectory was manually determined by setting the row, column positions of the centroid at every time point for 98 time frames. The trajectory was designed so that it would represent different neutrophil behaviours: some moments were very oriented and had movements with uniform distance between time frames, whilst others were less uniform and would move at different velocities, some were tortuous whilst others were straight.

Each time frame consisted of 11 slices of z-stack each with 275 x 275 pixels, where the neutrophil was formed by Gaussian distributions of higher intensities than the background and <strong>Poisson noise </strong>(check the corresponding sets with <strong>smaller </strong>regular shapes with Gaussian noise and irregular shapes with Poisson noise).

 

Files corresponding to the sets with irregular shapes and Poisson noise (noise increases from 1 to 5):


	<strong>    Ground Truth       syntheticData_L_mat_La </strong>
	<strong>    First data set         syntheticData_L1_mat_Re</strong>
	<strong>    Second data set     syntheticData_L2_mat_Re</strong>
	<strong>    Third data set       syntheticData_L3_mat_Re</strong>
	<strong>    Fourth data set     syntheticData_L4_mat_Re</strong>
	<strong>    Fifth data set        syntheticData_L5_mat_Re</strong>


 

Corresponding GIF files are also included as illustrations of the cells in motion.

 

Main Reference:

<strong><em>PhagoSight</em>: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model</strong> <br>
Henry KM, Pase L, Ramos-Lopez CF, Lieschke GJ, Renshaw SA, Reyes-Aldasoro CC. (2013) <em>PhagoSight</em>: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model. PLOS ONE 8(8): e72636. https://doi.org/10.1371/journal.pone.0072636
DOI: 10.5281/zenodo.2653734
title: Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol restrained to the membrane core

description: Membranes consisting of 260 DAPC and 28 (10 mol%) cholesterol molecules were simulated at various temperatures of 285, 298, 310, 320, and 333 K. Notably, one cholesterol molecule was restrained to the membrane core. The CHARMM36 force field [1] was used and the membranes were generated using CHARMM-GUI [2].

For simulations without a restrained cholesterol, see the other upload at DOI:

The simulations were run for 2 microseconds using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file (note that the temperature varies between simulations).

The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data:


	Topology files (top) and molecular definitions (itp)
	Index files (ndx)
	A common run parameter file (mdp)
	A run input file (tpr)
	Trajectory file (xtc) written every 100 ps
	Energy file (edr)
	Log file (log)
	Final structure file (gro)
	Continue point file (cpt)


The files are named LLLL_AA_CHOLXX_CORE_TTT.FFF, where


	LLLL is the type of phospholipid
	AA stands for all atom (Coarse-grained data in a separate upload)
	CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)
	TTT is the temperature
	FFF is the tile type (see above)


Note that topologies/index files are the same regardless of temperature, and hence their file names do not have the TTT section.

[1] <strong>DOI: </strong>10.1021/jp101759q

[2] <strong>DOI: </strong>10.1021/acs.jctc.5b00935

[3] <strong>DOI: </strong>10.1016/j.softx.2015.06.001
DOI: 10.5281/zenodo.2653735
title: Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol restrained to the membrane core

description: Membranes consisting of 260 DAPC and 28 (10 mol%) cholesterol molecules were simulated at various temperatures of 285, 298, 310, 320, and 333 K. Notably, one cholesterol molecule was restrained to the membrane core. The CHARMM36 force field [1] was used and the membranes were generated using CHARMM-GUI [2].

For simulations without a restrained cholesterol, see the other upload at DOI:

The simulations were run for 2 microseconds using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file (note that the temperature varies between simulations).

The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data:


	Topology files (top) and molecular definitions (itp)
	Index files (ndx)
	A common run parameter file (mdp)
	A run input file (tpr)
	Trajectory file (xtc) written every 100 ps
	Energy file (edr)
	Log file (log)
	Final structure file (gro)
	Continue point file (cpt)


The files are named LLLL_AA_CHOLXX_CORE_TTT.FFF, where


	LLLL is the type of phospholipid
	AA stands for all atom (Coarse-grained data in a separate upload)
	CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)
	TTT is the temperature
	FFF is the tile type (see above)


Note that topologies/index files are the same regardless of temperature, and hence their file names do not have the TTT section.

[1] <strong>DOI: </strong>10.1021/jp101759q

[2] <strong>DOI: </strong>10.1021/acs.jctc.5b00935

[3] <strong>DOI: </strong>10.1016/j.softx.2015.06.001
DOI: 10.25919/5cc6eff7ecd65
title: Parkes observations for project P991 semester 2019APRS_03

description: Finding radio pulsars orbiting near Sgr A* is a major goal of pulsar surveys with existing telescopes and future telescopes such as the Square Kilometer Array (SKA). The discovery of such pulsars will allow us to measure relativistic effects through timing of pulsars in tight orbits around Sgr A*, to characterise the distribution of dark matter near Sgr A*, to study the stellar population in the GC region and to probe the scattering region around Sgr A*. Although several surveys of the GC region have done, the Ultra-Wideband Low (UWL) receiver provides us a much wider frequency coverage with great sensitivity and therefore it is an excellent chance to revisit the GC region. At around 4GHz, a survey with UWL will achieve a sensitivity significantly higher than previous Parkes and Green Bank surveys, especially for pulsars with short spin periods and high dispersion measures.
DOI: 10.5519/qd.o2z1dqar
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (6531 records)
DOI: 10.18739/a28w3824w
title: High resolution photogrammetric data of Chamberlin Glacier and the Lake Peters watershed, Alaska, 2015-2017

description: Airborne photogrammetric data were acquired two times in 2015 (April 23 and July 5), three times in 2016 (April 19, July 11, and August 5), and three times in 2017 (April 28, June 27, and September 3). These data were used to create digital elevation models (DEMs) with postings of 50 cm provided in NAD83(2011) (North American Datum) NAVD88 (North American Vertical Datum) Geoid 12B (unless otherwise specified). When conditions permitted (April 23, 2015; July 5, 2015; April 19, 2016; April 28, 2017), the entire Carnivore Creek watershed was acquired. On all other dates, only the eastern side of the valley, where the catchment glaciers are located, was captured. These data were acquired using a Nikon DSLR (digital single-lens reflex) attached to a survey grade GNSS (Global Navigation Satellite System) on board a manned aircraft, providing photo-center position to 10 cm or better and thus eliminating the need for ground control. These DEMs were used to create difference DEMs that can be used to measure snowpack thickness throughout the entire watershed as well as glacier surface elevation change.
DOI: 10.25430/researchdata.cab.unipd.it.00000126
title: Subtyping of Primary Aldosteronism in the AVIS-2 Study:
Assessment of Selectivity and Lateralisation. Supplemental Material

description: Journal of Clinical Endocrinology and Metabolism Submission Supplemental Material–Apr2019
DOI: 10.5281/zenodo.2653768
title: Frequency list for comparing IE613 data with SE607

description: This is a sample of a list of clean frequencies away from loud RFI used with tutorials for beamModelTester.
DOI: 10.5281/zenodo.2653769
title: Frequency list for comparing IE613 data with SE607

description: This is a sample of a list of clean frequencies away from loud RFI used with tutorials for beamModelTester.