Promoting dietary changes for achieving health and sustainability targets

Globally, about 21–37% of total greenhouse gas (GHG) emissions are attributable to food systems. Dietary-related non-communicable diseases have increased significantly from 1990–2019 at a global scale. To achieve carbon emissions targets, increase resilience, and improve health there is a need to increase the sustainability of agricultural practises and change dietary habits. By considering these challenges together and focusing on a closer connection between consumers and sustainable production, we can benefit from a positive interaction between them. Using the 2019 EAT Lancet Commission dietary guidelines, this study analysed interview data and food diaries collected from members of Community Supported Agriculture (CSA) schemes and the wider UK population. By comparing the environmental sustainability and nutritional quality of their respective diets, we found that CSA members consumed diets closer to the EAT Lancet recommendations than controls. We identified significant differences in daily intakes of meat; dairy; vegetables; legumes; and sugar, and the diets of CSA members emitted on average 28% less CO2 compared to controls. We propose that agricultural and wider social and economic policies that increase the accessibility of CSAs for a more diverse demographic could support achieving health, biodiversity, and zero-emission policy targets

Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates

The developers of the Ontology of Biomedical Investigations (OBI) primarily use Protégé for editing. However, adding many classes with similar patterns of logical definition is time consuming, error prone, and requires the editor to have some expertise in OWL. Therefore, the process is poorly suited for a large number of domain experts who have limited experience Protégé and ontology development. We have developed a procedure to ease this task and allow such domain experts to add terms to the ontology in a way that both effectively includes complex logical definitions yet requires minimal manual intervention by OBI developers. The procedure is based on editing a Quick Term Template in a spreadsheet format which is subsequently converted into an OWL file. This procedure promises to be a robust and scalable approach for ontology enrichment

Deep Learning Enables Accurate Automatic Sleep Staging Based on Ambulatory Forehead EEG

We have previously developed an ambulatory electrode set (AES) for the measurement of electroencephalography (EEG), electrooculography (EOG), and electromyography (EMG). The AES has been proven to be suitable for manual sleep staging and self-application in in-home polysomnography (PSG). To further facilitate the diagnostics of various sleep disorders, this study aimed to utilize a deep learning-based automated sleep staging approach for EEG signals acquired with the AES. The present neural network architecture comprises a combination of convolutional and recurrent neural networks previously shown to achieve excellent sleep scoring accuracy with a single standard EEG channel (F4-M1). In this study, the model was re-trained and tested with 135 EEG signals recorded with AES. The recordings were conducted for subjects suspected of sleep apnea or sleep bruxism. The performance of the deep learning model was evaluated with 10-fold cross-validation using manual scoring of the AES signals as a reference. The accuracy of the neural network sleep staging was 79.7% (kappa = 0.729) for five sleep stages (W, N1, N2, N3, and R), 84.1% (kappa = 0.773) for four sleep stages (W, light sleep, deep sleep, R), and 89.1% (kappa = 0.801) for three sleep stages (W, NREM, R). The utilized neural network was able to accurately determine sleep stages based on EEG channels measured with the AES. The accuracy is comparable to the inter-scorer agreement of standard EEG scorings between international sleep centers. The automatic AES-based sleep staging could potentially improve the availability of PSG studies by facilitating the arrangement of self-administrated in-home PSGs.Peer reviewe

Occurrence, function and evolutionary origins of ‘2A-like’ sequences in virus genomes

2A is an oligopeptide sequence mediating a ribosome ‘skipping’ effect, producing an apparent ‘cleavage’ of polyproteins. First identified and characterized in picornaviruses, ‘2A-like’ sequences are found in other mammalian viruses and a wide range of insect viruses. Databases were analysed using a motif conserved amongst 2A/2A-like sequences. The newly identified 2A-like sequences (30 aa) were inserted into a reporter polyprotein to determine their cleavage activity. Our analyses showed that these sequences fall into two categories. The majority mediated very high (complete) cleavage to separate proteins and a few sequences mediated cleavage with lower efficiency, generating appreciable levels of the uncleaved form. Phylogenetic analyses of 2A-like sequences and RNA-dependent RNA polymerases (RdRps) indicated multiple, independent, acquisitions of these sequences at different stages during virus evolution. Within a virus family, 2A sequences are (probably) homologous, but diverge due to other evolutionary pressures. Amongst different families, however, 2A/2A-like sequences appear to be homoplasic

Modeling biomedical experimental processes with OBI

BACKGROUND: Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange and information retrieval. RESULTS: The Ontology for Biomedical Investigations (OBI), developed as a global, cross-community effort, provides a resource that represents biomedical investigations in an explicit and integrative framework. Here we detail three real-world applications of OBI, provide detailed modeling information and explain how to use OBI. CONCLUSION: We demonstrate how OBI can be applied to different biomedical investigations to both facilitate interpretation of the experimental process and increase the computational processing and integration within the Semantic Web. The logical definitions of the entities involved allow computers to unambiguously understand and integrate different biological experimental processes and their relevant components. AVAILABILITY: OBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.ow

Characterisation of Immune and Neuroinflammatory Changes Associated with Chemotherapy-Induced Peripheral Neuropathy

Chemotherapy-induced peripheral neuropathy (CIPN) and associated neuropathic pain is a debilitating adverse effect of cancer treatment. Current understanding of the mechanisms underpinning CIPN is limited and there are no effective treatment strategies. In this study, we treated male C57BL/6J mice with 4 cycles of either Paclitaxel (PTX) or Oxaliplatin (OXA) over a week and tested pain hypersensitivity and changes in peripheral immune responses and neuroinflammation on days 7 and 13 post 1st injection. We found that both PTX and OXA caused significant mechanical allodynia. In the periphery, PTX and OXA significantly increased circulating CD4+ and CD8+ T-cell populations. OXA caused a significant increase in the percentage of interleukin-4+ lymphocytes in the spleen and significant down-regulation of regulatory T (T-reg) cells in the inguinal lymph nodes. However, conditional depletion of T-reg cells in OXA-treated transgenic DEREG mice had no additional effect on pain sensitivity. Furthermore, there was no leukocyte infiltration into the nervous system of OXA- or PTX-treated mice. In the peripheral nervous system, PTX induced expression of the neuronal injury marker activating transcription factor-3 in IB4+ and NF200+ sensory neurons as well as an increase in the chemokines CCL2 and CCL3 in the lumbar dorsal root ganglion. In the central nervous system, PTX induced significant astrocyte activation in the spinal cord dorsal horn, and both PTX and OXA caused reduction of P2ry12+ homeostatic microglia, with no measurable changes in IBA-1+ microglia/macrophages in the dorsal and ventral horns. We also found that PTX induced up-regulation of several inflammatory cytokines and chemokines (TNF-α, IFN-γ, CCL11, CCL4, CCL3, IL-12p70 and GM-CSF) in the spinal cord. Overall, these findings suggest that PTX and OXA cause distinct pathological changes in the periphery and nervous system, which may contribute to chemotherapy-induced neuropathic pain

Implications and impacts of aligning regional agriculture with a healthy diet

One of the most intractable challenges currently facing agricultural systems is the need to produce sufficient food for all to enjoy a healthy balanced diet while minimising impacts to the environment. Balancing these competing goals is especially intractable because most food systems are not locally bounded. This study aims to investigate the likely impacts on production, profit and the environment that result from aligning food systems to a healthy diet, as defined by EAT-Lancet. For this, we consider two distinct areas of the UK, one in East Anglia and the other in South Wales. These two regions reflect different ecosystems and therefore differing specialisations in UK agriculture. We used the Rothamsted Landscape Model (a detailed agroecosystems process-based model) to predict soil carbon dynamics, nutrient flows and crop production for the dominant crops grown in these regions, and the IPCC inventory models to estimate emissions from six livestock systems. Two scenarios were considered, one in which the study regions had to meet healthy diet requirements independently of each other and another in which they could do so collectively. To map their production to healthy diets, both study areas require increases in the production of plant proteins and reductions in the production of red meat. While changes in production can feed more people a healthy diet compared to the business-as-usual state, the overall calories produced reduces dramatically. Emissions and leaching decrease under the healthy diet scenarios and pesticide impacts remain largely unchanged. We show that local infrastructure and environment have a bearing on how “localised” food systems can be without running into substantial constraints. Whilst isolation of the farming system to a regional level, as explored here, is unlikely to be practical, we nevertheless demonstrate that aligning agricultural production towards healthier diets can generate food systems with many associated benefits in terms of agroecosystems' health and resilience to shocks in the food supply chain

Expressions 2001

https://openspace.dmacc.edu/expressions/1020/thumbnail.jp