cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10518083
title: emacs-gc-stats: Does garbage collection actually slow down Emacs?

description: This dataset contains raw data, reproducible analysis (Org file), and presentation sources (Org file) for "emacs-gc-stats: Does garbage collection actually slow down Emacs?" presented at EmacsConf 2023: https://emacsconf.org/2023/talks/gc/
The file structure (inside the compressed emacs-gc-stats.tar.gz):

analysis.org contains the Org sources to generate all the plots
presentation.org contains the Org source of the presentation
0.eld - 129.eld contain the raw submitted data
*.svg files are annotated graphs prepared for the presentation
gc-duration/ contains processed statistics of GC duration
gc-duration-evo/ contains statistics of GC evolution over time
gc-merged/ contains statistics of agglomerated GCs
gc-pause/ contains statistics of GC frequency
dat/ contains filtered raw data in tabulated format prepared for Gnuplot
DOI: 10.6084/m9.figshare.25002824
title: Supplementary Material for: Genome-wide analysis of DNA methylation in pseudomyxoma peritonei originated from appendiceal neoplasms

description: Introduction:
Pseudomyxoma peritonei (PMP) is a disease characterized by progressive accumulation of intraperitoneal mucinous ascites produced by neoplasms in the abdominal cavity. Since the prognosis of patients with PMP remain unsatisfactory, the development of effective therapeutic drug(s) is a matter of pressing concern. Genetic analyses of PMP have clarified the frequent activation of GNAS and/or KRAS. However, the involvement of global epigenetic alterations in PMPs has not been reported.

Methods:
To clarify the genetic background of the 15 PMP tumors, we performed genetic analysis using AmpliSeq Cancer HotSpot Panel v2. We further investigated global DNA methylation in the 15 tumors and eight non-cancerous colonic epithelial cells using Methylation EPIC array BeadChip (Infinium 850k) containing a total of 865,918 probes. 

Results:
This is the first report of comprehensive DNA methylation profiles of PMPs in the world. We clarified that the 15 PMPs could be classified into at least two epigenotypes, unique methylation epigenotype (UME) and normal-like methylation epigenotype (NLME), and that genes associated with neuronal development and synaptic signaling may be involved in the development of PMPs. In addition, we identified a set of hypermethylation marker genes such as HOXD1 and TSPYL5 in the 15 PMPs.

Conclusions:
These findings may help the understanding of the molecular mechanism(s) of PMP and contribute to the development of therapeutic strategies for this life-threatening disease.
DOI: 10.6084/m9.figshare.25002830
title: Supplementary Material for: Genome-wide analysis of DNA methylation in pseudomyxoma peritonei originated from appendiceal neoplasms

description: Introduction:
Pseudomyxoma peritonei (PMP) is a disease characterized by progressive accumulation of intraperitoneal mucinous ascites produced by neoplasms in the abdominal cavity. Since the prognosis of patients with PMP remain unsatisfactory, the development of effective therapeutic drug(s) is a matter of pressing concern. Genetic analyses of PMP have clarified the frequent activation of GNAS and/or KRAS. However, the involvement of global epigenetic alterations in PMPs has not been reported.

Methods:
To clarify the genetic background of the 15 PMP tumors, we performed genetic analysis using AmpliSeq Cancer HotSpot Panel v2. We further investigated global DNA methylation in the 15 tumors and eight non-cancerous colonic epithelial cells using Methylation EPIC array BeadChip (Infinium 850k) containing a total of 865,918 probes. 

Results:
This is the first report of comprehensive DNA methylation profiles of PMPs in the world. We clarified that the 15 PMPs could be classified into at least two epigenotypes, unique methylation epigenotype (UME) and normal-like methylation epigenotype (NLME), and that genes associated with neuronal development and synaptic signaling may be involved in the development of PMPs. In addition, we identified a set of hypermethylation marker genes such as HOXD1 and TSPYL5 in the 15 PMPs.

Conclusions:
These findings may help the understanding of the molecular mechanism(s) of PMP and contribute to the development of therapeutic strategies for this life-threatening disease.
DOI: 10.6084/m9.figshare.25002830.v1
title: Supplementary Material for: Genome-wide analysis of DNA methylation in pseudomyxoma peritonei originated from appendiceal neoplasms

description: Introduction:
Pseudomyxoma peritonei (PMP) is a disease characterized by progressive accumulation of intraperitoneal mucinous ascites produced by neoplasms in the abdominal cavity. Since the prognosis of patients with PMP remain unsatisfactory, the development of effective therapeutic drug(s) is a matter of pressing concern. Genetic analyses of PMP have clarified the frequent activation of GNAS and/or KRAS. However, the involvement of global epigenetic alterations in PMPs has not been reported.

Methods:
To clarify the genetic background of the 15 PMP tumors, we performed genetic analysis using AmpliSeq Cancer HotSpot Panel v2. We further investigated global DNA methylation in the 15 tumors and eight non-cancerous colonic epithelial cells using Methylation EPIC array BeadChip (Infinium 850k) containing a total of 865,918 probes. 

Results:
This is the first report of comprehensive DNA methylation profiles of PMPs in the world. We clarified that the 15 PMPs could be classified into at least two epigenotypes, unique methylation epigenotype (UME) and normal-like methylation epigenotype (NLME), and that genes associated with neuronal development and synaptic signaling may be involved in the development of PMPs. In addition, we identified a set of hypermethylation marker genes such as HOXD1 and TSPYL5 in the 15 PMPs.

Conclusions:
These findings may help the understanding of the molecular mechanism(s) of PMP and contribute to the development of therapeutic strategies for this life-threatening disease.
DOI: 10.5281/zenodo.10516596
title: Dataset for article titled "Topography effect on seismic waveform tomography: A quantitative study"

description: These files support a manuscript entitled "Topography effect on seismic waveform tomography: A quantitative study", by Kaiyue Zheng, Yi Wang and Li Zhao. This research has been supported by the Natural Science Foundation of China (Grants 42021003, 41974046 and 42104052), Shanghai Sheshan National Geophysical Observatory (No. SSOP202106) and Shandong Key Laboratory of Mining Disaster Prevention and Control, Shandong University of Science and Technology (No. SMDPC202202).
DOI: 10.5281/zenodo.10516597
title: Dataset for article titled "Topography effect on seismic waveform tomography: A quantitative study"

description: These files support a manuscript entitled "Topography effect on seismic waveform tomography: A quantitative study", by Kaiyue Zheng, Yi Wang and Li Zhao. This research has been supported by the Natural Science Foundation of China (Grants 42021003, 41974046 and 42104052), Shanghai Sheshan National Geophysical Observatory (No. SSOP202106) and Shandong Key Laboratory of Mining Disaster Prevention and Control, Shandong University of Science and Technology (No. SMDPC202202).
DOI: 10.57745/mbxyjz
title: ExpeComModData.csv

description: Data set including all data collected during the experiments. One line is an observation and one column is a variable. Variables are described in the expeComModVariables.csv file.
DOI: 10.57745/bbrmi0
title: expeComModVariables.csv

description: Description of each variable of the dataset (in expeComModData.csv file).
DOI: 10.5281/zenodo.10517652
title: Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties

description: The data for manuscript "Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties" are deposited here.

FOLDER GrowthFolder contains all biological replicates for co-culture cell growth experiments. Each file contains growth data for LNCaP, LNCaP-abl or Fibroblast cells for all technical replicates within that biological replicate. The first block contains the raw GFP signal from the wells for each technical relicate. The second block contains the technical replicate data normalized to the time-point of initial cell growth. The third block contains the mean and standard deviation over technical replicates for each combination of cells (click on the excel-cells to find which wells were included).Mean data was used for particle swarm optimization, Figures 3 and 4, and Supplementary Figures 1,2,3,4 and 5.

FOLDER ApoptosisFolder contains all biological replicates for each apoptosis experiment of LNCaP cells. In each file, the first block contains the raw red object count form the wells for each technical replicate. The second block contains the mean and standard deviation over tehcnical replicates. Data was used in Supplementary Figure 2.

FOLDER Hormone conditions. Folder contains the single biological replicate for variation of hormone conditions for each cell type in the different co-cultures. Each file contains LNCaP growth for all technical replicates. The first block contains the raw GFP signal from the wells for each technical relicate. The second block contains the data normalized to the time-point of initial cell growth. The third block contains the mean and standard deviation over technical replicates for each combination of cells (click on the excel-cells to find which wells were included).Data was used in Figure 4.
DOI: 10.5281/zenodo.10517653
title: Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties

description: The data for manuscript "Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties" are deposited here.

FOLDER GrowthFolder contains all biological replicates for co-culture cell growth experiments. Each file contains growth data for LNCaP, LNCaP-abl or Fibroblast cells for all technical replicates within that biological replicate. The first block contains the raw GFP signal from the wells for each technical relicate. The second block contains the technical replicate data normalized to the time-point of initial cell growth. The third block contains the mean and standard deviation over technical replicates for each combination of cells (click on the excel-cells to find which wells were included).Mean data was used for particle swarm optimization, Figures 3 and 4, and Supplementary Figures 1,2,3,4 and 5.

FOLDER ApoptosisFolder contains all biological replicates for each apoptosis experiment of LNCaP cells. In each file, the first block contains the raw red object count form the wells for each technical replicate. The second block contains the mean and standard deviation over tehcnical replicates. Data was used in Supplementary Figure 2.

FOLDER Hormone conditions. Folder contains the single biological replicate for variation of hormone conditions for each cell type in the different co-cultures. Each file contains LNCaP growth for all technical replicates. The first block contains the raw GFP signal from the wells for each technical relicate. The second block contains the data normalized to the time-point of initial cell growth. The third block contains the mean and standard deviation over technical replicates for each combination of cells (click on the excel-cells to find which wells were included).Data was used in Figure 4.
DOI: 10.5281/zenodo.10518002
title: Dataset related to the article "N-acetylcysteine Amide AD4/NACA and Thioredoxin Mimetic Peptides Inhibit Platelet Aggregation and Protect against Oxidative Stress"

description: This record contains raw data related to the article "N-acetylcysteine Amide AD4/NACA and Thioredoxin Mimetic Peptides Inhibit Platelet Aggregation and Protect against Oxidative Stress"

Abstract: In the present study, we tested the effect of small-molecular-weight redox molecules oncollagen-induced platelet aggregation. We used N-acetylcysteine amide (AD4/NACA), the amideform of N-acetylcysteine (NAC), a thiol antioxidant with improved lipophilicity and bioavailabilitycompared to NAC, and the thioredoxin-mimetic (TXM) peptides, TXM-CB3, TXM-CB13, andTXM-CB30. All compounds significantly inhibited platelet aggregation induced by collagen, withTXM-peptides and AD4 being more effective than NAC. The levels of TxB2 and 12-HETE, the mainmetabolites derived from the cyclooxygenase and lipoxygenase pathways following platelet activation,were significantly reduced in the presence of AD4, TXM peptides, or NAC, when tested at thehighest concentration (0.6 mM). The effects of AD4, TXM-peptides, and NAC were also tested onthe clotting time (CT) of whole blood. TXM-CB3 and TXM-CB30 showed the greatest increase in CT.Furthermore, two representative compounds, TXM-CB3 and NAC, showed an increase in the antioxidantfree sulfhydryl groups of plasma detected via Ellman’s method, suggesting a contributionof plasma factors to the antiaggregating effects. Our results suggest that these small-molecularweightredox peptides might become useful for the prevention and/or treatment of oxidative stressconditions associated with platelet activation.
DOI: 10.5281/zenodo.10518003
title: Dataset related to the article "N-acetylcysteine Amide AD4/NACA and Thioredoxin Mimetic Peptides Inhibit Platelet Aggregation and Protect against Oxidative Stress"

description: This record contains raw data related to the article "N-acetylcysteine Amide AD4/NACA and Thioredoxin Mimetic Peptides Inhibit Platelet Aggregation and Protect against Oxidative Stress"

Abstract: In the present study, we tested the effect of small-molecular-weight redox molecules oncollagen-induced platelet aggregation. We used N-acetylcysteine amide (AD4/NACA), the amideform of N-acetylcysteine (NAC), a thiol antioxidant with improved lipophilicity and bioavailabilitycompared to NAC, and the thioredoxin-mimetic (TXM) peptides, TXM-CB3, TXM-CB13, andTXM-CB30. All compounds significantly inhibited platelet aggregation induced by collagen, withTXM-peptides and AD4 being more effective than NAC. The levels of TxB2 and 12-HETE, the mainmetabolites derived from the cyclooxygenase and lipoxygenase pathways following platelet activation,were significantly reduced in the presence of AD4, TXM peptides, or NAC, when tested at thehighest concentration (0.6 mM). The effects of AD4, TXM-peptides, and NAC were also tested onthe clotting time (CT) of whole blood. TXM-CB3 and TXM-CB30 showed the greatest increase in CT.Furthermore, two representative compounds, TXM-CB3 and NAC, showed an increase in the antioxidantfree sulfhydryl groups of plasma detected via Ellman’s method, suggesting a contributionof plasma factors to the antiaggregating effects. Our results suggest that these small-molecularweightredox peptides might become useful for the prevention and/or treatment of oxidative stressconditions associated with platelet activation.
DOI: 10.5281/zenodo.8254456
title: empty_60SDS_micelle_CHARMM36_TIP3P_10psSF_307K_replica2

description: empty_60SDS_micelle_CHARMM36_TIP3P_10psSF_307K_replica2
DOI: 10.5281/zenodo.8254457
title: empty_60SDS_micelle_CHARMM36_TIP3P_10psSF_307K_replica2

description: empty_60SDS_micelle_CHARMM36_TIP3P_10psSF_307K_replica2
DOI: 10.5281/zenodo.8254449
title: empty_60SDS_micelle_CHARMM36_TIP3P_10psSF_307K_replica1

description: empty_60SDS_micelle_CHARMM36_TIP3P_10psSF_307K_replica1
DOI: 10.5281/zenodo.8254450
title: empty_60SDS_micelle_CHARMM36_TIP3P_10psSF_307K_replica1

description: empty_60SDS_micelle_CHARMM36_TIP3P_10psSF_307K_replica1
DOI: 10.5281/zenodo.8183840
title: hMff_micelle_60SDS_CHARMM_310K_Na_Neut_OPC_replica3

description: hMff_micelle_60SDS_CHARMM_310K_Na_Neut_OPC_replica3
DOI: 10.5281/zenodo.8183841
title: hMff_micelle_60SDS_CHARMM_310K_Na_Neut_OPC_replica3

description: hMff_micelle_60SDS_CHARMM_310K_Na_Neut_OPC_replica3
DOI: 10.5281/zenodo.8183834
title: hMff_micelle_60SDS_CHARMM_310K_Na_Neut_OPC_replica2

description: hMff_micelle_60SDS_CHARMM_310K_Na_Neut_OPC_replica2
DOI: 10.5281/zenodo.8183835
title: hMff_micelle_60SDS_CHARMM_310K_Na_Neut_OPC_replica2

description: hMff_micelle_60SDS_CHARMM_310K_Na_Neut_OPC_replica2
DOI: 10.5281/zenodo.10023762
title: Diffraction data for SeMet-RmSBP (Radiation damage study)

description: Diffraction dataset for SeMet-RmSBP
DOI: 10.5281/zenodo.10023763
title: Diffraction data for SeMet-RmSBP (Radiation damage study)

description: Diffraction dataset for SeMet-RmSBP
DOI: 10.5281/zenodo.8183832
title: hMff_micelle_50SDS_CHARMM_310K_Na_Neut_OPC_replica3

description: hMff_micelle_50SDS_CHARMM_310K_Na_Neut_OPC_replica3
DOI: 10.5281/zenodo.8183833
title: hMff_micelle_50SDS_CHARMM_310K_Na_Neut_OPC_replica3

description: hMff_micelle_50SDS_CHARMM_310K_Na_Neut_OPC_replica3
DOI: 10.5281/zenodo.8183826
title: hMff_micelle_45SDS_CHARMM_310K_Na_Neut_OPC_replica3

description: hMff_micelle_45SDS_CHARMM_310K_Na_Neut_OPC_replica3
DOI: 10.5281/zenodo.8183827
title: hMff_micelle_45SDS_CHARMM_310K_Na_Neut_OPC_replica3

description: hMff_micelle_45SDS_CHARMM_310K_Na_Neut_OPC_replica3
DOI: 10.5281/zenodo.8183822
title: hMff_micelle_45SDS_CHARMM_310K_Na_Neut_OPC_replica2

description: hMff_micelle_45SDS_CHARMM_310K_Na_Neut_OPC_replica2
DOI: 10.5281/zenodo.8183823
title: hMff_micelle_45SDS_CHARMM_310K_Na_Neut_OPC_replica2

description: hMff_micelle_45SDS_CHARMM_310K_Na_Neut_OPC_replica2
DOI: 10.5281/zenodo.8183818
title: hMff_micelle_40SDS_CHARMM_310K_Na_Neut_OPC_replica3

description: hMff_micelle_40SDS_CHARMM_310K_Na_Neut_OPC_replica3
DOI: 10.5281/zenodo.8183819
title: hMff_micelle_40SDS_CHARMM_310K_Na_Neut_OPC_replica3

description: hMff_micelle_40SDS_CHARMM_310K_Na_Neut_OPC_replica3
DOI: 10.5281/zenodo.8183814
title: hMff_micelle_40SDS_CHARMM_310K_Na_Neut_OPC_replica2

description: hMff_micelle_40SDS_CHARMM_310K_Na_Neut_OPC_replica2
DOI: 10.5281/zenodo.8183815
title: hMff_micelle_40SDS_CHARMM_310K_Na_Neut_OPC_replica2

description: hMff_micelle_40SDS_CHARMM_310K_Na_Neut_OPC_replica2
DOI: 10.5281/zenodo.10517696
title: A dataset to assess Microsoft Copilot Answers in the Context of Swiss, Bavarian and Hesse Elections.

description: This dataset allows to assess the emerging challenges posed by Generative Artificial Intelligence, when doing Active Retrieval  Augmented Generation (RAG), especially when summarizing trustworthy sources on the internet. As a case study, we focus on Microsoft Copilot, an innovative software that integrates Large Language Models (LLMs) and Search Engines (SE) making advanced AI accessible to the general public. The core contribution of this paper is the presentation of the largest public database to date of RAG responses to user prompts, collected during the 2023 electoral campaigns in the Swiss, Bavaria and Hesse. This dataset was compiled with the assistance of a group of experts who posed realistic voter questions and conducted fact-checking of Microsoft Copilot's responses. It contains prompts and answers in English, German, French and Italian. All the collection happened during the electoral  campaign, between 21 August 2023 and 2 October 2023. The paper makes available the full set of 5,561 pairs of prompts and answers, including the quoted URLs for the source referenced in the answers. In addition to the dataset itself,  we provide 1374 answers labeled by a group of experts who rated the accuracy of the answers in providing factual information. This resource is intended to facilitate further research into the performance of LLMs in the context of elections, defined as "high-risk scenario" by the Digital Service Act (DSA).
DOI: 10.5281/zenodo.10517938
title: A dataset to assess Microsoft Copilot Answers in the Context of Swiss, Bavarian and Hesse Elections.

description: This dataset allows to assess the emerging challenges posed by Generative Artificial Intelligence, when doing Active Retrieval  Augmented Generation (RAG), especially when summarizing trustworthy sources on the internet. As a case study, we focus on Microsoft Copilot, an innovative software that integrates Large Language Models (LLMs) and Search Engines (SE) making advanced AI accessible to the general public. The core contribution of this paper is the presentation of the largest public database to date of RAG responses to user prompts, collected during the 2023 electoral campaigns in the Swiss, Bavaria and Hesse. This dataset was compiled with the assistance of a group of experts who posed realistic voter questions and conducted fact-checking of Microsoft Copilot's responses. It contains prompts and answers in English, German, French and Italian. All the collection happened during the electoral  campaign, between 21 August 2023 and 2 October 2023. The paper makes available the full set of 5,561 pairs of prompts and answers, including the quoted URLs for the source referenced in the answers. In addition to the dataset itself,  we provide 1374 answers labeled by a group of experts who rated the accuracy of the answers in providing factual information. This resource is intended to facilitate further research into the performance of LLMs in the context of elections, defined as "high-risk scenario" by the Digital Service Act (DSA).
DOI: 10.34740/kaggle/dsv/7413164
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.5281/zenodo.8183802
title: GWALP_monomer_micelle_80SDS_CHARMM_310K_Na_Neut_OPC_replica2

description: GWALP_monomer_micelle_80SDS_CHARMM_310K_Na_Neut_OPC_replica2
DOI: 10.5281/zenodo.8183803
title: GWALP_monomer_micelle_80SDS_CHARMM_310K_Na_Neut_OPC_replica2

description: GWALP_monomer_micelle_80SDS_CHARMM_310K_Na_Neut_OPC_replica2
DOI: 10.6084/m9.figshare.25002906
title: Using the geoheritage framework to explore the intersection of diverse legacies at Grand Caverns, Virginia, USA

description: A sample of the current point cloud for Grand Caverns.
DOI: 10.6084/m9.figshare.25002906.v1
title: Using the geoheritage framework to explore the intersection of diverse legacies at Grand Caverns, Virginia, USA

description: A sample of the current point cloud for Grand Caverns.
DOI: 10.5281/zenodo.8182795
title: eElab_micelle_40SDS_CHARMM_310K_Na_Neut_OPC_replica1

description: eElab_micelle_40SDS_CHARMM_310K_Na_Neut_OPC_replica1
DOI: 10.5281/zenodo.8182796
title: eElab_micelle_40SDS_CHARMM_310K_Na_Neut_OPC_replica1

description: eElab_micelle_40SDS_CHARMM_310K_Na_Neut_OPC_replica1
DOI: 10.5281/zenodo.8401867
title: Centre frequencies and uncertainties for "Evidence for a kilometre-scale seismically slow layer atop the core-mantle boundary from normal modes"

description: A table containing the centre frequencies and uncertainties used for the study presented in "Evidence for a kilometre-scale seismically slow layer atop the core-mantle boundary from normal modes". This table is the same as is contained in the supplementary materials of that paper.

Russell, S., Irving, J. C. E., Jagt, L., & Cottaar, S. (2023). Evidence for a kilometer-scale seismically slow layer atop the core-mantle boundary from normal modes. Geophysical Research Letters, 50, e2023GL105684. https://doi.org/10.1029/2023GL105684
DOI: 10.5281/zenodo.8401868
title: Centre frequencies and uncertainties for "Evidence for a kilometre-scale seismically slow layer atop the core-mantle boundary from normal modes"

description: A table containing the centre frequencies and uncertainties used for the study presented in "Evidence for a kilometre-scale seismically slow layer atop the core-mantle boundary from normal modes". This table is the same as is contained in the supplementary materials of that paper.

Russell, S., Irving, J. C. E., Jagt, L., & Cottaar, S. (2023). Evidence for a kilometer-scale seismically slow layer atop the core-mantle boundary from normal modes. Geophysical Research Letters, 50, e2023GL105684. https://doi.org/10.1029/2023GL105684