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Can pruning improve agent-based models' calibration? An application to HPVsim
Get PDFAgent-Based Models (ABMs) have gained popularity over the COVID-19 epidemic, but their efficient calibration remains challenging. Here we propose a novel calibration architecture by investigating the role of pruning in ABM calibration. We use a recently developed model for human papillomavirus (HPV) transmission and focus on its integrated calibration framework, Optuna. Simulating six synthetic datasets of various temporal skewness, with six pruners, we show that more aggressive pruners perform best (in terms of loss function at end of calibration) for very-back-heavy datasets, while median pruners are better for more-front-heavy datasets. For more balanced datasets most of the pruners perform similarly to no pruning. However, across all datasets pruning notably sped up calibration, in many cases without compromising on - or even improving upon - the optimal found parameter set. We validate our results through application to real-life data. Finally, we discuss approaches for improving “bad pruners” for balanced datasets. Our proof-of-principle study shows that pruners can improve ABMs’ calibration. As ABMs are becoming more widely used in epidemiological modelling, designing the next level of pandemic preparedness strategies will need to address efficient calibration; we believe pruning is a cornerstone for this.Peer reviewe
Between win-win and the manufacturing of consent : collaborative governance as a lightning rod in cannabis policy
Get PDFScholarship on collaborative governance emphasizes the importance of creating win-win situations as a way of generating policy innovation and effective problem-solving. However, the dynamics of collaboration are often more complicated than discovering mutual gains. An analysis of Cannabis legalization in the San Francisco Bay Area finds that “getting to yes” is often a subtle mixture of finding common ground and the manufacturing of consent. This means that some participants take the role of entrepreneurs in the collaborative process and push discursive dynamics towards a dominant perspective. Exploring the importance of power and politics in collaborative governance, the case illuminates how arena design, discourse, and coalition-building shape the scope and character of consensus formationPeer reviewe
JWST/NIRCam transmission spectroscopy of the nearby sub-Earth GJ 341b
Get PDFFunding: J.K. acknowledges financial support from Imperial College London through an Imperial College Research Fellowship grant.We present a JWST/NIRCam transmission spectrum from 3.9-5.0 μm of the recently-validated sub-Earth GJ 341b (Rp = 0.92 R⊕, Teq = 540 K) orbiting a nearby bright M1 star (d = 10.4 pc, Kmag =5.6). We use three independent pipelines to reduce the data from the three JWST visits and perform several tests to check for the significance of an atmosphere. Overall, our analysis does not uncover evidence of an atmosphere. Our null hypothesis tests find that none of our pipelines' transmission spectra can rule out a flat line, although there is weak evidence for a Gaussian feature in two spectra from different pipelines (at 2.3 and 2.9σ). However, the candidate features are seen at different wavelengths (4.3 μm vs 4.7 μm), and our retrieval analysis finds that different gas species can explain these features in the two reductions (CO2 at 3.1σ compared to O3 at 2.9σ), suggesting that they are not real astrophysical signals. Our forward model analysis rules out a low mean molecular weight atmosphere (< 350x solar metallicity) to at least 3σ, and disfavors CH4-dominated atmospheres at 1-3σ, depending on the reduction. Instead, the forward models find our transmission spectra are consistent with no atmosphere, a hazy atmosphere, or an atmosphere containing a species that does not have prominent molecular bands across the NIRCam/F444W bandpass, such as a water-dominated atmosphere. Our results demonstrate the unequivocal need for two or more transit observations analyzed with multiple reduction pipelines, alongside rigorous statistical tests, to determine the robustness of molecular detections for small exoplanet atmospheres.Peer reviewe
Widespread and diverging patterns of change in local phylogenetic diversity
Get PDFFunding: This work was supported by the Leverhulme Trust, RC-2018- 021 and Natural Sciences and Engineering Research Council of Canada.Aim: Ecosystems are witnessing drastic changes in biodiversity worldwide. However, it is still unclear whether changes in phylogenetic diversity—a measure of the evolutionary relationships among species—reflect observed changes in species richness. Specifically, we ask whether changes in local phylogenetic diversity correlate with changes in species richness and examine if major taxonomic groups show diverging trends. Location: Global. Methods: We estimate how local phylogenetic diversity has changed compared to species richness and whether there were diverging patterns across taxonomic groups. We use a database of compiled assemblage time series from around the world, BioTIME. We use assemblage total evolutionary history (Faith's phylogenetic diversity; PD) as well as average relatedness (mean pairwise distance and mean nearest taxon distance; MPD and MNTD, respectively) as measures of phylogenetic diversity and report taxon-level and assemblage-level posterior slope estimates from a Bayesian hierarchical model. We report trends in four major taxonomic groups: fish, birds, terrestrial mammals and terrestrial plants. Results: We found strong evidence of widespread increases in MPD across fish and bird assemblages, reflecting decreases in average relatedness and strong evidence of a decrease of MPD in mammals, indicating the opposite. Conversely, we did not find consistent directional change in MNTD, though null average trends included notable positive and negative trends across studies and regions. We also found moderate evidence that SR and PD were increasing in fish assemblages, while they were decreasing in mammals. Main Conclusions: Our findings suggest that changes in species composition are significantly altering the evolutionary makeup of assemblages at the local scale and that overall patterns diverge within and across taxonomic groups. We suggest potential drivers of these changes but highlight that our results are more generalisable for fish and birds than for mammals and plants, given the variation in geographical coverage and sample size.Peer reviewe
A conceptual framework for measuring ecological novelty
Get PDFFunding: This work was funded by ARC Discovery Early Career Research Award DE240100398 awarded to TLS and ARC Discovery Project DP210100804 awarded to JMP and WK. AEM, MD & AMP acknowledge support from the Leverhulme Trust (RPG-2019-402). The Sistema Nacional de Investigación of SENACYT (Panamá) supported AO. JLB was supported by the National Science Foundation (EAR-1750597). TH was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, project number HE 5893/8-1).Background: Human pressures are driving the emergence of unprecedented, ‘novel’, ecological and environmental systems. The concept of novel (eco)systems is well accepted by the scientific community, but the use and measurement of novelty has outgrown initial definitions and critiques. There are still unresolved methodological and conceptual differences in quantifying novelty that prevent a unified research approach. Framework: Here we present a conceptual framework and guidelines to unify past and future measurement of ecological novelty. Under this framework, novelty is a property of an ecological or environmental entity of interest. Novelty is quantified as the comparison between the target entity and a reference set, measured as the summary of degrees of difference across one or more dimensions. Choices in these components, particularly the reference set, can change resulting novelty measurements and inferences. Showcase: We provide a case-study to showcase our framework, measuring pre- and post-European novelty in 99 pollen assemblages in Midwest USA forests. We paired this quantitative exploration with a five-step process designed to improve the utility and outcomes of novelty analyses. Conclusions: Quantitative novelty has immense value in studies of abrupt ecological change, linking climatic and ecological change, biotic interactions and invasions, species range shifts and fundamental theories. Our framework offers a unified overview and is also primed for integration into management and restoration workflows, providing consistent and robust measurements of novelty to support decision making, priority setting and resource allocation.Peer reviewe
Rewilding Charlotte Brontë : Jane Eyre, interpretation and literary historiography
Get PDFWhat characterised the initial, feverish response to Charlotte Brontë’s Jane Eyre (1847), this article argues, was an acknowledgement of the book’s wildness: its strange, disconcerting unwillingness to assert conventional mores and expectations. Even the negative responses decrying the book as demoniacally immoral called attention to how wild the narrative initially appeared. The article asserts that, starting with Victorian writers such as Elizabeth Gaskell, successive generations of critics elevated Brontë and her most famous work into the heights of the British poetic canon by propagating a tamed, domesticated mythology that viewed Brontë as a long-suffering waif and Jane Eyre as a pious book about the importance of self-denial and enduring suffering. The article asserts how writers, notably Victorian ‘men of letters’ such as Matthew Arnold and Charles Kingsley, made Brontë and her moorland environs appear unthreatening, and it emphasises how recent scholars and critics have succeeded in ‘rewilding’ Brontë, reawakening the intriguingly disorienting strangeness that was so evident to Jane Eyre’s initial readers.Peer reviewe
Semiconductor nanolasers in living cells
Get PDFIn recent years there have been significant advancements in the miniaturisation of semiconductor laser devices, with optimised structures reaching extremely low thresholds, and operating at room temperature. This progress has enabled the demonstration of intracellular lasers, where miniaturised lasers are operated within living cells. Further developments in this new field focused on the optimisation of laser geometries as a potential method to increase the intensity and spectral resolution provided, over conventional biophotonic imaging approaches, using e.g. fluorophores and quantum dots. These intracellular lasers provide opportunities for sensing and multiplexing that were not possible with established techniques.
The focus of this PhD was on integrating these two research frontiers. It involved the fabrication, characterisation, and application of III-V, semiconductor nanodisk whispering gallery mode (WGM) lasers. These were processed to be biocompatible and applied as a biophotonic tool. The tiny resonator volumes - substantially smaller than the nucleus of a cell - could be easily integrated into a variety of cell types, including neurons and immune T-cells that had not been previously capable of internalising lasers. The minimal resonator volume allowed inserting multiple lasers within cells, as they moved through confined environments, such as micro-pore epithelial analogues. Furthermore, the unique properties of WGM lasers were exploited to investigate cell dynamics as an intracellular local refractive index sensor.
The realised lasers exhibited excellent properties, with high signal to noise ratios and very low laser thresholds (~0.13pJ). This was achieved by exploiting the large optical gain and high refractive index of GaInP/AlGaInP multi-quantum wells. In this work, the versatility of these lasers as a photonic platform was demonstrated by embedding them into transferable membranes. This was applied as a sensor for investigating epsilon near zero (ENZ) metamaterials and their optical enhancement properties, and additionally allowed the fabrication of different laser cavity designs such as a random network laser, to investigate the properties of random lasing
Will the drone always get through? Offensive myths and defensive realities
Get PDFFunding: The authors would like the acknowledge the financial support of the Italian Ministry of Foreign Affairs and International Cooperation and of the NATO Defense College, which permitted the authors to carry out this study.Do emerging and disruptive technologies yield an offensive advantage? This is a question of central theoretical and substantive relevance. For the most part, however, the literature on this topic has not investigated empirically whether such technologies make attacking easier than defending, but it has largely assumed that they do. At the same time, work on the offense–defense balance has primarily focused on land conflicts, thus offering little understanding of the effect of technological change in other domains, such as the air and sea. In this article we address these gaps by investigating whether current- and next-generation drones shift the offense–defense balance toward the offense or toward offense dominance, as many assume—that is, whether drone technology can or will defeat current- and next-generation air defense systems. To answer these questions, we have explored the literature in radar engineering, electromagnetism, signal processing, and air defense operation. Our analysis challenges the existing consensus about the present and raises questions about the future. Our findings also demonstrate how important it is for the field of security studies to embrace greater interdisciplinarity in order to explore pressing policy and theoretical questions.Peer reviewe
Is the Modified Dental Anxiety Scale (MDAS) a single or two construct measure? : A theoretical and pragmatic perspective
Get PDFBackground: The MDAS questionnaire is one of a number of scales available to assess dental anxiety. It is widely used and translated into many world languages, however it lacks an explicit theoretical backdrop to the content and structure of the measure. This paper draws upon original expositions of dental anxiety: how it develops, is maintained and how this draws attention to a re-evaluation of the measure. To assist this inspection it was proposed to investigate a two latent construct formulation through a stepwise analysis using data from a representative survey of English respondents on their oral health (the Adult Dental Health Survey). Aim: To present a brief theoretical framework to underpin the measure and, as part of this study’s objectives, to provide some evidence to support the measure’s potential two-construct structure. Method: Narrative re- view, structural equation modelling and testing of specific associations to indicate a two latent con- struct formulation. Data included the MDAS items (where items 1 and 2 comprise the Anticipatory subscale, and items 3 to 5 describe the Treatment-related subscale). These items were completed by the representative sample of respondents from the most recent Adult Dental Health Survey conducted in 2009. Results: The two latent construct solution for describing dental anxiety was sup- ported. The Anticipated and Treatment-related subscales could be discriminated although were strongly correlated demonstrating overlap. Comparison of how each construct varied across the three age groups suggests an interesting heterogeneity. In addition, the two constructs behaved differently when acknowledging previous experience of respondents’ last dental visit. Anticipatory Dental Anxiety was more strongly related to Oral Health Related Quality of Life (OHRQoL) than Treatment-related Dental Anxiety as predicted. This partial evidence from empirical data and previous reports in other studies suggests that the separation of the MDAS measure into the two subscales may be warranted. Discussion: Researchers are recommended to report not only the total score of the MDAS in their studies but consider also presenting the two subscale scores, namely: Anticipatory and Treatment-related Dental Anxiety. Further work is indicated to determine if clinicians may find the subscales of use when assessing their patients.Peer reviewe
Bank business model identification, evolution and outcomes : evidence for South Africa
Get PDFFunding: The research carried out in this paper was funded by the South African Reserve Bank.This paper presents the findings of an investigation of the type, evolution and impacts on performance of bank business models in South Africa. We identify the various business models used by South African banks using data on the monthly balance sheets of commercial banks made available by the South African Reserve Bank between 1993 and 2022. We cluster banks into different business models based on the composition of their balance sheets. Based on these clusters, we identify business models oriented to wholesale and retail funding, as well as to universal, investment and interbank activities. Overall, our clustering exercise returns six distinct business models. We observe large differences in terms of business size, performance and risk profiles across the business models. We also analyse the evolution of business models over time. The results suggest that banks exhibit relatively stable business models, but where transition exists it tends to be between certain business models. Increased risk is associated with a higher probability of banks shifting business models.Peer reviewe
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