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Open Access Publications from the University of California

Scholarly Works (12 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2021)

Spectroscopy methods are widely used for system characterization. Typically a perturbationsignal is introduced to the system, and corresponding outputs are detected. The underlying properties of a system can be determined by comparing the output to the input. This work employs advanced statistical methods to improve overall performance of such methods applied to energy transport and storage, in terms of accuracy, time efficiency and cost for spectroscopy methods to characterize thermal and electrochemical systems.

The rest part of this work reports a custom spectroscopy system that employs periodicheating to characterize thermal diffusivity under ambient conditions; the technique is also known as Angstrom's method. We employ forced convection to reduce variation in convective heat transfer losses along the heat propagation direction to enable the experiment to be conducted outside vacuum. We employ IR thermography to for data-rich temperature detection and further introduce a Bayesian framework for uncertainty quantification and uncertainty reduction with increased data. We demonstrate accurate results (< 5% error) for multiple short metal strips.

In the second part we extend the room temperature spectroscopy approach to high temperatures.For high-temperature characterization, the testing environment is difficult to control precisely; therefore, additional unknowns exist in the physical model as compared to low-temperature measurements. In addition, nonlinear radiation loss are present, and the transient heat transfer process must be modeled numerically. Solving the inverse problem using conventional regression approaches is challenging because the solutions are not unique and lack uncertainty estimates. Therefore, we develop a Bayesian framework to solve the inverse problem. The main challenges overcome are: (1) probing the posterior distribution given a computationally expensive forward model and (2) achieving convergence in the sampling process for a model with a relatively high number of unknowns. In this study we report a computationally efficient parametric surrogate model to accelerate the Bayesian analysis and employ a No-U-Turn sampler to achieve good convergence in the sampling process. The custom instrument exhibits high accuracy (approx. 5% error) and requires only 10 min. obtain steady high-temperature results, compared to several hours using conventional methods and commercial instruments.

Lastly we demonstrate a broadband spectroscopy instrument for electrochemical impedancespectroscopy (EIS) measurements for supercapacitors. Measuring EIS is challenging because (1) low-frequency scans are time consuming and (2) impedance of supercapacitors typically changes by several orders of magnitude across a wide frequency band. The custom instrument employs a broadband exponential chirp signal for rapid frequency scanning. To account for large impedance variations, we report a custom circuit for automatically adaptable impedance matching during measurements. The custom instrument is accurate and exhibits four times measurement time reduction and ten times cost reduction compared to leading commercial instruments.

    Cover page: Rapid thermal and electrochemical characterization with low measurement uncertainty
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2020)

    Background

    Antimicrobial resistance is a serious public health problem. Fecal carriage of drug-resistant bacteria has been suggested as an important source of antimicrobial resistant genes (ARGs). We aimed to identify risk factors associated with fecal carriage of drug-resistant commensal Escherichia coli among healthy adult population.

    Methods

    We conducted a systematic review and meta-analysis following the PRISMA guideline. We identified observational studies published from 2014 to 2019 through PubMed, Embase, and Web of Science. Studies were eligible if they investigated and reported risk factors and accompanying measure of associations for fecal carriage of drug-resistant E. coli for healthy population aged 18-65. Data on risk factors assessed in three or more studies were extracted.

    Results

    Fifteen of 395 studies involving 11480 healthy individuals were included. The pooled prevalence of drug-resistant Enterobacteriaceae was 14% (95% confidence interval [CI] 8-23%). Antimicrobial use within the 12 months prior to stool culture (odds ratio [OR] 1.84 [95%CI 1.35-2.51]), diarrhea symptoms (OR 1.56 [95%CI 1.09-2.25]), travel to India (OR 4.15 [95%CI 2.54-6.78]), and vegetarian diet (OR 1.60 [95%CI 1.00(1.0043)-2.56(2.5587)]) were associated with increased risk of fecal carriage of drug-resistant E. coli. Among travellers, antimicrobial use (OR 2.81 [95%CI 1.47-5.36]), diarrhea symptoms (OR 1.65 [95%CI 1.02-2.68]), travel to India (OR 3.80 [95%CI 2.23-6.47]), and vegetarian diet (OR 1.92 [95%CI 1.13-3.26]) were associated with increased risk. Among general adult population, antimicrobial use (OR 1.51 [95%CI 1.17-1.94]), diarrhea symptoms (OR 1.53 [95%CI 1.27-1.84]), and travel to Southeast Asia (OR 1.67 [95%CI 1.02-2.73]) were associated with the increased risk of drug-resistant E. coli carriage.

    Conclusions

    The findings indicate that dietary habit as well as past antimicrobial use and travel to high-risk country are associated with the risk of fecal carriage of drug-resistant commensal E. coli.
      Cover page: Risk factors for fecal carriage of drug-resistant Escherichia coli: a systematic review and meta-analysis
      • Article
      • Peer Reviewed
      UCLA Previously Published Works (2022)
      Abstract This work reports a method to measure thermal diffusivity of thin disk samples at high temperatures (approximately 900–1150 K) using a modified Ångström's method. Conventionally, samples are heated indirectly from the surroundings to reach high temperatures for such measurements, and this process is time-consuming, typically requiring hours to reach stable temperatures. In this work, samples are heated directly in a custom instrument by a concentrated light source and are able to reach high steady-periodic temperatures in approximately 10 min, thus enabling rapid thermal diffusivity characterization. Further, existing Ångström's methods for high temperature characterization use thermocouples for temperature detection that are commonly attached to samples via drilling and welding, which are destructive to samples and introduce thermal anomalies. We use an infrared camera calibrated to 2000 °C for noncontact, nondestructive, and data-rich temperature measurements and present an image analysis approach to process the infrared (IR) data that significantly reduces random noise in temperature measurements. We extract amplitude and phase from processed temperature profiles and demonstrate that these metrics are insensitive to uncertainty in emissivity. Previous studies commonly use regression approaches for parameter estimation that are ill-posed (i.e., nonunique solutions) and lack rigorous characterization of parameter uncertainties. Here, we employ a surrogate-accelerated Bayesian framework and a “no-U-turn” sampler for uncertainty quantification. The reported results are validated using graphite and copper disks and exhibit excellent agreement within 5% as compared to reference values obtained by other methods.
        Cover page: High-Temperature Thermal Diffusivity Measurements Using a Modified Ångström's Method With Transient Infrared Thermography
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2009)
        Secondary metabolites play an important role in host plant resistance to insects, and insects, in turn, may develop mechanisms to counter plant resistance mechanisms. In this study, we investigated the toxicity of gramine to the cereal aphid Sitobion avenae and some enzymatic responses of S. avenae to this alkaloid. When S. avenae fed on an artificial diet containing gramine, mortality occurred in a dose-dependent manner. The LC50 of gramine was determined to be 1.248 mM. In response to gramine, S. avenae developed increased activities of carboxylesterase and glutathione S-transferase, two important detoxification enzymes. The activities of both enzymes were positively correlated with the concentration of dietary gramine. In addition, the activities of peroxidase and polypheolic oxidase, two important oxidoreductase enzymes in S. avenae, increased in response to gramine; however, catalase activity decreased when insects were exposed to higher levels of dietary gramine. The potential role of gramine in host plant resistance and S. avenae counter-resistance is discussed.
          Cover page: Detoxification of Gramine by the Cereal Aphid Sitobion avenae
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2020)
          Community-acquired urinary tract infections (UTIs) are one of the most common bacterial infections worldwide. Escherichia coli is the most common cause of community-acquired UTI. In general, UTI results from E. coli in the intestine that enters the bladder via the urethra. However, whether these E. coli strains that cause UTI represent members of the intestinal commensal E. coli or a distinct subgroup of pathogenic E. coli remains unestablished. Here, we analyzed E. coli isolates from fecal samples of healthy volunteers and urine samples of UTI patients obtained from a university-affiliated health center. The E. coli isolates were genotyped by multilocus sequence typing (MLST). From May to October 2018, we analyzed 89 E. coli isolates from 76 (75%) rectal swabs from 113 unique healthy volunteers. We also analyzed 106 (27%) E. coli isolates from 398 unique urine samples collected between August and October 2018. Fecal and urine E. coli isolates each contained 31 distinct sequence types (STs). Nine STs were shared by fecal and urine E. coli isolates, which accounted for approximately 50% of urine isolates typed by MLST. Among the shared genotypes, ST10 and ST131 were significantly more frequently found in fecal samples, whereas ST95 and ST127 were significantly more frequently recovered from UTI samples. ST73 was found only among urine samples. These E. coli genotypes clustered and fluctuated over time. These observations suggest that E. coli genotypes found to cause UTI transiently colonize the intestine and that their primary reservoir may reside outside of the human intestine.
            Cover page: Multilocus sequence typing of Escherichia coli isolates from urinary tract infection patients and from fecal samples of healthy subjects in a college community
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2020)
            The genome sequence of a uropathogenic Escherichia coli sequence type 420 strain isolated from a patient with urinary tract infection in northern California is described here. The draft genome sequence includes a 4.8-Mb chromosome, accompanied by a 114-kb plasmid containing IncFIB/IncFII/Col156 and a 35-kb plasmid containing IncN3.
              Cover page: Draft Genome Sequence of an Escherichia coli Sequence Type 420 Isolate from a Patient with Urinary Tract Infection in Northern California
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2018)
              The Early Triassic Chaohu Fauna from Anhui Province, China, contains the oldest record of Mesozoic marine reptiles, such as Cartorhynchus and Sclerocormus. Most specimens from the fauna belong to the ichthyosauriform Chaohusaurus, more specifically resembling C. chaoxianensis. However, a wide range of morphological variation exists within about 40 skeletons that have been prepared, likely reflecting mixed signals from both sexual and taxonomic differences. We test whether the sexual and taxonomic signals are separable based on quantification, aided by the knowledge of sexual dimorphism in extant marine tetrapods. There are two different suites of dimorphism that divide the specimens differently from each other yet consistently within each suite, resulting in four morphotypes in combination, likely representing two sexes of two taxa. Presumed males have larger 'organ of prehension' sensu Darwin, specifically limbs in the present case, for a given body length. This sexing criterion is supported by the only specimen of a gravid female, which belongs to the morphotype with short limbs. Males also have larger skulls for the trunk length compared to females. This study demonstrates that sexual and taxonomic signals are separable in fossil reptiles, with a sufficient sample size and careful analyses.
                Cover page: Separating sexual dimorphism from other morphological variation in a specimen complex of fossil marine reptiles (Reptilia, Ichthyosauriformes, Chaohusaurus)
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2015)
                Neuronal atrophy in neurodegenerative diseases is commonly viewed as an early event in a continuum that ultimately results in neuronal loss. In a mouse model of the polyglutamine disorder spinocerebellar ataxia type 1 (SCA1), we tested the hypothesis that cerebellar Purkinje neuron atrophy serves an adaptive role rather than being simply a nonspecific response to injury. In acute cerebellar slices from SCA1 mice, we find that Purkinje neuron pacemaker firing is initially normal but, with the onset of motor dysfunction, becomes disrupted, accompanied by abnormal depolarization. Remarkably, subsequent Purkinje cell atrophy is associated with a restoration of pacemaker firing. The early inability of Purkinje neurons to support repetitive spiking is due to unopposed calcium currents resulting from a reduction in large-conductance calcium-activated potassium (BK) and subthreshold-activated potassium channels. The subsequent restoration of SCA1 Purkinje neuron firing correlates with the recovery of the density of these potassium channels that accompanies cell atrophy. Supporting a critical role for BK channels, viral-mediated increases in BK channel expression in SCA1 Purkinje neurons improves motor dysfunction and partially restores Purkinje neuron morphology. Cerebellar perfusion of flufenamic acid, an agent that restores the depolarized membrane potential of SCA1 Purkinje neurons by activating potassium channels, prevents Purkinje neuron dendritic atrophy. These results suggest that Purkinje neuron dendritic remodeling in ataxia is an adaptive response to increases in intrinsic membrane excitability. Similar adaptive remodeling could apply to other vulnerable neuronal populations in neurodegenerative disease.

                Significance statement

                In neurodegenerative disease, neuronal atrophy has long been assumed to be an early nonspecific event preceding neuronal loss. However, in a mouse model of spinocerebellar ataxia type 1 (SCA1), we identify a previously unappreciated compensatory role for neuronal shrinkage. Purkinje neuron firing in these mice is initially normal, but is followed by abnormal membrane depolarization resulting from a reduction in potassium channels. Subsequently, these electrophysiological effects are counteracted by cell atrophy, which by restoring normal potassium channel membrane density, re-establishes pacemaker firing. Reversing the initial membrane depolarization improved motor function and Purkinje neuron morphology in the SCA1 mice. These results suggest that Purkinje neuron remodeling in ataxia is an active compensatory response that serves to normalize intrinsic membrane excitability.
                  Cover page: Neuronal Atrophy Early in Degenerative Ataxia Is a Compensatory Mechanism to Regulate Membrane Excitability
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2020)
                  Marine tetrapods quickly diversified and were established as marine top predators after the end-Permian Mass extinction (EPME). Ichthyosaurs were the forerunner of this rapid radiation but the main drivers of the diversification are poorly understood. Cartorhynchus lenticarpus is a basal ichthyosauriform with the least degree of aquatic adaptation, holding a key to identifying such a driver. The unique specimen appeared edentulous based on what was exposed but a CT scanning revealed that the species indeed had rounded teeth that are nearly perpendicular to the jaw rami, and thus completely concealed in lateral view. There are three dental rows per jaw ramus, and the root lacks infoldings of the dentine typical of ichthyopterygians. The well-developed and worn molariform dentition with three tooth rows supports the previous inference that the specimen is not of a juvenile. The premaxilla and the corresponding part of the dentary are edentulous. Molariform dentition evolved three to five times independently within Ichthyosauriformes in the Early and Middle Triassic. Convergent exploitation of hard-shelled invertebrates by different subclades of ichthyosauriforms likely fueled the rapid taxonomic diversification of the group after EPME.
                    Cover page: Repeated evolution of durophagy during ichthyosaur radiation after mass extinction indicated by hidden dentition
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2016)
                    Contrary to the fast radiation of most metazoans after the end-Permian mass extinction, it is believed that early marine reptiles evolved slowly during the same time interval. However, emerging discoveries of Early Triassic marine reptiles are questioning this traditional view. Here we present an aberrant basal ichthyosauriform with a hitherto unknown body design that suggests a fast radiation of early marine reptiles. The new species is larger than coeval marine reptiles and has an extremely small head and a long tail without a fluke. Its heavily-built body bears flattened and overlapping gastral elements reminiscent of hupehsuchians. A phylogenetic analysis places the new species at the base of ichthyosauriforms, as the sister taxon of Cartorhynchus with which it shares a short snout with rostrally extended nasals. It now appears that ichthyosauriforms evolved rapidly within the first one million years of their evolution, in the Spathian (Early Triassic), and their true diversity has yet to be fully uncovered. Early ichthyosauromorphs quickly became extinct near the Early-Middle Triassic boundary, during the last large environmental perturbation after the end-Permian extinction involving redox fluctuations, sea level changes and volcanism. Marine reptile faunas shifted from ichthyosauromorph-dominated to sauropterygian-dominated composition after the perturbation.
                      Cover page: A large aberrant stem ichthyosauriform indicating early rise and demise of ichthyosauromorphs in the wake of the end-Permian extinction
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