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Open Access Publications from the University of California

Scholarly Works (38 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2012)

Automatic analysis of biological image datasets is one of the important achievements of applied image processing research. Feature extraction in volumetric bioimages obtained from numerous biomedical imaging techniques is becoming extremely critical for biologists and medical professionals to find the answers to many problems. In this work, we show how to extract effective features in two kinds of volumetric bioimages - plant shoot apical meristem(SAM) cell images taken by Confocal Laser Scanning Microscopy (CLSM) and the nematode images taken by Differential Interference Contrast Microscopy.

For actively developing tissues, a computational platform capable of automatically segmenting and tracking cells in the volumetric image stacks is very critical to obtaining high-throughput and quantitative spatiotemporal measurements of a range of cell behaviors, which will lead to a better understanding of the underlying dynamics of morphogenesis. The cells in the SAM are tightly clustered in space and have very similar shapes and intensity distributions, thus choosing reliable features to compute cell correspondences in space and time can be very challenging. In our research we propose a local graph matching based method to track the cells both spatially and temporally, and identify cell divisions. The geometric structure and topology of the cells' relative positions are efficiently exploited as the basic feature to match the cells. Furthermore, we build a joint segmentation and tracking system, where the tracking output acts as an indicator of the quality of segmentation and, in turn, the optimized segmentation can be improved to obtain better tracking results. In the end, the cell correspondences across multiple slices and time windows are fused together to obtain the final cell lineages. Experiments on multiple plant datasets show the proposed image analysis pipeline can effectively segment and track the SAMs cells.

Another contribution of this work on volumetric bioimages analysis lies in multilinear feature extraction and classification for nematode Digital Multi-focal Images (DMI). In such images, morphological information for a transparent specimen is captured in the form of a stack of high quality images, representing individual focal planes through the specimen's body. We present a method that can effectively exploit the entire information in the stack using the 3D X-Ray projections at different viewing angles. These DMI stacks represent the effect of different factors - shape, texture, viewpoint, different instances within the same class and different classes of specimens. For this purpose, we embed the 3D X-Ray Transform within a multilinear framework and propose a Multilinear X-Ray Transform feature representation. The experimental results on the nematode DMI data show that the proposed feature extraction and analysis method can give reliable recognition rate on a real-life database.

    Cover page: Feature Extraction in Volumetric Bioimages
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2020)
    Coronavirus disease 2019 (COVID-19) has resulted in considerable morbidity and mortality worldwide since December 2019. In order to explore the effects of comorbid chronic diseases on clinical outcomes of COVID-19, a search was conducted in PubMed, Ovid MEDLINE, EMBASE, CDC, and NIH databases to April 25, 2020. A total of 24 peer-reviewed articles, including 10948 COVID-19 cases were selected. We found diabetes was present in 10.0%, coronary artery disease/cardiovascular disease (CAD/CVD) was in 8.0%, and hypertension was in 20.0%, which were much higher than that of chronic pulmonary disease (3.0%). Specifically, preexisting chronic conditions are strongly correlated with disease severity [Odds ratio (OR) 3.50, 95% CI 1.78 to 6.90], and being admitted to intensive care unit (ICU) (OR 3.36, 95% CI 1.67 to 6.76); in addition, compared to COVID-19 patients with no preexisting chronic diseases, COVID-19 patients who present with either diabetes, hypertension, CAD/CVD, or chronic pulmonary disease have a higher risk of developing severe disease, with an OR of 2.61 (95% CI 1.93 to 3.52), 2.84 (95% CI 2.22 to 3.63), 4.18 (95% CI 2.87 to 6.09) and 3.83 (95% CI 2.15 to 6.80), respectively. Surprisingly, we found no correlation between chronic conditions and increased risk of mortality (OR 2.09, 95% CI 0.26 to16.67). Taken together, cardio-metabolic diseases, such as diabetes, hypertension and CAD/CVD were more common than chronic pulmonary disease in COVID-19 patients, however, each comorbid disease was correlated with increased disease severity. After active treatment, increased risk of mortality in patients with preexisting chronic diseases may reduce.
      Cover page: Comorbid Chronic Diseases are Strongly Correlated with Disease Severity among COVID-19 Patients: A Systematic Review and Meta-Analysis.
      • Article
      • Peer Reviewed
      UC San Francisco Previously Published Works (2003)

      Background

      Oocyte cortical granules are important in the fertilization of numerous species including mammals. Relatively little is known about the composition, migration, and pre-fertilization release of mammalian oocyte cortical granules.

      Results

      Results obtained with confocal scanning laser microscopy indicated that mouse oocytes have at least two populations of cortical granules, one that bound both the lectin LCA and the antibody ABL2 and one that bound only LCA. Both types of granules were synthesized at the same time during oocyte maturation suggesting that the ABL2 antigen is targeted to specific granules by a sorting sequence. The distribution of both populations of cortical granules was then studied during the germinal vesicle to metaphase II transition. As the oocytes entered metaphase I, the first cortical granule free domain, which was devoid of both populations of cortical granules, formed over the spindle. During first polar body extrusion, a subpopulation of LCA-binding granules became concentrated in the cleavage furrow and underwent exocytosis prior to fertilization. Granules that bound ABL2 were not exocytosed at this time. Much of the LCA-binding exudate from the release at the cleavage furrow was retained in the perivitelline space near the region of exocytosis and was deduced to contain at least three polypeptides with approximate molecular weights of 90, 62, and 56 kDa. A second cortical granule free domain developed following pre-fertilization exocytosis and subsequently continued to increase in area as both, LCA and LCA/ ABL2-binding granules near the spindle became redistributed toward the equator of the oocyte. The pre-fertilization release of cortical granules did not affect binding of sperm to the overlying zona pellucida.

      Conclusions

      Our data show that mouse oocytes contain at least two populations of cortical granules and that a subset of LCA-binding cortical granules is released at a specific time (during extrusion of the first polar body) and place (around the cleavage furrow) prior to fertilization. The observations indicate that the functions of the cortical granules are more complex than previously realized and include events occurring prior to gamete membrane fusion.
        Cover page: Biochemical heterogeneity, migration, and pre-fertilization release of mouse oocyte cortical granules
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2005)

        Background

        While mammalian cortical granules are important in fertilization, their biochemical composition and functions are not fully understood. We previously showed that the ABL2 antibody, made against zona free mouse blastocysts, binds to a 75-kDa cortical granule protein (p75) present in a subpopulation of mouse cortical granules. The purpose of this study was to identify and characterize p75, examine its distribution in unfertilized oocytes and preimplantation embryos, and investigate its biological role in fertilization.

        Results

        To identify p75, the protein was immunoprecipitated from ovarian lysates with the ABL2 antibody and analyzed by tandem mass spectrometry (MS/MS). A partial amino acid sequence (VLIGGSFY) was obtained, searched against the NCBI nonredundant database using two independent programs, and matched to mouse peptidylarginine deiminase (PAD). When PAD antibody was used to probe western blots of p75, the antibody detected a single protein band with a molecular weight of 75 kDa, confirming our mass spectrometric identification of p75. Immunohistochemistry demonstrated that PAD was present in the cortical granules of unfertilized oocytes and was released from activated and in vivo fertilized oocytes. After its release, PAD was observed in the perivitelline space, and some PAD remained associated with the oolemma and blastomeres' plasma membranes as a peripheral membrane protein until the blastocyst stage of development. In vitro treatment of 2-cell embryos with the ABL2 antibody or a PAD specific antibody retarded preimplantation development, suggesting that cortical granule PAD plays a role after its release in preimplantation cleavage and early embryonic development.

        Conclusion

        Our data showed that PAD is present in the cortical granules of mouse oocytes, is released extracellularly during the cortical reaction, and remains associated with the blastomeres' surfaces as a peripheral membrane protein until the blastocyst stage of development. Our in vitro study supports the idea that extracellular PAD functions in preimplantation development.
          Cover page: Peptidylarginine deiminase (PAD) is a mouse cortical granule protein that plays a role in preimplantation embryonic development.
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2022)

          Objective

          The Global Leader Initiative on Malnutrition (GLIM) criteria have been recommended for malnutrition diagnosis recently, for which the first step is malnutrition risk screening with any validated tool. This study aims to investigate the incidence of nutritional risk and malnutrition in Crohn's disease inpatients and compare the suitability of Nutritional Risk Screening 2002 (NRS-2002) and Malnutrition Universal Screening Tool (MUST) as the first-step screening tool for GLIM criteria.

          Methods

          We retrospectively analyzed the clinical data of Crohn's disease inpatients in our hospital from August 2016 to December 2019. NRS-2002 and MUST were used for nutritional screening at the time of admission. GLIM and Patient Generated-Subjective Global Assessment (PG-SGA) were used for malnutrition assessment, respectively. Patients without nutritional risk screened by NRS-2002 but with malnutrition risk screened by MUST were especially screened out. The appendicular skeletal muscle mass index (ASMI), fat-free mass index (FFMI), body fat percent (BFP), and body cell mass (BCM) were measured by the Biospace Inbody S10 composition analyzer.

          Results

          A total of 146 Crohn's disease patients were enrolled, of which 62.3 and 89.7% had nutritional or malnutrition risk according to NRS-2002 and MUST, respectively. The prevalence of malnutrition assessed by GLIM was 59.6% (87 cases) and 82.2% (120 cases) when NRS-2002 and MUST were used as the first step of GLIM respectively. Meanwhile, 99 patients (67.8%) had malnutrition when assessed by PG-SGA. There were 41 patients who were not at nutritional risk according to NRS-2002 but were at malnutrition risk determined by MUST. At last, 33 patients were GLIM-defined, and 16 patients were PG-SGA-defined malnutrition among the 41 patients.

          Conclusion

          The nutritional risk or malnutrition is common in Crohn's disease inpatients. It is recommended to use a variety of nutritional assessment tools for Crohn's disease inpatients. MUST can be used as a good supplement for the patients with a score of NRS-2002 lower than 3 in order to decrease the miss rate of GLIM-defined malnutrition.
            Cover page: GLIM criteria using NRS-2002 and MUST as the first step adequately diagnose the malnutrition in Crohn's disease inpatients: A retrospective study.
            • Article
            • Peer Reviewed
            UC Riverside Previously Published Works (2021)
            Most person re-identification methods, being supervised techniques, suffer from the burden of massive annotation requirement. Unsupervised methods overcome this need for labeled data, but perform poorly compared to the supervised alternatives. In order to cope with this issue, we introduce the problem of learning person re-identification models from videos with weak supervision. The weak nature of the supervision arises from the requirement of video-level labels, i.e. person identities who appear in the video, in contrast to the more precise frame-level annotations. Towards this goal, we propose a multiple instance attention learning framework for person re-identification using such video-level labels. Specifically, we first cast the video person re-identification task into a multiple instance learning setting, in which person images in a video are collected into a bag. The relations between videos with similar labels can be utilized to identify persons, on top of that, we introduce a co-person attention mechanism which mines the similarity correlations between videos with person identities in common. The attention weights are obtained based on all person images instead of person tracklets in a video, making our learned model less affected by noisy annotations. Extensive experiments demonstrate the superiority of the proposed method over the related methods on two weakly labeled person re-identification datasets.
              • Article
              • Peer Reviewed
              UC Irvine Previously Published Works (2013)
              In vitro culture of Plasmodium falciparum gametocytes is essential for studying sexual development of the parasite. Here we describe a simple method for producing synchronous gametocyte culture without contamination of asexual stages. This method employs heparin's activity in blocking merozoite invasion of erythrocytes to eliminate asexual stage parasites from gametocyte culture. We show that following induction of gametocyte formation, addition of heparin in culture medium for four days effectively eliminates asexual stages and produces pure, synchronous cultures of gametocytes. Compared with the commonly used N-acetylglucosamine treatment method, heparin treatment requires shorter time to eliminate asexual stages and causes significantly less hemolysis in late stage gametocyte cultures.
                Cover page: Plasmodium falciparum: Generation of pure gametocyte culture by heparin treatmentCreative Commons 'BY' version 4.0 license
                • Article
                • Peer Reviewed
                UCLA Previously Published Works (2023)

                Objectives

                Evaluation and follow-up of idiopathic pulmonary fibrosis (IPF) mainly rely on high-resolution computed tomography (HRCT) and pulmonary function tests (PFTs). The elastic registration technique can quantitatively assess lung shrinkage. We aimed to investigate the correlation between lung shrinkage and morphological and functional deterioration in IPF.

                Methods

                Patients with IPF who underwent at least two HRCT scans and PFTs were retrospectively included. Elastic registration was performed on the baseline and follow-up HRCTs to obtain deformation maps of the whole lung. Jacobian determinants were calculated from the deformation fields and after logarithm transformation, log_jac values were represented on color maps to describe morphological deterioration, and to assess the correlation between log_jac values and PFTs.

                Results

                A total of 69 patients with IPF (male 66) were included. Jacobian maps demonstrated constriction of the lung parenchyma marked at the lung base in patients who were deteriorated on visual and PFT assessment. The log_jac values were significantly reduced in the deteriorated patients compared to the stable patients. Mean log_jac values showed positive correlation with baseline percentage of predicted vital capacity (VC%) (r = 0.394, p < 0.05) and percentage of predicted forced vital capacity (FVC%) (r = 0.395, p < 0.05). Additionally, the mean log_jac values were positively correlated with pulmonary vascular volume (r = 0.438, p < 0.01) and the number of pulmonary vascular branches (r = 0.326, p < 0.01).

                Conclusions

                Elastic registration between baseline and follow-up HRCT was helpful to quantitatively assess the morphological deterioration of lung shrinkage in IPF, and the quantitative indicator log_jac values were significantly correlated with PFTs.

                Key points

                • The elastic registration on HRCT was helpful to quantitatively assess the deterioration of IPF. • Jacobian logarithm was significantly reduced in deteriorated patients and mean log_jac values were correlated with PFTs. • The mean log_jac values were related to the changes of pulmonary vascular volume and the number of vascular branches.
                  Cover page: Lung shrinking assessment on HRCT with elastic registration technique for monitoring idiopathic pulmonary fibrosis
                  • Article
                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2013)

                  Objective

                  To perform a meta-analysis exploring the correlation between the apparent diffusion coefficient (ADC) and tumor cellularity in patients.

                  Materials and methods

                  We searched medical and scientific literature databases for studies discussing the correlation between the ADC and tumor cellularity in patients. Only studies that were published in English or Chinese prior to November 2012 were considered for inclusion. Summary correlation coefficient (r) values were extracted from each study, and 95% confidence intervals (CIs) were calculated. Sensitivity and subgroup analyses were performed to investigate potential heterogeneity.

                  Results

                  Of 189 studies, 28 were included in the meta-analysis, comprising 729 patients. The pooled r for all studies was -0.57 (95% CI: -0.62, -0.52), indicating notable heterogeneity (P<0.001). After the sensitivity analysis, two studies were excluded, and the pooled r was -0.61 (95% CI: -0.66, -0.56) and was not significantly heterogeneous (P = 0.127). Regarding tumor type subgroup analysis, there were sufficient data to support a strong negative correlation between the ADC and cellularity for brain tumors. There was no notable evidence of publication bias.

                  Conclusions

                  There is a strong negative correlation between the ADC and tumor cellularity in patients, particularly in the brain. However, larger, prospective studies are warranted to validate these findings in other cancer types.
                    Cover page: The Correlation between Apparent Diffusion Coefficient and Tumor Cellularity in Patients: A Meta-Analysis
                    • Article
                    • Peer Reviewed
                    UC San Diego Previously Published Works (2018)
                    Myeloid-derived suppressor cells (MDSCs) are a heterogeneous group of myeloid cells that suppress T-cell activity in a tumor microenvironment. However, the suppressive function of MDSCs on B cells and its underlying mechanism remain unclear. Here, we show that in 4T1 breast cancer mice, a significantly increased number of MDSCs, in parallel with splenic B cells, are accumulated when compared to normal mice. In the presence of MDSCs, the surface molecules of B cells are remolded, with checkpoint-related molecules such as PD-1 and PD-L1 changing prominently. MDSCs also emerge as vital regulators in B-cell immune functions such as proliferation, apoptosis and the abilities to secrete antibodies and cytokines. Our study further identifies that MDSCs can transform normal B cells to a subtype of immuno- regulatory B cells (Bregs) which inhibit T-cell response. Furthermore, we identified a novel kind of Bregs with a specific phenotype PD-1-PD-L1+CD19+, which exert the greatest suppressive effects on T cells in comparison with the previously reported Bregs characterized as CD1d+CD5+CD19+, CD5+CD19+ and Interleukin (IL)-10-secreting B cells. Our results highlight that MDSCs regulate B-cell response and may serve as a therapeutic approach in anti-tumor treatment. Investigation of this new Breg subtype extends our understanding of regulation of T-cell response and sheds new light on anti-tumor immunity and immune therapy.
                      Cover page: A novel MDSC-induced PD-1−PD-L1+ B-cell subset in breast tumor microenvironment possesses immuno-suppressive properties
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