A new entropy measure based on the Renyi entropy rate using Gaussian kernels

The concept of entropy rate is well defined in dynamical systems theory but is impossible to apply it directly to finite real world data sets. With this in mind, Pincus developed Approximate Entropy (ApEn), which uses ideas from Eckmann and Ruelle to create a regularity measure based on entropy rate that can be used to determine the influence of chaotic behaviour in a real world signal. However, this measure was found not to be robust and so an improved formulation known as the Sample Entropy (SampEn) was created by Richman and Moorman to address these issues. We have developed a new, related, regularity measure which is not based on the theory provided by Eckmann and Ruelle and proves a more well-behaved measure of complexity than the previous measures whilst still retaining a low computational cost

Intensifying Melbourne

Cities are often said to be the engines of the global economy in an age of rapid urbanization. Car-dependent cities - particularly those that characterize North America and Australasia - are largely cities of suburban sprawl, freeways, shopping malls and poor public transport. They are also cities of great opportunity for significant reductions in carbon emissions through transit-oriented intensification within existing suburbs combined with improvements to transit services and shifts to active modes of transport. Such development,however, depends on a multi-scalar understanding that links the shaping of built form and public space at an urban design scale to larger scales of metropolitan structure and urban flows. This research project is an investigation of how such urban design and transport opportunities might be developed in Melbourne. We seek to show how transit-related problems and opportunities at different scales interconnect to form synergies and alliances both between projects and between scales. Through a series of design research studies we explore scenarios for the transformation of suburban railway stations, tram corridors, private shopping malls, university campuses and post-industrial zones. The analysis is undertaken within a theoretical framework of self-organization, emergence, complexity, adaptation and assemblage. Design research at every scale is argued to be a necessary link in the process of unlocking capacities for urban transformation

Acclimatization to high-variance habitats does not enhance physiological tolerance of two key Caribbean corals to future temperature and pH

Corals are acclimatized to populate dynamic habitats that neighbour coral reefs. Habitats such as seagrass beds exhibit broad diel changes in temperature and pH that routinely expose corals to conditions predicted for reefs over the next 50–100 years. However, whether such acclimatization effectively enhances physiological tolerance to, and hence provides refuge against, future climate scenarios remains unknown. Also, whether corals living in low-variance habitats can tolerate present-day high-variance conditions remains untested. We experimentally examined how pH and temperature predicted for the year 2100 affects the growth and physiology of two dominant Caribbean corals (Acropora palmata and Porites astreoides) native to habitats with intrinsically low (outer-reef terrace, LV) and/or high (neighbouring seagrass, HV) environmental variance. Under present-day temperature and pH, growth and metabolic rates (calcification, respiration and photosynthesis) were unchanged for HV versus LV populations. Superimposing future climate scenarios onto the HV and LV conditions did not result in any enhanced tolerance to colonies native to HV. Calcification rates were always lower for elevated temperature and/or reduced pH. Together, these results suggest that seagrass habitats may not serve as refugia against climate change if the magnitude of future temperature and pH changes is equivalent to neighbouring reef habitats

Beyond attention: deriving biologically interpretable insights from weakly-supervised multiple-instance learning models

Recent advances in attention-based multiple instance learning (MIL) have improved our insights into the tissue regions that models rely on to make predictions in digital pathology. However, the interpretability of these approaches is still limited. In particular, they do not report whether high-attention regions are positively or negatively associated with the class labels or how well these regions correspond to previously established clinical and biological knowledge. We address this by introducing a post-training methodology to analyse MIL models. Firstly, we introduce prediction-attention-weighted (PAW) maps by combining tile-level attention and prediction scores produced by a refined encoder, allowing us to quantify the predictive contribution of high-attention regions. Secondly, we introduce a biological feature instantiation technique by integrating PAW maps with nuclei segmentation masks. This further improves interpretability by providing biologically meaningful features related to the cellular organisation of the tissue and facilitates comparisons with known clinical features. We illustrate the utility of our approach by comparing PAW maps obtained for prostate cancer diagnosis (i.e. samples containing malignant tissue, 381/516 tissue samples) and prognosis (i.e. samples from patients with biochemical recurrence following surgery, 98/663 tissue samples) in a cohort of patients from the international cancer genome consortium (ICGC UK Prostate Group). Our approach reveals that regions that are predictive of adverse prognosis do not tend to co-locate with the tumour regions, indicating that non-cancer cells should also be studied when evaluating prognosis

Making the great transformation, November 13, 14, and 15, 2003

This repository item contains a single issue of the Pardee Conference Series, a publication series that began publishing in 2006 by the Boston University Frederick S. Pardee Center for the Study of the Longer-Range Future. This Conference took place during November 13, 14, and 15, 2003. Co-organized by Cutler Cleveland and Adil Najam.The conference discussants and participants analyze why transitions happen, and why they matter. Transitions are those wide-ranging changes in human organization and well being that can be convincingly attributed to a concerted set of choices that make the world that was significantly and recognizably different from the world that becomes. Transition scholars argue that that history does not just stumble along a pre-determined path, but that human ingenuity and entrepreneurship have the ability to fundamentally alter its direction. However, our ability to ‘will’ such transitions remains in doubt. These doubts cannot be removed until we have a better understanding of how transitions work

Genomic evolution and transcriptional changes in the evolution of prostate cancer into neuroendocrine and ductal carcinoma types

Prostate cancer is typically of acinar adenocarcinoma type but can occasionally present as neuroendocrine and/or ductal type carcinoma. These are associated with clinically aggressive disease, and the former often arises on a background of androgen deprivation therapy, although it can also arise de novo. Two prostate cancer cases were sequenced by exome capture from archival tissue. Case 1 was de novo small cell neuroendocrine carcinoma and ductal adenocarcinoma with three longitudinal samples over 5 years. Case 2 was a single time point after the development of treatment-related neuroendocrine prostate carcinoma. Case 1 showed whole genome doubling in all samples and focal amplification of AR in all samples except the first time point. Phylogenetic analysis revealed a common ancestry for ductal and small cell carcinoma. Case 2 showed 13q loss (involving RB1) in both adenocarcinoma and small cell carcinoma regions, and 3p gain, 4p loss, and 17p loss (involving TP53) in the latter. By using highly curated samples, we demonstrate for the first time that small-cell neuroendocrine and ductal prostatic carcinoma can have a common ancestry. We highlight whole genome doubling in a patient with prostate cancer relapse, reinforcing its poor prognostic nature

The public health implications of the Paris Agreement: a modelling study.

BACKGROUND: nationally determined contributions (NDCs) serve to meet the goals of the Paris Agreement of staying "well below 2°C", which could also yield substantial health co-benefits in the process. However, existing NDC commitments are inadequate to achieve this goal. Placing health as a key focus of the NDCs could present an opportunity to increase ambition and realise health co-benefits. We modelled scenarios to analyse the health co-benefits of NDCs for the year 2040 for nine representative countries (ie, Brazil, China, Germany, India, Indonesia, Nigeria, South Africa, the UK, and the USA) that were selected for their contribution to global greenhouse gas emissions and their global or regional influence. METHODS: Modelling the energy, food and agriculture, and transport sectors, and mortality related to risk factors of air pollution, diet, and physical activity, we analysed the health co-benefits of existing NDCs and related policies (ie, the current pathways scenario) for 2040 in nine countries around the world. We compared these health co-benefits with two alternative scenarios, one consistent with the goal of the Paris Agreement and the Sustainable Development Goals (ie, the sustainable pathways scenario), and one in line with the sustainable pathways scenario, but also placing health as a central focus of the policies (ie, the health in all climate policies scenario). FINDINGS: Compared with the current pathways scenario, the sustainable pathways scenario resulted in an annual reduction of 1·18 million air pollution-related deaths, 5·86 million diet-related deaths, and 1·15 million deaths due to physical inactivity, across the nine countries, by 2040. Adopting the more ambitious health in all climate policies scenario would result in a further reduction of 462 000 annual deaths attributable to air pollution, 572 000 annual deaths attributable to diet, and 943 000 annual deaths attributable to physical inactivity. These benefits were attributable to the mitigation of direct greenhouse gas emissions and the commensurate actions that reduce exposure to harmful pollutants, as well as improved diets and safe physical activity. INTERPRETATION: A greater consideration of health in the NDCs and climate change mitigation policies has the potential to yield considerable health benefits as well as achieve the "well below 2°C" commitment across a range of regional and economic contexts. FUNDING: This work was in part funded through an unrestricted grant from the Wellcome Trust (award number 209734/Z/17/Z) and supported by an Engineering and Physical Sciences Research Council grant (grant number EP/R035288/1)

The public health implications of the Paris Agreement: a modelling study.

BACKGROUND: nationally determined contributions (NDCs) serve to meet the goals of the Paris Agreement of staying "well below 2°C", which could also yield substantial health co-benefits in the process. However, existing NDC commitments are inadequate to achieve this goal. Placing health as a key focus of the NDCs could present an opportunity to increase ambition and realise health co-benefits. We modelled scenarios to analyse the health co-benefits of NDCs for the year 2040 for nine representative countries (ie, Brazil, China, Germany, India, Indonesia, Nigeria, South Africa, the UK, and the USA) that were selected for their contribution to global greenhouse gas emissions and their global or regional influence. METHODS: Modelling the energy, food and agriculture, and transport sectors, and mortality related to risk factors of air pollution, diet, and physical activity, we analysed the health co-benefits of existing NDCs and related policies (ie, the current pathways scenario) for 2040 in nine countries around the world. We compared these health co-benefits with two alternative scenarios, one consistent with the goal of the Paris Agreement and the Sustainable Development Goals (ie, the sustainable pathways scenario), and one in line with the sustainable pathways scenario, but also placing health as a central focus of the policies (ie, the health in all climate policies scenario). FINDINGS: Compared with the current pathways scenario, the sustainable pathways scenario resulted in an annual reduction of 1·18 million air pollution-related deaths, 5·86 million diet-related deaths, and 1·15 million deaths due to physical inactivity, across the nine countries, by 2040. Adopting the more ambitious health in all climate policies scenario would result in a further reduction of 462 000 annual deaths attributable to air pollution, 572 000 annual deaths attributable to diet, and 943 000 annual deaths attributable to physical inactivity. These benefits were attributable to the mitigation of direct greenhouse gas emissions and the commensurate actions that reduce exposure to harmful pollutants, as well as improved diets and safe physical activity. INTERPRETATION: A greater consideration of health in the NDCs and climate change mitigation policies has the potential to yield considerable health benefits as well as achieve the "well below 2°C" commitment across a range of regional and economic contexts. FUNDING: This work was in part funded through an unrestricted grant from the Wellcome Trust (award number 209734/Z/17/Z) and supported by an Engineering and Physical Sciences Research Council grant (grant number EP/R035288/1)

Public health benefits of strategies to reduce greenhouse-gas emissions: overview and implications for policy makers

This Series has examined the health implications of policies aimed at tackling climate change. Assessments of mitigation strategies in four domains-household energy, transport, food and agriculture, and electricity generation-suggest an important message: that actions to reduce greenhouse-gas emissions often, although not always, entail net benefits for health. In some cases, the potential benefits seem to be substantial. This evidence provides an additional and immediate rationale for reductions in greenhouse-gas emissions beyond that of climate change mitigation alone. Climate change is an increasing and evolving threat to the health of populations worldwide. At the same time, major public health burdens remain in many regions. Climate change therefore adds further urgency to the task of addressing international health priorities, such as the UN Millennium Development Goals. Recognition that mitigation strategies can have substantial benefits for both health and climate protection offers the possibility of policy choices that are potentially both more cost effective and socially attractive than are those that address these priorities independently