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Relying on a single summary statistic to assess model performance may not be enough to fully understand whether a model really performed well! AUC 100% True Positive Rate AUC = 0.9 TSS 0% False Positive Rate 100% Evaluation (exploring) the SDMs’ performance (behaviour) more precisely!! Comparison of different modelling techniques…! Spatial distribution of errors (local evaluation of model performance) 10 species were simulated and mapped into Spain! SI2=0.5 * (SI.L1.E1+SI.Ga.E2) SI6=SI.L1.E1*SI.Ga.E2 15 models (including ensemble approaches) for presence/absence & presence-only data were used! Global statistics Local statistics Model Uncertainty AUC TSS Sensitivity Specificity Fuzzy map comparison Niche similarity Known truth! Predicted! Known truth! Predicted! Presence-only Bioclim Niche space Geographic space Maxent Known truth BRT Maxent Bioclim Ensemble Presence-Absence GLM BRT Ensemble_PO Ensemble I FuzzyMatch Model Uncertainty (between model inconsistency) Presence Absence Presence Only Model Uncertainty (Within model inconsistency) Putting all together!!!! the ensemble-based model strongly outperforms the other models either when accuracy or uncertainty in the predictions is a matter! The set of evaluation methods we introduced can be useful for further investigations of model behaviours and provide deeper insights into the causes of varying model performances! 18 © 2007 Jane Genovese. All rights reserved. Page 1 ABOUT JANE GENOVESE Jane Genovese is a public speaker, university graduate of Law and Arts (majoring in Psychology) and passionate global warming advocate. She became concerned about global warming after reading an article on Artic Eskimos losing their way of life due to rapid climate change. This motivated her to study Environmental law and International Environmental law at university. Shortly after, she created the “Global Warming: Too Hot to Handle?” workshop and this book with her mother, Sharon. In her spare time, Jane enjoys salsa dancing, watching good documentaries and going to the gym. Contact Details PO Box 32 Bullcreek Post Office Bullcreek Western Australia 6149 Web: http://www.live-the-solution.com Email: jane@learningfundamentals.com.au © 2007 Jane Genovese. All rights reserved. Page 2 ACKNOWLEDGEMENTS I would like to thank my family for their passion and commitment to do whatever they can to combat global warming. Without their concern and stand, this book would not have been possible. They have inspired me to be responsible for my actions and future. Special thanks to my mum for the countless hours she spent illustrating this book and to my dad and brother for all their help too. Thanks to my environmental law lecturers as well as Ben Rose and Al Gore for waking me up to the climate crisis and calling me into action. Thanks to the team at PublicityShip.com.au for all their support and inspiring me with the idea of creating this ebook. Special thanks also to my wonderful Master Mind Alliance group (Chris, Ned and Bridget). Thanks to Rob and Brenda at Environment House. Their commitment to helping the community live greener and cleaner lives is an ongoing source of inspiration. I would also like to thank my good friends, Zayd Azmi, Dean Lasslet and Gerald Zeng, for their feedback and help in compiling the book. This book is for you all. Jane Genovese © 2007 Jane Genovese. All rights reserved. Page 3 HOW TO USE THIS BOOK This book contains a series of mind maps. You may be thinking ‘What is a mind map?’ A mind map is a creative way of displaying information, which involves exaggerated images, different colours and curved lines radiating from a central idea. Why have I bothered to use mind maps? A mind map is an effective way of learning new information. The colours, branches and images stimulate your mind and allow you to remember information more easily. Mind maps also give you an overview of a large subject area and help you to make connections faster between different ideas. I know how easy it is to become overwhelmed and confused when reading about climate change, and I don’t want this to happen to others. It was never my intention to make fun of this serious topic through the use of mind maps, just to simply illuminate the subject and make it easier for people from all walks of life to understand. That’s why I have included mind maps. As you read this book, start by looking at the mind map at the beginning of each chapter. These will give you the essence of what the chapter is about and the text will then deepen your understanding. If you have trouble understanding any content, I recommend you create a mind map yourself. For a step-by- step guide on how to mind map, visit MINIREVIEW Combinatorial approaches to protein stability and structure Thomas J. Magliery 1 and Lynne Regan 1,2 1 Department of Molecular Biophysics & Biochemistry and 2 Department of Chemistry, Yale University, New Haven, CT, USA Why do proteins adopt the conformations that they do, and what determines their stabilities? While we have come to some understanding of the forces that underlie protein architecture, a precise, predictive, physicochemical explanation is still elusive. Two obstacles to addressing these questions are the unfathomable vastness of protein sequence space, and the difficulty in making direct phy- sical measurements on large numbers of protein variants. Here, we review combinatorial methods that have been applied to problems in protein biophysics over the last 15 years. The effects of hydrophobic core composition, the most important determinant of structure and stabil- ity, are still poorly understood. Particular attention is given to core composition as addressed by library methods. Increasingly useful screens and selections, in combination with modern high-throughput approaches borrowed from genomics and proteomics efforts, are making the empirical, statistical correlation between sequence and structure a tractable problem for the coming years. Introduction Understanding the basis of protein stability and structure is a problem of fundamental chemical and physical signi- ficance. In addition, such knowledge is critical for numerous biomedical applications, including but not limited to the preparation of stable protein-based therapeutics and the treatment of pathologies related to mutated, unstable proteins [1–4]. The importance of this issue has led to considerable study, at least since the first protein crystal structures were determined [5–7]. In spite of such attention, a satisfactory understanding of how proteins adopt the conformations that they do is still far from complete. Why has it been so difficult to develop a precise physicochemical model of protein structure? To the extent that it is true that the in vivo conformation of proteins is encoded entirely by the primary structure, a sufficiently broad survey of protein variants must contain, in the limit, all that we need to know to understand the basis of protein stability. The problem is that the number of possible protein variants is incomprehensibly large, the biophysical charac- terization of proteins is slow, and the resulting paucity of data makes it difficult to parameterize potential functions correlating structure and sequence. Sequence space for even a very small protein (e.g. 50 amino acids or 6 kDa) is mind- bogglingly large (one molecule each of the 10 65 variants wouldweighinat10 39 tonnes; approximately the mass of the Milky Way galaxy). We currently lack the theoretical framework to quantitatively predict the effects of even a single point mutation, even for the simplest protein-like structures, such as coiled-coils. Remarkable computational successes, such as the in silico redesigns of a zinc-free Ôzinc fingerÕ [8] and a right-handed coiled-coil [9], belie the fact that we cannot reliably predict the effects of hydrophobic core mutations (even if we can distinguish some destabilized variants from some stable ones) [10,11]. Indeed, there is still widespread debate about the restrictiveness of stereochem- ical constraints of the amino acids on the ability to achieve stable protein structures, with extreme views favoring the dominance of hydrophobic surface burial (like an oil droplet) [12] or the difficulty of achieving intimate van der Waals packing (like a jigsaw puzzle) [13]. The problem can therefore be framed simply: we need a way to (a) [...]... Byram Karasu, also morbidly obese, died at the age of 56 This tale of two fathers is in the background of the volume as the authors seek to assess the many factors that contribute to obesity and its control The Gravity of Weight is a model of scholarly inquiry that describes and analyzes, in a critical manner, an enormous amount of information With the possible exception of a few references that may... know about the complex subject of weight Statistics can never account for everyone Nevertheless, our book, The Gravity of Weight: A Clinical Guide to Weight Loss and Maintenance, is our attempt to explain some of these discrepancies and explore particularly why, for most people, it is so difficult to lose weight and maintain that loss No one has all the answers, but an understanding of the science, of. .. can actually achieve and maintain is probably within a fairly limited range, but even a 5% to 10% loss of weight can have substantial health benefits Nevertheless, many people cannot lose even the 10% that can be an achievable and reasonable goal and keep it off indefinitely And many people have every wish to remain a certain weight yet find themselves overeating, often with considerable guilt before and. .. control, and weight maintenance seem to apply better to animals that do not have the advanced cortical brains we have We can limit an animal’s food intake, for example, and give it regular exercise, and the animal will lose weight and maintain that loss, assuming its food and exercise regimens continue to be regulated Human beings, however, are different We are not only beneficiaries of our remarkable evolution... endemic rather than epidemic, and she notes that although there has been a rise in the prevalence of obesity over the past twenty or so years, a survey done in the early 1960s actually found that 45% of the U.S population was overweight at that time In fact, back in the 1950s Breslow (1952) was already warning of the dangers of overweight and its relationship to increased mortality He said, The American... dyslipidemia), hypertension, adult-onset diabetes, and even gout, all symptoms of metabolic abnormalities His own father had died at the age of 62 from a sudden myocardial infarction, so my father had a strong genetic risk factor as well What was in my father’s favor, though, was that he had always believed in the importance of exercise, particularly walking and weight lifting, well before it was fashionable... and to explain why the control of body weight and its maintenance are “so daunting for so many people.” The problems that they raise and the analyses that they conduct go far to realize this goal Early in the book, I was struck by the discussion of two problems in the understanding of obesity The first RESEARC H Open Access Downscaling future climate scenarios to fine scales for hydrologic and ecological modeling and analysis Lorraine E Flint * and Alan L Flint Abstract Introduction: Evaluating the environ mental impacts of climate change on water resources and biological components of the landscape is an integral part of hydrologic and ecological investigations, and the resultant land and resource management in the twenty-first century. Impacts of both climate and simulated hydrologic parameters on ecological processes are relevant at scales that reflect the heterogeneity and complexity of landscapes. At present, simulations of climate change available from global climate models [GCMs] require downscaling for hydrologic or ecological applications. Methods: Using statistically downscaled future climate projections developed using constructed analogues, a methodology was developed to further downscale the projections spatially using a gradient-inverse-distance- squared approach for application to hydrologic modeling at 270-m spatial resolution. Results: This paper illustrates a methodology to downscale and bias-correct national GCMs to subkilometer scales that are applicable to fine-scale environmental processes. Four scenarios were chosen to bracket the range of future emissions put forth by the Intergovernmental Panel on Climate Change. Fine-scale applications of downscaled datasets of ecological and hydrologic correlations to variation in climate are illustrated. Conclusions: The methodology, which includes a sequence of rigorous analyses and calculations, is intended to reduce the addition of uncertainty to the climate data as a result of the downscaling while providing the fine-scale climate information necessary for ecological analyses. It results in new but consistent data sets for the US at 4 km, the southwest US at 270 m, and California at 90 m and illustrates the utility of fine-scale downscaling to analyses of ecological processes influenced by topographic complexity. Keywords: downscaling, climate change, spatial scale, scenarios Background and introduction Climate change has become an integral part of conduct- ing hydr ologic and ecological stud ies in the twenty-first century. In general, the best scient ific evidence suggests that global warming has been occurring and will con- tinue to occur during this century no matter what man- agement approaches to ameliorate climate change are implemented (California Department of Water Resources 2008). Were we to eliminate all anthropo- genic greenhouse gas emissions today, about half of the anthropogenic CO 2 would be removed from the atmo- sphere within 30 years, but the remaining atmospheric CO 2 would remain for centuries (IPCC 2007). To assess the impacts of climate change, many global socio-eco- nomic scenarios are being developed by the Intergovern- mental Panel on Climate Change [IPCC] to provide climate scenarios that take into account estimates of possible magnitudes of greenhouse gas emissions that are responsible for much of the climate change. These scenarios are used as boundary conditions for global cli- mate models [GCMs] that provide us with insight into how human behavior in the future may influence changes in climate. These GCMs lack orographic detail, having a coarse spatial resolution with a grid-cell size on the order ... it be informative enough? Relying on a single summary statistic to assess model performance may not be enough to fully understand whether a model really performed well! AUC 100% True Positive... distribution of errors (local evaluation of model performance) 10 species were simulated and mapped into Spain! SI2=0.5 * (SI.L1.E1+SI.Ga.E2) SI6=SI.L1.E1*SI.Ga.E2 15 models (including ensemble... AUC TSS Sensitivity Specificity Fuzzy map comparison Niche similarity Known truth! Predicted! Known truth! Predicted! Presence-only Bioclim Niche space Geographic space Maxent Known truth BRT