cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25582/data.2022-03.2444773/1939437
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2444825/1940173
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2444806/1940198
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2444795/1940259
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2444759/1940264
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2444810/1941085
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2444769/1941106
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2444791/1941185
title: Data for EMSL Project 51132 from March 2022
DOI: 10.6084/m9.figshare.20454462.v2
title: Statistical Shape Model of the Tibia.

description: This project provides a freely accessible three-dimensional statistical shape model (SSM) of the tibia, the coded scripts for generating a SSM and the segmented surface models of the cortical and trabecular bone. Further, it provides three potential applications for the SSM. Please see the associated read-me files for further details. <br> Please cite our work if you use this code or data.<br> (Preprint) Keast, M., Bonacci, J., & Fox, A. (2022). Geometric variation of the human tibia-fibula: A public dataset of tibia-fibula surface meshes and statistical shape model. <em>BioRxiv</em>, 2022.08.04.502722. https://doi.org/10.1101/2022.08.04.502722<br>
DOI: 10.5281/zenodo.7679463
title: List of appendix cystic fibrosis and CBAVD research paper

description: This is the dataset list of cystic fibrosis inside sperm wioth with <strong>congenital</strong> bilateral absence of the <strong>vas</strong> <strong>deferens (CBAVD)</strong>
DOI: 10.5281/zenodo.7679462
title: List of appendix cystic fibrosis and CBAVD research paper

description: This is the dataset list of cystic fibrosis inside sperm wioth with <strong>congenital</strong> bilateral absence of the <strong>vas</strong> <strong>deferens (CBAVD)</strong>
DOI: 10.5281/zenodo.7339586
title: Supplementary material for Journal of Fungi (Jof-2078054)

description: Supplementary material for Journal of Fungi (Jof-2078054). Supplementary Figures S1-S6; and Tables S1, S2 and S3.
DOI: 10.5281/zenodo.7679505
title: Supplementary material for Journal of Fungi (Jof-2078054)

description: Supplementary material for Journal of Fungi (Jof-2078054). Supplementary Figures S1-S6; and Tables S1, S2 and S3.
DOI: 10.6084/m9.figshare.21799793.v9
title: Precision Oncology-Based Targeting of Signaling Pathways Toward a Holistic Approach to Cancer Therapeutics

description: The mutational changes occurring in the regulatory genes responsible for the maintenance of optimal cell growth and proliferation gradually lead to cancer progression and metastasis. Furthermore, patients with the same cancer types often respond differently to different cancer therapies, indicating the need for a patient-specific treatment regimen for the disease. Precision oncology is the new field of cancer research that relies on genetic profiling of individual tumors to identify targetable alterations for custom-tailored personalized treatment of the disease. It is to rely upon the genomic study of cancer cells to get a clear picture of the prognosis and pathways involved in disease progression and to look for the means to selectively target them for a cure. This article intends to briefly explain the foundations and frontiers of precision oncology in the context of technological advances being made in this direction to assess its scope and importance in the realization of a proper cure for cancer.
DOI: 10.26060/g6aq-6r35
title: NZEnvDS_Priestley Taylor v1.0
DOI: 10.5281/zenodo.7058984
title: Dataset of the 1976 Ms 7.3 Chaldiran earthquake

description: The dataset, used in the study of the 1976 Ms 7.3 Chaldiran earthquake by Lu and Zhou (2023), includes KeyHole (KH-4B and KH-9) ortho-images, post-earthquake Pleiades data (1-m DEM and ortho-image) and a 30-m ALOS DEM.
DOI: 10.5281/zenodo.7050477
title: Dataset of the 1976 Ms 7.3 Chaldiran earthquake

description: The dataset, used in the study of the 1976 Ms 7.3 Chaldiran earthquake by Lu and Zhou (2023), includes KeyHole (KH-4B and KH-9) ortho-images, post-earthquake Pleiades data (1-m DEM and ortho-image) and a 30-m ALOS DEM.
DOI: 10.5281/zenodo.6542266
title: Exploration, representation and rationalization of the conformational phase-space of N-glycans

description: Collection of structure and trajectory files of free N-glycans simulated in solution using either the CHARMM36m or GLYCAM06j force field. Simulations are either plain MD or enhanced sampled via the combination of replica exchange methods REST-RECT.
description: {"references": ["Gil-Ley, A. & Bussi, G. Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering. J Chem Theory Comput 11, 1077\u20131085 (2015).", "Wang, L., Friesner, R. A. & Berne, B. J. Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2). J Phys Chem B 115, 9431\u20138 (2011)."]}
DOI: 10.5281/zenodo.6542267
title: Exploration, representation and rationalization of the conformational phase-space of N-glycans

description: Collection of structure and trajectory files of free N-glycans simulated in solution using either the CHARMM36m or GLYCAM06j force field. Simulations are either plain MD or enhanced sampled via the combination of replica exchange methods REST-RECT.
description: {"references": ["Gil-Ley, A. & Bussi, G. Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering. J Chem Theory Comput 11, 1077\u20131085 (2015).", "Wang, L., Friesner, R. A. & Berne, B. J. Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2). J Phys Chem B 115, 9431\u20138 (2011)."]}
DOI: 10.6084/m9.figshare.22180546
title: unigenes of D.cambodiana treatment with UV-B

description: Unigenes of D.cambodiana treatment with UV-B
DOI: 10.6084/m9.figshare.22180546.v1
title: unigenes of D.cambodiana treatment with UV-B

description: Unigenes of D.cambodiana treatment with UV-B
DOI: 10.34740/kaggle/dsv/4394911
title: FLSea VI
DOI: 10.25345/c5ww77891
title: MassIVE MSV000091367 - ClpP ADEP1 Native Mass Spectrometry
title: Native mass spectrometry experiments of ClpP and ADEP1. Direct infusion with formic acid / ammonium acetat buffer (pH ~ 4).
DOI: 10.6084/m9.figshare.21505677.v1
title: Untitled Item

description: Supplemental Files
DOI: 10.34740/kaggle/dsv/5071896
title: 💥📰 Daily Breaking News Twitter Dataset
DOI: 10.6084/m9.figshare.21505677
title: Untitled Item

description: Supplemental Files
DOI: 10.6084/m9.figshare.21505677.v3
title: Untitled Item

description: Supplemental Files
DOI: 10.6084/m9.figshare.21505677.v2
title: Untitled Item

description: Supplemental Files
DOI: 10.6084/m9.figshare.21505653
title: Supplemental File 1. DroughtDB Plant Drought Stress Genes Fasta File

description: Supplemental File 1. DroughtDB Plant Drought Stress Genes Fasta File
DOI: 10.6084/m9.figshare.21505653.v1
title: Supplemental File 1. DroughtDB Plant Drought Stress Genes Fasta File

description: Supplemental File 1. DroughtDB Plant Drought Stress Genes Fasta File
DOI: 10.6084/m9.figshare.21505653.v2
title: Supplemental File 1. DroughtDB Plant Drought Stress Genes Fasta File

description: Supplemental File 1. DroughtDB Plant Drought Stress Genes Fasta File
DOI: 10.34740/kaggle/dsv/5071900
title: 🇺🇦 Ukraine Conflict Twitter Dataset
DOI: 10.6084/m9.figshare.22178414.v1
title: Data file 1

description: The excel dataset shows the data collected from 613 medical students from India about their knowledge, attitude and practice towards COVID-19
DOI: 10.5517/ccdc.csd.cc2fbwm9
title: CCDC 2244791: Experimental Crystal Structure Determination

description: Related Article: Debiao Huo|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.21781511
title: Leukocyte DNA methylation in Alzheimer´s disease associated genes: replication of findings from neuronal cells

description: Differences in gene-wide DNA methylation of the Alzheimer’s disease (AD)-associated genes <i>BIN1, HLA-DRB5, SORL1, SLC24A4</i>, and <i>ABCA7</i> are reported to be associated with AD in post-mortem brain samples. We investigated whether the same associations could be found in leukocytes collected pre-mortem. Using cohort data of 544 Swedish twins (204 dementia diagnoses), we replicated the findings in <i>HLA-DRB5</i> and <i>SLC24A4</i> at <i>P</i> &lt; 0.05. However, co-twin control analyses indicated that the associations were partly explained by familial confounding. Thus, DNA methylation differences in <i>HLA-DRB5</i> and <i>SLC24A4</i> are present in both neuronal cells and leukocytes, and not fully explained familial factors.
DOI: 10.6084/m9.figshare.21781511.v1
title: Leukocyte DNA methylation in Alzheimer´s disease associated genes: replication of findings from neuronal cells

description: Differences in gene-wide DNA methylation of the Alzheimer’s disease (AD)-associated genes <i>BIN1, HLA-DRB5, SORL1, SLC24A4</i>, and <i>ABCA7</i> are reported to be associated with AD in post-mortem brain samples. We investigated whether the same associations could be found in leukocytes collected pre-mortem. Using cohort data of 544 Swedish twins (204 dementia diagnoses), we replicated the findings in <i>HLA-DRB5</i> and <i>SLC24A4</i> at <i>P</i> &lt; 0.05. However, co-twin control analyses indicated that the associations were partly explained by familial confounding. Thus, DNA methylation differences in <i>HLA-DRB5</i> and <i>SLC24A4</i> are present in both neuronal cells and leukocytes, and not fully explained familial factors.
DOI: 10.6084/m9.figshare.21665636
title: Exploration of genome-wide DNA methylation profiles in night shift workers

description: The past decades, studies indicated that night shift work is associated with adverse health effects, however, molecular mechanisms underlying these effects are poorly understood. A few previous studies have hypothesized a role for DNA-methylation (DNAm) in this relationship. We performed a cross-sectional epigenome-wide association study, to investigate if night shift work is associated with genome-wide DNAm changes and DNAm-based biological age acceleration, based on previously developed so-called ‘epigenetic clocks.’ Short term (2–6 years) and intermediate term (10–16 years) night shift workers, along with age and sex matched dayworkers (non-shift workers) were selected from the Lifelines Cohort Study. For genome-wide methylation analysis the Infinium Methylation EPIC array (Ilumina) was used. Linear regression analyses were used to detect differences in methylation at individual CpG-sites associated with night shift work. Pathway analysis was performed based on KEGG pathways and predictions of age acceleration in night shift workers were performed based on four previously developed epigenetic age calculators. Only in women, differences in methylation at individual CpG-sites were observed between night shift workers and non-shift workers. Most of these differentially methylated positions (DMPs) were observed in intermediate term night shift workers. Pathway analysis shows involvement of pathways related to circadian rhythm and cellular senescence. Increased age acceleration was observed only in short-term night shift workers (men and women). This might be indicative of adaptation to night shift work or a so-called healthy worker effect. In conclusion, these results show that DNA methylation changes are associated with night shift work, specifically in women.
DOI: 10.6084/m9.figshare.21665636.v1
title: Exploration of genome-wide DNA methylation profiles in night shift workers

description: The past decades, studies indicated that night shift work is associated with adverse health effects, however, molecular mechanisms underlying these effects are poorly understood. A few previous studies have hypothesized a role for DNA-methylation (DNAm) in this relationship. We performed a cross-sectional epigenome-wide association study, to investigate if night shift work is associated with genome-wide DNAm changes and DNAm-based biological age acceleration, based on previously developed so-called ‘epigenetic clocks.’ Short term (2–6 years) and intermediate term (10–16 years) night shift workers, along with age and sex matched dayworkers (non-shift workers) were selected from the Lifelines Cohort Study. For genome-wide methylation analysis the Infinium Methylation EPIC array (Ilumina) was used. Linear regression analyses were used to detect differences in methylation at individual CpG-sites associated with night shift work. Pathway analysis was performed based on KEGG pathways and predictions of age acceleration in night shift workers were performed based on four previously developed epigenetic age calculators. Only in women, differences in methylation at individual CpG-sites were observed between night shift workers and non-shift workers. Most of these differentially methylated positions (DMPs) were observed in intermediate term night shift workers. Pathway analysis shows involvement of pathways related to circadian rhythm and cellular senescence. Increased age acceleration was observed only in short-term night shift workers (men and women). This might be indicative of adaptation to night shift work or a so-called healthy worker effect. In conclusion, these results show that DNA methylation changes are associated with night shift work, specifically in women.
DOI: 10.6084/m9.figshare.21571349
title: Assessment of aberrant DNA methylation two years after paediatric critical illness: a pre-planned secondary analysis of the international PEPaNIC trial

description: Critically ill children requiring intensive care suffer from impaired physical/neurocognitive development 2 y later, partially preventable by omitting early use of parenteral nutrition (early-PN) in the paediatric intensive-care-unit (PICU). Altered methylation of DNA from peripheral blood during PICU-stay provided a molecular basis hereof. Whether DNA-methylation of former PICU patients, assessed 2 y after critical illness, is different from that of healthy children remained unknown. In a pre-planned secondary analysis of the PEPaNIC-RCT (clinicaltrials.gov-NCT01536275) 2-year follow-up, we assessed buccal-mucosal DNA-methylation (Infinium-HumanMethylation-EPIC-BeadChip) of former PICU-patients (N = 406 early-PN; N = 414 late-PN) and matched healthy children (N = 392). CpG-sites differentially methylated between groups were identified with multivariable linear regression and differentially methylated DNA-regions via clustering of differentially methylated CpG-sites using kernel-estimates. Analyses were adjusted for technical variation and baseline risk factors, and corrected for multiple testing (false-discovery-rate &lt;0.05). Differentially methylated genes were functionally annotated (KEGG-pathway database), and allocated to three classes depending on involvement in physical/neurocognitive development, critical illness and intensive medical care, or pre-PICU-admission disorders. As compared with matched healthy children, former PICU-patients showed significantly different DNA-methylation at 4047 CpG-sites (2186 genes) and 494 DNA-regions (468 genes), with most CpG-sites being hypomethylated (90.3%) and with an average absolute 2% effect-size, irrespective of timing of PN initiation. Of the differentially methylated KEGG-pathways, 41.2% were related to physical/neurocognitive development, 32.8% to critical illness and intensive medical care and 26.0% to pre-PICU-admission disorders. Two years after critical illness in children, buccal-mucosal DNA showed abnormal methylation of CpG-sites and DNA-regions located in pathways known to be important for physical/neurocognitive development.
DOI: 10.6084/m9.figshare.21571349.v1
title: Assessment of aberrant DNA methylation two years after paediatric critical illness: a pre-planned secondary analysis of the international PEPaNIC trial

description: Critically ill children requiring intensive care suffer from impaired physical/neurocognitive development 2 y later, partially preventable by omitting early use of parenteral nutrition (early-PN) in the paediatric intensive-care-unit (PICU). Altered methylation of DNA from peripheral blood during PICU-stay provided a molecular basis hereof. Whether DNA-methylation of former PICU patients, assessed 2 y after critical illness, is different from that of healthy children remained unknown. In a pre-planned secondary analysis of the PEPaNIC-RCT (clinicaltrials.gov-NCT01536275) 2-year follow-up, we assessed buccal-mucosal DNA-methylation (Infinium-HumanMethylation-EPIC-BeadChip) of former PICU-patients (N = 406 early-PN; N = 414 late-PN) and matched healthy children (N = 392). CpG-sites differentially methylated between groups were identified with multivariable linear regression and differentially methylated DNA-regions via clustering of differentially methylated CpG-sites using kernel-estimates. Analyses were adjusted for technical variation and baseline risk factors, and corrected for multiple testing (false-discovery-rate &lt;0.05). Differentially methylated genes were functionally annotated (KEGG-pathway database), and allocated to three classes depending on involvement in physical/neurocognitive development, critical illness and intensive medical care, or pre-PICU-admission disorders. As compared with matched healthy children, former PICU-patients showed significantly different DNA-methylation at 4047 CpG-sites (2186 genes) and 494 DNA-regions (468 genes), with most CpG-sites being hypomethylated (90.3%) and with an average absolute 2% effect-size, irrespective of timing of PN initiation. Of the differentially methylated KEGG-pathways, 41.2% were related to physical/neurocognitive development, 32.8% to critical illness and intensive medical care and 26.0% to pre-PICU-admission disorders. Two years after critical illness in children, buccal-mucosal DNA showed abnormal methylation of CpG-sites and DNA-regions located in pathways known to be important for physical/neurocognitive development.
DOI: 10.6084/m9.figshare.21781498.v2
title: Non-pathogenic microbiota accelerate age-related CpG Island methylation in colonic mucosa

description: DNA methylation is an epigenetic process altered in cancer and ageing. Age-related methylation drift can be used to estimate lifespan and can be influenced by extrinsic factors such as diet. Here, we report that non-pathogenic microbiota accelerate age-related methylation drift in the colon when compared with germ-free mice. DNA methylation analyses showed that microbiota and IL10KO were associated with changes in 5% and 4.1% of CpG sites, while mice with both factors had 18% alterations. Microbiota, IL10KO, and their combination altered 0.4%, 0.4%, and 4% of CpG island methylation, respectively. These are comparable to what is seen in colon cancer. Ageing changes were accelerated in the IL10KO mice with microbiota, and the affected genes were more likely to be altered in colon cancer. Thus, the microbiota affect DNA methylation of the colon in patterns reminiscent of what is observed in ageing and colorectal cancer.
DOI: 10.6084/m9.figshare.21781498
title: Non-pathogenic microbiota accelerate age-related CpG Island methylation in colonic mucosa

description: DNA methylation is an epigenetic process altered in cancer and ageing. Age-related methylation drift can be used to estimate lifespan and can be influenced by extrinsic factors such as diet. Here, we report that non-pathogenic microbiota accelerate age-related methylation drift in the colon when compared with germ-free mice. DNA methylation analyses showed that microbiota and IL10KO were associated with changes in 5% and 4.1% of CpG sites, while mice with both factors had 18% alterations. Microbiota, IL10KO, and their combination altered 0.4%, 0.4%, and 4% of CpG island methylation, respectively. These are comparable to what is seen in colon cancer. Ageing changes were accelerated in the IL10KO mice with microbiota, and the affected genes were more likely to be altered in colon cancer. Thus, the microbiota affect DNA methylation of the colon in patterns reminiscent of what is observed in ageing and colorectal cancer.
DOI: 10.6084/m9.figshare.21813773
title: Identification and comparison of m6A modifications in glioblastoma non-coding RNAs with MeRIP-seq and Nanopore dRNA-seq

description: The most prominent RNA modification – N6-methyladenosine (m6A) – affects gene regulation and cancer progression. The extent and effect of m6A on long non-coding RNAs (lncRNAs) is, however, still not clear. The most established method for m6A detection is methylated RNA immunoprecipitation and sequencing (MeRIP-seq). However, Oxford Nanopore Technologies recently developed direct RNA-seq (dRNA-seq) method, allowing m6A identification at higher resolution and in its native form. We performed whole transcriptome sequencing of the glioblastoma cell line U87-MG with both MeRIP-seq and dRNA-seq. For MeRIP-seq, m6A peaks were identified using nf-core/chipseq, and for dRNA-seq – EpiNano pipeline. MeRIP-seq analysis revealed <i>5086</i> lncRNAs transcripts, while dRNA-seq identified 336 lncRNAs transcripts from which 556 and 198 were found to be m6A modified, respectively. While 24 lncRNAs with m6A overlapped between two methods. Gliovis database analysis revealed that the expression of the major part of identified overlapping lncRNAs was associated with glioma grade or patient survival prognosis. We found that the frequency of m6A occurrence in lncRNAs varied more than 9-fold throughout the provided list of 24 modified lncRNAs. The highest m6A frequency was detected in <i>MIR1915HG, THAP9-AS1, MALAT1, NORAD1</i>, and <i>NEAT1 (</i>49–88nt), while <i>MIR99AHG, SNHG3, LOXL1-AS1, ILF3-DT</i> showed the lowest m6A frequency (445–261nt). Taken together, (1) we provide a high accuracy list of 24 m6A modified lncRNAs of U87-MG cells; (2) we conclude that MeRIP-seq is more suitable for an initial m6A screening study, due to its higher lncRNA coverage, whereas dRNA-seq is most useful when more in-depth analysis of m6A quantity and precise location is of interest. <b>Abbreviations:</b> (dRNA-seq) direct RNA-seq, (GBM) glioblastoma, (LGG) low-grade glioma, (lncRNAs) long non-coding RNAs, (m6A) N6-methyladenosine, (MeRIP-seq) methylated RNA immunoprecipitation and sequencing, (ncRNA) non-coding RNA, (ONT) Oxford Nanopore Technologi; Lietuvos Mokslo Taryba