RCMVis: A Visual Analytics System for Route Choice Modeling.

We present RCMVis, a visual analytics system to support interactive Route Choice Modeling analysis. It aims to model which characteristics of routes, such as distance and the number of traffic lights, affect travelers' route choice behaviors and how much they affect the choice during their trips. Through close collaboration with domain experts, we designed a visual analytics framework for Route Choice Modeling. The framework supports three interactive analysis stages: exploration, modeling, and reasoning. In the exploration stage, we help analysts interactively explore trip data from multiple origin-destination (OD) pairs and choose a subset of data they want to focus on. To this end, we provide coordinated multiple OD views with different foci that allow analysts to inspect, rank, and compare OD pairs in terms of their multidimensional attributes. In the modeling stage, we integrate a k-medoids clustering method and a path-size logit model into our system to enable analysts to model route choice behaviors from trips with support for feature selection, hyperparameter tuning, and model comparison. Finally, in the reasoning stage, we help analysts rationalize and refine the model by selectively inspecting the trips that strongly support the modeling result. For evaluation, we conducted a case study and interviews with domain experts. The domain experts discovered unexpected insights from numerous modeling results, allowing them to explore the hyperparameter space more effectively to gain better results. In addition, they gained OD- and road-level insights into which data mainly supported the modeling result, enabling further discussion of the model.

Association between CYP2D6 phenotype and recurrence of Plasmodium vivax infection in south Korean patients.

BACKGROUND: Primaquine is activated by CYP2D6 in the hepatocytes. In Korea, primaquine is the only hypnozoitocidal agent used for patients with vivax malaria. Thus, patients with poor CYP2D6 activity could have an increased risk of primaquine failure and subsequent relapse. The study sought to identify the association between CYP2D6 phenotype and recurrence of malaria in Korean patients. METHODS: A total of 102 patients with vivax malaria were prospectively enrolled from eight institutions in Korea. An additional 38 blood samples from patients with recurred vivax malaria were provided by the Korea Disease Control and Prevention Agency. Malaria recurrence was defined as more than one episode of vivax malaria in the same or consecutive years. CYP2D6 star alleles, phenotypes, and activity scores were examined. RESULTS: Genotyping for CYP2D6 was successful in 101 of the prospectively enrolled patients and 38 samples from the Korea Disease Control and Prevention Agency, of which 91 were included in the no-recurrence group and 48 were included in the recurrence group. Reduced CYP2D6 activity (intermediate metabolizer) phenotype was more common in the recurrence group than in the no-recurrence group (OR, 2.33 (95% CI, 1.14-4.77); p = 0.02). Patients with lower CYP2D6 activity had a higher probability of recurrence (p = 0.029). CONCLUSION: This study suggests that CYP2D6 polymorphism may affect primaquine efficacy and thus Plasmodium vivax recurrence in Korea.

Travel pattern-based bus trip origin-destination estimation using smart card data.

Smart card data are widely used in generating the origin and destination (O-D) matrix for public transit, which contains important information for transportation planning and operation. However, the generation of the O-D matrix is limited by the smart card data information that includes the boarding (origin) information without the alighting (destination) information. To solve this problem, trip chain methods have been proposed, thereby greatly contributing in estimating the destination using the smart card data. Nevertheless, unlinked trips, that is, trips with unknown destinations, are a persisting issue. The purpose of this study is to develop a method for estimating the destination of unlinked trips, in which trip chain methods cannot be applied, using temporal travel patterns and historical boarding records of the passengers based on long-term smart card data. The passengers were clustered by k-means clustering, and the time-of-day travel patterns were estimated for each cluster using a Gaussian mixture model. The travel patterns were formulated to estimate the destination of the passengers from the smart card data. The proposed method was verified using the 2018 smart card data collected in Sejong City, South Korea. The existing trip chain method matched the destinations of 60.0% of the total trips, whereas the proposed method improved the matching to 74.9% by additionally matching the destinations of 37.2% of the unlinked trips.

Recent Incidence of Paragonimus westermani Metacercariae in Freshwater Crayfish, Cambaroides similis, from Two Enzootic Sites in Jeollanam-do, Korea.

An epidemiological study was performed to know the recent infection status of Paragonimus westermani metacercariae (PwMc) in freshwater crayfish, Cambaroides similis, from 2 streams in Jeollanam-do, Republic of Korea. Crayfish were collected from creeks in Bogil-do (Island), Wando-gun, and in a creek near Daeheung Temple in Haenam-gun. The infection rate of crayfish with PwMc in Bogil-do was 89.8%, and the metacercarial burden was 37 PwMc per the infected crayfish. Crayfish in a creek near Daeheung Temple were larger and twice heavier than those in Bogil-do. Of them, 96.5% were infected with PwMc. An average of 140 metacercariae was found in the infected crayfish, almost quadruple to those of Bogil-do. There was a strong correlation between the number of PwMc and body weight of the crayfish. These results suggest that P. westermani metacercariae are still prevalent in crayfish of the 2 regions in Jeollanam-do, Korea.

The unique distribution of the Plasmodium vivax merozoite surface protein 1 in parasite isolates with short and long latent periods from the Republic of Korea.

BACKGROUND: Vivax malaria occurring in the Republic of Korea is occasionally characterized by a long latent infection induced by hypnozoites in the liver. So far, the mechanisms responsible for short and long latent infections of vivax malaria are not known. Therefore, the present study classified the parasite isolates according to the long and short latent periods and then analysed the genetic diversity of the Plasmodium vivax merozoite surface protein 1 (PvMSP-1). METHODS: Blood samples containing P. vivax isolates were collected from 465 patients from 2011 to 2013 at health centers in the Republic of Korea. PvMSP-1 gene sequences were analysed in groups classified by the collection year, and short or long latent periods. The samples in short and long latent periods were selected by the timing of vivax malaria occurrence, July-August and January-May, respectively. RESULTS: Three PvMSP-1 types (Sal-1, Belem, and recombinant) were observed in P. vivax isolates collected from 2011 to 2013. Interestingly, the recombinant and Sal-1 types were dominant in vivax malaria of the long and short latent periods, respectively. In addition, the S-b like subtype of the PvMSP-1 Sal-1 type was first identified in 2013. CONCLUSION: This study revealed that the genetic type of PvMSP-1 is likely related to the duration of its latent period. Moreover, trends of the genetic types of PvMSP-1 seem to be stable in recent years compared with those of previous years in which various new types were observed.

Development and efficacy of real-time PCR in the diagnosis of vivax malaria using field samples in the Republic of Korea.

The development of sensitive, rapid, and accurate diagnostic methods for vivax malaria is essential for the effective control of malaria in the Republic of Korea, where vivax malaria patients usually show low parasitemia. In this study, a TaqMan-based real-time polymerase chain reaction (PCR) method was established and compared with other PCR-based assays, including nested PCR, loop-mediated isothermal amplification, and multiplex PCR, using samples from febrile patients with suspected vivax malaria. The established real-time PCR had a high sensitivity (99.6%) and specificity (100%). Therefore, this sensitive, specific, rapid, and quantitative real-time PCR method could be used for the routine diagnosis of vivax malaria in the laboratory of the Korea National Institute of Health.

First evaluation of glucose-6-phosphate dehydrogenase (G6PD) deficiency in vivax malaria endemic regions in the Republic of Korea.

BACKGROUND: Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human enzyme defect and affects more than 400 million people worldwide. This deficiency is believed to protect against malaria because its global distribution is similar. However, this genetic disorder may be associated with potential hemolytic anemia after treatment with anti-malarials, primaquine or other 8-aminoquinolines. Although primaquine is used for malaria prevention, no study has previously investigated the prevalence of G6PD variants and G6PD deficiency in the Republic of Korea (ROK). METHODS: Two commercialized test kits (Trinity G-6-PDH and CareStart G6PD test) were used for G6PD deficiency screening. The seven common G6PD variants were investigated by DiaPlexC kit in blood samples obtained living in vivax malaria endemic regions in the ROK. RESULTS: Of 1,044 blood samples tested using the CareStart G6PD test, none were positive for G6PD deficiency. However, a slightly elevated level of G6PD activity was observed in 14 of 1,031 samples tested with the Trinity G-6-PDH test. Forty-nine of the 298 samples with non-specific amplification by DiaPlexC kit were confirmed by sequencing to be negative for the G6PD variants. CONCLUSIONS: No G6PD deficiency was observed using phenotypic- or genetic-based tests in individuals residing in vivax malaria endemic regions in the ROK. Because massive chemoprophylaxis using primaquine has been performed in the ROK military to kill hypnozoites responsible for relapse and latent stage vivax malaria, further regular monitoring is essential for the safe administration of primaquine.

First characterization of Plasmodium vivax liver stage antigen (PvLSA) using synthetic peptides.

BACKGROUND: Plasmodium vivax is the most widespread human malaria in tropical and subtropical countries, including the Republic of Korea. Vivax malaria is characterized by hypnozoite relapse and long latency infection by the retained liver stage of P. vivax, and somewhat surprisingly, little is known of the liver stage antigens of this parasite. Here, we report for the first time the characterization of a liver stage antigen of P. vivax (PvLSA). METHODS: Five peptides located inside PvLSA were synthesized, and specific anti-sera to the respective peptides were used to localize PvLSA on P. vivax parasites in human liver cells by immunofluorescence. Western blotting and enzyme-linked immunosorbent assay were performed using the five peptides and sera collected from vivax malaria patients and from normal healthy controls. RESULTS: PvLSA was localized on P. vivax parasites in human liver cells. Vivax malaria-infected patients were detected using the five peptides by western blotting. Furthermore, the peptides reacted with the sera of vivax malaria patients. CONCLUSIONS: These results suggest that PvLSA may function during the liver stage of P. vivax.

Comparison of rapid diagnostic tests for the detection of Plasmodium vivax malaria in South Korea.

South Korea is one of many countries with endemic Plasmodium vivax malaria. Here we report the evaluation of four rapid diagnostic tests (RDTs) for diagnosis of this disease. A total of 253 subjects were enrolled in the study. The sensitivities, specificities and agreement frequencies were estimated by comparing the four RDTs against the standard of nested-PCR and microscopic examination. The CareStart(TM) and SD Bioline had higher test sensitivities (99.4 and 98.8%, respectively) compared with the NanoSign and Asan Easy tests (93.0 and 94.7%, respectively). The CareStart(TM) and SD Bioline tests could detect P. vivax in samples with parasite densities <150/µl, which was a slightly better performance than the other two RDTs. The quantitative accuracy of the four RDTs was also estimated by comparing results with P. vivax counts from blood samples. Lower test price would result in increased use of these RDTs in the field. The results of this study contribute valuable information that will aid in the selection of a diagnostic method for the detection of malaria.

Rapid dissemination of newly introduced Plasmodium vivax genotypes in South Korea.

Reemerged Plasmodium vivax malaria in South Korea has not yet been eradicated despite continuous governmental efforts. It has rather become an endemic disease. Our study aimed to determine the genetic diversity in P. vivax merozoite surface protein-1 (PvMSP-1) and circumsporozoite protein (PvCSP) genes over an extended period after its reemergence to its current status. Sequence analysis of PvMSP-1 gene sequences from the 632 P. vivax isolates during 1996-2007 indicates that most isolates recently obtained were different from isolates obtained in the initial reemergence period. There was initially only one subtype (recombinant) present but its subtypes have varied since 2000; six MSP-1 subtypes were recently found. A similar variation was observed by CSP gene analysis; a new CSP subtype was found. Understanding genetic variation patterns of the parasite may help to analyze trends and assess extent of endemic malaria in South Korea.

Outbreak of vivax malaria in areas adjacent to the demilitarized zone, South Korea, 1998.

Malaria had been eradicated in the Republic of Korea (South Korea) by the late 1970s. In 1993, a soldier was infected with Plasmodium vivax malaria in the Demilitarized Zone (DMZ; the border area between North and South Korea), and since then, the number of cases has been steadily increasing year after year. In 1998, 3,932 vivax malaria cases were microscopically confirmed, affecting 2,784 (70.8%) soldiers (including discharged soldiers) and 1,148 (29.2%) civilians. These cases occurred throughout the year, peaking in July (30.1%) and August (30.5%). Most of the patients were infected in areas in or near the DMZ. Taking into consideration entomologic, socioecologic, and epidemiologic factors, it is postulated that there has been an epidemic of malaria in North Korea since 1993, with the number of cases increasing yearly; the continuous infiltration across the DMZ from North Korea of infected female mosquitoes of the vector species Anopheles sinensis resulted in an outbreak of vivax malaria in the DMZ of South Korea.