cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13379028
title: Temporal genome-wide DNA methylation signature of post-smolt Pacific salmon challenged with <i>Piscirickettsia salmonis</i>

description: Piscirickettsiosis is the most important bacterial disease in the Chilean salmon industry, which has sorted several efforts to its control, generating enormous economic losses. Epigenetic alterations, such as DNA methylation, can play a relevant role in the modulation of the metazoans response to pathogens. Bacterial disease may activate global and local immune responses generating intricate responses with significant biological impact in the host. However, it is scarcely understood how bacterial infections influence fish epigenetic alterations. In the present study, we utilized Pacific salmon and Piscirickettsiosis as model, to gain understanding into the dynamics of DNA methylation among fish-bacterial infection interactions. A genome-wide analysis of DNA methylation patterns in female spleen tissue of Pacific salmon was achieved by reduced representation bisulphite sequencing from a time course design. We determined 2,251, 1,918, and 2,516 differentially methylated regions DMRs among infected and control Pacific salmon in 1 dpi, 5 dpi, and 15 dpi, respectively. The mean methylation difference per DMR among control and infected groups was of ~35%, with an oscillatory pattern of hypo, hyper, and hypomethylation across the disease. DMCs, among the control and infected group, showed that they were statistically enriched in intergenic regions and depleted in exons. Functional annotation of the DMR genes demonstrated three KEGG principal categories, associated directly with the host response to pathogens infections. Our results provide the first evidence of epigenetic variation in fish provoked by bacterial infection and demonstrate that this variation can be modulated across the disease.
DOI: 10.6084/m9.figshare.13379028.v1
title: Temporal genome-wide DNA methylation signature of post-smolt Pacific salmon challenged with <i>Piscirickettsia salmonis</i>

description: Piscirickettsiosis is the most important bacterial disease in the Chilean salmon industry, which has sorted several efforts to its control, generating enormous economic losses. Epigenetic alterations, such as DNA methylation, can play a relevant role in the modulation of the metazoans response to pathogens. Bacterial disease may activate global and local immune responses generating intricate responses with significant biological impact in the host. However, it is scarcely understood how bacterial infections influence fish epigenetic alterations. In the present study, we utilized Pacific salmon and Piscirickettsiosis as model, to gain understanding into the dynamics of DNA methylation among fish-bacterial infection interactions. A genome-wide analysis of DNA methylation patterns in female spleen tissue of Pacific salmon was achieved by reduced representation bisulphite sequencing from a time course design. We determined 2,251, 1,918, and 2,516 differentially methylated regions DMRs among infected and control Pacific salmon in 1 dpi, 5 dpi, and 15 dpi, respectively. The mean methylation difference per DMR among control and infected groups was of ~35%, with an oscillatory pattern of hypo, hyper, and hypomethylation across the disease. DMCs, among the control and infected group, showed that they were statistically enriched in intergenic regions and depleted in exons. Functional annotation of the DMR genes demonstrated three KEGG principal categories, associated directly with the host response to pathogens infections. Our results provide the first evidence of epigenetic variation in fish provoked by bacterial infection and demonstrate that this variation can be modulated across the disease.
DOI: 10.6084/m9.figshare.13359693
title: Derivation and investigation of the first human cell-based model of Beckwith-Wiedemann syndrome

description: Genomic imprinting is a rare form of gene expression in mammals in which a small number of genes are expressed in a parent-of-origin-specific manner. The aetiology of human imprinting disorders is diverse and includes chromosomal abnormalities, mutations, and epigenetic dysregulation of imprinted genes. The most common human imprinting disorder is Beckwith-Wiedemann syndrome (BWS), frequently caused by uniparental isodisomy and DNA methylation alterations. Because these lesions cannot be easily engineered, induced pluripotent stem cells (iPSC) are a compelling alternative. Here, we describe the first iPSC model derived from patients with BWS. Due to the mosaic nature of BWS patients, both BWS and non-BWS iPSC lines were derived from the same patient’s fibroblasts. Importantly, we determine that DNA methylation and gene expression patterns of the imprinted region in the iPSC lines reflect the parental cells and are stable over time. Additionally, we demonstrate that differential expression in insulin signalling, cell proliferation, and cell cycle pathways was seen in hepatocyte lineages derived from BWS lines compared to controls. Thus, this cell based-model can be used to investigate the role of imprinting in the pathogenesis of BWS in disease-relevant cell types.
DOI: 10.6084/m9.figshare.13377011.v1
title: DNA methylation aging clocks and pancreatic cancer risk: pooled analysis of three prospective nested case-control studies

description: DNA methylation (DNAm) age may reflect age-related variations in biological changes and abnormalities related to aging. DNAm age acceleration measures have been associated with a number of cancers, but to our knowledge, have not been examined in relation to pancreatic cancer risk or survival. DNAm levels in leukocytes of prediagnostic blood samples of 393 pancreatic cancer cases and 431 matched controls, pooled from three large prospective cohort studies, were used to estimate DNAm age, epigenetic age acceleration (AA) and intrinsic epigenetic age acceleration (IEAA) metrics. Logistic regression and Cox proportional hazard regression models were used to examine the relationship between the various AA and IEAA metrics and pancreatic cancer risk and survival, respectively. The results showed that pancreatic cancer risk was significantly increased across all IEAA metrics, ranging from 83% to 95% increased risk when comparing the third and highest quartiles to the lowest quartile of IEAA. Consistent with these findings, the results from multivariate spline regression analyses showed non-linear relationships between all three IEAA metrics and pancreatic cancer risk with apparent threshold effect including 2 turning points at minimal and at maximal risks, respectively. There is no evidence of significant association between pancreatic cancer survival and any of the epigenetic AA or IEAA metrics. Our results indicate DNAm age acceleration, measured in blood prior to cancer diagnosis, is associated with an increased risk of pancreatic cancer in a complex nonlinear, dose-response manner. Epigenetic IEAA metrics may be a useful addition to current methods for pancreatic cancer risk prediction.
DOI: 10.6084/m9.figshare.13359693.v2
title: Derivation and investigation of the first human cell-based model of Beckwith-Wiedemann syndrome

description: Genomic imprinting is a rare form of gene expression in mammals in which a small number of genes are expressed in a parent-of-origin-specific manner. The aetiology of human imprinting disorders is diverse and includes chromosomal abnormalities, mutations, and epigenetic dysregulation of imprinted genes. The most common human imprinting disorder is Beckwith-Wiedemann syndrome (BWS), frequently caused by uniparental isodisomy and DNA methylation alterations. Because these lesions cannot be easily engineered, induced pluripotent stem cells (iPSC) are a compelling alternative. Here, we describe the first iPSC model derived from patients with BWS. Due to the mosaic nature of BWS patients, both BWS and non-BWS iPSC lines were derived from the same patient’s fibroblasts. Importantly, we determine that DNA methylation and gene expression patterns of the imprinted region in the iPSC lines reflect the parental cells and are stable over time. Additionally, we demonstrate that differential expression in insulin signalling, cell proliferation, and cell cycle pathways was seen in hepatocyte lineages derived from BWS lines compared to controls. Thus, this cell based-model can be used to investigate the role of imprinting in the pathogenesis of BWS in disease-relevant cell types.
DOI: 10.6084/m9.figshare.13359693.v1
title: Derivation and investigation of the first human cell-based model of Beckwith-Wiedemann syndrome

description: Genomic imprinting is a rare form of gene expression in mammals in which a small number of genes are expressed in a parent-of-origin-specific manner. The etiology of human imprinting disorders is diverse and includes chromosomal abnormalities, mutations, and epigenetic dysregulation of imprinted genes. The most common human imprinting disorder is Beckwith-Wiedemann syndrome (BWS), frequently caused by uniparental isodisomy and DNA methylation alterations. Because these lesions cannot be easily engineered, induced pluripotent stem cells (iPSC) are a compelling alternative. Here, we describe the first iPSC model derived from patients with BWS. Due to the mosaic nature of BWS patients, both BWS and non-BWS iPSC lines were derived from the same patient’s fibroblasts. Importantly, we determine that DNA methylation and gene expression patterns of the imprinted region in the iPSC lines reflect the parental cells and are stable over time. Additionally, we demonstrate that differential expression in insulin signaling, cell proliferation, and cell cycle pathways was seen in hepatocyte lineages derived from BWS lines compared to controls. Thus, this cell based-model can be used to investigate the role of imprinting in the pathogenesis of BWS in disease-relevant cell types.
DOI: 10.26126/intervals.4iswpd
title: [Raw Data] ATP content in bronchial tissues and liver spheroids

description: This dataset was generated in a study where a new physiological aerosol exposure system was developed (combining a multi-organs-on-a-chip system, air–liquid interface 3D lung tissues, liver spheroids, and a direct aerosol exposure system) to assess the impact of 1R6F CS and THS 2.2 aerosol on xenobiotic metabolism.
The viability was measured using CellTiter-Glo® reagent (Promega, Madison, WI, USA) and the luminescence was measured using a FLUOstar Omega plate reader (BMG Labtech, Ortenberg, Germany).
This dataset includes single measurements for each sample.
DOI: 10.26126/intervals.uob3ut
title: [Raw Data] CYP Activity

description: This dataset was generated in a study where a new physiological aerosol exposure system was developed (combining a multi-organs-on-a-chip system, air–liquid interface 3D lung tissues, liver spheroids, and a direct aerosol exposure system) to assess the impact of 1R6F CS and THS 2.2 aerosol on xenobiotic metabolism. 
CYP1A1/1B1, CYP1A2, and CYP3A4 enzyme activities were measured using the P450-Glo™ kit (Promega), and CYP1A2, CYP2B6, CYP2C9, CYP2C19, CYP2D6, and CYP3A4 were measured by incubating cells with a cocktail containing 104 µM phenacetin, 400 µM bupropion, 36 µM diclofenac, 80 µM (S)-mephenytoin, 36 µM bufuralol, and 100 µM testosterone and analyzed using LC-MS.
This dataset includes single measurements for each sample.
DOI: 10.26126/intervals.ch4ecu
title: [Raw Data] LDH released in the medium

description: This dataset was generated in a study where a new physiological aerosol exposure system was developed (combining a multi-organs-on-a-chip system, air–liquid interface 3D lung tissues, liver spheroids, and a direct aerosol exposure system) to assess the impact of 1R6F CS and THS 2.2 aerosol on xenobiotic metabolism. 
The viability of bronchial tissues and liver spheroids cultured in the same circuit were measured using the LDH-Glo™ Cytotoxicity Assay (Promega, Madison, WI, USA).
This dataset includes single measurements for each sample.
DOI: 10.26126/intervals.moqlpm
title: [Raw Data] Nicotine measurements in aqueous fractions

description: This dataset was generated in a study where a new physiological aerosol exposure system was developed (combining a multi-organs-on-a-chip system, air–liquid interface 3D lung tissues, liver spheroids, and a direct aerosol exposure system) to assess the impact of 1R6F CS and THS 2.2 aerosol on xenobiotic metabolism. 
The concentration of nicotine in the aqueous fractions following exposure was measured.
This dataset includes single measurements for each sample.
DOI: 10.26126/intervals.68h2hn
title: [Raw Data] TEER measurements

description: This dataset was generated in a study where a new physiological aerosol exposure system was developed (combining a multi-organs-on-a-chip system, air–liquid interface 3D lung tissues, liver spheroids, and a direct aerosol exposure system) to assess the impact of 1R6F CS and THS 2.2 aerosol on xenobiotic metabolism. 
TEER was measured by using an EndOhm-6 chamber (WPI, Sarasota, FL, USA) connected to an EVOM™ Epithelial Voltohmmeter (WPI).
This dataset includes single measurements for each sample.
DOI: 10.21227/k06q-3t33
title: SDN DDOS ATTACK IMAGE DATASET

description: It is now widely known fact that the Cloud computing and Software defined network paradigms have received a wide acceptance from researchers, academia and the industry. But the wider acceptance of cloud computing and SDN paradigms are hampered by increasing security threats. One of the several facts is that the advancements in processing facilities currently available are implicitly helping the attackers to attack in various directions. For example, it is visible that the conventional DoS attacks are now extended to cloud environments as DDoS attacks. With a huge number of security threats that are continuously occurring in computer networks and environments such as software defined networks (SDN) and Cloud computing, there is a demand to address security solutions that have a better reliability when compared to existing security solutions that are designed by considering datasets that did not meet the assessment and evaluation criterion which must be considered during the design of IDS systems. In [2], Nisha Ahuja, Gaurav Singal, and Debajyoti Mukhopadhyay have generated DDoS attack dataset for Software Defined Networks. This dataset was generated using mininet emulator. The dataset is available in the form of csv file(.csv) . The original version of dataset consists of 104345 traffic instances defined over 23 features.For evaluating performance of ML and DL based Intrusion Detection System, we have converted the DDOS attack SDN Dataset [3] in csv format to SDN DDoS attack image dataset consisting of network traffic image instances. Each traffic image instance in SDN DDoS attack image dataset is of 5x5 pixel size.
DOI: 10.6084/m9.figshare.17057615.v1
title: Bryophyte presence-absence and their environment data

description: They are dataset on moss and liverwort presence-absence and their environment data
DOI: 10.25345/c55k4f
title: MassIVE MSV000088481 - Proteomic analysis of renal cancer secretome
title: Introduction/aim: Renal cell cancer (RCC) is the most frequent kidney malignancy. Here, we aimed to analyze RCC secretome to find key molecules involved in tumor microenvironment regulation. Methods: Conditioned media from five RCC-derived cell lines (Caki-1, KIJ-265T, KIJ-308T, 786-O, and A498) and a non-cancerous proximal tubules (RPTEC) were used for mass spectrometry based proteomic analysis. The results were evaluated using Gene Onthology algorithms. Results: When compared with RPTEC, CM of Caki-1 and KIJ265T contained 587 and 802 aberrantly expressed proteins, respectively. Remarkably, there were 360 proteins commonly found in CM from Caki-1 and KIJ265T cells, with striking 348 proteins with changes in similar directions. 786-O CM expressed 612, A498 569, and KIJ308T 802 proteins. All cell lines shared 124 aberrantly expressed CM proteins, with 119 proteins with changes in the same direction. Top commonly downregulated proteins included SCIN, CBR4, MUC1, PELP1, LSM1, while top upregulated proteins were BZW2, COLGALT1, EEF1A2, CSDE1, INHBA, and STAT1. GO analysis of cellular components related to the identified proteins revealed that 63 proteins were associated with extracellular exosomes. Conclusion: Different RCC cell lines secrete proteins, commonly altered when compared with normal kidney proximal tubules. 53% of these proteins are associated with extracellular exosomes.
DOI: 10.5281/zenodo.5746885
title: Supplementary Data The Critical Need to Foster Reproducibility

description: Supplementary Data for the article: "The Critical Need to Foster Reproducibility"
DOI: 10.5281/zenodo.5746884
title: Supplementary Data The Critical Need to Foster Reproducibility

description: Supplementary Data for the article: "The Critical Need to Foster Reproducibility"
DOI: 10.5517/ccdc.csd.cc24004b
title: CCDC 1966210: Experimental Crystal Structure Determination

description: Related Article: Tuğba Aycan, Filiz Öztürk, Nilgün Özdemir, Hümeyra Paşaoğlu|2020|Int. J.Adv. in Eng. and Pure Sci.|32|42|doi:10.7240/jeps.580978
DOI: 10.5517/ccdc.csd.cc25h1nd
title: CCDC 2010463: Experimental Crystal Structure Determination

description: Related Article: Luca Polacchi, Arnaud Brosseau, Régis Guillot, Rémi Métivier, Clemence Allain|2021|Phys.Chem.Chem.Phys.(PCCP)|23|25188|doi:10.1039/D1CP03458H
DOI: 10.5281/zenodo.5746898
title: Benchmarking eliminative radiomic feature selection for head and neck lymph node classification - Supplemental data

description: Supplementary files for the publication "Benchmarking eliminative radiomic feature selection for head and neck lymph node classification"
DOI: 10.5281/zenodo.5746897
title: Benchmarking eliminative radiomic feature selection for head and neck lymph node classification - Supplemental data

description: Supplementary files for the publication "Benchmarking eliminative radiomic feature selection for head and neck lymph node classification"
DOI: 10.6084/m9.figshare.17104364
title: Intubation

description: it is novel technique
DOI: 10.6084/m9.figshare.17104364.v1
title: Intubation

description: dataset
DOI: 10.6084/m9.figshare.14414554.v1
title: Affective Affordances: Exploring Facebook Reactions as Emotional Responses to Hyperpartisan Political News

description: This research examines the key characteristics of hyperpartisan news pages on Facebook and how audiences interact with politically polarized content through the visual-emotional shorthand of Facebook Reactions. Through a quantitative content analysis of 4,236 posts shared by the most popular hyperpartisan U.S. Facebook pages before, during, and after the 2016 U.S. Presidential Election, the researchers introduce the concept of affective affordances to analyse emotional reactions elicited through Facebook Reactions in response to right- and left-leaning Facebook news posts, as well as the political topics, rhetorical devices, stylistic devices and emotionally charged content that are most likely to elicit emotional responses and inspire shares and comments from audiences in reaction to liberal and conservative content. The results are interpreted in light of the theory of affective intelligence.
DOI: 10.5281/zenodo.5734960
title: BirdScan Community Reference Dataset

description: This repository contains the reference dataset of labelled (or otherwise useful) echo samples acquired with a BirdScan MR1 radar. This dataset enables classification of the radar echoes acquired with a BirdScan MR1 into a number of biological groups of interests (as well as the removal of non-biological targets). Files and their contents: <em>TrainingData.csv</em> and<em> TrainingData.rds</em> files:<br> These files contain the actual training dataset, with the labels and all radar-derived features. We use a .csv file as this is compatible cross-platform and programming languages. We also include an .rds file for the R users. <em>ReclassTable.csv</em>:<br> This file contains the table that is used to sort the original ‘labelHuman’ labels into the hierarchical label system, i.e., columns ‘labelHa1’ to ‘labelHa6’. <em>MR1_ML_Tool_Documentation_v1.2.pdf</em>:<br> This file contains a description of the features in the dataset, as well as the classification and wingbeat frequency estimation algorithms and parameter settings that are currently being used in the SBRS software that is delivered along with the BirdScan radar. <em>Signatures.zip</em>:<br> This zip file contains a folder with the echo signature and north files associated to each of the samples in the TrainingData.csv (and .rds) file.<br> Files in the folder follow a strict directory and filenaming structure, i.e., <em>%Y_%m_%d\siteCode-echoID_sig.da</em>t and <em>%Y_%m_%d\siteCode-echoID_north.dat</em><br> For example: 2015_09_07\MOL-echo324_0000001606_sig.dat and 2015_09_07\MOL-echo324_0000001606_north.dat. <em>license.txt</em>:<br> This file contains the license applying to the data.
DOI: 10.6084/m9.figshare.17098877.v3
title: Mass-wasting-inferred Variability of 130,000-year Indian Summer Monsoon Intensity from Deposits in the Southeast Tibetan Plateau

description: A large proportion (~80%) of the Indian subcontinent’s precipitation comes from the Indian summer monsoon (ISM), which influences one-fifth of the world’s population. A long-term reliable proxy for ISM is fundamental to understanding previous global climate change. We establish a mass-wasting-inferred proxy to examine the paleohydrogeology (river undercutting history) of the Southeast Tibetan Plateau and reconstruct the variability of ISM intensity (precipitation) in the past 130,000 years. Our data suggest that mass-wasting events, which provides us sufficient samples for paleoclimate research, are prone to dramatic climate changes, especially extreme climate environments. The Southeast Tibetan Plateau was subjected to at least four distinct ISM intensity phases in the past 130,000 years. We conclude that ISM intensity has a cyclicity featured by the Earth’s orbit with obliquity, and that ISM intensity transformation lags the global ice volume (sea level) change by 8–15 kyrs.
DOI: 10.5281/zenodo.5746923
title: Azotea Dataset

description: Latest monthly AZOTEA reduced CSV files
DOI: 10.5281/zenodo.4423137
title: Azotea Dataset

description: Latest monthly AZOTEA reduced CSV files
DOI: 10.6084/m9.figshare.17098877.v5
title: Mass-wasting-inferred Variability of 130,000-year Indian Summer Monsoon Intensity from Deposits in the Southeast Tibetan Plateau

description: A large proportion (~80%) of the Indian subcontinent’s precipitation comes from the Indian summer monsoon (ISM), which influences one-fifth of the world’s population. A long-term reliable proxy for ISM is fundamental to understanding previous global climate change. We establish a mass-wasting-inferred proxy to examine the paleohydrogeology (river undercutting history) of the Southeast Tibetan Plateau and reconstruct the variability of ISM intensity (precipitation) in the past 130,000 years. Our data suggest that mass-wasting events, which provides us sufficient samples for paleoclimate research, are prone to dramatic climate changes, especially extreme climate environments. The Southeast Tibetan Plateau was subjected to at least four distinct ISM intensity phases in the past 130,000 years. We conclude that ISM intensity has a cyclicity featured by the Earth’s orbit with obliquity, and that ISM intensity transformation lags the global ice volume (sea level) change by 8–15 kyrs.