cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/by4gbgr9gd.2
title: PCAWG Intra-Tumor Heterogeneity Simulations

description: This resource contains the simutated samples that go with the paper `Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes` which is available at the URL in the Related Links section below. Please find a full description of these data in the supplementary information of this paper, as well as the full author list and credit for creation of these data. Please find below a description of the included files. PhylogicNDT500: Note difference between directories marked with and without "_all". It is recommended to not use files in "_all" directories, as they contain mutations below the detection limit of 3 variant reads. * Copynumber: Segments/ directory - Subclonal copynumber is encoded via multiple reports of the same segment with a different CCF * Variants: VCF/ directory - These follow PCAWG consensus basic read count annotations * Purity/ploidy: PP_Table/ directory * Truth clusters: Subclonal_Structure/ directory * Truth assignments: Mut_Assign/ directory * Truth mutations: Mafs_Real_Info/ directory SimClone1000 - testing: * Copynumber: *_segments.txt in each sample directory - There is no subclonal copynumber * Variants: *.vcf - These follow PCAWG consensus basic read count annotations * Purity/ploidy: Included purity_ploidy.txt file SimClone1000 - truth: * Every simulation has its own directory tree. * Truth clusters (cluster position in CCF): [samplename]/simulated_0001/truth_tree/simulated_0001_subclonal_structure.txt * Truth assignments: [samplename]/simulated_0001/truth_tree/simulated_0001_mutation_assignments.txt * Truth mutations: [samplename]/simulated_0001/simulated_0001_0001/truth/simulated_0001_0001_multiplicity.txt
DOI: 10.5281/zenodo.4696304
title: Figure 1 from article Crystals "Cadmium Telluride Nanocomposite Films Formation from Thermal Decomposition of Cadmium Carboxylate Precursor and Their Photoluminescence Shift from Green to Red"

description: The dataset includes two files: the word file describes the type of sample and the procedures used to pick up the data; the excel file includes the raw data used to obtain the plots of figure 1. In the following is reported the caption of figure 1 as wrote in the paper. Normalized emission spectra of CdTe QDs synthetized in film at different temperatures: 120 C (black line), 150 C (blue line) and 180 C (purple line): (a) at 5 min and (b) 20 min.
DOI: 10.5281/zenodo.4696303
title: Figure 1 from article Crystals "Cadmium Telluride Nanocomposite Films Formation from Thermal Decomposition of Cadmium Carboxylate Precursor and Their Photoluminescence Shift from Green to Red"

description: The dataset includes two files: the word file describes the type of sample and the procedures used to pick up the data; the excel file includes the raw data used to obtain the plots of figure 1. In the following is reported the caption of figure 1 as wrote in the paper. Normalized emission spectra of CdTe QDs synthetized in film at different temperatures: 120 C (black line), 150 C (blue line) and 180 C (purple line): (a) at 5 min and (b) 20 min.
DOI: 10.5281/zenodo.4696361
title: Figure 2 from article Cadmium Telluride Nanocomposite Films Formation from Thermal Decomposition of Cadmium Carboxylate Precursor and Their Photoluminescence Shift from Green to Red

description: The dataset includes two files: the word file describes the type of sample and the procedures used to pick up the data; the excel file includes the raw data used to obtain the plots of figure 2. In the following is reported the caption of figure 2 as wrote in the paper: Absorption and normalized PL spectra of films annealed at 150 C for (a) 5, (b) 10, (c) 20, (d) 30, (e) 60, and (f) 120 min under vacuum. Inset: photographs of the films acquired under UV lamp at 365 nm.
DOI: 10.5281/zenodo.4696360
title: Figure 2 from article Cadmium Telluride Nanocomposite Films Formation from Thermal Decomposition of Cadmium Carboxylate Precursor and Their Photoluminescence Shift from Green to Red

description: The dataset includes two files: the word file describes the type of sample and the procedures used to pick up the data; the excel file includes the raw data used to obtain the plots of figure 2. In the following is reported the caption of figure 2 as wrote in the paper: Absorption and normalized PL spectra of films annealed at 150 C for (a) 5, (b) 10, (c) 20, (d) 30, (e) 60, and (f) 120 min under vacuum. Inset: photographs of the films acquired under UV lamp at 365 nm.
DOI: 10.5281/zenodo.4696390
title: Figure 3 from paper Crystals Cadmium Telluride Nanocomposite Films Formation from Thermal Decomposition of Cadmium Carboxylate Precursor and Their Photoluminescence Shift from Green to Red

description: The dataset includes two files: the word file describes the type of sample and the procedures used to pick up the data; the excel file includes the raw data used to obtain the plots of figure 3. In the following is reported the description of figure 3 as wrote in the paper: <strong>Estimated average size of the CdTe nanocrystals (d) as a function of the annealing time.</strong>
DOI: 10.5281/zenodo.4696389
title: Figure 3 from paper Crystals Cadmium Telluride Nanocomposite Films Formation from Thermal Decomposition of Cadmium Carboxylate Precursor and Their Photoluminescence Shift from Green to Red

description: The dataset includes two files: the word file describes the type of sample and the procedures used to pick up the data; the excel file includes the raw data used to obtain the plots of figure 3. In the following is reported the description of figure 3 as wrote in the paper: <strong>Estimated average size of the CdTe nanocrystals (d) as a function of the annealing time.</strong>
DOI: 10.5281/zenodo.4697054
title: Figure 4 from article Crystals "Cadmium Telluride Nanocomposite Films Formation from Thermal Decomposition of Cadmium Carboxylate Precursor and Their Photoluminescence Shift from Green to Red

description: The dataset includes two files: the word file describes the type of sample and the procedures used to pick up the data; the excel file includes the raw data used to obtain the plots of figure 4. In the following is reported the description of figure 4 as wrote in the paper. PL peak position as a function of CdTe QDs size grown in film (the first linear fit for the growth of CdTe QDs from 5 to 20 min is reported as solid line and circles; the second linear fit for the growth of CdTe QDs from 30 to 120 min is reported as solid line and spheres).
DOI: 10.5281/zenodo.4697053
title: Figure 4 from article Crystals "Cadmium Telluride Nanocomposite Films Formation from Thermal Decomposition of Cadmium Carboxylate Precursor and Their Photoluminescence Shift from Green to Red

description: The dataset includes two files: the word file describes the type of sample and the procedures used to pick up the data; the excel file includes the raw data used to obtain the plots of figure 4. In the following is reported the description of figure 4 as wrote in the paper. PL peak position as a function of CdTe QDs size grown in film (the first linear fit for the growth of CdTe QDs from 5 to 20 min is reported as solid line and circles; the second linear fit for the growth of CdTe QDs from 30 to 120 min is reported as solid line and spheres).
DOI: 10.25380/iastate.14439494
title: Texture data of Additively Manufactured Ti-6Al-4V (Different Scanning Strategies)

description: Electron Backscatter Diffraction data collected from 3 electron-beam Ti-6-Al-4V AM samples, using 3 different additive manufacturing techniques: raster (L), Dehoff (D) and random (R), at three different heights (bottom, middle and top) of the builds.<br>
DOI: 10.25380/iastate.14439494.v1
title: Texture data of Additively Manufactured Ti-6Al-4V (Different Scanning Strategies)

description: Electron Backscatter Diffraction data collected from 3 electron-beam Ti-6-Al-4V AM samples, using 3 different additive manufacturing techniques: raster (L), Dehoff (D) and random (R), at three different heights (bottom, middle and top) of the builds.<br>
DOI: 10.6084/m9.figshare.14442284
title: Enzyme activity in seasonal snow, Snowy Range, WY

description: This dataset includes locations of snow sample collections in the Snowy Range, WY, snow chemistry data and potential microbial extracellular enzyme activity from enzyme assays.
DOI: 10.6084/m9.figshare.14442284.v1
title: Enzyme activity in seasonal snow, Snowy Range, WY

description: This dataset includes locations of snow sample collections in the Snowy Range, WY, snow chemistry data and potential microbial extracellular enzyme activity from enzyme assays.
DOI: 10.15468/rjmthu
title: Two new species of Tingidae (Insecta: Heteroptera) from Papua New Guinea

description: This dataset contains the digitized treatments in Plazi based on the original journal article Guilbert, Eric (2021): Two new species of Tingidae (Insecta: Heteroptera) from Papua New Guinea. Zootaxa 4952 (3): 589-595, DOI: https://doi.org/10.11646/zootaxa.4952.3.11
DOI: 10.5281/zenodo.4697690
title: Silent Misconfiguration Study

description: Silent Misconfiguration Study
DOI: 10.5281/zenodo.4697689
title: Silent Misconfiguration Study

description: Silent Misconfiguration Study
DOI: 10.25345/c5d232
title: MassIVE MSV000087218 - AlgP is associated with Polyphosphate Granules During Nitrogen Starvation in Pseudomonas aeruginosa
title: Nitrogen starvation results in polyphosphate accumulation in Pseudomonas aeruginosa. Using Percoll gradient centrifugation, we pelleted polyphosphate granules and compared their composition to the unfractionated cell lysate using mass spectrometry. Among the enriched proteins was the alginate regulatory protein AlgP. Its unusual amino-acid composition, overall charge, and physicochemical properties lead us to further investigate its role in granule association and spacing in Pseudomonas aeruginosa.
DOI: 10.15468/2h5sms
title: Redescriptions and new species in the ‘ Austrosignum-Munnogonium’ complex sensu Just & Wilson (2007), mainly from the Southern Hemisphere (Crustacea Isopoda: Paramunnidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Just, Jean, Wilson, George D. F. (2021): Redescriptions and new species in the ‘ Austrosignum-Munnogonium’ complex sensu Just & Wilson (2007), mainly from the Southern Hemisphere (Crustacea Isopoda: Paramunnidae). Zootaxa 4952 (3): 401-447, DOI: https://doi.org/10.11646/zootaxa.4952.3.1
DOI: 10.6073/pasta/070bbb849cd6ca77fc623be7fa0ba0bc
title: Soil temperature data from the Arctic LTER Moist Acidic Tussock Experimental plots from 2008 to 2020, Toolik Filed Station, North Slope, Alaska.

description: Soil temperature data from the 1989 LTER Moist Acidic Tussock (MAT89) Experimental plots. The logging station was installed in 1990 in block 2 of a four block experimental block design. The plots are located on a hillside near Toolik Lake (68 38' N, 149 36'W). Two replicates depth profiles (10, 20 ,40 centimeters) were installed in each block 2 experimental plots. Frost heaving has caused uncertain depths of measurements for many of the profiles. This data set cotains oly the control profiles from 2011 to 2020.
DOI: 10.21227/ac97-8m18
title: CATARACTS

description: A fundamental building block of any computer-assisted interventions (CAI) is the ability to automatically understand what the surgeons are performing throughout the surgery. In other words, recognizing the surgical activities being performed or the tools being used by the surgeon can be deemed as an essential steps toward CAI. The main motivation for these tasks is to design efficient solutions for surgical workflow analysis. The CATARACTS dataset was proposed in this context. This dataset consists of 50 cataract surgery. It was annotated for two main tasks: surgical tool presence detection and surgical activity recognition. It was divided into two sets (train, test) for the surgical tool presence detection task and 3 sets (train, dev, test) for the activity recognition task. This dataset was used in three different: CATARACTS2017, CATARACTS2018 and CATARACTS2020. The ground truth of the test sets of these challenges are now released so the community can use it to benchmark algorithms for sugical workflow analysis.
DOI: 10.15468/peuwan
title: Distribution, habitats, and redescription of the rare mite species Iphidonopsis sculptus Gwiazdowicz, 2004 (Mesostigmata: Ascidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Makarova, Olga L., Marchenko, Irina I., Lindquist, Evert E. (2021): Distribution, habitats, and redescription of the rare mite species Iphidonopsis sculptus Gwiazdowicz, 2004 (Mesostigmata: Ascidae). Zootaxa 4952 (3): 448-464, DOI: https://doi.org/10.11646/zootaxa.4952.3.2
DOI: 10.3886/e119446v81
title: COVID-19 US State Policy Database

description: For questions or comments about the database please contact:<br>Alexandra Skinner <br>skinnera@bu.edu <br>Research Fellow & Database Manager<br>Department of Health Law, Policy & Management <br>Boston University School of Public Health<br><br>Database of state policies on closures, shelter-in-place orders, housing protections, changes to Medicaid and SNAP, physical distancing closures, reopening, and more created by researchers at the Boston University School of Public Health. Policies included are state-wide directives or mandates, not guidance or recommendations. In order for a policy to be included, it must apply to the entire state. We are working quickly to go through state government websites to make the policy database as complete and accurate as possible in a rapidly changing policy context. If you use data on a given policy, we encourage you to triangulate based on additional sources of policy data and to review the source documentation to consider the coding decisions that are right for your work. Of course, please email us if you note a discrepancy so we can improve the database for everyone. State policy source documentation can be found at: tinyurl.com/statepolicysources.
description: State policies. Smallest Geographic Unit: State
description: other; Contributors: Megan Cole Brahim, Noa Krawczyk, Carolyn Hoffman, Claire Corkish, Elizabeth Ferrara, Elizabeth Long, Emily Baroni, Faith Contador, Hannah Simon, Morgan Simko, Rachel Scheckman, Sarah Brewer, Sue Kulkarni, Felicia Heykoop, Manish Patel, Aishwarya Vidyasagaran, Andrew Chiao, Cara Safon, Samantha Burkhart, Harry Jung, Victor Lee, Marina MacKinnon, Aarohi Rede, Marie Vearling, Sophie Li, Christina Wang, Tim Levengood, María Jordán P. Emma Chistolini
DOI: 10.25345/c58b9v
title: MassIVE MSV000087219 - Oncogene Regulated Release of Extracellular Vesicles
title: Oncogenes can alter metabolism by changing the balance between anabolic and catabolic processes. However, how oncogenes regulate tumor cell biomass remains poorly understood. Using isogenic MCF10A cells transformed with nine different oncogenes, we show that specific oncogenes reduce the biomass of cancer cells by promoting EV release. While MYC and AURKB elicited the highest number of EVs, each oncogene selectively altered the protein composition of released EVs. Likewise, oncogenes alter secreted miRNAs. MYC overexpressing cells require ceramide, while AURKB require ESCRT to release high levels of EVs. We identify an inverse relationship between MYC upregulation and activation of the RAS/MEK/ERK signaling pathway for regulating EV release in some tumor cells. Finally, lysosome genes and activity are downregulated in the context of MYC and AURKB, suggesting that cellular contents instead of being degraded, were released via EVs. Thus, oncogene mediated biomass regulation via differential EV release is a new metabolic phenotype.
DOI: 10.6084/m9.figshare.14071283
title: SACT template

description: We establsihed the SACT template by using a large sample of diffusion data of school-age children (380 participants). We provided two types of diffusion tensor (DT) templates. One is for the entire age range (6-12 years old), another one is for each specific age.Under the downloaded data, four folders are corresponding to different kinds of templates. Specifically, SACT includes the tensor template of the entire age range (‘SACT_06_12_DT.nii.gz’) which is in the same space as the CHN-PD template (https://helab.bnu.edu.cn/chn-pd/). The corresponding fractional anisotropy (FA) and trace map (3*Mean diffusivity, MD) are also available (‘SACT_06_12_DT_fa.nii.gz’, ‘SACT_06_12_DT_tr.nii.gz’). The ‘SACT_06_12_mask.nii.gz’ is the brain mask. Similarly, age-specific templates can be found in the age-specific folders, e.g., ‘/Age_Specific_SACT/Age_06_07’. Here, ‘06_07’ stands for the age range between 6 years old and 7 years old. To conveniently use the SACT template with tensor-based registration methods (DTI-TK), we also provided the corresponding templates which are padded with zeros to ensure the matrix size of the template as 256*256*256, which are available under the folders ended with ‘DTI_TK’.Moreover, the tensor templates are organized as six tensor components stored in the lower triangular order, i.e., Dxx, Dyx, Dyy, Dzx, Dzy, and Dzz. It is in the same order as the one specified by the NIfTI standard. The unit of diffusivity is 10-3mm2.s-1.Finally, to conveniently and accurately use the SACT template for the TBSS (ref. 1) analysis, we provided the ‘SACT_LowerCingulum_1mm.nii.gz’ under the ‘TBSS’ folder of each template. As the mask of the lower cingulum would be required for the skeleton process (ref. 1), we compensated the difference between SACT template and FMRIB58_FA template by registering the FMRIB58_FA template to the corresponding SACT template. Then, the warp field were applied to the mask of the lower cingulum corresponding to the FMRIB58_FA template.<br>Ref.1:S.M. Smith, M. Jenkinson, H. Johansen-Berg, D. Rueckert, T.E. Nichols, C.E. Mackay, K.E. Watkins, O. Ciccarelli, M.Z. Cader, P.M. Matthews, and T.E.J. Behrens. Tract-based spatial statistics: Voxelwise analysis of multi-subject diffusion data. NeuroImage, 31:1487-1505, 2006.
DOI: 10.6073/pasta/ab4694e723c4c3f94792bec64141c00f
title: Soil temperature data from the control Arctic LTER Moist Acidic Tussock (MAT89) Experimental plots from 2008 to 2020, Toolik Field Station, North Slope, Alaska.

description: Soil temperature data from the 1989 LTER Moist Acidic Tussock (MAT89) Experimental plots. The logging station was installed in 1990 in block 2 of a four block experimental block design. The plots are located on a hillside near Toolik Lake (68 38' N, 149 36'W). Two replicates depth profiles (10, 20 ,40 centimeters) were installed in each block 2 experimental plots. Frost heaving has caused uncertain depths of measurements for many of the profiles. This data set contains only the control profiles from 2008 to 2020.
DOI: 10.5517/ccdc.csd.cc24zz7c
title: CCDC 1995973: Experimental Crystal Structure Determination

description: Related Article: Lukas Klemmer, Anna-Lena Thömmes, Michael Zimmer, Volker Huch, Bernd Morgenstern, David Scheschkewitz |2021|Nature Chemistry|13|373|doi:10.1038/s41557-021-00639-9
DOI: 10.5517/ccdc.csd.cc24zz8d
title: CCDC 1995974: Experimental Crystal Structure Determination

description: Related Article: Lukas Klemmer, Anna-Lena Thömmes, Michael Zimmer, Volker Huch, Bernd Morgenstern, David Scheschkewitz |2021|Nature Chemistry|13|373|doi:10.1038/s41557-021-00639-9
DOI: 10.5517/ccdc.csd.cc25c9kf
title: CCDC 2006864: Experimental Crystal Structure Determination

description: Related Article: Narendra Kumar Vaishanv, Mohd Khalid Zaheer, Sandeep Kumar, Ruchir Kant, Kishor Mohanan|2021|J.Org.Chem.|86|5630|doi:10.1021/acs.joc.1c00109
DOI: 10.5517/ccdc.csd.cc25fl6f
title: CCDC 2009054: Experimental Crystal Structure Determination

description: Related Article: Narendra Kumar Vaishanv, Mohd Khalid Zaheer, Sandeep Kumar, Ruchir Kant, Kishor Mohanan|2021|J.Org.Chem.|86|5630|doi:10.1021/acs.joc.1c00109
DOI: 10.6073/pasta/5bec91673a0bd177777381b490247241
title: Soil temperatures and moisture for Arctic Long Term Experimental Research (ARC LTER) heath experimental plots, Toolik Field Station, North Slope Alaska for 2001-2018.

description: Soil temperatures at 2 depths, 5 and 10 cm, canopy temperatures and soil moisture at 10 cm were measured in a heath tundra Arctic Long Term Experimental Research (ARC-LTER) site at Toolik Lake Field Station, North slope, Alaska. Air temperature and relative humidity and global radiation were also measured but are presented in another dataset. Only control and nutrient addition (nitrogen plus phosphorus ) treatments plots were measured .
DOI: 10.6084/m9.figshare.14435030
title: true_16s_99_rdp.fa

description: Here are the file of RDP database for Qiime2 (in development because some errors are still encountered...) <br>
DOI: 10.6084/m9.figshare.14435030.v1
title: true_16s_99_rdp.fa

description: Here are the file of RDP database for Qiime2 (in development because some errors are still encountered...) <br>
DOI: 10.6084/m9.figshare.14442567
title: The Block-Poisson Estimator for Optimally Tuned Exact Subsampling MCMC

description: Speeding up Markov Chain Monte Carlo (MCMC) for datasets with many observations by data subsampling has recently received considerable attention. A pseudo-marginal MCMC method is proposed that estimates the likelihood by data subsampling using a block-Poisson estimator. The estimator is a product of Poisson estimators, allowing us to update a single block of subsample indicators in each MCMC iteration so that a desired correlation is achieved between the logs of successive likelihood estimates. This is important since pseudo-marginal MCMC with positively correlated likelihood estimates can use substantially smaller subsamples without adversely affecting the sampling efficiency. The block-Poisson estimator is unbiased but not necessarily positive, so the algorithm runs the MCMC on the absolute value of the likelihood estimator and uses an importance sampling correction to obtain consistent estimates of the posterior mean of any function of the parameters. Our article derives guidelines to select the optimal tuning parameters for our method and shows that it compares very favourably to regular MCMC without subsampling, and to two other recently proposed exact subsampling approaches in the literature.
DOI: 10.6084/m9.figshare.14442567.v1
title: The Block-Poisson Estimator for Optimally Tuned Exact Subsampling MCMC

description: Speeding up Markov Chain Monte Carlo (MCMC) for datasets with many observations by data subsampling has recently received considerable attention. A pseudo-marginal MCMC method is proposed that estimates the likelihood by data subsampling using a block-Poisson estimator. The estimator is a product of Poisson estimators, allowing us to update a single block of subsample indicators in each MCMC iteration so that a desired correlation is achieved between the logs of successive likelihood estimates. This is important since pseudo-marginal MCMC with positively correlated likelihood estimates can use substantially smaller subsamples without adversely affecting the sampling efficiency. The block-Poisson estimator is unbiased but not necessarily positive, so the algorithm runs the MCMC on the absolute value of the likelihood estimator and uses an importance sampling correction to obtain consistent estimates of the posterior mean of any function of the parameters. Our article derives guidelines to select the optimal tuning parameters for our method and shows that it compares very favourably to regular MCMC without subsampling, and to two other recently proposed exact subsampling approaches in the literature.