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Radnovich R, Scott D, Patel AT, Olson R, Dasa V, Segal N, Lane NE, Shrock K, Naranjo J, Darr K, Surowitz R, Choo J, Valadie A, Harrell R, Wei N, Metyas S. Cryoneurolysis to treat the pain and symptoms of knee osteoarthritis: a multicenter, randomized, double-blind, sham-controlled trial. Osteoarthritis Cartilage 2017; 25:1247-1256. [PMID: 28336454 DOI: 10.1016/j.joca.2017.03.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Evaluate the efficacy and safety/tolerability of cryoneurolysis for reduction of pain and symptoms associated with knee osteoarthritis (OA). DESIGN Randomized, double-blind, sham-controlled, multicenter trial with a 6-month follow-up in patients with mild-to-moderate knee OA. Patients were randomized 2:1 to cryoneurolysis targeting the infrapatellar branch of the saphenous nerve (IPBSN) or sham treatment. The primary endpoint was the change from baseline to Day 30 in the Western Ontario and McMaster Osteoarthritis Index (WOMAC) pain score adjusted by the baseline score and site. Secondary endpoints, including visual analogue scale (VAS) pain score and total WOMAC score, were tested in a pre-defined order. RESULTS The intent-to-treat (ITT) population consisted of 180 patients (n = 121 active treatment, n = 59 sham treatment). Compared to the sham group, patients who received active treatment had a statistically significant greater change from baseline in the WOMAC pain subscale score at Day 30 (P = 0.0004), Day 60 (P = 0.0176), and Day 90 (P = 0.0061). Patients deemed WOMAC pain responders at Day 120 continued to experience a statistically significant treatment effect at Day 150. Most expected side effects were mild in severity and resolved within 30 days. The incidence of device- or procedure-related adverse events was similar in the two treatment groups with no occurrence of serious or unanticipated adverse device effects (ADE). CONCLUSIONS Cryoneurolysis of the IPBSN resulted in statistically significant decreased knee pain and improved symptoms compared to sham treatment for up to 150 days, and appeared safe and well tolerated.
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Kwon BC, Kim H, Wall E, Choo J, Park H, Endert A. AxiSketcher: Interactive Nonlinear Axis Mapping of Visualizations through User Drawings. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2017; 23:221-230. [PMID: 27514048 DOI: 10.1109/tvcg.2016.2598446] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Visual analytics techniques help users explore high-dimensional data. However, it is often challenging for users to express their domain knowledge in order to steer the underlying data model, especially when they have little attribute-level knowledge. Furthermore, users' complex, high-level domain knowledge, compared to low-level attributes, posits even greater challenges. To overcome these challenges, we introduce a technique to interpret a user's drawings with an interactive, nonlinear axis mapping approach called AxiSketcher. This technique enables users to impose their domain knowledge on a visualization by allowing interaction with data entries rather than with data attributes. The proposed interaction is performed through directly sketching lines over the visualization. Using this technique, users can draw lines over selected data points, and the system forms the axes that represent a nonlinear, weighted combination of multidimensional attributes. In this paper, we describe our techniques in three areas: 1) the design space of sketching methods for eliciting users' nonlinear domain knowledge; 2) the underlying model that translates users' input, extracts patterns behind the selected data points, and results in nonlinear axes reflecting users' complex intent; and 3) the interactive visualization for viewing, assessing, and reconstructing the newly formed, nonlinear axes.
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Kim M, Kang K, Park D, Choo J, Elmqvist N. TopicLens: Efficient Multi-Level Visual Topic Exploration of Large-Scale Document Collections. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2017; 23:151-160. [PMID: 27875138 DOI: 10.1109/tvcg.2016.2598445] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Topic modeling, which reveals underlying topics of a document corpus, has been actively adopted in visual analytics for large-scale document collections. However, due to its significant processing time and non-interactive nature, topic modeling has so far not been tightly integrated into a visual analytics workflow. Instead, most such systems are limited to utilizing a fixed, initial set of topics. Motivated by this gap in the literature, we propose a novel interaction technique called TopicLens that allows a user to dynamically explore data through a lens interface where topic modeling and the corresponding 2D embedding are efficiently computed on the fly. To support this interaction in real time while maintaining view consistency, we propose a novel efficient topic modeling method and a semi-supervised 2D embedding algorithm. Our work is based on improving state-of-the-art methods such as nonnegative matrix factorization and t-distributed stochastic neighbor embedding. Furthermore, we have built a web-based visual analytics system integrated with TopicLens. We use this system to measure the performance and the visualization quality of our proposed methods. We provide several scenarios showcasing the capability of TopicLens using real-world datasets.
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Huh J, Kwon BC, Kim SH, Lee S, Choo J, Kim J, Choi MJ, Yi JS. Personas in online health communities. J Biomed Inform 2016; 63:212-225. [PMID: 27568913 DOI: 10.1016/j.jbi.2016.08.019] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 11/29/2022]
Abstract
Many researchers and practitioners use online health communities (OHCs) to influence health behavior and provide patients with social support. One of the biggest challenges in this approach, however, is the rate of attrition. OHCs face similar problems as other social media platforms where user migration happens unless tailored content and appropriate socialization is supported. To provide tailored support for each OHC user, we developed personas in OHCs illustrating users' needs and requirements in OHC use. To develop OHC personas, we first interviewed 16 OHC users and administrators to qualitatively understand varying user needs in OHC. Based on their responses, we developed an online survey to systematically investigate OHC personas. We received 184 survey responses from OHC users, which informed their values and their OHC use patterns. We performed open coding analysis with the interview data and cluster analysis with the survey data and consolidated the analyses of the two datasets. Four personas emerged-Caretakers, Opportunists, Scientists, and Adventurers. The results inform users' interaction behavior and attitude patterns with OHCs. We discuss implications for how these personas inform OHCs in delivering personalized informational and emotional support.
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Wong ML, Inserra A, Lewis MD, Mastronardi CA, Leong L, Choo J, Kentish S, Xie P, Morrison M, Wesselingh SL, Rogers GB, Licinio J. Inflammasome signaling affects anxiety- and depressive-like behavior and gut microbiome composition. Mol Psychiatry 2016; 21:797-805. [PMID: 27090302 PMCID: PMC4879188 DOI: 10.1038/mp.2016.46] [Citation(s) in RCA: 360] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 02/19/2016] [Accepted: 02/22/2016] [Indexed: 12/13/2022]
Abstract
The inflammasome is hypothesized to be a key mediator of the response to physiological and psychological stressors, and its dysregulation may be implicated in major depressive disorder. Inflammasome activation causes the maturation of caspase-1 and activation of interleukin (IL)-1β and IL-18, two proinflammatory cytokines involved in neuroimmunomodulation, neuroinflammation and neurodegeneration. In this study, C57BL/6 mice with genetic deficiency or pharmacological inhibition of caspase-1 were screened for anxiety- and depressive-like behaviors, and locomotion at baseline and after chronic stress. We found that genetic deficiency of caspase-1 decreased depressive- and anxiety-like behaviors, and conversely increased locomotor activity and skills. Caspase-1 deficiency also prevented the exacerbation of depressive-like behaviors following chronic stress. Furthermore, pharmacological caspase-1 antagonism with minocycline ameliorated stress-induced depressive-like behavior in wild-type mice. Interestingly, chronic stress or pharmacological inhibition of caspase-1 per se altered the fecal microbiome in a very similar manner. When stressed mice were treated with minocycline, the observed gut microbiota changes included increase in relative abundance of Akkermansia spp. and Blautia spp., which are compatible with beneficial effects of attenuated inflammation and rebalance of gut microbiota, respectively, and the increment in Lachnospiracea abundance was consistent with microbiota changes of caspase-1 deficiency. Our results suggest that the protective effect of caspase-1 inhibition involves the modulation of the relationship between stress and gut microbiota composition, and establishes the basis for a gut microbiota-inflammasome-brain axis, whereby the gut microbiota via inflammasome signaling modulate pathways that will alter brain function, and affect depressive- and anxiety-like behaviors. Our data also suggest that further elucidation of the gut microbiota-inflammasome-brain axis may offer novel therapeutic targets for psychiatric disorders.
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Jones T, Moore T, Rose H, Choo J. (512) The impact of virtual reality on chronic pain. THE JOURNAL OF PAIN 2016. [DOI: 10.1016/j.jpain.2016.01.319] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kwon BC, Kim SH, Lee S, Choo J, Huh J, Yi JS. VisOHC: Designing Visual Analytics for Online Health Communities. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2016; 22:71-80. [PMID: 26529688 PMCID: PMC4638132 DOI: 10.1109/tvcg.2015.2467555] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Through online health communities (OHCs), patients and caregivers exchange their illness experiences and strategies for overcoming the illness, and provide emotional support. To facilitate healthy and lively conversations in these communities, their members should be continuously monitored and nurtured by OHC administrators. The main challenge of OHC administrators' tasks lies in understanding the diverse dimensions of conversation threads that lead to productive discussions in their communities. In this paper, we present a design study in which three domain expert groups participated, an OHC researcher and two OHC administrators of online health communities, which was conducted to find with a visual analytic solution. Through our design study, we characterized the domain goals of OHC administrators and derived tasks to achieve these goals. As a result of this study, we propose a system called VisOHC, which visualizes individual OHC conversation threads as collapsed boxes-a visual metaphor of conversation threads. In addition, we augmented the posters' reply authorship network with marks and/or beams to show conversation dynamics within threads. We also developed unique measures tailored to the characteristics of OHCs, which can be encoded for thread visualizations at the users' requests. Our observation of the two administrators while using VisOHC showed that it supports their tasks and reveals interesting insights into online health communities. Finally, we share our methodological lessons on probing visual designs together with domain experts by allowing them to freely encode measurements into visual variables.
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El-Saed A, Masaki K, Okamura T, Evans RW, Nakamura Y, Willcox BJ, Lee S, Maegawa H, Seto TB, Choo J, Fujiyoshi A, Miura K, Kuller LH, Ueshima H, Sekikawa A. The Associations of C-Reactive Protein with Serum Levels of Polyunsaturated Fatty Acids and Trans Fatty Acids Among Middle-Aged Men from Three Populations. J Nutr Health Aging 2016; 20:16-21. [PMID: 26728928 DOI: 10.1007/s12603-016-0670-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND C-reactive protein (CRP) and many fatty acids (FAs) have been linked to cardiovascular disease. Associations of serum CRP with FAs in different populations have not been established. METHODS Participants were 926 men aged 40-49 (2002-2006) from a population-based sample; 310 Whites from Pennsylvania, U.S., 313 Japanese from Shiga, Japan, and 303 Japanese Americans from Hawaii, U.S. Serum CRP (mg/L) was measured using immunosorbent assay while serum FAs (%) were measured using capillary-gas-liquid chromatography. RESULTS Whites had CRP (mg/L) levels higher than Japanese with Japanese Americans in-between (age-adjusted geometric mean "GM" 0.96, 0.38, 0.66, respectively). Whites had also higher levels of total n-6 FAs (%) and trans fatty acids (TFAs) but lower levels of marine-derived n-3 FAs compared to Japanese (41.78 vs. 35.05, 1.04 vs. 0.58, and 3.85 vs. 9.29, respectively). Japanese Americans had FAs levels in-between the other two populations. Whites had significant inverse trends between CRP and tertiles of total n-6 FAs (GM 1.20, 0.91 and 0.80; p=0.002) and marine-derived n-3 FAs (GM 1.22, 1.00 and 0.72; p<0.001) but a significant positive trend with TFAs (GM 0.80, 0.95 and 1.15; p=0.007). Japanese had a significant inverse trend between CRP and only total n-6 FAs (GM 0.50, 0.35 and 0.31; p<0.001). Japanese Americans had CRP associations with n-3 FAs, n-6 FAs, and TFAs similar to but weaker than Whites. CONCLUSIONS With the exception of consistent inverse association of CRP with total n-6 FAs, there are considerable variations across the three populations in the associations of CRP with different FAs.
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Kim H, Choo J, Park H, Endert A. InterAxis: Steering Scatterplot Axes via Observation-Level Interaction. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2016; 22:131-140. [PMID: 26357399 DOI: 10.1109/tvcg.2015.2467615] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Scatterplots are effective visualization techniques for multidimensional data that use two (or three) axes to visualize data items as a point at its corresponding x and y Cartesian coordinates. Typically, each axis is bound to a single data attribute. Interactive exploration occurs by changing the data attributes bound to each of these axes. In the case of using scatterplots to visualize the outputs of dimension reduction techniques, the x and y axes are combinations of the true, high-dimensional data. For these spatializations, the axes present usability challenges in terms of interpretability and interactivity. That is, understanding the axes and interacting with them to make adjustments can be challenging. In this paper, we present InterAxis, a visual analytics technique to properly interpret, define, and change an axis in a user-driven manner. Users are given the ability to define and modify axes by dragging data items to either side of the x or y axes. from which the system computes a linear combination of data attributes and binds it to the axis. Further, users can directly tune the positive and negative contribution to these complex axes by using the visualization of data attributes that correspond to each axis. We describe the details of our technique and demonstrate the intended usage through two scenarios.
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Choo J, Augenstein A, Nadar M, Afflick E, Kasdan M, Wilhelmi B. Anatomic Landmarks of the Distal Radioulnar Joint. EPLASTY 2015; 15:e36. [PMID: 26301001 PMCID: PMC4539850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
HYPOTHESIS Using Lister's tubercle and the ulnar styloid as landmarks, accurate localization of the distal radioulnar joint can be achieved without the need for an image-guided approach. METHODS Cadaveric dissection of 16 upper extremities was performed to measure the relationships between the ulnar styloid, Lister's tubercle, and the distal radioulnar joint. In each specimen, the location of the distal radioulnar joint (point A) in relation to Lister's tubercle and the ulnar styloid was determined as follows: (1) the perpendicular distance between the distal radioulnar joint and ulnar styloid-Lister's tubercle was measured; (2) with A' marking the intersection of this distance and the ulnar styloid-Lister's tubercle line, the location of the distal radioulnar joint along the ulnar styloid-Lister's tubercle axis was determined by comparing ulnar styloid-A' and A'-Lister's tubercle with ulnar styloid-Lister's tubercle. RESULTS The mean distance between ulnar styloid-Lister's tubercle was 4.3 ± 0.4 cm. The mean perpendicular distance between the distal radioulnar joint and the ulnar styloid-Lister's tubercle line was 0.2 ± 0.1 cm proximal to the ulnar styloid-Lister's tubercle line. The ratio of ulnar styloid-A' and A'-Lister's tubercle to ulnar styloid-Lister's tubercle was 0.5 ± 0.03 and 0.5 ± 0.03, respectively. CONCLUSIONS Simple relationships between the ulnar styloid and Lister's tubercle serve as reliable landmarks for locating the distal radioulnar joint. The distal radioulnar joint is centered about the midpoint of the ulnar styloid-Lister's tubercle axis and slightly proximal to it. This may improve the accuracy and efficacy of corticosteroid injections in the treatment of distal radioulnar joint arthritis without the need for image guidance.
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Chowdhry S, Davis J, Boyd T, Choo J, Brooks RM, Kelishadi SS, Tutela JP, Yonick D, Wilhelmi BJ. Safe Tummy Tuck: Anatomy and Strategy to Avoid Injury to the Lateral Femoral Cutaneous Nerve During Abdominoplasty. EPLASTY 2015; 15:e22. [PMID: 26171094 PMCID: PMC4473816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
BACKGROUND Abdominoplasty is one of the most common aesthetic procedures performed in the United States. While poor contour and unsatisfactory cosmetic result have been recognized, neuropathic pain from lateral femoral cutaneous nerve injury has been poorly described. We aim to improve outcomes by using an anatomical study to develop a strategy to avoid injury to the lateral femoral cutaneous nerve in abdominoplasty. METHODS Twenty-three fresh cadaver abdomens were dissected to evaluate the course of the lateral femoral cutaneous nerve, using 2.5× loupe magnification. Measurements were taken from the nerve to the anterior superior iliac spine and from the pubic symphysis to the lateral femoral cutaneous nerve. Recordings of the relationship of the nerve to the inguinal ligament and depth at scarpa's fascia were also made. Statistical analysis was performed to find average distances with a standard deviation. RESULTS On average, the distance from the lateral femoral cutaneous nerve to the anterior superior iliac spine was 3.62 (SD = 1.32) cm and 13.58 (SD = 2.41) cm from the pubic symphysis in line with the inguinal ligament. The lateral femoral cutaneous nerve was found at the inguinal ligament 80% of the time and 20% of the time superior to the ligament and always deep to scarpa's fascia. CONCLUSION Abdominoplasty carries a high patient and surgeon satisfaction rate. The plastic surgeon is continuously challenged to identify ways to improve outcomes, efficiency, and morbidity. Minimal and careful dissection in the area around 4 cm of the anterior superior iliac spine in addition to preserving scarpa's fascia near the inguinal ligament may serve as key strategies to avoiding lateral femoral cutaneous nerve injury.
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El-Saed A, Masaki K, Okamura T, Evans RW, Nakamura Y, Willcox BJ, Lee S, Maegawa H, Seto TB, Choo J, Fujiyoshi A, Miura K, Kuller LH, Ueshima H, Sekikawa A. The associations of C-reactive protein with serum levels of polyunsaturated fatty acids and trans fatty acids among middle-aged men from three populations. J Nutr Health Aging 2015. [DOI: 10.1007/s12603-015-0551-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Choo J, Sparks B, Kasdan M, Wilhelmi B. Composite grafting of a distal thumb amputation: a case report and review of literature. EPLASTY 2015; 15:e5. [PMID: 25848442 PMCID: PMC4347358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVE We report a case in which an avulsion-amputation of the thumb proximal to the lunula was repaired by reattaching the amputated segment as a composite graft. The graft demonstrated complete survival with only a minimal sacrifice in length. METHODS A 23-year-old man presented 4 hours after an avulsion injury of the thumb with associated distal and proximal phalanx fractures. The amputated segment included the sterile and germinal matrix. He underwent defatting and composite grafting of the amputated segment followed by K-wire fixation of his proximal phalanx fracture. RESULTS In his 1-week follow-up, the patient's composite graft-including his nail bed-demonstrated complete survival. At one month, the composite graft maintained stable soft tissue coverage and showed signs of nail plate regrowth. Four months after repair, he was able to return to light duty and was advanced to full duty within 5 months. He continued to report gradually improving hypersensitivity at the margins of the graft and stiffness of the interphalangeal joint. At five months he regained full mobility of his carpometacarpal joint. The range of motion of his interphalangeal and metacarpophalangeal joint were 0 to 10 degrees and 0 to 25 degrees, respectively. He was able to oppose his thumb to all 4 digits. Six months after repair, he demonstrated protective sensation of the tip of the thumb. CONCLUSION Composite grafting of the thumb, even in less than ideal cases, can still provide useful length for function as a opposable post and can be considered in reconstruction of thumb amputations at or proximal to the lunula.
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Kim H, Choo J, Reddy CK, Park H. Doubly supervised embedding based on class labels and intrinsic clusters for high-dimensional data visualization. Neurocomputing 2015. [DOI: 10.1016/j.neucom.2014.09.064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Dressler OJ, Yang T, Chang SI, Choo J, Wootton RCR, deMello AJ. Continuous and low error-rate passive synchronization of pre-formed droplets. RSC Adv 2015. [DOI: 10.1039/c5ra08044d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A microfluidic droplet-handling architecture for the synchronization of asynchronous, mis-matched, pre-formed droplet streams is demonstrated.
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Choo J, Lee C, Reddy CK, Park H. UTOPIAN: user-driven topic modeling based on interactive nonnegative matrix factorization. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2013; 19:1992-2001. [PMID: 24051765 DOI: 10.1109/tvcg.2013.212] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Topic modeling has been widely used for analyzing text document collections. Recently, there have been significant advancements in various topic modeling techniques, particularly in the form of probabilistic graphical modeling. State-of-the-art techniques such as Latent Dirichlet Allocation (LDA) have been successfully applied in visual text analytics. However, most of the widely-used methods based on probabilistic modeling have drawbacks in terms of consistency from multiple runs and empirical convergence. Furthermore, due to the complicatedness in the formulation and the algorithm, LDA cannot easily incorporate various types of user feedback. To tackle this problem, we propose a reliable and flexible visual analytics system for topic modeling called UTOPIAN (User-driven Topic modeling based on Interactive Nonnegative Matrix Factorization). Centered around its semi-supervised formulation, UTOPIAN enables users to interact with the topic modeling method and steer the result in a user-driven manner. We demonstrate the capability of UTOPIAN via several usage scenarios with real-world document corpuses such as InfoVis/VAST paper data set and product review data sets.
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Görg C, Liu Z, Kihm J, Choo J, Park H, Stasko J. Combining computational analyses and interactive visualization for document exploration and sensemaking in jigsaw. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2013; 19:1646-1663. [PMID: 23267206 DOI: 10.1109/tvcg.2012.324] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Investigators across many disciplines and organizations must sift through large collections of text documents to understand and piece together information. Whether they are fighting crime, curing diseases, deciding what car to buy, or researching a new field, inevitably investigators will encounter text documents. Taking a visual analytics approach, we integrate multiple text analysis algorithms with a suite of interactive visualizations to provide a flexible and powerful environment that allows analysts to explore collections of documents while sensemaking. Our particular focus is on the process of integrating automated analyses with interactive visualizations in a smooth and fluid manner. We illustrate this integration through two example scenarios: an academic researcher examining InfoVis and VAST conference papers and a consumer exploring car reviews while pondering a purchase decision. Finally, we provide lessons learned toward the design and implementation of visual analytics systems for document exploration and understanding.
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Choo J, Park H. Customizing computational methods for visual analytics with big data. IEEE COMPUTER GRAPHICS AND APPLICATIONS 2013; 33:22-28. [PMID: 24808056 DOI: 10.1109/mcg.2013.39] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The volume of available data has been growing exponentially, increasing data problem's complexity and obscurity. In response, visual analytics (VA) has gained attention, yet its solutions haven't scaled well for big data. Computational methods can improve VA's scalability by giving users compact, meaningful information about the input data. However, the significant computation time these methods require hinders real-time interactive visualization of big data. By addressing crucial discrepancies between these methods and VA regarding precision and convergence, researchers have proposed ways to customize them for VA. These approaches, which include low-precision computation and iteration-level interactive visualization, ensure real-time interactive VA for big data.
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Hwang SY, Cho SH, Cho DY, Lee M, Choo J, Jung KH, Maeng JH, Chai YG, Yoon WJ, Lee EK. Time-lapse, single cell based confocal imaging analysis of caspase activation and phosphatidylserine flipping during cellular apoptosis. Biotech Histochem 2010; 86:181-7. [DOI: 10.3109/10520291003648367] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Abstract
The cases of two patients with hyperthyroidism and acute left ventricular (LV) dysfunction with segmental wall motion abnormalities resulting in heart failure are reported. Both had electrocardiographic changes mimicking ischemic coronary artery disease. Treatment with antithyroid medications, beta blockers, and angiotensin-converting enzyme inhibitors rapidly restored LV function. The rapid reversibility suggests a role for myocardial stunning, an important entity to recognize in hyperthyroidism since this form of LV dysfunction can be reversed with appropriate treatment.
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Lee D, Kim S, Kim H, Choo J, Song J, Han J, Kim H, Lee J. Early prediction of response in patients with advanced/metastatic non-small cell lung cancer during chemotherapy with FDG-PET-CT. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.13154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
13154 Background: To evaluate the use of 18-fluorodeoxyglucose positron emission tomography-computed tomography (PET-CT) for prediction of response and survival early during the course of treatment in patients with advanced/metastatic NSCLC. Methods: Between May 2004 and November 2005, 31 patients (gender, 23M, 8F; stage, 2IIIB/29IV, histology, 6 squamous cell ca, 22 adenoca, 3 NOS; age median 57 (30–73 y)) with histopathologically proven NSCLC stage IIIB/IV were enrolled into this study. PET-CT was performed prior to and after one cycle of treatment. Early changes of primary tumor FDG-uptake measured by standardized uptake values (SUV) were correlated with best response to therapy as assessed by CT scan according to WHO response criteria. Results: Patients underwent standard treatment with gemcitabine/vinorelbine (15), gemcitabine/cisplatin (1) gemcitabine/vinorelbine/cisplatin (1), irinotecan/cisplatin (9) or gefitinib (5). In the 25 patients evaluable for response, other 6 patients ongoing, 9 patients achieved a partial response (36%), 5 showed stable diseases and 11 were progressive. Using a cut-off value of 20% reduction of FDG-uptake as a criterion for a response in PET-CT, subsequent best response was predicted with a sensitivity of 88.9% and a specificity of 87.5%. The positive predictive value of a metabolic response was 80.0% and the negative predictive value 93.3%, respectively. There was a significant correlation between the decrease of tumor metabolic activity and subsequent best response (p< 0.001). The median time to progression for PET-CT responder was 10.1 months when compared with that of non-responders with 2.6 months (log-rank p=0.009). Conclusions: Using FDG-PET best response to standard treatment and patient outcome can be predicted very early and therefore, the use of PET-CT may allow to reduce side effects and costs of ineffective therapy in non-responding patients No significant financial relationships to disclose.
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Briscoe T, Duncan J, Cock M, Choo J, Rice G, Harding R, Scheerlinck JPY, Rees S. Activation of NF-κB transcription factor in the preterm ovine brain and placenta after acute LPS exposure. J Neurosci Res 2006; 83:567-74. [PMID: 16435393 DOI: 10.1002/jnr.20757] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Intrauterine infection may be causally related to inflammation and injury of the fetal brain, however the mechanisms by which this occurs are unclear. We have investigated whether nuclear factor (NF)-kappaB, a transcription factor for proinflammatory cytokines, is activated in the fetal brain after acute LPS-exposure. At 95 days of gestation (term = approximately 147 days), 5 fetuses received a single intravenous bolus dose of LPS (1 microg/kg); 6 fetuses served as controls. Fetal blood samples were taken hourly for 6 hr post LPS-exposure to assess physiological status. Ewes and fetuses were then euthanased, placental and brain tissue examined histologically, and NF-kappaB activation assessed in several regions of the fetal brain using an electromobility shift assay (EMSA). Oxidative stress was measured using lipid peroxidation and 8-isoprostane biochemical assays and brain cytokine concentrations analysed by enzyme linked immunosorbent assay (ELISA). LPS-exposed fetuses (relative to controls) were hypoxemic and the haematocrit and lactate levels had increased. In the brains of LPS-exposed fetuses compared to controls, NF-kappaB binding activity was elevated in the hippocampus and the thalamus/basal ganglia; 8-isoprostane levels were elevated overall (P < 0.05) in the parietal/occipital/temporal lobes and thalamus/basal ganglia. TNF-alpha and IL-6 concentrations were not elevated, however, there was a tendency for an elevation of IFN-gamma concentrations in the thalamus/basal ganglia. IFN-gamma concentration was elevated (P < 0.05) in the plasma 4 hr after LPS-exposure. In the placenta, NF-kappaB binding activity was increased (P < 0.05). We conclude that acute systemic administration of LPS leads to increased binding activity of NF-kappaB subunits in specific regions of the fetal brain and in the placenta, but that there is no clear-cut relationship between this elevation and vulnerability to endotoxic damage.
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Dickler A, Kirk M, Choo J, Hsi W, Chu J, Dowlatshahi K, Francescatti D, Schott S, Nguyen C. Cosmetic outcome and incidence of infection with the mammosite breast brachytherapy applicator. Int J Radiat Oncol Biol Phys 2004. [DOI: 10.1016/j.ijrobp.2004.07.271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Dickler A, Kirk M, Choo J, Hsi W, Chu J, Nguyen C, Dowlat K. Treatment volume and dose optimization of the mammosite breast brachytherapy applicator. Int J Radiat Oncol Biol Phys 2003. [DOI: 10.1016/s0360-3016(03)01181-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Choo J, Laane J, Majors R, Villarreal JR. Far-infrared spectra and ring--puckering potential energy function of 4H-pyran. Conformations and bonding of 1,4-cyclohexadiene and its oxygen analogs. J Am Chem Soc 2002. [DOI: 10.1021/ja00071a056] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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