179566 research outputs found
Sort by
Adapting a global conservation perspectives assessment for local relevance: Evaluating perspectives on protected area management across diverse groups in South Africa
Get PDFConservation governance has traditionally focussed on biological and scientific expertise while often avoiding value-based conflicts. However, ignoring the value dimension overlooks conservation's dual nature. Understanding the values that guide the actions and narratives of conservationists and those interested in or affected by conservation is crucial for fostering better understanding, relationships and resolving conflicts. Few studies have directly compared the conservation values of those employed in conservation and other groups. This gap makes it difficult to identify and address value differences between them, potentially leading to distrust and conflict.We adapted an existing instrument used to assess global conservation perspectives to evaluate local challenges and trade-offs faced by protected areas (PAs) in South Africa. Our Conservation Perspectives Assessment Tool (CPAT) consists of 55 Likert-scale statements, which enabled us to identify key conservation dimensions and assess perspective differences between South African conservation agency staff, national park visitors and other conservation professionals.Descriptive statistics, followed by exploratory and confirmatory factor analyses, unveiled four major conservation dimensions: people and community-centric conservation, capitalism-driven conservation, ecocentric conservation and compassionate conservation. These dimensions underlie many decisions and trade-offs PA managers make routinely.Group membership (professional conservationist/visitor), gender, age and location (national/international) are intricately linked to these dimensions. Groups explored here generally scored high on ecocentric conservation, fostering common ground for dialogue among these groups, yet divergence emerged between groups on specific aspects (e.g. compassionate conservation; community-centric conservation), highlighting differences both within and between groups.Synthesis and application: Our approach can be used to develop further locally contextualised CPATs for conservation agencies to reflect on their values, identify areas of internal agreement or disagreement, address internal conflicts and assess alignment with certain interest groups. It emphasises that conservation is not solely about ecological science but is heavily influenced by the varied values, perspectives and characteristics of interest groups. Considering these insights, we recommend that conservation agencies must understand, respect and navigate these differences; adapt to societal and ideological shifts when needed; and be transparent about their values in decision-making. In addition to biological and scientific knowledge, there is a need to incorporate adaptive, value-based approaches that acknowledge the diversity of perspectives within and beyond the conservation community
Fluctuating selection among years in a wild insect (Gryllus campestris)
No full textTemporal or spatial variation in selection has the potential to explain long standing evolutionary problems such as evolutionary stasis and the maintenance of genetic variation. Long-term field studies of plants and wild vertebrates have provided some insights, but multigenerational measures of selection in wild invertebrates remain scarce. Short-lived ectothermic animals are likely to experience more pronounced environmental variation across generations than longer-lived and endothermic species. As a result, variation in selection may be particularly significant in these groups. Over ten years, we have monitored an individually tagged population of wild crickets (Gryllus campestris) using a network of up to 133 day-night video cameras. The over a million hours of video that we watched allowed us to capture detailed information about naturally and sexually selected traits and life-history parameters. Over ten discrete generations, population size ranged from 51 to 546 adults. There were also substantial differences among years in the average values of traits including adult emergence date, body size, lifespan, and several behavioral traits. We combined measurements of these traits with individual fitness, measured as the number of adult offspring inferred from genetic-marker-based parentage assignments. This revealed substantial variation in selection gradients across years in several traits, with evidence that in one trait, adult emergence date, selection switched from positive to negative among years. Our findings suggest that fluctuations in selection gradients are common but complete reversals in the direction of selection may not be very frequent.Temporal or spatial variation in selection has the potential to explain long standing evolutionary problems such as evolutionary stasis and the maintenance of genetic variation. Long-term field studies of plants and wild vertebrates have provided some insights, but multigenerational measures of selection in wild invertebrates remain scarce. Short-lived ectothermic animals are likely to experience more pronounced environmental variation across generations than longer-lived and endothermic species. As a result, variation in selection may be particularly significant in these groups. Over ten years, we have monitored an individually tagged population of wild crickets (Gryllus campestris) using a network of up to 133 day-night video cameras. The over a million hours of video that we watched allowed us to capture detailed information about naturally and sexually selected traits and life-history parameters. Over ten discrete generations, population size ranged from 51 to 546 adults. There were also substantial differences among years in the average values of traits including adult emergence date, body size, lifespan, and several behavioral traits. We combined measurements of these traits with individual fitness, measured as the number of adult offspring inferred from genetic-marker-based parentage assignments. This revealed substantial variation in selection gradients across years in several traits, with evidence that in one trait, adult emergence date, selection switched from positive to negative among years. Our findings suggest that fluctuations in selection gradients are common but complete reversals in the direction of selection may not be very frequent.Rodríguez-Muñoz, Rolando; Hopwood, Paul; Slate, Jon et al. (2025). Fluctuating selection among years in a wild insect (Gryllus campestris) [Dataset]. Dryad. https://doi.org/10.5061/dryad.rxwdbrvm
CryoEM structure of rice nucleosome containing a H4 variant chimera
No full textPDB ID: 8Q16 DOI Citation: Sotelo-Parrilla, P., Hari Sundar G, V., Raju, S., Jha, S., Gireesh, A., Gut, F., Vinothkumar, K.R., Berger, F., Shivaprasad, P.V., Jeyaprakash, A.A., (2025) CryoEM structure of rice nucleosome containing a H4 variant chimera doi: https://doi.org/10.2210/pdb8q16/pd
Assessment paper on high impact climate events, tipping points and irreversible regional impacts
No full textThis presentation was given by Gabi Hegerl at the TipESM and ClimTip Joint Conference.Hegerl, G. (2025, April 24). Assessment paper on high impact climate events, tipping points and irreversible regional impacts. Zenodo. https://doi.org/10.5281/zenodo.1527405
Standard Operating Procedures (SOPs) for Senescence and Mitochondrial Function Assays in Cellular Models of Parkinson's Disease and Ageing
No full textThis collection comprises Standard Operating Procedures (SOPs) developed by the PD-AGE network for assessing key cellular processes relevant to Parkinson's disease (PD) and ageing. These SOPs cover assays for: Senescence and Inflammaging: β-Galactosidase activity, γ-H2AX foci detection, Senescence-Associated Secretory Phenotype (SASP) factor measurement (e.g., IL-6, IL-8), P16 and P21 protein detection, telomere length measurement, HMGB1 detection, and Lamin B1 detection. Mitochondrial Function: Mitochondrial DNA (mtDNA) damage detection, mitochondrial morphology analysis, and mitochondrial respiration measurement. These SOPs are designed to promote methodological rigour, consistency, and reproducibility across research groups investigating the interplay between ageing and PD using cellular models. Subtitle (English) Mitochondrial Respiration Measuring in Adherent Patient-Derived Cells Subtitle (English) Mitochondrial DNA (mtDNA) Mutation Detection - quantitative Polymerase chain Reaction (qPCR) Subtitle (English) Mitochondrial Morphology Analysis via High-Content Imaging Subtitle (English) Assessment of cell cycle-arresting proteins P21 and P16 by western blot Subtitle (English) Detection of Senescence-Associated β Galactosidase in cultured cells Subtitle (English) Immunocytochemical detection of γH2AX DNA damage foci in fixed cells Subtitle (English) Detection of the Senescence-Associated Secretory Phenotype (SASP) Subtitle (English) Senescent markers immunocytochemistry (HMGB1, Lamin A, Lamin B1, p16INK4a) in fixed cells Subtitle (English) Southern blot-based Telomere Restriction Fragment AssayBury, A. G., Olejnik, A., Tocco, C., Saurat, N., Hockemeyer, D., Schwamborn, J. C., Studer, L., Giorgio Mastroberardino, P., Bolognin, S., Kunath, T., Korolchuk, V. I., Drouin-Ouellet, J., & Mortiboys, H. (2025). Standard Operating Procedures (SOPs) for Senescence and Mitochondrial Function Assays in Cellular Models of Parkinson's Disease and Ageing. Zenodo. https://doi.org/10.5281/zenodo.1505660
DNA methylation is a key determinant of response to targeted and immune checkpoint therapies in metastatic renal cell carcinoma
No full textAbstract The response to targeted therapies and immune checkpoint inhibitors for patients suffering from metastatic clear cell renal cell carcinoma (ccRCC) is heterogeneous and currently not predictable in clinic. We conducted a meta-analysis of 700 ccRCCs profiled by DNA methylation to compare the ability ofseveral published probe signatures to cluster patients into hyper- and hypomethylation subtypes. To gain further insights into the biological relevance of these subtypes, we characterized them using matched RNA sequencing profiles. We studied differences affecting biological pathways, transcriptional regulators, tumor microenvironment composition, and the expression levels of enzymes known to control cytosine DNA methylation. Then, to facilitate the clinical translation of these findings, we developed predictive models capable of inferring ccRCC methylation subtypes from specific gene expression markers. Finally, we evaluated the association between the predicted DNA methylation subtypes and patient responses to ccRCC therapies. We showed that the hyper-methylated tumors exhibited a worse prognosis, a higher fraction of cycling tumor cells and a lower activity of homeobox transcription factors. To translate the use of DNA methylation information into a clinical setting, we developed a simple model accurately predicting the ccRCC methylation subtypes (AUC-ROCs of 0.91) from two gene expression ratios (IGF2BP3/PCCA, TNNT1/TMEM88). In addition, these methylation subtypes were significantly associated with the therapeutic outcome of patients to anti-PD-1, mTOR inhibitor or tyrosine kinase inhibitor therapies. Overall, our framework for predicting the ccRCC DNA methylation subtypes from targeted gene expression data is easy to translate in clinic and contributes to better personalization of ccRCC therapies. Code repository This repository contains data and code in order to reproduce the entire data analysis from the article entitled "DNA methylation is a key determinant of response to targeted and immune checkpoint therapies in metastatic renal cell carcinoma" (bioRxiv 2024.11.05.622095; doi: https://doi.org/10.1101/2024.11.05.622095). CodeNotebook.zip This archive contains all the Jupyter notebooks needed to reproduce data analyses. SingularityImage.sif To seamlessly reproduce the entire workflow of Jupyter notebooks without dependency issues, you can use the Singularity image. To open a Jupyter Lab session and execute the notebooks from the CodeNotebook directory (uncompressed) mounted inside the Singularity image, please run this command: singularity exec --bind /pathTo/CodeNotebook/:/home/pathInside/mnt SingularityImage.sif jupyter lab --no-browser --NotebookApp.iopub_data_rate_limit=1.0e10 Please, note that due to dependencies between the notebook results, you should follow the numbering to run each notebook. So, run the "5.a.*", then the "5.b.*", and so on. For any issues and questions, please contact Florian Jeanneret and Christophe Battail.Jeanneret, F., Schoch, S., Ballester, P., Symeonides, S. N., Laird, A., Axelson, H., PFLIEGER, D., & Battail, C. (2025). DNA methylation is a key determinant of response to targeted and immune checkpoint therapies in metastatic renal cell carcinoma. Zenodo. https://doi.org/10.5281/zenodo.1505257
Analytic Expressions of Master Integrals for Higgs Production Through Gluon Fusion at NLO in the EW Coupling
No full textWe consider mixed strong-electroweak corrections to Higgs production via gluon fusion, in which the Higgs boson couples to the top quark. Using the method of differential equations, we compute all of the master integrals that contribute to this process at two loops through weight six, keeping full analytic dependence on the top quark, Higgs, W, and Z boson masses. We present the results for these master integrals in terms of iterated integrals whose kernels depend on elliptic curves.Marzucca, R., McLeod, A., & Nega, C. (2025). Analytic Expressions of Master Integrals for Higgs Production Through Gluon Fusion at NLO in the EW Coupling [Data set]. Zenodo. https://doi.org/10.5281/zenodo.1484361
Data Repository - A single-molecule fluorescence assay for ion transport across lipid bilayers
No full textData repository associated to publication. N.B. Data files are reported in sets of 10 files with the same root name and the suffix numbered 2-10.Edwards, D. (2025). Data Repository - A single-molecule fluorescence assay for ion transport across lipid bilayers [Data set]. Zenodo. https://doi.org/10.5281/zenodo.1509653
pablosanchezmart/Sanchez-Martinez-etal-2025-Amazon-rainforest-ecohydrological-adjustment: Sanchez-Martinez et al. 2025
No full textCode used to analize data in the paper titled "Amazon rainforest collapse under experimental drought averted by ecohydrological adjustment", published in Nature in Ecology and Evolution in 2025Pablo Sanchez-Martinez. (2025). pablosanchezmart/Sanchez-Martinez-etal-2025-Amazon-rainforest-ecohydrological-adjustment: Sanchez-Martinez et al. 2025 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.1509126
FIGURE 42 in An integrative taxonomic approach to describe Andricus pseudomultiplicatus sp. nov. and establish new synonymies in Andricus Hartig, 1840 (Hymenoptera: Cynipidae: Cynipini)
No full textFIGURE 42. Maximum likelihood phylogeny of selected Western Palaearctic Andricus species, based on a concatenation of cytochrome b and long-wavelength opsin DNA sequences. Numbers above nodes provide ultra-fast bootstrap support values; terminal names correspond to individuals whose details are in Table 1. Shaded boxes indicate the limits of focal taxa discussed in the main text: A. truncicolus (sexual and asexual individuals indicated), A. conificus (sexual and asexual individuals indicated) and A. pseudomultiplicatus sp. nov..Sottile, S., Nicholls, J. A., Stone, G. N., & Cerasa, G. (2025). FIGURE 42 in An integrative taxonomic approach to describe Andricus pseudomultiplicatus sp. nov. and establish new synonymies in Andricus Hartig, 1840 (Hymenoptera: Cynipidae: Cynipini). In Zootaxa (Vol. 5609, Number 4, pp. 451–478). Zenodo. https://doi.org/10.5281/zenodo.1521536
Access Repository Dashboard
Do you manage Edinburgh Research Explorer? Access insider analytics, issue reports and manage access to outputs from your repository in the CORE Repository Dashboard!