Office of Research, UC Riverside
UCR Federal Grants  
3/11/2022


Principal Investigator:
Yates, Tuppett
Professor of Psychology
Psychology

Award#
008416-002

Project Period
7/15/2016 - 6/30/2019

Funding Agency
NATIONAL SCIENCE FOUNDATION

Summary
Children's beliefs and expectations about their relationships with their parents are related to their ability to adapt to new situations, experiences, and relationships, including those with peers and teachers. The goal of this project is to investigate the link between children's understanding of their relationships with their parents and their ability to adapt to the challenges of early adolescence. Early adolescence is a period of significant change in children's family dynamics as they begin to pursue autonomy and an independent identity. Young adolescents also encounter new social and academic challenges as they navigate the transition to middle school. This project will evaluate how youths' thoughts and feelings about their relationships with their mothers relate to their own self-concept, self-regulation, school adjustment, and social competence. The outcomes will be compared to these children's same measures at earlier points in their development.

This project will extend an ongoing NSF-supported study of 250 mother-child dyads (50% female children; 95.2% longitudinal retention) from multiple ethnoracial groups (88.8% non-White) and variable risk backgrounds (e.g., 36.7% poverty, 28% maltreated) who completed laboratory and school assessments of representation, adjustment, and parent-child relationship quality at ages 4, 5, 6, 7, 8, and 10. The current funds will support an early adolescent data wave at age 12 to assess multiple facets of youths' representations in terms of what they think and feel (i.e., the content of their representation) and how they organize their thoughts and feelings (i.e., the coherence of representation) to understand how representational processes may carry experience from the family setting to broader educational and social contexts. In addition to evaluating core developmental assumptions, expected scientific tools and findings will refine contemporary risk identification and screening approaches by providing efficient and culturally valid assessment tools that can be readily transported to clinical and field (e.g., school) settings.
(Abstract from NSF)

3/11/2022


Principal Investigator:
Xu, Shizhong
Distinguished Professor and Geneticist
Botany and Plant Sciences

Award#
007433-002

Project Period
7/1/2015 - 6/30/2018

Funding Agency
NATIONAL SCIENCE FOUNDATION

Summary
Understanding the mechanisms of genotype and phenotype (G2P) associations has been an important and challenging task in modern biology. The challenge lies in the high-dimensional gene variables and the complexity of gene regulation and interactions that collectively define particular phenotypes (also called traits). The project will develop innovative methods, tools and bioinformatics systems to decipher the plant G2P associations through integrative genome-scale biological network and genome-wide association analysis. A breakthrough in this work will lead to a systems-level understanding of how biological processes, pathways and complex traits in plants are hierarchically regulated. Advancing such fundamental knowledge will greatly benefit modern genome-assisted plant breeding by providing the underlying regulatory mechanisms and key regulators of agriculturally important traits. This in turn will have great potential to be translated into new means of improving plant quality and production for agriculture, thus benefiting society as a whole. Cutting-edge technologies will be developed to study G2P associations in plants, providing excellent opportunities for training undergraduates, graduates and postdocs in interdisciplinary fields such as computational biology, bioinformatics, plant genomics, and statistical genetics, at the three institutes. Underrepresented minorities and women will be especially targeted in the recruitment of the project. The research will form the basis of the proposed educational workshops centering on bioinformatics and statistical genetics. Creative and innovative hands-on outreach activities will be arranged through the three institutes? outreach programs with local K-12 schools to inspire young minds to become bioinformatics scientists.

Innovative methods will be developed to analyze genome-scale biological networks and genome-wide associations through a fully integrated bioinformatics platform, enabling the discovery of G2P associations in plants. Specific aims of the project include 1) to develop novel top-down and bottom-up graphical Gaussian model (GGM) algorithms to reconstruct the hierarchical gene networks that control biological processes and pathways; 2) to develop models and algorithms that enable large-scale marker-trait association analysis with high precision using novel statistical genetics approaches; and 3) to develop a Graph-search-empowered integrative bioinformatics platform to facilitate the integration, deciphering and discovery of G2P associations. To validate our approaches and tools, public data from genome-wide plant 'omics' studies and genome-wide association studies (GWAS) will be integrated and analyzed, associating traits with SNP markers and fine-tuning the prediction of phenotype-associated hierarchical and/or pleiotropic regulators and functional networks. The novel knowledge and analytic methods and tools yielded from this project will be disseminated into the public at large through presentations, publications and web applications. All the tools and data resources will be made freely available at http://plantgrn.org/ to the plant research communities, accelerating plant bioinformatics and plant science research, education and applications.
(Abstract from NSF)

3/11/2022


Principal Investigator:
Tsutsui, Hideaki
Associate Professor
Mechanical Engineering

Award#
008305-003

Project Period
7/5/2017 - 6/30/2019

Funding Agency
NATIONAL SCIENCE FOUNDATION

Summary
PI: Tsutsui, Hideaki
Proposal No: 1606181

This project proposes to develop a paper-based molecular sensing platform. The primary advantages are its low cost and ease of use. The proposed work is expected to broadly expand the capability and applications of paper-based sensors for a variety of fields, such as medical, agricultural, and environmental testing and diagnosis.



Paper-based microfluidic devices have recently emerged as promising sensing platforms for serving the diagnostic needs in many sectors of society. Advantages of paper-based microfluidic sensors include fast detection, ease of fabrication and use, minimal instrument requirements, lightweight, portability, and low cost. However, its widespread use beyond research laboratories has been hampered because of a lack of highly sensitive detection methods that can be easily implemented on a paper substrate. The overall goal of this project is to develop a label-free, highly sensitive, chemiresistive nanosensor platform. This goal will be achieved through a series of research tasks: 1) development of an ultrasensitive carbon nanotube chemiresistive biosensor on paper; 2) development of an effective fluid handling technology; and 3) integration and demonstration of label-free, multiplexed detection of cardiac biomarkers as model antigens. Intellectual merits include a highly sensitive sensing element made of semiconducting single-walled carbon nanotubes and technological innovations of microfluidic transport, which collectively enable the proposed nanosensor. Broader impact of the research program is expansion of the capability and applications of the paper-based microfluidic-facilitated biosensors. In particular, the proposed label-free chemiresistive biosensor array is expected to be highly sensitive, facile, and economical. It is also expected to be readily applicable to the multiplexed detection of analytes in a variety of complex fluid matrices such as food, water, plants, and body fluids. In conjunction with research activities, this project will develop and integrate several outreach and educational activities, including new curricula development on paper-based microfluidic biosensors, research training of both undergraduate and graduate students, particularly underrepresented minorities and women, and outreach efforts to engage K-12 teachers and students of the Inland Empire region of California.
(Abstract from NSF)

3/11/2022


Principal Investigator:
Switzer, Christopher Y
Professor of Chemistry
Chemistry

Award#
006408-003

Project Period
9/1/2013 - 8/31/2016

Funding Agency
NATIONAL SCIENCE FOUNDATION

Summary
With this award, the Chemistry of Life Processes Program in the Chemistry Division is funding Dr. Christopher Switzer at the University of California-Riverside, to develop metal mediated base pairs that are capable of participating in information transfer reactions alongside their natural counterparts. To accomplish this objective, metal mediated base pair motifs will be developed with optimal shape and size for acceptance by natural enzymes. The work under the award will build on preliminary studies by the PI's laboratory to create a next generation metal mediated base pair capable of such function. This next generation base pair uses a tridentate purine-like component and a monodentate pyrimidine-like component to coordinate a divalent metal ion, such as Cu2+. The function of metal mediated base pairs with natural polymerase enzymes will be explored and optimized by employing a range of different monodentate nucleotides chosen on the basis of synthetic expediency and known optimal design features.

Watson-Crick base pairs encode genetic information in all organisms. While natural base pairs rely on hydrogen bonds for recognition, other weak or reversible interactions hold promise for the creation of non-standard base pairs. Metal-mediated bonds have been shown recently to replace hydrogen bonds between non-standard bases in the DNA helix. The next steps in the progression to achieve functional metal-mediated base pairs are therefore now within reach. The program of study will provide a solid training ground for graduate students in chemical biology. Additionally, research opportunities for undergraduate students will be offered during the proposal period, including a summer undergraduate research position for underrepresented minorities or women.
(Abstract from NSF)

3/11/2022


Principal Investigator:
Stajich, Jason
Professor
Microbiology & Plant Pathology

Award#
008080-002

Project Period
4/1/2016 - 3/31/2019

Funding Agency
NATIONAL SCIENCE FOUNDATION

Summary
The anaerobic gut fungi (AGF) differ from all other groups of fungi by having a restricted habitat (the rumen and alimentary tract of herbivores), and by growing in the absence of atmospheric oxygen. They have evolved hundreds of millions of years ago and represent one of the oldest fungal groups. However, the evolutionary history of anaerobic fungi is currently unclear. Specifically, the exact relationship between anaerobic fungi and other fungal groups, as well as the timing and sequence of events that lead to their sequestration into the herbivorous gut remain unclear. Further, it is not exactly known how the retention of anaerobic fungi in the herbivorous gut has affected their genomes and evolution. This project will tackle these questions by sequencing the genomes of a large, diverse collection of anaerobic fungi, and analyzing the data produced using a wide range of computational procedures. The project will engage multiple high school and undergraduate students in research, with special effort to engage minority (especially Native American) students to advance the participation of underrepresented groups in STEM disciplines. 


Overall research progress on anaerobic fungi has been slow, and sequencing of AGF genomes has been hampered by their extremely high AT content and the proliferation of intergenic repeats in their genomes. This project will utilize a new approach that combines multiple sequencing technologies to sequence the genomes and transcriptomes of a large and diverse collection of anaerobic fungal isolates. This research will utilize the data generated to conduct an extensive phylogenomic analysis, aiming to resolve their evolutionary history within the fungal tree of life, correlate the timing of AGF diversification events to the evolution of their herbivorous hosts, resolve the diversification pattern of anaerobic fungal genera, and investigate the impact of the unique habitat and evolutionary trajectory on their genomic architecture. The proposed efforts will lead to significant advances in the understanding of the history of this peculiar group of fungi and factors driving their evolution. Further, the genomic and transcriptomic data obtained would be of extreme interest to a broader group of scientists working in the areas of biofuel research, animal nutrition, and molecular biology of fungi.
(Abstract from NSF)

3/11/2022


Principal Investigator:
Stajich, Jason
Professor
Microbiology & Plant Pathology

Award#
007015-003

Project Period
1/1/2015 - 12/31/2018

Funding Agency
NATIONAL SCIENCE FOUNDATION

Summary
Fungi comprise one of the most successful groups of life on Earth. They inhabit most of the world's environments, where they perform numerous functions (e.g., nutrient cycling, foundations of food webs, etc.) that are central to healthy ecosystems. Importantly, fungi interact with all other forms of life, including plants, animals and bacteria -- in associations that range from beneficial to antagonistic. Zygomycete fungi, the focus of this research project, are an ancient group in which most of the morphological and ecological traits associated with Kingdom Fungi first arose, but their evolutionary history and ecological associations have not yet been well resolved. This project will reconstruct the genealogical relationships of this earliest branch in fungal evolutionary history, resolve the origins of symbiotic relationships between plants and zygomycetes, reveal how complex body plans evolved in the group, elucidate mechanisms of mating genetics between organisms with complex and differing life cycles, and develop genomic barcodes to facilitate identification of unknown fungi. The results of this research will contribute to many scientific disciplines and to society. Expanding and maintaining expertise on these fungi is critical for the field of biology, human health and productivity, and safe food production. This project includes training of the next generation of mycologists, dissemination of information on basic fungal biology, development of teaching resources, expansion of biological database and web resources, development of research materials including strain cultures and genomes for the wider scientific community, and broadening of participation of underrepresented groups in STEM disciplines.

Zygomycetes are filamentous fungi that lack flagella and that produce simple but defined reproductive structures. An initial analysis of zygomycete genomes support the hypothesis that the group is a pivotal transition point between certain flagellated Fungi and their specific life histories, and what became the dominant eukaryotic terrestrial clade of Fungi (the fleshy fungi, e.g., mushrooms). Because the zygomycetes are the first terrestrial fungi that exhibit fruiting bodies, understanding how these structures evolved will provide a basis for understanding the origins of complex morphogenesis (e.g., multicellularity) in the Fungi, as well as the evolution of complex life histories. Zygomycetes also display a diversity of ecological relationships with plants (mycorrhizae), animals (pathogens) and bacteria (endosymbionts). Resolving the phylogenetic origins of these interactions will provide an evolutionary framework for elucidating molecular and biochemical mechanisms that govern these interactions, and in doing so, will have direct impacts on research into natural and managed ecosystems and human welfare. This research will also refine molecular environmental sampling techniques, resulting in a more accurate census of zygomycete biodiversity, especially in soil ecosystems. By gathering orders of magnitude more genome-scale data and integrating it with biochemical, morphological, subcellular, and fossil data layers, this elusive region of the fungal genealogy of life will be illuminated and will provide a foundation for broad scale biological research.
(Abstract from NSF)

3/11/2022


Principal Investigator:
Rey, Sergio
Adjunct Professor
Faculty Initiatives

Award#
009475-002

Project Period
7/31/2017 - 8/31/2020

Funding Agency
NATIONAL SCIENCE FOUNDATION

Summary
This research project will advance the way in which neighborhoods are defined in urban social science research. The definition of a socioeconomic neighborhood is an important and central issue across many research domains. Neighborhoods serve as the organizational units to frame empirical research that has examined a wide array of issues, including the ability of social networks to produce collective efficacy in a spatial context, the relationships between concentrated poverty traps and violence, spatial sorting and segregation, and the role of neighborhoods as seeds for wider urban economic development. Despite this importance, consensus has not yet emerged regarding how to operationalize neighborhoods in practice. Moreover, the role of spatial structure largely has been ignored in existing approaches to neighborhood definition. This project will produce new methods for neighborhood identification and analysis that draw on recent developments in geographic information science and spatial statistics. These new methods will enhance the urban social science toolkit enabling researchers to carry out empirical work that can be replicated, thereby moving urban policy research onto stronger analytic foundations. The new methods and analytics will be implemented in a publicly available open-source longitudinal neighborhood analysis package. The project will provide training to a post-doctoral research associate and will include a partnership between academia and industry, with applications to commercial market segmentation and analysis.

This research project will advance understanding of the spatial dimensions of neighborhoods. The project will focus on three central aims. First, a number of underexamined issues associated with defining neighborhoods in spatial and temporal contexts will be investigated. These issues are related to the lack of a spatially explicit approach to neighborhood definition in the current literature and the impacts of ignoring the dynamics of spatial clustering and heterogeneity. The second aim is to develop new methods for neighborhood delineation and analysis that address these issues. These new methods will include local measures to identify hot-spots of neighborhood change within individual urban areas as well as global measures that summarize the overall amount of spatial change in a given metropolitan area. The third area of activity will be the implementation of the new methods for neighborhood delineation in an open-source framework to provide social scientists with a platform of flexible, scalable, and advanced spatio-temporal clustering methods that support replication and enhance the existing infrastructure of social science research on urban dynamics.
(Abstract from NSF)

3/11/2022


Principal Investigator:
Ren, Shaolei
Associate Professor
Electrical & Computer Eng

Award#
008313-002

Project Period
7/15/2016 - 6/30/2019

Funding Agency
NATIONAL SCIENCE FOUNDATION

Summary
Microgrids are localized grids that have become an integral component of future smart grids. Meanwhile, datacenters have been expanding enormously to support the exploding digital economy worldwide, emerging as significant energy consumers that are commonly co-located with a diverse set of non-datacenter loads in microgrids. Nonetheless, prior research on datacenter energy management, although encouraging, has traditionally viewed datacenters as isolated stand-alone facilities and rarely considered their physical interconnection with other loads. On the other hand, the rich literature on microgrid energy management has primarily focused on non-datacenter loads (e.g., thermostatically controlled loads), while treating energy-intensive datacenters as miscellaneous loads and ignoring their unique global-routing capabilities. This lack of integration and coordination between datacenter and non-datacenter loads poses a series of challenges to microgrid management, such as high peak demand, waste of on-site renewables, and even potential threats to the stability of main grids.

This project seeks to address the challenges and optimize microgrid energy management for minimizing the energy cost and facilitating demand responses to better protect the main grid. Towards this end, this project takes a transformative shift from the current view that treats datacenter and non-datacenter loads separately, to an integrated approach that holistically coordinates both datacenter and non-datacenter loads in microgrids. Specifically, this project investigates two complementary research thrusts. First, when the microgrid operator can directly schedule the loads, this project investigates novel control algorithms to holistically manage both datacenter and non-datacenter loads, while taking into account datacenters spatial-routing and heterogeneous communications capabilities. Second, when the loads are managed by self-interested entities, this project studies market mechanisms to coordinate both datacenter and non-datacenter loads for microgrid-level efficiency.

This project advances the existing research on microgrid energy management by transforming datacenters' role in microgrids from miscellaneous loads into a valuable asset with high scheduling flexibilities. It can catalyze a shift in the way that microgrids evolve, bearing great economic, environmental and societal impacts. This project will also incorporate the research into existing courses and provide abundant opportunities to nurture and attract students, especially those from under-represented groups, to engage in research careers.
(Abstract from NSF)

3/11/2022


Principal Investigator:
Rankin, Erin
Professor of Entomlogy
Entomology

Award#
008066-002

Project Period
7/1/2016 - 6/30/2019

Funding Agency
NATIONAL SCIENCE FOUNDATION

Summary
Invasive species are one of the main drivers of global environmental change. Consequently, there is growing interest in understanding how invaders damage ecosystems and in developing management strategies to minimize their effects. Through manipulative field experiments and native-introduced range comparisons, this research will investigate how and when invasive yellowjackets express variation in their life cycle, specifically, whether their colonies die back (senescence) each year, or are perennial colonies. This project contributes to understanding of life cycle variation in insects, how such flexibility mediates ecological processes at the landscape scale, and what factors interact to influence perenniality. The research will help inform predictions as to how impacts of species invasions may respond to climate change. Furthermore, this project will provide insights into transmission of common diseases of wasps and their bee prey. As yellowjackets can be public nuisances, revealing the causes of perenniality may lead to the development of control methods that prevent the emergence of perenniality in this species and potentially in other species. In addition to providing research opportunities for undergraduates, the researchers will develop an educational activity on invasive social insects for K-6 children about the biology and potential hazards posed by social wasps.

This project focuses on invasive social wasps that have structural effects on the ecosystems that they invade. These wasps express plasticity in key life history traits (e.g. annual or perennial colony phenology), which greatly magnifies their ecological impacts. The researchers explicitly test how ecological and climatic factors interact to affect shifts in invader life history traits and ultimately modify invasion impacts. Specifically this research investigates how yellowjacket foraging behavior and colony phenology shift in response to diet subsidies, artificial warming of the nest to simulate mild climate, or both subsidies and artificial warming. Coupling such manipulations with landscape-scale prey population sampling, this project also quantifies subsequent invasion impacts on native prey. These experiments will provide insights as to how yellowjackets may respond to changes in pollinator populations and climate change. Furthermore, researchers will determine whether wasp consumption of honey bees influences pathogen load; this is particularly important as honey bee pathogens are increasingly detected in non-honey bee species. Pathogen screening will help distinguish whether (a) wasps increase their pathogen load by consuming bees, (b) whether wasps transmit pathogens through predation and raiding of beehives, and (c) identify differences in pathology between annual and perennial colonies. Understanding the factors affecting life history is vital for predicting how trait evolution or plasticity may respond to future global climate change.
(Abstract from NSF)

3/11/2022


Principal Investigator:
Qian, Zhiyun
Professor
Computer Science & Engineering

Award#
008513-002

Project Period
10/1/2016 - 9/30/2019

Funding Agency
NATIONAL SCIENCE FOUNDATION

Summary
Use of encrypted Web traffic is growing at an unprecedented rate. While enhancing user privacy, Secure Hypertext Transfer Protocol (HTTPS) makes it difficult for middleboxes that are commonly used by Internet service providers and mobile carriers to operate, because numerous beneficial middlebox functions (e.g., caching, web page optimization) rely on accessing the unencrypted traffic content. To overcome this challenge, this project develops a system aiming for a practical, ready-to-deploy solution that allows middleboxes to selectively inspect and manipulate HTTPS traffic while still respect the privacy requirements of users. This research will lead to new and continuous innovations in network services that are hard or impossible to achieve today.

The system has two prominent features. First, it is only deployed at client hosts as an operating system (OS) service, as well as on middleboxes. In addition to being transparent to applications, it does not change the encryption protocol or anything on the server side. Therefore, the system can be easily deployed by, for example, regular OS update pushed by mobile carriers. Second, the system allows clients to control what information the middlebox can access. Doing so provides least privileges to middleboxes for performing their functions. In addition, the proposed system is easy to use, secure, and incurs low overhead.

Developing these technologies will facilitate our understanding of the possible design space to allow coordinated, secure, and efficient manipulation of HTTPS traffic, ultimately leading to improved Internet user experience and privacy. The PIs will incorporate knowledge and results developed in this project into both undergraduate and graduate courses in networking, mobile computing and network security.
(Abstract from NSF)

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