cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.35193
title: Popc @ 310K, Varying Amounts Of Nacl. Slipids With Ecc-Scaled Ions

description: Simulations of a POPC bilayer with varying amounts of NaCl.<br>
These simulations were performed as a part of the NMRlipids<br>
project (http://nmrlipids.blogspot.fi). The goal was to study <br>
the effect of salt on the order parameters of the lipid head <br>
group and the glycerol backbone. The obtained results are <br>
reported in the blog.

A POPC bilayer consisting of 200 lipids (100 per leaflet) is <br>
simulated in the presence of NaCl. Concentrations of 130, 300, <br>
500, 750, and 1000 mM are employed. The Slipids model [1–3] is <br>
employed for lipids, tip3p model for water, and the recent ion <br>
parameters by Kohagen et al. [4] for NaCl. 

The Slipids force field parameters were downloaded from<br>
http://mmkluster.fos.su.se/slipids/

The ion parameters are available at<br>
https://bitbucket.org/hseara/ions/

––––––––––––––––––––––––––––––––––––––––––––––––––––––

The files are named based on the concentration of NaCl<br>
and are in GROMACS format. Trajectories (.xtc) are <br>
100 ns long with data saved every 100 ps. Additionally,<br>
initial structures (.gro), topology (.top), index (.ndx)<br>
and binary run input files for GROMACS v. 4.6–&gt; (.tpr)<br>
are provided. The run parameter file (.mdp) is general<br>
for all systems.

––––––––––––––––––––––––––––––––––––––––––––––––––––––

[1] Derivation and Systematic Validation of a Refined <br>
All-Atom Force Field for Phosphatidylcholine Lipids<br>
Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br>
The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br>
DOI: 10.1021/jp212503e

 

[2] An Extension and Further Validation of an All-Atomistic <br>
Force Field for Biological Membranes<br>
Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br>
Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br>
DOI: 10.1021/ct300342n

 

[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br>
Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br>
Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br>
DOI: 10.1021/ct300777p

 

[4] Accounting for Electronic Polarization Effects in Aqueous Sodium <br>
Chloride via Molecular Dynamics Aided by Neutron Scattering<br>
Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth<br>
The Journal of Physical Chemistry B Article ASAP<br>
DOI: 10.1021/acs.jpcb.5b0522
DOI: 10.5281/zenodo.35275
title: Popc @ 310K, 130 Mm Of Nacl. Slipids With Ions By Smith & Dang

description: Simulations of a POPC bilayer with 130 mM of NaCl. <br>
The goal was to study the effect of salt on the order <br>
parameters of the lipid head group and the glycerol <br>
backbone. The obtained results are reported in the <br>
NMRlipids blog at http://nmrlipids.blogspot.fi

A POPC bilayer consisting of 200 lipids (100 per leaflet) <br>
is simulated in the presence of 130 mM NaCl. The Slipids <br>
model [1–3] is employed for lipids, tip3p model for water, <br>
and the ion parameters by Smith and Dang [4] for NaCl. 

The Slipids force field parameters were downloaded from<br>
http://mmkluster.fos.su.se/slipids/

The ion parameters are available at<br>
https://bitbucket.org/hseara/ions/

––––––––––––––––––––––––––––––––––––––––––––––––––––––

The files are in GROMACS format. Trajectory (.xtc) is <br>
100 ns long with data saved every 100 ps. Additionally,<br>
the initial structure (.gro), topology (.top), index<br>
file (.ndx), simulation paremeter file (.mdp), binary <br>
run input file for GROMACS v. 4.6–&gt; (.tpr) and the <br>
energy output file (.edr) are provided. 

––––––––––––––––––––––––––––––––––––––––––––––––––––––

[1] Derivation and Systematic Validation of a Refined <br>
All-Atom Force Field for Phosphatidylcholine Lipids<br>
Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br>
The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br>
DOI: 10.1021/jp212503e

[2] An Extension and Further Validation of an All-Atomistic <br>
Force Field for Biological Membranes<br>
Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br>
Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br>
DOI: 10.1021/ct300342n

[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br>
Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br>
Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br>
DOI: 10.1021/ct300777p

[4] Computer simulations of NaCl association in polarizable water<br>
David E. Smith and Liem X. Dang <br>
The Journal of Chemical Physics 1994 100, 3757-3766<br>
DOI: 10.1063/1.466363
DOI: 10.5281/zenodo.35350
title: The Literary Geographies Of Christine De Pizan (Geo-Data)

description: This geodata set gives the place names found in the corpus of writings of Christine de Pizan, woman writer of the late 14th and early 15th centuries. It accompanies an eponymous essay forthcoming in the Modern Language Association's Approaches to Teaching Christine de Pizan volume.
DOI: 10.5281/zenodo.35370
title: Data For Manuscript "Changes In P300 Latency And Amplitude Reflect Expertise Acquisition In A Football Visuomotor Learning Task"

description: Open-access data for the manuscript "Changes in P300 Latency and Amplitude Reflect Expertise Acquisition in a Football Visuomotor Learning Task". Includes:

Grand Average dEEG file containing data from all days and all conditions. .csv file outputs used for all analyses. .rmd file detailing the statistical workflow used to obtain the stats presented in the manuscript.
DOI: 10.5281/zenodo.35375
title: Currently Available Scaffolds And Mmp Cores In Chembl 20

description: All target-based BM scaffolds (K<sub>i</sub>: 35,872; IC<sub>50</sub>: 74,379), CSKs (K<sub>i</sub>: 23,056; IC<sub>50</sub>: 49,216), MMP cores (K<sub>i</sub>: 42,104; IC<sub>50</sub>: 73,616), and retrosynthetic MMP cores (K<sub>i</sub>: 19,040; IC<sub>50</sub>: 32,382) for high confident bioactive compounds extracted from ChEMBL version 20 are provided herein.
DOI: 10.5281/zenodo.35379
title: Partial Density Profiles Of Lipids And Ions

description: Partial density profiles of lipids and ions calculated using the script available on Zenodo. Each simulated system contains 600 DPPC molecules, 150 mM NaCl and 30 waters/lipid. The ion model is the one described by Roux. The analysis has been performed over the last 40 ns of each 100 ns trajectory. All simulations have been performed with the Slipids force field.
DOI: 10.5281/zenodo.51404
title: Moma Collection - Automatic Monthly Update

description: The Artworks dataset contains 128,074 records, representing all of the works that have been accessioned into MoMA’s collection and cataloged in our database. It includes basic metadata for each work, including title, artist, date made, medium, dimensions, and date acquired by the Museum. Some of these records have incomplete information and are noted as “not Curator Approved.” The Artists dataset contains 14,839 records, representing all the artists who have work in MoMA's collection and have been cataloged in our database. It includes basic metadata for each artist, including name, nationality, gender (labeled "code"), birth year, death year, Wiki QID, and Getty ULAN ID.
DOI: 10.5281/zenodo.51494
title: Optimization Of Spect/Ct Based Lung Dose Calculation For Holmium-166 Hepatic Radioembolization

description: <strong>Background</strong>: Quantitative SPECT of the lungs after intra-arterial hepatic radioembolization using Holmium-166 (<sup>166</sup>Ho)microspheres is essential to assess therapy safety. A SPECT estimated lung absorbed dose resulting from radioembolization of more than 30 Gy is a contra-indication for therapy. Earlier we showed the superiority of Monte Carlo-based iterative reconstructions over conventional reconstructions due to its quantitative nature, required for dosimetry, at the cost of substantial computation times. In clinical routine, however, the limited available time between scout imaging and therapy constrains its application. To reduce computation times, we investigated the minimum number of iterations required to guarantee a clinical acceptable accuracy in lung dose estimation using patient and phantom data.

<strong>Methods</strong>: <sup>166</sup>Ho scout SPECT data (range: 222-283 MBq) were used from 9 patients. SPECT images were Monte Carlo-based OSEM reconstructed (iterations: 30, subsets: 8). Additionally, the 4D XCAT anthropomorphic phantom was used to mimic SPECT studies with an injected scout activity of 250 MBq and with varying lung doses ranging from 0 to 15.6 mGy/MBq. These studies were reconstructed in the same way as the patient data.

<strong>Results: </strong>In all patients the lung absorbed dose upon OSEM convergence ranged from 0 to 0.025 mGy/MBq, and ranged from 0.002 to 0.078 mGy/MBq after five iterations, still well below the allowed 30 Gy in case treatment was proceeded. In the phantom data, the estimated lung dose ranged from 0.004 to 15 mGy/MBq upon convergence and from 0.03 to 13.9 mGy/MBq after five iterations, simulating situations well below and above an estimated treatment lung dose of 30 Gy. Importantly, the lung absorbed dose upon OSEM convergence was underestimated by 15% as compared to the actual simulated lung dose, and the dose after five OSEM iterations was underestimated by 9% as compared to the dose upon convergence. Both underestimations were irrespective of the magnitude of the lung dose and thus can be easily corrected for.

<strong>Conclusions</strong>: The number of OSEM iterations necessary for a quantitative estimate of the lung dose can be reduced from 30 to 5. The resulting six fold reduction in calculation time enables data processing of the scout images before therapy administration.
DOI: 10.5281/zenodo.51553
title: Contour Method Dataset For As-Deposited And Rolled Wire+Arc Additive Manufacturing Ti–6Al–4V Components

description: This is an archive of the raw metrology of the EDM cut surface data files used for the contour method analysis of Wire+Arc Additive Manufacture (WAAM) Ti6Al4V components appearing in: "Residual stress of as-deposited and rolled wire+arc additive manufacturing Ti–6Al–4V components" by F. Martina, M. J. Roy, B. A. Szost, S. Terzi, P. A. Colegrove, S. W. Williams, P. J. Withers, J. Meyer and M. Hofmann.

The files are described by their filenames and side of each EDM cut. For example, 'Control_1.dat' refers to one side of the cut performed on the as-deposited specimen, while '50kN_1.dat' refers to one side of a specimen rolled at 50 kN load, etc.

Data is in the form of a point cloud with one point per line, whitespace delimited in microns. Data was captured with a Nanofocus CF-4 laser profilometer sensor with point spacing 30 µm apart. Data with z coordinates below or above 500 µm are considered outside of the surface detection limits.
DOI: 10.5281/zenodo.51563
title: Deferoxamine Regulates Neuroinflammation And Iron Homeostasis In A Mouse Model Of Postoperative Cognitive Dysfunction

description: The raw data of the manuscript” Deferoxamine Regulates Neuroinflammation and Iron Homeostasis in a Mouse Model of Postoperative Cognitive Dysfunction”
DOI: 10.5281/zenodo.51569
title: Icebridge Topography Data From Petty Et Al., 2016, Tc.

description: Data used to assess Arctic sea ice topography using high-resolution IceBridge laser (ATM) data, from the following publication:

Petty, A. A., M. C. Tsamados, N. T. Kurtz, S. L. Farrell, T. Newman, J. Harbeck, D. L. Feltham, J. A. Richter-Menge (2016), Characterizing Arctic sea ice topography using high-resolution IceBridge data, The Cryosphere, doi:10.5194/tcd-9-6495-2015.

Processing scripts available at at https://github.com/akpetty/ibtopo2016
DOI: 10.5281/zenodo.51603
title: Databases

description: Databases S1-S13
DOI: 10.5281/zenodo.35475
title: Leaf Processing Behavior In Atta Leafcutter Ants: 90% Of Leaf Cutting Takes Place Inside The Nest, And Ants Select Pieces That Require Less Cutting

description: Leafcutter ants cut trimmings from plants, carry them to their underground nests, and cut them into smaller pieces before inoculating them with a fungus that serves as a primary food source for the colony. Cutting is energetically costly, so the amount of cutting is important in understanding foraging energetics. Estimates of the cutting density, meters of cutting per square meter of leaf, were made from samples of transported leaf cuttings and of fungal substrate from field colonies of <em>Atta cephalotes</em> and <em>Atta colombica</em>. To investigate cutting inside the nest, we made leaf-processing observations of our laboratory colony, <em>A. cephalotes</em>. We did not observe the commonly reported reduction of the leaf fragments into a pulp, which would greatly increase the energy cost of processing. Video clips of processing behaviors, including behaviors that have not previously been described, are linked. An estimated 2.9 (+0.3) kilometers of cutting with mandibles was required to reduce a square meter of leaf to fungal substrate. Only about 12% (+ 1%) of this cutting took place outside of the nest. The cutting density and energy cost is lower for leaf material with higher ratios of perimeter to area, so we tested for, and found that the laboratory ants had a preference for leaves that were pre-cut into smaller pieces.  Estimates suggest that the energy required to transport and cut up the leaf material is comparable to the metabolic energy available from the fungus grown on the leaves, and so conservation of energy is likely a particularly strong selective pressure for leafcutter ants.
DOI: 10.5281/zenodo.35484
title: Cabo Verde Fogo Volcano Interferogram November 2014

description: A volcano eruption in Fogo Island, Cabo Verde, began on 23 Nov 2014, affecting the people living in Chã das Caldeiras, the volcano crater area. An estimated 1,000 people have been evacuated from the area, of which 838 have been relocated in temporary accommodation centres and in houses built in the aftermath of the 1995 eruption.
DOI: 10.5281/zenodo.51022
title: Dataset: Six Years Ground-Based Remote Sensing Of Microphysical Properties Of Stratiform Liquid Clouds At Mace Head, Ireland

description: A total of 118 stratiform water clouds observed by ground-based remote sensing instruments at the Mace Head Atmospheric Research Station at the West coast of Ireland from 2009 to 2015 were analyzed in terms of microphysical and optical characteristics as well as the impact of aerosols on these properties. The microphysical and optical cloud properties in the files were obtained using the algorithm SYRSOC (SYnergistic Remote Sensing Of Clouds).
DOI: 10.5281/zenodo.51252
title: Openaire Lod Dump

description: OpenAIRE LOD Dump
DOI: 10.5281/zenodo.51440
title: Openaire Lod Dump

description: OpenAIRE LOD Dump
DOI: 10.5281/zenodo.51651
title: Genetic Risk Factors For Restenosis After Percutaneous Coronary Intervention In Kazakh Population

description: QuantStudio 12K Flex (Life Technologies) raw data files
DOI: 10.5281/zenodo.51689
title: Differential Cytotoxicity Induced By The Titanium(Iv)Salan Complex Tc52In G2-Phase Independent Of Dna Damage

description: Chemotherapy is one of the major treatment modalities for cancer. Metal-based compounds such as derivatives of cisplatin are in the front line of therapy against a subset of cancers, but their use is restricted by severe side-effects and the induction of resistance in treated tumors. Subsequent research focused on development of cytotoxic metal-complexes without cross-resistance to cisplatin and reduced side-effects. This led to the discovery of first-generation titanium(IV)salan complexes, which reached clinical trials but lacked efficacy. New-generation titanium (IV)salan-complexes show promising anti-tumor activity in mice, but their molecular mechanism of cytotoxicity is completely unknown.

4 different human cell lines were analyzed in their responses to a toxic (Tc52) and a structurally highly related but non-toxic (Tc53) titanium(IV)salan complex. Viability assays were used to reveal a suitable treatment range, flow-cytometry analysis was performed to monitor the impact of dosage and treatment time on cell-cycle distribution and cell death. Potential DNA strand break induction and crosslinking was investigated by immunostaining of damage markers as well as automated fluorometric analysis of DNA unwinding. Changes in nuclear morphology were analyzed by DAPI staining. Acidic beta-galactosidase activity together with morphological changes was monitored to detect cellular senescence. Western blotting was used to analyze induction of pro-apoptotic markers such as activated caspase7 and cleavage of PARP1, and general stress kinase p38.

Here we show that the titanium(IV)salan Tc52 is effective in inducing cell death in the lower micromolar range. Surprisingly, Tc52 does not target DNA contrary to expectations deduced from the reported activity of other titanium complexes. Instead, Tc52 application interferes with progression from G2-phase into mitosis and induces apoptotic cell death in tested tumor cells. Contrarily, human fibroblasts undergo senescence in a time and dose-dependent manner. As deduced from fluorescence studies, the potential cellular target seems to be the cytoskeleton.

In summary, we could demonstrate in four different human cell lines that tumor cells were specifically killed without induction of major cytotoxicity in non-tumorigenic cells. Absence of DNA damaging activity and the cell-cycle block in G2 instead of mitosis makes Tc52 an attractive compound for further investigations in cancer treatment.
DOI: 10.5281/zenodo.35563
title: The Egocentric Nature Of Action-Sound Associations

description: These are the data of the corresponding manuscript: "The egocentric nature of action-sound associations" by Nicole Navolio, Guillaume Lemaitre, Alain Forget, and Laurie M. Heller.

These are Matlab .mat files. Each file corresponds to one participant. There are four variables:

- Accuracy: 0 = incorrect answer; 1= correct answer

- Time: response time in ms. 

- Congruency: type of trial. 1 = incongruent, 2=congruent, 3=nosound

- Order: trial order.

Each variable is Nx2 matrix. N is the number of trials. First line is up gesture, second line is right gesture.
DOI: 10.5281/zenodo.35568
title: A List Of Collection Codes And Corresponding Bold Numbers To Sixty New Dragonfly And Damselfly Species From Africa

description: These files contain the data and accession numbers used in the following publication:

Dijkstra, Klaas-Douwe B. et al.. (2015). Sixty new dragonfly and damselfly species from Africa (Odonata). Odonatologica 44(4): 447-678. doi:10.5281/zenodo.35388

Contents

- Lab (BOLD numbers)<br>
- Vouchers<br>
- Taxonomy<br>
- Specimen details<br>
- CollectionData

 

uploaded for Odonatologica by Plazi
DOI: 10.5281/zenodo.35577
title: Dataset For Sensorless Drive Diagnosis

description: Electric current drive signals are measured. The drive has intact and defective components. This results in 11 different classes with different conditions. Each condition has been measured several times by different operating conditions, this means by different speeds, load moments and load forces. The current signals are measured with a current probe and an oscilloscope on two phases.
description: Relevant paper:

[1]	F. Paschke, C. Bayer, M. Bator, U. Mönks, A. Dicks, O. Enge-Rosenblatt, and V. Lohweg, “Sensorlose Zustandsüberwachung an Synchronmotoren,” in Proceedings 23. Workshop Computational Intelligence, Karlsruhe: KIT Scientific Publishing, 2013, pp. 211–225.
[2]	C. Bayer, M. Bator, U. Mönks, A. Dicks, O. Enge-Rosenblatt, and V. Lohweg, “Sensorless Drive Diagnosis Using Automated Feature Extraction, Significance Ranking and Reduction,” in 18th IEEE Int. Conf. on Emerging Technologies and Factory Automation (ETFA 2013): IEEE, 2013, pp. 1–4.
DOI: 10.5281/zenodo.35584
title: Diversity Of Bacterial Communities On Four Frequently Used Surfaces In A Large Brazilian Teaching Hospital

description: Frequently used hand-touch surfaces in hospital settings have been implicated as a vehicle of microbial transmission. In this study, we aimed to investigate the overall bacterial population on four frequently used surfaces using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Surface samples were collected from four sites, namely elevator buttons (EB), bank machine keyboard buttons (BMKB), restroom surfaces, and the employee biometric time clock system (EBTCS), in a large public and teaching hospital in Sao Paulo. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Actinobacteria and Proteobacteria, with a total of 926 bacterial families and 2832 bacterial genera. Moreover, our analysis revealed the presence of some potential pathogenic bacterial genera, including <em>Salmonella enterica</em>, <em>Klebsiella pneumoniae</em>, and <em>Staphylococcus aureus</em>. The presence of these pathogens in frequently used surfaces enhances the risk of exposure to any susceptible individuals. Some of the factors that may contribute to the richness of bacterial diversity on these surfaces are poor personal hygiene and ineffective routine schedules of cleaning, sanitizing, and disinfecting. Strict standards of infection control in hospitals and increased public education about hand hygiene are recommended to decrease the risk of transmission in hospitals among patients.
DOI: 10.5281/zenodo.51700
title: Hemoglobin Metabolism After Hemorrhagic Stroke

description: Raw data from research on hemoglobin metabolism in the pathophysiology of hemorrhagic stroke
DOI: 10.5281/zenodo.51704
title: Tavush Children Dataset

description: This data was gathered from 6 months to 6 year old children information gathered in 2013 from Berd Region in Armenia. For more information and data dictionary please contact: arinbalalian@gmail.com
DOI: 10.5281/zenodo.51864
title: Sample Data

description: Sample data
DOI: 10.5281/zenodo.51900
title: Jissn Downhill Running Data

description: Data for study entitled: The Effects of a Multi-Ingredient Supplement on Markers of Muscle Damage and Inflammation Following Downhill Running in Females.
DOI: 10.5281/zenodo.51956
title: Raw Diffraction Images Of A Crystal Of Ferulic Acid Esterase (Fae) Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using The Esrf Robodiff Goniometer

description: In order to demonstrate the data collection capabilities of the RoboDiff diffraction data were collected from a crystal of FAE to demonstrate the suitability of the beamline MASSIF-1 and RoboDiff for ab initio phasing experiments using diffraction data collected at wavelengths at or remote from the absorption edges of the anomalous scattering elements contained in crystals.
DOI: 10.13012/b2idb-1968634_v1
title: Library Publishing Services: Survey Data on User Studies Practices

description: This data set includes survey responses collected during 2015 from academic libraries with library publishing services. Each institution responded to questions related to its use of user studies or information about readers in order to shape digital publication design, formats, and interfaces. Survey data was supplemented with institutional categories to facilitate comparison across institutional types.
DOI: 10.5281/zenodo.15989
title: Scorep Mg A 64

description: Sample Scorep trace in pj_dump format.
DOI: 10.5281/zenodo.35655
title: Dataset For: Spinal Motion And Muscle Activity During Active Trunk Movements - Comparing Sheep And Humans Adopting Upright And Quadrupedal Postures

description: Datasets used for the manuscript "Spinal motion and muscle activity during active trunk movements - comparing sheep and humans adopting upright and quadrupedal postures", accepted in PLOS ONE
DOI: 10.5281/zenodo.35672
title: Propofol_Fetal_Maternal_Pk

description: Propofol fetal maternal PK data
DOI: 10.5281/zenodo.52569
title: Developmental Stress Elicits Preference For Methamphetamine In The Spontaneously Hypertensive Rat Model Of Attention-Deficit/Hyperactivity Disorder

description: The raw data of the manuscript, "Developmental stress elicits preference for methamphetamine in the spontaneously hypertensive rat model of attention-deficit/hyperactivity disorder".