cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7380017
title: Piper longum transcriptomes generated using transXpress

description: Piper longum transcriptome assemblies created and annotated using transXpress with rnaSPAdes and Trinity assemblers.
description: The transcriptome was assembled from reads from SRA with following IDs: SRR10362954, SRR10583928, SRR10362953. Github repository for transXpress: https://github.com/transXpress/transXpress
description: {"references": ["Fallon et al., transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation, BMC Bioinformatics 2023"]}
DOI: 10.5281/zenodo.7380016
title: Piper longum transcriptomes generated using transXpress

description: Piper longum transcriptome assemblies created and annotated using transXpress with rnaSPAdes and Trinity assemblers.
description: The transcriptome was assembled from reads from SRA with following IDs: SRR10362954, SRR10583928, SRR10362953. Github repository for transXpress: https://github.com/transXpress/transXpress
description: {"references": ["Fallon et al., transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation, BMC Bioinformatics 2023"]}
DOI: 10.48670/moi-00230
title: Global Ocean Chlorophyll-a trend map from Observations Reprocessing
DOI: 10.25381/cput.21542346
title: Performance and optimisation of a jet loop reactor’s pilot plant for the treatment of acid mine water using South African coal fly ash.

description: 2021FEBEREC-STD-054 <br> The dataset uploaded are the chemical kinetics as well as the resullts optained after different analyses.
DOI: 10.25381/cput.21542346.v1
title: Performance and optimisation of a jet loop reactor’s pilot plant for the treatment of acid mine water using South African coal fly ash.

description: 2021FEBEREC-STD-054 <br> The dataset uploaded are the chemical kinetics as well as the resullts optained after different analyses.
DOI: 10.48670/moi-00259
title: Mediterranean Sea Chlorophyll-a time series and trend from Observations Reprocessing
DOI: 10.48670/moi-00260
title: Mediterranean Sea Chlorophyll-a trend map from Observations Reprocessing
DOI: 10.5519/qd.a57rrqbz
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (418 records)
DOI: 10.5519/qd.l21jnlaz
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (166 records)
DOI: 10.5281/zenodo.7352051
title: Endometrium Carcinoma Pipelle biopsies

description: The dataset consists of n=91 digital pathology whole-slide images (WSI) of endometrium carcinoma Pipelle biopsies, stained with hematoxylin and eosin (H&E) at Radboud University Medical Centers, Nijmegen (The Netherlands). The WSIs were scanned with a 3DHistech P1000 scanners at 0.25 um/px spacing, originally stored in MRXS file format. However, the WSIs made available here have been converted to TIFF format with a maximum spacing of 0.5 um/px. This was done to make slides broadly accessible (since MRXS files are sometimes not compatible with some digital pathology viewers or APIs). In order to fit into the Zenodo requirements, the 91 slides are compressed into a .rar file. Together with the data, we have released a web-based evaluation platform via the grand-challenge.org platform, which can be found at this link: https://endo-aid.grand-challenge.org/. In this way, researchers can download the WSI from Zenodo, process them with their algorithm to predict a single grading score for each slide, compile the predictions as indicated on the grand-challenge.org page, and submit them, to compare the results with the opinion of a panel of fifteen pathologists. The data is released under CC BY-NC 4.0 license
DOI: 10.5281/zenodo.7380460
title: Monitoring NBS for coastal erosion and marine flooding: the Emilia-Romagna case study

description: The study was conducted in the context of the OPERANDUM project which is an H2020 project which aims at providing tools and methodologies for the assessment of NBS efficiency around the world. As NBS will be tested an artificial dune built with natural materials. The artificial dune is an engineered structure that will mimic the functioning of natural dunes. Its aims are reducing both natural dune erosion and flooding in adjacent coastal lowlands. It consists of a barrier between the sea and land, in a similar way to a seawall. Unlike the latter, the NBS are ‘dynamic’, i.e. the dune/beach system interacts a great deal and is constantly undergoing small adjustments in response to changes in wind and wave climate or sea level. Its construction involves the placement of sediment from dredged sources on the beach and it will be reinforced with a structure composed of biodegradable material. Different typologies of experimental solutions are foreseen. The Bellocchio Beach at Lido di Spina (Italy) was initially chosen for the study, however the Volano beach was selected as the new study area because of the strong erosion caused by an intense storm event in December 2020 at Bellocchio. The dune was built on the Volano beach and monitoring surveys were carried out on this new site. A morphological monitoring aimed to assess the beach evolution and the performance of the NBS were performed. Monitoring of morphology evolution of shoreline and inland area provide information about impact of the NBS on coastal erosion. Furthermore, the changes in the form of the work give information about the resistance of the NBS to wave attacks. Sedimentological campaigns have been planned in order to provide information regarding the texture of the sediments present in the area detected and possibly highlight changes after the construction of the dune. Three monitoring campaigns were carried out before, immediately after and six months later the construction of the dune (January, May and October 2022). All data were analysed to assess local coastal dynamics and NBS evolution. The monitoring consisted of: topographic and bathymetric surveys (GNSS and multibeam/singlebeam echosounder) to generate DTMs of the entire area (10 m cell size); aerial photogrammetric surveys by UAV for the production of orthophotos and high resolutions DTMs of the emerged beach (1m cell size) and of the dune area (0.2 m cell size); sediment sampling and grain size analysis. Surveys show that morphological and sedimentological changes are determined mostly by anthropic actions to the beach and seabed maintenance (artificial winter banks and Sacca di Goro channel). Regarding the dune area no significant changes in morphology were observed due to the limited period between the surveys. Appreciable signals were detected, such as the natural recolonization by pioneer plant species and the slight sand accumulation on the dune foot. This dataset consists of data related to monitoring activities.
DOI: 10.5281/zenodo.7380459
title: Monitoring NBS for coastal erosion and marine flooding: the Emilia-Romagna case study

description: The study was conducted in the context of the OPERANDUM project which is an H2020 project which aims at providing tools and methodologies for the assessment of NBS efficiency around the world. As NBS will be tested an artificial dune built with natural materials. The artificial dune is an engineered structure that will mimic the functioning of natural dunes. Its aims are reducing both natural dune erosion and flooding in adjacent coastal lowlands. It consists of a barrier between the sea and land, in a similar way to a seawall. Unlike the latter, the NBS are ‘dynamic’, i.e. the dune/beach system interacts a great deal and is constantly undergoing small adjustments in response to changes in wind and wave climate or sea level. Its construction involves the placement of sediment from dredged sources on the beach and it will be reinforced with a structure composed of biodegradable material. Different typologies of experimental solutions are foreseen. The Bellocchio Beach at Lido di Spina (Italy) was initially chosen for the study, however the Volano beach was selected as the new study area because of the strong erosion caused by an intense storm event in December 2020 at Bellocchio. The dune was built on the Volano beach and monitoring surveys were carried out on this new site. A morphological monitoring aimed to assess the beach evolution and the performance of the NBS were performed. Monitoring of morphology evolution of shoreline and inland area provide information about impact of the NBS on coastal erosion. Furthermore, the changes in the form of the work give information about the resistance of the NBS to wave attacks. Sedimentological campaigns have been planned in order to provide information regarding the texture of the sediments present in the area detected and possibly highlight changes after the construction of the dune. Three monitoring campaigns were carried out before, immediately after and six months later the construction of the dune (January, May and October 2022). All data were analysed to assess local coastal dynamics and NBS evolution. The monitoring consisted of: topographic and bathymetric surveys (GNSS and multibeam/singlebeam echosounder) to generate DTMs of the entire area (10 m cell size); aerial photogrammetric surveys by UAV for the production of orthophotos and high resolutions DTMs of the emerged beach (1m cell size) and of the dune area (0.2 m cell size); sediment sampling and grain size analysis. Surveys show that morphological and sedimentological changes are determined mostly by anthropic actions to the beach and seabed maintenance (artificial winter banks and Sacca di Goro channel). Regarding the dune area no significant changes in morphology were observed due to the limited period between the surveys. Appreciable signals were detected, such as the natural recolonization by pioneer plant species and the slight sand accumulation on the dune foot. This dataset consists of data related to monitoring activities.
DOI: 10.5281/zenodo.7380536
title: Monthly average profiles of Distributed Temperature Sensing at Thwaites Eastern Ice Shelf

description: Monthly average profiles of Distributed Temperature Sensing (DTS) for Thwaites Eastern Ice Shelf used in Dotto et al. (under review). The profiles are from April 2020, September 2020 and February 2021. DTS utilizes a fibre-optic cable installed within the ice and through the ocean, and it uses Raman backscattered photons to estimate the in situ temperature of the fiber (Hausner et al 2011). The DTS interrogators (Silixa XT-DTS, Silixa LLC. Elstree, UK) used a spatial sampling of 25 cm. Each DTS profile uses a 1-minute integration time to reduce signal to noise. Independent temperature measurements from the MicroCATs are employed to calibrate the backscatter signal (Tyler et al., 2013; Hausner et al 2011). Hausner, M. B., Suárez, F., Glander, K. E., van de Giesen, N., Selker, J. S. & Tyler, S. W. Calibrating single-ended fiber-optic Raman spectra distributed temperature sensing data. Sensors (Basel), 11(11), 10,859–10,879 (2011). Tyler, S. W., Holland, D. M., Zagorodnov, V., Stern, A. A., Sladek, C., Kobs, S., White, S., Suárez, F. & Bryenton, J. Using distributed temperature sensors to monitor an Antarctic ice shelf and sub-ice-shelf cavity. Journal of Glaciology, 59(215), 583–591 (2013). Dotto, T. S., Heywood, K., Hall, R. et al. Ocean variability beneath Thwaites Eastern Ice Shelf driven by the Pine Island Bay Gyre strength, 11 October 2022, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-1466534/v1]
DOI: 10.25919/nmty-sf74
title: Parkes observations for project P1170 semester 2022OCTS_10

description: We request 15.5 hours of observations with the Parkes UWL receiver to search for giant pulses (GPs) in all seven pulsars in the Southern sky which are known to exhibit this phenomenon. The UWL receiver is particularly well-suited to such a study, since some GPs from known emitters have been found to be very narrow-band and so the observed emission rate is likely to be highly frequency-dependent. Additionally, the wide bandwidth allows one to detect spectral structures such as the 'banding' effect recently observed in GPs from some pulsars, similar to that observed in the spectra of fast radio bursts. These observations should provide a wealth of information about the underlying GP emission mechanism, and a stringent test of current theories.
DOI: 10.5281/zenodo.7380292
title: DADA2 formatted eHOMD 16S rRNA gene sequences databse

description: eHOMD Refseq database (V15.22) formated to be used with dada2 <em>i.e.</em>, dada2::assignTaxonomy(seqs, "eHOMD_RefSeq_dada2_V15.22.fasta.gz" ) and dada2::addSpecies(taxa, "eHOMD_RefSeq_dada2_assign_species_V15.22.fasta.gz", verbose=TRUE) Alternatively, you could use the metabaRpipe R package to directly update the taxonomy of a phyloseq object see: https://github.com/fconstancias/metabaRpipe#2-addingreplacing-taxonomical-table-in-a-phyloseq-object Example below:<br> source("https://raw.githubusercontent.com/fconstancias/metabaRpipe-source/master/Rscripts/functions.R") readRDS("dada2/phyloseq.RDS") %&gt;%<br> phyloseq_dada2_tax(physeq = .,<br> threshold = 60,<br> db ="~/metabaRpipe/databases/eHOMD_RefSeq_dada2_V15.22.fasta.gz",<br> db_species ="~/metabaRpipe/databases/eHOMD_RefSeq_dada2_assign_species_V15.22.fasta.gz",<br> nthreads = 2,<br> full_return = FALSE) -&gt; physeq_eHOMD_tax
description: {"references": ["Isabel Fern\u00e1ndez Escapa, Tsute Chen, Yanmei Huang, Prasad Gajare, Floyd E Dewhirst, and Katherine P Lemon. New insights into human nostril microbiome from the expanded Human Oral Microbiome Database (eHOMD): a resource for species-level identification of microbiome data from the aerodigestive tract. DOI: 10.1128/mSystems.00187-18. Online Open Access: https://msystems.asm.org/content/3/6/e00187-18", "F. Escapa, I., Huang, Y., Chen, T., Lin, M., Kokaras, A., Dewhirst F.E., Lemon, K.P. (2020) Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets. Microbiome 8, 65. Online Open Access https://doi.org/10.1186/s40168-020-00841-w", "Callahan, B., McMurdie, P., Rosen, M. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13, 581\u2013583 (2016). https://doi.org/10.1038/nmeth.3869"]}
DOI: 10.5281/zenodo.7380291
title: DADA2 formatted eHOMD 16S rRNA gene sequences databse

description: eHOMD Refseq database (V15.22) formated to be used with dada2 <em>i.e.</em>, dada2::assignTaxonomy(seqs, "eHOMD_RefSeq_dada2_V15.22.fasta.gz" ) and dada2::addSpecies(taxa, "eHOMD_RefSeq_dada2_assign_species_V15.22.fasta.gz", verbose=TRUE) Alternatively, you could use the metabaRpipe R package to directly update the taxonomy of a phyloseq object see: https://github.com/fconstancias/metabaRpipe#2-addingreplacing-taxonomical-table-in-a-phyloseq-object Example below:<br> source("https://raw.githubusercontent.com/fconstancias/metabaRpipe-source/master/Rscripts/functions.R") readRDS("dada2/phyloseq.RDS") %&gt;%<br> phyloseq_dada2_tax(physeq = .,<br> threshold = 60,<br> db ="~/metabaRpipe/databases/eHOMD_RefSeq_dada2_V15.22.fasta.gz",<br> db_species ="~/metabaRpipe/databases/eHOMD_RefSeq_dada2_assign_species_V15.22.fasta.gz",<br> nthreads = 2,<br> full_return = FALSE) -&gt; physeq_eHOMD_tax
description: {"references": ["Isabel Fern\u00e1ndez Escapa, Tsute Chen, Yanmei Huang, Prasad Gajare, Floyd E Dewhirst, and Katherine P Lemon. New insights into human nostril microbiome from the expanded Human Oral Microbiome Database (eHOMD): a resource for species-level identification of microbiome data from the aerodigestive tract. DOI: 10.1128/mSystems.00187-18. Online Open Access: https://msystems.asm.org/content/3/6/e00187-18", "F. Escapa, I., Huang, Y., Chen, T., Lin, M., Kokaras, A., Dewhirst F.E., Lemon, K.P. (2020) Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets. Microbiome 8, 65. Online Open Access https://doi.org/10.1186/s40168-020-00841-w", "Callahan, B., McMurdie, P., Rosen, M. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13, 581\u2013583 (2016). https://doi.org/10.1038/nmeth.3869"]}
DOI: 10.7910/dvn/jq9c9l
title: A factorial survey for assessing the effects of verbal administrative language on citizen perceptions

description: Data for journal publication Eckhard, S. & Friedrich, L. (2022). Linguistic features of public service encounters: How spoken administrative language affects citizen satisfaction. Journal of Public Administration Research and Theory
DOI: 10.6084/m9.figshare.20625171
title: Supplementary Material for: Approaches to Identify Factors Associated with Pubertal Timing in Self-Limited Delayed Puberty

description: Introduction: Children with self-limited delayed puberty (constitutional delay) enter puberty after variable waiting times, and the factors associated with their eventual pubertal timing are not well understood. Methods: We conducted a retrospective study of 99 girls and 228 boys with self-limited delayed puberty (DP) at an academic medical center between 2000 and 2015. To define features and potential subtypes of self-limited DP, we performed group-based trajectory modeling on childhood growth and latent-variable factor analysis on clinical characteristics. We then conducted time-to-event analyses to identify associations with pubertal timing. Results: We identified two distinct growth trajectories in individuals with self-limited DP: one with stable and the other with declining height percentiles. Latent-variable factor analysis identified five factors underlying clinical variation that appear to correspond to genetic height potential, body mass index, childhood growth, parental pubertal delay, and medical issues (attention-deficit/hyperactivity disorder and inhaled glucocorticoid use). We observed correlations between pubertal timing and bone age (p=0.01), childhood height (p=0.004), and midparental target height (p&lt;0.001), but not with parental pubertal delay or with testosterone treatment in boys. Conclusions: By illustrating the heterogeneity within self-limited DP and identifying factors underlying this heterogeneity, our study suggests that there may be multiple causes of self-limited DP. However, our ability to determine when puberty will eventually occur remains limited. Dissecting self-limited DP into its component subtypes may inform future studies of the mechanisms contributing to pubertal delay as well as studies of the short- and long-term outcomes of self-limited DP.
DOI: 10.6084/m9.figshare.20625171.v1
title: Supplementary Material for: Approaches to Identify Factors Associated with Pubertal Timing in Self-Limited Delayed Puberty

description: Introduction: Children with self-limited delayed puberty (constitutional delay) enter puberty after variable waiting times, and the factors associated with their eventual pubertal timing are not well understood. Methods: We conducted a retrospective study of 99 girls and 228 boys with self-limited delayed puberty (DP) at an academic medical center between 2000 and 2015. To define features and potential subtypes of self-limited DP, we performed group-based trajectory modeling on childhood growth and latent-variable factor analysis on clinical characteristics. We then conducted time-to-event analyses to identify associations with pubertal timing. Results: We identified two distinct growth trajectories in individuals with self-limited DP: one with stable and the other with declining height percentiles. Latent-variable factor analysis identified five factors underlying clinical variation that appear to correspond to genetic height potential, body mass index, childhood growth, parental pubertal delay, and medical issues (attention-deficit/hyperactivity disorder and inhaled glucocorticoid use). We observed correlations between pubertal timing and bone age (p=0.01), childhood height (p=0.004), and midparental target height (p&lt;0.001), but not with parental pubertal delay or with testosterone treatment in boys. Conclusions: By illustrating the heterogeneity within self-limited DP and identifying factors underlying this heterogeneity, our study suggests that there may be multiple causes of self-limited DP. However, our ability to determine when puberty will eventually occur remains limited. Dissecting self-limited DP into its component subtypes may inform future studies of the mechanisms contributing to pubertal delay as well as studies of the short- and long-term outcomes of self-limited DP.
DOI: 10.6084/m9.figshare.21647129.v1
title: Supplementary Material for: Two Years with COVID-19: The Electronic Frailty Index Identifies High-Risk Patients in the Stockholm GeroCovid Study

description: <b><i>Introduction:</i></b> Frailty, a measure of biological aging, has been linked to worse COVID-19 outcomes. However, as the mortality differs across the COVID-19 waves, it is less clear whether a medical record-based electronic frailty index (eFI) that we have previously developed for older adults could be used for risk stratification in hospitalized COVID-19 patients. <b><i>Objectives:</i></b> The aim of the study was to examine the association of frailty with mortality, readmission, and length of stay in older COVID-19 patients and to compare the predictive accuracy of the eFI to other frailty and comorbidity measures. <b><i>Methods:</i></b> This was a retrospective cohort study using electronic health records (EHRs) from nine geriatric clinics in Stockholm, Sweden, comprising 3,980 COVID-19 patients (mean age 81.6 years) admitted between March 2020 and March 2022. Frailty was assessed using a 48-item eFI developed for Swedish geriatric patients, the Clinical Frailty Scale, and the Hospital Frailty Risk Score. Comorbidity was measured using the Charlson Comorbidity Index. We analyzed in-hospital mortality and 30-day readmission using logistic regression, 30-day and 6-month mortality using Cox regression, and the length of stay using linear regression. Predictive accuracy of the logistic regression and Cox models was evaluated by area under the receiver operating characteristic curve (AUC) and Harrell’s C-statistic, respectively. <b><i>Results:</i></b> Across the study period, the in-hospital mortality rate decreased from 13.9% in the first wave to 3.6% in the latest (Omicron) wave. Controlling for age and sex, a 10% increment in the eFI was significantly associated with higher risks of in-hospital mortality (odds ratio = 2.95; 95% confidence interval = 2.42–3.62), 30-day mortality (hazard ratio [HR] = 2.39; 2.08–2.74), 6-month mortality (HR = 2.29; 2.04–2.56), and a longer length of stay (β-coefficient = 2.00; 1.65–2.34) but not with 30-day readmission. The association between the eFI and in-hospital mortality remained robust across the waves, even after the vaccination rollout. Among all measures, the eFI had the best discrimination for in-hospital (AUC = 0.780), 30-day (Harrell’s C = 0.733), and 6-month mortality (Harrell’s C = 0.719). <b><i>Conclusion:</i></b> An eFI based on routinely collected EHRs can be applied in identifying high-risk older COVID-19 patients during the continuing pandemic.
DOI: 10.6084/m9.figshare.21647171
title: JGR_Data_Share_202212.zip

description: The VLF observation data at GWS