cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5506413
title: RNA modification 5-methylcytosine (m5C) is associated with small RNA biogenesis in Arabidopsis thaliana

description: <strong>Small RNAs (sRNAs) are essential in regulating the development in plants and animals. While the biogenesis pathways of many sRNAs is clear, the biogenesis pathway for novel small RNAs like tRNA- and rRNA-derived fragments (tRFs and rRFs) is less so. Many diverse cellular RNAs including mRNAs, long-non-coding RNAs, tRNAs and rRNAs in plants have covalent post-transcriptional modifications and their function is only starting to be elucidated. Here, we determine if the RNA modification 5-methylcytosine (m<sup>5</sup>C) plays a role in sRNA biogenesis in <em>Arabidopsis thaliana</em>. To this effect, we Illumina-sequenced sRNAs from wild type and m5C methyltransferase mutant <em>tRNA methyltransferase 4b </em>(<em>trm4b</em>). Our bioinformatics analysis identified 158 sRNAs loci that increased in abundance and two sRNA loci that decreased in abundance in the <em>trm4b</em> compared to the wild type control. Comparison with RNA bisulphite sequencing data confirmed that most of the top differentially abundant sRNAs have m<sup>5</sup>C sites. In summary, our results suggest that m<sup>5</sup>C RNA modifications is associated with sRNA biogenesis in <em>Arabidopsis thaliana</em>.</strong>
description: This dataset consist of the source code used for the unpublished manuscript of the same title. The datasets associated with this code have not been uploaded to any data repository as its unpublished. For enquiries and updates, please contact the corresponding author Dr. Iain Searle (iain.searle@adelaide.edu.au) This is also included as part of Pei Qin Ng's thesis examination for the qualification of Doctor of Philosophy (PhD) at the University of Adelaide.
DOI: 10.5281/zenodo.5506434
title: Raw Data for IntoValue Dataset

description: Raw Data for IntoValue Dataset This data deposit includes large raw data used for the "IntoValue" dataset, which underlies several projects at the QUEST Center for Responsible Research in the Berlin Institute of Health (BIH) @ Charité. An initial version of the IntoValue dataset is available in Zenodo: https://doi.org/10.5281/zenodo.5141342. Based on this initial version, the dataset is actively developed and maintained in GitHub: https://github.com/maia-sh/intovalue-data. This Zenodo deposit serves to store large raw data files for individual trials and are used in that GitHub repository. These data are deposited for computational reproducibility and documentation; they are not intended to be used for additional projects and do not reflect the most current/accurate data available from each source. This deposit contains raw data from the following sources: <strong>PubMed</strong> (<code>pubmed.zip</code>): PubMed XML files are provided courtesty of the U.S. National Library of Medicine and were accessed via the Entrez Programming Utilities (E-utilities) API. The files were downloaded on 2021-08-15 and do not reflect the most current/accurate data available from NLM. The following scripts were used to download and create these files: get-pubmed.R; download-pubmed.R. <strong>ClinicalTrials.gov</strong> (<code>ctgov.zip</code>): ClinicalTrials.gov was accessed via the Clinical Trials Transformation Initiative (CTTI) Aggregate Content of ClinicalTrials.gov (AACT) via its PostgreSQL database API.The API was queried and CSV files were generated on 2021-08-15. The following scripts were used to download and create these files: get-aact.R; aact-functions.R. <strong>German Clinical Trials Registry (DRKS)</strong> (<code>drks.zip</code>): DRKS does not provide an API and was webscrapped on 2021-08-15. The following scripts were used to download and create these XML files: get-drks.R; drks-functions.R
description: This work was funded under a grant from the Federal Ministry of Education and Research of Germany (Bundesministerium für Bildung und Forschung - BMBF) [01PW18012].
DOI: 10.5517/ccdc.csd.cc20f9sk
title: CCDC 1859838: Experimental Crystal Structure Determination

description: Related Article: Rana Sanii, Ewa Patyk-Kaźmierczak, Carol Hua, Shaza Darwish, Tony Pham, Katherine A. Forrest, Brian Space, Michael J. Zaworotko|2021|Cryst.Growth Des.|21|4927|doi:10.1021/acs.cgd.1c00353
DOI: 10.6085/aa/srkx00_xxxitv2xlsr02_20190620.40.1
title: (:unkn)
DOI: 10.18112/openneuro.ds003555.v1.0.2
title: Dataset of EEG recordings of pediatric patients with epilepsy based on the 10-20 system
DOI: 10.6084/m9.figshare.16615948
title: Glasshouse trial data for sex and flowers: testing the resource dependant selection hypothesis for flower sex allocation

description: Glasshouse trial data for sex and flowers: testing the resource dependant selection hypothesis for flower sex allocation
DOI: 10.6084/m9.figshare.16615948.v1
title: Glasshouse trial data for sex and flowers: testing the resource dependant selection hypothesis for flower sex allocation

description: Glasshouse trial data for sex and flowers: testing the resource dependant selection hypothesis for flower sex allocation
DOI: 10.6084/m9.figshare.16615960
title: Supplementary Material for: Association of the Degree of Erythroid Expansion and Maturation Arrest with the Clinical Severity of β<sup>0</sup>-Thalassemia/Hemoglobin E Patients

description: <b><i>Introduction:</i></b> β-Thalassemia/hemoglobin E represents one-half of all the clinically severe β-thalassemias worldwide. Despite similar genetic backgrounds, patients show clinical heterogeneity ranging from nearly asymptomatic to transfusion-dependent thalassemia. The underlying disease modifying factors remain largely obscure. <b><i>Methods:</i></b> To elucidate the correlation between ineffective erythropoiesis and β<sup>0</sup>-thalassemia/hemoglobin E (HbE) disease severity, in vitro culture of erythroid cells derived from patients with different clinical symptoms was established. Cell proliferation, viability, and differentiation were investigated. To identify potential molecular mechanisms leading to the arrested erythroid maturation, the expression levels of erythropoiesis modifying factors were measured. <b><i>Results:</i></b> The β<sup>0</sup>-thalassemia/HbE cells exhibited enhanced proliferation, limited differentiation, and impaired erythroid terminal maturation but did not show accelerated erythroblast differentiation and increased cell death. Erythroblasts derived from mild patients showed the highest proliferation rate with a faster cell division time, while erythroblasts derived from severe patients displayed extremely delayed erythroid maturation. Downregulation of growth differentiation factor 11 and FOXO3a was observed in mild β<sup>0</sup>-thalassemia/HbE erythroblasts, while upregulation of heat shock protein 70 and activin receptor 2A was revealed in severe erythroblasts. <b><i>Discussion/Conclusion:</i></b> The degree of erythroid expansion and maturation arrest contributes to the severity of β<sup>0</sup>-thalassemia/HbE patients, accounting for the disease heterogeneity. The findings suggest a restoration of erythroid maturation as a promising targeted therapy for severe patients.
DOI: 10.6084/m9.figshare.16615960.v1
title: Supplementary Material for: Association of the Degree of Erythroid Expansion and Maturation Arrest with the Clinical Severity of β<sup>0</sup>-Thalassemia/Hemoglobin E Patients

description: <b><i>Introduction:</i></b> β-Thalassemia/hemoglobin E represents one-half of all the clinically severe β-thalassemias worldwide. Despite similar genetic backgrounds, patients show clinical heterogeneity ranging from nearly asymptomatic to transfusion-dependent thalassemia. The underlying disease modifying factors remain largely obscure. <b><i>Methods:</i></b> To elucidate the correlation between ineffective erythropoiesis and β<sup>0</sup>-thalassemia/hemoglobin E (HbE) disease severity, in vitro culture of erythroid cells derived from patients with different clinical symptoms was established. Cell proliferation, viability, and differentiation were investigated. To identify potential molecular mechanisms leading to the arrested erythroid maturation, the expression levels of erythropoiesis modifying factors were measured. <b><i>Results:</i></b> The β<sup>0</sup>-thalassemia/HbE cells exhibited enhanced proliferation, limited differentiation, and impaired erythroid terminal maturation but did not show accelerated erythroblast differentiation and increased cell death. Erythroblasts derived from mild patients showed the highest proliferation rate with a faster cell division time, while erythroblasts derived from severe patients displayed extremely delayed erythroid maturation. Downregulation of growth differentiation factor 11 and FOXO3a was observed in mild β<sup>0</sup>-thalassemia/HbE erythroblasts, while upregulation of heat shock protein 70 and activin receptor 2A was revealed in severe erythroblasts. <b><i>Discussion/Conclusion:</i></b> The degree of erythroid expansion and maturation arrest contributes to the severity of β<sup>0</sup>-thalassemia/HbE patients, accounting for the disease heterogeneity. The findings suggest a restoration of erythroid maturation as a promising targeted therapy for severe patients.
DOI: 10.6084/m9.figshare.16615951
title: DSP analysis - Stroma Areactive Invasion Front Areas (SARIFA) – a new prognostic biomarker in gastric cancer related to tumor-promoting adipocytes

description: DSP transcriptome analysis: Stroma Areactive Invasion Front Areas (SARIFA) - ein neuer prognostischer Biomarker bei Magenkrebs im Zusammenhang mit tumorpromovierenden Adipozyten
DOI: 10.6084/m9.figshare.16615966
title: 2021_For_FigShare.xlsx

description: Here, using energy-subtractive synchrotron radiation tomography, we measured, the distribution of an inert gas (Xe) in the <i>in vivo</i> rabbit lung during Xe washin breathing maneuvers. The effects of convective flow rate, diffusion, and cardiac motion were also assessed. Fractal analysis of resulting gas concentration and tissue-density maps revealed that fractal dimension was always smaller for Xe than for tissue density, and that only for the gas, a length scale existed where fractal dimension approached unity. The length scale where this occurred was seen to correspond to that of a rabbit acinus, the terminal structure comprising only alveolated airways.
DOI: 10.3886/e127521v1-96220
title: 2020 Perceived Stress and Cognitive Failure in Chinese Adolescents

description: 435 Chinese adolescents were tested with perceived stress scale,cognitive failure scale, negative affect scale and mobile phone addiction scale.
DOI: 10.6084/m9.figshare.16615984
title: Macroinvertebrate biomass in the water column of constructed ponds in the Whangamarino wetland

description: Macroinvertebrate biomass in the water column of constructed ponds in the Whangamarino wetland<br><br><b>Quality control:</b> Habitat type; Identification QA; Identified by; Net mesh size; Sampling method; Sampling protocol; Sorting QA; Sorting protocol<br><br><b>Type of waterbody:</b> Wetland<br><br><b>Variables:</b> Macroinvertebrates Biomass; Sampling effort<br><br><b>Start date:</b> 2013-07-16<br><br><b>End date:</b> 2013-09-03<br><br><b>Region:</b> Waikato<br><br><b>Wetland:</b> Constructed pond in the Whangamarino wetland<br><br>This dataset was originally hosted in the LERNZdb freshwater data repository that was developed as part of the Lake Ecosystem Restoration New Zealand (LERNZ) project run by the Environmental Research Institute at the University of Waikato, New Zealand. <br><br>In retrieving LERNZdb material you agree that you rely on the data at your own risk; the University of Waikato offers no warranty or representation that the data is fit for any particular purpose, or free from defects, and will not be liable for any losses or damages whatsoever including any indirect, special, incidental or consequential damages incurred by you arising out of the use of the database or in reliance on the data retrieved. You agree that data is not of a kind ordinarily supplied for personal or domestic purposes, and that the Consumer Guarantees Act 1993 does not apply.
DOI: 10.6084/m9.figshare.16615969
title: Supplementary Material for: DNA Methylation Profile of the <b><i>SREBF2</i></b> Gene in Human Fetal Aortas

description: Increasing evidence suggests that maternal cholesterol represents an important risk factor for atherosclerotic disease in offspring already during pregnancy, although the underlying mechanisms have not yet been elucidated. Eighteen human fetal aorta samples were collected from the spontaneously aborted fetuses of normal cholesterolemic and hypercholesterolemic mothers. Maternal total cholesterol levels were assessed during hospitalization. DNA methylation profiling of the whole <i>SREBF2</i> gene CpG island was performed (<i>p</i> value &lt;0.05). The Mann-Whitney U test was used for comparison between the 2 groups. For the first time, our study revealed that in fetal aortas obtained from hypercholesterolemic mothers, the <i>SREBF2</i> gene shows 4 significant differentially hypermethylated sites in the 5′UTR-CpG island. This finding indicates that more effective long-term primary cardiovascular prevention programs need to be designed for the offspring of mothers with hypercholesterolemia. Further studies should be conducted to clarify the epigenetic mechanisms underlying the association between early atherogenesis and maternal hypercholesterolemia during pregnancy.
DOI: 10.6084/m9.figshare.16615969.v1
title: Supplementary Material for: DNA Methylation Profile of the <b><i>SREBF2</i></b> Gene in Human Fetal Aortas

description: Increasing evidence suggests that maternal cholesterol represents an important risk factor for atherosclerotic disease in offspring already during pregnancy, although the underlying mechanisms have not yet been elucidated. Eighteen human fetal aorta samples were collected from the spontaneously aborted fetuses of normal cholesterolemic and hypercholesterolemic mothers. Maternal total cholesterol levels were assessed during hospitalization. DNA methylation profiling of the whole <i>SREBF2</i> gene CpG island was performed (<i>p</i> value &lt;0.05). The Mann-Whitney U test was used for comparison between the 2 groups. For the first time, our study revealed that in fetal aortas obtained from hypercholesterolemic mothers, the <i>SREBF2</i> gene shows 4 significant differentially hypermethylated sites in the 5′UTR-CpG island. This finding indicates that more effective long-term primary cardiovascular prevention programs need to be designed for the offspring of mothers with hypercholesterolemia. Further studies should be conducted to clarify the epigenetic mechanisms underlying the association between early atherogenesis and maternal hypercholesterolemia during pregnancy.
DOI: 10.22011/strenda_db.tqx5cm
title: Discovery of a Kojibiose Phophorylase in E. coli

description: Beta-phosphoglucomutase (Beta-PGM), P77366, 2-O-(alpha-D-glucopyranosyl)-D-glycerate + phosphate = alpha-D-glucopyranose 1-phosphate + D-glycerate
DOI: 10.22011/strenda_db.0toyql
title: Discovery of a Kojibiose Phophorylase in E. coli

description: YcjT, P77154, 2-alpha-D-glucosyl-D-glucose + phosphate = D-glucose + beta-D-glucose 1-phosphate
DOI: 10.22011/strenda_db.gfjqzc
title: Discovery of a Kojibiose Phophorylase in E. coli

description: Beta-phosphoglucomutase (Beta-PGM), P77366, null
DOI: 10.22023/mdx.15125133.v1
title: Initial questionnaire for Smart Home User

description: Survey questionnaire
DOI: 10.22023/mdx.15125133
title: Initial questionnaire for Smart Home User

description: Survey questionnaire
DOI: 10.22023/mdx.11822046.v1
title: Validation 2: Enhance the Understanding of the home using the UTL approach

description: This part of the validation is supplementary of the validation part one. Three participants participated in this validation process.
DOI: 10.22023/mdx.11822046
title: Validation 2: Enhance the Understanding of the home using the UTL approach

description: This part of the validation is supplementary of the validation part one. Three participants participated in this validation process.
DOI: 10.5281/zenodo.5503996
title: Ultrahigh vacuum packaging and surface cleaning for quantum devices

description: Datasets associated with the paper "Ultrahigh vacuum packaging and surface cleaning for quantum devices". Datasets for the plots in Figures 4, 5, 6 and Table I are provided. Toc.pdf links the data to the figures and adds information on how the data can be reproduced.
DOI: 10.5281/zenodo.5503995
title: Ultrahigh vacuum packaging and surface cleaning for quantum devices

description: Datasets associated with the paper "Ultrahigh vacuum packaging and surface cleaning for quantum devices". Datasets for the plots in Figures 4, 5, 6 and Table I are provided. Toc.pdf links the data to the figures and adds information on how the data can be reproduced.
DOI: 10.6084/m9.figshare.16615993
title: Posttraumatic growth, positive psychology, perceived spousal support, and psychological complications in head and neck cancer: Evaluating their association in a longitudinal study

description: Head and neck cancer (HNC) specifically, refers to malignant tumor which develop around the head and neck area, such as the throat, mouth, nose and ear. HNC contributes to a wide range of psychosocial issues, such as depression, anxiety, substance use disorder, suicide, conflict in interpersonal relationship, damage to self-esteem, social isolation, and facial disfigurement. Hence, it is associated with various psychological complications such as depression, anxiety and posttraumatic stress disorder. Notwithstanding to these negative impacts of HNC, positive psychology such as posttraumatic growth (PTG), hope, and optimism have been reported in HNC patients. Higher degree of positive psychology may resulting in better appreciation of life, improved interpersonal relationship, greater spiritual development, more possibilities in life, and enhancement of the personal strength of HNC patients. However, data on how positive psychology is related to psychological complications of HNC across time is lacking. This longitudinal study examined the trends of positive psychology (such as PTG, hope, and optimism), perceived spousal support, and psychological complications (such as depression, anxiety, and posttraumatic stress symptoms); and determined the association between these positive psychology, psychological complications, and PTG across two timelines among a cohort of HNC patients. We found that a total of 175 HNC respondents exhibited increasing trend of positive psychology and perceived spousal support, while reported reducing trend of psychological complications between baseline and follow up assessments. Greater degree of hope and perceived spousal support contributed to higher degree of PTG across time. Conversely, higher severity of anxiety symptoms was associated with lower degree of PTG over time. This study indicates the pivotal role of incorporating psychosocial interventions into the treatment regimen to enhance the degree of hope and perceived spousal support as well as reducing anxiety symptoms severity, which in turn will facilitate the development of PTG and improve the mental well-being of HNC patients.
DOI: 10.6084/m9.figshare.16615993.v1
title: Posttraumatic growth, positive psychology, perceived spousal support, and psychological complications in head and neck cancer: Evaluating their association in a longitudinal study

description: Head and neck cancer (HNC) specifically, refers to malignant tumor which develop around the head and neck area, such as the throat, mouth, nose and ear. HNC contributes to a wide range of psychosocial issues, such as depression, anxiety, substance use disorder, suicide, conflict in interpersonal relationship, damage to self-esteem, social isolation, and facial disfigurement. Hence, it is associated with various psychological complications such as depression, anxiety and posttraumatic stress disorder. Notwithstanding to these negative impacts of HNC, positive psychology such as posttraumatic growth (PTG), hope, and optimism have been reported in HNC patients. Higher degree of positive psychology may resulting in better appreciation of life, improved interpersonal relationship, greater spiritual development, more possibilities in life, and enhancement of the personal strength of HNC patients. However, data on how positive psychology is related to psychological complications of HNC across time is lacking. This longitudinal study examined the trends of positive psychology (such as PTG, hope, and optimism), perceived spousal support, and psychological complications (such as depression, anxiety, and posttraumatic stress symptoms); and determined the association between these positive psychology, psychological complications, and PTG across two timelines among a cohort of HNC patients. We found that a total of 175 HNC respondents exhibited increasing trend of positive psychology and perceived spousal support, while reported reducing trend of psychological complications between baseline and follow up assessments. Greater degree of hope and perceived spousal support contributed to higher degree of PTG across time. Conversely, higher severity of anxiety symptoms was associated with lower degree of PTG over time. This study indicates the pivotal role of incorporating psychosocial interventions into the treatment regimen to enhance the degree of hope and perceived spousal support as well as reducing anxiety symptoms severity, which in turn will facilitate the development of PTG and improve the mental well-being of HNC patients.
DOI: 10.5281/zenodo.5504655
title: Identity Based Proxy Re-encryption Source Code for Security and Privacy in Connected Vehicle

description: This is a source code for identity based proxy re-encryption using special string attribute for connected vehicle and Privacy, designed in python using Charm Cryptographic library using Pairing Group ss512 and 1024 bits.
DOI: 10.5281/zenodo.5504654
title: Identity Based Proxy Re-encryption Source Code for Security and Privacy in Connected Vehicle

description: This is a source code for identity based proxy re-encryption using special string attribute for connected vehicle and Privacy, designed in python using Charm Cryptographic library using Pairing Group ss512 and 1024 bits.
DOI: 10.6084/m9.figshare.16615981
title: Amphibians sampled for chytrid fungus in Suriname

description: Overview of species sampled during 3 years in Suriname for <i>Batrachochytrium dendrobatidis</i>
DOI: 10.6084/m9.figshare.16615981.v1
title: Amphibians sampled for chytrid fungus in Suriname

description: Overview of species sampled during 3 years in Suriname for <i>Batrachochytrium dendrobatidis</i>