cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12631588
title: Dataset for Investigation of Thermospheric Response to Geomagnetic Storms Using GITM-OVATION Prime and -FTA model With Comparison to GOLD and SABER Observations

description: Dataset Overview

This dataset accompanies the research paper titled " Investigation of Thermospheric Response to Geomagnetic Storms Using GITM-OVATION Prime and -FTA model With Comparison to GOLD and SABER Observations" and contains all the necessary data and scripts required to reproduce the results presented in the paper. The dataset is organized by figure numbers, corresponding directly to the figures in the paper, making it straightforward to locate and generate the specific results.

Structure of the Dataset

The dataset is divided into multiple folders, each named according to the figure numbers in the paper (e.g., Figure_1, Figure_2, etc.). Inside each of these folders, you will find:



Data Files: These files contain the raw and processed data used to generate the figures.

Scripts: MATLAB scripts (e.g., Figure_2*.m) that process the data and generate the respective figures.

Readme.txt: A text file providing detailed instructions on how to use the data and scripts, including any dependencies or specific steps required.


Instructions for Reproducing Figures





Download the Dataset:



Download the entire dataset or specific figure folders as needed.





Prepare Your Environment:



Ensure that MATLAB is installed on your local machine.

Verify that all necessary MATLAB toolboxes and dependencies are installed, as specified in the Readme.txt files within each figure folder.





Generate Figures:



Navigate to the directory where the dataset is saved.

Open MATLAB and set the current directory to the folder containing the downloaded data and scripts.

Run the script corresponding to the figure you wish to generate. For example, to generate Figure 1, navigate to the Figure_1 folder and run the Figure_1*.m.





Refer to Readme.txt for Further Details:



Each figure folder contains a Readme.txt file with additional details, including specific instructions, data descriptions, and any figure-specific requirements or notes.




By following these steps, you can successfully reproduce the figures and results presented in the paper "Paper 1 vs Paper 2" using the provided dataset and scripts. If you encounter any issues or have questions, refer to the Readme.txt files or contact the authors for further assistance.
DOI: 10.5281/zenodo.13760831
title: Efficient parameterization of transferable Atomic Cluster Expansion for water

description: This collection contains files associated with  Journal of Chemical Theory and Computation. "Efficient parameterization of transferable Atomic Cluster Expansion for water" (2024) paper:

- ACE potentials for water.

-Active set inverted (ASI) for the ACE potential

- Training dataset that was used for fitting Atomic Cluster Expansion potential.
DOI: 10.5281/zenodo.13869398
title: Plasma circulating microRNA-expression quantitative trait loci (eQTLs) data in the Rotterdam Study

description: The dataset contains GWAS summary statistics for 2,083 plasma circulating microRNAs, obtained from nearly 2,178 participants of the Rotterdam Study. The dataset includes three files, as outlined below:

File1: SNP_reference_file_maf0.01_Rsq0.7.txt

A reference file for SNPs with good imputation quality (Rsq > 0.7)  and minor allele frequency > 0.01 among participants included in our GWAS in the Rotterdam Study (N=2,178). The headers are:

SNP: rsID

chr: chromosome number according to GRCh37

bp: basepair position according to GRCh37

effect_allele: effect allele

other_allele: other allele

eaf: effect allele frequency

File2: miReQTLs_1e-5_maf0.01_Rsq0.7.txt

Summary statistics for all SNPs significantly associated with 2083 miRNAs (p-value < 1e-5), filtered by minor allele frequency > 0.01 and Rsq > 0.7. The headers are:

SNP: rsID

beta: effect estimate

se: standard error

pval: p-value

miRNA: miRNA ID

File3: miReQTLs_nominal_sig.csv.gz

Summary statistics for all SNPs nominally associated with 2083 miRNAs (p-value < 0.05). The headers are:

RSID: SNP ID

p-value: p-value

phenotype: miRNA

SE: standard error

BETA: effect estimate

 

The SNP allelic information and frequency can be found in the reference file (File1). 

For more information, please contact: m.ghanbari@erasmusmc.nl
DOI: 10.5281/zenodo.4014322
title: Marine plankton show threshold extinction response to Neogene climate change

description: Taxonomic occurrence datasets to accompany the article entitled "Marine plankton show threshold extinction response to Neogene climate change." Spreadsheets contain International Ocean Discovery Program (IODP) site information, sample names, depth in meters below the seafloor (mbsf), age (in millions of years), and the number of occurrences of each taxon per sample. For the eastern equatorial Pacific (EEP) dataset, ages were calculated using the astronomically-tuned model of Tian <em>et al.</em> (2018). Southern Ocean (SO) age information comes from the Neptune Sandbox Berlin (NSB) database (Renaudie <em>et al. </em>2020), with age model quality reported as: very good (VG), good (G), medium (M), or poor (P). Only species-level data associated with "very good" age models were analyzed in our study; however, here we provide all data at the species and genus level, with age models of any quality.
description: {"references": ["Tian, J. et al. Paleoceanography of the east equatorial Pacific over the past 16 Myr and Pacific\u2013Atlantic comparison: High resolution benthic foraminiferal \u03b418O and \u03b413C records at IODP Site U1337. Earth Planet. Sci. Lett. 499, 185\u2013196 (2018).", "Renaudie, J., Lazarus, D. & Diver, P. NSB (Neptune Sandbox Berlin): An expanded and improved database of marine planktonic microfossil data and deep-sea stratigraphy. Palaeontol. Electron. 23, a11 (2020)."]}
DOI: 10.5445/ir/1000120666
title: Datasets to: The seasonal cycle of ice-nucleating particles linked to the abundance of biogenic aerosol in boreal forests
DOI: 10.5883/bold:ads7120
title: Overview of Barcode Index Number - BOLD:ADS7120

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.6084/m9.figshare.26977306
title: Supplementary Material for: A Case of CUP with Malignant Pleural Effusion: Overcoming Diagnostic and Therapeutic Hurdles with Chemotherapy

description: Introduction: Cancers of unknown primary (CUP) present a diagnostic challenge, as their origin is unidentified at diagnosis. Massive pleural effusion (MPE), indicative of lung metastasis in CUP, categorizes the condition into an unfavorable subset with a poor prognosis. Patients in this subset may exhibit a lower response to specific therapies.
Case Presentation: A 62-year-old woman presented with cough, severe dyspnea, and MPE in the left lung evident. Thoracocentesis was performed, extracting 1200 mL of hemorrhagic fluid, followed by the placement of an indwelling pleural catheter. The cytological examination of the pleural effusion indicated an adenocarcinoma, with immunohistochemistry revealing positive CK-7 and negative CK-20, Napsin A, and TTF-1. Additionally, elevated levels of Ca-125 (1605 U/mL) and Ca 15-3 (242 U/mL) raised suspicion of gynecological malignancy. Thorax and abdominal CT scans, breast, and thyroid ultrasounds showed no signs of malignancy, leading to the diagnosis of CUP. The patient's performance status according to the Eastern Cooperative Oncology Group (ECOG) score was 4. Initial carboplatin 5 AUC and paclitaxel 175 mg/m2 administration resulted in improvement in performance status with ECOG score of 1, alleviation of dyspnea, reduction in pleural effusion one week after chemotherapy, with minimal effusion observed at three weeks, and Ca-125 levels decreased to 33.6 U/mL thereafter.
Discussion: Empiric chemotherapy using carboplatin and paclitaxel is a feasible option for managing CUP with MPE mimicking gynecological malignancies with elevated Ca-125 and Ca 15-3 markers; initiating chemotherapy in poor performance status patients is beneficial with proper clinical judgment.
DOI: 10.6084/m9.figshare.27053038
title: Supplementary Material for: Lysinuric Protein Intolerance: not only a disorder for pediatric nephrologists. Case report.

description: Introduction. Lysinuric Protein Intolerance (LPI) is a multisystemic inborn error of metabolism with a variable clinical expressivity, that usually begins in childhood with growth failure and gastroenterological/neurological problems related to the altered urea cycle and later complications involving the renal, pulmonary and immuno-hematological systems. 
Case report: We present the case of a 40-year-old woman suffering from chronic kidney disease in the context of a LPI, whose diagnosis was challenging because the signs of the disease were always blurred and the patient never manifested critical episodes typical of this multisystemic disease. In addition to renal disease, splenomegaly, thrombocytopenia, elevated lactate dehydrogenase (LDH), hyperferritinemia and hypertriglyceridemia were also present. A thorough investigation of the patient’s food preferences revealed her spontaneous aversion to protein-containing foods and excessive drowsiness during the occurrence of infectious episodes or on the rare occasions of excessive protein intake, although without ever coming to medical attention. These nuanced signs led us to suspect an impairment of the urea cycle and ultimately allowed us to narrow down the diagnosis to LPI through biochemical and genetic investigations. 
Conclusion. Nephrologists should consider LPI in the differential diagnosis, whenever a patient presents with mixed proteinuria, tubular dysfunction and/or chronic kidney failure of unknown origin. In these circumstances, we suggest looking for other signs such as growth failure, signs and symptoms ascribed to urea-cycle impairment, pulmonary involvement, hepatosplenomegaly and laboratory alterations such as pancytopenia, hyperferritinemia, lipid abnormalities, elevated LDH.
DOI: 10.6084/m9.figshare.27124476
title: Supplementary Material for: Optimal strategies for screening common birth defects in children of lower- and middle-income countries: a systematic review

description: Introduction
Congenital anomalies are one of the major causes of the global burden of diseases, and low- and middle-income countries (LMIC) are disproportionately affected. This review assesses the prenatal and postnatal screening methods and compares the prevalence of major congenital anomalies in LMICs. 
Methodology
We conducted a systematic search in MEDLINE/PubMed, CINAHL, Cochrane databases of systematic reviews, clinical trials.gov for relevant studies using Medical Subject Headings (MESH) and keywords. We categorized the studies into different systems and screening methods depending on the time the tests were conducted (prenatal or post-natal). The studies were then subjected to detailed descriptive analysis. 
Results
A total of 59 studies were selected for analysis; these focused on screening methods for congenital anomalies and compared their prevalence with regards to different systems. The most common screening techniques both prenatal and post-natal included antenatal ultrasound, fetal echocardiography, pulse oximetry and clinical examination. The most common congenital abnormalities involved the central nervous system (neural tube defects) and musculoskeletal (clubfoot), followed by gastrointestinal (omphalocele and gastroschisis) and cardiovascular (structural heart defect) . Overall, different systems had varying prevalences of different birth defects, ranging from 0.28 to 8.5%. In contrast, the prevalence of musculoskeletal system disorders varied from 1.01% to 3.96%, in the cardiovascular system from 0.57% to 10.4%, and in the urogenital group from 0.83% to 5.9%.
Conclusion:
The review highlights the lack of screening programs and studies especially in the primary and secondary care settings in LMICs, and limited studies do indicate a high burden of various congenital anomalies. There is a need for guidelines and programs in global maternal and child health programs to include timely screening and management of common birth defects in LMICs.
DOI: 10.6084/m9.figshare.27144996
title: Supplementary Material for: Virus Induced Voracity: Uncovering Hyperphagia Post Herpes Simplex Virus Type 1

description: Herpes simplex virus type 1 (HSV-1) is the leading cause of sporadic fatal encephalitis, typically presenting with temporal lobe abnormalities. We report a 25-year-old woman with a 10-day history of fever, headache, and vomiting, progressing to confusion, visual hallucinations and drowsiness. She had a history of meningoencephalitis at age eight and well-controlled focal seizures. Upon admission, her GCS score was E3V5M3, and the MRI showed hyperintensities in both temporal lobes with diffusion restriction. EEG indicated generalised slowing, and CSF analysis revealed lymphocytic pleocytosis with elevated protein levels. Viral encephalitis was suspected, and intravenous acyclovir was initiated. CSF PCR confirmed HSV-1. By the end of 1st week, she became afebrile and showed improved awareness but developed hyperphagia for both edible and non-edible objects. She received 21 days of acyclovir with significant improvement in consciousness but only partial improvement in over eating. HSV-1 affects the bilateral medial temporal lobes, insular cortex, and cingulate gyrus. An MRI confirmed these findings in this patient. Hyperphagia, a rare complication of HSV encephalitis, is a part of Kluver-Bucy Syndrome (KBS), typically associated with other cognitive dysfunctions. Despite early treatment, hyperphagia persisted partially, emphasising the need for rapid diagnosis and treatment to prevent severe outcomes. The case highlights that acute onset hyperphagia can be an isolated complication of HSV encephalitis, requiring tailored therapeutic strategies. Follow-up showed significant weight gain with moderate improvement in hyperphagia, underscoring the challenges in managing this condition.
DOI: 10.26165/juelich-data/hdveef
title: In-vivo mGluR5 and GABAA Receptor Specific Parametric PET Atlas of the Human Brain

description: This Dataset holds the results of the manuscript entitled "mGluR5 and GABAA Receptor Specific Parametric PET Atlas Construction - PET/MR Data Processing Pipeline, Validation and Application". In this study, we propose a comprehensive processing pipeline for the construction of standard space, in vivo distributions of non-displaceable binding potential (BPND), and total distribution volume (VT) based on simultaneously acquired bolus-infusion positron emission tomography (PET) and magnetic resonance imaging (MR) data. The pipeline was applied to [11C]ABP688-PET/MR (13 healthy male non- smokers, 26.6 ± 7.0 years) and [11C]Flumazenil-PET/MR (10 healthy males, 25.8 ± 3.0 years) data. Activity concentration templates, as well as VT and BPND atlases of mGluR5 and GABAA, were generated from these data. An evaluation of PET-to-PET registrations based on the new maps showed higher registration accuracy compared to registrations based on the commonly used [15O]H2O-template distributed with SPM12. Thus, we conclude that the resulting maps can be used for further research and the proposedpipeline is a viable tool for the construction of standardized PET data distributions. The maps were released to aid further research, by providing healthy in vivo references for the two mentioned neuroreceptor systems which may be used to assess associations with psychiatric and neurologic diseases. In addition, templates of normalized activity concentration distribution were released which were shown to benefit direct PET to PET registration for tracer-specific data.
DOI: 10.4121/12957986
title: Climate Policy Database

description: The Climate Policy Database collects information on currently adopted policies related to climate change mitigation from countries worldwide. The objective of the website is to provide an open, collaborative platform for information access, policy analysis and good-practice sharing. All data can be downloaded via the policies page.
DOI: 10.5281/zenodo.13364985
title: Experimental dataset for Liu et al. "Patterns of (micro)nutrient limitation across the South Pacific Ocean"

description: Dataset of ocean nutrient addition bioassay experiments. Accompanies publication: 'Patterns of (micro)nutrient limitation across the South Pacific Ocean' by Liu et al.
DOI: 10.5281/zenodo.13382821
title: TTV Data Extraction

description: This data set contains TTV (threats to validity) analysis extracted from 91 studies.
DOI: 10.5281/zenodo.7191424
title: Database that contains all images (plus 180 more) employed in the article: "Image features for quality analysis of thick blood smears employed in malaria diagnosis"

description: We share with you a bank of images obtained from microscopic fields of thick blood smears employed in the malaria diagnosis, and also the .csv file that contains the labels for each image. The images are saved with a unique name that is found in the first column of the .csv file. The second column contains the labels from each image, according to their unique names. The labeling process was done with the online toolbox Labelbox. Labelbox, "Labelbox," Online, 2020. [Online]. Available: https://labelbox.com If you are interested in using our database, cite our article as a way to recognize our work. We will be grateful for that. CITATION: Fong Amaris, W.M., Martinez, C., Cortés-Cortés, L.J. et al. Image features for quality analysis of thick blood smears employed in malaria diagnosis. Malar J 21, 74 (2022). https://doi.org/10.1186/s12936-022-04064-2 URL of our paper: https://malariajournal.biomedcentral.com/articles/10.1186/s12936-022-04064-2 <strong>--- This is the link where you can find our images Bank: https://drive.google.com/drive/folders/1Qrv0e4bSEtkeqtPABz-klQp-6D6OjU-X?usp=sharing </strong> It is important you to know that along with this .txt file, we are sharing the .csv file that contains 600 names of images (in the first column) with their respective labels (second column aside) This file corresponds to the instructions of an extended label file related to 600 images (and 600 new labels) in contrast to our previous label file with 420 labels from 420 images (https://www.researchgate.net/publication/359439520_Database420LabelsInstructionstxt ; https://www.researchgate.net/publication/359438904_Database420Labelscsv). Best Regards
DOI: 10.5883/bold:ads7172
title: Overview of Barcode Index Number - BOLD:ADS7172

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:ads7174
title: Overview of Barcode Index Number - BOLD:ADS7174

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.6084/m9.figshare.27254964
title: Supplementary Material for: Discovering Novel Loci of Chronic Kidney Disease via Principal Component Analysis based Multiple-trait Genome‑wide Association Study

description: Introduction
Chronic kidney diseases (CKD) encompass a spectrum of complex pathophysiological processes. While numerous genome-wide association studies (GWASs) have focused on individual traits such as albuminuria, estimated glomerular filtration rate (eGFR), and eGFR change, there remains a paucity of genetic studies integrating these traits collectively for comprehensive evaluation.
Methods
In this study, we performed individual GWASs for albuminuria, baseline eGFR, and eGFR slope utilizing data from non-diabetic individuals enrolled from the Taiwan Biobank (TWB). Subsequently, we employed principal component analysis to transform these three quantitative traits into principal components (PCs) and performed GWAS based on these principal components (PC-based GWAS).
Results
The individual GWAS analyses of albuminuria, baseline eGFR, and eGFR slope identified 10, 13, and 210 candidate loci respectively, with 2, 3, and 99 of them representing previously reported loci. PC-based GWAS identified additional 20 novel candidate loci linked to CKD (P-values ranging from 5.8 × 10−7 to 9.1 × 10−6). Notably, 4 of these 20 single nucleotide polymorphisms (rs9332641, rs10737429, rs117231653, and rs73360624) exhibited significant associations with kidney expression quantitative trait loci.
Conclusion
To our knowledge, this study represents the first PC-based GWAS integrating albuminuria, baseline eGFR, and eGFR slope. Our approach found 20 novel candidate loci suggestively associated with CKD, underscoring the value of integrating multiple kidney traits in unraveling the pathophysiology of this complex disorder.
DOI: 10.18434/mds2-2344
title: Transmission electron microscope tomographic data of aligned carbon nanotubes in epoxy at volume fractions of 0.44%, 2.6%, 4%, and 6.9%.
DOI: 10.5065/d68s4n4h
title: Snow on the Alaska North Slope Grids, Version 1.0

description: This data report is a summary of snow-survey information collected during a trip to the Arctic Slope on April 9-14, 2003. The data were all collected as part of the Biocomplexity of Frost-Boil Ecosystems study (Walker et al. 2003, in press). Snow is an important factor affecting soil-surface temperatures during the winter. These data will be used to help model the influence of snow on frost heave. The data collected included 
 1. Snow depth and soil temperature information from 106 permanent plots (releves) that are part of a vegetation classification study. 
 2. Snow density and snow-water-equivalent (SWE) measurements from the midpoints of the four sides of each of twelve 10x10-m grids at Happy Valley, Sagwon, Franklin Bluffs, Deadhorse, West Dock, and Howe Island. 
 3. Snow depths at every meter within the grids. 
 4. Snow profile descriptions from each grid.
DOI: 10.5281/zenodo.10469663
title: Datasets to: Measurement report: Introduction to the HyICE-2018 campaign for the measurements of ice nucleating particles in the boreal forest of Hyytiälä

description: This repository contains the datasets used in the study 'Measurement report: Introduction to the HyICE-2018 campaign for the measurements of ice nucleating particles in the boreal forest of Hyytiälä'. Detailed information and technical aspects of the data can be found in the publication.

Update (version 2 - January 2024): The repository was updated and now contains the complete HyICE-2018 datasets for the instruments uL-NIPI and PINE.
DOI: 10.5281/zenodo.10984085
title: Nests of Northern Wheatears Oenanthe oenanthe in Val Piora, Switzerland (2019 to 2022)

description: Nests and pseudo-absence sites of Northern Wheatears Oenanthe oenanthe in Val Piora, Switzerland (2019 to 2022) with habitat predictors and success
DOI: 10.5281/zenodo.11002996
title: Land and atmospheric drivers of the 2023 flood in India