cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22266313.v2
title: Human lung organoids reveal donor-dependent variability in susceptibility to SARS-CoV-2 variants of concern

description: The emergence of SARS-CoV-2 variants of concern (VOC) Delta (B.1.617.2) and Omicron (B.1.1.529) raised global health concerns about increased pathogenicity. The ability of viruses to replicate in the lower respiratory tract (LRT) is often associated with severe clinical disease, making this an important site to consider when evaluating pathogenicity of SARS-CoV-2 VOCs. Distal human lung organoids (hLOs) are three-dimensional primary cell culture systems that enable the study of physiologically relevant LRT epithelium, including alveolar type II cells. Using hLOs derived from four human donors, we compared the fitness and pathogenicity of SARS-CoV-2 VOC Delta and Omicron, along with an ancestral clade B variant containing the D614G substitution in spike, and evaluated donor-dependent differences in susceptibility to infection. We observed substantial attenuation of Omicron in hLOs and demonstrated enhanced susceptibility to Omicron and D614G replication in hLOs from one donor. Transcriptomic analysis revealed that increased susceptibility to SARS-CoV-2 infection in these hLOs was associated with reduced tonic interferon signaling activity. Overall, we show that hLOs are a useful model to evaluate SARS-CoV-2 VOC fitness and pathogenicity. Additionally, we propose that hLOs may serve as a unique system to model the heterogeneity of SARS-CoV-2 pathogenesis in humans.
DOI: 10.17632/xxmfhk9rzg
title: Local electron tomography using angular variations of surface tangents: Stomo version 2

description: Abstract In a recent publication, we investigated the prospect of measuring the outer three-dimensional (3D) shapes of nano-scale atom probe specimens from tilt-series of images collected in the transmission electron microscope. For this purpose alone, an algorithm and simplified reconstruction theory were developed to circumvent issues that arise in commercial “back-projection” computations in this context. In our approach, we give up the difficult task of computing the complete 3D continuum structur... Title of program: STOMO version 2 Catalogue Id: AEFS_v2_0 Nature of problem A local electron tomography algorithm of specimens for which conventional back projection may fail and or data for which there is a limited angular range (which would otherwise cause significant 'missing-wedge' artefacts). The algorithm does not solve the tomography back projection problem but rather locally reconstructs the 3D morphology of surfaces defined by varied scattering densities. Versions of this program held in the CPC repository in Mendeley Data AEFS_v1_0; STOMO version 1.0; 10.1016/j.cpc.2009.10.023 AEFS_v2_0; STOMO version 2; 10.1016/j.cpc.2011.11.008 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17605/osf.io/jrqpz
title: Assessing Medical Errors in HIV/AIDS Treatment Among Young Adults in Sub-Saharan Africa: A Scoping Review Protocol

description: The study is a systematic investigation aimed at mapping the existing literature on medical errors within the context of HIV/AIDS treatment for young adults in Sub-Saharan Africa. Despite advancements in antiretroviral therapy (ART), medical errors remain a significant threat to patient safety, exacerbated by the complexities of treatment regimens and socioeconomic challenges prevalent in the region. This scoping review will explore the types, prevalence, and impacts of medical errors, as well as the demographic factors influencing these occurrences. Additionally, it will identify underlying causes and implications for treatment outcomes and patient safety.
DOI: 10.6084/m9.figshare.14865702.v1
title: Supplementary Material for: The Burden of Dementia due to Down Syndrome, Parkinson’s Disease, Stroke, and Traumatic Brain Injury: A Systematic Analysis for the Global Burden of Disease Study 2019

description: <b><i>Background:</i></b> In light of the increasing trend in the global number of individuals affected by dementia and the lack of any available disease-modifying therapies, it is necessary to fully understand and quantify the global burden of dementia. This work aimed to estimate the proportion of dementia due to Down syndrome, Parkinson’s disease, clinical stroke, and traumatic brain injury (TBI), globally and by world region, in order to better understand the contribution of clinical diseases to dementia prevalence. <b><i>Methods:</i></b> Through literature review, we obtained data on the relative risk of dementia with each condition and estimated relative risks by age using a Bayesian meta-regression tool. We then calculated population attributable fractions (PAFs), or the proportion of dementia attributable to each condition, using the estimates of relative risk and prevalence estimates for each condition from the Global Burden of Disease Study 2019. Finally, we multiplied these estimates by dementia prevalence to calculate the number of dementia cases attributable to each condition. <b><i>Findings:</i></b> For each clinical condition, the relative risk of dementia decreased with age. Relative risks were highest for Down syndrome, followed by Parkinson’s disease, stroke, and TBI. However, due to the high prevalence of stroke, the PAF for dementia due to stroke was highest. Together, Down syndrome, Parkinson’s disease, stroke, and TBI explained 10.0% (95% UI: 6.0–16.5) of the global prevalence of dementia. <b><i>Interpretation:</i></b> Ten percent of dementia prevalence globally could be explained by Down syndrome, Parkinson’s disease, stroke, and TBI. The quantification of the proportion of dementia attributable to these 4 conditions constitutes a small contribution to our overall understanding of what causes dementia. However, epidemiological research into modifiable risk factors as well as basic science research focused on elucidating intervention approaches to prevent or delay the neuropathological changes that commonly characterize dementia will be critically important in future efforts to prevent and treat disease.
DOI: 10.6084/m9.figshare.19499030.v4
title: Fasta and phylogenetic tree files of Virome of illegally trafficked Malayan pangolins reveals pangolin-associated viral lineages and infection with known pathogens of humans

description: Fasta and phylogenetic tree files of Virome of illegally trafficked Malayan pangolins reveals pangolin-associated viral lineages and infection with known pathogens of humans
DOI: 10.6084/m9.figshare.20220087.v1
title: SciSciNet_PaperFields

description: SciSciNet_PaperFields
DOI: 10.6084/m9.figshare.23791050.v1
title: Supplementary Material for: Association of maternal cigarette smoking with neonatal death: a population-based cohort study

description: Background: Maternal pregnancy smoking have adverse perinatal outcomes and the relationship between maternal smoking and neonatal death have not been fully elucidated. We aimed to examine the risk of neonatal death in relation to maternal smoking and to quantify potential mediators of these associations. Methods: We did a population-based cohort study using Period Linked Birth-Infant Death data from 2016 to 2019 in the US National Vital Statistics System. The exposure was maternal smoking status. The main outcome was neonatal death. Association between maternal smoking and neonatal death was estimated through logistic regression. Mediation analysis was performed to assess the extent to which the association between maternal smoking and neonatal death was mediated by neonatal complications. Results: The final sample consisted of 14717020 mothers with live singleton births. The overall neonatal mortality rate was 2.2 per 1000 live births. Maternal pregnancy smoking was associated with an increased risk of neonatal death (aOR, 1.33 [95%CI, 1.28-1.38]; P&lt;.001), while smoking cessation during the whole pregnancy showed a comparable risk of neonatal death with non-smokers (aOR,1.06 [95%CI, 0.99-1.14]; P=0.116). Mediation analysis indicated that the association between pregnancy smoking and neonatal death might be mainly mediated by preterm birth and low Apgar score at 5min. Conclusions: Maternal pregnancy smoking, regardless of pregnancy trimester and intensity, was associated with increased risk of neonatal death. Efforts are needed for policymakers to promote smoking cessation before pregnancy and professional perinatal care should be provided for those who smoked during pregnancy.
DOI: 10.6084/m9.figshare.9906512.v1
title: Data-Chen-JGR

description: This dataset contains Py-GC-MS/MS data, Geochip data and PLFA data.
DOI: 10.6084/m9.figshare.9962765.v2
title: Harmonised LUCAS in-situ land cover and use database for field surveys from 2006 to 2018 in the European Union

description: d'Andrimont, R., Yordanov, M., Martinez-Sanchez, L., Eiselt, B., Palmieri, A., Dominici, P., Gallego, J., Reuter, H.I., Joebges, C., Lemoine, G. and van der Velde, M., 2020. <b>Harmonised LUCAS in-situ land cover and use database for field surveys from 2006 to 2018 in the European Union</b>.<br><b><br></b>LUCAS_harmonised<b><br></b>├── 0_releaseNote.txt├── 1_table│ ├── lucas_harmo_exif.zip│ ├── lucas_harmo_uf_2006.zip│ ├── lucas_harmo_uf_2009.zip│ ├── lucas_harmo_uf_2012.zip│ ├── lucas_harmo_uf_2015.zip│ ├── lucas_harmo_uf_2018.zip│ └── lucas_harmo_uf.zip├── 2_geometry│ ├── LUCAS_gps_geom.zip│ ├── LUCAS_th_geom.zip│ └── LUCAS_trans_geom.zip├── 3_supporting│ ├── C3_legends.xls│ ├── lucas_harmo_record_descriptor.xls│ └── LUCAS-Variable_and_Classification_Changes.xlsx└── 4_mappings ├── 2006_lucas_harmo_allVars.csv ├── 2009_lucas_harmo_allVars.csv ├── 2012_lucas_harmo_allVars.csv ├── 2015_lucas_harmo_allVars.csv ├── 2018_lucas_harmo_allVars.csv ├── columnRename.csv ├── manChangedVars.csv └── RecodeVars.csv
DOI: 10.6084/m9.figshare.28481033.v1
title: Supplementary Material for: A Pilot Study to Evaluate the Role of Obesity and Genetic Variants in Serum C-Reactive Protein Response to an Acute Fructose Load

description: 33 Introduction: Excess fructose intake has been linked to increased risk for dyslipidemia, insulin, 
34 resistance, hyperuricemia, inflammation, and obesity. In this human study, we investigated if serum 
35 CRP concentrations change after fructose consumption, and whether genetic variants and 
36 obesity status influences this change. Methods: Blood was drawn before and at four time points 
37 after administration of a fructose load (n=57). Serum concentrations of CRP were measured, 
38 and 11 single nucleotides polymorphisms (SNPs) (rs1205, rs1417938, rs1470515, rs3093068,
39 rs6588158, rs16842568, rs2259820, rs157581, rs2794521, rs3093062, rs17700633), 
40 previously associated with serum CRP were genotyped and assessed for their association with 
41 CRP levels. Results: Participants identifying as White (n = 37) had higher mean CRP levels across 
42 all time points compared to those identifying as Black (n = 20). Participants with obesity (BMI ≥ 30 
43 kg/m2) (n = 25) were younger and had higher mean CRP levels throughout the study period 
44 compared to those without (n = 32). All SNPs were in Hardy-Weinberg Equilibrium and their 
45 effect allele frequencies ranged between 11and 96%. Baseline CRP was associated with CRP 
46 SNPs rs1417938 and rs2794521 (p &lt;0.005), with rs2794521 also associated with CRP response to 
47 fructose challenge (p &lt; 0.005). The variability in responses to fructose and genetic associations 
48 were mainly observed in individuals without obesity. Obesity status was associated with early 
49 changes in CRP (0-30 min and 30-60min) whereas CRP SNPs were associated with later changes 
50 (60-120min and 120-180 min). Conclusion: Changes in serum CRP were associated with obesity
51 status or SNPs based on the time elapsed since fructose ingestion. Larger studies are needed to
52 confirm and validate these associations.
53 
54
DOI: 10.6084/m9.figshare.7881059.v1
title: Ricardo Henriques talk at University of Birmingham 2019 - Democratising Live-Cell Compatible High-Speed Super-Resolution Microscopy

description: A copy of my lecture at University of Birmingham in 2019 titled "Democratising Live-Cell Compatible High-Speed Super-Resolution Microscopy". This recent publication highlights a large portion of the work shown in the presentation: https://iopscience.iop.org/article/10.1088/1361-6463/ab0261/meta
DOI: 10.6084/m9.figshare.3530633.v1
title: Data Paper. Data Paper

description: File List Recruitment_data_97-07.txt -- recruitment data from experimental plots on sheltered intertidal shores in the Gulf of Maine 1997–2007. ASCII text, tab delimited. No compression scheme was used. Description Experimental clearings in macroalgal (<em>Ascophyllum nodosum</em>) stands were made at 12 sites in 1996 to determine if mussel beds and macroalgal stands on sheltered intertidal shores of New England represent alternative community states. Sites were located on Swan’s Island, Maine, USA. At each site an uncleared control plot and four sizes of circular clearings, which mimicked ice scour events, were established. The purpose of this data set is to provide access to recruitment data collected in the experimental plots from 1997 to 2007. <i>Key words: alternative stable states; barnacles; community ecology; Gulf of Maine; LTREB data; mussels; recruitment; rocky intertidal shores; seaweed.</i>
DOI: 10.6084/m9.figshare.12444686.v1
title: Bitter fruits of hard labour: diet metabarcoding and telemetry reveal that urban songbirds travel further for lower-quality food

description: These are the data used in Jarrett et al (2020). All data files have their individual metadata tabs. Descriptions of all methods can be found in the linked article and associated supplementary materials. The R code used for statistical analysis is also included. The bioinformatics code can be shared by contacting Andreanna Welch at a.j.welch@durham.ac.uk
DOI: 10.6084/m9.figshare.28794500.v1
title: extrusion data

description: Research data on Extrusion Process Fault Detection Based on Current Signal Analysis and DWT
DOI: 10.6084/m9.figshare.12486350.v2
title: Dataset for the manuscript "Deriving the absorption of brown carbon from multiple wavelengths: The effect of black carbon morphologies " by Luo et al.

description: This is the Dataset for the manuscript "Deriving the absorption of brown carbon from multiple wavelengths: The effect of black carbon morphologies " by Luo et al.
DOI: 10.6084/m9.figshare.26384536.v1
title: Working capital Management_Malaysian <i>SMEs_</i> P2P lending

description: Using an exploratory approach, we observed 125 loan applications from October 2023 to February 2024 from Funding Societies, Malaysia’s largest P2P platform. We used descriptive and correlation analyses to determine the characteristics of MSMEs that use P2P platforms to obtain working capital. We found that these firms were repeat platform users, whereby only 40 MSMEs had made the 125 borrowings at an average interest rate of 13%. Most firms were from the wholesale and retail industry while account payable financing was the most popular type of working capital financing. We found that these MSMEs issued Islamic accounts payable notes at relatively high interest rates, considering the low amounts borrowed and low tenures on these Islamic notes. We found that these MSMEs were mostly 6 to 10 years old hence, few young firms used P2P lending. There was no micro-enterprise among these firms. We observed that manufacturing MSMEs outperformed those in the wholesale and retail sectors in terms of revenue, revenue growth, and average growth margin in 2020 and 2021. In the correlation analysis among 22 financial and non-financial variables, we found 23 combinations that were negatively correlated and 69 combinations that were positively correlated. These findings have varied implications among the different P2P lending stakeholders. This is the first exploratory study to give deeper insights into the features of MSMEs that use P2P online lending to obtain working capital in Malaysia.
DOI: 10.6084/m9.figshare.19640892.v4
title: Datas of study

description: We evaluated oxidative stress parameters and DNA damage before and after treatment in children with B12 deficiency in this study.
DOI: 10.6084/m9.figshare.1299451.v2
title: Open Access Journals 2014, DOAJ subset

description: Prepared for "Idealism and Opportunism: The State of Open Access Journals," <em>Library Technology Reports</em>, 2015 (to appear later this year). Data on 7,301 journals listed in the <em>Directory of Open Access Journals</em> as of May 7, 2014 that could be reviewed using English. Data gathered by direct (visual) checking of journal sites. Article counts approximate in some cases. See data_key sheet for code explanations. Additional commentary in <em>Cites & Insights</em> 14:10, 14:11, 15:1 and 15:3 (not yet published)
DOI: 10.6084/m9.figshare.7081268.v3
title: Unmasking Technology Skills Divide (TSD) as an Emerging Digital Divide Within the ICT Framework

description: The digital divide is a common term used to describe the inequalities that exist with respect to the use of Internet and other telecommunication services, but as these inequalities lessen with more availability of information communication technology (ICT) and mobile devices, a new complication arises in the form of technology skills divide (TSD). The researchers sought to address TSD in a manner like that of the digital divide. They looked to modeling technology skills for high school teachers in an era of exponential growth in ICT and how this can create a rise in TSD for high school teachers in the United States. Through a research synthesis, using data from a study conducted by PBS in 2012 on “teacher technology use”, the researchers found TSD can be viewed as an entropy in technology skills of teachers created by the rapid changes and exponential growth in ICT. Specific technology needs and demands vary across business/industry and many industries have specific needs that are unique to their organization. Technology as a tool is used to increase productivity and should be infused and integrated with the curriculum to enhance student learning. Innovations in ICT has resulted in new technological skills, new attitudes, new learning styles, and new expectations regarding technology in the classroom. In this poster the researchers examine phases of TSD modeled against that of the Digital Divide framework. This research intends to be a practical step towards advancing theory, practice, and policy regarding TSD. <br>MethodsData was pulled form two sources: (1) Study by PBS on ‘teachers technology use’ which surveyed 503 US Pre-K-12 teachers in a web-based interview with a marginal error of +/- 4.4% at a 95% confidence level. (2) Through the United States Department of Education and the National Center for Education Statistics, titled “Teachers’ Use of Educational Technology in U.S. Public Schools, 2009”.
DOI: 10.6084/m9.figshare.7098077.v1
title: Supplementary Material for: Biochemical and Morphological Characterization of a Neurodevelopmental Disorder-Related Mono-ADP-Ribosylhydrolase, MACRO Domain Containing 2

description: MACRO Domain Containing 2 (MacroD2) is a neurodevelopmental disorder-related mono-ADP-ribosylhydrolase. Molecular features of this protein in neural tissues are largely unknown. In this study, we generated a specific antibody against MacroD2, and carried out expression and morphological analyses of the molecule during mouse brain development. In Western blotting, 2 MacroD2 isoforms with molecular masses of ∼70 and ∼75 kDa started to be expressed at embryonic day 16.5, reached the maximal level at postnatal day 8, and then gradually decreased through P30. In contrast, other isoforms with molecular masses of ∼110 and ∼140 kDa gradually increased during embryonic to postnatal development. In immunohistochemical analyses, MacroD2 was strongly detected in cortical neurons in layer II–V at P0 and P7, while the protein expression decreased significantly in the neurons at P30. Immunofluorescence analyses revealed that MacroD2 was mainly distributed in the soma and to a lesser extent in the axon and dendrite of immature primary cultured mouse hippocampal neurons. On the other hand, in the matured hippocampal neurons, while MacroD2 was detected in the soma, it displayed in dendrites a punctate distribution pattern with a partial colocalization with synaptic markers, synaptophysin, and PSD95. The obtained results indicate that MacroD2 is expressed and may have a physiological role in the central nervous system during brain development.
DOI: 10.6084/m9.figshare.14907909.v1
title: Missing value analysis - PTB Brazil

description: missing value analysis of the PTB dataset
DOI: 10.6084/m9.figshare.14998650.v1
title: Manual analysis of FRAP data for diffusion in PVA manuscript

description: Manually entered data of diffusivity coefficients, etc., from FRAP analysis of solutes diffusing within hydrogels.
DOI: 10.6084/m9.figshare.12627659.v1
title: Data from: Habitat disturbance can alter forest understory bird activity patterns: a regional-scale assessment with camera-traps

description: Original data from:Fontúrbel, F.E., J.I. Orellana, G.B. Rodríguez-Gómez, C.A. Tabilo & G.J. Castaño-Villa (2021) Habitat disturbance can alter activity patterns of forest understory birds: a regional-scale assessment with camera-traps. Forest Ecology and Management <b>479</b> (1): 1186618. doi: 10.1016/j.foreco.2020.118618<br>Please see the readme.txt file for further details.
DOI: 10.6084/m9.figshare.5383699.v1
title: HFMD-orignal.xlsx

description: Economic burden and health related quality of life for Hand, Foot and Mouth Disease in China
DOI: 10.17632/rt2gmzbvmz
title: Tetraploidwheat_220Indx21347SNPs

description: Filtered SNP variants of 220 tetraploid wheat accessions in VCF format.
DOI: 10.6084/m9.figshare.26793697.v1
title: Chromosome-level genome assembly of Parachromis managuensis

description: Chromosome-level genome assembly of Parachromis managuensis using PacBio HiFi and Hi-C sequencing.
DOI: 10.6084/m9.figshare.17878589.v1
title: phishing_url_test

description: The phishing url dataset contains synthetic data of urls - some regular and some used for phishing. This is the test dataset.<br>The dataset is based on the project (https://github.com/Rohith-2/url_classification_dl) byRohith Ramakrishnan (https://www.linkedin.com/in/rohith-ramakrishnan-54094a1a0/) and others, accompanied bya blog post (https://medium.com/nerd-for-tech/url-feature-engineering-and-classification-66c0512fb34d&gt;).<br>The dataset is released under Creative Commons Zero v1.0 Universal (CC0 1.0).
DOI: 10.6084/m9.figshare.22965200.v1
title: QDM magnetic microscopy dataset of a speleothem from Morocco

description: The dataset was measured on a Quantum Diamond Microscope (QDM) at Harvard University, using a stalagmite from Wintimdouine cave (Morroco). <br> We performed a magnetic map over a sample section of approximately 1410 μm × 2256 μm with a grid spacing of 2.35 μm and a sensor-sample distance of approximately 5 μm, totaling 576,000 data points. The data were taken in projected magnetic microscopy (PMM) mode and converted to the vertical component of magnetic field (𝑏𝑧). <br> In this sample, the magnetic remanence is carried by magnetite and hematite. We apply two IRM pulse fields parallel to the sample surface, 2.7 T and 0.3 T, respectively, toward the +Y and -Y directions. The high coercivity grains (hematite) would point towards +Y and the low coercivity ones (magnetite) would align in the -Y direction.