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Open Access Publications from the University of California

Scholarly Works (36 results)

  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2019)
OBJECTIVE:To assess the efficacy of transdermal lidocaine as a treatment for chronic subjective tinnitus as measured by the Tinnitus Functional Index (TFI). STUDY DESIGN:Pilot, prospective efficacy trial. SETTING:Tertiary care hospital. PATIENTS:Men and women, over the age of 18 with chronic subjective tinnitus for >6 months. INTERVENTION:Daily application of commercially available transdermal lidocaine patch. OUTCOME MEASURE:Change in the TFI. RESULTS:The average pre-treatment TFI score was 56.2. After 1 month the average TFI decreased to 41 (p < 0.05). The scores dropped to 34 and 35 after 2 and 3 months of treatment respectively. Despite improvement in symptoms of tinnitus, most patients did not continue the study after the first month, dropping out due to the size, discomfort, and appearance of the lidocaine patch, failure to follow-up and lack of perceived benefit from treatment. CONCLUSIONS:In this preliminary study, 5% transdermal lidocaine appears to be a potential treatment for chronic subjective tinnitus. The majority of subjects who completed 1 month of treatment had clinically significantly improved tinnitus. These findings are confounded however by the small sample size and significant drop out rate.
    Cover page: Transdermal lidocaine as treatment for chronic subjective tinnitus: A pilot study
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2021)

    The aim of this study was to test the hypothesis that endovascular aspiration thrombectomy of right atrial thrombus (RAT) using the AngioVac device is as safe and effective in patients with cancer as those without cancer.

    RAT is a uniquely challenging clinical presentation of venous thromboembolism due to its low incidence and historically high-risk of mortality due to thrombus propagation into the pulmonary arteries. There is a lack of consensus regarding management, particularly in high-risk cancer patients. Endovascular aspiration thrombectomy utilizing the AngioVac device is effective in removal of right atrial thrombus and may be a safer option for patients with cancer in whom avoidance of higher-risk intervention is preferred.

    This was an institutional review board-approved retrospective single-center case control study of patients with RAT who underwent AngioVac aspiration thrombectomy between August 2013 and July 2020. Analysis of patient demographics and clinical characteristics, thrombus-related factors, and operative details was performed. Primary endpoints included survival, safety, and technical success.

    A total of 44 patients met inclusion criteria, 20 of whom with active malignancy. The oncology group had a significantly higher Charlson comorbidity index (P = 0.01). Comparative outcomes between the oncology and non-oncology group showed no difference in survival (P = 0.8) or technical success (OR 3, 95% CI 0.83-10.9). There were 9 complications, including 6 minor, 1 moderate, 1 severe, and 1 death.

    AngioVac aspiration thrombectomy of RAT is as safe and effective in patients with cancer as those without cancer.

      Cover page: AngioVac Aspiration Thrombectomy of Right Atrial Thrombus is Safe and Effective in Cancer Patients.
      • Article
      • Peer Reviewed
      Clinical Practice and Cases in Emergency Medicine, Volume 2, Issue 3 (2018)
      A 56-year-old female presented to the emergency department with evolving cardiac tamponade after receiving alteplase for acute ischemic stroke. This is the first case report of cardiac tamponade from thrombolytics in the setting of recent pacemaker placement. Point-of-care ultra sound was usedto make the diagnosis quickly and expedite the patient to the operating room where a pericardial window was performed.
        Cover page: Alteplase Causing Cardiac Tamponade in the Setting of Recent Cardiac Pacemaker PlacementCreative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2015)

        Purpose

        To identify which patients and canines are involved in dog bites of the head and neck, and how they impact health systems.

        Materials and methods

        This is a single center, retrospective cohort study conducted from January 2012 to June 2013 in an academic, tertiary care center situated between multiple suburban and urban communities. Patients were identified by queried search for all bite-related diagnoses codes.

        Results

        334 unique dog bites were identified, of which 101 involved the head and neck. The mean patient age was 15.1±18.1years. Of the more than 8 different breeds identified, one-third were caused by pit bull terriers and resulted in the highest rate of consultation (94%) and had 5 times the relative rate of surgical intervention. Unlike all other breeds, pit bull terriers were relatively more likely to attack an unknown individual (+31%), and without provocation (+48%). Injuries of the head and neck had an average follow-up of 1.26±2.4 visits, and average specialty follow-up of 3.1±3.5 visits.

        Conclusions

        The patients most likely to suffer dog bite injuries of the head and neck are children. Although a number of dog breeds were identified, the largest group were pit bull terriers, whose resultant injuries were more severe and resulted from unprovoked, unknown dogs. More severe injuries required a greater number of interventions, a greater number of inpatient physicians, and more outpatient follow-up encounters. Healthcare utilization and costs associated with dog bites warrant further investigation.
          Cover page: Dog bites of the head and neck: an evaluation of a common pediatric trauma and associated treatment
          • Article
          • Peer Reviewed
          UC Santa Cruz Previously Published Works (2017)
          Liver cancer has the second highest worldwide cancer mortality rate and has limited therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases by whole-exome sequencing and DNA copy number analyses, and we analyzed 196 HCC cases by DNA methylation, RNA, miRNA, and proteomic expression also. DNA sequencing and mutation analysis identified significantly mutated genes, including LZTR1, EEF1A1, SF3B1, and SMARCA4. Significant alterations by mutation or downregulation by hypermethylation in genes likely to result in HCC metabolic reprogramming (ALB, APOB, and CPS1) were observed. Integrative molecular HCC subtyping incorporating unsupervised clustering of five data platforms identified three subtypes, one of which was associated with poorer prognosis in three HCC cohorts. Integrated analyses enabled development of a p53 target gene expression signature correlating with poor survival. Potential therapeutic targets for which inhibitors exist include WNT signaling, MDM4, MET, VEGFA, MCL1, IDH1, TERT, and immune checkpoint proteins CTLA-4, PD-1, and PD-L1.
            Cover page: Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma
            • Article
            • Peer Reviewed
            UC Santa Cruz Previously Published Works (2017)
            Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.
              Cover page: Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles
              • Article
              • Peer Reviewed
              UC San Francisco Previously Published Works (2018)
              (Cell Reports 23, 313–326; April 3, 2018) In the originally published version of this article, the author list contained two errors. Specifically, David J. Kwiatkowski was misspelled as David J. Kwaitkowski, and William Y. Kim was inadvertently written as William T. Kim. Both names have been corrected online. The authors regret this error.
                Creative Commons 'BY' version 4.0 license
                • Article
                • Peer Reviewed
                UC San Francisco Previously Published Works (2019)
                (Immunity 48, 812–830.e1–e14; April 17, 2018) In the originally published version of this article, the authors neglected to include Younes Mokrab and Aaron M. Newman as co-authors and misspelled the names of authors Charles S. Rabkin and Ilya Shmulevich. The author names have been corrected here and online. In addition, the concluding sentence of the subsection “Immune Signature Compilation” in the Method Details in the original published article was deemed unclear because it did not specify differences among the gene set scoring methods. The concluding sentences now reads “Gene sets from Bindea et al., Senbabaoglu et al., and the MSigDB C7 collection were scored using single-sample gene set enrichment (ssGSEA) analysis (Barbie et al., 2009), as implemented in the GSVA R package (Hänzelmann et al., 2013). All other signatures were scored using methods found in the associated citations.”
                  Creative Commons 'BY' version 4.0 license
                  • Article
                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2018)
                  (Cell 173, 371–385.e1–e9; April 5, 2018) It has come to our attention that we made two errors in preparation of this manuscript. First, in the STAR Methods, under the subheading of “Hypermutators and Immune Infiltrates” within the “Quantification and Statistical Analysis” section, we inadvertently referred to Figures S7A–S7C for data corresponding to sample stratification by hypermutator status alone in the last sentence. It should have referred to Figure S6A–S6C. Second, the lists of highly frequent missense mutations for COAD (colon adenocarcinoma) and READ (rectum adenocarcinoma) displayed in Figure S7 were incorrect because when we ordered the mutations in the initial analysis, we mistakenly combined the two cancer types COAD and READ for analysis, despite the fact that they were listed as two separate cancer types in the x-axis of the figure. After re-ordering the mutations by frequency for COAD and READ independently, information on highly frequent missense mutations for each of these cancer types is different and updated now in the revised Figure S7. These errors don't change the major conclusions of the paper and have been corrected online. We apologize for any confusion they may have caused. [Figure-presented]
                    Creative Commons 'BY' version 4.0 license
                    • Article
                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2018)
                    The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 8928 tumor samples across 33 cancer types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed in most cancers. Across cancer types, global enhancer activity was positively associated with aneuploidy, but not mutation load, suggesting a hypothesis centered on "chromatin-state" to explain their interplay. Integrating eQTL, mRNA co-expression, and Hi-C data analysis, we developed a computational method to infer causal enhancer-gene interactions, revealing enhancers of clinically actionable genes. Having identified an enhancer ∼140 kb downstream of PD-L1, a major immunotherapy target, we validated it experimentally. This study provides a systematic view of enhancer activity in diverse tumor contexts and suggests the clinical implications of enhancers.
                      Cover page: A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples
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