Using systemic models in games and simulations for participatory planning

Planning for large Indian cities presents a complex problem to planners due to a number of factors, three of them being the scale of the cities, the diversity of people and the inequity among the population. Effective participatory approaches to planning aim to address the inherent inequity (stemming from levels of income, class, caste, gender, etc.) among stakeholders by including the needs of the marginalised. Such methods should allow for the collection of people’s aspirations, their needs and preferences, this leads to a set of outcomes that can then be negotiated between the stakeholders. In traditional approaches, in order to develop plans or implement urban infrastructure, a pilot project is created/implemented for each plan option, based on the input from different people, and to test them in the real world. For example, selecting a small region in the city to test a bus rapid transit system (BRT) to check for its efficacy and acceptance. However, apart from the financial and other resource costs, it requires changes to governance and administrative processes in order to create, monitor and analyse such a pilot. This makes the pilot-based approach expensive and time-consuming. Recently, the ethical concerns of pilots and randomised control trials have been well documented. Simulation models address these gaps by allowing us to test for certain conditions. However, most of these modelling techniques available today were developed in a western context for a western city dweller. These assumptions related to income & expenditure, types of livelihoods, aspirations, type of governance and road network & topology, has influenced the methods of planning. Due to the diversity and the differences in the model assumptions, most plans developed using such techniques either tend to have skewed results or are not relevant to the context. A new method is required in order to include the contextual assumptions and thus develop tools and methods that are able to inform the planner about the context and limitations to work within. In this article, we demonstrate the use of approaches from systems dynamics modelling and the use of participatory modelling to build models of people and processes for the development of neighbourhood level plans. We then demonstrate how such models can be used in two ways, 1) As a basis for the design of serious games, to elicit preferences, biases and aspirations from people and, 2) As simulation planning tools to develop planning scenarios which can be used to explore different outcomes. We provide examples of both these methods as a means to develop and discover the fundamental context for planning in India

Evolution of compound eye morphology underlies differences in vision between closely related Drosophila species

Background: Insects have evolved complex visual systems and display an astonishing range of adaptations for diverse ecological niches. Species of Drosophila melanogaster subgroup exhibit extensive intra- and interspecific differences in compound eye size. These differences provide an excellent opportunity to better understand variation in insect eye structure and the impact on vision. Here we further explored the difference in eye size between D. mauritiana and its sibling species D. simulans. Results: We confirmed that D. mauritiana have rapidly evolved larger eyes as a result of more and wider ommatidia than D. simulans since they recently diverged approximately 240,000 years ago. The functional impact of eye size, and specifically ommatidia size, is often only estimated based on the rigid surface morphology of the compound eye. Therefore, we used 3D synchrotron radiation tomography to measure optical parameters in 3D, predict optical capacity, and compare the modelled vision to in vivo optomotor responses. Our optical models predicted higher contrast sensitivity for D. mauritiana, which we verified by presenting sinusoidal gratings to tethered flies in a flight arena. Similarly, we confirmed the higher spatial acuity predicted for Drosophila simulans with smaller ommatidia and found evidence for higher temporal resolution. Conclusions: Our study demonstrates that even subtle differences in ommatidia size between closely related Drosophila species can impact the vision of these insects. Therefore, further comparative studies of intra- and interspecific variation in eye morphology and the consequences for vision among other Drosophila species, other dipterans and other insects are needed to better understand compound eye structure–function and how the diversification of eye size, shape, and function has helped insects to adapt to the vast range of ecological niches

Pleiotropic functions of the tumor- and metastasis-suppressing Matrix Metalloproteinase-8 in mammary cancer in MMTV-PyMT transgenic mice

Matrix metalloproteinase-8 (MMP-8; neutrophil collagenase) is an important regulator of innate immunity which has onco-suppressive actions in numerous tumor types

NMNAT1 Mutations Cause Leber Congenital Amaurosis

Leber congenital amaurosis (LCA) is an infantile-onset form of inherited retinal degeneration characterized by severe vision loss. Two-thirds of LCA cases are caused by mutations in 17 known disease genes (RetNet Retinal Information Network). Using exome sequencing, we identified a homozygous missense mutation (c.25G>A, p.Val9Met) in NMNAT1 as likely disease-causing in two siblings of a consanguineous Pakistani kindred affected by LCA. This mutation segregated with disease in their kindred, including in three other children with LCA. NMNAT1 resides in the previously identified LCA9 locus and encodes the nuclear isoform of nicotinamide mononucleotide adenylyltransferase, a rate-limiting enzyme in nicotinamide adenine dinucleotide $(NAD^+)$ biosynthesis. Functional studies showed the p.Val9Met mutation decreased NMNAT1 enzyme activity. Sequencing NMNAT1 in 284 unrelated LCA families identified 14 rare mutations in 13 additional affected individuals. These results are the first to link an NMNAT isoform to disease and indicate that NMNAT1 mutations cause LCA

Projects in Applied Data Science: Fall 2019

This document contains semester projects for students in CSCI 4381/7000 Data ScienceProjects. This course explores concepts and techniques for design, formulation and execution ofpractical, applied data science. Topics covered include experimental design, statistical analysisand predictive modeling, machine learning, data visualization, scientific writing and presentation.During the class, students selected a semester-long project to acquire, analyze, and understanddata in support of a research question. In addition to traditional lectures, students read anddiscussed published papers on data science topics, practiced skills in recitation sessions, andentertained guest lectures from expert data scientists in the field. Outside of these readings andrecitations, students were allowed to work on their projects exclusively and were supported withmeetings, peer-discussion and copyediting. In terms of the scope of the final product, undergraduate students were asked to perform aresearch or engineering task of some complexity while graduate students were additionallyrequired to perform a survey of related work, demonstrate some novelty in their approach, anddescribe the position of their contribution within the broader literature. All students whoperformed at or above these expectations were offered the opportunity to contribute their paperfor publication in this technical summary. The diversity of the papers herein is representative of the diversity of interests of the students inthe class. There is no common trend among the papers submitted and each takes a differenttopic to task. Students made use of open data or worked with organizations to acquire data.Several students pivoted their projects early on due to limitations and difficulties in data access--- a real-world challenge in practical data science. The projects herein range from analyzingtraffic in cities, restaurant trends and Facebook responses to smartphone accelerometer data,scaling laws in higher education, and bicycle trends in Boulder, Colorado. Analysis approachesare similarly varied: visualization, statistical analysis and modeling, machine learning,reinforcement learning, etc.. Most papers can be understood as exploratory data analysis,although some emphasize interactive visualization and others emphasize statistical modelingand prediction aimed at testing a well-defined research question. To inform the style of theirapproach, students read papers from a broad sampling of original research. They used thesereadings to build an understanding of approaches to presentation and analysis in the modernscientific literature. One paper was held out from this compendium so that it could be submittedfor publication to a peer-reviewed venue. Please direct questions/comments on individual papers to the student authors when contactinformation has been made available.</p

Evolution of compound eye morphology underlies differences in vision between closely related Drosophila species

Background. Insects have evolved complex visual systems and display an astonishing range of adaptations for diverse ecological niches. Species of Drosophila melanogaster subgroup exhibit extensive intra- and interspecific differences in compound eye size. These differences provide an excellent opportunity to better understand variation in insect eye structure and the impact on vision. Here we further explored the difference in eye size between D. mauritiana and its sibling species D. simulans. Results. We confirmed that D. mauritiana have rapidly evolved larger eyes as a result of more and wider ommatidia than D. simulans since they recently diverged approximately 240,000 years ago. The functional impact of eye size, and specifically ommatidia size, is often only estimated based on the rigid surface morphology of the compound eye. Therefore, we used 3D synchrotron radiation tomography to measure optical parameters in 3D, predict optical capacity, and compare the modelled vision to in vivo optomotor responses. Our optical models predicted higher contrast sensitivity for D. mauritiana, which we verified by presenting sinusoidal gratings to tethered flies in a flight arena. Similarly, we confirmed the higher spatial acuity predicted for Drosophila simulans with smaller ommatidia and found evidence for higher temporal resolution. Conclusions. Our study demonstrates that even subtle differences in ommatidia size between closely related Drosophila species can impact the vision of these insects. Therefore, further comparative studies of intra- and interspecific variation in eye morphology and the consequences for vision among other Drosophila species, other dipterans and other insects are needed to better understand compound eye structure–function and how the diversification of eye size, shape, and function has helped insects to adapt to the vast range of ecological niches

Co-regulatory expression quantitative trait loci mapping: method and application to endometrial cancer

<p>Abstract</p> <p>Background</p> <p>Expression quantitative trait loci (eQTL) studies have helped identify the genetic determinants of gene expression. Understanding the potential interacting mechanisms underlying such findings, however, is challenging.</p> <p>Methods</p> <p>We describe a method to identify the <it>trans-</it>acting drivers of multiple gene co-expression, which reflects the action of regulatory molecules. This method-termed <it>co-regulatory expression quantitative trait locus </it>(creQTL) <it>mapping</it>-allows for evaluation of a more focused set of phenotypes within a clear biological context than conventional eQTL mapping.</p> <p>Results</p> <p>Applying this method to a study of endometrial cancer revealed regulatory mechanisms supported by the literature: a creQTL between a locus upstream of STARD13/DLC2 and a group of seven IFNβ-induced genes. This suggests that the Rho-GTPase encoded by STARD13 regulates IFNβ-induced genes and the DNA damage response.</p> <p>Conclusions</p> <p>Because of the importance of IFNβ in cancer, our results suggest that creQTL may provide a finer picture of gene regulation and may reveal additional molecular targets for intervention. An open source R implementation of the method is available at <url>http://sites.google.com/site/kenkompass/</url>.</p