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Ecology and environment predict spatially stratified risk of H5 highly pathogenic avian influenza clade 2.3.4.4b in wild birds across Europe
<p>The data in this repository were used to conduct the analysis outlined in the following bioRxiv preprint:</p> <ul> <li>Sarah Hayes, Joe Hilton, Joaquin Mould-Quevedo, Christl Donnelly, Matthew Baylis, Liam Brierley (2025) "Ecology and environment predict spatially stratified risk of H5 highly pathogenic avian influenza clade 2.3.4.4b in wild birds across Europe" <em>bioRxiv</em> doi:10.1101/2024.07.17.603912</li> </ul> <p>The codes used for the analyses are available at https://github.com/sarahhayes/avian_flu_sdm/ </p> <p>The following lookup table can be used to cross-reference between the variable descriptions in Tables 1 and 2 of the preprint and the files in this repository:</p> <p> </p> <table> <tbody> <tr> <td> <h3> Variable description </h3> </td> <td> <h3> Filename </h3> </td> </tr> <tr> <td> Minimum elevation (metres above sea level) </td> <td> elevation_min_10kres.tif </td> </tr> <tr> <td> Maximum elevation (metres above sea level) </td> <td> elevation_max_10kres.tif </td> </tr> <tr> <td> Difference between minimum and maximum elevation </td> <td> elevation_diff_10kres.tif </td> </tr> <tr> <td> Modal elevation (metres above sea level) </td> <td> elevation_mode_10kres.tif </td> </tr> <tr> <td> Normalised Difference Vegetation Index (NDVI) </td> <td> ndvi_*_quart_2022_eco_rasts.tif </td> </tr> <tr> <td> Land cover </td> <td> landcover_output_full_2022_10kres.tif </td> </tr> <tr> <td> Distance to coast </td> <td> dist_to_coast_10kres.csv </td> </tr> <tr> <td> Distance to inland water </td> <td> dist_to_water_output_10kres.csv </td> </tr> <tr> <td> Relative humidity </td> <td> mean_relative_humidity_q*_10kres_eco_quarts.tif </td> </tr> <tr> <td>Seasonal weighted mean of the month-wise difference in the minimum temperature and maximum temperature (degrees Celsius) </td> <td> mean_diff_*_quart_eco_rasts.tif </td> </tr> <tr> <td>Seasonal weighted mean of monthly mean temperatures (degrees Celsius) (Mean monthly temperature for each month calculated using: Mean temperature = Minimum temperature + diurnal range/2)</td> <td> mean_mean_*_quart_eco_rasts.tif </td> </tr> <tr> <td>Seasonal temperature variation (degrees Celsius)<br>(Difference between the maximum and minimum of<br>mean monthly temperature values across months<br>majority-represented within the season)</td> <td> variation_in_quarterly_mean_temp_q*_eco_rasts.tif </td> </tr> <tr> <td> Precipitation </td> <td> mean_prec_*_quart_eco_rasts.tif </td> </tr> <tr> <td>Seasonal mean of daily zero-degree isotherm (metres<br>above sea level) </td> <td> isotherm_mean_q*_eco_rasts.tif </td> </tr> <tr> <td>Number of days the zerodegree isotherm was below 1 metre at midday at Coordinated Universal Time (UTC) </td> <td> isotherm_midday_days_below1_q*_eco_quarts.tif </td> </tr> <tr> <td> Chicken density </td> <td> chicken_density_2010_10kres.tif </td> </tr> <tr> <td> Duck density </td> <td> duck_density_2010_10kres.tif </td> </tr> <tr> <td> <em>Anatinae</em> (dabbling ducks) </td> <td> anatinae_rast_eco_bds.tif </td> </tr> <tr> <td> <em>Anserinae</em> (swans and geese) </td> <td> anserinae_rast_eco_bds.tif </td> </tr> <tr> <td> <em>Ardeidae</em> (herons) </td> <td> ardeidae_rast_eco_bds.tif </td> </tr> <tr> <td> <em>Arenaria/Calidris</em> (turnstones and sandpipers) </td> <td> arenaria_calidris_rast_eco_bds.tif </td> </tr> <tr> <td> <em>Aythyini</em> (diving ducks)</td> <td> aythyini_rast_eco_bds.tif</td> </tr> <tr> <td> Laridae (gulls) </td> <td> laridae_rast_eco_bds.tif </td> </tr> <tr> <td> Percentage time spent feeding within 2m of water surface </td> <td> around_surf_rast_eco_bds.tif </td> </tr> <tr> <td> Percentage time spent feeding >2m below water surface </td> <td> below_surf_rast_eco_bds.tif </td> </tr> <tr> <td> Percentage diet plants </td> <td> plant_rast_eco_bds.tif </td> </tr> <tr> <td> Percentage diet scavenging </td> <td> scav_rast_eco_bds.tif </td> </tr> <tr> <td> Percentage diet endothermic vertebrates </td> <td> vend_rast_eco_bds.tif </td> </tr> <tr> <td> Congregative </td> <td> cong_rast_eco_bds.tif </td> </tr> <tr> <td> Migratory </td> <td> migr_rast_eco_bds.tif </td> </tr> <tr> <td> Below threshold phylogenetic distance to known host species </td> <td> host_dist_rast_eco_bds.tif </td> </tr> <tr> <td> Species richness </td> <td> species_richness_rast_eco_bds.tif </td> </tr> </tbody> </table>
Dataset of "TWIST1 expression is associated with high-risk neuroblastoma and promotes primary and metastatic tumor growth"
<p>The embryonic transcription factors TWIST1/2 are frequently overexpressed in cancer, acting as multifunctional oncogenes. Here we investigate their role in neuroblastoma (NB), a heterogeneous childhood malignancy ranging from spontaneous regression to dismal outcomes despite multimodal therapy. We first reveal the association of TWIST1 expression with poor survival and metastasis in primary NB, while TWIST2 correlates with good prognosis. Secondly, suppression of TWIST1 by CRISPR/Cas9 results in a reduction of tumor growth and metastasis in immunocompromised mice. Moreover, TWIST1 knock-out tumors displays a less aggressive cellular morphology and a reduced disruption of the extracellular matrix (ECM) reticulin network. Additionally, we identify a TWIST1-mediated transcriptional program associated with dismal outcome in NB and involved in the control of pathways mainly linked to the signaling, migration, adhesion, the organization of the ECM, and the tumor cells versus tumor stroma crosstalk. Taken together, our findings identified TWIST1 as novel therapeutic target in NB.</p>
Dataset for "TWIST1 expression is associated with high-risk neuroblastoma and promotes primary and metastatic tumor growth"
<p>The embryonic transcription factors TWIST1/2 are frequently overexpressed in cancer, acting as multifunctional oncogenes. Here we investigate their role in neuroblastoma (NB), a heterogeneous childhood malignancy ranging from spontaneous regression to dismal outcomes despite multimodal therapy. We first reveal the association of TWIST1 expression with poor survival and metastasis in primary NB, while TWIST2 correlates with good prognosis. Secondly, suppression of TWIST1 by CRISPR/Cas9 results in a reduction of tumor growth and metastasis in immunocompromised mice. Moreover, TWIST1 knock-out tumors displays a less aggressive cellular morphology and a reduced disruption of the extracellular matrix (ECM) reticulin network. Additionally, we identify a TWIST1-mediated transcriptional program associated with dismal outcome in NB and involved in the control of pathways mainly linked to the signaling, migration, adhesion, the organization of the ECM, and the tumor cells versus tumor stroma crosstalk. Taken together, our findings confirm TWIST1 as promising therapeutic target in NB.</p> <p>This dataset comprise images (.ndpi files) of anti-F4/80 IHC staining used for the quantification of macrophages in subcutaneous and orthotopic neuroblastoma xenografts derived from SK-N-Be2c cells expressing TWIST1 or knocked out for TWIST1 through CRISR/Cas9.</p>
Materials for "Poor nutritional condition promotes high-risk behaviours: A systematic review and meta-analysis"
<p>This contains a permanent record of dataset and analysis code for the study:</p> <p>Moran, N. P., Sánchez‐Tójar, A., Schielzeth, H., & Reinhold, K. (2021). Poor nutritional condition promotes high‐risk behaviours: a systematic review and meta‐analysis. <em>Biological Reviews</em>, <em>96</em>(1), 269-288.</p> <p>Full data analysis records are available on https://osf.io/3tphj/</p> <p>This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 836937. Also, this research was funded by the German Research Foundation (DFG) as part of the SFB TRR 212 (NC³) – Project numbers 316099922 and 396782608.</p>
Clinical evidence for high-risk CE-marked medical devices for glucose management: a systematic review and meta-analysis
<p><strong><span>Aims: </span></strong><span>High-risk medical devices are increasingly used in diabetes management, but<span><span> there are no specific European recommendations on how they should be evaluated. Within</span></span> the Coordinating Research and Evidence for Medical Devices (CORE-MD) project, we conducted a systematic review and meta-analysis evaluating CE-marked high-risk devices for glucose management. </span></p> <p><strong><span>Materials and Methods: </span></strong><span>We<span> identified interventional and observational studies evaluating the </span>efficacy and safety of 8 automated insulin delivery (AID) systems, 2 implantable insulin pumps, and 3 implantable continuous glucose monitoring (CGM) devices.<span> </span></span><span>We meta-analysed randomized controlled trials (RCTs) comparing AID systems with other treatments.</span></p> <p><strong><span>Results:</span></strong><span> 99 studies published from 2009–2022 were included, comprising 83 on AID systems, 6 on insulin pumps, and 10 on CGM; 43% reported industry funding;30% were pre-market; 45% had a comparator group. 33% were RCTs, 25% non-randomized trials, and 41% observational studies. Median sample size was 52 (interquartile range 25–111), age 37.8 years (17–45.5), and study duration 13 weeks (4.5–26). AID systems lowered HbA1c by 0.3 percentage points (absolute mean difference [MD]=-0.3; 9 RCTs; I<sup>2</sup>=85%) and increased time in target range for sensor glucose level by 10.5 percentage points (MD=10.5; 14 RCTs; I<sup>2</sup>=89%). 69% of studies reported on at least one safety outcome.</span></p> <p><strong><span>Conclusions:</span></strong><span> High-risk devices for glucose monitoring or insulin dosing, in particular AID systems, improve glucose control safely but evidence on diabetes-related end organ damage is lacking due to short study durations. Methodological heterogeneity highlights the need for d<span><span>eveloping standards for future pre- and post-market investigations of diabetes-specific high-risk medical devices.</span></span></span></p>
Additional data: Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring
<p>This repository provides additional data for the manuscript titled "Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring", currently under revision at Nature Genetics. The primary data cohort has been deposited in the HTAN data portal. This repository includes processed 10x Xenium spatial transcriptomic data for six TH-MYCN mice (three chemotherapy-treated and three treatment-naive) as well as processed scRNA-seq data for CHLA15 and CHLA20 neuroblastoma (NBL) cells. The scRNA-seq data includes mono-cultured, co-cultured cells with THP-1 macrophages, and co-culture cells treated with Afatinib/CRM197. </p>
Competitive growth experiments with a high-lipid Chlamydomonas reinhardtii mutant strain and its wild-type to predict industrial and ecological risks
<p>Key microalgal species are currently being exploited as biomanufacturing platforms using mass cultivation systems. The opportunities to enhance productivity levels or produce non-native compounds are increasing as genetic manipulation and metabolic engineering tools are rapidly advancing. Regardless of the end product, there are both environmental and industrial risks associated to open pond cultivation of mutant microalgal strains. A mutant escape could be detrimental to local biodiversity and increase the risk of algal blooms. Similarly, if the cultivation pond is invaded by a wild-type microalgae or the mutant reverts to wild-type phenotypes, productivity could be impacted. To investigate these potential risks, a response surface methodology was applied to determine the competitive outcome of two <em>Chlamydomonas reinhardtii</em> strains, a wild-type (CC-124) and a high-lipid accumulating mutant (CC-4333), grown in mixotrophic conditions, with differing levels of nitrogen and initial wild-type to mutant ratios. Results of the growth experiments show that mutant cells have double the exponential growth rate of the wild-type in monoculture. However, due to a slower transition from lag phase to exponential phase, mutant cells are outcompeted by the wild-type in every co-culture treatment. This suggests that, under the conditions tested, outdoor cultivation of the <em>C. reinhardtii</em> cell wall-deficient mutant strains does not carry a significant environmental risk to its wild-type in an escape scenario. Furthermore, lipid results show the mutant strain accumulates over 200% more TAGs per cell, at 50 mg/L NH<sub>4</sub>Cl, compared to the wild-type, therefore, the fragility of the mutant strain could impact on overall industrial productivity.</p>
Cracks in the mirror hypothesis: high specularity does not reduce detection or predation risk
<p>Some animals, including certain fish, beetles, spiders and Lepidoptera chrysalises, have such shiny or glossy surfaces that they appear almost mirror-like. A compelling but unsubstantiated hypothesis is that a highly specular or mirror-like appearance enhances survival by reflecting the surrounding environment and reducing detectability.</p> <p>We tested this hypothesis by asking human participants to wear a mobile eye-tracking device and locate highly realistic mirror-green and diffuse-green replica beetles against a variety of backgrounds in a natural forest environment. We also tested whether a mirror-like appearance enhances survival to wild predators by monitoring survival of mirror-green and diffuse-green replica beetles in a forested habitat and an open habitat.</p> <p>Human participants showed no difference in the detection probability or detection latency of mirror versus diffuse replica beetles, indicating that mirror-like appearance does not impair prey capture. The field predation experiment found no difference in survival between the mirror and diffuse replica beetles in forested environments. Similarly, there was no difference in survival when beetles were deployed in open habitat where there is no background to reflect, indicating that predators detect and do not actively avoid mirror-like beetles.</p> <p>Our results suggest that a mirror-like appearance does not reduce attack by predators. Instead, highly specular, mirror-like surfaces may have evolved for an alternate visual function or as a secondary consequence of selection for a non-visual function, such as thermoregulation.</p>
High-Resolution Vector-borne Disease Infection Risk Mapping with Area-to-Point Kriging and Species Distribution Modeling - Datasets
<p>Datasets and notebooks used in the publication High-Resolution Vector-borne Disease Infection Risk Mapping with Area-to-Point Kriging and Species Distribution Modeling</p>
Fig. 2 a in Circulating dengue virus serotypes and vertical transmission in AEdES larvae during outbreak and inter-outbreak seasons in a high dengue risk area of Sri Lanka
Fig. 2 a Distribution of dengue cases in the Kegalle District and Mawanella MOH area, Sri Lanka from December 2015 to March 2017. b Distribution of DENV serotypes in patients and distribution of Aedes mosquito larvae in and around the residences of dengue patients in Mawanella from December 2015 to March 2017. Abbreviations: DENV1, -2, -3, -4, DENV serotypes 1, 2, 3, 4
Model fields supporting the publication "Integrated Assessment of the Risks to Ocean Acidification in the Northern High Latitudes: Regional Comparison of Exposure, Sensitivity and Adaptive Capacity of Pelagic Calcifiers"
<p>These are the model outputs supporting the described manuscript. They include monthly averaged output of aragonite saturation state for each year during the 10-year hindcast. Also included is the particle tracking output, for both the Bering Sea and the Gulf of Alaska, as described in the manuscript.</p>
Data of "Impact of temporal correlations on high risk outbreaks of independent and cooperative SIR dynamics"
<p>The data reported in the paper: Sajjadi et al. (2021) Impact of temporal correlations on high risk outbreaks of independent and cooperative SIR dynamics. PLoS ONE 16(7): e0253563. https://doi.org/10.1371/journal.pone.0253563<br> Each directory contains the data illustrated in one figure. The data structure and properties are described in .info files within each directory.</p> <p><br> All the simulations, analyses and illustrations have been conducted via the Epyc package (written in C++ and Python), developed by Sina Sajjadi. Epyc is available under GPLv3, at https://github.com/Sepante/Epyc.</p>
Health Risks Forecast of Regional Air Pollution on Allergic Rhinitis: High-Resolution City-Scale Simulations in Changchun, China
<p>Here presented the forcasted results of Potential Morbidity Risk Index (PMRI) for the personal patients with allerigc rhinitis and the public health administrations, and these results are supplied to the published paper of "Health Risks Forecast of Regional Air Pollution on Allergic Rhinitis: High-Resolution City-Scale Simulations in Changchun, China".</p>
Data from Zeppenfeld et al. 2023: "Winter storm risk assessment in forests with high resolution gust speed data", Eur. J. For. Res.
<p>Single-tree damage data from winter storm event "Lothar" 1999 in Baden-Wurttemberg, Germany. The data set includes the response (damage or no damage) and covariates for model parametrisation as described in Zeppenfeld et al. (2023).</p>
Telemedicine in High-Risk Cardiovascular Patients Post-ACS
ClinicalTrials.gov study NCT05015634. IPD Sharing: NO. Countries: 1. Publications: 9.
Dabrafenib With Trametinib in the Adjuvant Treatment of High-risk BRAF V600 Mutation-positive Melanoma (COMBI-AD).
ClinicalTrials.gov study NCT01682083. IPD Sharing: YES. Countries: 25. Publications: 9.
Trial to Assess the Effect of Long Term Dosing of Inclisiran in Subjects With High CV Risk and Elevated LDL-C
ClinicalTrials.gov study NCT03814187. IPD Sharing: YES. Countries: 13. Publications: 2.
Triple Combination Therapy in High Risk Crohn's Disease (CD)
ClinicalTrials.gov study NCT02764762. IPD Sharing: YES. Countries: 2. Publications: 1.
Study of Efficacy and Safety of MBG453 in Combination With Azacitidine in Subjects With Intermediate, High or Very High Risk Myelodysplastic Syndrome (MDS) as Per IPSS-R, or Chronic Myelomonocytic Leu
ClinicalTrials.gov study NCT04266301. IPD Sharing: YES. Countries: 36. Publications: 1.
Study of Efficacy and Safety of Inclisiran in Japanese Participants With High Cardiovascular Risk and Elevated LDL-C
ClinicalTrials.gov study NCT04666298. IPD Sharing: YES. Countries: 1. Publications: 1.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.