cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14246903.v1
title: Circ_0000518 contributes to breast cancer development depending on the regulation of miR-1258/ZEB1 axis

description: Breast cancer (BC) is a common malignancy in women. We aimed to investigate the role of circular RNA_0000518 (circRNA_0000518) in BC progression and its associated mechanism. Real-time quantitative polymerase chain reaction (RT-qPCR) and Western blot assay were utilized to measure RNA and protein expression. Cell proliferation was assessed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and colony formation assay. Transwell assays were conducted to analyze cell motility. Intermolecular interaction was verified via dual-luciferase reporter assay and RNA-pull down assay. Circ_0000518 expression was up-regulated in BC tissues and cell lines. Circ_0000518 interference suppressed the proliferation, migration, invasion and glycolytic metabolism and promoted the apoptosis of BC cells. Circ_0000518 acted as a molecular sponge for microRNA-1258 (miR-1258), and circ_0000518 interference-mediated effects in BC cells were largely alleviated by the addition of anti-miR-1258. MiR-1258 interacted with the 3′ untranslated region (3′UTR) of zinc finger E-box binding homeobox 1 (ZEB1) in BC cells, and miR-1258 suppressed the malignant behaviors of BC cells partly through down-regulating ZEB1. Circ_0000518 interference significantly suppressed the growth of xenograft tumors <i>in vivo</i>. Circ_0000518/miR-1258/ZEB1 signaling cascade was identified in this study for the first time. Circ_0000518 contributed to BC progression by binding to miR-1258 to induce ZEB1 expression.
DOI: 10.25919/8pr7-z525
title: Eukaryote, Prokaryote and Metazoan datasets for comparing DNA extraction protocols for environmental DNA-based monitoring of sediment biota

description: 18S rDNA (Eukaryote), 16S rDNA (Prokaryote) and COI (Metazoan) amplicons data from sediment DNA used to compare DNA extraction protocols for the purpose of environmental DNA-based monitoring of sediment biota. DNA was extracted using two extraction methods (with variations in the initial volume of material): a bespoke method targeting only extracellular DNA and a commercially available kit-based method for extracting total DNA. 16S Prokaryote amplicons were amplified with primers 515F (5’-GTGYCAGCMGCCGCGGTAA-3’) and 806R (5’-GGACTACNVGGGTWTCTAAT-3’) (Parada et al. 2016; Apprill et al. 2015). 18S Eukaryote amplicons were amplified with primers All18SF (5’-GGTGCATGGCCGTTCTTAGT-3’) and All18SR (5’-CATCTAAGGGCATCACAGACC-3') (Hardy et al. 2010). COI Metazoa amplicons were amplified with primers mlCOIintF (5’-GGWACWGGWTGAACWGTWTAYCCYCC-3’) and jgHCO2198 (5’-TAIACYTCIGGRTGICCRAARAAYCA-3’) (Leray et al. 2013). Sequences were obtained by a 2 x 250 bp paired-end sequencing on Illumina MiSeq 2500 platform. https://www.publish.csiro.au/MF/justaccepted/MF20269
DOI: 10.25919/5f880e342fda6
title: CCS - CCS1 Mooring data November 2019 deployment

description: Project Overview: A range of solutions will be required to reach globally agreed emissions reductions targets for carbon dioxide (CO2). Carbon capture and storage (CCS) is part of the suite of technologies that will contribute to lowering atmospheric emissions of CO2 from Australia's energy system. There are a wide variety of technologies at various stages of technical and commercial readiness, with more development underway for cost effective CO2 capture and storage. Our research will provide new knowledge to inform cost-efficient measurement, monitoring and verification (MMV) of the environment of CCS projects in coastal waters. --o-- Description: Measurements are made Seabird Seaphox (for dissolved oxygen, pH, Seawater Temperature and Salinity), mounted on a lander. The Seaphox takes a reading every hour in the UTC hour and is transmitted real time through acoustic and/or 3G modems. The Seaphox consists of a SeaFET (pH) and SBE-37-SMP-ODO CTD (SW temperature, Salinity and Dissolved Oxygen [SBE63]). Relevant component details: make, model, serial number, firmware version, settings: Sensor | Make | Model | Serial Number | Calibration pH, DO,T and S sensor | Seabird Seaphox | SeaFET | 444 | 2017-05, factory calibrated, verified by CSIRO lab pH, DO,T and S sensor | Seabird Seaphox | SBE-37-SMP-ODO | 15643 | 2017-05, factory calibrated, verified by CSIRO lab pH, DO,T and S sensor | Seabird Seaphox | SBE-63 | 1697 | 2017-05, factory calibrated, verified by CSIRO lab Calibration Information (if applicable) SBE 37 (T, S, DO) and the SeaFET (pH) are calibrated by the factory and verified in the CSIRO laboratory. The pH reported in the files is flagged questionable for the pre-deployment calibrated data due to possible calibration changes which can occur after deployment pH (calibrated) is further processed after the recovery using in situ bottle sample where available, using Total Alkalinity (TA) and Dissolved Inorganic Carbon (DIC), which will be converted to pH using CO2SYS, where the Lueker k1k2 dissociation constant is used. Location: 38.2607167S 147.41965E
DOI: 10.25919/5f880e34333b4
title: CCS - CCS2 Mooring data November 2019 deployment

description: Project Overview: A range of solutions will be required to reach globally agreed emissions reductions targets for carbon dioxide (CO2). Carbon capture and storage (CCS) is part of the suite of technologies that will contribute to lowering atmospheric emissions of CO2 from Australia's energy system. There are a wide variety of technologies at various stages of technical and commercial readiness, with more development underway for cost effective CO2 capture and storage. Our research will provide new knowledge to inform cost-efficient measurement, monitoring and verification (MMV) of the environment of CCS projects in coastal waters. --o-- Description: Measurements are made Seabird Seaphox (for dissolved oxygen, pH, Seawater Temperature and Salinity), mounted on a lander. The Seaphox takes a reading every hour in the UTC hour and is transmitted real time through acoustic and/or 3G modems. The Seaphox consists of a SeaFET (pH) and SBE-37-SMP-ODO CTD (SW temperature, Salinity and Dissolved Oxygen [SBE63]). Relevant component details: make, model, serial number, firmware version, settings: Sensor | Make | Model | Serial Number | Calibration pH, DO,T and S sensor | Seabird Seaphox | SeaFET | 1031 |2019-04, factory calibrated pH, DO,T and S sensor | Seabird Seaphox | SBE-37-SMP-ODO | 15559 | 2019-04, factory calibrated pH, DO,T and S sensor | Seabird Seaphox | SBE-63 | 1689 | 2019-04, factory calibrated Calibration Information (if applicable) SBE 37 (T, S, DO) and the SeaFET (pH) are calibrated by the factory and verified in the CSIRO laboratory. The pH reported in the files is flagged questionable for the pre-deployment calibrated data due to possible calibration changes which can occur after deployment pH (calibrated) is further processed after the recovery using in situ bottle sample where available, using Total Alkalinity (TA) and Dissolved Inorganic Carbon (DIC), which will be converted to pH using CO2SYS, where the Lueker k1k2 dissociation constant is used. Location: 38.2588333S 147.4220333E
DOI: 10.25919/5f880e5ca9b71
title: CCS - CCS8 Mooring data November 2019 deployment

description: Project Overview: A range of solutions will be required to reach globally agreed emissions reductions targets for carbon dioxide (CO2). Carbon capture and storage (CCS) is part of the suite of technologies that will contribute to lowering atmospheric emissions of CO2 from Australia's energy system. There are a wide variety of technologies at various stages of technical and commercial readiness, with more development underway for cost effective CO2 capture and storage. Our research will provide new knowledge to inform cost-efficient measurement, monitoring and verification (MMV) of the environment of CCS projects in coastal waters. --o-- Description: Measurements are made Seabird Seaphox (for dissolved oxygen, pH, Seawater Temperature and Salinity), mounted on a lander. The Seaphox takes a reading every hour in the UTC hour and is transmitted real time through acoustic and/or 3G modems. The Seaphox consists of a SeaFET (pH) and SBE-37-SMP-ODO CTD (SW temperature, Salinity and Dissolved Oxygen [SBE63]). Relevant component details: make, model, serial number, firmware version, settings: Sensor | Make | Model | Serial Number | Calibration pH, DO,T and S sensor | Seabird Seaphox | SeaFET | 1002 |2019-04, factory calibrated pH, DO,T and S sensor | Seabird Seaphox | SBE-37-SMP-ODO | 15567 | 2019-04, factory calibrated pH, DO,T and S sensor | Seabird Seaphox | SBE-63 | 1683 | 2019-04, factory calibrated Calibration Information (if applicable) SBE 37 (T, S, DO) and the SeaFET (pH) are calibrated by the factory and verified in the CSIRO laboratory. The pH reported in the files is flagged questionable for the pre-deployment calibrated data due to possible calibration changes which can occur after deployment pH (calibrated) is further processed after the recovery using in situ bottle sample where available, using Total Alkalinity (TA) and Dissolved Inorganic Carbon (DIC), which will be converted to pH using CO2SYS, where the Lueker k1k2 dissociation constant is used. Location: 38.2564S 147.3372E
DOI: 10.5281/zenodo.4620534
title: The ECS-FVCOM results and also the input variables of FMGDM, the initial particles and satellite pictures

description: The data for the manuscript: A Lagrangian-based Floating Macro<br> -algal Growth and Drift Model (FMGDM v1.0): application in the<br> green tides of the Yellow Sea. <br> -----------------------------------------------------------------------------<br> Updata: 2021/03/18 -----------------------------------------------------------------------------<br> Part 1: The ECS-FVCOM results and also the input variables of FMGDM<br> Part 2: The initial particles position imformation (lat, lon, depth)<br> Part 3: The satellite pictures of green tides in YS, 2014 and 2015
DOI: 10.25919/s767-q790
title: Data for paper "An error model for long-range ensemble forecasts of ephemeral rivers"

description: Observations and retrospective forecasts for 50 catchments used in the paper: Bennett JC, Wang QJ, Robertson DE, Bridgart R, Lerat J, Li M, Michael K (accepted) An error model for long-range ensemble forecasts of ephemeral rivers. Accepted for publication in Advances in Water Resources, March 2021
DOI: 10.6084/m9.figshare.14247101
title: Supplementary Material for: Dietary Fibers and Proteins Modulate Behavior via the Activation of Intestinal Gluconeogenesis

description: <b><i>Introduction:</i></b> Several studies have suggested that diet, especially the one enriched in microbiota-fermented fibers or fat, regulates behavior. The underlying mechanisms are currently unknown. We previously reported that certain macronutrients (fermentable fiber and protein) regulate energy homeostasis via the activation of intestinal gluconeogenesis (IGN), which generates a neural signal to the brain. We hypothesized that these nutriments might control behavior using the same gut-brain circuit. <b><i>Methods:</i></b> Wild-type and IGN-deficient mice were fed chow or diets enriched in protein or fiber. Changes in their behavior were assessed using suited tests. Hippocampal neurogenesis, extracellular levels of serotonin, and protein expression levels were assessed by immunofluorescence, in vivo dialysis, and Western blotting, respectively. IGN was rescued by infusing glucose into the portal vein of IGN-deficient mice. <b><i>Results:</i></b> We show here that both fiber- and protein-enriched diets exert beneficial actions on anxiety-like and depressive-like behaviors. These benefits do not occur in mice lacking IGN. Consistently, IGN-deficient mice display hallmarks of depressive-like disorders, including decreased hippocampal neurogenesis, basal hyperactivity, and deregulation of the hypothalamic-pituitary-adrenal axis, which are associated with increased expression of the precursor of corticotropin-releasing hormone in the hypothalamus and decreased expression of the glucocorticoid receptor in the hippocampus. These neurobiological alterations are corrected by portal glucose infusion mimicking IGN. <b><i>Conclusion:</i></b> IGN translates nutritional information, allowing the brain to finely coordinate energy metabolism and behavior.
DOI: 10.6084/m9.figshare.13580870
title: <sup>13</sup>C NMR chemical shifts in substituted benzenes: analysis using natural perturbation orbitals and substitution effects

description: The natural perturbation orbital (NPO) method, combined with the gauge-including atomic orbital (GIAO), was applied to nuclear magnetic resonance (NMR) chemical shifts. The substituent effects of electron-donating (NH<sub>2</sub>) and electron-withdrawing (NO<sub>2</sub>) groups on the <sup>13</sup>C NMR chemical shifts of monosubstituted benzenes were analysed using NPOs. <sup>13</sup>C chemical shifts at the <i>ortho</i>-, <i>meta</i>- and <i>para</i>-positions were efficiently decomposed into contributions from two NPO pairs (σx−πx∗, σy−πy∗). These contributions were further divided into two factors, namely electron density in the vicinity of resonance nuclei and orbital energy gaps. Trends in the electron density matched with the <i>ortho</i>-, <i>meta</i>- and <i>para</i>-directions of the substituent effects. Specifically, NH<sub>2</sub> shielded the <i>ortho</i>- and <i>para</i>-carbons, while NO<sub>2</sub> deshielded the same carbons. The orbital energy gaps of <i>ortho</i>-carbons in NH<sub>2</sub>- and NO<sub>2</sub>-benzenes were significantly decreased, showing that these substituents shielded the <i>ortho</i>-carbons.
DOI: 10.6084/m9.figshare.13580870.v1
title: <sup>13</sup>C NMR chemical shifts in substituted benzenes: analysis using natural perturbation orbitals and substitution effects

description: The natural perturbation orbital (NPO) method, combined with the gauge-including atomic orbital (GIAO), was applied to nuclear magnetic resonance (NMR) chemical shifts. The substituent effects of electron-donating (NH<sub>2</sub>) and electron-withdrawing (NO<sub>2</sub>) groups on the <sup>13</sup>C NMR chemical shifts of monosubstituted benzenes were analysed using NPOs. <sup>13</sup>C chemical shifts at the <i>ortho</i>-, <i>meta</i>- and <i>para</i>-positions were efficiently decomposed into contributions from two NPO pairs (σx−πx∗, σy−πy∗). These contributions were further divided into two factors, namely electron density in the vicinity of resonance nuclei and orbital energy gaps. Trends in the electron density matched with the <i>ortho</i>-, <i>meta</i>- and <i>para</i>-directions of the substituent effects. Specifically, NH<sub>2</sub> shielded the <i>ortho</i>- and <i>para</i>-carbons, while NO<sub>2</sub> deshielded the same carbons. The orbital energy gaps of <i>ortho</i>-carbons in NH<sub>2</sub>- and NO<sub>2</sub>-benzenes were significantly decreased, showing that these substituents shielded the <i>ortho</i>-carbons.
DOI: 10.5281/zenodo.4616092
title: Literature review: source data

description: Source data: included papers in the literature review
DOI: 10.5281/zenodo.4616091
title: Literature review: source data

description: Source data: included papers in the literature review
DOI: 10.6084/m9.figshare.14247122
title: Supplementary Material for: Pre-Stroke Cholinesterase Inhibitor Treatment Is Beneficially Associated with Functional Outcome in Patients with Acute Ischemic Stroke and Pre-Stroke Dementia: The Fukuoka Stroke Registry

description: <b><i>Introduction:</i></b> Pre-stroke dementia is significantly associated with poor stroke outcome. Cholinesterase inhibitors (ChEIs) might reduce the risk of stroke in patients with dementia. However, the association between pre-stroke ChEI treatment and stroke outcome remains unresolved. Therefore, we aimed to determine this association in patients with acute ischemic stroke and pre-stroke dementia. <b><i>Methods:</i></b> We enrolled 805 patients with pre-stroke dementia among 13,167 with ischemic stroke within 7 days of onset who were registered in the Fukuoka Stroke Registry between June 2007 and May 2019 and were independent in basic activities of daily living (ADLs) before admission. Primary and secondary study outcomes were poor functional outcome (modified Rankin Scale [mRS] score: 3–6) at 3 months after stroke onset and neurological deterioration (≥2-point increase in the NIH Stroke Scale [NIHSS] during hospitalization), respectively. Logistic regression analysis was used to evaluate associations between pre-stroke ChEI treatment and study outcomes. To improve covariate imbalance, we further conducted a propensity score (PS)-matched cohort study. <b><i>Results:</i></b> Among the participants, 212 (26.3%) had pre-stroke ChEI treatment. Treatment was negatively associated with poor functional outcome (odds ratio: 0.68 [95% confidence interval: 0.46–0.99]) and neurological deterioration (0.52 [0.31–0.88]) after adjusting for potential confounding factors. In the PS-matched cohort study, the same trends were observed between pre-stroke ChEI treatment and poor functional outcome (0.61 [0.40–0.92]) and between the treatment and neurological deterioration (0.47 [0.25–0.86]). <b><i>Conclusions:</i></b> Our findings suggest that pre-stroke ChEI treatment is associated with reduced risks for poor functional outcome and neurological deterioration after acute ischemic stroke in patients with pre-stroke dementia who are independent in basic ADLs before the onset of stroke.
DOI: 10.25910/3ka2-1r16
title: Calcium-sensing receptors control CYP27B1-luciferase expression. Transcriptional and post-transcriptional mechanisms
DOI: 10.5281/zenodo.3929102
title: Pulse labelling of deep soil layers in forest with 13CH4: testing a new method for tracing methane in the upper horizons, understorey vegetation and tree stems using laserbased spectrometry

description: Methane is one the main greenhouse gases and upland forests are one of its main biological sinks. However, vegetation could reduce this sink by allowing a direct path for the methane produced in deep soils to escape into the atmosphere. By tracing emissions with <sup>13</sup>CH<sub>4</sub>, we show for the first time that methane emitted by trees in upland forest could have a deep soil origin even though the soil is an overall methane sink. However, we found that the trees and understorey vegetation at our site had only a small impact on the methane budget.
DOI: 10.5281/zenodo.3929101
title: Pulse labelling of deep soil layers in forest with 13CH4: testing a new method for tracing methane in the upper horizons, understorey vegetation and tree stems using laserbased spectrometry

description: Methane is one the main greenhouse gases and upland forests are one of its main biological sinks. However, vegetation could reduce this sink by allowing a direct path for the methane produced in deep soils to escape into the atmosphere. By tracing emissions with <sup>13</sup>CH<sub>4</sub>, we show for the first time that methane emitted by trees in upland forest could have a deep soil origin even though the soil is an overall methane sink. However, we found that the trees and understorey vegetation at our site had only a small impact on the methane budget.
DOI: 10.5281/zenodo.4559067
title: Datasets: density estimation using deep generative neural network

description: Datasets used in Roundtrip paper. Source code can be found at https://github.com/kimmo1019/Roundtrip UCI datasets: AReM/data.npy: Activity Recognition data collected from Multi sensors. Data size (42239, 6) CASP/data.npy: Protein Tertiary Structure data. Data size (45730, 9) BANK/data.npy: Financial data collected from clients. Data size (45211, 17) YPMSD/data.npy: Audio data of various songs. Data size (515345,90) HEPMASS/train.csv and HEPMASS/test.csv: Data of high-energy particles. ODDS contains three outlier detection datasets Shuttle, Mammography and ForestCover. mnist.tar.gz: MNIST datasets cifar10.tar.gz: CIFAR-10 datasets Pretrained models:uncompress pre_trained_models.tar.gz under the Roundtrip model.
DOI: 10.5281/zenodo.3747144
title: Datasets: density estimation using deep generative neural network

description: Datasets used in Roundtrip paper. Source code can be found at https://github.com/kimmo1019/Roundtrip UCI datasets: AReM/data.npy: Activity Recognition data collected from Multi sensors. Data size (42239, 6) CASP/data.npy: Protein Tertiary Structure data. Data size (45730, 9) BANK/data.npy: Financial data collected from clients. Data size (45211, 17) YPMSD/data.npy: Audio data of various songs. Data size (515345,90) HEPMASS/train.csv and HEPMASS/test.csv: Data of high-energy particles. ODDS contains three outlier detection datasets Shuttle, Mammography and ForestCover. mnist.tar.gz: MNIST datasets cifar10.tar.gz: CIFAR-10 datasets Pretrained models:uncompress pre_trained_models.tar.gz under the Roundtrip model.
DOI: 10.48370/ofd/9ojloj
title: Wierzba trójpręcikowa (Salix triandra L.), 3405

description: Herbarium
DOI: 10.6084/m9.figshare.13397585
title: Insight into chronic pain in the United States: descriptive results from the Prescription Opioid Misuse and Abuse Questionnaire (POMAQ) validation study

description: A chronic pain patient sample living in the United States who participated in a cross-sectional study to evaluate the validity and reproducibility of the Prescription Opioid Misuse and Abuse Questionnaire is characterized. Patients with chronic pain identified through electronic medical records as refilling at least one opioid prescription within the prior 3 months were recruited from five United States Department of Defense Military Health System clinics. Patients completed the Prescription Opioid Misuse and Abuse Questionnaire, Brief Pain Inventory-Short Form, Medical Outcomes Study: 36-item Short Form, and sociodemographic questions online. Clinical characteristics and electronic medical records for 1 year prior to consent were collected. 809 (86.2%) participants completed the Prescription Opioid Misuse and Abuse Questionnaire. Mean (± standard deviation) age was 55.4 ± 12.7 years; the majority female (55.5%) and white (74.8%). Mean duration of chronic pain was 14.7 ± 10.5 years; the most common pain conditions were lower back pain (76.6%), neck or shoulder pain (60.3%), and osteoarthritis (38.7%). The most commonly prescribed opioids were oxycodone (35.7%), tramadol (34.5%), and hydrocodone (26.9%); 54.8% took one opioid, 44.9% took 2 or more opioids. Participants’ health status was poor; pain severity and interference were moderate. Electronic medical record data revealed high healthcare resource utilization. This chronic pain population was severely impacted by their pain condition(s).