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Validation of two swabbing methods to sample DNA for genotyping Atlantic bluefin tuna (Thunnus thynnus)
Get PDFIn fisheries, genetic based assignment of individuals to their population of origin can benefit efforts aimed at monitoring and managing stocks. Assignment combined with knowledge of the migration history of individuals can provide powerful insights into mechanisms of genetic mixing, for which refined sampling methods are required to minimise any impacts. In this study we tested two minimally invasive swabbing techniques for sampling DNA when attaching electronic satellite tags to Atlantic bluefin tuna (Thunnus thynnus) for migration studies. First, DNA was sampled by skin swabbing (hereafter skin swabs) individuals from which there were corresponding fin clip samples. Second, swabs were taken from the applicator poles used to attach electronic tags (hereafter pole swabs). Quantification of DNA from the different sources revealed decreasing yields moving from fin clips, to skin swabs, to pole swabs. The utility of the DNA obtained by both swabbing methods for individual genotyping was then assessed by sequencing of the mtDNA control region and genotyping of six microsatellite loci. In all cases successful genotyping was achieved. For mtDNA an 868 bp fragment was successfully amplified in all samples with 775 bp aligned across individuals revealing 26 haplotypes (overall haplotype diversity = 0.987). All six microsatellites were successfully amplified including a largest allele size of 291 bp. mtDNA and microsatellite genotypes for the skin swabs matched with the corresponding fin clip samples. Although no tissue replicates were available for the pole swab samples the genotypes obtained were unambiguous, consistent across repeated PCRs, and reported no evidence of PCR issues such as large allele drop out. Overall, the genetic data suggested high variability among individuals sampled, comparable to levels of genetic diversity seen within the species' Atlantic range. The study demonstrates that non-invasive sampling can be used to obtain DNA for population assignment studies and that valuable material can be sampled from tagging equipment.</p
Workshop report:One Health challenges and knowledge gaps in the control of intracellular infections with a focus on tuberculosis and leishmaniasis
Get PDFThe VALIDATE Network brings together scientists addressing vaccine development for neglected infectious diseases caused by intracellular pathogens. In September 2023, the first workshop on One Health approaches to research and capacity building was held in Paarl, South Africa, with a focus on tuberculosis and leishmaniasis. Thirty-two scientists from 15 countries presented and discussed broad topics pertinent to zoonotic diseases, cross-species disease transmission, disease mitigation strategies, inequitable access to medicines and health technologies, and health system challenges in One Health. In this report, we summarize the gaps, challenges, and opportunities identified during the 2023 VALIDATE One Health workshop. We anticipate that the experiences and dialogues will be informative for animal, human, and environmental health investigators to guide the development of research projects and vaccine development with a One Health vision.</p
Towards Breast Cancer Diagnosis Using Multiple Mammography Views
Get PDFThis study introduces a novel computer aided diagnosis system to diagnose breast cancer using two mammography views as input i.e. MLO and CC. The pipeline consists of a convolutional autoencoder that is trained to extract features from different mammograms’ views, and one-dimensional convolutional neural network to classify the input embeddings into two classes i.e. benign or malignant. We compare the one-dimensional convolutional neural network classification results with a support vector machine trained on the same latent embeddings. We conclude that the combination of autoencoders and one-dimensional convolutional neural networks yields the best classification accuracy on the test set of the INbreast dataset
Effect of potent inhibitors of phenylalanine ammonia-lyase and PVP on in vitro morphogenesis of Fagopyrum tataricum
Get PDFBackground: Fagopyrum tataricum (Tartary buckwheat) is known for its high phenolic content, particularly rutin. High concentrations of these compounds secreted in the tissue culture medium can lead to its darkening and the eventual death of explants in in vitro cultures. This study aims to enhance the morphogenesis of F. tataricum callus cultures by utilising phenylalanine ammonia-lyase (PAL) inhibitors and polyvinylpyrrolidone (PVP) to mitigate oxidative browning and improve tissue viability.Results:We analysed the response of protoplasts isolated from morphogenic callus to media supplemented with varying concentrations of PAL inhibitors (AIP, AOPP, OBHA) and PVP. The flow cytometry results revealed that 10 µM AIP and 1% PVP yielded exclusively diploid plants, whereas higher concentrations (100 µM AIP and 3% PVP) failed to regenerate plants. Moreover, AOPP and OBHA addition resulted in the regeneration of tetraploid plants. Further analysis of proembryogenic cell complexes (PECCs) isolated from Tartary buckwheat morphogenic calli responses to AIP and PVP indicated that 100 µM AIP was most effective for plant regeneration. Metabolomic analysis showed that AIP treatments reduced phenolic compounds, notably rutin, and increased the GSH/GSSG ratio, indicating reduced oxidative stress. Gene expression analysis highlighted elevated expression of somatic embryogenesis-related genes (LEC2, BBM) and WUSCHEL in AIP-treated callus.Conclusions: This study demonstrates that AIP enhances the regeneration potential of F. tataricum callus cultures, offering valuable insights for optimising tissue culture techniques for industrial crops. Additionally, we have detailed the metabolomic changes in calli treated with PVP and AIP, highlighting their impact on metabolism.<p/
Genotypic Differences in Soil Carbon Stocks Under Miscanthus:Implications for Carbon Sequestration and Plant Breeding
Get PDFBiomass crops provide renewable material for bioproducts and energy generation with the potential for negative greenhouse gas emissions through bioenergy with carbon capture and storage. Miscanthus spp. is a perennial crop with rapid biomass production and low inputs. However, uncertainty exists over impacts on soil organic carbon (SOC) stocks in conversion from agricultural grasslands, and the interaction between divergent Miscanthus species and SOC sequestration. As a C4 plant (in contrast to C3 temperate grassland species) the fate of Miscanthus derived carbon can be traced in the soil through its isotopic signature. Taking advantage of this, we use soil cores (pre and post conversion) to investigate species groupings and genotypic effect on SOC stocks in a rare long-term field trial located in the UK. Results show that 10 years after conversion from a managed grass pasture to Miscanthus, expected SOC losses due to cultivation were recovered (Miscanthus spp. mean of 82 Mg C ha−1 compared to pre-conversion stocks of 79 Mg C ha−1, 0–30 cm soil depth) but significant variation in SOC between genotypes was observed (a difference of 32 Mg C ha−1 between the highest and lowest). Of the plant traits investigated, a large rhizome mass was correlated with C4 carbon, and leaf litter was associated with increased SOC. As well as providing empirical data for the impact on SOC in a likely land use conversion, our findings show a genotypic influence on SOC sequestration processes, revealing the potential of Miscanthus selection to maximise climate mitigation benefits. With only 2 of the 13 genotypes identified as sequestering lower SOC compared to the others, there remains a wide genotypic base to select from. Yield is a primary breeding target (commercially and for increased CO2 uptake); we demonstrate that high yield need not be at the expense of low soil carbon.</p
A ‘Hawk in Holy Orders’:the fourteenth-century Marcher cleric who instigated a rebellion
No full textCross-cultural evidence that intergroup conflict heightens preferences for dominant leaders:A 25-country study
Get PDFAcross societies and across history, seemingly dominant, authoritarian leaders have emerged frequently, often rising to power based on widespread popular support. One prominent theory holds that evolved psychological mechanisms of followership regulate citizens' leadership preferences such that dominant individuals are intuitively attributed leadership qualities when followers face intergroup conflicts like war. A key hypothesis based on this theory is that followers across the world should upregulate their preferences for dominant leaders the more they perceive the present situation as conflict-ridden. From this conflict hypothesis, we generate and test four concrete predictions using a novel dataset including 5008 participants residing in 25 countries from different world regions (consisting of a mix of convenience and approximately representative country-specific samples). Specifically, we combine experimental techniques, validated psychological scales, and macro-level indicators of intergroup conflict to gauge people's preferences for dominant leadership. Across four independent tests, results broadly support the notion that the presence of intergroup conflict increases follower preferences for dominant leaders. Thus, our results provide robust cross-cultural support for the existence of an adaptive, tribal followership psychology, a finding that has various implications for understanding contemporary politics and international relations.</p
Enhancing Dongba Pictograph Recognition Using Convolutional Neural Networks and Data Augmentation Techniques
Get PDFThe recognition of Dongba pictographs presents significant challenges due to the pitfalls in traditional feature extraction methods, classification algorithms’ high complexity, and generalization ability. This study proposes a convolutional neural network (CNN)-based image classification method to enhance the accuracy and efficiency of Dongba pictograph recognition. The research begins with collecting and manually categorizing Dongba pictograph images, followed by these preprocessing steps to improve image quality: normalization, grayscale conversion, filtering, denoising, and binarization. The dataset, comprising 70,000 image samples, is categorized into 18 classes based on shape characteristics and manual annotations. A CNN model is then trained using a dataset that is split into training (with 70% of all the samples), validation (20%), and test (10%) sets. In particular, data augmentation techniques, including rotation, affine transformation, scaling, and translation, are applied to enhance classification accuracy. Experimental results demonstrate that the proposed model achieves a classification accuracy of 99.43% and consistently outperforms other conventional methods, with its performance peaking at 99.84% under optimized training conditions—specifically, with 75 training epochs and a batch size of 512. This study provides a robust and efficient solution for automatically classifying Dongba pictographs, contributing to their digital preservation and scholarly research. By leveraging deep learning techniques, the proposed approach facilitates the rapid and precise identification of Dongba hieroglyphs, supporting the ongoing efforts in cultural heritage preservation and the broader application of artificial intelligence in linguistic studies.</p
Opportunities and challenges for monitoring terrestrial biodiversity in the robotics age
Get PDFWith biodiversity loss escalating globally, a step change is needed in our capacity to accurately monitor species populations across ecosystems. Robotic and autonomous systems (RAS) offer technological solutions that may substantially advance terrestrial biodiversity monitoring, but this potential is yet to be considered systematically. We used a modified Delphi technique to synthesize knowledge from 98 biodiversity experts and 31 RAS experts, who identified the major methodological barriers that currently hinder monitoring, and explored the opportunities and challenges that RAS offer in overcoming these barriers. Biodiversity experts identified four barrier categories: site access, species and individual identification, data handling and storage, and power and network availability. Robotics experts highlighted technologies that could overcome these barriers and identified the developments needed to facilitate RAS-based autonomous biodiversity monitoring. Some existing RAS could be optimized relatively easily to survey species but would require development to be suitable for monitoring of more ‘difficult’ taxa and robust enough to work under uncontrolled conditions within ecosystems. Other nascent technologies (for instance, new sensors and biodegradable robots) need accelerated research. Overall, it was felt that RAS could lead to major progress in monitoring of terrestrial biodiversity by supplementing rather than supplanting existing methods. Transdisciplinarity needs to be fostered between biodiversity and RAS experts so that future ideas and technologies can be codeveloped effectively.</p
The enigmatic ‘Newall boulder’ excavated at Stonehenge in 1924:New data and correcting the record
Get PDFSome authors have questioned whether the bluestone megaliths present at the Stonehenge Neolithic stone circle were transported from their source area in north Pembrokeshire, over 200 km to the west, by ice, rather than humans. There is scant evidence for either hypothesis and much debate on the matter since the 1990s has involved the so-called ‘Newall boulder’, a stone collected in 1924 by Lt-Col Hawley. Initial studies considered the boulder to be a glacial erratic and hence supported the ice transport hypothesis. More recent work discounted this interpretation and proposed that the boulder was a piece of rhyolite debitage, itself derived from a broken-up monolith, most likely Stone 32d, originally sourced from Craig Rhos-y-Felin, in north Pembrokeshire although this has been challenged in a recent study.This paper aims to clarify the record regarding previous studies on the Newall boulder and samples taken from it for analysis and to correct errors of fact introduced into the current literature. Petrographic, automated SEM-EDS analysis and portable XRF investigation (including new analyses) relating to the characteristics and composition of the Newall boulder are presented, supporting (a) the interpretation that its original source was Craig Rhos-y-Felin, in north Pembrokeshire and (b) that there is no evidence to support an interpretation that it is a glacial erratic. In addition, it is shown that the overall non-sarsen lithological assemblage at Stonehenge is restricted, supporting derivation by human activity from a limited number of sites, predominantly from west Wales, but also NE Scotland, and not derived from glacial erratics