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Open Access Publications from the University of California

Scholarly Works (37 results)

  • Article
  • Peer Reviewed
UC Santa Barbara Previously Published Works (2010)
Fungal pathogens can regulate the abundance and distribution of natural plant populations by inhibiting the growth, survival, and reproduction of their hosts. The abiotic environment is a crucial component in host–pathogen interactions in natural plant populations as favorable conditions drive pathogen development, reproduction, and persistence. Foliar plant pathogens, such as fungal lesions referred to generically as “leaf spot disease,” are particularly responsive to increased moisture levels, but the manner in which the abiotic environment drives disease dynamics, and how these diseases regulate natural plant populations, is not fully understood. We investigate (1) the impact of ambient soil moisture and diffuse light on the prevalence of a leaf spot pathogen (Phyllosticta sp.) in a natural population of Polygonatum biflorum, an understory herb native to deciduous forest understories in the eastern US, and (2) the effects of the fungal pathogen on the survival, growth, and abundance of the plants. We tracked six P. biflorum populations and disease incidence, as well as soil moisture and diffuse light, between 2003 and 2005 in the understory deciduous forest of the southern Appalachian Mountains, North Carolina, USA. Results show that both the occurrence of P. biflorum and the prevalence of P. biflorum leaf spot disease are highest where soil moisture is intermediate and diffuse light is lowest. Disease occurrence depends upon plant presence, but it also adversely impacts plant survival, abundance, and growth. These results suggest that leaf spot disease is likely to impact population dynamics, which in turn vary as a function of environmental drivers.
    Cover page: Soil moisture mediated interaction between Polygonatum biflorum and leaf spot disease
    • Thesis
    • Peer Reviewed
    UC Irvine Electronic Theses and Dissertations (2017)

    Cardiovascular disease (CVD) is the number one killer in the world, yet one third of CVD-related deaths occur in asymptomatic individuals and one fifth of these individuals bear no previous diagnosis of CVD [1]. New methods that provide a better understanding of CVD risk factors and detect asymptomatic disease could save many lives. In this work, I introduce diffuse optical spectroscopic imaging (DOSI) as a new method for non-invasively assessing “silent” CVD and CVD risk. DOSI is a quantitative, model-based technique that utilizes a broadband wavelength range, corrects for light scattering, and probes several centimeters into tissue. DOSI is particularly relevant for cardiovascular disease research because it measures absolute concentrations of the primary light absorber in blood, hemoglobin, as well as the oxygenation state of hemoglobin, lipid content, and water content. These features of DOSI allow for hemodynamic measurements, compositional analysis, and reliable comparisons across operators, instruments, and even separate institutions.

    I demonstrate a diffuse optical spectroscopic vascular health assessment which samples three important features of vascular health: body composition, tissue metabolism, and vascular reactivity. In a pilot study of body composition assessment, DOSI is used to track alterations in human muscle tissue following 5-weeks of resistance training. These assessments of muscle are compared to dual-energy x-ray absorptiometry (DXA), a standard body composition assessment technique. A similar approach is used in a study of 103 individuals but is extended to sample the whole body. Using DOSI assessments at 12 anatomical locations, a method is developed to predict whole-body fat and lean soft tissue percentage. Next, I study hemodynamics in a cohort of healthy volunteers using a vascular occlusion technique. This study characterizes the range of tissue metabolism we expect to see in healthy individuals and identifies how adipose tissue thickness affects DOSI assessments. Finally, preliminary data on vascular reactivity from patients with confirmed vascular disease is presented and I propose a framework for future vascular health assessments with DOSI.

      Cover page: Development of Non-Invasive, Functional, Optical Imaging for Monitoring and Detecting Cardiovascular DiseaseCreative Commons 'BY-NC-ND' version 4.0 license
      • Article
      • Peer Reviewed
      UC San Francisco Previously Published Works (2015)
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2013)
        Frequency domain optical spectroscopy in the diffusive regime is currently being investigated for biomedical applications including tumor detection, therapy monitoring, exercise metabolism, and others. Analog homodyne or heterodyne detection of sinusoidally modulated signals have been the predominant method for measuring phase and amplitude of photon density waves that have traversed through tissue. Here we demonstrate the feasibility of utilizing direct digital sampling of modulated signals using a 3.6 Gigasample/second 12 bit Analog to Digital Converter. Digitally synthesized modulated signals between 50MHz and 400MHz were measured on tissue simulating phantoms at six near-infrared wavelengths. An amplitude and phase precision of 1% and 0.6 degrees were achieved during drift tests. Amplitude, phase, scattering and absorption values were compared with a well-characterized network analyzer based diffuse optical device. Measured optical properties measured with both systems were within 3.6% for absorption and 2.8% for scattering over a range of biologically relevant values. Direct digital sampling represents a viable method for frequency domain diffuse optical spectroscopy and has the potential to reduce system complexity, size, and cost.
          Cover page: Feasibility of direct digital sampling for diffuse optical frequency domain spectroscopy in tissueCreative Commons 'BY' version 4.0 license
          • Article
          Recent Work (2007)

          Deer-vehicle collisions are on the rise and are a costly side-effect of increasing deer populations and expanding transportation systems. We evaluated the efficacy of sound as a deterrent for reducing deer-vehicle collisions by observing the behavioral response of captive and free-ranging white-tailed deer (Odocoileus virginianus) to 5 pure-tone sound treatments: 0.28 kHz, 1 kHz, 8 kHz, 15 kHz, and 28 kHz. We conducted preliminary trials with semi-tame deer at the University of Georgia Captive Deer Research Facility. We exposed 8 deer in a 0.25-ha outside paddock and 5 deer in individual stalls (2.7 m x 4.8 m) to the various treatments at >70 dB Sound Pressure Level. We recorded 406 observations and determined that the behavior of captive deer did not change when presented with any of the 5 pure-tone sound treatments. We also conducted field trials at Berry College Wildlife Refuge, Georgia and gathered 319 behavioral observations of free-ranging deer relative to a moving automobile (56.45 kph). The automobile was fitted with a sound-producing device and speakers that emitted one of the pure-tone sound treatments or no sound treatment as a control. For the 1 kHz, 8 kHz, 15 kHz, and 28 kHz sound treatments, we observed no change in deer behavior relative to the control. When exposed to the 0.28 kHz treatment, deer reacted in a manner more likely to cause deer-vehicle collisions. Our results indicate that deer within 10 m of roadways did not alter their behavior in response to the pure-tone sound treatments we tested in a manner that would prevent deer-vehicle collisions. Commercially available wildlife warning whistles (aka deer whistles) are purported to emit similar consistent, continuous sounds as pure tones at various frequencies within the range of those presented in this study. Our data suggests that deer-whistles, as they are purported to operate, are likely not effective in preventing deer-vehicle collisions.

            Cover page: Behavioral Responses of White-tailed Deer to Vehicle Mounted Sound-Producing Devices
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2011)

            Background

            Retroperitoneal tumors are often massive and can involve adjacent organs and/or vital structures, making them difficult to resect. Completeness of resection is within the surgeon's control and critical for long-term survival, particularly for malignant disease. Few studies directly address strategies for complete and safe resection of challenging retroperitoneal tumors.

            Methods

            Fifty-six patients representing 63 cases of primary or recurrent retroperitoneal tumor resection between 2004-2009 were identified and a retrospective chart review was performed. Rates of complete resection, use of adjunct procedures, and perioperative complications were recorded.

            Results

            In 95% of cases, complete resection was achieved. Fifty-eight percent of these cases required en bloc multi-organ resection, and 8% required major vascular resection. Complete resection rates were higher for primary versus recurrent disease. Adjunct procedures (ureteral stents, femoral nerve monitoring, posterior laminotomy, etc.) were used in 54% of cases. Major postoperative complications occurred in 16% of cases, and one patient died (2% mortality).

            Conclusions

            Complete resection of challenging retroperitoneal tumors is feasible and can be done safely with important pre- and intraoperative considerations in mind.
              Cover page: Complete and safe resection of challenging retroperitoneal tumors: anticipation of multi-organ and major vascular resection and use of adjunct procedures
              • Article
              • Peer Reviewed
              Abstract Background Retroperitoneal tumors are often massive and can involve adjacent organs and/or vital structures, making them difficult to resect. Completeness of resection is within the surgeon's control and critical for long-term survival, particularly for malignant disease. Few studies directly address strategies for complete and safe resection of challenging retroperitoneal tumors. Methods Fifty-six patients representing 63 cases of primary or recurrent retroperitoneal tumor resection between 2004-2009 were identified and a retrospective chart review was performed. Rates of complete resection, use of adjunct procedures, and perioperative complications were recorded. Results In 95% of cases, complete resection was achieved. Fifty-eight percent of these cases required en bloc multi-organ resection, and 8% required major vascular resection. Complete resection rates were higher for primary versus recurrent disease. Adjunct procedures (ureteral stents, femoral nerve monitoring, posterior laminotomy, etc.) were used in 54% of cases. Major postoperative complications occurred in 16% of cases, and one patient died (2% mortality). Conclusions Complete resection of challenging retroperitoneal tumors is feasible and can be done safely with important pre- and intraoperative considerations in mind.
                Cover page: Complete and safe resection of challenging retroperitoneal tumors: anticipation of multi-organ and major vascular resection and use of adjunct procedures
                • Article
                • Peer Reviewed
                UC Irvine Previously Published Works (2017)
                Frequency-domain photon migration (FDPM) uses modulated laser light to measure the bulk optical properties of turbid media and is increasingly applied for noninvasive functional medical imaging in the near-infrared. Although semiconductor edge-emitting laser diodes have been traditionally used as miniature light sources for this application, we show that vertical-cavity surface-emitting lasers (VCSELs) exhibit output power and modulation performance characteristics suitable for FDPM measurements of tissue optical properties at modulation frequencies exceeding 1 GHz. We also show that an array of multiple VCSEL devices can be coherently modulated at frequencies suitable for FDPM and can improve optical power. In addition, their small size and simple packaging make them an attractive choice as components in wearable sensors and clinical FDPM-based optical spectroscopy systems. We demonstrate the benefits of VCSEL technology by fabricating and testing a unique, compact VCSEL-based optical probe with an integrated avalanche photodiode. We demonstrate sensitivity of the VCSEL-based probe to subcutaneous tissue hemodynamics that was induced during an arterial cuff occlusion of the upper arm in a human subject.
                  Cover page: Vertical-cavity surface-emitting laser sources for gigahertz-bandwidth, multiwavelength frequency-domain photon migration
                  • Article
                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2013)
                  SALL2- a member of the Spalt gene family- is a poorly characterized transcription factor found deregulated in various cancers, which suggests it plays a role in the disease. We previously identified SALL2 as a novel interacting protein of neurotrophin rece
                    • Article
                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2022)
                    Tumour Necrosis Factor (TNF) potently induces a transient inflammatory response that must be downregulated once any invasive stimulus has resolved. Yet, how TNF-induced inflammation is shut down in normal cells is incompletely understood. The present study shows that STAT3 was activated in mouse embryo fibroblasts (MEFs) by treatment with TNF or an agonist antibody to TNFR1. STAT3 activation was inhibited by pharmacological inhibition of the Jak2 tyrosine kinase that associates with TNFR1. To identify STAT3 target genes, global transcriptome analysis by RNA sequencing was performed in wild-type MEFs and MEFs from STAT3 knockout (STAT3KO ) mice that were stimulated with TNF, and the results were validated at the protein level by using multiplex cytokine assays and immunoblotting. After TNF stimulation, STAT3KO MEFs showed greater gene and protein induction of the inflammatory chemokines Ccl2, Cxcl1 and Cxcl10 than WT MEFs. These observations show that, by activating STAT3, TNF selectively modulates expression of a cohort of chemokines that promote inflammation. The greater induction by TNF of chemokines in STAT3KO than WT MEFs suggested that TNF induced an inhibitory protein in WT MEFs. Consistent with this possibility, STAT3 activation by TNFR1 increased the expression of Tnfaip3/A20, a ubiquitin modifying enzyme that inhibits inflammation, in WT MEFs but not in STAT3KO MEFs. Moreover, enforced expression of Tnfaip3/A20 in STAT3KO MEFs suppressed proinflammatory chemokine expression induced by TNF. Our observations identify Tnfaip3/A20 as a new downstream target for STAT3 which limits the induction of Ccl2, Cxcl1 and Cxcl10 and inflammation induced by TNF.
                      Cover page: STAT3 regulates inflammatory cytokine production downstream of TNFR1 by inducing expression of TNFAIP3/A20
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