cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8061668
title: [Datasets] Evaluación de la capacidad predictiva de modelos de aprendizaje supervisado para la clasificación de pacientes con cáncer colorrectal

description: <strong>DATASETS INFO</strong> Dataset on colorectal cancer and hydroxymethylation levels ready to be used in machine learning algorithms. This dataset was generated using data from Walker NJ, Rashid M, Yu S, et al. [Dataset] Hydroxymethylation profile of cell free DNA is a biomarker for early colorectal cancer. Accessed May 17, 2023. https://zenodo.org/record/5170265#.ZGSpgHZBxD-. <strong>ABSTRACT</strong><br> Colorectal cancer (CRC) is the second most common cause of cancer death, accounting for 9.5% of all cancer deaths. In addition to patient age, other potential risk factors should be considered to correctly identify the target population for CRC screening programmes. The identification of these risk factors would allow a personalised and accurate approach for each patient that would help improve the survival rate. Thus, the main objective of this study was to identify useful risk biomarkers for the early detection of CRC using machine learning algorithms. For this purpose, we compared the predictive ability of different supervised machine learning models, such as gradient boosting, support vector machines (SVM) or random forest, using a public dataset on hydroxymethylation levels in the enhancer regions in CRC patients, AAR and controls. In addition, we evaluated the suitability of K-means for the identification of CRC patient subgroups using this dataset. The results of this work suggested that the best supervised model to differentiate CRC patients from controls, using hydroxymethylation data, was a SVM model with linear kernel, whose sensitivity was 58% after setting the specificity to 95%, improving the model presented in the article from which the dataset was extracted. In addition, enhancers that regulate the expression of genes such as MYSM1 or SP1, or those that regulate genes encoding proteins involved in pathways such as TGF-β and integrin pathways, were identified as the most relevant enhancers when classifying samples into CRC or control. On the other hand, the use of K-means identified 6 clusters among the samples in the hydroxymethylation dataset. Two of these clusters were mainly composed of samples with CCR, however, these clusters were not associated with a specific stage of development, and the differentiation between clusters was not clear, obtaining very close clusters. Thus, we can conclude that hydroxymethylation data were useful for the identification of CRC biomarkers, obtaining promising results by supervised machine learning approaches. However, these results should be interpreted as preliminary, requiring validation in an external cohort and molecular analysis of the biomarkers identified.
DOI: 10.5281/zenodo.8061648
title: Spectral data used in "Stratospheric-trace-gas-profile retrievals from balloon-borne limb imaging of mid-infrared emission spectra"

description: The calibrated spectral data used in the trace gas retrievals by the Limb Imaging Fourier Transform Spectrometer Experiment (LIFE).
DOI: 10.5281/zenodo.8061647
title: Spectral data used in "Stratospheric-trace-gas-profile retrievals from balloon-borne limb imaging of mid-infrared emission spectra"

description: The calibrated spectral data used in the trace gas retrievals by the Limb Imaging Fourier Transform Spectrometer Experiment (LIFE).
DOI: 10.6073/pasta/f5777f4bc02159bfaa5a53094ebbbf56
title: North Temperate Lakes LTER: Sediment Deposition - Trout Lake Area 1986 - current

description: Settling particulate matter is collected using sediment traps deployed in the hypolimnion at the deepest part of the lake. Duplicate traps are set at one station in Trout, Sparkling and Crystal lakes. Traps are deployed during the ice-free period for four-week intervals. Mass deposition rates are calculated from the dry-weight of material collected, and mass flux is reported as mg per meter-squared per day. Sampling Frequency: every four weeks during ice-free season. Number of sites: 3.
DOI: 10.6084/m9.figshare.3761562.v2622
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.25739/1n89-rd43
title: Carolyn_Lawrence_Dill_GOMAP_Maize_MaizeGDB_CML103_NAM_1.0_October_2022.r1

description: This dataset generated by GOMAP is a high-coverage and reproducible functional annotation set based on Gene Ontology (GO) term assignments that covers all gene models in MaizeGDB Zea mays CML103 genome with a median of 10 annotations per gene model with 99.99% coverage. It was created in October of 2022.
DOI: 10.25739/e6hc-0406
title: Carolyn_Lawrence_Dill_GOMAP_Maize_MaizeGDB_CML228_NAM_1.0_October_2022.r1

description: This dataset generated by GOMAP is a high-coverage and reproducible functional annotation set based on Gene Ontology (GO) term assignments that covers all gene models in MaizeGDB Zea mays CML228 genome with a median of 10 annotations per gene model with 100% coverage. It was created in October of 2022.
DOI: 10.25739/be28-vs34
title: Bangladesh CNN - LSTM Model Data

description: This dataset contains the data necessary to reproduce the model results published in the paper ["**Giezendanner et al.** , *Inferring the past: a combined CNN--LSTM deep learning framework to fuse satellites for historical inundation mapping*, CVPR 23 Earthvision workshop"](https://openaccess.thecvf.com/content/CVPR2023W/EarthVision/html/Giezendanner_Inferring_the_Past_A_Combined_CNN-LSTM_Deep_Learning_Framework_To_CVPRW_2023_paper.html). The code is available on [GitHub](https://github.com/GieziJo/cvpr23-earthvision-CNN-LSTM-Inundation).
DOI: 10.25345/c59p2wh0f
title: MassIVE MSV000092220 - Mapping proteome trafficking in living cells via TransitID
title: The ability to map trafficking for thousands of endogenous proteins at once in living cells would reveal biology currently invisible to both microscopy and mass spectrometry. Here we report TransitID, a method for unbiased mapping of endogenous proteome trafficking with nanometer spatial resolution in living cells. Two proximity labeling (PL) enzymes, TurboID and APEX, are targeted to source and destination compartments, and PL with each enzyme is performed in tandem via sequential addition of their small-molecule substrates. Mass spectrometry identifies the proteins tagged by both enzymes. Using TransitID, we mapped proteome trafficking between cytosol and mitochondria, cytosol and nucleus, and nucleolus and stress granules, uncovering a role for stress granules in protecting the transcription factor JUN from oxidative stress. TransitID also identifies proteins that signal intercellularly between macrophages and cancer cells. TransitID is a powerful method for distinguishing protein populations based on compartment or cell type of origin.
DOI: 10.25921/8m8f-6e80
title: EK80 Water Column Sonar Data Collected During PC1901
DOI: 10.17045/sthlmuni.21724262.v2
title: Robertson et al., 2023. AJP Endocrinology and Metabolism Data

description: Data for Robertson et al: <strong>"Turning up the heat”: Role of neurotrophic batokines in the postnatal maturation and remodelling of brown adipose tissue in deer mice</strong> Activation of brown adipose tissue (BAT) thermogenesis impacts energy balance and must be tightly regulated. Several neurotrophic factors, expressed in BAT of adult laboratory rodents, have been implicated in remodelling the sympathetic neural network to enhance thermogenesis (e.g., NGF, NRG4 and S100b). Here, we compare for the first time the relative roles of three neurotropic ‘batokines’ in establishing/remodelling innervation during postnatal development and adult cold stress. We used lab-reared <em>P. maniculatus,</em> which rely heavily on BAT-based thermogenesis for survival in the wild, beginning between postnatal days (P) 8 and 10. BAT sympathetic innervation was enhanced from P6-10, and exogenous NGF, NRG4, and S100b stimulated neurite outgrowth from P6 sympathetic neurons. Endogenous BAT protein stores and/or gene expression of NRG4, S100b, and calsyntenin-3ß (which regulates S100b secretion), remained high and constant during development. However, endogenous NGF was low and <em>ngf</em> mRNA was undetectable. Conditioned media (CM) from cultured P10 BAT slices stimulated neurite outgrowth from sympathetic neurons <em>in vitro</em> that was inhibited by antibodies against all three growth factors. P10 CM had significant amounts of secreted NRG4 and S100b protein, but not NGF. By contrast, BAT slices from cold-acclimated <em>adult</em>s released significant amounts of all three factors relative to thermoneutral controls. These data suggest that while neurotrophic batokines regulate sympathetic innervation <em>in vivo</em>, their relative contributions differ depending on life stage. They also provide novel insight into the regulation of BAT remodelling and BAT’s secretory role, which are both critical to our understanding of mammalian energy homeostasis.
DOI: 10.17045/sthlmuni.21724262
title: Robertson et al., 2023. AJP Endocrinology and Metabolism Data

description: Data for Robertson et al: <strong>"Turning up the heat”: Role of neurotrophic batokines in the postnatal maturation and remodelling of brown adipose tissue in deer mice</strong> Activation of brown adipose tissue (BAT) thermogenesis impacts energy balance and must be tightly regulated. Several neurotrophic factors, expressed in BAT of adult laboratory rodents, have been implicated in remodelling the sympathetic neural network to enhance thermogenesis (e.g., NGF, NRG4 and S100b). Here, we compare for the first time the relative roles of three neurotropic ‘batokines’ in establishing/remodelling innervation during postnatal development and adult cold stress. We used lab-reared <em>P. maniculatus,</em> which rely heavily on BAT-based thermogenesis for survival in the wild, beginning between postnatal days (P) 8 and 10. BAT sympathetic innervation was enhanced from P6-10, and exogenous NGF, NRG4, and S100b stimulated neurite outgrowth from P6 sympathetic neurons. Endogenous BAT protein stores and/or gene expression of NRG4, S100b, and calsyntenin-3ß (which regulates S100b secretion), remained high and constant during development. However, endogenous NGF was low and <em>ngf</em> mRNA was undetectable. Conditioned media (CM) from cultured P10 BAT slices stimulated neurite outgrowth from sympathetic neurons <em>in vitro</em> that was inhibited by antibodies against all three growth factors. P10 CM had significant amounts of secreted NRG4 and S100b protein, but not NGF. By contrast, BAT slices from cold-acclimated <em>adult</em>s released significant amounts of all three factors relative to thermoneutral controls. These data suggest that while neurotrophic batokines regulate sympathetic innervation <em>in vivo</em>, their relative contributions differ depending on life stage. They also provide novel insight into the regulation of BAT remodelling and BAT’s secretory role, which are both critical to our understanding of mammalian energy homeostasis.
DOI: 10.17045/sthlmuni.21724262.v1
title: Robertson et al., 2023. AJP Endocrinology and Metabolism Data

description: Data for Robertson et al: <strong>"Turning up the heat”: Role of neurotrophic batokines in the postnatal maturation and remodelling of brown adipose tissue in deer mice</strong> Activation of brown adipose tissue (BAT) thermogenesis impacts energy balance and must be tightly regulated. Several neurotrophic factors, expressed in BAT of adult laboratory rodents, have been implicated in remodelling the sympathetic neural network to enhance thermogenesis (e.g., NGF, NRG4 and S100b). Here, we compare for the first time the relative roles of three neurotropic ‘batokines’ in establishing/remodelling innervation during postnatal development and adult cold stress. We used lab-reared <em>P. maniculatus,</em> which rely heavily on BAT-based thermogenesis for survival in the wild, beginning between postnatal days (P) 8 and 10. BAT sympathetic innervation was enhanced from P6-10, and exogenous NGF, NRG4, and S100b stimulated neurite outgrowth from P6 sympathetic neurons. Endogenous BAT protein stores and/or gene expression of NRG4, S100b, and calsyntenin-3ß (which regulates S100b secretion), remained high and constant during development. However, endogenous NGF was low and <em>ngf</em> mRNA was undetectable. Conditioned media (CM) from cultured P10 BAT slices stimulated neurite outgrowth from sympathetic neurons <em>in vitro</em> that was inhibited by antibodies against all three growth factors. P10 CM had significant amounts of secreted NRG4 and S100b protein, but not NGF. By contrast, BAT slices from cold-acclimated <em>adult</em>s released significant amounts of all three factors relative to thermoneutral controls. These data suggest that while neurotrophic batokines regulate sympathetic innervation <em>in vivo</em>, their relative contributions differ depending on life stage. They also provide novel insight into the regulation of BAT remodelling and BAT’s secretory role, which are both critical to our understanding of mammalian energy homeostasis.
DOI: 10.6084/m9.figshare.21260013
title: CBAM Allies Dataset

description: The carbon border adjustment mechanism (CBAM) of the European Union (EU) will raise the export costs faced by some its trading partners. Their reactions will vary depending on their export structure, the carbon intensity of their economy, national climate policy stance, adaptive capacity, and trade agreements with the EU. CBAM may function like an undeclared climate club, and those countries that are most eager to join the club could play an important role in giving it the critical mass to survive. This dataset is used to assess which countries are likely to be most supportive of the EU’s CBAM by constructing a multidimensional index. <br>
DOI: 10.25921/qjh6-n461
title: EK80 Water Column Sonar Data Collected During PC1903
DOI: 10.34943/03d02b19-b895-4dc4-bc05-2b61d60d8fee
title: Cascadia Seaweed Burrough Point Reference Site Oxygen Sensor Deployed 2022-03-08

description: The JFE Rinko ARO-FT (SN 0EAK007) was deployed on 2022-03-08 at Cascadia Seaweed Burrough Point Reference Site. The Burrough Point Farm Reference Site in Barkley Sound is used to obtain ambient measurements as a comparison to the nearby seaweed farm. This device is a Oxygen Sensor. Oxygen sensors measure dissolved oxygen concentration in seawater. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.34943/5b52ec79-97db-4f9a-a45d-f2e068227940
title: Cascadia Seaweed Burrough Point Reference Site Fluorometer Deployed 2022-03-08

description: The Turner Cyclops-7F Fluorometer (S/N 900331) was deployed on 2022-03-08 at Cascadia Seaweed Burrough Point Reference Site. The Burrough Point Farm Reference Site in Barkley Sound is used to obtain ambient measurements as a comparison to the nearby seaweed farm. This device is a Fluorometer. Fluorometers measure the amount of stimulated electromagnetic radiation (fluorescence) produced by pulses of electromagnetic radiation emitted into the water column. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.34943/3476bb51-1f54-471b-b03b-7bf99fbcbea5
title: Cascadia Seaweed Burrough Point Reference Site Turbidity Meter Deployed 2022-03-08

description: The Turner Cyclops-7F Fluorometer (S/N 900269) was deployed on 2022-03-08 at Cascadia Seaweed Burrough Point Reference Site. The Burrough Point Farm Reference Site in Barkley Sound is used to obtain ambient measurements as a comparison to the nearby seaweed farm. This device is a Turbidity Meter. Turbidity meters are sensors that detect scattered light from suspended particles in water. The amount of scattered light that reaches the detector is proportional to the turbidity or particle concentration in the water. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.34943/515740d1-3278-4be2-8a2b-ce8959c63017
title: Cascadia Seaweed Burrough Point Reference Site Radiometer Deployed 2022-03-08

description: The LI-COR LI-192 Underwater Quantum Sensor UWQ10717 was deployed on 2022-03-08 at Cascadia Seaweed Burrough Point Reference Site. The Burrough Point Farm Reference Site in Barkley Sound is used to obtain ambient measurements as a comparison to the nearby seaweed farm. This device is a Radiometer. Radiometers collect measurements of electromagnetic radiation in the ocean environment. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.18739/a26q1sj67
title: HELiX Uncrewed Aircraft System data from the Multidisciplinary drifting Observatory for the Study of the Arctic Climate (MOSAiC) campaign, surface features classification based on multispectral imagery data. 2020.

description: The surface classification is obtained from orthomosaic images of the surface during the Multidisciplinary drifting Observatory for the Study of the Arctic Climate (MOSAiC) campaign. The HELiX Uncrewed Aircraft System (UAS) flew above the sea ice during the summertime of 2020. The images are available for download at https://arcticdata.io/data/10.18739/A2RV0D21Z/ and the description of the images is detailed in Hamilton et al., 2021 (DOI: 10.18739/A2T727H3V). Images are obtained in 5 spectral bands: blue, green, red, red edge and NIR. Three categories of surface types are defined in the dataset: ocean, melt pond, and snow/bare ice. The study focuses on orthomosaic images from gird and profile UAS flights. For each orthomosaic, samples of identifiable features are selected for each surface type in each spectral band. Based on these samples, the threshold to separate open water from melt ponds is defined in the blue channel and the threshold to separate melt ponds from snow/bare ice surface is defined in the NIR channel. More details of the methodology, correction, and uncertainty to define surface features can be found in Calmer et al., 2023 (https://doi.org/10.1525/elementa.2023.00001). The results of the surface classification are used to calculate the melt pond fraction associated with the scene captured by each orthomosaic image.
DOI: 10.21227/53t5-fw17
title: Hansard

description: This research studies the stance classification task of parliamentary debates with the aims to analyse how parliamentarians argue on different debate topic, what is their political stance, and the impact of homophily with respect to their party affiliation. A state-level Australian Hansard data is collected focusing on debates related to obesity and food marketing policies in Australia. It covers 6 states and 1 territory (NT is excluded) from the period 1/1/2020 to 1/1/ 2022. The raw data is stored in .jsonlist for each of the 6 states and 1 territory after data extraction from PDF and HTML files, resulting in the length of  645,594. The data contains the following attributes: data, fileIdx, idx, keywords, filename, state, title, house, utterance, speaker, text, source, party.
DOI: 10.25921/nck9-j467
title: EM304 Water Column Sonar Data Collected During RICHARD2023L4
DOI: 10.6084/m9.figshare.23549502
title: T. molitor-Development.xlsx

description: Data for the development of Tenebrio at different temperatures.
DOI: 10.6084/m9.figshare.23549502.v1
title: T. molitor-Development.xlsx

description: Data for the development of Tenebrio at different temperatures.
DOI: 10.25921/qjn3-4758
title: EM2040 Water Column Sonar Data Collected During RICHARD2023L4
DOI: 10.6084/m9.figshare.23549529
title: Supplementary Material for: Prevalence of Hidradenitis Suppurativa in an African population: Validation of a screening questionnaire in Lagos, Nigeria

description: Background: Epidemiologic Hidradenitis Suppurativa (HS) studies from Africa are lacking. This study aimed at uncovering the prevalence of HS in Lagos, Nigeria, validate an HS screening questionnaire, and to contribute to the Global Hidradenitis Suppurativa Atlas (GHiSA). Methods: This was a cross-sectional study of 802 healthy adults accompanying their relations to the outpatient clinic of Family Medicine and Ophthalmology at the Lagos State University Teaching Hospital in Lagos, Nigeria following ethical approval. Verbal and written consent were obtained prior to inclusion of study participants. The study was conducted using a validated screening questionnaire. Screen positive and randomly selected screen negative participants were clinically examined. Severity was categorized using the Hurley Score. Results: The prevalence of HS in the sample was 2.2% (18/802; 95% CI:1.4% - 3.5%) with no gender predominance. The mean age in the HS group was 34 years (IQR 28-42), and the median BMI of the HS patients was 27.0 (IQR 21.4-28.6). There was no significant difference in BMI between the HS and control group. The screening questionnaire had a sensitivity of 1 (18/18), specificity of 0.8 (20/25), positive predictive value of 0.8 (18/23), and a negative predictive value of 1 (20/20). The axilla was the predominant site of affection (66.7%), and all HS patients were classified as mild disease (Hurley Score I). Conclusion: The prevalence of HS in Lagos, Nigeria was 2.2% and, in this population, BMI did not appear to be a risk factor. The axilla was the most affected site, and all patients had a mild disease severity (Hurley Score I). Finally, the HS screening questionnaire is a suitable tool in population surveys.
DOI: 10.6084/m9.figshare.23549529.v1
title: Supplementary Material for: Prevalence of Hidradenitis Suppurativa in an African population: Validation of a screening questionnaire in Lagos, Nigeria

description: Background: Epidemiologic Hidradenitis Suppurativa (HS) studies from Africa are lacking. This study aimed at uncovering the prevalence of HS in Lagos, Nigeria, validate an HS screening questionnaire, and to contribute to the Global Hidradenitis Suppurativa Atlas (GHiSA). Methods: This was a cross-sectional study of 802 healthy adults accompanying their relations to the outpatient clinic of Family Medicine and Ophthalmology at the Lagos State University Teaching Hospital in Lagos, Nigeria following ethical approval. Verbal and written consent were obtained prior to inclusion of study participants. The study was conducted using a validated screening questionnaire. Screen positive and randomly selected screen negative participants were clinically examined. Severity was categorized using the Hurley Score. Results: The prevalence of HS in the sample was 2.2% (18/802; 95% CI:1.4% - 3.5%) with no gender predominance. The mean age in the HS group was 34 years (IQR 28-42), and the median BMI of the HS patients was 27.0 (IQR 21.4-28.6). There was no significant difference in BMI between the HS and control group. The screening questionnaire had a sensitivity of 1 (18/18), specificity of 0.8 (20/25), positive predictive value of 0.8 (18/23), and a negative predictive value of 1 (20/20). The axilla was the predominant site of affection (66.7%), and all HS patients were classified as mild disease (Hurley Score I). Conclusion: The prevalence of HS in Lagos, Nigeria was 2.2% and, in this population, BMI did not appear to be a risk factor. The axilla was the most affected site, and all patients had a mild disease severity (Hurley Score I). Finally, the HS screening questionnaire is a suitable tool in population surveys.