cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.833825.v1
title: MegaJournal Data October 2013

description: This data was used in a Presentation to UBC Open on 10/22/2013 (see the livestreamed video at: http://mediasitemob1.mediagroup.ubc.ca/Mediasite/Play/2cdc95b2d56a4c56a6606a6c116a58b01d) and in a blog post for Creative Commons New Zealand on 10/23/2013 (see http://creativecommons.org.nz/2013/10/open-access-megajournals-have-they-changed-everything/). View the PPT with synced audio at: http://www.slideshare.net/PBinfield/oa-mega-journals-ubc-open-event Blurb for the talk: The Open Access ‘Megajournal’ (a class of journal defined by the success of PLOS ONE) is a reasonably recent phenomenon, but one that some observers believe is poised to change the publishing world very rapidly. A megajournal is typically understood to be an online-only journal; covering a very broad subject area; selecting content based only on scientific and methodological soundness; and with a business model which allows each article to cover its own costs. With these attributes, megajournals are not limited in potential output and as such are able to grow commensurate with any growth in submissions. PLOS ONE pioneered this category of journal and is currently expected to publish in excess of 30,000 articles in 2013 alone – possibly approaching 3% of all STM articles published that year. Recognizing the success of this model, many other publishers (such as Nature, Springer, SAGE, BioONE, PeerJ, , BMJ, F1000 and so on) have launched similar journals and each of these publishers is seeing their megajournal grow in volume, month on month. In many ways, the growth of the megajournal has been one of the most visible successes of the open access movement.
DOI: 10.6084/m9.figshare.7325180.v1
title: Evaluation of Knowledge Graph Embedding Approaches for Drug-Drug Interaction Prediction using Linked Open Data

description: Current approaches to identifying drug-drug interactions (DDIs), which involve clinical evaluation of drugs and post-marketing surveillance, are unable to provide complete, accurate information, nor do they alert the public to potentially dangerous DDIs before the drugs reach the market. Predicting potential drug-drug interaction helps reduce unanticipated drug interactions and drug development costs and optimizes the drug design process. Many bioinformatics databases have begun to present their data as Linked Open Data (LOD), a graph data model, using Semantic Web technologies. The knowledge graphs provide a powerful model for defining the data, in addition to making it possible to use underlying graph structure for extraction of meaningful information. In this work, we have applied Knowledge Graph (KG) Embedding approaches to extract feature vector representation of drugs using LOD to predict potential drug-drug interactions. We have investigated the effect of different embedding methods on the DDI prediction and showed that the knowledge embeddings are powerful predictors and comparable to current state-of-the-art methods for inferring new DDIs. We have applied Logistic Regression, Naive Bayes and Random Forest on Drugbank KG with the 10-fold traditional cross validation (CV) using RDF2Vec, TransE and TransD. RDF2Vec with uniform weighting surpass other embedding methods.
DOI: 10.6084/m9.figshare.3523421.v1
title: Appendix C. A table of tadpole performance by treatment, pond, and year.

description: A table of tadpole performance by treatment, pond, and year.
DOI: 10.6084/m9.figshare.16995052.v1
title: Supplementary Material for: Innate Immune Training with Bacterial Extracts Enhances Lung Macrophage Recruitment to Protect from Betacoronavirus Infection

description: Training of the innate immune system with orally ingested bacterial extracts was demonstrated to have beneficial effects on infection clearance and disease outcome. The aim of our study was to identify cellular and molecular processes responsible for these immunological benefits. We used a murine coronavirus (MCoV) A59 mouse model treated with the immune activating bacterial extract Broncho-Vaxom (BV) OM-85. Tissue samples were analysed with qPCR, RNA sequencing, histology, and flow cytometry. After BV OM-85 treatment, interstitial macrophages accumulated in lung tissue leading to a faster response of type I interferon (IFN) signalling after MCoV infection resulting in overall lung tissue protection. Moreover, RNA sequencing showed that lung tissue from mice receiving BV OM-85 resembled an intermediate stage between healthy and viral infected lung tissue at day 4, indicating a faster return to normal tissue homoeostasis. The pharmacologic effect was mimicked by adoptively transferring naive lung macrophages into lungs from recipient mice before virus infection. The beneficial effect of BV OM-85 was abolished when inhibiting initial type I IFN signalling. Overall, our data suggest that BV OM-85 enhances lung macrophages allowing for a faster IFN response towards a viral challenge as part of the oral-induced innate immune system training.
DOI: 10.6084/m9.figshare.27051142.v1
title: Code repository

description: Jupyter notebooks with code for the paper titled: "A combined lifestyle intervention induces a sensitization of the blood transcriptomic response to a nutrient challenge"
DOI: 10.6084/m9.figshare.28692668.v1
title: Transaction fees Bitcoin 2024

description: Bitcoin transaction fees in 2024
DOI: 10.6084/m9.figshare.24493939.v1
title: Supplementary Material for: Hepcidin removal during Continuous Renal Replacement Therapy

description: Introduction: Patients with acute kidney injury (AKI) or end stage kidney disease (ESKD) may require continuous renal replacement therapy (CRRT) as a supportive intervention. While CRRT is effective at achieving solute control and fluid balance, the indiscriminate nature of this procedure raises the possibility that beneficial substances may similarly be removed. Hepcidin, an antimicrobial peptide with pivotal roles in iron homeostasis and pathogen clearance, has biochemical properties amenable to direct removal via CRRT. We hypothesized that serum hepcidin levels would significantly decrease after initiation of CRRT. Methods: In this prospective, observational trial, we enrolled 13 patients who required CRRT: 11 due to stage 3 AKI, and 2 due to critical illness in the setting of ESKD. Plasma was collected at the time of enrollment, and then plasma and effluent were collected at 10 AM on the following 3 days. Plasma samples were also collected from healthy controls, and we compared hepcidin concentrations in those with renal disease compared to normal controls, evaluated trends in hepcidin levels over time, and calculated the hepcidin sieving coefficient. Results: Plasma hepcidin levels were significantly higher in patients initiating CRRT than in normal controls (158±60 vs 17±3 ng/mL respectively, p&lt;0.001). Hepcidin levels were highest prior to CRRT initiation (158±60 ng/mL), and were significantly lower on day 1 (102±24 ng/mL, p&lt;0.001) and day 2 (56±14 ng/mL, p&lt;0.001) before leveling out on day 3 (51±11 ng/mL). The median sieving coefficient was consistent at 0.82-0.83 for each of 3 days. Conclusions: CRRT initiation is associated with significant decreases in plasma hepcidin levels over the first 2 days of treatment regardless of indication for CRRT, or presence of underlying ESKD. Since reduced hepcidin levels are associated with increased mortality and our data implicate CRRT in hepcidin removal, larger clinical studies evaluating relevant clinical outcomes based on hepcidin trends in this population should be pursued.
DOI: 10.6084/m9.figshare.25584585.v1
title: Test Suite of PHPLang

description: Test Suite of "New PHP Language Features Make Your Static Code Analysis Tools Miss Vulnerabilities"<br>If you use this test suite, please cite@INPROCEEDINGS{phplang-lin,<br>author={Wang, Lin and Zhang, Yuan and Tan, Xin and Ye, Shengke and Yang, Min},<br>booktitle={2024 IEEE International Conference on Software Maintenance and Evolution (ICSME)},<br>title={New PHP Language Features Make Your Static Code Analysis Tools Miss Vulnerabilities},<br>year={2024},<br>volume={},<br>number={},<br>pages={63-74},<br>keywords={Software maintenance;Codes;Systematics;Source coding;Scalability;Programming;Feature extraction;Rendering (computer graphics);Market research;Stakeholders;PHP Language Feature;Static Code Analysis;Web Security;Vulnerability Detection},<br>doi={10.1109/ICSME58944.2024.00017}}<br><br>
DOI: 10.6084/m9.figshare.23133422.v1
title: Quercus ithaburensis chorology

description: Distribution map of <em>Quercus ithaburensis</em>. <br> <br> <br> These maps were produced by combining numerous and heterogeneous data collected from atlas monographs providing complete species distribution maps, from national to regional atlases, occurrence geo-databases, scientific and grey literature. <br> The maps were created using ESRI shapefiles (*.shp, *.shx, *.dbf, *.prj files) archived in the ZIP file. Species range is mapped with polygon features (name suffix "plg"), which define continuous areas of occupancy of the species, and with point features (name suffix "pnt"), which identify more fragmented and isolated populations. If synanthropic occurrences are reported outside the species natural range, additional point and/or polygon shapefiles are also present (suffix "syn"). <br> Polygon borders delimiting species ranges are generalized across the mainland and sea boundaries. This offers the possibility to mask sea areas or to clip and extract the terrestrial range parts using GIS data layers of the users' choice. <br> An additional version of polygon ranges are clipped with a coastline (name suffix "clip"), which have been derived from Natural Earth dataset "Admin 0 - Countries" 1:50M version 4.1.0 (https://www.naturalearthdata.com). <br> <br> <br> Please cite as: Caudullo, G., Welk, E., San-Miguel-Ayanz, J., 2017. Chorological maps for the main European woody species. Data in Brief 12, 662-666. DOI: doi.org/10.1016/j.dib.2017.05.007 <br> <br> <br> Additional information and used references are on 'supplementary materials' document: <br> https://doi.org/10.6084/m9.figshare.5091901 <br> <br> <br> Chorological maps are part of the "European Atlas of Forest Tree Species" project: <br> https://w3id.org/mtv/FISE-Comm/v01
DOI: 10.6084/m9.figshare.28211441.v3
title: Nitrogen-induced changes in different mycorrhiza-dominated forests

description: This dataset contains the types of mycorrhiza and the effects of nitrogen addition on forest ecosystems covered in the article.
DOI: 10.34740/kaggle/dsv/11634276
title: Earthquakes in Indonesia
DOI: 10.6084/m9.figshare.4807054.v1
title: Socioeconomic Impacts of Climatic Change on Paddy Cultivation: An Empirical Investigation in Malaysia

description: AbstractThe changing natures of climatic factors have different impacts on agriculture based on areas,periods and crops. Farmers are the most vulnerable group who are affected both directly andindirectly through climatic changes. In the study area in Malaysia, climatic changes have adverseimpacts on farmers. Due to climatic change productivity and profitability of paddy cultivationhave declined in the Integrated Agricultural Development Area, North-West Selangar. Farmersperceive that paddy cultivation is no longer profitable due to low productivity as a result ofclimatic changes. They now prefer full-time to part-time engagement in paddy cultivation. Heavygovernment subsidy and encouragement are not enough; it requires increase in productivity andprofitability of paddy cultivation for making its viable and sustainable sector. All efforts ofmitigation and adaptation must be pursued to counter the adverse impacts of climatic changesand increase the productivity of paddy cultivation in the area. It is observed that there is a highdegree of income inequality among the paddy farmers in the study area.
DOI: 10.6084/m9.figshare.28147040.v1
title: Odorant and gustatory receptor sequences of Diabrotica virgifera virgifera

description: FASTA files for DNA and amino acid sequences of manually annotated odorant and gustatory sequences of Diabrotica virgifera virgifera Leconte. Genomic sequences were annotated using the PGI_DIABVI_V3a genome assembly.
DOI: 10.25413/sun.28804154.v1
title: Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma

description: Tuberculosis (TB) remains a global public health threat. Understanding the dynamics of host-pathogen interactions within TB granulomas will assist in identifying what leads to the successful elimination of infection. <i>In vitro</i> TB models provide a controllable environment to study these granuloma dynamics. Previously we developed a biomimetic 3D spheroid granuloma model that controls bacteria better than a traditional monolayer culture counterpart. We used agent-based simulations to predict the mechanistic reason for this difference. Our calibrated simulations were able to predict heterogeneous bacterial dynamics that are consistent with experimental data. In one group of simulations, spheroids are found to have higher macrophage activation than their traditional counterparts, leading to better bacterial control. This higher macrophage activation in the spheroids was not due to higher counts of activated T cells, instead fewer activated T cells were able to activate more macrophages due to the proximity of these cells to each other within the spheroid. In a second group of simulations, spheroids again have more macrophage activation but also more T cell activation, specifically CD8+ T cells. This higher level of CD8+ T cell activation is predicted to be due to the proximity of these cells to the cells that activate them. Multiple mechanisms of control were predicted. Simulations removing individual mechanisms show that one group of simulations has a CD4+ T cell dominant response, while the other has a mixed/CD8+ T cell dominant response. Lastly, we demonstrated that in spheroids the initial structure and movement rules work synergistically to reduce bacterial load. These findings provide valuable insights into how the structural complexity of <i>in vitro</i> models impacts immune responses. Moreover, our study has implications for engineering more physiologically relevant <i>in vitro</i> models and advancing our understanding of TB pathogenesis and potential therapeutic interventions.
DOI: 10.6084/m9.figshare.5127796.v1
title: Supplementary Material for: Pre-Sleep and Sleeping Platform Construction Behavior in Captive Orangutans (<b><i>Pongo </i></b>spp<b><i>.</i></b>): Implications for Ape Health and Welfare

description: The nightly construction of a ‘nest' or sleeping platform is a behavior that has been observed in every wild great ape population studied, yet in captivity, few analyses have been performed on sleep related behavior. Here, we report on such behavior in three female and two male captive orangutans (<i>Pongo</i> spp.), in a natural light setting, at the Indianapolis Zoo. Behavioral samples were generated, using infrared cameras for a total of 47 nights (136.25 h), in summer (n = 25) and winter (n = 22) periods. To characterize sleep behaviors, we used all-occurrence sampling to generate platform construction episodes (n = 217). Orangutans used a total of 2.4 (SD = 1.2) techniques and 7.5 (SD = 6.3) actions to construct a sleeping platform; they spent 10.1 min (SD - 9.9 min) making the platform and showed a 77% preference for ground (vs. elevated) sleep sites. Comparisons between summer and winter platform construction showed winter start times (17:12 h) to be significantly earlier and longer in duration than summer start times (17:56 h). Orangutans should be provisioned with seasonally appropriate, high quality materials suitable for construction of sleeping platforms to increase sleep quality and improve animal health and welfare.
DOI: 10.6084/m9.figshare.5999627.v1
title: Supplementary Material for: Longitudinal Melanonychia: Differences in Etiology Are Associated with Patient Age at Diagnosis

description: <b><i>Background:</i></b> Longitudinal melanonychia (LM) may occur as a result of nail apparatus melanoma. Knowledge of etiology plays an important role in the management of LM. <b><i>Objectives:</i></b> The study is aimed to compare the diagnosis of LM in different age groups. <b><i>Methods:</i></b> We collected 63 cases (45 adults and 18 children) with LM who underwent nail matrix biopsy or excision in a 21-year cohort and assessed their clinicopathological features. <b><i>Results:</i></b> Melanomas in adults and children were 40% and none, while nevi accounted for 15.6% in adults and 94.4% in children. There was a statistically significant difference between the average age at diagnosis for melanoma (54.5 ± 13.3 years) and nevus (15.2 ± 18.5 years). Logistic regression related the occurrence of melanoma to older ages with a relative risk of 1.2 compared to nevus, but no cutoffs between age groups could be deﬁned between LM-associated nevus and melanoma. <b><i>Conclusion:</i></b> The adult group has a significantly higher risk of melanoma, while children with LM show mostly nonmelanoma etiologies. Tissue proof is more warranted in adult cases, and it is needed in selected cases of children with LM.
DOI: 10.6084/m9.figshare.27022705.v1
title: 年平均 RE

description: 使用 ETR 模型融合 CHIRPS、CPC、CN05.1、CHM、ERA5 数据集得到的年降雨侵蚀率RE_yyyy代表当年的 RE yyyy
DOI: 10.6084/m9.figshare.20065676.v1
title: Supplementary Material for: Twist2 Reduced NLRP3-Induced Inflammation of Infantile Pneumonia via Regulation of Mitochondrial Permeability Transition by FOXO1

description: <b><i>Background:</i></b> Infantile pneumonia is an acute inflammatory lesion of the lung caused by mycoplasma pneumonia. Indeed, Twist2 signaling pathway controls inflammatory reaction, oxidative stress, and other biological reaction. However, the regulation of Twist2 on the inflammation in infantile pneumonia remains unclear. This study explained that the function and mechanism of Twist2 in infantile pneumonia. <b><i>Methods:</i></b> The subjects included the serum samples of 12 patients with infantile pneumonia and normal healthy volunteers from <i>Hunan Children’s Hospital</i>. Besides, mice were given with lipopolysaccharide (LPS) into the lung. Moreover, RAW264.7 macrophages were stimulated with LPS for 4 h and added to the culture medium. <b><i>Results:</i></b> In present study, in serum of patients with infantile pneumonia or lung tissue of mice model with infantile pneumonia, TWIST2 expression was lessened. Apart from that, TWIST2 protein could reduce the inflammatory reaction in mice model with infantile pneumonia, resulting in an inhibition in lung injury. Conversely, over-expression of TWIST2 also decreased inflammatory reaction in macrophages model via the regulation of FOXO1/NLRP3 pathway. Downregulation of TWIST2 promoted the inflammation in macrophages model by the regulation of FOXO1/NLRP3 pathway. <b><i>Conclusion:</i></b> According to the findings, present study have identified that the TWIST2 could reduce the inflammation of infantile pneumonia by NLRP3 inflammasome through the regulation of mitochondrial permeability transition and the induction of FOXO1 expression.
DOI: 10.6084/m9.figshare.19336346.v2
title: RTSIF dataset

description: Satellite-retrieved solar-induced chlorophyll fluorescence (SIF) can be a valuable proxy for photosynthesis. TROPOspheric Monitoring Instrument (TROPOMI) on the Copernicus Sentinel-5P mission enables significant improvements in measuring SIF, but the short temporal coverage of the data records has limited its applications in long-term studies. This dataset uses machine learning to reconstruct TROPOMI SIF (RTSIF) for 2001-2020 with a spatial resolution of 0.05° and a temporal resolution of 8 days. Our machine learning model has high accuracy on the training and testing data (R<sup>2</sup> = 0.907, regression slope = 1.001). The RTSIF dataset is in good agreement with the original TROPOMI SIF, and its accuracy is further validated against tower-based SIF. The RTSIF dataset is also compared with other satellite-derived SIF (GOME-2 SIF and OCO-2 SIF). Comparing RTSIF with Gross Primary Production (GPP) illustrates the potential of RTSIF for estimating carbon fluxes. We anticipate that this new dataset will be valuable in assessing long-term terrestrial photosynthesis and constraining the global carbon budget and associated water fluxes.
DOI: 10.6084/m9.figshare.7592930.v1
title: Steady-state kinetics for the peroxidase mimicking (Fig.6)

description: The reaction rate as a function of (b) [H<sub>2</sub>O<sub>2</sub>] and (c) [TMB] in the acetate buffer (0.1 M, pH 4) suspension of AKCN (0.5 g L<sup>-1</sup>) with TMB and H<sub>2</sub>O<sub>2</sub> for 10 min incubation.
DOI: 10.6084/m9.figshare.19614255.v1
title: Supplementary Material for: Criteria for Continuous Kidney Replacement Therapy Cessation in ICU Patients

description: <b><i>Introduction:</i></b> In intensive care unit (ICU) patients with acute kidney injury, specific recommendations to guide the decision to cease continuous kidney replacement therapy (CKRT) are lacking. <b><i>Methods:</i></b> We performed a survey to identify criteria currently used to cease CKRT in real-life clinical practice in the Netherlands. We used an online questionnaire with multiple choice questions designed with web-based software from SurveyMonkey. <b><i>Results:</i></b> We received 169 completed questionnaires from intensivists (<i>n</i> = 126) and nephrologists (<i>n</i> = 43). Essential determinants for the cessation of CKRT were a spontaneously increasing diuresis (indicated by 92% of the respondents), absence of fluid overload (indicated by 88% of the respondents), and improvement in creatinine clearance (indicated by 61% of the respondents; intensivists 56%; nephrologists 77%, <i>p</i> = 0.03). Most often mentioned cut-off values used for increase in diuresis were 0.25 and 0.5 mL/kg/h (35% and 33%, respectively). Actual CKRT cessation was often postponed until the filter clots or until circuit disconnection is needed because of patient transport for diagnostic or intervention procedures (indicated by 58% of the respondents). Expected discharge from the ICU was the most frequently reported determinant to switch from CKRT to hemodialysis (indicated by 67% of the respondents). <b><i>Conclusions:</i></b> CKRT cessation in clinical practice is mostly based on spontaneously increasing diuresis, absence of fluid overload, and improvement in creatinine clearance and is often delayed until filter clotting or disconnection of the circuit because of logistic reasons.
DOI: 10.6084/m9.figshare.26880589.v1
title: Supplemental Tables 1-5 Formal Degree Programs in Physiology Promote Careers of Clinical Scientists and Benefit Basic Science Departments

description: Twenty-two year follow-up of surgical trainees pursuing bench laboratory science and PhD in Physiology in a Surgery Department within a single public medical school. The sources and resources include selection, funding, physiology classroom work, and laboratory studies with personal involvement by faculty that have seldom been recorded, especially with longer-term career outcomes. These selected Ph.D. candidates have subsequently pursued several lines of activity, many with distinguished careers and major influences upon future generations of academic surgeons.