cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/x4r2y8kwjv
title: Nicotinamide Mononucleotide Ameliorates Alzheimer’s Disease Symptoms through Modulation of Gut Microbiota in APP/PS1 Mice

description: Research Hypothesis:
NMN supplementation can alleviate AD symptoms in APP/PS1 mice by modulating gut microbiota and its metabolites, influencing brain health through the gut-brain axis.
Data Collection and Methodology:
APP/PS1 (AD) and C57BL/6 (NC) mice were divided into four groups: ADNMN, ADPBS, NCNMN, and NCPBS. Experiments included microbiota analysis (DNA extraction, sequencing, MENs, PCA, LEfSe), metabolite analysis (HPLC-MS/MS), pathological analysis (Alcian Blue staining, immunohistochemistry), ROS detection, RNA sequencing for GO and KEGG enrichment, Morris water maze test for spatial memory, ATP and mitochondrial complex I activity measurement, and Western blotting for protein expression.
Notable Findings:
1. NMN restored intestinal flora structure and composition in AD mice, increasing MEN complexity and resilience. PCA showed similarity to normal controls, and LEfSe identified reduced bacteria (Catellicoccus, Lactobacillus_aviarius, and uncultured_bacterium) levels in ADNMN.
2. After 16 weeks of NMN treatment, most metabolite changes in AD mice reversed, with Acylcarnitine 14:1, Corticosterone, and Taurine showing significant improvement. Spearman correlation analysis revealed that Bacteroides, uncultured-bacterium-c-Gammaproteobacteria, and Campylobacter were key genera affecting metabolite differences between ADNMN and ADPBS groups. In ADNMN, Bacteroides and Enterorhabdus correlated positively with LysoPI 18:0, LysoPE 12:0, and DHA methyl ester, while in ADPBS, Gemella correlated positively with LysoPG 16:0, Cer (AP) 33:2, LysoPG 18:1, and LysoPI 20:3. 
3.NMN altered metabolic pathways in AD mice, promoting nervous system development and reducing abnormal immune activation. Key microbial taxa were identified, with metabolites impacting AD development.
4. NMN increased goblet cell counts in both AD and healthy mice, enhancing the mucus barrier to protect against microbial invasion. RNA-Seq analysis showed elevated expression of mucus-related genes (Clca1 and Fcgbp) in the ADNMN group. NMN also partially reversed downregulated genes in AD mice, upregulating immune and cell adhesion pathways while downregulating oxidative stress and lipid metabolism genes. In vivo imaging showed NMN reduces colon ROS, lessening oxidative stress damage in AD mice. 
5. In the MWM test, ADPBS mice had worse performance than NCPBS mice during training (days 1-5). NMN improved metrics for both groups. On day 6, ADPBS mice showed cognitive impairments, but NMN helped restore their spatial memory.
6.NMN mitigated brain inflammation and oxidative stress in AD mice through pathway regulation, reducing lipids, azelaic acid metabolism, and key acids.
7. NMN restored ATP levels and mitochondrial complex I activity in AD mice's hippocampus. It also enhanced synaptic density and reversed synaptic dysfunction by increasing presynaptic and postsynaptic protein expression.
DOI: 10.6084/m9.figshare.1554708.v2
title: Example of use of DataCite #1

description: Datasets' DOIs and authors' ORCIDs.
DOI: 10.6084/m9.figshare.23142422.v1
title: Supplementary Material for: Central Retinal Vein Occlusion after mRNA COVID-19 Vaccination

description: A 47-year-old man presented with visual loss in the right eye 8 h after the first dose of a coronavirus disease 2019 (COVID-19) vaccine developed by Pfizer/BioNTech (BNT162b2). The best corrected visual acuity (BCVA) was 20/200. Fundus examination showed dilated and tortuous retinal veins at the posterior pole, retinal hemorrhages throughout the fundus, and macular edema. Fluorescein angiography showed multiple hypofluorescent spots that appeared to be fluorescent block due to retinal hemorrhages and hyperfluorescent leakage from the retinal veins. The eye was diagnosed with central retinal vein occlusion (CRVO). For the treatment of macular edema, intravitreal injection of aflibercept (IVA) was administered and treated with one plus pro re nata regimen. Five IVAs were performed over a 10-month follow-up period, with resolution of macular edema, and the BCVA recovered to 20/20. The patient was young and had no history of diabetes mellitus, hypertension, or atherosclerotic diseases, and his blood tests showed no abnormal findings. Both antigen test and polymerase chain reaction test for COVID-19 were negative, and the antibody test was positive due to vaccination. The development of CRVO in this patient may have been related to COVID-19 vaccination, and the appropriate IVA treatment resulted in a good visual prognosis.
DOI: 10.60893/figshare.apm.28821839.v1
title: Supplement

description: Supplement methods and figures
DOI: 10.17632/kw6d5jvp6z
title: DHX15 inhibits mouse APOBEC3 deamination activity

description: APOBEC3 family proteins are critical host proteins that counteract and prevent the replication
of retroviruses and other viruses through cytidine deamination. Human APOBEC3G inactivates
HIV-1 through the introduction of lethal mutations to viral genomes. In contrast, mouse
APOBEC3 does not induce DNA hypermutation of murine retroviruses, although it retains
functional cytidine deaminase activity. Why mouse APOBEC3 does not effectively deaminate
MLV is still unknown. In this study, we found that the dead box helicase DHX15 interacts with
mouse APOBEC3 and inhibits its deamination activity. DHX15 was packaged into virions
independent of its binding with APOBEC3. Moreover, DHX15 knockdown inhibited MLV
replication and resulted in more G-to-A mutations in proviral DNA. Finally, DHX15 knockdown
induced DNA damage in murine cells, suggesting that it plays a role in preserving genome
integrity in cells expressing mouse APOBEC3 protein.
DOI: 10.6084/m9.figshare.14827584.v1
title: QM9_DGL_Atoms format

description: QM9 dataset from DGL in JARVIS-Tools Atoms format<br>https://www.nature.com/articles/sdata201422<br>
DOI: 10.6084/m9.figshare.26065444.v2
title: Photogrammetric reconstruction of MHNRS-Pa-1 (Myobradypterygius hauthali) ichthyosaur from southern Chilean Patagonia.

description: The data correspond to a photogrammetric reconstruction of an ichthyosaur excavated in the border of the Tyndall Glacier in southernmost chilean Patagonia. The ichthyosaur is almost completely exposed from the sediment and each of its bones are articulated. The specimen correspond to a female pregnant with one embryo also exposed from the sediment. This specimen correspond to the first complete excavated ichthyosaur from Chile and the single pregnant ichthyosaur record of 131.07 +/- 0.07 million year in the planet.The complete article has been submitted to the Journal of Vertebrate of Paleontology.
DOI: 10.6084/m9.figshare.27214161.v1
title: Govt Expenditure in Healthcare Industry and Cancer Data for 18 Countries

description: The following 3 datasets consist of <b>cancer incidence and mortality data</b> for males and females and <b>government healthcare expenses</b> for 9 rich countries and 9 moderate countries. This dataset was taken from "<b>International Agency for Research on Cancer</b>" and "<b>Global Health Expenditure Database</b>" by WHO.
DOI: 10.6084/m9.figshare.29066402.v1
title: Scopus Design Thinking & Creative Thinking.csv

description: Design thinking and creative thinking skills have a significant impact on fostering innovation across various fields, especially education and technology development. However, the mapping of research related to these two concepts still requires a comprehensive understanding to identify global collaboration trends and patterns. This study aims to examine the thematic trends, evolution of concepts, and collaborative connections between countries through a bibliometric method. To map keyword, author, and international collaboration networks, keywords were analyzed using Scopus database and VOS viewer software. Design thinking relates more to innovation, design education, and sustainability, whereas creative thinking relates more to problem solving, active learning, and critical thinking according to the analysis. Trends include the United States, China and Indonesia as being dominant in terms of international scientific collaboration, and a prospective strengthening of ties between European and East Asian countries. The visualization of knowledge networks and the mapping of international collaborations is the second key contribution of this research and providing opportunities for fure research. It is anticipated that this finding will be a reference for researchers and practitioners in conducting more integrated and useful research in the future.
DOI: 10.17632/y3dgh36zt9
title: SASe

description: Operating code and design files for the subsurface automated sampler for environmental DNA (SASe)
DOI: 10.6084/m9.figshare.14703639.v1
title: mnist+context

description: The dataset consists of MNIST digits set on either noisy backgrounds, with noise a Gaussian random variable, or MNIST digits set on a more naturalistic background from the CIFAR-10 dataset. A parameter that makes the task more difficult is digit transparency; as we increase transparency, the background interferes with the digit and the identity of the digit becomes more ambiguous. The goal is to perform image classification so that neural networks (NN) correctly identify the MNIST digit despite the different backgrounds. <br>
DOI: 10.6084/m9.figshare.22494478.v1
title: RAW DATA.zip

description: Raw data files include CCK8,PCR,WB,IF and ELISA.
DOI: 10.6084/m9.figshare.25888096.v1
title: Tribolium confusum Male and Female coverage

description: Illumina and PacBio sequencing coverage over draft genome assembly of Tribolium confusum
DOI: 10.6084/m9.figshare.25980112.v2
title: FMO-SCOP-29Jun2022

description: <b>Quantum chemical dataset for representative protein folds by the fragment molecular orbital method</b><br>Please refer to the paper for details. [submitted]<br>
DOI: 10.6084/m9.figshare.26077015.v1
title: Machine Learning Materials Properties with Accurate Predictions, Uncertainty Estimates, Domain Guidance, and Persistent Online Accessibility

description: We develop random forest ML models for 33 materials properties spanning an array of data sources (computational and experimental) and property types (electrical, mechanical, thermodynamic, etc.). All models have calibrated ensemble error bars to quantify prediction uncertainty and domain of applicability guidance enabled by kernel-density-estimate-based feature distance measures. All data and models are publicly hosted on the Garden-AI infrastructure, which provides an easy-to-use, persistent interface for model dissemination that permits models to be invoked with only a few lines of Python code.
DOI: 10.6084/m9.figshare.28207571.v1
title: Auto Insurance Fraud Detection

description: Auto Insurance Fraud Detection: Dataset and BQABA algorithm python code
DOI: 10.6084/m9.figshare.853801_d11
title: README.txt

description: The Global Integrated Drought Monitoring and Prediction System (GIDMaPS) provides near real-time drought information based on multiple drought indicators and input data sets (http://drought.eng.uci.edu/). In this package, the folder names indicate the drought index and the source of data (INDEX_SOURCE). Index options are: 1-PSI: Multivariate Standardized Drought Index (MSDI) based on Precipitation (P) and Soil Moisture (S). 2-SSI: Standardized Soil Moisture Index 3-SPI: Standardized Precipitation Index. In each folder the files are named as INDEXYYYYMM.asc, where YYYY= year; MM= month, and INDEX = PSI, SSI, SPI.
<br>
GIDMaPS is presented in [Hao et al, 2014]. The deatails of MSDI, SSI and SPI are discussed in [Hao and AghaKouchak 2013a, 2013b]. GIDMaPS data has been used in [Damberg and AghaKouchak, 2013].
 
<strong>References</strong>
[1] Hao Z., AghaKouchak A., Nakhjiri N., Farahmand A., 2014, Global Integrated Drought Monitoring and Prediction System, Scientific Data, 1: 140001, doi: 10.1038/sdata.2014.1.
<br>
[2]  Hao Z., AghaKouchak A., 2013a, A Nonparametric Multivariate Multi-Index Drought Monitoring Framework,Journal of Hydrometeorology, doi:10.1175/JHM-D-12-0160.1.
<br>
[3]  Hao Z., AghaKouchak A., 2013b, Multivariate Standardized Drought Index: A Parametric Multi-Index Model,Advances in Water Resources, 57, 12-18, doi: 10.1016/j.advwatres.2013.03.009.
<br>
[4]  Damberg L., AghaKouchak A., 2013, Global Trends and Patterns of Droughts from Space, Theoretical and Applied Climatology, doi: 10.1007/s00704-013-1019-5. 
<br>
DOI: 10.17632/mm9w4yybz3
title: The proteomic landscape of genotoxic stress-induced micronuclei. MacDonald et al.

description: Uncropped microscopy and immunoblot data
DOI: 10.6084/m9.figshare.11669514.v1
title: Genome Annotation of Cerasus humilis

description: This dataset is generated from the genome annotation results of Cerasus humilis. The format is GFF3, and all protein coding genes are included in this dataset. It could be used in the genetic studies of Cerasus humilis in the future.
DOI: 10.6084/m9.figshare.20523210.v1
title: pithecophaga_jefferyi_spades_01.fasta.gz

description: .....
DOI: 10.6084/m9.figshare.26214821.v2
title: Potential intensification of permafrost carbon feedback under net-zero and negative emissions

description: Using the CESM2 model, a simulated dataset was created to investigate the response of the permafrost carbon cycle to net-zero and negative emissions through an emission-driven carbon dioxide removal simulation in the study titled <i>"</i><i>Potential intensification of permafrost carbon feedback under net-zero and negative emissions</i><i>".</i>
DOI: 10.6084/m9.figshare.5123935.v1
title: Supplementary Material for: Staging of Mental Disorders: Systematic Review

description: <b><i>Background:</i></b> The staging method, whereby a disorder is characterized according to its seriousness, extension, development and features, is attracting increasing attention in clinical psychology and psychiatry. The aim of this systematic review was to critically summarize the tools that are available for reproducing and standardizing the clinical intuitions that are involved in a staging formulation. <b><i>Methods:</i></b> A comprehensive research was conducted on the MEDLINE, PsycINFO, EMBASE and Cochrane databases from inception to May 2012. The following search terms were used: ‘stage/staging’ AND ‘psychiatric disorder/mental disorder/schizophrenia/mood disorder/anxiety disorder/substance use disorder/eating disorder’. <b><i>Results:</i></b> A total of 78 studies were identified for inclusion in the review. We discussed studies addressing or related to the issue of staging in a number of mental disorders (schizophrenia, unipolar depression, bipolar disorder, panic disorder, substance use disorders, anorexia and bulimia nervosa). The literature indicates that disorders have a longitudinal development or a treatment history that can be categorized according to stages. We proposed staging formulations for the above-mentioned psychiatric disorders. <b><i>Conclusion:</i></b> Staging models offer innovative assessment tools for clinical psychologists and psychiatrists. Characterizing each stage of an illness demarcates major prognostic and therapeutic differences among patients who otherwise seem to be deceptively similar since they share the same psychiatric diagnosis. A stage 0 to denote an at-risk condition does not appear to be warranted at the current state of research.
DOI: 10.60893/figshare.jcp.28742432.v1
title: Supplementary Material

description: Supplementary Material
DOI: 10.17632/9vx554yd34
title: Series representation of differential elastic scattering cross section for electrons: Applications in theoretical models of electron transport in condensed matter

description: Quantitative applications of surface sensitive electron spectroscopies require availability of reliable theoretical models describing electron transport in the surface region of solids. An important effect to be accounted for in these models is the phenomenon of elastic scattering of signal electrons on atoms constituting a studied solid. A convenient representation of the elastic scattering cross sections (DCS) for a given interaction is the expansion into the series of Legendre polynomials. Knowledge of the expansion coefficient provides a useful tool for the software developers when a large number of the DCSs is needed in the course of calculations. The enclosed computer program AL_CREATE makes possible to calculate the expansion coefficients from three different algorithms. Much attention is devoted to evaluate the accuracy of the DCSs. High accuracy of the DCS is reported when the expansion coefficients are calculated from the relativistic phase shifts. The database of these coefficients for all elements and for the energy range from 50 eV to 20 keV is accompanying the program AL_CREATE. Taking advantage of smooth variation of expansion coefficients with energy, this database makes possible a convenient and accurate determination of the expansion coefficients for any analytical conditions. It is shown that a number of different parameters needed for quantification of electron spectroscopies can be expressed by a relatively simple formalism based on known expansion coefficients. An attention is drawn to a possibility of creating a universal sampler of the elastic scattering angles that requires only the input of the complete series of expansion coefficients. This would greatly facilitate development of programs designed for Monte Carlo simulations of electron transport. A proposition of such a generator is implemented in the program SAMPLER which is also enclosed to the present report. The program AL_CREATE has an option of testing the performance of this generator. It is shown that the frequency histogram reproduces the DCS even when a sharp and narrow features are observed.
DOI: 10.6084/m9.figshare.21269130.v1
title: Motor unit data for Soleus and Medial Gastrocnemius from HD EMG

description: <strong>Matlab files (.mat)</strong> holding the data (motor unit firings) after cutting the segments and pairing between muscles and within muscles for coherence analyses. <br> These are not the raw HD EMG data, but instead the<strong> motor unit spike trains + metadata</strong>, after motor units were paired for coherence analyses. <br> Includes <strong>README file</strong> explaining data organisation and abbreviations.
DOI: 10.6084/m9.figshare.25592400.v1
title: Cultural Heritage Models for Benchmarking MVS Algorithms

description: This is a collection of in total 14 3D Models and point clouds that were used to benchmark multi-view stereo algorithms in combination with autonomous adaptive view planning.The models originate from the <i>Virtual Museums of Małopolska</i> and were originally shared with a CC0 license. The models were pre-processed to fit a cube of approximately 1x1x1 units (e.g. meters). Each model is located in a sub folder that contains the following data:<b>model.obj</b>: The model with UV coordinates that is used for rendering.<b>reference_model.ply</b>: The same model in ply format that is used as reference geometry<b>points.ply</b>: A point cloud of 1 million points that were sampled on the model<b>diffuse.png</b>: The diffuse texture
DOI: 10.6084/m9.figshare.25746771.v1
title: UdonPred Data

description: Datasets used to train the UdonPred Method.UdonPred is a predictive model for protein disorder, leveraging embeddings from the pre-trained protein language model ProstT5. This model variant has been trained using a novel dataset of nuclear magnetic resonance (NMR) spectroscopy chemical shifts from the Biological Magnetic Resonance Data Bank (BMRB). It employs the TriZOD scoring scheme, which quantifies disorder by assigning G-scores that identify deviations from the chemical shifts expected in random coil configurations. UdonPred was subsequently fine-tuned using data from the DisProt database.UdonPred is available at: https://github.com/JSchlensok/udonpred<br>TriZOD G-Scores method is available at: https://github.com/MarkusHaak/trizod
DOI: 10.6084/m9.figshare.26831818.v4
title: Merge conflicts dataset used in SBES 2022 paper

description: This is the dataset used in the paper https://doi.org/10.1145/3555228.3555229.
DOI: 10.17632/gcy5p3ddfb
title: PICPANTHER: A simple, concise implementation of the relativistic moment implicit particle-in-cell method

description: Abstract A three-dimensional, parallelized implementation of the electromagnetic relativistic moment implicit particle-in-cell method in Cartesian geometry (Noguchi et al., 2007) is presented. Particular care was taken to keep the C++11 codebase simple, concise, and approachable. GMRES is used as a field solver and during the Newton–Krylov iteration of the particle pusher. Drifting Maxwellian problem setups are available while more complex simulations can be implemented easily. Several test runs are d... Title of program: PICPANTHER Catalogue Id: AEVA_v1_0 Nature of problem Kinetic simulations of collisionless plasma mostly need to resolve the smallest scales in a plasma, limiting the problem domains that can be tackled. The Courant-Friedrichs-Lewy condition poses further problems. Explicit algorithms require large amounts of computational power to cope with these restrictions. Implementations of implicit algorithms, on the other hand, are very complex. Very few implicit codes are openly available and approachable. Fully relativistic, three-dimensional electromagne ... Versions of this program held in the CPC repository in Mendeley Data AEVA_v1_0; PICPANTHER; 10.1016/j.cpc.2014.11.010 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/jvgvp3my5g
title: Graph diffusion based on Quantum cuts algorithm for butterfly segmentation 

description: We present the contrast maps results obtained by our graph based diffusion process that exploits efficiently wave functions in the Schrodinger equation in a mono-layered undirected graph using the public Leeds Butterfly dataset (J. Wang, K. Markert, M. Everingham, Learning models for object recognition from natural language descriptions. Proc. br. Mach. Vis. Conf., (2009), pp. 2.1-2.11, https://doi.org/10.5244/C.23.2.). The dataset contains 832 ecological images on which each one represents a single butterfly in its natural environment. There is ten species of butterflies in the dataset and a distribution of 55 to 100 photographs is repertoried in each of them. The images are characterized by several artifacts that complicate the segmentation task like the presence of irrelevant objects, the shadow effect, the variation of illumination and the high similarity between some background and butterfly regions. Our algorithm evaluates the regional contrast based on Quantum cuts theory  by performing a diffusion process of intensity scores from the foreground template towards the image borders. The obtained contrast maps allow to extract efficiently the butterfly regions and supress the background areas. In order to evaluate visually the performance of our algorithm, ground truth images are provided.

Folders descriptions:
-> Images: Color ecological images. 
-> Ground Truth: The real position of butterflies in the images.
-> Contrast Maps: Results returned by our algorithm.  
-> Contrast Estimation: a compressed folder containing the above folders
DOI: 10.4225/03/5726f9e6aad6e
title: Bima as Dewa Ruci - Wayang Kulit (shadow puppet)

description: Bima as Dewa Ruci, his inner God-self. Leather shadow puppet in Yogyakarta style.