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This report is the consolidated work of an interdisciplinary course project in CEE494/598, CON598, and SOS598, Urban Infrastructure Anatomy and Sustainable Development. In Fall 2012, the course at Arizona State University used sustainability research frameworks and life-cycle assessment methods to evaluate the comprehensive benefits and costs when transit-oriented development is

This report is the consolidated work of an interdisciplinary course project in CEE494/598, CON598, and SOS598, Urban Infrastructure Anatomy and Sustainable Development. In Fall 2012, the course at Arizona State University used sustainability research frameworks and life-cycle assessment methods to evaluate the comprehensive benefits and costs when transit-oriented development is infilled along the proposed light rail transit line expansion. In each case, and in every variation of possible future scenarios, there were distinct life-cycle benefits from both developing in more dense urban structures and reducing automobile travel in the process.

Results from the report are superseded by our publication in Environmental Science and Technology.

Created2012-12
Description

Public transit systems are often accepted as energy and environmental improvements to automobile travel, however, few life cycle assessments exist to understand the effects of implementation of transit policy decisions. To better inform decision-makers, this project evaluates the decision to construct and operate public transportation systems and the expected energy

Public transit systems are often accepted as energy and environmental improvements to automobile travel, however, few life cycle assessments exist to understand the effects of implementation of transit policy decisions. To better inform decision-makers, this project evaluates the decision to construct and operate public transportation systems and the expected energy and environmental benefits over continued automobile use. The public transit systems are selected based on screening criteria. Initial screening included advanced implementation (5 to 10 years so change in ridership could be observed), similar geographic regions to ensure consistency of analysis parameters, common transit agencies or authorities to ensure a consistent management culture, and modes reflecting large infrastructure investments to provide an opportunity for robust life cycle assessment of large impact components. An in-depth screening process including consideration of data availability, project age, energy consumption, infrastructure information, access and egress information, and socio-demographic characteristics was used as the second filter. The results of this selection process led to Los Angeles Metro’s Orange and Gold lines.

In this study, the life cycle assessment framework is used to evaluate energy inputs and emissions of greenhouse gases, particulate matter (10 and 2.5 microns), sulfur dioxide, nitrogen oxides, volatile organic compounds, and carbon monoxide. For the Orange line, Gold line, and competing automobile trip, an analysis system boundary that includes vehicle, infrastructure, and energy production components is specified. Life cycle energy use and emissions inventories are developed for each mode considering direct (vehicle operation), ancillary (non-vehicle operation including vehicle maintenance, infrastructure construction, infrastructure operation, etc.), and supply chain processes and services. In addition to greenhouse gas emissions, the inventories are linked to their potential for respiratory impacts and smog formation, and the time it takes to payback in the lifetime of each transit system.

Results show that for energy use and greenhouse gas emissions, the inclusion of life cycle components increases the footprint between 42% and 91% from vehicle propulsion exclusively. Conventional air emissions show much more dramatic increases highlighting the effectiveness of “tailpipe” environmental policy. Within the life cycle, vehicle operation is often small compared to other components. Particulate matter emissions increase between 270% and 5400%. Sulfur dioxide emissions increase by several orders of magnitude for the on road modes due to electricity use throughout the life cycle. NOx emissions increase between 31% and 760% due to supply chain truck and rail transport. VOC emissions increase due to infrastructure material production and placement by 420% and 1500%. CO emissions increase by between 20% and 320%. The dominating contributions from life cycle components show that the decision to build an infrastructure and operate a transportation mode in Los Angeles has impacts far outside of the city and region. Life cycle results are initially compared at each system’s average occupancy and a breakeven analysis is performed to compare the range at which modes are energy and environmentally competitive.

The results show that including a broad suite of energy and environmental indicators produces potential tradeoffs that are critical to decision makers. While the Orange and Gold line require less energy and produce fewer greenhouse gas emissions per passenger mile traveled than the automobile, this ordering is not necessarily the case for the conventional air emissions. It is possible that a policy that focuses on one pollutant may increase another, highlighting the need for a broad set of indicators and life cycle thinking when making transportation infrastructure decisions.

Description

The goal of this working paper is to provide the methodological background for several upcoming reports and peer-reviewed journal publications. This manuscript only provides background methodology and does not show or interpret any of the results that are being generated by the research team. The methodology is consistent with the

The goal of this working paper is to provide the methodological background for several upcoming reports and peer-reviewed journal publications. This manuscript only provides background methodology and does not show or interpret any of the results that are being generated by the research team. The methodology is consistent with the transportation LCA approach developed by the author in previous research. The discussion in this working paper provides the detailed background data and steps used by the research team for their assessment of Los Angeles Metro transit lines and a competing automobile trip.

Created2012-07-30
Description

Public transportation systems are often part of strategies to reduce urban environmental impacts from passenger transportation, yet comprehensive energy and environmental life-cycle measures, including upfront infrastructure effects and indirect and supply chain processes, are rarely considered. Using the new bus rapid transit and light rail lines in Los Angeles, near-term

Public transportation systems are often part of strategies to reduce urban environmental impacts from passenger transportation, yet comprehensive energy and environmental life-cycle measures, including upfront infrastructure effects and indirect and supply chain processes, are rarely considered. Using the new bus rapid transit and light rail lines in Los Angeles, near-term and long-term life-cycle impact assessments are developed, including consideration of reduced automobile travel. Energy consumption and emissions of greenhouse gases and criteria pollutants are assessed, as well the potential for smog and respiratory impacts.

Results show that life-cycle infrastructure, vehicle, and energy production components significantly increase the footprint of each mode (by 48–100% for energy and greenhouse gases, and up to 6200% for environmental impacts), and emerging technologies and renewable electricity standards will significantly reduce impacts. Life-cycle results are identified as either local (in Los Angeles) or remote, and show how the decision to build and operate a transit system in a city produces environmental impacts far outside of geopolitical boundaries. Ensuring shifts of between 20–30% of transit riders from automobiles will result in passenger transportation greenhouse gas reductions for the city, and the larger the shift, the quicker the payback, which should be considered for time-specific environmental goals.

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Description

In an extreme heat event, people can go to air-conditioned public facilities if residential air-conditioning is not available. Residences that heat slowly may also mitigate health effects, particularly in neighborhoods with social vulnerability. We explored the contributions of social vulnerability and these infrastructures to heat mortality in Maricopa County and

In an extreme heat event, people can go to air-conditioned public facilities if residential air-conditioning is not available. Residences that heat slowly may also mitigate health effects, particularly in neighborhoods with social vulnerability. We explored the contributions of social vulnerability and these infrastructures to heat mortality in Maricopa County and whether these relationships are sensitive to temperature. Using Poisson regression modeling with heat-related mortality as the outcome, we assessed the interaction of increasing temperature with social vulnerability, access to publicly available air conditioned space, home air conditioning and the thermal properties of residences. As temperatures increase, mortality from heat-related illness increases less in census tracts with more publicly accessible cooled spaces. Mortality from all internal causes of death did not have this association. Building thermal protection was not associated with mortality. Social vulnerability was still associated with mortality after adjusting for the infrastructure variables. To reduce heat-related mortality, the use of public cooled spaces might be expanded to target the most vulnerable.

ContributorsEisenman, David P. (Author) / Wilhalme, Holly (Author) / Tseng, Chi-Hong (Author) / Chester, Mikhail Vin (Author) / English, Paul (Author) / Pincetl, Stephanie Sabine, 1952- (Author) / Fraser, Andrew (Author) / Vangala, Sitaram (Author) / Dhaliwal, Satvinder K. (Author)
Created2016-08-03
Description

Better methods are necessary to fully account for anthropogenic impacts on ecosystems and the essential services provided by ecosystems that sustain human life. Current methods for assessing sustainability, such as life cycle assessment (LCA), typically focus on easily quantifiable indicators such as air emissions with no accounting for the essential

Better methods are necessary to fully account for anthropogenic impacts on ecosystems and the essential services provided by ecosystems that sustain human life. Current methods for assessing sustainability, such as life cycle assessment (LCA), typically focus on easily quantifiable indicators such as air emissions with no accounting for the essential ecosystem benefits that support human or industrial processes. For this reason, more comprehensive, transparent, and robust methods are necessary for holistic understanding of urban technosphere and ecosphere systems, including their interfaces. Incorporating ecosystem service indicators into LCA is an important step in spanning this knowledge gap.

For urban systems, many built environment processes have been investigated but need to be expanded with life cycle assessment for understanding ecosphere impacts. To pilot these new methods, a material inventory of the building infrastructure of Phoenix, Arizona can be coupled with LCA to gain perspective on the impacts assessment for built structures in Phoenix. This inventory will identify the origins of materials stocks, and the solid and air emissions waste associated with their raw material extraction, processing, and construction and identify key areas of future research necessary to fully account for ecosystem services in urban sustainability assessments. Based on this preliminary study, the ecosystem service impacts of metropolitan Phoenix stretch far beyond the county boundaries. A life cycle accounting of the Phoenix’s embedded building materials will inform policy and decision makers, assist with community education, and inform the urban sustainability community of consequences.

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Description
Background
Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the

Background
Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment on the pace of biological discovery. It is thus imperative to design an automated system for efficient image annotation and comparison.
Results
We present a computational framework to perform anatomical keywords annotation for Drosophila gene expression images. The spatial sparse coding approach is used to represent local patches of images in comparison with the well-known bag-of-words (BoW) method. Three pooling functions including max pooling, average pooling and Sqrt (square root of mean squared statistics) pooling are employed to transform the sparse codes to image features. Based on the constructed features, we develop both an image-level scheme and a group-level scheme to tackle the key challenges in annotating Drosophila gene expression pattern images automatically. To deal with the imbalanced data distribution inherent in image annotation tasks, the undersampling method is applied together with majority vote. Results on Drosophila embryonic expression pattern images verify the efficacy of our approach.
Conclusion
In our experiment, the three pooling functions perform comparably well in feature dimension reduction. The undersampling with majority vote is shown to be effective in tackling the problem of imbalanced data. Moreover, combining sparse coding and image-level scheme leads to consistent performance improvement in keywords annotation.
ContributorsSun, Qian (Author) / Muckatira, Sherin (Author) / Yuan, Lei (Author) / Ji, Shuiwang (Author) / Newfeld, Stuart (Author) / Kumar, Sudhir (Author) / Ye, Jieping (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / Ira A. Fulton Schools of Engineering (Contributor)
Created2013-12-03
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Description
Background
“Stoichioproteomics” relates the elemental composition of proteins and proteomes to variation in the physiological and ecological environment. To help harness and explore the wealth of hypotheses made possible under this framework, we introduce GRASP (http://www.graspdb.net), a public bioinformatic knowledgebase containing information on the frequencies of 20 amino acids and atomic

Background
“Stoichioproteomics” relates the elemental composition of proteins and proteomes to variation in the physiological and ecological environment. To help harness and explore the wealth of hypotheses made possible under this framework, we introduce GRASP (http://www.graspdb.net), a public bioinformatic knowledgebase containing information on the frequencies of 20 amino acids and atomic composition of their side chains. GRASP integrates comparative protein composition data with annotation data from multiple public databases. Currently, GRASP includes information on proteins of 12 sequenced Drosophila (fruit fly) proteomes, which will be expanded to include increasingly diverse organisms over time. In this paper we illustrate the potential of GRASP for testing stoichioproteomic hypotheses by conducting an exploratory investigation into the composition of 12 Drosophila proteomes, testing the prediction that protein atomic content is associated with species ecology and with protein expression levels.
Results
Elements varied predictably along multivariate axes. Species were broadly similar, with the D. willistoni proteome a clear outlier. As expected, individual protein atomic content within proteomes was influenced by protein function and amino acid biochemistry. Evolution in elemental composition across the phylogeny followed less predictable patterns, but was associated with broad ecological variation in diet. Using expression data available for D. melanogaster, we found evidence consistent with selection for efficient usage of elements within the proteome: as expected, nitrogen content was reduced in highly expressed proteins in most tissues, most strongly in the gut, where nutrients are assimilated, and least strongly in the germline.
Conclusions
The patterns identified here using GRASP provide a foundation on which to base future research into the evolution of atomic composition in Drosophila and other taxa.
ContributorsGilbert, James D. J. (Author) / Acquisti, Claudia (Author) / Martinson, Holly M. (Author) / Elser, James (Author) / Kumar, Sudhir (Author) / Fagan, William F. (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2013-09-04
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Description
Background
Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS,

Background
Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.
Results
For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.
Conclusions
SISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.
ContributorsSchwartz, Rachel (Author) / Harkins, Kelly (Author) / Stone, Anne (Author) / Cartwright, Reed (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (Contributor)
Created2015-06-11