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Huang A.,Mahidol University | Hoonlor A.,AFRIMS
20th International Computer Science and Engineering Conference: Smart Ubiquitos Computing and Knowledge, ICSEC 2016 | Year: 2016

The essence of bioinformatics is to research, develop, or apply computational tools to biology related data. We confirmed in this paper that bioinformatics tools have been emerging exponentially from 1988-2016. To aide in tool discovery, many directories were established. Though the number of citations to the tools were provided in some directories, none describe how the tools were used. Currently reviewing the literature in a continuous manner remains the key method to keep up with the rapidly changing best practices. To reduce this burden, we proposed a method to systematically gather the documented usage from literature and analyzed them such that the active tool combinations can be derived. Implementation of our method found a total of 4,832 bioinformatics tools, published during 1988-2016, with known PubMed unique identifiers. From January to July 2016, the tools were cited in 13,619 publications. From those publications, 57 function sets (i.e. analysis patterns) were deduced by clustering the usage instances according to the tool functionalities used. A total of 666 tool combinations were observed from those function sets. The top five function sets consisted of 30-98 combinations each; the additional 43 function sets contained 2-9 combinations. The nonhomogeneous tool preferences elicits the search for their influential factors to guide the improvement of tool discovery methods. © 2016 IEEE.

Cui L.,Pennsylvania State University | Cui L.,Chongqing Normal University | Yan G.,University of California at Irvine | Yan G.,Chongqing Normal University | And 18 more authors.
Acta Tropica | Year: 2012

The Greater Mekong Subregion (GMS), comprised of six countries including Cambodia, China's Yunnan Province, Lao PDR, Myanmar (Burma), Thailand and Vietnam, is one of the most threatening foci of malaria. Since the initiation of the WHO's Mekong Malaria Program a decade ago, malaria situation in the GMS has greatly improved, reflected in the continuous decline in annual malaria incidence and deaths. However, as many nations are moving towards malaria elimination, the GMS nations still face great challenges. Malaria epidemiology in this region exhibits enormous geographical heterogeneity with Myanmar and Cambodia remaining high-burden countries. Within each country, malaria distribution is also patchy, exemplified by 'border malaria' and 'forest malaria' with high transmission occurring along international borders and in forests or forest fringes, respectively. 'Border malaria' is extremely difficult to monitor, and frequent malaria introductions by migratory human populations constitute a major threat to neighboring, malaria-eliminating countries. Therefore, coordination between neighboring countries is essential for malaria elimination from the entire region. In addition to these operational difficulties, malaria control in the GMS also encounters several technological challenges. Contemporary malaria control measures rely heavily on effective chemotherapy and insecticide control of vector mosquitoes. However, the spread of multidrug resistance and potential emergence of artemisinin resistance in Plasmodium falciparum make resistance management a high priority in the GMS. This situation is further worsened by the circulation of counterfeit and substandard artemisinin-related drugs. In most endemic areas of the GMS, P. falciparum and Plasmodium vivax coexist, and in recent malaria control history, P. vivax has demonstrated remarkable resilience to control measures. Deployment of the only registered drug (primaquine) for the radical cure of vivax malaria is severely undermined due to high prevalence of glucose-6-phosphate dehydrogenase deficiency in target human populations. In the GMS, the dramatically different ecologies, diverse vector systems, and insecticide resistance render traditional mosquito control less efficient. Here we attempt to review the changing malaria epidemiology in the GMS, analyze the vector systems and patterns of malaria transmission, and identify the major challenges the malaria control community faces on its way to malaria elimination. © 2011 Elsevier B.V.

Cui L.,Pennsylvania State University | Cui L.,Chongqing Normal University | Yan G.,University of California at Irvine | Yan G.,Chongqing Normal University | And 11 more authors.
Acta Tropica | Year: 2012

Despite significant improvement in the malaria situation of the Greater Mekong Subregion (GMS), malaria control for the region continues to face a multitude of challenges. The extremely patchy malaria distribution, especially along international borders, makes disease surveillance and targeted control difficult. The vector systems are also diverse with dramatic differences in habitat ecology, biting behavior, and vectorial capacity, and there is a lack of effective transmission surveillance and control tools. Finally, in an era of heavy deployment of artemisinin-based combination therapies, the region acts as an epicenter of drug resistance, with the emergence of artemisinin resistant Plasmodium falciparum posing a threat to both regional and global malaria elimination campaigns. This problem is further exacerbated by the circulation of counterfeit and substandard artemisinin drugs. Accordingly, this Southeast Asian Malaria Research Center, consisting of a consortium of US and regional research institutions, has proposed four interlinked projects to address these most urgent problems in malaria control. The aims of these projects will help to substantially improve our understanding of malaria epidemiology, vector systems and their roles in malaria transmission, as well as the mechanisms of drug resistance in parasites. Through the training of next-generation scientists in malaria research, this program will help build up and strengthen regional research infrastructure and capacities, which are essential for sustained malaria control in this region. © 2011 Elsevier B.V.

Chuangchaiya S.,Mahidol University | Jangpatarapongsa K.,Mahidol University | Sattabongkot J.,AFRIMS | Pattanapanyasat K.,Mahidol University | And 4 more authors.
Clinical and Experimental Immunology | Year: 2010

Summary Plasmodium falciparum infection causes transient immunosuppression during the parasitaemic stage. However, the immune response during simultaneous infections with both P. vivax and P. falciparum has been investigated rarely. In particular, it is not clear whether the host's immune response to malaria will be different when infected with a single or mixed malaria species. Phenotypes of T cells from mixed P. vivax-P. falciparum (PV-PF) infection were characterized by flow cytometry, and anti-malarial antibodies in the plasma were determined by an enzyme-linked immunosorbent assay. We found the percentage of CD3 +δ2+-T cell receptor (TCR) T cells in the acute-mixed PV-PF infection and single P. vivax infection three times higher than in the single P. falciparum infection. This implied that P. vivax might lead to the host immune response to the production of effector T killer cells. During the parasitaemic stage, the mixed PV-PF infection had the highest number of plasma antibodies against both P. vivax and P. falciparum. Interestingly, plasma from the group of single P. vivax or P. falciparum malaria infections had both anti-P. vivax and anti-P. falciparum antibodies. In addition, antigenic cross-reactivity of P. vivax or P. falciparum resulting in antibodies against both malaria species was shown in the supernatant of lymphocyte cultures cross-stimulated with either antigen of P. vivax or P. falciparum. The role of δ2 ± TCR T cells and the antibodies against both species during acute mixed malaria infection could have an impact on the immunity to malaria infection. © 2009 British Society for Immunology.

Loan H.K.,Institute Pasteur | Cuong N.V.,University of Oxford | Takhampunya R.,AFRIMS | Klangthong K.,AFRIMS | And 8 more authors.
Vector-Borne and Zoonotic Diseases | Year: 2015

A survey of Bartonella spp. from 275 rats purchased in food markets (n=150) and trapped in different ecosystems (rice field, forest, and animal farms) (n=125) was carried out during October, 2012-March, 2013, in the Mekong Delta of Vietnam. The overall Bartonella spp. prevalence detected by culture and PCR in blood was 14.9% (10.7-19.1%), the highest corresponding to Rattus tanezumi (49.2%), followed by Rattus norvegicus (20.7%). Trapped rats were also investigated for the presence and type of chiggers (larvae of trombiculid mites), and Bartonella spp. were investigated on chigger pools collected from each rat by RT-PCR. A total of five Bartonella spp. were identified in rats, three of which (B. elizabethae, B. rattimassiliensis, and B. tribocorum) are known zoonotic pathogens. Among trapped rats, factors independently associated with increased prevalence of Bartonella spp. included: (1) Rat species (R. tanezumi); (2) the number of Trombiculini-Blankaartia and Schoengastiini-Ascoschoengastia mites found on rats; and (3) the habitat of the rat (i.e., forest/fields vs. animal farms). The prevalence of Bartonella infection among chiggers from Bartonella spp.-positive R. tanezumi rats was 5/25 (25%), compared with 1/27 (3.7%) among Bartonella spp.-negative R. tanezumi rats (relative risk [RR]=5.4, 95% confidence interval [CI] 0.68-43.09). The finding of Bartonella spp.-positive chiggers on Bartonella spp.-negative rats is strongly suggestive of a transovarial transmission cycle. Rats are ubiquitous in areas of human activity and farms in the Mekong Delta; in addition, trapping and trading of rats for food is common. To correctly assess the human risks due to rat trapping, marketing, and carcass dressing, further studies are needed to establish the routes of transmission and cycle of infection. The widespread presence of these zoonotic pathogens in rats and the abundance of human - rat interactions suggest that surveillance efforts should be enhanced to detect any human cases of Bartonella infection that may arise. © 2015, Mary Ann Liebert, Inc.

Takhampunya R.,AFRIMS | Tippayachai B.,AFRIMS | Promsathaporn S.,AFRIMS | Leepitakrat S.,AFRIMS | And 6 more authors.
American Journal of Tropical Medicine and Hygiene | Year: 2014

Characterization of the 56-kDa type-specific antigen (TSA) genes of Orientia tsutsugamushi (OT) from three naturally infected, laboratory-reared mite colonies comprising three species (Leptotrombidium deliense [Ld], Leptotrombidium imphalum [Li], and Leptotrombidium chiangraiensis [Lc]) has revealed the presence of single and coexisting OT genotypes found in individual chiggers. The Karp genotype was found in all of the chiggers examined, whereas Gilliam and UT302 genotypes were only observed in combination with the Karp genotype. From analysis of these OT genotypes after transmission from chiggers to mice it was determined that with the Lc and Li mites, the OT genotype composition in the rodent spleens post-infection had not changed and therefore resembled that observed in the feeding chiggers. However, only the Karp genotype was found in rodents after feeding by Ld chiggers carrying Karp and Gilliam genotypes. The current findings reveal a complex association among the host, pathogen, and vector. Copyright © 2014 by The American Society of Tropical Medicine and Hygiene.

Khemawoot P.,AFRIMS | Saunders D.,AFRIMS | Rasameesoraj M.,AFRIMS | Melendez V.,U.S. Army | And 4 more authors.
Antimicrobial Agents and Chemotherapy | Year: 2011

The pharmacokinetics, oral bioavailability, and ex vivo antimalarial activity of mirincamycin isomers in a healthy rhesus monkey model were assessed to support lead optimization of novel nonhemolytic drugs for radical cure and causal prophylaxis of malaria. Fourteen male rhesus monkeys were randomized to four groups, which included cis and trans isomers by the oral and intravenous routes, with vehicle-only controls for each dosing route. Concentration-time data were collected for 7 days and were analyzed by noncompartmental analysis. cis-Mirincamycin had an absolute oral bioavailability of 13.6%, which was slightly higher than that of trans-mirincamycin (11.7%), but this difference was not statistically significant. There was a statistically significant difference between the area under the concentration-time curve from zero to 48 h (AUC 0-48) of cis-mirincamycin and that of trans-mirincamycin after oral dosing. When cultured in vitro with the W2 clone of Plasmodium falciparum, the 50% inhibitory concentrations for cis-mirincamycin, trans-mirincamycin, and dihydroartemisinin were 11,300, 12,300, and 2.30 nM, respectively. However, when dosed primate plasma was cultured ex vivo against the W2 clone, both isomers had much greater relative potencies than their in vitro activities relative to results for dihydroartemisinin, an increase of approximately 100-fold for the cis isomer and 150-fold for the trans isomer. Further, oral ex vivo activity was significantly higher than intravenous activity for both isomers, particularly during the first 90 min following dosing, suggesting the first-pass formation of one or more metabolites with blood-stage antimalarial activity. Identification of the metabolic pathways and metabolites may help to further delineate the properties of this class of drugs with previously demonstrated liver-stage antimalarial activity. Copyright © 2011, American Society for Microbiology. All Rights Reserved.

Bethell D.,AFRIMS | Se Y.,AFRIMS | Lon C.,AFRIMS | Socheat D.,Center for Parasitology | And 13 more authors.
Clinical Infectious Diseases | Year: 2010

Background. Fears of emerging artemisinin resistance in western Cambodia have prompted a series of clinical trials investigating whether slow responses to antimalarial treatment can be overcome by increasing doses of drug. Methods. Patients with uncomplicated malaria were allocated 1 of 3 oral artesunate monotherapy regimens (2, 4, or 6 mg/kg/day for 7 days) and were observed for 42 days. A series of safety measures, including complete blood count on days 0, 3, 6, and 14, was implemented because of a lack of safety data for these experimental doses. Results. After 3 doses, geometric mean absolute neutrophil counts were reduced in all groups, and 2 patients required artesunate to be discontinued because of neutropenia (absolute neutrophil count, <1.0×103 cells/μL). Recipients of the 6 mg/kg/day dosage had significantly lower geometric mean absolute neutrophil counts than did recipients of the 2 and 4 mg/kg/day dosages at 6 and 14 days (P<.001 for each). Overall, 5 (19%) of 26 patients who received the 6 mg/kg/day dosage became neutropenic within 14 days, triggering a cohort-halting rule and ending the trial early. Pharmacokinetic data from neutropenic patients showed wide variance, with plasma clearance occurring significantly slower in neutropenic patients than in nonneutropenic patients. Conclusions. Artesunate remains a crucial drug for the treatment of malaria, and determining optimal dosing regimens is vital to overcome emerging resistant parasite strains along the Thai-Cambodian border. However, future experimental dosing studies must be designed with care, because the safety of such regimens can no longer be assumed. The artemisinin derivatives remain one of the safest classes of antimalarial drugs, but this study demonstrates that the dosing limit may have been reached. © 2010 by the Infectious Diseases Society of America. All rights reserved.

Lurchachaiwong W.,AFRIMS | McCardle W.,AFRIMS | Chan T.-C.,Naval Medical Research Center | Schuster A.L.,AFRIMS | And 2 more authors.
Vector-Borne and Zoonotic Diseases | Year: 2015

Currently, no vaccine has been developed to protect humans from naturally acquired heterologous Orientia tsutsugamushi infections. To enhance the validity of vaccine candidates, we are developing a murine chigger challenge model with the O. tsutsugamushi Lc-1-infected Leptotrombidium chiangraiensis Line-1. To this end, an intraperitoneal (i.p.) murine challenge model using an O. tsutsugamushi Lc-1 isolate was developed for eventual validation of the chigger challenge model. We have determined that the murine lethal dose that kills 50% of the challenged mice (MuLD50) of a liver/spleen homogenate developed from O. tsutsugamushi Lc-1-infected ICR Swiss mice to be 10-6.9. Employing different inoculum doses of this homogenate, the bacterial load using quantitative real-time PCR (qPCR) was determined to range from 60 to 1.6 × 105 genome equivalent copies (GEC)/μL of liver and 33.4 to 2.2 × 105 GEC/μL of spleen tissue. The clinical outcomes relative to homogenate dose levels followed a dose-dependent pattern. The successful development and characterization of the O. tsutsugamushi Lc-1 i.p. challenge model will assist in the development and validation of a mouse chigger challenge scrub typhus model. © Copyright 2015, Mary Ann Liebert, Inc. 2015.

Roobsoong W.,Mahidol University | Roytrakul S.,National Center for Genetic Engineering and Biotechnology | Sattabongkot J.,AFRIMS | Li J.,Virginia Polytechnic Institute and State University | And 2 more authors.
Journal of Proteomics | Year: 2011

With the genome of the malaria parasite Plasmodium vivax sequenced, it is important to determine the proteomes of the parasite in order to assist efforts in antigen and drug target discovery. Since a method for continuous culture of P. vivax parasite is not available, we tried to study the proteome of the erythrocytic stages using fresh parasite isolates from patients. In schizont-enriched samples, 316 proteins were confidently identified by tandem mass spectrometry. Almost 50% of the identified proteins were hypothetical, while other major categories include proteins with binding function, protein fate, protein synthesis, metabolism and cellular transport. To identify proteins that are recognized by host humoral immunity, parasite proteins were separated by two-dimensional gel electrophoresis and screened by Western blot using an immune serum from a P. vivax patient. Mass spectrometry analysis of protein spots recognized by the serum identified four potential antigens including PV24. The recombinant protein PV24 was recognized by antibodies from vivax malaria patients even during the convalescent period, indicating that PV24 could elicit long-lasting antibody responses in P. vivax patients. © 2011 Elsevier B.V.

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