cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/x44cvwpw9h
title: Siphoned apart: A portfolio perspective on order flow segmentation

description: This code replicates all figures in the paper.
DOI: 10.17632/yky9zd5hr5
title: UHPLC-MS/MS quantification of atractyligenin glycosides in Arabica coffee and coffee brew

description: The data comprise the raw data to the publication "UHPLC-MS/MS quantification of atractyligenin glycosides in Arabica coffee and coffee brew" submitted to the "Journal of Food Composition and Analysis".
Find the article here: https://doi.org/10.1016/j.jfca.2025.107432

Atractyligenin and its glycosides are coffee-specific diterpene glycosides with particular abundance in C. arabica, C. liberica, and C. stenophylla. We developed a UHPLC-MS/MS method and sample extraction protocol for their quantification in roasted coffee samples. During method development, we assessed the linear range, instrumental Limit of Detection and Limit of Quantification, and precision and accuracy in spiked analyte-free liquid and solid matrix. We evaluated precision and repeatability in authentic samples. Aqueous extraction approximated completion after 30 min of incubation at 95°C. We analyzed a sample set of Arabica coffee from Colombia and coffee brews using the method. The data showed that Arabica coffee from Colombia contained 2.2 – 4.1 µmol/g atractyligenin derivatives. 2-O-β-D-glucosylatractyligenin was the principal constituent (46.8 - 63.6%), followed by 3'-O-β-D-glucosyl-2'-O-isovaleryl-2-O-β-D-glucosylatractyligenin (18.9 - 35.7%). Atractyligenin accounted for 5.5 - 14.8% and 2'-O-isovaleryl-2-O-β-D-glucosylatractyligenin for 6.0 - 12.1%. The four compounds were nearly quantitatively extracted during coffee brewing. Extraction rates were 79.1 - 98.3%.
The data show that these coffee-specific diterpenoids are extracted and ingested with the coffee brew. After ingestion atractyligenin glycosides are subject to metabolic breakdown, leading to coffee-specific metabolites, e.g., atractyligenin-19-O-glucuronide, in the plasma and urine.
In conclusion these coffee-specific diterpenoids form coffee-specific metabolites that could be exploited as dietary biomarkers indicating recent coffee consumption. Such dietary biomarkers are of importance in nutritional intervention studies on, e.g., the health impact of regular coffee consumption.
- NMR spectra of the compounds 2´-O-isovaleryl-2-O-β-D-glucosylatractyligenin obtained by acidic hydrolysis of atractyloside
- NMR spectra of the compounds 2´-O-isovaleryl-2-O-β-D-glucosylcarboxyatractyligenin obtained by acidic hydrolysis of 4´-desulfocarboxyatractylic acid
- validation data of the developed UHPLC-MS/MS method (linear range, LoD. LoQ, precision and accuracy in analyte-free matrix, precision in authentic samples)
- quantitative data on the concentrations of atractyligenin and its glycosides in roasted Arabica coffee from Colombia and coffee brews (French Press, Turkish coffee, Espresso coffee, Cold Brew).
- experimental data on lipophilicity of atractyligenin and its glycosides in terms of water:n-octanol coefficient.
DOI: 10.6084/m9.figshare.21581619.v1
title: Synthetic spectra training data

description: Training dataset to train ML/DL models for classification of synthetic spectra
DOI: 10.6084/m9.figshare.21587145.v1
title: Increases in intraspecific body size variation are common amongst North American mammals and birds between 1880 and 2020

description: Many studies have documented the average body size of animals declining over time. Compared to mean body size, less is known about long-term changes in intraspecific trait variation (ITV), which is also important to understanding species’ ability to cope with environmental challenges. Based on 393,499 specimen records from 380 species collected in North America between 1880-2020, we found that body size ITV increased by 9.59% for mammals (n=302) and 30.67% for birds (n=78); human-harvested species had higher probability of ITV increase. The observed increasing ITV in many species suggests possible niche expansion and potential buffering effects against downsizing, but it risks increased maladaptation to rapidly changing environments. The results demonstrate that trait mean and variance do not necessarily respond in similar ways to anthropogenic pressures, and both should be considered.
DOI: 10.6084/m9.figshare.28429457.v1
title: Nepali Ethnic Groups Facial Emotion Dataset

description: This dataset consists of 1,045 images capturing various emotions, including happy, sad, disgust, fearful, neutral, surprised, and angry, featuring individuals from diverse cultural and ethnic backgrounds in Nepal.
DOI: 10.6084/m9.figshare.7363160.v1
title: Surveillance of Antimicrobial Resistance of Proteus spp. in a Tertiary Hospital in Nepal

description: This is the dataset for publication of "<b>Surveillance of Antimicrobial Resistance of <i>Proteus</i> spp. in a Tertiary Hospital in Nepal".</b>
DOI: 10.17632/4tmbsx7kk6
title: Data for: Assessing changes in US public trust in science amid the COVID-19 pandemic

description: Dataset associated with the noted study. Data are provided in raw form (e.g., please be aware of the need to reverse code some variables). A codebook is appended.
DOI: 10.6084/m9.figshare.4868117.v1
title: L1_BP_MAN_new23_GABRA6_X.xlsx

description: GABA in depression
DOI: 10.17632/69sh42vz3c
title: Supplement data for analyzing risk transmission in renewable energy incidents

description: Datasets for building REI-BNs,
1.REI datasets: two datasets with massive renewable energy incidents are used,  one is hand-annotated and the other is unsupervised, both of them are collected from several news websites.
2.REI ontology: an ontology with well-defined REI risk elements and subjects that widely distribute in renewable energy systems, social systems, and ecosystems.
3. Extracted quintuplets: entities and relations extracted from the REI datasets via the StanfordOpenIE5.1 system
DOI: 10.17632/6cv77bry6m
title: The genomic and immune landscapes of lethal metastatic breast cancer

description: Supplemental information for: The genomic and immune landscapes of lethal metastatic breast cancer
DOI: 10.6084/m9.figshare.14104502.v2
title: cryptoAD.ref.passed.vcf

description: Cryptococcus SNPs between JEC21 and H99 in vcf file. vcf file generated from aligning genome assemblies of H99 and JEC21. Analysis conducted using parsnp and harvest tools
DOI: 10.6084/m9.figshare.3822309.v3
title: European average tree height gridded data 2000-2010

description: Average height in meters of all trees in a cell. Also, standard deviation and standard error.
DOI: 10.6084/m9.figshare.5509501.v1
title: Comparison of Vai script (pdf version)

description: This dataset is a comprehensive diachronic comparison of the Vai script of Liberia, as derived from sixteen sources dated between 1834 and 2005. It can be viewed as a webpage at https://ftp.shh.mpg.de/kelly/Vai.html.<br>A sortable docx version can also be downloaded from figshare. <br>Please note that a subset of these graphemes have been traced as svg vector images. You can download them here: https://doi.org/10.6084/m9.figshare.5897158.v1<br>The same graphemes with a black background can be found here: https://doi.org/10.6084/m9.figshare.5901337.v1
DOI: 10.17632/vsfhggggfb
title: PubMed articles (Title, abstract, authors) that used questionnaire to assess audio/visual telemedicine consultation experiences

description: We conducted a systematic review search in PubMed for studies that used questionnaires to assess audio/visual telemedicine consultation experiences.
DOI: 10.6084/m9.figshare.23647623.v1
title: Supplementary Materials for: Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification

description: Title: Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification <br> Author list: Xudong Yang, Xu Zhang, Tiantian Xue, Xiaoxia Zhang, Fusheng Yang, Jianghong Yu, Steven B. Janssens, Shengxiang Yu (yushengxiang@ibcas.ac.cn) <br> Four_traits_states.csv: States summary of four traits. <br> Species_distribution_points_to_extract_climate_data.csv: The longitude and latitude data obtained for each species were used to extract corresponding climate variables. <br> R_Hydrangeeae_biogeography.zip: The main R language codes involved in this study. <br> MCC.tre: Timetree of Hydrangeeae
DOI: 10.6084/m9.figshare.26406418.v1
title: Household fuel use and adverse pregnancy outcomes

description: This prospective follow up was conducted in Eastern Ethiopia with the aim detecting adverse pregnancy outcomes to improve maternal and child health. The data contained maternal sociodemographic characteristics, maternal obstetrics and health conditions during pregnancy and child birth information as well as child related data.
DOI: 10.6084/m9.figshare.27674034.v1
title: Submitted to AGU: Forecasting Groundwater Level by Characterizing Multiple Spatial Dependencies of Environmental Factors Using Graph-based Deep Learning

description: Submitted to AGU: Forecasting Groundwater Level by Characterizing Multiple Spatial Dependencies of Environmental Factors Using Graph-based Deep LearningThe specific datasets and code
DOI: 10.6084/m9.figshare.28079867.v1
title: Friction Data

description: friction data
DOI: 10.6084/m9.figshare.29106731.v1
title: Project.zip

description: Supporting materials for Neurips2025 submission
DOI: 10.6084/m9.figshare.5450602.v1
title: Drosophila 25 species phylogeny

description: We used the peptide sequences for 25 Drosophila species along with an outgroup species, <i>Musca domestica</i>, that were available on NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/) and FlyBase (ftp://flybase.net/12_species_analysis/genomes/) as of April 21, 2017. We employed the clustering algorithm MCL to predict orthologous groups of peptides and used the 1,634 ortho-groups that were predicted as being single-copy in all species for phylogeny reconstruction. These groups were aligned with PASTA and the alignments were concatenated and given to RAxML with the PROTGAMMAJTTF model to estimate the species topology and relative branch lengths. Other methods based on individual gene trees (average consensus and ASTRAL) resulted in the exact same topology. We then used r8s to estimate branch lengths in terms of millions of years with three calibration points: 49-59 mya for the common ancestor of <i>D. pseudoobscura</i> and <i>D. melanogaster</i>, 64-74 mya for the common ancestor of <i>D. grimshawi</i> and <i>D. melanogaster</i>, and 156 mya for the common ancestor of <i>D. melanogaster</i> and <i>Musca domestica</i>.<br><br>File summary:<br>1. drosophila-25spec-concordance-factor-tree.png<br>An image of the phylogeny with branches scaled by relative number of substitutions. Nodes are labeled with concordance factors. Concordance factors are calculated for each node in the species phylogeny as: (# of gene trees with that node / total # of gene trees).<br><br>2. drosophila-25spec-node-age-tree.png<br>An image of the phylogeny with branches scaled by millions of years. Nodes are labeled with their ages in millions of years.<br><br>3. drosophila-25spec-time-tree.tre<br>The Newick string of the phylogeny with branches scaled by millions of years. Nodes are labeled with concordance factors.<br><br>4. drosophila-25spec-tree.tre<br>The Newick string of the phylogeny with branches scaled by relative number of substitutions. Nodes are labeled with concordance factors.<br>
DOI: 10.17632/85fdtx3kr5
title: Salvador Urban Network Transportation (SUNT)

description: Efficient public transportation management is essential for the development of large urban centers, providing several benefits such as comprehensive coverage of population mobility, the decrease of transport costs, better control of traffic congestion, and significant reduction of environmental impact limiting gas emissions and pollution. Realizing these benefits requires a deeply understanding the population and transit patterns and the adoption of approaches to model multiple relations and characteristics efficiently. This work addresses these challenges by providing a novel dataset that includes various public transportation components from three different systems: regular buses, subway, and BRT (Bus Rapid Transit). Our dataset comprises daily information from about 710,000 passengers in Salvador, one of Brazil's largest cities, and local public transportation data with approximately 2,000 vehicles operating across nearly 400 lines, connecting almost 3,000 stops and stations. With data collected from March 2024 to March 2025 at a frequency lower than one minute, SUNT stands as one of the largest, most comprehensive, and openly available urban datasets in the literature.
DOI: 10.17632/x8t4gn6mt6
title: Indonesian Tweets Dataset for Identifying Emotion Changes Among Twitter Users Following the Onset of the COVID-19

description: Tweet data was collected using the Twitter API services based on a point location with a radius of 10 km to obtain high tweet intensity in strategic locations. The location for data collection was the Setiabudi area, Jakarta, Indonesia, obtained by rounding the latitude value to -6.22 and longitude to 106.83; this location point was chosen via probability sampling to enhance the analysis process, as this area was most affected by COVID-19 cases in Indonesia during the pandemic.

Data collection was divided into two periods: before the COVID-19 outbreak (i.e., December 2019 to March 2020) and the beginning of the COVID-19 outbreak (i.e., March 2020 to June 2020). This study considered the first day of the COVID-19 pandemic in Indonesia to be March 14, 2020, according to the rules released by the Indonesian government. This mechanism resulted large and varied data, as a data filtering process based on a specific context was not conducted. Then, our work performed three steps of data reduction to obtain the appropriate data dimensions; a) select active users based on tweet intensity, b) remove tweet data with a word count below five, and c) eliminate data based on the suitability of discussion topics. The data used in the modeling process has passed three stages of data reduction. 

Linear with our work, there are three labeling processes: discussion topic, emotion and sentiment. For discussion topic labeling, this data performed a topic modeling mechanism using the LDA algorithm.  On the other hand, for emotion and sentiment labeling, three annotators manually labeled the data and used the majority vote strategy for the final class label on sample data. In our annotation strategy, for emotion labeling, each annotator was asked to annotate the individual tweets as "Happiness", "Love", "Fear", "Sadness", and "Anger". While for sentiment labeling, each tweet has been annotated into three predetermined category, namely "Positive", "Negative", and "Neutral".
DOI: 10.6084/m9.figshare.16437054.v7
title: A 30-m annual maize phenology dataset from 1985 to 2020 in China

description: maize phenolgoy indicators
DOI: 10.6084/m9.figshare.21350088.v3
title: Fibrosis data

description: The raw data in the study involved 40 patients with chronic liver diseases requiring liver biopsies at the Gastroenterology Clinic at referral hospital and 40 healthy controls with comparable age, sex and body mass index.
DOI: 10.6084/m9.figshare.25138820.v1
title: Experimental Samples of Dynamic Creep Test

description: A set of 118 experiment samples of dynamic creep tests was collected from the Asphalt Mixtures and Bitumen Research Center at the Iran University of Science and Technology.
DOI: 10.6084/m9.figshare.29086454.v1
title: VS-FPM: large-format, label-free virtual histopathology microscopy

description: <b>Abstract</b>By generating realistic histologically stained images from label-free image data, virtual staining (VS) methods have the potential to streamline clinical workflows, improve image consistency and enable new ways of visualizing and analysing tissues. This article describes a new VS approach based on the application of conditional generative adversarial networks to translate high-resolution phase images of unstained tissues, recovered using Fourier ptychographic microscopy (FPM), into brightfield H&E images. Compared to other label-free imaging methods, FPM offers unique advantages for VS as it allows simultaneous capture of sample amplitude and phase information, simplifying the pixelwise registration required for supervised training. FPM combines high spatial resolution with a large field of view and a large depth of field making it well suited to large format imaging of histological tissues. The method is readily implemented by modifying a conventional brightfield microscope using simple, low-cost optoelectronic hardware. Using colonic polyps as a test case, we compare FPM and VS-FPM images to brightfield whole slide images (WSIs) captured using a pathology slide scanner. Our results show that FPM images captured at 4x magnification have a spatial resolution equivalent to WSIs captured at 20x magnification and virtual H&E images of unstained tissues generated using VS-FPM closely match brightfield images of the same tissue sections captured after chemical staining, enabling pathological assessment and diagnosis.<b>Dataset:</b>This dataset contains pathology images of intestinal polyps from 3 patients. For each polyp section, there is are 4 registered images, 3 of which are chemically stained with H&E: WSI (captured with a NanoZoomer S360MD), FPM reconstructed amplitude and raw 4x brightfield. The 4th image is virtually stained from FPM phase images of unstained tissue.<br>
DOI: 10.6084/m9.figshare.7713245.v4
title: NCOMMS-18-36895B_code_data

description: <b>Hauenstein2019_code_data.zip</b><br>Code and data to reproduce the analysis:- p1_analysis contains all r-scripts to reproduce the analysis and produce figures presented in the manuscript.- p1_data includes all data which are accessed from within the r-scripts in p1_analysis<br><b>NCOMMS-18-36895B_supplementary_results.pdf</b>Region- and site-specific annual estimates of the proportion of illegally killed elephants (PIKE) and conservation targets.<br>
DOI: 10.7274/28766582.v1
title: Learning on Graphs with Robustness, Efficiency and Adaptability

description: Graphs are ubiquitous data structures that capture complex relationships among entities in real-world systems, including social networks, biological networks, transportation systems, and e-commerce platforms. With the rapid growth of graph data, numerous challenges and tasks have emerged, significantly impacting everyday life. While Graph Neural Networks (GNNs) have become the dominant approach for addressing these challenges, they face critical limitations in robustness, efficiency, and adaptability that restrict their broader application.

This thesis systematically addresses these limitations to develop more powerful GNN models. To improve robustness, this thesis investigates GNNs from both model and data perspectives. On the model side, it identifies dataset shift as a fundamental issue and proposes a corresponding solution. On the data side, it introduces a data augmentation method to generate predictive and concise graph representations. To enhance efficiency, the thesis presents techniques that improve GNN expressiveness through efficient graph structural estimation. Additionally, it proposes a novel training paradigm that bypasses the conventional gradient descent process, allowing GNNs to fit directly to data. To improve adaptability, the thesis explores methods for GNNs to generalize to new data and tasks. Specifically, it introduces a framework for link prediction that can adapt to arbitrary graphs during inference. Furthermore, it develops a practical application of GNNs for predictive tasks in relational databases. By addressing these limitations, this thesis advances the robustness, efficiency, and adaptability of GNNs, expanding their applicability in diverse real-world scenarios.
DOI: 10.17632/rrnz8p6rvw
title: Digital Repression Index 2003-2022

description: The data describes global patterns of digital repression from 2003-2022 and incorporates two composite indexes: a latent construct of digital repression and a latent construct of digital repression capacity. Key issues addressed by this data: Which countries are deploying digital repression techniques and how prevalent is their use? What is the relationship between regime type and digital repression? How might we understand the relationship between specific types of repression (violating political liberties, physical violence committed by the state, or curtailing private civil liberties) and digital repression? How does the deployment of individual components of digital repression differ by political system and regime type?
DOI: 10.6084/m9.figshare.27900702.v1
title: Supplementary Material for: Effects of a protease inhibitor camostat mesilate on gut microbial function in patients with irritable bowel syndrome: A pilot randomized placebo-controlled study

description: Introduction: Increased fecal protease activity which may induce visceral hypersensitivity has been observed in patients with irritable bowel syndrome (IBS). Serine proteases modulate FK506 binding protein (FKBP)-type peptidylprolyl cis-trans isomerase (PPIase) activity associated with immune and glucocorticoid receptor functions. The aims were to investigate whether camostat mesilate (CM), a serine protease inhibitor, modifies fecal bacterial function associated with FKBP-type PPIases ameliorates in patients with IBS. 
Methods: Randomly assigned 16 patients with IBS received 200 mg po tid of CM and 16 patients received placebo for 14 days. Self-reported adequate relief (AR) as a primary endpoint, IBS Symptom Severity Scale (IBS-SSS) and colonic motor and pain thresholds to colorectal distention were assessed before and after treatment. The fecal bacterial content was inferred from 16S rRNA gene sequence data using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. 
Results: CM significantly increased the relative abundance of Streptococcus and the functional abundances of serine protease and FKBP-type PPIase FklB and SlyD more than placebo after treatment. CM treatment was not superior to placebo in proportion of AR although colonic motor response partially changed. 
Conclusion: CM modulated the fecal microbiome composition and functional potentials that are related to FKBP-type PPIase activity in IBS patients. These findings suggest that protease inhibitors may modify gut microbial function along with abnormal immunological and/or stress responses that underlie pathophysiology of IBS.
DOI: 10.26188/5b7c83f3dc239
title: Database of environmental flow coefficients for construction materials

description: PLEASE NOTE THAT THIS DATABASE HAS BEEN SUPERSEDED BY THE EPiC DATABASE, AVAILABLE AT https://doi.org/10.26188/5dc228ef98c5a<br>This database of environmental flow coefficients has been compiled to assist in the quantification of embodied (indirect) flows associated with construction projects. Coefficients have been produced for the following flows:<br>- energy- water- waste- greenhouse gas emissions- land- material resources<br>The coefficients represent the quantity of a certain flow (e.g. energy) associated with (or embodied in) the production of a certain material (i.e. also known as a material's embodied enegy in this case).<br><br>Coefficients can be multiplied by available material quantities extracted as part of a bill of materials to determine the embodied flows for a particular construction project.<br>These coefficients have been compiled using a path exchange hybrid approach, utilising best available process and input-output data. Further details about their compilation can be found in the associated report.<br>Latest database and report will be uploaded shortly.
DOI: 10.6084/m9.figshare.29069453.v1
title: Chromosome-level genome assembly of <i>Phlomoides rotata</i>

description: Genome assembly and annotation of <i>Phlomoides rotata</i>