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I-Corps: Hand-held Assistive Mobility Device for the Visually Impaired Using Sensors to Feel Obstacles From a Distance and Track Their Movements
Biology; TAMU; https://hdl.handle.net/20.500.14641/548; National Science Foundation
The broader impact/commercial potential of this I-Corps project is the development of a hand-held assistive mobility device for the visually impaired. The Center for Disease Control (CDC) estimates that approximately 12 million people over the age of 40 suffer from visual impairment in the United States. Vision impairment and loss of sight are among the top 10 disabilities for individuals over the age of 18 and can have a substantial social and economic toll including, but not limited to, significant loss of productivity and diminished quality of life. Further, the annual economic impact of major vision problems in those 40 and older is estimated to be $145 billion. The proposed device holds the potential to significantly improve mobility, accessibility, and quality of life for the millions of people with no or low-vision that currently use an assistive mobility device such as the widely used ?white cane.? The technology also offers potential benefits to people working in low-visibility or disaster conditions, such as emergency first-responders or military personnel. This I-Corps project is based on the development of a hand-held device that uses remote sensing technology to control a dynamic tactile display on the hand, allowing the visually impaired to detect and classify obstacles in their environment sooner and more broadly than is possible using current assistive technology devices. Unlike existing technologies that involve touching or poking items with a white cane or rely on the individual to follow auditory cues, this device may enable individuals to feel the presence of obstacles and targets from a distance, including the relative location of multiple obstacles and being able to track the relative movements of nearby obstacles and targets. The proposed technology is an extension of research into optimized graphical displays of information derived from Sound Navigation and Ranging (SONAR) and Light Detection and Ranging (LIDAR)-based sensor systems. People in low-vision situations may be better equipped to rapidly process and exploit multi-channel spatial information when it is delivered via the hand instead of the ear. The proposed technology exploits the natural active-sensing behaviors used by humans when they reach out to explore their environment. 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.
Collaborative Research: Linking Atmospheric CO2 to Millennial Changes in Atmospheric and Oceanic Circulation in the Eastern Equatorial Pacific Ocean over the Past 100 kyr
Geology And Geophysics; TAMU; https://hdl.handle.net/20.500.14641/205; National Science Foundation
To understand future climate change, we must know how climate varied in the past. One of the biggest unknowns about past climate is the origin of atmospheric carbon dioxide (CO2) variability over global warm-cold cycles. This project will address potential causes of the varying atmospheric carbon dioxide by focusing on changes in the efficiency of fertilization of the surface ocean, and how, and if, that is related to changes in the deep-ocean. Furthermore, the research will investigate both the "how" of varying carbon dioxide with the "where", namely the Eastern Equatorial Pacific (EEP), an important region of the world ocean where, today, significant CO2 is exhaled to the atmosphere and the greatest rates of phytoplankton growth are found. The project will contribute to an improved understanding of global climate change and important Earth systems connected to the tropical Pacific Ocean. On the broadest of levels, understanding the past dynamics of Earth's carbon cycle is of fundamental importance to inform and guide societal policy-making in an increasing CO2 world. The project will support the educational and professional development of graduate and undergraduate students and results will be incorporated into the curriculum of undergraduate and graduate classes. In addition, a series of YouTube videos will be developed that are aimed at communicating the importance of how past climate variability informs us about climate's future variability and its potential impact on our lives. The project seeks to answer questions related to: 1) where and how atmospheric carbon dioxide was sequestered from the atmosphere, or ventilated from the ocean, on millennial timescales, and 2) how these carbon dynamics are related to both changes in atmospheric and oceanic circulation over the last glacial period and into the deglacial and Holocene. To address these objectives, an integrated suite of multiple proxies will be measured in two high accumulation rate sediment cores previously collected from the EEP. These proxies include: authigenic uranium as a proxy for bottom water oxygenation and radiocarbon ages of benthic foraminifera as a proxy for changes in the age of deep water in the EEP, 231Pa/230Th ratios and excess Ba fluxes as proxies for productivity, excess 230Th-derived 232Th flux as a proxy for dust flux, B/Ca ratios in planktonic foraminifera as a proxy for carbonate ion concentration of surface water, and Nd and Pb isotope ratios as a proxy for the provenance of the dust source of the detrital component of the sediment and, therefore, an index of Intertropical Convergence Zone migration. By investigating the storage of a respired carbon pool in the deep ocean during cold periods of the last glacial period (i.e., from ~71,000 to 14,000 years ago), in conjunction with probing how this storage relates to changes in export production and potential iron fertilization, the research will shed light on the mechanistic links between ocean (stratification/ventilation) and atmospheric (wind belt shifts) circulation and the modification of atmospheric CO2 levels. 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.
Mirror image DNA circuitry for complex microRNA analysis in live cells
Chemistry; TAMU; https://hdl.handle.net/20.500.14641/200; DHHS-NIH-National Institute of BioMedical Imaging and BioEngineering
Project Summary/Abstract MicroRNAs (miRNAs) are short, noncoding RNAs that play a critical role in post-transcriptional regulation of gene expression. Consequently, aberrant miRNA expression levels are associated with a wide range of human diseases, the most prominent of which is cancer. Cancer cells are often associated with the simultaneous up- and-down regulation of several miRNAs relative to normal cells of the same tissue, and these “signatures” can reveal significant information about the underlying disease. Thus, nucleic acid analysis technologies aimed at profiling miRNA expression patterns in living cells and tissues hold great promise for early cancer detection and diagnosis. However, prevailing methods for detecting nucleic acids in living systems are generally limited to the detection of a single nucleic acid target, thereby precluding their use in more complex pattern- recognition applications. A promising solution to this problem is molecular circuitry, and specifically, DNA strand-displacement circuits that can be programmed to generate optical and/or chemical “outputs” in response to specific combinations of nucleic acid “inputs”. Unfortunately, exogenously delivered DNA has a cellular half- life on the order of minutes and is susceptible to unintended interactions with cellular macromolecules, all of which adversely affect the performance of the device. As a consequence, it remains enormously challenging to execute complex and useful tasks in living systems using DNA-based circuits. Herein, the PI provides an innovative solution to this problem: mirror image DNA. Mirror image DNA (referred to as L-DNA) has the same physical and chemical properties as its natural counterpart, D-DNA, yet as a reflection, it is completely invisible to the stereospecific environment of cells (i.e. L-DNA is resistant to both nuclease degradation and off-target interactions with cellular components). Consequently, DNA-based circuitry constructed from L-DNA is expected to operate free from cellular interference, thereby overcoming the primary barrier to engineering complex and reliable functionality. On this basis, the PI proposes to develop a series of autonomous L-DNA-based circuits capable of recognizing and reporting specific miRNA expression patterns in live human cells. The immediate goal of this work is to uncover fundamental relationships between circuit design and cellular delivery methods, which together represent a critical first step towards constructing more complex intracellular devices. As the project progresses, the complexity of the L-DNA circuitry will be gradually increased through the introduction of L-DNA-based logic gate motifs that will be arranged to compute the presence of specific combinations of up to four different miRNAs. If successful, this work will signify a major advance in the area of intracellular DNA computing and provide a strong foundation for future applications aimed at “intelligent” disease diagnosis.
CDS&E-MSS: Recovery of High-Dimensional Structured Functions
Mathematics; TAMU; https://hdl.handle.net/20.500.14641/323; National Science Foundation
Many scientific problems of crucial importance for the United States involve a very large number of parameters. This high dimensionality has long been a challenge for the numerical treatment of physical, chemical, and biological processes, and now it also represents an obstacle in data science, especially for the task of extracting useful information from only a limited amount of observations. Propitiously, the high-dimensional objects prevailing in real-life problems often possess some underlying structure simplifying their manipulation. The purpose of this project is to exploit this structure in order to develop a consistent theoretical framework and to conceive novel computational methods for the exact recovery (or good approximation) of the high-dimensional objects sketchily acquired. More specifically, the objects considered in this project are functions of very many variables. Handling them via traditional numerical methods is doomed by the so-called curse of dimensionality. But modern ideas such as sparsity and variable reduction make it possible to bypass the curse and thus are revolutionizing the approach to high-dimensional problems. Building upon the fundamentals from the theory of compressive sensing, the project will consider sparse recovery and simultaneously structured recovery as part of the more general recovery of high-dimensional functions depending on few reduced variables. The research strategy starts by investigating the theoretical limitations of any recovery method within a model, then continues by refining the model through confrontation with real-life problems, and finishes by implementing the algorithms proven to perform optimally. Since the project features interactions with several applied fields (in particular, Engineering and Bioinformatics), the novel numerical methods are to be tested in these areas, which will in turn provide fresh mathematical insight. A final part of the project is devoted to the integration of emerging concepts into the culture of the next scientific generation and in particular to the training of mathematicians in computational and data-related aspects.
Clumped Isotope Reordering Kinetics in Carbonate Minerals: The key to accurate ocean paleotemperatures and basin thermal histories
Geology And Geophysics; TAMU; https://hdl.handle.net/20.500.14641/225; National Science Foundation
One of the most exciting new ideas in geochemistry is to measure two rare isotopes in calcium carbonate instead of just one and "clump" them together. This provides a new and powerful tool to study the temperature of ancient oceans and sediments and will help scientists looking at climate change, plate tectonics, and petroleum exploration. This study will help identify the calcium carbonate minerals most likely to preserve ancient temperatures. It will also provide the chemical information needed to use two minerals at the same time to better estimate the temperature history of the rocks. This project will develop this new tool by connecting atom-level processes with observed chemical reactions. The study will improve temperature estimates of ancient oceans and the temperature history of rocks related to petroleum reservoirs. The project will train graduate and undergraduate students and will add a new section of a capstone undergraduate course that will introduce seniors to the field. The project will also engage chemistry graduate and undergraduate students from underrepresented minority groups One of the most exciting developments in geochemistry in the 21st century is the ability to measure the relative abundance of molecules with two rare isotopes ("clumped isotopes") in calcium carbonate minerals (e.g., calcite) and apply this technique to reveal the temperatures of ancient oceans or the burial temperatures of sediments now exposed at the surface. A major complication in clumped isotope paleothermometry however is reequilibration (reordering) of the signatures at elevated temperatures (>100oC) on million-year timescales. While complicating paleoclimate studies, this reordering provides great potential for measuring rates of burial, uplift, and exhumation of geologic formations, but only if the rates (kinetics) of reordering are well understood. Currently, only the reordering kinetics of the mineral calcite (CaCO3) has been studied in detail. To address this knowledge gap, experiments will be conducted in which different minerals are heated and the rate at which they reorder is measured. The mechanisms of clumped isotope reordering will be examined at an atomistic level using a range of sophisticated chemical techniques such as programmable heated-stage synchrotron X-ray diffraction, total scattering, Raman spectroscopy, and scanning transmission X-ray microscopy, in conjunction with advanced models for atomic bonding. Correlating atomic characteristics with kinetic parameters and mineralogical characterization will allow determination of detailed equations governing the rates of reordering in a variety of carbonate minerals. The project will train graduate and undergraduate students and will add a new section of a capstone undergraduate course that will introduce seniors to the field. The project will also engage chemistry graduate and undergraduate students from underrepresented minority groups 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.
Innate Immune Signaling and Type I Interferon Responses as Novel Modifiers of Mitochondrial Disease Pathology
Microbial Pathogenesis And Immunology; TAMHSC; https://hdl.handle.net/20.500.14641/248; DOD-Army-Medical Research and Materiel Command
Fiscal Year 2016 Peer Reviewed Medical Research Program Topic Area: Mitochondrial Disease Mitochondrial diseases are a group of disorders caused by the malfunction of cellular organelles called mitochondria. Because mitochondria are responsible for generating the energy that powers vital cellular processes, mitochondrial malfunction can result in extensive disease throughout the body, including the nervous, musculoskeletal, digestive, and reproductive systems. Much of the research on mitochondrial disease has focused on the role of mitochondria in energy generation. However, recent studies have shown that mitochondria are key regulators of the immune system and orchestrate many aspects of inflammation during viral or bacterial illness, as well as in non-infectious diseases. In fact, abnormal inflammatory responses have been implicated in a number of diverse pathologies, some of which are present in the multi-organ disease of patients afflicted with mitochondrial syndromes. It is therefore possible that mitochondrial dysfunction aberrantly engages the immune system, resulting in inflammatory responses that exacerbate the pathology of mitochondrial disorders. To test this hypothesis, we will use a mouse model of mitochondrial disease (called POLG-mutator mice) that mirrors pathology seen in human patients with mitochondrial disease. We will use an array of techniques to characterize inflammatory responses through the progression of disease in these mice. Next, we will use POLG-mutator mice deficient in key immune signaling pathways to determine whether the absence of these pathways attenuates mitochondrial dysfunction and disease, thus demonstrating their importance in driving it. Based on preliminary studies, we predict that inhibition of the immune system will slow or alleviate pathology in this mouse model of mitochondrial disease. This proposal is innovative in several ways. First, it will examine the novel, unexplored paradigm that inflammatory mechanisms exacerbate multi-organ pathology in mitochondrial disorders and will provide a robust foundation for future research that focuses on immune pathology of mitochondrial diseases in other experimental and clinical settings. Second, there are presently no cures for many mitochondrial disorders, and few treatments are available to slow the progression of these diseases. This research may lay the foundation for studies exploring the therapeutic targeting of inflammatory pathways as a means to attenuate multi-system pathology of mitochondrial diseases.
New Color Centers in Diamond: Towards Broadband Quantum Memories
Physics And Astronomy; TAMU; https://hdl.handle.net/20.500.14641/318; National Science Foundation
Information technologies are among the main pillars of society, and information security is becoming more important. One direction for improving the security of future information systems is to utilize quantum communication lines. Based on laws of nature, such lines do not allow non-traceable copying of the information transmitted. But the same physics that makes them secure (i.e. the non-cloning theorem) also forbids the use of classical repeaters, which in turn limits communication distance and speed. This issue may be overcome by using quantum repeaters, the key ingredient of which is a quantum memory device. The aim of this project is to develop a novel solid-state quantum memory based on quantum states of color centers in diamond. This project will utilize theoretical and experimental advances developed at Texas A&M University both for the memory access protocol and for its physical implementation. This research project will strengthen the US presence in the field of optical ensemble-based solid-state quantum memories. It will also help train the next generation of scientists in this dynamically developing interdisciplinary field of research. Graduate and undergraduate students will get involved in the investigations through participation in the experiments, developing theoretical models, programming, collecting and interpreting experimental data, and numerical simulations. The investigators will also incorporate the obtained results into courses. This project focuses on new color centers, namely, Germanium Vacancies and Silicon Vacancies in diamond (GeV and SiV) for pioneering experimental realization of an ensemble based broadband quantum memory in diamond. This realization will be achieved using a new approach to quantum memory based on a discrete spatial chirp of a control field that has recently been suggested by the co-PIs. The outcome of this work, a single-photon solid-state interface, will be a milestone on the way to a scalable universal optical quantum computer. In comparison to existing technologies, like rare-earth doped crystals and nitrogen vacancy centers in diamond (NV), SiV and GeV have stronger optical interaction and less spectral diffusion (and inhomogeneous linewidths). The stronger zero-phonon line gives more efficient interaction of a single photon with a single silicon-vacancy, while a narrow inhomogeneous line broadening favors ensemble-based quantum memories. Other advantages of GeV and SiV are the presence of polarization selection rules and large (160 GHz and 50 GHz accordingly) energy level splitting in the ground state. The last one allows for large storage bandwidth. It is worth pointing out that multi-GHz vs MHz bandwidth is a key advantage of an optical over RF quantum networks (i.e. superconducting circuits (SCC)). The only disadvantage of GeV and SiV is a shorter electron-spin coherence time. However, it has been shown that this can be dramatically increased, up to 13 ms, by cooling SiV down to 100 mK. 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.
Finite Element Approximations of Bending Actuated Devices
Mathematics; TAMU; https://hdl.handle.net/20.500.14641/630; National Science Foundation
The ability to generate complex deformations from relatively small energies has tremendous applications in micro-engineering and biomedical science. This research focuses on developing and implementing mathematical algorithms able to predict and optimize the deformation of elastic films, chosen for their potential in the production of robust and light-weight micro-scale devices. The deformations considered are triggered by exposing to external stimuli either polymers with different expansion characteristics or manufactured gels with residual stresses. Devices based on these technologies are, for instance, employed as drug delivery vesicles, cell encapsulation devices, sensors, bio-muscles and as proxies for tissue growth. In addition to these applications in biomedical science, the development of autonomous foldable structures such as self-deployable sun sails in spacecraft or deployable aircrafts, photovoltaic devices, actuators, micromotors, microgrippers, microvalves, microswimmers are very popular interests in the engineering community this research is likely to have impact on. The proposed study focuses on thin devices where bending is the principal mechanism for, possibly large, deformations. The mathematical models are derived as the two dimensional limit of thin three dimensional hyper-elastic solids. They are characterized by energy densities dominated by bending, expressed geometrically as the film's second fundamental form. In addition to the difficulties inherent in the non-divergence form of this fourth order system, fully non-linear geometrical constraints must be taken into account in the context of large deformations. The aim of this research is to derive mathematical models when not available for the targeted application, and to design, analyze and implement finite element based algorithms for their approximations. The entire process from the mathematical analysis to the actual highly parallel implementation of finite element algorithms is covered. Hence, analytical tools borrowed from differential geometry and calculus of variation are blended with numerical analysis and delicate computational efforts to achieve efficient and practical algorithms. The ability to generate complex deformations from relatively small energies has tremendous application in micro-engineering and biomedical science. The algorithms resulting from the proposed research - and in particular their relatively effortless implementations - are likely to have impact in these areas. To mention a few applications, devices based on bilayers of polymers or prestrained films are employed as drug delivery vesicles, cell encapsulation devices, sensors, bio-muscles and as proxies for tissue growth. In addition to these applications in biomedical science, the development of autonomous foldable structures such as self-deployable sun sails in spacecraft or deployable aircrafts, photovoltaic devices, engineered scaffolds, actuators, micromotors, microgrippers, microvalves, microswimmers are very popular research interests in the engineering community. 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.
Assessing the influence of background state and climate variability on tropical cyclones using initialized ensembles and mesh refinement in E3SM
Atmospheric Sciences; TAMU; https://hdl.handle.net/20.500.14641/227; DOE-Office Of Science
The scientific goal of this project is to assess the influence of the background state and horizontal resolution of climate models on the simulation of extreme events like intense precipitation, tropical cyclones, atmospheric rivers, and heatwaves. The main results are: - Initialized ensembles of 4-week forecasts using a climate model (E3SM) show that dynamic (flow) and thermodynamic (moisture) biases asymptote to their climatological values at different rates—dynamic bias grows rapidly and approaches its climatological value within about 2 weeks whereas the thermodynamic bias takes about 4 weeks. - Moisture bias has a bigger impact on extreme events like tropical cyclones and intense precipitation than flow bias, and this impact is non-monotonic over bias evolution time. - Climate models are capable of simulating the flow features associated with unprecedented extreme events like the Western North America heatwave of June 2021, but moisture biases can weaken the surface manifestation of extreme heatwaves. Reducing model bias may be more important than increasing model resolution in improving the fidelity of heatwave simulations in climate models. - Climate models are capable of simulating weather patterns associated with “power droughts”, i.e., periods with low solar and wind power generation, provided model biases in the simulation of the background state can be corrected. - Regional mesh refinement can improve the simulation of extreme weather events but model biases may still persist.
NSFOCE-BSF: Collaborative Research: The Role and Mechanisms of Nuclei-induced Calcium Carbonate Precipitation in the Coastal Carbon Cycle: A First In-depth Study
Marine Science; TAMUG; https://hdl.handle.net/20.500.14641/665; National Science Foundation
The formation of calcium carbonate (CaCO3) in seawater is a fundamental pathway in the marine carbon cycle. Calcium carbonate formation may occur through biological production (calcification by organisms building shells or skeletal material) or through non-biological (abiotic, or chemical) processes. Although most surface seawater in both open and coastal waters is supersaturated in calcium carbonate, several factors inhibit the abiotic production of calcium carbonate. Therefore the current paradigm is that most calcium carbonate formation in seawater is biological. However, laboratory experiments have demonstrated that addition of solid-phase particles to supersaturated seawater promotes nuclei-induced CaCO3 precipitation (NICP) by providing "seeds" for precipitation. NICP has been demonstrated in the Little Bahama Banks during events of re-suspension of CaCO3-rich sediments. Until very recently, essentially no evidence has shown that NICP occurs in typical marine systems where suspended particles have relatively low CaCO3 content. A recent study by the Israeli partners in this project provides evidence that NICP may play a significant role in the carbon budget in the Red Sea, as a result of an influx of particulate material caused by flash floods and potentially airborne dusts. Such a finding suggests that NICP may be an important CaCO3 formation pathway that has been mostly ignored in the ocean carbon cycle. The goal of this project is to conduct the first comprehensive, in-depth study to evaluate the significance of NICP in the oceans. The project is an international collaboration between U.S. and Israeli scientists, jointly funded by NSF and the U.S.-Israel Binational Science Foundation. A postdoctoral researcher whose Ph.D. work forms the foundation for this study will be supported through this project. An Israeli masters-level student and one U.S. minority undergraduate intern will be advised and trained in this project. The project will use an integrated approach to assess different mechanisms that may result in NICP, including riverine sediment input, land-derived particle influx via flash floods, bottom sediment resuspension, and atmospheric dust input. Field investigations will be done in a suite of coastal environments: the northern Red Sea, the Mississippi and Sabine River plumes and Galveston Bay in the northern Gulf of Mexico, each of which receive significant quantities of non-carbonate rich sediments. The investigators will also conduct controlled laboratory experiments to verify and extend field observations. If NICP is shown to be significant, this finding could promote a reexamination of important parts of the carbon cycle and the response of the ocean carbon system to ongoing perturbations.
P30 Yr 2 Pilot- Public Opinion Survey on Environmental Health Risk Perceptions and Policy Preferences
Institute For Science, Techology And Pub; TAMU; https://hdl.handle.net/20.500.14641/506; DHHS-NIH-National Institute of Environmental Health Sciences
Project Overview: The Community, Regulation, and Policy Team conducted an online representative national public opinion survey with representative oversamples in Texas, Harris County, and Hidalgo County. This survey used theoretically based questions to tap into public knowledge, trust, concerns, and policy preferences regarding environmentally based individual and community health threats. The team will use the results of this survey to find out: 1. What people know about the role of the environment in their health status 2. How familiar people are with specific environmental health threats in their communities and those that may pose more specific threats for particularly vulnerable populations 3. Public trust in science and government 4. Public expectations of government and the private sector to reduce and adapt to these threats Furthermore, the data collected from this survey can be used to help frame current and future scientific research, extending its reach and relevance, and to help guide community engagement activities. We will collaborate with the TiCER scientists to identify solutions that could be implemented for specific environmental health threats and identified public health problems.
EarthCube Data Infrastructure: Collaborative Proposal: A unified experimental-natural digital data system for analysis of rock microstructures
Geology And Geophysics; TAMU; https://hdl.handle.net/20.500.14641/381; National Science Foundation
When viewed at the micro-scale, rocks reveal structures that help to interpret the processes and forces responsible for their formation. These microstructures help to explain phenomena that occur at the scale of mountains and tectonic plates. Interpretation of microstructures formed in nature during deformation is aided by comparison with those formed during experiments, under known conditions of pressure, temperature, stress, strain and strain rate, and experimental rock deformation benefits from the ground truth offered through comparison with rocks deformed in nature. However, the ability to search for relevant naturally or experimentally deformed microstructures is hindered by the lack of any database that contains these data. The researchers collaborating on this project will develop a single digital data system for rock microstructures to facilitate the critical interaction between and among the communities that study naturally and experimentally deformed rocks. To aid in the comparison of microstructures formed in nature and experiment, the researchers will link to commonly used analytical tools and develop a pilot project for automatic comparison of microstructures using machine learning. Rock microstructures relate processes at the microscopic scale to phenomena at the outcrop, orogen, and plate scales and reveal the relationships among stress, strain, and strain rate. Quantitative rheological information is obtained through linked studies of naturally formed microstructures with those created during rock deformation experiments under known conditions. The project will develop a single digital data system for both naturally and experimentally deformed rock microstructure data to facilitate comparison of microstructures from different environments. A linked data system will facilitate interaction between practitioners of experimental deformation, those studying natural deformation and the cyberscience community. The data system will leverage the StraboSpot data system currently under development in Structural Geology and Tectonics. To develop this system requires: 1) Modification of the StraboSpot data system to accept microstructural data from both naturally and experimentally deformed rocks; and 2) Linking the microstructural data to its geologic context ? either in nature, or its experimental data/parameters. The researchers will engage the rock deformation community with the goal of establishing data standards and protocols for data collection, and integrate our work with ongoing efforts to establish protocols and techniques for automated metadata collection and digital data storage. To analyze the microstructures studied and/or generated by these communities, we will ensure StraboSpot data output is compatible with commonly used microstructural tools. They will develop a pilot project for comparing and analyzing microstructures from different environments using machine-learning
Yr. 2 IHSFC Voucher - Generate a Tll1-flox transgenic mouse
Ibt - Ctr For Epigenetics & Disease Prev; TAMU; https://hdl.handle.net/20.500.14641/409; DHHS-NIH-National Institute of Environmental Health Sciences
We received 2 clones from EuMMCR, performed several rounds of injections, but couldn’t obtain a good male chimera. The only chimera we got was a low percent female that usually don’t produce germline. We subcloned these clones in presence of a special medium that helps ES cells retain totipotency and performed karyotyping to confirm that the subclones don’t have any abnormalities. We then injected two best subclones and obtained 3 male chimeras with 90-95% coat contribution from the ES cells. The chimeras were set up to breed with B6N females and one of them produced germline heterozygous. More litters will be screened in the nearest future.
Epigenetic Regulation of Seasonal Behavior in Insects
Biology; TAMU; https://hdl.handle.net/20.500.14641/206; National Science Foundation
Many animals change their behavior in response to seasonal changes in the environment. The molecular nature of the changes that occur in the brain to alter behavior in a seasonal manner remains poorly understood. This project will examine epigenetic changes, i.e. changes in external modifications to DNA, that turn behavior-regulating genes on or off in a season-dependent manner. The work will be carried out using behavioral approaches and DNA sequencing of the genome of the long-distance migratory monarch butterfly, Danaus plexippus. The monarch exhibits extreme seasonal behavioral changes at the individual level in response to changing daylength and temperature. Migratory monarch butterflies accomplish an extraordinary journey of 2,000 miles from the United States to their overwintering sites in Mexico by flying southward in the fall. In the spring, migratory butterflies flip their flight orientation northward and return to the United States. This project will reveal seasonal epigenetic changes to the genome in the brains of these seasonal forms. These findings will provide insight into the molecular mechanisms underlying seasonal migration and the production of distinct seasonal flight orientations, and may be applicable to other migratory species. They could also have implications for conservation strategies to help preserve the iconic monarch migration, a spectacular yet threatened biological phenomenon. The project will provide valuable research training for students interested in animal behavior, neuroscience, and bioinformatics, including students from groups underrepresented in STEM fields. The researchers will also develop outreach activities devoted to increase public awareness for the need of monarch habitat conservation efforts. Seasonal behavioral adaptations are key to the ecological success of many animals. The behavioral plasticity observed in individuals in response to seasonal changes in the environment strongly suggests that epigenetics play a crucial role in shaping seasonal behavior. However, the epigenetic changes that link brain function to seasonal regulation of behavior remain largely unknown. This project will leverage the remarkable seasonal plasticity of monarch butterfly migratory behavior in response to seasonal changes in the environment (daylength, temperature) to delineate the genome-wide epigenetic architecture in the brain that underlies seasonal migratory behavior and flight orientation. The goal of the project is to identify active cis-regulatory elements (CREs) and putative transcription factors (TFs) that mediate differential gene expression in the brains of non-migrants, fall migrants and spring remigrants. The researchers will use fall migrants and fall migrants reprogrammed into spring remigrants in controlled conditions and a combination of next-generation sequencing technologies. Genes differentially expressed in the brains of these seasonal forms will be identified by RNA-seq, and open genomic regulatory regions and CREs that mediate this differential expression will be identified by ATAC-seq and ChIP-seq of histone marks. Candidate transcription factors (TFs) responsible for the seasonal behavioral reprogramming will ultimately be identified through DNA genomic footprinting within CREs. The project will have broad societal impacts through outreach activities devoted to increase public awareness for the need of monarch habitat conservation efforts, and research training of students interested in animal behavior, neuroscience, and bioinformatics. 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.
Oral delivery of insulin using ligand-directed nanoparticles that do not compete with physiological ligands
Cop - Pharmaceutical Sciences; TAMU; https://hdl.handle.net/20.500.14641/447; DHHS-NIH-National Institute of Diabetes and Digestive and Kidney Disorders
Project Summary The primary focus of managing type 2 diabetes (T2D) has traditionally been the strict control of blood glucose using one or multiple orally administered medications. Drugs currently used to treat T2D range from pharmaceutical agents that increase insulin secretion or sensitivity, to those that decrease hepatic gluconeogenesis or intestinal carbohydrate absorption. Agents that are more recent include glucagon-like peptide-1 (GLP-1) analogues, which inhibit the breakdown of endogenous GLP-1 by dipeptidyl peptidase-IV (DPP-IV), and sodium-glucose cotransporter-2 (SGLT-2) inhibitors, which block normal glucose reabsorption in the kidneys. According to the United Kingdom Prospective Diabetes Study (UKPDS 33), even though the efficacy of these drugs in preventing microvascular complications of T2D (e.g., retinopathy, neuropathy and nephropathy) has been partially established, their role in preventing macrovascular complications (e.g., coronary heart disease and stroke) remains elusive. Moreover, the same study points out that 50 percent of patients originally controlled with a single drug acquired tolerance and needed the addition of a second drug after three years, and by nine years, about 75 percent of patients needed multiple therapies to achieve the target HbA1c value. There is significant evidence that in some T2D patients, despite taking medications, the ?-cell function undergoes continuous decline and eventually fails entirely, leaving these patients the only option of insulin therapy. Rather than being used as a treatment of last resort however, the clinical and research communities are recognizing that early initiation of insulin therapy in T2D patients will correct all of the underlying pathogenic mechanisms such as increased ?-cell apoptosis, glucotoxicity, lipotoxicity, and inflammation. Major drawbacks of early insulin injections for T2D include risks of cardiovascular disease, weight gain and hypoglycemia, stemming from irregular or incorrect dosing, lack of time in the physician's schedule to manage insulin therapy, and most importantly, patient non-compliance. Successful oral delivery of insulin is therefore a therapeutic Holy Grail as its inherent ease of administration mimicking natural secretion process potentially obviates or minimizes many of the drawbacks, and should reduce much of the burden of managing T2D by health care professionals. However, gastric instability and lack of transport across tightly packed epithelium and overlying mucus are formidable challenges to successful intestinal absorption of insulin. The work enabled by previous findings, in which oral delivery of insulin using ligand-directed nanoparticles that do not compete with physiological ligands led to improved therapeutic outcomes compared to conventional nanoparticles. In this project, the technology is further developed by investigating, how fine-tuning the nanoparticle composition affect the drug disposition and therapeutic outcomes, under the influence of commonly experienced physiological and pathophysiology conditions. In doing so, the project will establish 1) optimal non-competitive nanoparticle chemistry, 2) active drug delivery under pertinent physiological conditions, and 3) the therapeutic window of oral insulin in T2D.
Modulation of peptidergic neurons by the gluconeogenic enzyme Glucose-6-Phosphatase
Molecular And Cellular Medicine; TAMHSC; https://hdl.handle.net/20.500.14641/238; National Institutes of Health
Neuropeptides (NPs) play crucial roles in behavior and physiology. NPs are short proteins that are stored and released from Large Dense Core Vesicles of peptidergic neurons. Peptidergic neurons activate neural circuits that regulate and modulate a range of physiological processes and impact an array of behaviors, including feeding, social interactions, circadian behavior and others. Some peptidergic neurons can express multiple NPs, and most contain also small Synaptic Vesicles that release classic neurotransmitters. An additional level of complexity is imparted by various degrees of NP processing, which can occur prior or after their release (i.e. regulated transport, localization, processing etc.). Thus, peptidergic neurons are multimodal that can convey information within the nervous system. In addition, some NPs act also as neurohormones and can signal to tissues other than the CNS. Even though the functions of many NPs have been characterized and their receptors have been identified, little is known about how their activity is modulated. In the fruit fly Drosophila, cell fate of many peptidergic neurons is dependent on the transcriptional activator Dimmed (DIMM). The recent discovery that many DIMM positive neurons express G6P-GAL4, a marker for cells expressing the highly conserved enzyme Glucose-6-phosphatase (G6P), implies that G6P has a non-canonical role in Drosophila. G6P is better known for its role in gluconeogenesis, a process restricted to the liver and kidney of mammals, for the generation of glucose from non-carbohydrate precursors to maintain blood glucose homeostasis when animals are food-deprived. Initial characterization of Drosophila G6P has established that G6P-expressing peptidergic neurons have gluconeogenic capacity and are able to use alanine as a substrate to generate glucose. Moreover, G6P is necessary for NP accumulation in neural processes, and preliminary data presented in this application reveal that G6P is required in these neurons to generate appropriately sized Golgi complexes. Based on these data, G6P (and by inference gluconeogenesis) are proposed to play a critical role in peptidergic neurons, presumably in the biogenesis of Golgi and/or LDCV structures, to affect NP release, thereby modulating physiological and behavioral processes. Importantly, mammals harbor, three G6P genes, only one of which (G6PC1) is involved in hepatic gluconeogenesis. The other two genes, G6PC2 and G6PC3, are expressed in secretory cells of other tissues, including the brain and CNS. The function of these non-canonical mammalian G6P genes is not known, but given their similarities to Drosophila G6P with regard to expression and cellular context, it is intriguing to posit that the G6PC2 and G6PC3 enzymes have similar roles in mammals as the single G6P enzyme in the fly CNS. !
COVID-19: RAPID: Collaborative Research: Optimizing non-pharmaceutical and pharmaceutical interventions for controlling COVID-19 at the community-level
Veterinary Integrative Biosciences; TAMU; https://hdl.handle.net/20.500.14641/446; National Science Foundation
During emerging infectious disease outbreaks, such as the current novel coronavirus (COVID-19) pandemic, mathematical models are important tools to help inform public health recommendations and best utilization of limited resources. This research will develop and analyze data-driven mathematical models to predict the spread and evaluate the success of various public health intervention strategies to control COVID-19 in the US and abroad. The models will account for the characteristics of the pathogen, the variation of transmission that occur within community and in hospital settings, and geographical difference in transmission. The broader impacts from these models will provide real-time information to assist public health officials and decision-makers in making critical decisions on COVID-19 control policies and resource allocation. Standard modeling approach such as compartmental population-based approach may not be suitable for modeling the spread of COVID-19, due to the high-level of heterogeneity of such systems, disease pathways, population makeup, host interactions on different levels of organization (household, workplace/school, social activities), and adaptive features of human behavior. The investigators will employ an individual-based modeling approach (IBM) that will accommodate such local heterogeneities. The investigators will use social, demographic, and epidemiological data of COVID-19 cases in the US and Korea, as well as hospital-level and city-level contact tracing data of COVID-19 in Wuhan, China, to parameterize their models. First, they will develop an IBM hospital-based model to explore different hospital-based interventions for mitigating the risk of nosocomial transmission of COVID-19 between patients and healthcare workers. Second, they will develop an IBM community-based model to evaluate and identify optimal non-pharmaceutical and potential pharmaceutical interventions for COVID-19 control in different local communities (city-county scale). The non-pharmaceutical interventions will include, amongst others: case isolation at home or hospitals, voluntary self-quarantine, stopping mass gathering, closure of schools, universities, or workplaces, and social distancing such as reduction of contacts, wearing of protective masks, and reduction of individuals' movements. Pharmaceutical interventions will include novel vaccines and antiviral therapies. This RAPID award is made by the Ecology and Evolution of Infectious Diseases Program in the Division of Environmental Biology, using funds from the Coronavirus Aid, Relief, and Economic Security (CARES) Act 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.
HPV and Cancer mHealth Prevention Education for HIV Positive Women Pilot Study
Health And Kinesiology; TAMU; https://hdl.handle.net/20.500.14641/425; DHHS-NIH-National Cancer Institute
DESCRIPTION (provided by applicant): The candidate is a research assistant professor with academic training in health promotion, education, and behavior, as well as postdoctoral training in HIV/AIDS prevention, health disparities, and health services research. She also has data management expertise and clinical immunology experience. The candidate has completed two pilot studies that examined HPV infection and cervical cancer prevention knowledge, beliefs and screening behaviors among women living with HIV (WLH). The candidate is seeking additional training needed to develop and implement effective cancer health (including mHealth) communication and community navigation strategies to improve WLH's timely use of cancer screening, diagnostic and treatment services and procedures. The candidate's long-term goal is to obtain extramural research funding for her independent research program focusing on the prevention and control of HPV-mediated cancers among WLH over the next 5-10 years. Promotion to associate professor (tenure- or research-track) is an intermediate goal that the candidate is striving to attain within the next five years. A combination of formal didactic trainig and experiential learning opportunities will be used to acquire cancer prevention and control research skills in the following areas: cancer health (including mHealth) communication, cancer epidemiology, HPV-mediated cancer biology, community navigation, advanced epidemiological research skills (e.g., social epidemiology, n- of-1 research study designs, and, multilevel modeling). The candidate will use the cancer prevention and control research and health communication knowledge and skills acquired through the proposed career development award to conduct formative research needed to inform intervention development in which she will examine cancer health information seeking and sharing among WLH as well as their non-clinical HIV service providers (e.g., HIV/STI risk reduction counselors). Non-clinical HIV service providers will be included because, in addition to the fact that these individuals are already promoting safe sexual practices among WLH, they are also able to reach marginalized groups of WLH such as those who are homeless. This includes sheltered and unsheltered homeless WLH. The candidate's mentors and co-mentors have scientific expertise and community-based participatory research experience that will increase the likelihood of the proposed specific aims being successfully completed. The candidate will first examine HPV-mediated cancer prevention knowledge, beliefs and behaviors, as well as cancer health communication seeking and sharing behaviors (including the use of technology to find health information) (Aim 1). These formative research data will then be used to inform the development (Aim 2) and subsequent pilot testing and evaluation (Aim 3) of an HPV- mediated cancer prevention mHealth education intervention aimed at training WLH who already serve as peer leaders and non-clinical HIV service providers to use mHealth tools and community navigation strategies to disseminate HPV-mediated cancer prevention education. As community navigators, these individuals will use cancer health (including mHealth) communication and community navigation strategies to increase awareness about HPV-mediated cancer risk. This will include promoting cancer risk reducing behaviors such as safe sexual practices and the timely use of recommended cancer screening, diagnostic, and treatment services and procedures). Recall and reminder messages will be sent for screening and follow-up cancer care appointments. User-defined social support messages will also be sent to WLH who may be encountering access to cancer care barriers. The candidate will disseminate the scientific research findings to local, regional, national, and international audiences via presentations that she will give at scientific conferences and annual meetings as well as peer-reviewed publications that she will produce. Most relevant to the candidate's long-term goal of attaining research independence is increasing her number of peer-reviewed publications from her current publication rate of approximately three per year to four or more produced annually by the end of the 5-year training period and the submission of at least one grant proposal (e.g., R01-level funding) by the end of the 5-year training period. The proposed career development/training and research activities will enable the candidate to realize her long-term career goal of becoming an independent cancer researcher with expertise in using cancer health communication, community navigation, and mHealth technologies to address health system failures encountered by vulnerable, medically-underserved WLH along the cancer care continuum. Continued mentoring and opportunities for team science research collaborations will facilitate the candidate's successful progression to being an independent cancer researcher. WLH and non-clinical HIV service providers will be recruited from Ryan White funded clinics and AIDS-service organizations located in urban and rural geographical areas of South Carolina that represent a microcosm of disparities in HIV/AIDS, cancer, and other chronic illness that disproportionately burden medically underserved minority populations. Addressing health system failures that occur along the cancer care continuum that result in missed opportunities to prevent, detect, diagnose and treat HPV-mediated cancers will help to reduce the burden of cancer incidence and mortality among this high cancer risk, vulnerable group of WLH. The proposed HPV-mediated cancer mHealth prevention education intervention will be conducted in a community-based setting and builds upon an existing academic-community partnership between the candidate and a local AIDS-service organization. The candidate has a supportive, resource-intensive scientific environment for her cancer research training.
CombinaTexas 2020: A Combinatorics Conference for the South-Central U.S.
Mathematics; TAMU; https://hdl.handle.net/20.500.14641/350; National Science Foundation
The CombinaTexas 2020 conference will be held at Texas A&M University, College Station TX on April 10-11, 2020. The conference will feature six fifty-minute plenary lectures and a number of contributed talks in various areas of Combinatorics and Graph Theory. The aim of the CombinaTexas conference series is to enhance the educational and research atmosphere of combinatorialists in Texas and the surrounding states, increase communication between mathematicians of the region, and provide a forum for presentation and discussion of the most recent developments in the field of Combinatorics. CombinaTexas was established in 2000 and rotated among different institutions in the South Central United States until 2014. Since then it has been hosted at Texas A&M University. CombinaTexas 2020 is the nineteenth conference in this series. The topics of the CombinaTexas Series include all branches of Combinatorics, Graph Theory, and their connections to Algebra, Geometry, Probability Theory, and Computer Science. In 2020 the confirmed plenary speakers are Miklos Bona (University of Florida), Tri Lai (University of Nebraska- Lincoln), Chun-Hung Liu (Texas A&M University), Nathan Reading (North Carolina State University), Stephanie van Willigenburg (University of British Columbia), Josephine Yu (Georgia Institute of Technology). They will present research in enumerative combinatorics, combinatorial representation theory, cluster algebras, tiling theory, topological graph theory, and tropical geometry. About 70 participants are anticipated, with an estimated 20 contributed talks in parallel sessions. More information about the conference is available at the webpage https://www.math.tamu.edu/conferences/combinatexas/ 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.
Quantification of the Impacts of Saharan Dust on Atlantic Hurricanes Using Satellite Observations and Coupled Atmosphere-Ocean Model
Atmospheric Sciences; TAMU; https://hdl.handle.net/20.500.14641/504; NASA-Washington
Abstract: The radiative and microphysical effects of Saharan dust are believed to exert substantial impacts on the regional weather systems and climate in the Atlantic, but the current understanding of the dust effects on tropical cyclones (TCs) remains inadequate. This project aims at quantification of the impacts of Saharan dust on the evolution of Atlantic TCs by combining observational analysis and simulations with coupled atmosphere-ocean models. The dust impacts on TCs will be assessed from analysis of NASA satellite and aircraft measurements of aerosol and cloud properties in this region and simulations using a cloud-resolving Weather Research and Forecasting Model coupled with Regional Ocean Modeling System (CR-WRFROMS) and the National Center for Atmospheric Research (NCAR) coupled-Community Earth System Model (CESM). Specifically, the following research tasks are proposed: (1) analysis of dust measurements from the Multi-angle imaging SpectroRadiometer (MISR) and Moderate Resolution Imaging Spectroradiometer (MODIS), dust and cloud vertical profiles from the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) and CloudSat, and aircraft observational data from the NASA African Monsoon Multidisciplinary Activities Experiment (NAMMA) field campaign, Hurricane and Severe Storm Sentinel (HS3), and Genesis and Rapid Intensification Processes (GRIP) missions to evaluate the interaction between Saharan dust and TCs, select the case for model simulations, and perform inter-comparison between the model and observation, (2) quantification of the dust direct and indirect effects on Atlantic TCs using the CR-WRF-ROMS, and (3) assessment of the impacts of Saharan Air Layer (SAL) and African Easterly Waves (AEWs) on the TC trend using the coupled-CESM. Ultimately, the results from this proposed research will provide quantitative assessment of the impacts of Saharan dust on the genesis and intensification of Atlantic TCs and will facilitate more accurate future forecasting and climate projections of TCs in the Atlantic Basin.

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