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Connecting Researchers in Sharing and Re-Use of Research Data and Software: University of California Office of the President

Sponsor: University of California, Office of the President, Oakland

Guenter Waibel

[email protected] (Principal Investigator)

ABSTRACT

Open science practices have gained widespread adoption, globally, with the help of federal funding and publisher policies, as well as the increasing visibility and growing awareness of the value of sharing work. This has been largely evident in light of the current COVID19 pandemic, with data sharing driving many areas of research, and open software resources must evolve to meet the needs of researchers. To meet the emerging demands and growing requirements of the research community who need support for both data and software sharing, Dryad and California Digital Library partnered in 2018 and Dryad and Zenodo partnered in 2019. These partnerships have allowed for the three organizations to re-think the data and publishing processes, explore ways for data curation, software preservation, and for output re-use to be tied together more seamlessly.

This project is a one-day, invitational workshop bringing together researchers and adjacent community members with diverse backgrounds to discuss needs, challenges, and priorities for re-using research data and software. The goal of the meeting is to develop pathways for consistent engagement with individuals and groups across the diverse scientific disciplines in order to be connected with and responsive to researchers’ needs and goals. Meeting topics include dataset re-use, deposition guidance, curation standards and requirements, integrations and relationships between data and code, and advocacy and adoption. The anticipated outputs are a set of requirements and needs to better enable data and software sharing and re-use.

InventXRLearn TechResearchXR

SusChEM: Design Principles Inspired by Symmetry for Controlling Singlet Fission in Structurally Well-Defined Covalent Dimers: University of Colorado at Boulder

Niels Damrauer

[email protected]

In this project funded by the Chemical Structure, Dynamic & Mechanism B Program of the Chemistry Division, Professors Niels H. Damrauer and Tarek Sammakia of the Department of Chemistry and Biochemistry at the University of Colorado Boulder are synthesizing new organic molecular systems that contain two chromophores (i.e., parts of the molecules that can absorb light) and using spectroscopy to explore their photophysics. The goal is to develop design rules for how the arrangement of the chromophores controls excited state reactivity following visible light photoexcitation. The particular reaction of interest is important in certain next-generation strategies to increase the efficiency of solar cells by limiting waste heat production that generally occurs when higher energy solar photons are absorbed. This proposal establishes a fundamental research program where students are exposed to a considerable breadth of ideas in synthesis, spectroscopy, and applications of electronic structure theory. A specific outreach effort in collaboration with local high school teachers is part of the funded work that aims to provide sophisticated but affordable spectroscopic tools and curriculum ideas to Colorado high school science programs. <br/><br/>Singlet fission is a photophysical phenomenon observed in certain organic materials wherein light absorption produces a spin-allowed singlet excited state that then non-radiatively converts to a pair of triplet excitations. If these triplets can be further transformed to charge carriers, it is possible to envision device scenarios where the solar spectrum is more efficiently utilized compared to devices in operation today. This research is predicated on the idea that molecular dimers are the fundamental unit for singlet fission and that they can provide a platform wherein synthetic manipulations that control the spatial juxtaposition and covalent interaction of chromophores are called upon to affect key photophysical rate constants. The most important design opportunity that is being tested relates to dimer point group symmetry and the idea that it can control the interference (constructive vs. destructive) of pathways in the quantum mechanical description of diabatic coupling for singlet fission. Other strategies will call on substituents to affect the relative energy of charge transfer states.

 

ResearchXR

RAPID: Glycocalyx engineering to probe the role of mucin structure in coronavirus transmission and infection: University of Utah

Jessica Kramer

[email protected]

Project Non-Technical Abstract<br/><br/>With this award, the Biomaterials Program in the Division of Materials Research and the Chemistry of Life Processes Program in the Division of Chemistry are funding Dr. Jessica R. Kramer from The University of Utah to study the role of mucus composition in coronavirus (COV) transmission. COV-related diseases have emerged as a serious public health threat. Airborne droplets from an infected person?s cough, sneeze, or even talking are a major source of viral spread. These droplets stem from virus-laden mucosalivary fluid and land on the mucus membranes of the next potential host (mouth, airway, eyes) or on hard surfaces. There, the virus is dispersed for the next infection. Mucus is produced in hundreds of forms that vary between species, and even person-to-person. The forms present could affect how easily the viruses pass through the mucus membrane, especially since some types bind directly to COVs. Mucus forms could also affect the concentration and viability of COVs in airborne droplets. The goal of this project is to identify the forms of mucus that result in increased airborne COV transmission and infection. This will be accomplished by simulation of cough droplets produced from varied mucus and using human cells coated with varied mucus. This knowledge could lead to development of new therapeutics that disrupt COV-mucus binding, or identify populations more vulnerable to COV transmission and infection. <br/><br/><br/>Project Technical Abstract<br/><br/>This research project undertakes study of the role of mucin glycoprotein structures in coronavirus (COV) transmission via airborne particles, fomite objects, and in cellular entry through the glycocalyx. Epithelial tissue is coated with protective mucins that are secreted to form mucus and also tethered to the cell surface to form the glycocalyx. COVs must traverse these layers before entry into host cells for replication. Viral transmission through expelled airborne mucosalivary droplets is a major mode of transmission. Mucins are produced with a variety of attached glycans specific to each host. These glycans alter the viscoelasticity of mucosalivary fluid and directly bind to COV spike proteins. These factors could affect virus loading and viability in airborne particles and could affect docking and diffusion at the cell surface. However, such questions have been challenging to answer because native mucin glycosylation is poorly-defined and not tunable by current biological methods. The PI?s lab will synthesize mucin analogs with tunable COV-binding glycan patterns and will use them to engineer the glycocalyx of live cell surfaces. Coughs will be simulated and the role of mucin structure in airborne respiratory droplet COV transmission will be examined by characterization of droplet morphology, and viral loading and viability. Docking and diffusion at the cell surface, as well as replication, will be quantified on live epithelial cells.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

ResearchXR

RAPID Proposal: Psychological distance and risk perception related to the 2019 novel coronavirus (2019-nCoV) outbreak: SUNY at Buffalo

Janet Yang

[email protected]

This project assesses the American public?s perception of the 2019 novel coronavirus outbreak that originated from Wuhan, China. The focus of this research is to examine whether Americans? perception of the root cause of the outbreak, as well as whether they believe the outbreak is a distant issue for most Americans, will determine their risk perception and emotional responses to the outbreak. Further, this project examines the extent to which risk perception and emotions influence whether Americans seek information about this issue, share information with others, and support public health policies including international cooperation. The proposed research advances risk communication research, as well as enhances our understanding of strategic messaging design to benefit public health, prosperity and welfare.<br/><br/>The proposed research is an experimental survey to assess 1) how psychological distance (especially spatial and social distance) and causal attribution influence the U.S. public?s risk perception surrounding the 2019 novel coronavirus outbreak; 2) how mental construal of the outbreak determines Americans? emotional responses to the outbreak; 3) how risk perception and emotional responses influence risk communication behaviors and public support for U.S. involvement in providing aid; and 4) whether cultural cognition moderates these relationships. The research involves a survey, based on a nationally representative sample of 1,000 participants, who are randomly assigned to four experimental conditions. Psychological distance and causal attributions are the main experimental factors with cultural cognition as the primary moderator, while risk perception, emotional responses, communication behaviors, and support for U.S. response effort are the outcome variables. The outbreak provides a unique context to study public risk perception and risk communication behaviors. Although only a small number cases have been confirmed in the U.S. at the inception of the research, there is heightened media attention and the U.S. government has issued a travel ban to all foreign nationals who have been to mainland China. It is possible that social cognitive mechanisms, such as psychological distance, causal attribution, and cultural cognition will synergistically influence public risk perceptions and subsequent communication behaviors and support for public health policies. Exploring these mechanisms and their respective impacts can help us understand how to communicate better about a major disease outbreak in an interconnected world.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

ResearchXR

RAPID: A Longitudinal Study of Public Responses to the Coronavirus: University of Oregon Eugene

Ellen Peters

[email protected]

The coronavirus pandemic provides a rare opportunity to study public risk perceptions and risk-related behaviors in the midst of a World Health Organization Public Health Emergency of International Concern that could threaten the quality of life of a wide spectrum of Americans. Few emergencies within the United States have affected so many people. The situation is a rich opportunity because it is occurring in real-time and is highly dynamic, involving many players in our country and around the world. As a result, it allows the research team a chance to compare this health threat with other perceived disasters such as immigration, terrorism, and possible future public health emergencies. The public?s perceptions and risk-related behaviors seem likely to change over time in response to media coverage as well as actions from our own and foreign governments.<br/><br/>In one longitudinal study, the research team invites participants from Amazon Mechanical Turk to complete one survey each month for 5 months. The researchers query their risk perceptions and affective responses toward the coronavirus, frequency of discussions about the coronavirus with others, behavioral intentions towards hypothetical experimental vaccines and treatments, and support for possible policy solutions such as quarantine. The research also ascertains their intended travel plans and media exposure to the pandemic including how much they trust those sources. The team models the emotional, risk-perception, and behavioral responses of participants toward the coronavirus by using a latent variable growth curve model that examines the trajectories of variables over time. To establish causal links, the scholars also conduct a second related experiment that manipulates affect through narratives and examines its effects on risk perceptions, medical decisions, and policy decisions. Participants are assigned to a more negative or less negative condition, and mediation analysis is used to evaluate the manipulation?s effects. In these studies, theoretical links are made between risk perceptions, social amplification of risk, the affect heuristic and other functions of affect, and numeracy. There is a dynamic test of the three functions of affect by correlating current feelings over time with risk judgments, intended prevention and treatment behaviors, and support for policy options. Theoretical research on affect has not been tested in the setting of a world health emergency. This research results in deep mechanistic understanding of how emotions and media exposure influence vaccine and treatment choices as well as support for policies. Finally, the second study establishes causal links between affect and support for prevention, treatment, and policy strategies. The research tests the dynamic and causal power of the functions of affect and motivated reasoning in order to lay the groundwork for interventions for emotional responses to the coronavirus and future epidemics. The research also has important implications, including for communication methods, for other affect-rich decisions faced by the public and policy makers.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

ResearchXR

RAPID: Investigating the Causal Propositions of the Affect Heuristic During an Ongoing Pandemic: Decision Science Research Institute

William Burns

[email protected]

The unprecedented pandemic wrought by the coronavirus has infected many people around the world, triggering anxiety and panic and disrupting all facets of life. In addition to the growing numbers of cases and deaths, the social, economic, and political impacts are vast. Lacking a vaccine or effective therapeutic cure, the front line of defense against the spread of this disease depends on human behavior, following guidelines about social distancing, sanitation, and other recommended measures. There is great uncertainty about the future trajectory of the disease and its impacts. Against the backdrop of this catastrophic threat this research forecasts public perceptions of risks, including hopes and fears, using a new theoretical model based on what is known as ?the affect heuristic.? The researchers build and test this model in two ways that increase understanding of how positive and negative emotions, influenced by daily news reports, interact to guide behavior. Understanding the changing reactions to news information not only advances understanding of risk perception, but enables the creation of effective risk communication messages. The research provides insight into the behaviors that will determine the course of the disease and can help to mitigate its harmful social and economic impacts.<br/><br/>Studies have consistently found an inverse relationship between judgments of benefits and risks associated with a wide array of hazards. This relationship occurs because perceptions of risk and benefit are derived in opposite ways from an affective sense of the importance of the risk. This process became known as the affect heuristic. The causal dynamics that underlie the relationship between affect and perceived risks and benefits remain poorly understood. This project does three things: (1a) constructs a system dynamics simulation model that explicitly incorporates the informational feedback loops that allow affect to play this moderating role and (1b) simulates the trajectories of affect and perceived risk and benefits as the coronavirus pandemic unfolds, (2) constructs a hybrid agent-based model that incorporates findings from the systems model but allows for heterogeneity (e.g., different levels of medical vulnerability) among agents, and (3) conducts a longitudinal national panel to survey the public?s response to the pandemic over a 6 month period. These data together with data from an independent panel are be used to estimate and validate both models. This project has broad impacts because understanding how we manage our perceptions of risk and benefits is critical to the decisions we make and our behaviors. The project helps to explain this entanglement and predict public reaction to the current pandemic and, potentially, to other crises.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

ResearchXR

RAPID: Biophysical characterization of the native SARS-CoV-2 virion by atomistic simulations: University of Delaware

Juan Perilla

[email protected]

Since December 2019, a novel coronavirus (SARS-CoV-2) that emerged in China has become a global pandemic. Research into the molecular basis of SARS-CoV-2 is now essential to provide understanding of viral entry and infection of human cells, a first step in developing novel drugs and vaccines to combat SARS-CoV-2. The research supported through this RAPID award will enable the development of an all-atom molecular dynamic simulation of the virus that includes realistic predictions of the envelope, membrane and spike proteins of the virus, as well as simulations of the complex surfaces of the human cells that the virus infects. This research could have immediate impact on steps taken to halt the spread of SARS-CoV-2. Simulation results will be broadly and quickly disseminated to ensure impact of the research. In addition, the investigators will use this as a training opportunity for students at all levels. <br/><br/>This project will use to state of the art tools of computational virology to provide bio-physical characterization of the SARS-CoV-2 virion, revealing information relevant to the function and potential targeting and disruption of the virus. The PI proposes a study of the full-size viral envelope which can establish the effects of specific components of the virus, including its bilayer lipid composition, shedding light on the need for coronaviruses to remodel the host cell membrane for successful infection. Additionally the characterization of the native SARS-CoV-2 viral surface proteins, which represent key functional and antigenic sites, will form a good basis for development of an infectious SARS-CoV-2 virion and a platform to investigate a mechanism of host cell entry, in which coronaviruses bind to CD13 receptors in lipid rafts. Study of glycosylated S protein, proposed as one of the aspects of the work, will reveal details of epitope masking by the glycan shield, relevant to vaccine and antibody design, as well as the role of viral glycans in host cell adhesion in a second mechanism of cell entry mediated by S binding to ACE2 receptors. The work could have immediate impact of the current pandemic.<br/><br/>This RAPID award is cofounded by the Molecular Biophysics Program in the Division of Molecular and Cellular Biosciences and the EPSCoR Program.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

ResearchXR

Collaborative Research: A Bridge to Physics and Astronomy Doctorates for Students with Financial Need: Cal Poly Pomona Foundation, Inc.

Alexander Rudolph

[email protected]

With funding from the NSF's Scholarships in Science, Technology, Engineering, and Mathematics (S-STEM) program, this project at California State Polytechnic University Pomona (CalPoly Pomona) will support high-achieving, low-income students with demonstrated financial need. This project will fund 146 scholarships over five years for students who are pursuing bachelor's degrees in physics and astronomy. Participating scholars will join a cohort-based mentoring and undergraduate research program spanning a diverse network of more than 50 California higher education institutions. These institutions are dedicated to the goal of increasing the number of students pursuing PhDs in physics, astronomy, and associated STEM disciplines. Led by CalPoly Pomona and the University of California Irvine in Southern California, and by San Jose State University and the University of California Santa Cruz in Northern California, more than 140 physics and astronomy faculty at the 24 California State University (CSU) and University of California (UC) campuses in the bridge network will serve as mentors to scholars supported by the project. In addition to receiving biweekly mentoring and progress monitoring by pairs of one UC and one CSU professor, these scholars will also receive full need-based scholarships during their junior and senior years, monthly professional development workshops, and supervised research opportunities via the successful NSF-funded CAMPARE program.<br/><br/>Given the size and diversity of the California secondary education system, the success of this S-STEM Track 3 project will likely significantly increase the number of PhDs nationwide earned by underrepresented minorities in the fields of physics and astronomy. All low-income students enrolled in a participating CSU campus are eligible for this California Bridge (Cal-Bridge) program, which searches for students with unusual potential, using holistic review and research-based criteria developed by successful bridge programs such as the Fisk-Vanderbilt Master's-to-PhD Bridge program. Unlike other existing bridge programs, Cal-Bridge begins with students during their formative undergraduate years, focusing on preparation rather than remediation. This multifaceted support will mitigate known barriers to graduate school entry for high-achieving, motivated students from economically disadvantaged backgrounds, and will thus greatly increase the probability they complete their undergraduate degree and gain entry to PhD programs. The project also involves multi-method social science research to understand the networks of scholars and institutions formed because of partnerships between Minority/Hispanic Serving Institutions and Research Universities, and the effect of those networks on recruitment and admissions to participating UC physics and astronomy departments. Over the five-years, social network analysis and qualitative case study methods will be used to capture patterns in Cal-Bridge Scholars' graduate school admissions and enrollment, as well as in impediments to these outcomes. These results, along with the project's growing connections with institutions beyond California, will have the potential to influence the national landscape of equitable participation by low-income students in STEM higher education.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

ResearchXR

Criminal Record Questions on Job Applications as a Self-Selection Mechanism for Applying for Employment: Ohio State University

Michael Vuolo

[email protected]

Individuals with criminal records fare worse at obtaining employment compared to those with clean records. Experimental evidence shows that employers prefer those with clean records, and that persons of color with records are particularly discriminated against. While much is known about employer hiring preferences, little is known about whether applicants with criminal records avoid or prefer particular employers. In other words, individuals with criminal records may not even apply to certain positions due to perceived low odds of getting the job or because they fear being stigmatized by employers in the application process. Employment is one of the most critical bonds for preventing a return to crime. If individuals elect not to apply for certain positions, such choices will decrease the odds of forming this important bond. Understanding under what conditions individuals with records choose to apply for jobs is therefore central to efforts to help individuals reintegrate into society and prevent crime. <br/><br/> This research project will interview 140 individuals with criminal records recruited from criminal reentry organizations and halfway houses in the Columbus, OH metropolitan area. An interview guide and brief survey were developed through a pilot study completed in 2017. In-depth interviews will provide nuanced information regarding job search experiences and choices. The interviews query topics such as experiences with job searches both before and after having a criminal record, whether criminal records questions or background check statements on job applications prevent individuals from applying for positions, how forthcoming individuals are about their record in the application process, and what types of industries they seek out. The survey gathers complementary information on socio-demographics, criminal history, employment history, and personal difficulties in applying for jobs. Respondents will be re-interviewed six months later in order to understand whether new experiences in the labor market alter choices among those with records, whether this differs by background factors related to labor market outcomes such as race, and the underlying reasons for any changes in choices such as those related to stigma. This project directly addresses ongoing public policy debates regarding how best to provide individuals with criminal records a fair assessment in the job application process so that they can experience the benefits of the important social bond of employment, best epitomized by the Ban the Box movement (which seeks to eliminate criminal record questions from job applications). By moving the discussion from decisions of employers to those of applicants, these results may fundamentally change the way we think about and evaluate these policies.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

ResearchXR

CSU Noyce Phase II: Empowering Scholars and STEM Teachers: Colorado State University

Meena Balgopal

[email protected]

There is an established need for well-qualified teachers in high-need school districts, which are often located in rural or urban communities, and those with significant populations of English language learners. Over the five-year duration of the project, the Colorado State University (CSU) Noyce Phase 2 Scholarship Program will prepare 24 new secondary science, technology, engineering, or mathematics (STEM) teachers educated in social justice. Each Noyce Scholarship recipient will be working toward or will have earned a bachelor's degree in a STEM discipline, and will be enrolled in the CSU secondary teacher education program. Four CSU STEM colleges will work in partnership with local school districts, CSU Extension, and the 21 Colorado Boards of Cooperative Educational Services. The project will address three research questions to better understand the effectiveness of teacher preparation programs: (1) What is the longitudinal impact on recipients' teaching self-efficacy, perceptions of STEM and STEM teaching, teaching ability, and self-efficacy as a teacher mentor? (2) What impacts do the Phase 1 and Phase 2 models have on secondary student perceptions of STEM and their STEM learning as well as recipients' perceptions of their students' learning? (3) What impacts does the Phase 2 model have on teacher mentor perceptions of STEM and STEM teaching, mentoring self-efficacy, and teaching ability?<br/><br/>The project will work toward three overarching objectives. (1) Recruitment: The project will recruit first and second year STEM undergraduates to work at an existing summer STEM camp for under-served students and provide them with mentorship from experienced in-service STEM classroom teachers. Undergraduates enrolled in a first year mathematics seminar led by a mathematics education expert will be engaged in outreach programs for under-served students and will be encouraged to apply for a Noyce Scholarship.(2) Support: Scholarships of $10,000 will be awarded to outstanding juniors and seniors committed to teaching in high need schools. The project will leverage a strong statewide partnership with high-need schools through the CSU Alliance School Program to place successful graduates where they are needed most. (3) Community building: The project will foster a cohesive community of practitioners among the Noyce Scholars, a Cadre of Mentor STEM teachers, and teacher educators at CSU. Support for Noyce graduates and mentor teachers will include induction mentoring and professional development on inquiry-based and design-based STEM instruction and social justice in STEM. Through these objectives and the research agenda, the project will develop, improve, and maintain a pipeline to recruit and prepare STEM teachers for underserved schools.

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