Education & Certifications


  • Bachelor of Science, University of California, Los Angeles (2016)

All Publications


  • Decoding COVID-19 pneumonia: comparison of deep learning and radiomics CT image signatures. European journal of nuclear medicine and molecular imaging Wang, H., Wang, L., Lee, E. H., Zheng, J., Zhang, W., Halabi, S., Liu, C., Deng, K., Song, J., Yeom, K. W. 2020

    Abstract

    High-dimensional image features that underlie COVID-19 pneumonia remain opaque. We aim to compare feature engineering and deep learning methods to gain insights into the image features that drive CT-based for COVID-19 pneumonia prediction, and uncover CT image features significant for COVID-19 pneumonia from deep learning and radiomics framework.A total of 266 patients with COVID-19 and other viral pneumonia with clinical symptoms and CT signs similar to that of COVID-19 during the outbreak were retrospectively collected from three hospitals in China and the USA. All the pneumonia lesions on CT images were manually delineated by four radiologists. One hundred eighty-four patients (n = 93 COVID-19 positive; n = 91 COVID-19 negative; 24,216 pneumonia lesions from 12,001 CT image slices) from two hospitals from China served as discovery cohort for model development. Thirty-two patients (17 COVID-19 positive, 15 COVID-19 negative; 7883 pneumonia lesions from 3799 CT image slices) from a US hospital served as external validation cohort. A bi-directional adversarial network-based framework and PyRadiomics package were used to extract deep learning and radiomics features, respectively. Linear and Lasso classifiers were used to develop models predictive of COVID-19 versus non-COVID-19 viral pneumonia.120-dimensional deep learning image features and 120-dimensional radiomics features were extracted. Linear and Lasso classifiers identified 32 high-dimensional deep learning image features and 4 radiomics features associated with COVID-19 pneumonia diagnosis (P < 0.0001). Both models achieved sensitivity > 73% and specificity > 75% on external validation cohort with slight superior performance for radiomics Lasso classifier. Human expert diagnostic performance improved (increase by 16.5% and 11.6% in sensitivity and specificity, respectively) when using a combined deep learning-radiomics model.We uncover specific deep learning and radiomics features to add insight into interpretability of machine learning algorithms and compare deep learning and radiomics models for COVID-19 pneumonia that might serve to augment human diagnostic performance.

    View details for DOI 10.1007/s00259-020-05075-4

    View details for PubMedID 33094432

  • Association of Pediatric Acute-Onset Neuropsychiatric Syndrome With Microstructural Differences in Brain Regions Detected via Diffusion-Weighted Magnetic Resonance Imaging. JAMA network open Zheng, J., Frankovich, J., McKenna, E. S., Rowe, N. C., MacEachern, S. J., Ng, N. N., Tam, L. T., Moon, P. K., Gao, J., Thienemann, M., Forkert, N. D., Yeom, K. W. 2020; 3 (5): e204063

    Abstract

    Epidemiological studies indicate a link between obsessive-compulsive disorder and infections, particularly streptococcal pharyngitis. Pediatric acute-onset neuropsychiatric syndrome (PANS) manifests suddenly with obsessions, compulsions, and other behavioral disturbances, often after an infectious trigger. The current working model suggests a unifying inflammatory process involving the central nervous system, particularly the basal ganglia.To investigate whether diffusion-weighted magnetic resonance imaging (DWI) detects microstructural abnormalities across the brain regions of children with PANS.Case-control study performed at a single-center, multidisciplinary clinic in the United States focusing on the evaluation and treatment of children with PANS. Sixty consecutive patients who underwent 3 Tesla (T) magnetic resonance imaging (MRI) before immunomodulation from September 3, 2012, to March 30, 2018, were retrospectively reviewed for study inclusion. Six patients were excluded by blinded investigators because of imaging or motion artifacts, 3 patients for major pathologies, and 17 patients for suboptimal atlas image registration. In total, 34 patients with PANS before initiation of treatment were compared with 64 pediatric control participants.Using atlas-based MRI analysis, regional brain volume, diffusion, and cerebral blood flow were measured in the cerebral white matter, cerebral cortex, thalamus, caudate, putamen, pallidum, hippocampus, amygdala, nucleus accumbens, and brainstem. An age and sex-controlled multivariable analysis of covariance was used to compare patients with control participants.This study compared 34 patients with PANS (median age, 154 months; age range, 55-251 months; 17 girls and 17 boys) and 64 pediatric control participants (median age, 139 months; age range, 48-213 months); 41 girls and 23 boys). Multivariable analysis demonstrated a statistically significant difference in MRI parameters between patients with PANS and control participants (F21,74 = 6.91; P < .001; partial η2 = 0.662). All assessed brain regions had statistically significantly increased median diffusivity compared with 64 control participants. Specifically, the deep gray matter (eg, the thalamus, basal ganglia, and amygdala) demonstrated the most profound increases in diffusivity consistent with the cardinal clinical symptoms of obsessions, compulsions, emotional dysregulation, and sleep disturbances. No statistically significant differences were found regarding volume and cerebral blood flow.This study identifies cerebral microstructural differences in children with PANS in multiple brain structures, including the deep gray matter structures (eg, the thalamus, basal ganglia, and amygdala). Further study of MRI is warranted in prospective, clinical trials as a potential quantitative method for assessing patients under evaluation for PANS.

    View details for DOI 10.1001/jamanetworkopen.2020.4063

    View details for PubMedID 32364596

  • Cerebral volume and diffusion MRI changes in children with sensorineural hearing loss. NeuroImage. Clinical Moon, P. K., Qian, J. Z., McKenna, E., Xi, K., Rowe, N. C., Ng, N. N., Zheng, J., Tam, L. T., MacEachern, S. J., Ahmad, I., Cheng, A. G., Forkert, N. D., Yeom, K. W. 2020; 27: 102328

    Abstract

    Sensorineural hearing loss (SNHL) is the most prevalent congenital sensory deficit in children. Information regarding underlying brain microstructure could offer insight into neural development in deaf children and potentially guide therapies that optimize language development. We sought to quantitatively evaluate MRI-based cerebral volume and gray matter microstructure children with SNHL.We conducted a retrospective study of children with SNHL who obtained brain MRI at 3 T. The study cohort comprised 63 children with congenital SNHL without known focal brain lesion or structural abnormality (33 males; mean age 5.3 years; age range 1 to 11.8 years) and 64 age-matched controls without neurological, developmental, or MRI-based brain macrostructure abnormality. An atlas-based analysis was used to extract quantitative volume and median diffusivity (ADC) in the following brain regions: cerebral cortex, thalamus, caudate, putamen, globus pallidus, hippocampus, amygdala, nucleus accumbens, brain stem, and cerebral white matter. SNHL patients were further stratified by severity scores and hearing loss etiology.Children with SNHL showed higher median ADC of the cortex (p = .019), thalamus (p < .001), caudate (p = .005), and brainstem (p = .003) and smaller brainstem volumes (p = .007) compared to controls. Patients with profound bilateral SNHL did not show any significant differences compared to patients with milder bilateral SNHL, but both cohorts independently had smaller brainstem volumes compared to controls. Children with unilateral SNHL showed greater amygdala volumes compared to controls (p = .021), but no differences were found comparing unilateral SNHL to bilateral SNHL. Based on etiology for SNHL, patients with Pendrin mutations showed higher ADC values in the brainstem (p = .029, respectively); patients with Connexin 26 showed higher ADC values in both the thalamus (p < .001) and brainstem (p < .001) compared to controls.SNHL patients showed significant differences in diffusion and volume in brain subregions, with region-specific findings for patients with Connexin 26 and Pendrin mutations. Future longitudinal studies could examine macro- and microstructure changes in children with SNHL over development and potential predictive role for MRI after interventions including cochlear implant outcome.

    View details for DOI 10.1016/j.nicl.2020.102328

    View details for PubMedID 32622314

  • Eponyms are here to stay: Usage in the literature and among current neurology trainees. Neurology Zheng, J., Gold, C. A. 2020

    Abstract

    To assess the historical trends of medical eponym use in neurology literature and knowledge and attitudes among current trainees related to eponyms.A comprehensive list of medical eponyms compiled from multiple online and print sources was queried against the titles and abstracts of PubMed articles authored by neurologists to assess historical prevalence in the literature from 1988 to 2013. We also surveyed current neurology trainees and trainees who have matched for residency in neurology, but not yet started neurology training, on their familiarity and attitudes toward eponyms.The yearly prevalence of eponyms among neurologist-authored publications ranged from 15% and 25%, with a mean of 21%. The total number of unique eponyms appearing in titles and abstracts increased from 693 in 1988 to 1,076 in 2013, representing 1.8% average annual growth. Our survey showed that residents with at least 1 year of neurology training reported familiarity with significantly more eponyms than those before neurology training (p < 0.001). For familiar eponyms, most residents were either unaware of an alternative descriptor or preferred using the eponym. Despite recognizing both the benefits and drawbacks of eponyms, the vast majority of trainees stated that historical precedent, pervasiveness, and ease of use would drive the continued use of eponyms in neurology.Eponyms will remain a cornerstone in medical education and communication moving forward. Educators in neurology should consider how best to integrate useful eponyms and alternative descriptors into residency training to enhance knowledge acquisition and retention.

    View details for DOI 10.1212/WNL.0000000000008912

    View details for PubMedID 31896619

  • Pleiotropic jaw morphology links the evolution of mechanical modularity and functional feeding convergence in Lake Malawi cichlids. Proceedings. Biological sciences Hulsey, C. D., Alfaro, M. E., Zheng, J., Meyer, A., Holzman, R. 2019; 286 (1897): 20182358

    Abstract

    Complexity in how mechanistic variation translates into ecological novelty could be critical to organismal diversification. For instance, when multiple distinct morphologies can generate the same mechanical or functional phenotype, this could mitigate trade-offs and/or provide alternative ways to meet the same ecological challenge. To investigate how this type of complexity shapes diversity in a classic adaptive radiation, we tested several evolutionary consequences of the anterior jaw four-bar linkage for Lake Malawi cichlid trophic diversification. Using a novel phylogenetic framework, we demonstrated that different mechanical outputs of the same four jaw elements are evolutionarily associated with both jaw protrusion distance and jaw protrusion angle. However, these two functional aspects of jaw protrusion have evolved independently. Additionally, although four-bar morphology showed little evidence for attraction to optima, there was substantial evidence of adaptive peaks for emergent four-bar linkage mechanics and jaw protrusion abilities among Malawi feeding guilds. Finally, we highlighted a clear case of two cichlid species that have -independently evolved to graze algae in less than 2 Myr and have converged on similar jaw protrusion abilities as well as four-bar linkage mechanics, but have evolved these similarities via non-convergent four-bar morphologies.

    View details for PubMedID 30963830

    View details for PubMedCentralID PMC6408893

  • A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America MOLECULAR PHYLOGENETICS AND EVOLUTION Lima, M. M., de Sousa e Silva-Junior, J., Cerny, D., Buckner, J. C., Aleixo, A., Chang, J., Zheng, J., Alfaro, M. E., Martins, A., Di Fiore, A., Boubli, J. P., Alfaro, J. 2018; 124: 137–50

    Abstract

    Phylogenetic relationships amongst the robust capuchin monkeys (genus Sapajus) are poorly understood. Morphology-based taxonomies have recognized anywhere from one to twelve different species. The current IUCN (2017) classification lists eight robust capuchins: S. xanthosternos, S. nigritus, S. robustus, S. flavius, S. libidinosus, S. cay, S. apella and S. macrocephalus. Here, we assembled the first phylogenomic data set for Sapajus using ultra-conserved elements (UCEs) to reconstruct a capuchin phylogeny. All phylogenomic analyses strongly supported a deep divergence of Sapajus and Cebus clades within the capuchin monkeys, and provided support for Sapajus nigritus, S. robustus and S. xanthosternos as distinct species. However, the UCE phylogeny lumped the putative species S. cay, S. libidinosus, S. apella, S. macrocephalus, and S. flavius together as a single widespread lineage. A SNP phylogeny constructed from the UCE data was better resolved and recovered S. flavius and S. libidinosus as sister species; however, S. apella, S. macrocephalus, and S. cay individuals were recovered in two geographic clades, from northeastern and southwestern Amazon, rather than clustering by currently defined morphospecies. STRUCTURE analysis of population clustering revealed widespread admixture among Sapajus populations within the Amazon and even into the Cerrado and Atlantic Forest. Difficulty in assigning species by morphology may be a result of widespread population admixture facilitated through frequent movement across major rivers and even ecosystems by robust capuchin monkeys.

    View details for PubMedID 29545109

  • Phylogenomics of a putatively convergent novelty: did hypertrophied lips evolve once or repeatedly in Lake Malawi cichlid fishes? BMC evolutionary biology Darrin Hulsey, C., Zheng, J., Holzman, R., Alfaro, M. E., Olave, M., Meyer, A. 2018; 18 (1): 179

    Abstract

    Phylogenies provide critical information about convergence during adaptive radiation. To test whether there have been multiple origins of a distinctive trophic phenotype in one of the most rapidly radiating groups known, we used ultra-conserved elements (UCEs) to examine the evolutionary affinities of Lake Malawi cichlids lineages exhibiting greatly hypertrophied lips.The hypertrophied lip cichlids Cheilochromis euchilus, Eclectochromis ornatus, Placidochromis "Mbenji fatlip", and Placidochromis milomo are all nested within the non-mbuna clade of Malawi cichlids based on both concatenated sequence and single nucleotide polymorphism (SNP) inferred phylogenies. Lichnochromis acuticeps that exhibits slightly hypertrophied lips also appears to have evolutionary affinities to this group. However, Chilotilapia rhoadesii that lacks hypertrophied lips was recovered as nested within the species Cheilochromis euchilus. Species tree reconstructions and analyses of introgression provided largely ambiguous patterns of Malawi cichlid evolution.Contrary to mitochondrial DNA phylogenies, bifurcating trees based on our 1024 UCE loci supported close affinities of Lake Malawi lineages with hypertrophied lips. However, incomplete lineage sorting in Malawi tends to render these inferences more tenuous. Phylogenomic analyses will continue to provide powerful inferences about whether phenotypic novelties arose once or multiple times during adaptive radiation.

    View details for DOI 10.1186/s12862-018-1296-9

    View details for PubMedID 30486792

  • Assessing quality of care through client satisfaction at an interprofessional student-run free clinic JOURNAL OF INTERPROFESSIONAL CARE Asanad, K., Zheng, J., Chan-Golston, A., Tam, E., Bhetraratana, M., Lan, C., Zhao, M., Abdi, R., Abdi, F., Vasti, E., Prelip, M. L. 2018; 32 (2): 203–10

    Abstract

    Student-run free clinics (SRFCs) have become important contributors not only to improve access to primary-care services for homeless and uninsured populations but also to enhance health sciences student education. In order for SRFCs to reliably provide high quality healthcare services and educationally benefit students, it is imperative to assess client perceptions of the quality of care provided. The objective of this study was to evaluate the delivery of healthcare services through a client satisfaction questionnaire at the University of California, Los Angeles Mobile Clinic Project (UCLA MCP). From 2012 to 2015, 194 questionnaires that addressed demographic information, satisfaction with services and client outcomes were analysed. Satisfaction scores were evaluated on a four-point scale and differences in the composite satisfaction scores were assessed using Mann-Whitney U-tests. Half (50%) of the client respondents report that UCLA MCP is their primary source of health care (MCP primary care clients), while 81.3% reported that the clinic improved access to other healthcare resources. Overall, clients are highly satisfied with their experiences (Range: 3.5-3.9) and 62% have recommended our services to others. While MCP primary-care clients report significantly higher satisfaction scores than non-primary-care clients on average (p < 0.01), the mean composite scores for all subgroups are consistently high. The UCLA MCP clients perceive the clinic to provide high-quality healthcare services. This article presents a framework that may help other SRFCs evaluate clients' perception of the quality of their care, an essential building block for effective physician-client relationships.

    View details for PubMedID 29182406

  • Phylogenomic analysis of Lake Malawi cichlid fishes: Further evidence that the three-stage model of diversification does not fit Molecular Phylogenetics and Evolution Hulsey, D., Zheng, J., Faircloth, B. C., Meyer, A., Alfaro, M. E. 2017; 114: 40-48

    Abstract

    Adaptive radiations could often occur in discrete stages. For instance, the species flock of ∼1000 species of Lake Malawi cichlid fishes might have only diverged once between rocky and sandy environments during the initial stage of their diversification. All further diversification within the rock-dwelling (mbuna) or sand-dwelling (utaka) cichlids would have occurred during a subsequent second stage of extensive trophic evolution that was followed by a third stage of sexual trait divergence. We provide an improved phylogenetic framework for Malawi cichlids to test this three-stage hypothesis based on newly reconstructed phylogenetic relationships among 32 taxonomically disparate Malawi cichlids species. Using several reconstruction methods and 1037 ultra-conserved element (UCE) markers, we recovered a molecular phylogeny that confidently resolved relationships among most of the Malawi lineages sampled when a bifurcating framework was enforced. These bifurcating reconstructions also indicated that the sand-dwelling species Cyathochromis obliquidens was well-nested within the primarily rock-dwelling radiation known as the mbuna. In contrast to predictions from the three-stage model of vertebrate diversification, the recovered phylogeny reveals an initial colonization of rocky reefs, followed by substantial diversification of rock-dwelling lineages, and then at least one instance of subsequent evolution back into sandy habitats. This repeated evolution into major habitat types provides further evidence that the three-stage model of Malawi cichlid diversification has numerous exceptions.

    View details for DOI 10.1016/j.ympev.2017.05.027

  • Replicated divergence in cichlid radiations mirrors a major vertebrate innovation Proceedings of the Royal Society B: Biological Sciences McGee, M. D., Faircloth, B. C., Borstein, S. R., Zheng, J., Hulsey, D., Wainwright, P. C., Alfaro, M. E. 2016; 283 (1822)

    View details for DOI 10.1098/rspb.2015.1413