Food system resilience measurement: principles, framework and caveats

There is growing recognition that a better understanding of how food systems respond to crises is critical to build and protect the food security of local populations. But rigorous and reliable methods to measure food system resilience are still missing. In this paper, we build on the current literature to develop an analytical framework aimed at assessing the resilience of food systems at local level. The novel element of the analysis lies in the levels at which resilience is considered. Combining the individual actor level with the notion of 'emergent properties' of food systems, we argue that the overall resilience of food system results from processes that take place – and need to be measured – at both individual and system levels. The framework is structured around three components: (i) the mapping of the actors and the local food system; (ii) the assessment of the resilience of these actors and that of the food system, and (iii) the outcomes of this resilience, assessed in term of local population’s food security. For each of those components, indicators are proposed and the ways to collect them are discussed. The paper then presents the types of analyses that would be necessary to complete to gain a better understanding of the situation regarding the resilience of the local food system under consideration, including the analysis of “positive deviance” among food system actors. The paper concludes with a series of reflections about the caveats and challenges that one may face when attempting to assess food system resilience

Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease

Inherited retinal disease is a common cause of visual impairment and represents a highly heterogeneous group of conditions. Here, we present findings from a cohort of 722 individuals with inherited retinal disease, who have had whole-genome sequencing (n = 605), whole-exome sequencing (n = 72), or both (n = 45) performed, as part of the NIHR-BioResource Rare Diseases research study. We identified pathogenic variants (single-nucleotide variants, indels, or structural variants) for 404/722 (56%) individuals. Whole-genome sequencing gives unprecedented power to detect three categories of pathogenic variants in particular: structural variants, variants in GC-rich regions, which have significantly improved coverage compared to whole-exome sequencing, and variants in non-coding regulatory regions. In addition to previously reported pathogenic regulatory variants, we have identified a previously unreported pathogenic intronic variant in $\textit{CHM}$ in two males with choroideremia. We have also identified 19 genes not previously known to be associated with inherited retinal disease, which harbor biallelic predicted protein-truncating variants in unsolved cases. Whole-genome sequencing is an increasingly important comprehensive method with which to investigate the genetic causes of inherited retinal disease.This work was supported by The National Institute for Health Research England (NIHR) for the NIHR BioResource – Rare Diseases project (grant number RG65966). The Moorfields Eye Hospital cohort of patients and clinical and imaging data were ascertained and collected with the support of grants from the National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital, National Health Service Foundation Trust, and UCL Institute of Ophthalmology, Moorfields Eye Hospital Special Trustees, Moorfields Eye Charity, the Foundation Fighting Blindness (USA), and Retinitis Pigmentosa Fighting Blindness. M.M. is a recipient of an FFB Career Development Award. E.M. is supported by UCLH/UCL NIHR Biomedical Research Centre. F.L.R. and D.G. are supported by Cambridge NIHR Biomedical Research Centre

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements

Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder affecting 0.5–2% of pregnancies. The majority of cases present in the third trimester with pruritus, elevated serum bile acids and abnormal serum liver tests. ICP is associated with an increased risk of adverse outcomes, including spontaneous preterm birth and stillbirth. Whilst rare mutations affecting hepatobiliary transporters contribute to the aetiology of ICP, the role of common genetic variation in ICP has not been systematically characterised to date. Here, we perform genome-wide association studies (GWAS) and meta-analyses for ICP across three studies including 1138 cases and 153,642 controls. Eleven loci achieve genome-wide significance and have been further investigated and fine-mapped using functional genomics approaches. Our results pinpoint common sequence variation in liver-enriched genes and liver-specific cis-regulatory elements as contributing mechanisms to ICP susceptibility

Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia.

The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Cav2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca2+ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Cav2.2 in normal human neurodevelopment.MAK is funded by an NIHR Research Professorship and receives funding from the Wellcome Trust, Great Ormond Street Children's Hospital Charity, and Rosetrees Trust. E.M. received funding from the Rosetrees Trust (CD-A53) and Great Ormond Street Hospital Children's Charity. K.G. received funding from Temple Street Foundation. A.M. is funded by Great Ormond Street Hospital, the National Institute for Health Research (NIHR), and Biomedical Research Centre. F.L.R. and D.G. are funded by Cambridge Biomedical Research Centre. K.C. and A.S.J. are funded by NIHR Bioresource for Rare Diseases. The DDD Study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between the Wellcome Trust and the Department of Health, and the Wellcome Trust Sanger Institute (grant number WT098051). We acknowledge support from the UK Department of Health via the NIHR comprehensive Biomedical Research Centre award to Guy's and St. Thomas' National Health Service (NHS) Foundation Trust in partnership with King's College London. This research was also supported by the NIHR Great Ormond Street Hospital Biomedical Research Centre. J.H.C. is in receipt of an NIHR Senior Investigator Award. The research team acknowledges the support of the NIHR through the Comprehensive Clinical Research Network. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, Department of Health, or Wellcome Trust. E.R.M. acknowledges support from NIHR Cambridge Biomedical Research Centre, an NIHR Senior Investigator Award, and the University of Cambridge has received salary support in respect of E.R.M. from the NHS in the East of England through the Clinical Academic Reserve. I.E.S. is supported by the National Health and Medical Research Council of Australia (Program Grant and Practitioner Fellowship)

Resilience in Action: Adaptive Governance for Subaks, Rice Terraces, and Water Temples in Bali, Indonesia

Although there is a growing literature on resilience and collaborative approaches to ecosystem management, there are relatively few empirical case studies on the process of adaptive governance. Moreover, previous research offers limited insights into the conditions that facilitate new ecosystem management trajectories. By analyzing the emergence of an adaptive co-management initiative in Bali, the UNESCO World Heritage Cultural Landscape of Bali Province, this dissertation seeks to contribute to recent research on institutional governance approaches to enhance ecosystem management and social well-being. To that end, it addresses two questions. First, it identifies and explores three primary characteristics that fostered a new multi-level adaptive governance approach to cultural landscape management in Bali: the widespread perception of environmental crisis on the island that triggered collective action and the political will for a new form of ecosystem management; the emergence of a shared ideology--articulated in the Balinese Hindu philosophy of tri hita karana, or "the three causes of prosperity"--that unified diverse actors and actor networks and established a common platform for ecological resource management; and context-specific governance strategies that built on existing institutions and local-level initiatives. The second question centers on an analysis of the emergence of the management plan for the World Heritage site in Bali. The management plan was developed to support the Balinese subak in its struggle to adapt to current and future pressures that threaten to undermine the island's unique social-ecological system. For centuries, the subak have maintained Bali's terraced rice paddy landscape as a network of semi-autonomous irrigation associations, mediated through water temples. The adaptive co-management plan draws on principles of adaptive governance to connect subaks with other actors and actor groups across multiple institutional levels and regional jurisdictions. Research findings support the likelihood that the World Heritage initiative can promote transformative change in cultural landscape management in Bali. As the initiative develops, it will provide a fertile site for future research on adaptive governance, to better understand interdependent social-ecological relationships and the evolution of adaptive co-management approaches

Characterising a Custom-Built Radio Frequency PECVD Reactor to Vary the Mechanical Properties of TMDSO Films

Plasma-polymerised tetramethyldisiloxane (TMDSO) films are frequently applied as coatings for their abrasion resistance and barrier properties. By manipulating the deposition parameters, the chemical structure and thus mechanical properties of the films can also be controlled. These mechanical properties make them attractive as energy adsorbing layers for a range of applications, including carbon fibre composites. In this study, a new radio frequency (RF) plasma-enhanced chemical vapour deposition (PECVD) plasma reactor was designed with the capability to coat fibres with an energy adsorbing film. A key characterisation step for the system was establishing how the properties of the TMDSO films could be modified and compared with those deposited using a well-characterized microwave (MW) PECVD reactor. Film thickness and chemistry were determined with ellipsometry and X-ray photoelectron spectroscopy, respectively. The mechanical properties were investigated by nanoindentation and atomic force microscopy with peak-force quantitative nanomechanical mapping. The RF PECVD films had a greater range of Young’s modulus and hardness values than the MW PECVD films, with values as high as 56.4 GPa and 7.5 GPa, respectively. These results demonstrated the varied properties of TMDSO films that could in turn be deposited onto carbon fibres using a custom-built RF PECVD reactor

Niche construction on Bali: the gods of the countryside

Human niche construction encompasses both purely biological phenomena, such as the evolution of lactose tolerance, and dual inheritance theory, which investigates the transmission of cultural information. But does niche construction help to explain phenomena in which conscious intention also plays a role? The creation of the engineered landscape of Balinese rice terraces offers a test case. Population genetic analysis and archaeological evidence are used to investigate whether this phenomenon emerged historically from trial and error by generations of farmers, or alternatively was designed by Bali's rulers. In light of strong support for the former hypothesis, two models are developed to explore the emergence of functional structure at both local and global scales. As time goes forward and selected patterns of irrigation schedules are implemented, local variation in rice harvests influences future decisions by the farmers, creating a coupled human–natural system governed by feedback from the environment. This mathematical analysis received a measure of empirical support when government agricultural policies severed the local feedback channels, resulting in the almost instantaneous collapse of rice harvests. The historical process of niche construction may also have included an evolution of religious consciousness, reflected in the beliefs and practices of the water temple cult