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Open Access Publications from the University of California

Scholarly Works (12 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2010)

This thesis studies the performance of time delay estimation and the range-based localization schemes in wireless multipath channels. The research focuses on the localization schemes based on time-of-arrival and time-difference-of-arrival measurements. In multipath environments, time delay measurements suffer from the errors due to weak line-of-sight and rich non-line-of-sight (NLOS) signal paths. Instead of proposing range measurement algorithms, the thesis is devoted to develop theoretical performance lower bounds used as benchmarks to guide algorithm design and provide insight into the behavior of time delay estimation (TDE).

The author develops Ziv-Zakai bounds (ZZBs) on Bayesian estimation of time delay, for known pulsed signal and frequency hopping waveforms that propagate through unknown random multipath channels following Rayleigh/Rician distribution, with a uniform prior on the delay. The bounds do not assume channel knowledge at receivers, providing more realistic and tighter performance limits than the average bound that assumes channel knowledge. The ZZBs also present good performance prediction for maximum a posteriori estimator, tracking a wide range of signal-to-noise ratios. The ZZB for wideband frequency hopping waveforms reveals the performance benefit for TDE from frequency diversity over frequency-selective fading channels. To evaluate the ZZB, the author proposes a moment generating function approach. The closed-form expressions for independent flat-fading channels enable easy study of the effects of SNR, frequency diversity, and channel statistics on TDE.

The TDE errors lead to time-based ranging errors that in turn cause positioning errors and deteriorated localization performance. The thesis models the NLOS range measurement error as a deterministic or random positive bias, following widely adopted distributions for time delay over multipath channels. The error analysis for typical estimators shows that the MSE and bias performance is determined by the statistics of measurement bias and noise, the beacon array geometry and the estimator type.

    Cover page: Performance of Time Delay Estimation and Range-Based Localization in Wireless Channels
    • Thesis
    • Peer Reviewed
    UC Davis Electronic Theses and Dissertations (2021)

    Understanding the relationship between demand and traffic network flows under an uncertain setting is gaining more and more attention in the transportation science community. In this dissertation, we establish new theorems and methods for understanding the input-output relation of traffic network equilibrium problems under uncertainty. Approaching the problem from a fresh geometrical perspective, we provide new understanding of the uncertainty propagation process in the problem of traffic equilibrium. We first introduce a minimum norm solution mapping (MNSM) between travel demand and network flows and explore its mathematical properties in terms of well-defined, continuity, induced partition and connectivity. Under the linearity assumption of the link cost function, we provide a stable analytic formula of the MNSM together with the criterion of partition region determination. We then extend those results to more general cost functions by using epi-splines to incorporate more realistic situation of nonlinear link cost under congestion. The new results can also maintain good geometric inherent characteristics. After completing these fundamental analysis, we demonstrate how the MNSM can help understand the uncertainty propagation process through the push-forward measure induced by the MNSM and we prove that the approximation process maintains strong convergence of the push-forward measure. We also provide an effective algorithm to compute the MNSM which avoids massive enumeration. Several important application examples are provide in the end to demonstrate how the new analytical and numerical methods established in the dissertation can be used to provide engineering and policy insights for transportation network planning and management.

      Cover page: How does uncertainty propagate through a transportation network under equilibrium?
      • Article
      • Peer Reviewed
      LBL Publications (2017)
      Understanding fluids migration and leakage risk along the fault zone is necessary to guarantee the safety of CO2 geological storage. The validity of Darcy's law gets challenged in dealing with the flow in open fractures since the occurring of turbulence flow. In this study, we develop a 2D model with usage of T2Well, an integrated wellbore-reservoir simulator, to investigate the leakage problem along open fractures which are embedded in a fault zone from the deep injection reservoir to shallow aquifers. The results record a positive feedback of gas expansion and pressure response in fracture, which causes a quick downward propagation of highly gas saturated zone from the top of fracture and an easy gas breakthrough in the shallower aquifers. The decreasing of aperture size of fracture significantly enhances the leakage rates in fracture, but with less influences as aperture increases. In comparison, the Equivalent PorousMedia models show a good approximation with the momentum model of large apertures but poor for the small one. Nevertheless, the differences are small in terms of final CO2 distribution among various aquifers, suggesting that Darcy's law may be still "effective" in solving flow problem along fractures in a constant injection system at a large time scale.
        • Article
        • Peer Reviewed
        LBL Publications (2021)
        Transcriptional factor-based biosensors (TFBs) have been widely used in dynamic pathway control or high-throughput screening. Here, we systematically explored the tunability of a salicylic acid responsive regulator MarR from Escherichia coli aiming to explore its engineering potential. The effect of endogenous MarR in E. coli on the MarR-PmarO biosensor system was investigated. Furthermore, to investigate the function of marO binding boxes in this biosensor system, a series of hybrid promoters were constructed by placing the marO binding boxes in the strong constitutive pL promoter. The engineered hybrid promoters became responsive to MarR and salicylic acid. To further study the influence of each nucleotide in the marO box on MarR binding, we employed dynamic modeling to simulate the interaction and binding energy between each nucleotide in the marO boxes with the corresponding residues on MarR. Guided by the results of the simulation, we introduced mutations to key positions on the hybrid promoters and investigated corresponding dynamic performance. Two promoter variants I12AII4T and I12AII14T that exhibited improved responsive strengths and shifted dynamic ranges were obtained, which can be beneficial for future metabolic engineering research.
          Cover page: Exploring the Tunability and Dynamic Properties of MarR-PmarO Sensor System in Escherichia coli.
          • Article
          • Peer Reviewed
          UCLA Previously Published Works (2019)
          Many living organisms track light sources and halt their movement when alignment is achieved. This phenomenon, known as phototropism, occurs, for example, when plants self-orient to face the sun throughout the day. Although many artificial smart materials exhibit non-directional, nastic behaviour in response to an external stimulus, no synthetic material can intrinsically detect and accurately track the direction of the stimulus, that is, exhibit tropistic behaviour. Here we report an artificial phototropic system based on nanostructured stimuli-responsive polymers that can aim and align to the incident light direction in the three-dimensions over a broad temperature range. Such adaptive reconfiguration is realized through a built-in feedback loop rooted in the photothermal and mechanical properties of the material. This system is termed a sunflower-like biomimetic omnidirectional tracker (SunBOT). We show that an array of SunBOTs can, in principle, be used in solar vapour generation devices, as it achieves up to a 400% solar energy-harvesting enhancement over non-tropistic materials at oblique illumination angles. The principle behind our SunBOTs is universal and can be extended to many responsive materials and a broad range of stimuli.
            Cover page: Artificial phototropism for omnidirectional tracking and harvesting of light.
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2021)
            The cohesin complex has an essential role in maintaining genome organization. However, its role in gene regulation remains largely unresolved. Here we report that the cohesin release factor WAPL creates a pool of free cohesin, in a process known as cohesin turnover, which reloads it to cell-type-specific binding sites. Paradoxically, stabilization of cohesin binding, following WAPL ablation, results in depletion of cohesin from these cell-type-specific regions, loss of gene expression and differentiation. Chromosome conformation capture experiments show that cohesin turnover is important for maintaining promoter-enhancer loops. Binding of cohesin to cell-type-specific sites is dependent on the pioneer transcription factors OCT4 (POU5F1) and SOX2, but not NANOG. We show the importance of cohesin turnover in controlling transcription and propose that a cycle of cohesin loading and off-loading, instead of static cohesin binding, mediates promoter and enhancer interactions critical for gene regulation.
              Cover page: WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation
              • Article
              • Peer Reviewed
              LBL Publications (2019)
              The cardiogenic transcription factors (TFs) Mef2c, Gata4, and Tbx5 can directly reprogram fibroblasts to induced cardiac-like myocytes (iCLMs), presenting a potential source of cells for cardiac repair. While activity of these TFs is enhanced by Hand2 and Akt1, their genomic targets and interactions during reprogramming are not well studied. We performed genome-wide analyses of cardiogenic TF binding and enhancer profiling during cardiac reprogramming. We found that these TFs synergistically activate enhancers highlighted by Mef2c binding sites and that Hand2 and Akt1 coordinately recruit other TFs to enhancer elements. Intriguingly, these enhancer landscapes collectively resemble patterns of enhancer activation during embryonic cardiogenesis. We further constructed a cardiac reprogramming gene regulatory network and found repression of EGFR signaling pathway genes. Consistently, chemical inhibition of EGFR signaling augmented reprogramming. Thus, by defining epigenetic landscapes these findings reveal synergistic transcriptional activation across a broad landscape of cardiac enhancers and key signaling pathways that govern iCLM reprogramming.
                Cover page: Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers.
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2020)

                Purpose

                End-of-life (EOL) cancer care is costly, with challenges regarding intensity and place of care. We described EOL care and costs for patients with colorectal cancer (CRC) in the United States and the province of Ontario, Canada, to inform better care delivery.

                Methods

                Patients diagnosed with CRC from 2007 to 2013, who died of any cancer from 2007 to 2013 at age ≥ 66 years, were selected from the US SEER cancer registries linked to Medicare claims (n = 16,565) and the Ontario Cancer Registry linked to administrative health data (n = 6,587). We estimated total and resource-specific costs (2015 US dollars) from public payer perspectives over the last 360 days of life by 30-day periods, by stage at diagnosis (0-II, III, IV).

                Results

                In all months, especially 30 days before death, higher percentages of SEER-Medicare than Ontario patients received chemotherapy (15.7% v 8.0%), and imaging tests (39.4% v 31.1%). A higher percentage of Ontario patients were hospitalized (62.5% v 51.0%), but 43.2% of hospitalized SEER-Medicare patients had intensive care unit (ICU) admissions versus 17.9% of hospitalized Ontario patients. Cost differences between cohorts were greater for patients with stage IV disease. In the last 30 days, mean total costs for patients with stage IV disease were $15,881 (SEER-Medicare) and $12,034 (Ontario) versus $19,354 and $17,312 for stage 0-II. Hospitalization costs were higher for SEER-Medicare patients ($11,180 v $9,434), with lower daily hospital costs in Ontario ($1,067 v $2,004).

                Conclusion

                These findings suggest opportunities for reducing chemotherapy and ICU use in the United States and hospitalizations in Ontario.
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2014)

                  Background

                  The utilization and costs of home care services provided for people with colorectal cancer is not well-known. We conducted an analysis to determine the utilization and costs of such services associated with each stage of colorectal cancer among patients in the province of Ontario.

                  Methods

                  We included cases of colorectal cancer diagnosed in Ontario between Jan. 1, 2005, and Dec. 31, 2009. Data were extracted from the Ontario Cancer Registry and linked to data from a home care administrative database. The types of services used were stratified by stage of disease and by phase of care (initial phase = 180 d after diagnosis, terminal phase = 180 d before death, continuing phase = interval between initial and terminal phases). Overall utilization rates and costs were determined, and regression analysis was used to examine associated factors.

                  Results

                  A total of 36 195 patients had colorectal cancer diagnosed during the study period; the median age was 71 (interquartile range 61-79) years. Home care services were provided to 24 641 patients (68.1%). The number of services per patient-year was 27.5, at a cost of $2180 per patient-year. The number of services provided per patient-year increased with increasing disease severity at diagnosis (15.5 at stage I, 25.5 at stage II, 32.5 at stage III and 62.5 at stage IV; 22.6 for unstaged disease). The cost of services per patient-year also increased with disease severity at diagnosis ($1170 at stage I, $1995 at stage II, $2727 at stage III and $5541 at stage IV). Publicly funded home care services and associated costs decreased with increasing income group, but they increased among patients who had a history of high health resource utilization. The mean 30-day cost of home care services decreased from the initial phase of care ($323) to the continuing phase ($160) but increased during the terminal phase ($616).

                  Interpretation

                  More than two-thirds of the patients with colorectal cancer in this study used home care services. Those who received home care services used about 2 services per month in a one-year period, at a cost of about $2000 per year. This information can aid policy-makers in future decisions regarding resource allocations.
                    Cover page: Utilization and costs of home care for patients with colorectal cancer: a population-based study
                    • Article
                    • Peer Reviewed
                    LBL Publications (2019)
                    The cardiogenic transcription factors (TFs) Mef2c, Gata4, and Tbx5 can directly reprogram fibroblasts to induced cardiac-like myocytes (iCLMs), presenting a potential source of cells for cardiac repair. While activity of these TFs is enhanced by Hand2 and Akt1, their genomic targets and interactions during reprogramming are not well studied. We performed genome-wide analyses of cardiogenic TF binding and enhancer profiling during cardiac reprogramming. We found that these TFs synergistically activate enhancers highlighted by Mef2c binding sites and that Hand2 and Akt1 coordinately recruit other TFs to enhancer elements. Intriguingly, these enhancer landscapes collectively resemble patterns of enhancer activation during embryonic cardiogenesis. We further constructed a cardiac reprogramming gene regulatory network and found repression of EGFR signaling pathway genes. Consistently, chemical inhibition of EGFR signaling augmented reprogramming. Thus, by defining epigenetic landscapes these findings reveal synergistic transcriptional activation across a broad landscape of cardiac enhancers and key signaling pathways that govern iCLM reprogramming.
                      Cover page: Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers
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