cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27074809
title: Supplementary Material for: Plasma cytokines pattern as a prognostic marker for esophageal squamous cell carcinoma via unsupervised clustering analyses

description: Introduction: Cytokines such as Tumor necrosis factor-alpha (TNF-α), Interleukin 6 (IL6), Interferon-gamma (IFN-γ), Interleukin 17-alpha (IL17-α), and Interleukin 33 (IL33), play critical roles in immune responses, and may impact cancer prognosis in future. However, few studies have simultaneously explored the prognostic impact of these cytokines for cancer. In this study, we aim to apply the unsupervised clustering analysis to approach the correlation between the expression of these cytokines and the subsequent prognosis of patients with esophageal squamous cell carcinoma.

Methods: A robust clustering algorithm was used, the Gaussian Mixture Method, through the mclust R package to group patients based on the expression of their cytokines in plasma or tumors. The 324 NTU patients were grouped into 4 clusters, and the 179 GSE53625 patients were grouped into 3 clusters based on expression in plasma and tumors, respectively. Five- and three-year overall survival (OS) and progression free survival (PFS) curves of each cluster were compared. Univariate and multivariate Cox regression analyses were also performed.

Results: We successfully distinguished the multimodal distribution of cytokines through GMM clustering, and discovered the relationship between cytokines and clinical outcomes. We observed that NTU-G3 and NTU-G4 subgroups showed most variation in 5-, 3-year OS, and 5-, 3-year PFS with NTU-G3 being associated with poorer prognosis compared to NTU-G4 (P = 0.016, 0.0052, 0.0575, and 0.0168, respectively). NTU-G3 was characterized with higher TNF-α (median = 3.855, N=78) and lower IL33 (median = 0.000, N = 78), while NTU-G4 showed lower TNF-α (median = 1.76, N = 51) and higher IL33 (median = 1.070, N = 51). The difference was statistically significant for TNF-α and IL33, with P = 0.002 and P &lt;0.0001, respectively. A multivariate Cox-regression analysis revealed that GMM clustering and T/N stage were independent factors for prognosis, suggesting that the prognosis might be dependent on these cytokines. 

Conclusions: Our data suggest that expression patterns of IL33 and TNF-α in plasma might serve as a convenient marker to predict the prognosis of ESCC in the future.
DOI: 10.13026/25fx-f706
title: EHR-DS-QA: A Synthetic QA Dataset Derived from Medical Discharge Summaries for Enhanced Medical Information Retrieval Systems

description: This dataset was designed and created to enable advancements in healthcare-
focused large language models, particularly in the context of retrieval-
augmented clinical question-answering capabilities. Developed using a self-
constructed pipeline based on the 13-billion parameter Meta Llama 2 model,
this dataset encompasses 21466 medical discharge summaries extracted from the
MIMIC-IV-Note dataset, with 156599 synthetically generated question-and-answer
pairs, a subset of which was verified for accuracy by a physician. These pairs
were generated by providing the model with a discharge summary and instructing
it to generate question-and-answer pairs based on the contextual information
present in the summaries. This work aims to generate data in support of the
development of compact large language models capable of efficiently extracting
information from medical notes and discharge summaries, thus enabling
potential improvements for real-time decision-making processes in clinical
settings. Additionally, accompanying the dataset is code facilitating
question-and-answer pair generation from any medical and non-medical text.
Despite the robustness of the presented dataset, it has certain limitations.
The generation process was confined to a maximum context length of 6000 input
tokens, owing to hardware constraints. The large language model's nature in
generating these question-and-answer pairs may introduce an underlying bias or
a lack in diversity and complexity. Future iterations should focus on
rectifying these issues, possibly through diversified training and expanded
verification procedures as well as the employment of more powerful large
language models.
DOI: 10.14284/346
title: Global contourite distribution database, version 3

description: This product offers a global overview of contourite distribution. Contourites are sedimentary units which are deposited or substantially reworked by alongslope bottom currents. They refer to the lithological unit and the terminology reflects the grain size of the sediment. Drifts refer to the same sedimentary unit as a contourite, but the word 'drift' reflects the morphological appearance of the sedimentary unit. The product was elaborated digitizing the information from several hundred published scientific papers.
description: More info: https://www.marineregions.org/sources.php#contourite
DOI: 10.17188/1313928
title: Materials Data on SiC3 by Materials Project

description: SiC(C)2 crystallizes in the tetragonal I4/mmm space group. The structure is two-dimensional and consists of two C sheets oriented in the (0, 0, 1) direction and two SiC sheets oriented in the (0, 0, 1) direction. In each C sheet, C+1.33- is bonded in a square co-planar geometry to four equivalent C+1.33- atoms. All C–C bond lengths are 1.80 Å. In each SiC sheet, Si4+ is bonded in a square co-planar geometry to four equivalent C+1.33- atoms. All Si–C bond lengths are 1.80 Å. C+1.33- is bonded in a square co-planar geometry to four equivalent Si4+ atoms.
DOI: 10.18434/m32073
title: NIST's Integrated Colony Enumerator

description: This work involves only data processing software and does not involve data to publish. Data are acquired by the users of this software by the following methods. Two methods can be used to acquire images of agar plates with bacterial colonies grown. In the first, plates were placed on a flatbed scanner, covered by soft gloss paper (HP LaserJet soft gloss paper), and 8-bit grayscale images of the plates were obtained at 300 dpi (dots per inch; 118 dots per cm), 600 dpi (236 dots per cm), and 1,200 dpi (472 dots per cm). In the second approach, images are acquired with a digital camera. Images are acquired at the maximum resolution of the camera with no zoom. More details are described in the manual for the software.
DOI: 10.18712/nsd-nsd2971-v2
title: Norwegian Public Inquiry Commissions Dataset

description: The dataset is generated from available data (from The National Library of Norway and regjeringen.no) and gives an overview of all Official Norwegian Reports committees and working group, members, and secretaries between 1972 to 2020. It has many similarities to Sikts utvalgsdatabase. The registry is a combination of information from the Official Norwegian Reports, including the members and secretaries occupational title, name, and organizational/institutional affiliation. The dataset includes name of the registered and indirectly identifiable personal information.

The data was collected in connection with the research project EUREX (2016-2020), which was a collaboration between the University of Oslo and Leiden University. The project was funded by the Norwegian Research Council, the ISF-project is internally funded.
DOI: 10.25919/4jwj-na34
title: Soil and Landscape Grid National Soil Attribute Maps - Available Volumetric Water Capacity (Percent) (3 arc second resolution) Version 2

description: This is Version 2 of the Australian Available Volumetric Water Capacity (AWC) product of the Soil and Landscape Grid of Australia.

The map gives a modelled estimate of the spatial distribution of AWC soil hydraulic property in soils across Australia.

The Soil and Landscape Grid of Australia has produced a range of digital soil attribute products. Each product contains six digital soil attribute maps, and their upper and lower confidence limits, representing the soil attribute at six depths: 0-5cm, 5-15cm, 15-30cm, 30-60cm, 60-100cm and 100-200cm. These depths are consistent with the specifications of the GlobalSoilMap.net project (https://esoil.io/TERNLandscapes/Public/Pages/SLGA/Resources/GlobalSoilMap_specifications_december_2015_2.pdf). The digital soil attribute maps are in raster format at a resolution of 3 arc sec (~90 x 90 m pixels).

Detailed information about the Soil and Landscape Grid of Australia can be found at - https://esoil.io/TERNLandscapes/Public/Pages/SLGA/index.html

Attribute Definition: Available Volumetric Water Capacity
Units: percent;
Period (temporal coverage; approximately): 1950-2021;
Spatial resolution: 3 arc seconds (approx 90m);
Total number of gridded maps for this attribute: 18;
Number of pixels with coverage per layer: 2007M (49200 * 40800);
Data license : Creative Commons Attribution 4.0 (CC BY);
Target data standard: GlobalSoilMap specifications;
Format: Cloud Optimised GeoTIFF;
DOI: 10.26179/5d267d1ceb60c
title: Circum-Antarctic landfast sea ice extent, 2000-2018
DOI: 10.5067/modis/myd09.061
title: MODIS/Aqua Atmospherically Corrected Surface Reflectance 5-Min L2 Swath 250m, 500m, 1km
DOI: 10.5281/zenodo.10031633
title: Workflow I - Interactive Analysis - Three Analysed ROIS

description: This dataset contains the exported and processed data for an interactive Analysis Workflow that processes the Tribolium Dataset from https://publications.mpi-cbg.de/publications-sites/7207/
DOI: 10.5281/zenodo.10031807
title: Workflow III - Smart Microscopy - Adaptive monitoring of cell clusters

description: This Dataset contains images that were acquired during the adaptive monitoring of cell clusters forming in a dissociated cell culture.
DOI: 10.5281/zenodo.11379147
title: Daily Edge of Each Polynya in Antarctic (DEEP-AA)

description: The dataset of Daily Edge of Each Polynya in Antarctic (DEEP-AA) maps the area of each polynya daily. It uses a polynya tracking and identification method proposed by Lin et al., and effectively records the daily areas of both frequent and infrequent polynyas in wintertime (April to October). The DEEP-AA spans from 2003 to 2022 (2011.09.01-2012.07.31 missed). 

It should be noticed that ONLY the dataset of  SIC60_6.25km_20d.zip is recommended, and the other ones used only in sensitive anaylsis were NOT parameter tuned. Be careful to use sets other than SIC60_6.25km_20d.zip.

You can get the codfe to create the dataset from the Github release.

A description of the dataset has been published: Lin, Y. et al. A dataset of the daily edge of each polynya in the Antarctic. Sci. Data 11, 1006 (2024).

Contents in DEEP-AA



DEEP-AA



Subsets (*.zip)



Daily maps (DEEP_*.nc)

OverviewMap.mat

Input.txt






Subsets

Multiple subsets (*.zip) under various parameter settings are provided here. Among them, SIC60_6.25km_20d.zip is recommended. Its spatial resolution is 6.25 km (polar stereographic grid, EPSG code 3412) and the temporal resolution is 1 day. This subset is built based on sea ice concentration data from the University of Bremen (https://doi.org/10.1594/PANGAEA.919778, and https://doi.org/10.1594/PANGAEA.898400), combined with ERA5 2m air temperature (https://doi.org/10.24381/cds.adbb2d47), Circum-Antarctic landfast sea ice extent, 2000-2018 - version 2.2 (https://doi.org/doi:10.26179/5d267d1ceb60c), and U.S. National Ice Center Arctic and Antarctic Sea Ice Concentration and Climatologies in Gridded Format, Version 1 (https://doi.org/10.7265/46cc-3952).

The other subsets are the results of simple parameter modification (1 or 2 parameters) based on the setting of SIC60_6.25km_20d.zip. You can get detailed parameter settings in the Input.txt in every subset.

Files of each subset

Daily maps (DEEP_*.nc)

DEEP-AA provides a NetCDF file daily containing a polynya map for that day. We give each polynya a 9-bit unique ID that does not change over time, and in the daily maps, the area of each polynya is masked by its ID. The last bit of the ID also represents the attributes of the polynya: the even number indicates coastal polynya, odd number indicates open-ocean polynya.

In addition, the other open water, open sea, lands, etc. are also recorded in the maps. See details in the following table:




Value
Meanings


>0, even number
coastal polynya ID mask


>0, odd number
open-ocean polynya ID mask


-100
mask of landfast ice


-2
open sea


-1
the other open waters (not polynyas)


NaN or -999
mask of lands




 

OverviewMap.mat

An overview map of all polynyas identified. It maps all the Antarctic polynyas in that subset by their ID masks. You can run the MATLAB script PolynyaIDsFinder_Guide.m to view it and inquire about polynyas' IDs easily.

Input.txt

It records the parameters used to create the subset.
DOI: 10.5281/zenodo.12659826
title: Data for "Elevated urban energy risks due to climate-driven biophysical feedbacks"

description: This dataset contains the global multi-model urban climate and energy projections from Li et al. (2024), "Elevated urban energy risks due to climate-driven biophysical feedbacks", published in Nature Climate Change. It contains global monthly mean projections of urban 2-meter air temperature, and urban cooling and heating energy fluxes derived from 25 Earth system models (ESMs) participating in the Coupled Model Intercomparison Project Phase 6 (CMIP6). Details about how this dataset was generated are described in the article. This dataset may be useful for multiple communities interested in future energy risks, climate change impacts and vulnerability, and climate-sensitive adaptation and energy planning.

For more details, please refer to the README.md file included in the dataset.
DOI: 10.5281/zenodo.4635427
title: Floristic composition surrounding the footprint of eddy covariance and micrometeorology tower in the tropical dry forest, Tesopaco, Sonora (México)

description: The tropical dry forest (TDR) finds its northernmost distribution in Sonora. At 7.5 km east of Rosario de Tesopaco, a 13 m tower was installed (27.841319 N, -109.301264 W) with micrometeorological and eddy covariance measurements above the forest canopy. The tower was positioned in the center of a homogeneous terrain, ensuring the same coverage in at least 1 km in any direction. According to Köppen’s classification, the climate is warm semiarid, with a mean annual temperature of 22.1° C and 712 mm of annual (Rosario Tesopaco Climatological Station No. 00026100, Comisión Nacional del Agua), with most of the rainfall (80%) falling during the monsoon from June to October. A circular plot of 35.7 m of diameter was sampled to cover 1000 m<sup>2</sup> around the micrometeorological tower in 2009 (July). One hundred and four individuals were identified based on taxonomy, and the diameter at breast height (DBH) and height were measured for each individual.
DOI: 10.5281/zenodo.7668423
title: Global Fire Emissions Database (GFED5) Burned Area

description: The monthly GFED5 burned area data produced in this study are available in netCDF files. For years between 2001 and 2020, five layers of burned area (Norm: normal type, Crop: cropland burning, Defo: deforestation burning, Peat: peatland burning, Total: the sum of all burning) are provided at 0.25°×0.25° resolution. The ‘Norm’ layer contains burned areas in each grid cell (in km<sup>2</sup>) separated by 17 major land cover types. For the pre-MODIS era (1997-2000), only the ‘Total’ burned area layer with reduced spatial resolution (1°×1°) is provided. We also provide two global maps of burnable area (with water and snow/ice cover excluded) in each grid cell (0.25°×0.25° for the MODIS era and 1°×1° for the pre-MODIS era). Please refer to readme.html or readme.pdf for more detail about the dataset.
DOI: 10.5281/zenodo.8335354
title: Great Britain's primary substation service areas and annual domestic energy statistics

description: This geospatial data is a combination of Great Britain's 4436 primary substation service areas which have been parsed into a single shapefile for energy systems analysis. The original component datasets were provided by the six distribution network operator (DNO) companies in Great Britain (National Grid Electricity Distribution, Electricity North West Ltd, Scottish and Southern Electricity Networks, UK Power Networks, Scottish Power Energy Networks and Northern Power Grid). Attribution is given to the original data owners at each of these six DNOs and the resulting dataset from this work has been created and published under an open licence with each DNO's permission. The data is available to download as two geojson files in the WGS84 coordinate system. One is a streamlined version which just contains the polygons along with a unique primary identifier (UPID), primary substation name, DNO licence area and local authority. The other contains the polygons along with richer energy data which was aggregated to the primary substation level from publicly available Department for Energy Security and Net Zero, Office for National Statistics and National Grid ESO datasets. This data is also available to download in tabular form as a csv file. The meter numbers and consumption values are the means of those reported from 2015-2020. The substation polygons were those as received or publicly available as of the time period of this study (2021-22). Links to source datasets along with details on the creation methodology, use cases and significance of this dataset will be described in an upcoming manuscript which is under review for publication. Funding to support this work was received from the Engineering and Physical Sciences Research Council (EP/W008726/1) under the Gas Net New project and the Alan Turing Institute's Science of Cities and Regions Programme. Thanks are also given to the contributors of QGIS and the Geopandas Python library, both of which were used in this analysis.
DOI: 10.6084/m9.figshare.22233292.v1
title: Plate 1

description: These are the Cell Painting images from Plate 1. There are three channels: - DAPI (DNA/Nuclei) - GFP (ER) - RFP (Actin) There are two genotypes of cells (NF1+/+ and NF1-/-) that are split between columns 6 and 7, respectively. <br> Included in this dataset is the plate map file that contains all the metadata for this project. <br>
DOI: 10.6084/m9.figshare.22233700.v1
title: Plate 2

description: These are the Cell Painting images from Plate 2. There are three channels: - DAPI (DNA/Nuclei) - GFP (ER) - RFP (Actin) There are two genotypes of cells (NF1+/+ and NF1-/-) that are split between columns 1 and 6 for WT and 7 and 12 for Null for all rows in a 96-well plate. Included in this dataset is the plate map file that contains all the metadata for this project. <br> Note: These images have been corrected using CellProfiler to convert them from RGB tiff images to greyscale tiff images.
DOI: 10.6084/m9.figshare.22592890.v1
title: Plate 3 and Plate 3' (prime)

description: In this item, there are zip files containing images from plates 3 and 3'(prime). <br> There are 4 channels/stains: <br> - DAPI (DNA/Nuclei) - GFP (ER) - CY5 (Mitochondria) - RFP (Actin) <br> There are all 3 NF1 genotype of isogenic Schwann cells on both of these plates. <br> For more information on the data, please go to the GitHub repository for this project, nf1_cellpainting_data. <br> The metadata for both plates are included, with the naming convention "platemap_NF1_plate3.csv". Though the name of the file only has plate 3, this file is applicable to plate 3'(prime) as both have the same plate layout. <br> <br>
DOI: 10.6084/m9.figshare.25991356
title: Supplementary Material for: A Systematic Review and Meta-analysis on the prevalence of mild cognitive impairment and dementia in Mexico

description: Introduction: Age remains one of the major risk factors for the onset of mild cognitive impairment (MCI) and dementia. Studies on the prevalence of these conditions in Mexico used different methods, tools, and population with different health status. All these heterogeneous results may be a problem in identifying the true prevalence of MCI and dementia in Mexico. To our knowledge, there is not a systematic review available that presents essential figures on the prevalence of these conditions in Mexico. Therefore, we intend to access the maximum number of reports published on the topic and determine the prevalence of MCI and dementia in Mexican older adults. Methods: A systematic review using PubMed, Cochrane, Research Gate, Lilacs, and Scielo databases. Meta-analysis of the prevalence of MCI and dementia was analyzed using a random-effects model and presented in a forest plot among cross-sectional, epidemiological and pooled studies. Results: Sixteen articles were included. The overall prevalence of MCI of 18% (95% CI 0.10–0.27) was estimated from pooled information from 12 selected studies, in women 21% (95% CI 0.08–0.38), and in men 18% (95% CI 0.06–0.33). The overall prevalence of dementia of 10% (95% CI 0.06–0.14) was estimated from pooled information from 9 selected studies, in women 14% (95% CI 0.05–0.25), and in men 10% (95% CI 0.04–0.17). Conclusion: Mexican older individuals have a similar prevalence of dementia and MCI as reported by international data; nevertheless, the prevalence is higher than some Latin American Countries. Mexico has particular issues that must be resolved, such as, a lack of research in the southern regions of the country and the high incidence of comorbidities.
DOI: 10.6084/m9.figshare.26324098
title: Supplementary Material for: Palmitic acid modulation of the insulin-like growth factor system in hypothalamic astrocytes and neurons

description: Introduction: Insulin-like growth factor (IGF)1 and IGF2 have neuroprotective effects, but less is known regarding how other members of the IGF system, including IGF binding proteins (IGFBPs) and the regulatory proteinase pappalysin-1 (PAPP-A) and its endogenous inhibitor stanniocalcin-2 (STC2) participate in this process. Here we analyzed whether these members of the IGF system are modified in neurons and astrocytes in response to palmitic acid (PA), a fatty acid that induces cell stress when increased centrally.
Methods: Primary hypothalamic astrocyte cultures from male and female PND2 rats and the pro-opiomelanocortin (POMC) neuronal cell line, mHypoA-POMC/GFP-2, were treated with PA, IGF1 or both. To analyze the role of STC2 in astrocytes, siRNA assays were employed. 
Results: In astrocytes of both sexes, PA rapidly increased cell stress factors followed by increased Pappa and Stc2 mRNA levels and then a decrease in Igf1, Igf2 and Igfbp2 expression and cell number. Exogenous IGF1 did not revert these effects. In mHypoA-POMC/GFP-2 neurons, PA reduced cell number and Pomc and Igf1 mRNA levels, and increased Igfbp2 and Stc2, again with no effect of exogenous IGF1. PA increased STC2 expression, but no effect of decreasing its levels by interference assays or exogenous STC2 treatment in astrocytes were found.
Conclusions: The response of the IGF system to PA was cell and sex specific, but no protective effects of the IGFs were found. However, the modifications in hypothalamic PAPP-A and STC2 indicate that further studies are required to determine their role in the response to fatty acids and possibly in metabolic control.