Search tips
Search criteria

Results 1-12 (12)

Clipboard (0)

Select a Filter Below

Year of Publication
1.  Trauma training course: innovative teaching models and methods for training health workers in active conflict zones of Eastern Myanmar 
Myanmar has struggled through decades of internal conflict, which has negatively impacted the country’s health outcomes. Recent government changes have brought hope and reduced conflict. The ethnic minority groups have suffered the brunt of the health consequences and reside in regions that lack health infrastructure, resources, and providers. Due to the chronic lack of healthcare providers within conflict areas, health workers (HWs) have been trained in an effort to fill the void. Research has shown that these non-physician clinicians positively impact health outcomes in developing countries. These HWs are supported by community-based organizations in collaboration with foreign non-governmental organizations. Started in 2000, the trauma training course was developed to meet the educational needs of these HWs.
Essential procedures for HWs in conflict zones were identified, and teaching methods were adapted to develop models that were simple, reproducible, cost effective, and able to facilitate effective learning within the limitations of these challenging environments. This paper presents simulation models developed to teach trauma injury evaluation and management in resource-limited settings to HWs.
Material and construction of the models described include breathing, chest, cricothyroidotomy, circulation, wound repair, fracture/dislocation, splinting, fasciotomy/amputation, and an animal model. In 2013, a pre/post test and post-training evaluation were completed, which demonstrated an increase in understanding of the material and satisfaction with the training.
The simulation models described engage the HWs in clinical skills practice specific to injury management, which builds upon the HWs existing knowledge and facilitates an increased understanding of life-saving procedures. Through observation of the HW performance and HW feedback, these simulation models have increased the understanding of trauma management. Limitations include lack of a graduated learning system for the HWs, logistics, and time constraints. Despite the barriers faced, we feel that this is a necessary program that has reduced morbidity and mortality due to traumatic injury in the geographic areas that the HWs serve. With the changing political environment in Myanmar and the development of peace agreements between the government and the ethnic minority groups, these HWs can be integrated into Myanmar’s evolving health system.
PMCID: PMC4298949  PMID: 25624953
Trauma training; Simulation; Health worker; Myanmar; Conflict
2.  Thoughts and Progress 
Artificial organs  2012;36(8):10.1111/j.1525-1594.2012.01523.x.
Heart failure (HF) is increasing worldwide and represents a major burden in terms of health care resources and costs. Despite advances in medical care, prognosis with HF remains poor, especially in advanced stages. The large patient population with advanced HF and the limited number of donor organs stimulated the development of mechanical circulatory support (MCS) devices as a bridge to transplant and for destination therapy. However, MCS devices require a major operative intervention, cardiopulmonary bypass, and blood component exposure, which have been associated with significant adverse event rates, and long recovery periods. Miniaturization of MCS devices and the development of an efficient and reliable transcutaneous energy transfer system may provide the vehicle to overcome these limitations and usher in a new clinical paradigm in heart failure therapy by enabling less invasive beating heart surgical procedures for implantation, reduce cost, and improve patient outcomes and quality of life. Further, it is anticipated that future ventricular assist device technology will allow for a much wider application of the therapy in the treatment of heart failure including its use for myocardial recovery and as a platform for support for cell therapy in addition to permanent long-term support.
PMCID: PMC3810069  PMID: 22882443
Miniaturization; Ventricular assist device technology; Mechanical circulatory support; Heart failure; Review
3.  Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology 
Briefings in Bioinformatics  2009;11(1):40-79.
Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry.
PMCID: PMC2810111  PMID: 19955237
Genome informatics; Metabolic pathways; Pathway bioinformatics; Model organism databases; Genome databases; Biological networks; Regulatory networks
4.  Population‐based survey methods to quantify associations between human rights violations and health outcomes among internally displaced persons in eastern Burma 
Case reports of human rights violations have focused on individuals' experiences. Population‐based quantification of associations between rights indicators and health outcomes is rare and has not been documented in eastern Burma.
We describe the association between mortality and morbidity and the household‐level experience of human rights violations among internally displaced persons in eastern Burma.
Mobile health workers in conflict zones of eastern Burma conducted 1834 retrospective household surveys in 2004. Workers recorded data on vital events, mid‐upper arm circumference of young children, malaria parasitaemia status of respondents and household experience of various human rights violations during the previous 12 months.
Under‐5 mortality was 218 (95% confidence interval 135 to 301) per 1000 live births. Almost one‐third of households reported forced labour (32.6%). Forced displacement (8.9% of households) was associated with increased child mortality (odds ratio = 2.80), child malnutrition (odds ratio = 3.22) and landmine injury (odds ratio = 3.89). Theft or destruction of the food supply (reported by 25.2% of households) was associated with increased crude mortality (odds ratio = 1.58), malaria parasitaemia (odds ratio = 1.82), child malnutrition (odds ratio = 1.94) and landmine injury (odds ratio = 4.55). Multiple rights violations (14.4% of households) increased the risk of child (incidence rate ratio = 2.18) and crude (incidence rate ratio = 1.75) mortality and the odds of landmine injury (odds ratio = 19.8). Child mortality risk was increased more than fivefold (incidence rate ratio = 5.23) among families reporting three or more rights violations.
Widespread human rights violations in conflict zones in eastern Burma are associated with significantly increased morbidity and mortality. Population‐level associations can be quantified using standard epidemiological methods. This approach requires further validation and refinement elsewhere.
PMCID: PMC2652972  PMID: 17873229
Burma; mortality; human rights; internally displaced persons; malaria; landmines; civil conflict
5.  Molecular surveillance for drug-resistant Plasmodium falciparum in clinical and subclinical populations from three border regions of Burma/Myanmar: cross-sectional data and a systematic review of resistance studies 
Malaria Journal  2012;11:333.
Confirmation of artemisinin-delayed parasite clearance in Plasmodium falciparum along the Thai-Myanmar border has inspired a global response to contain and monitor drug resistance to avert the disastrous consequences of a potential spread to Africa. However, resistance data from Myanmar are sparse, particularly from high-risk areas where limited health services and decades of displacement create conditions for resistance to spread. Subclinical infections may represent an important reservoir for resistance genes that confer a fitness disadvantage relative to wild-type alleles. This study estimates the prevalence of resistance genotypes in three previously unstudied remote populations in Myanmar and tests the a priori hypothesis that resistance gene prevalence would be higher among isolates collected from subclinical infections than isolates collected from febrile clinical patients. A systematic review of resistance studies is provided for context.
Community health workers in Karen and Kachin States and an area spanning the Indo-Myanmar border collected dried blood spots from 988 febrile clinical patients and 4,591 villagers with subclinical infection participating in routine prevalence surveys. Samples positive for P. falciparum 18 s ribosomal RNA by real-time PCR were genotyped for P. falciparum multidrug resistance protein (pfmdr1) copy number and the pfcrt K76T polymorphism using multiplex real-time PCR.
Pfmdr1 copy number increase and the pfcrt K76 polymorphism were determined for 173 and 269 isolates, respectively. Mean pfmdr1 copy number was 1.2 (range: 0.7 to 3.7). Pfmdr1 copy number increase was present in 17.5%, 9.6% and 11.1% of isolates from Karen and Kachin States and the Indo-Myanmar border, respectively. Pfmdr1 amplification was more prevalent in subclinical isolates (20.3%) than clinical isolates (6.4%, odds ratio 3.7, 95% confidence interval 1.1 - 12.5). Pfcrt K76T prevalence ranged from 90-100%.
Community health workers can contribute to molecular surveillance of drug resistance in remote areas of Myanmar. Marginal and displaced populations under-represented among previous resistance investigations can and should be included in resistance surveillance efforts, particularly once genetic markers of artemisinin-delayed parasite clearance are identified. Subclinical infections may contribute to the epidemiology of drug resistance, but determination of gene amplification from desiccated filter samples requires further validation when DNA concentration is low.
PMCID: PMC3518194  PMID: 22992214
Malaria; Plasmodium falciparum; Artemisinin resistance; Genetic; Subclinical infection; Conflict; Myanmar
6.  Impact of Community-Based Maternal Health Workers on Coverage of Essential Maternal Health Interventions among Internally Displaced Communities in Eastern Burma: The MOM Project 
PLoS Medicine  2010;7(8):e1000317.
Mullany and colleagues report outcomes from a project involving delivery of community-based maternal health services in eastern Burma, and report substantial increases in coverage of care.
Access to essential maternal and reproductive health care is poor throughout Burma, but is particularly lacking among internally displaced communities in the eastern border regions. In such settings, innovative strategies for accessing vulnerable populations and delivering basic public health interventions are urgently needed.
Four ethnic health organizations from the Shan, Mon, Karen, and Karenni regions collaborated on a pilot project between 2005 and 2008 to examine the feasibility of an innovative three-tiered network of community-based providers for delivery of maternal health interventions in the complex emergency setting of eastern Burma. Two-stage cluster-sampling surveys among ever-married women of reproductive age (15–45 y) conducted before and after program implementation enabled evaluation of changes in coverage of essential antenatal care interventions, attendance at birth by those trained to manage complications, postnatal care, and family planning services.
Among 2,889 and 2,442 women of reproductive age in 2006 and 2008, respectively, population characteristics (age, marital status, ethnic distribution, literacy) were similar. Compared to baseline, women whose most recent pregnancy occurred during the implementation period were substantially more likely to receive antenatal care (71.8% versus 39.3%, prevalence rate ratio [PRR] = 1.83 [95% confidence interval (CI) 1.64–2.04]) and specific interventions such as urine testing (42.4% versus 15.7%, PRR = 2.69 [95% CI 2.69–3.54]), malaria screening (55.9% versus 21.9%, PRR = 2.88 [95% CI 2.15–3.85]), and deworming (58.2% versus 4.1%, PRR = 14.18 [95% CI 10.76–18.71]. Postnatal care visits within 7 d doubled. Use of modern methods to avoid pregnancy increased from 23.9% to 45.0% (PRR = 1.88 [95% CI 1.63–2.17]), and unmet need for contraception was reduced from 61.7% to 40.5%, a relative reduction of 35% (95% CI 28%–40%). Attendance at birth by those trained to deliver elements of emergency obstetric care increased almost 10-fold, from 5.1% to 48.7% (PRR = 9.55 [95% CI 7.21–12.64]).
Coverage of maternal health interventions and higher-level care at birth was substantially higher during the project period. The MOM Project's focus on task-shifting, capacity building, and empowerment at the community level might serve as a model approach for similarly constrained settings.
Please see later in the article for the Editors' Summary
Editors' Summary
Every minute, somewhere in the world, a woman dies of complications related to pregnancy and childbirth. Access to essential maternal and reproductive health care (including family planning) is particularly bad in war-torn countries. In Burma, for example, where there have been decades of conflict between the military junta and ethnic minority resistance groups, the maternal mortality rate (the number of deaths among women from pregnancy-related causes per 100,000 live births) is around 380, whereas in neighboring Thailand it is only 44. Maternal health is even worse in the Shan, Mon, Karen, and Karenni regions of eastern Burma where ethnic conflicts and enforced village relocations have internally displaced more than half a million people. Here, the maternal mortality rate is around 1,200. In an effort to improve access to maternal health services in these regions, community-based organizations in Burma, the Johns Hopkins Center for Public Health and Human Rights, and the Global Health Access Program undertook an innovative pilot project—the Mobile Obstetric Medics (MOM) project—between 2005 and 2008. Local health workers from 12 communities in eastern Burma received training in antenatal care, obstetrics (the care of women during childbirth), postnatal care, and family planning at the Mae Tao Clinic in Mae Sot, Thailand. These “maternal health workers” then returned to Burma where they trained local health workers and traditional birth attendants to provide maternal health care to their communities.
Why Was This Study Done?
Before the MOM project started, nearly 3,000 women living in the study communities were surveyed to evaluate the coverage of essential antenatal care interventions such as urine testing for infections during pregnancy, screening for malaria, and deworming; Urinary tract infections, malaria, and hookworm infections all increase the risk of poor maternal and neonatal outcomes. The preproject survey also evaluated how many births were attended by people able to deal with complications, and the provision of postnatal care and family planning services. In this study, the researchers undertake a similar postproject survey to evaluate the impact of MOM on the coverage of essential maternal health interventions among internally displaced communities in eastern Burma.
What Did the Researchers Do and Find?
Between October 2008 and December 2008, trained survey workers asked nearly 2,500 ever-married women of reproductive age from the project's study communities about their access to antenatal and postnatal care, skilled birth attendants, and family planning. The results of the postproject survey were then compared with those of the “baseline,” preproject survey. The general characteristics (age, marital status, ethnicity, and literacy) of the women included in the two surveys were very similar. However, 71.8% of the women whose most recent pregnancy occurred during the implementation period of the MOM project had received antenatal care compared to only 39.3% of women surveyed at baseline. Similarly, among the women questioned during the postproject survey, 42.4% had had their urine tested and 55.9% had been screened for malaria during pregnancy compared to only 15.7% and 21.9%, respectively, of the women questioned in the preproject survey. Deworming had increased from 4.1% to 58.2% during the project, postnatal care visits within 7 days had doubled, and attendance at birth by people trained to deal with obstetric emergencies had increased 10-fold from 5.1% to 48.7%. Finally, the use of modern contraception methods (slow-release contraceptives, oral contraceptives, and condoms) had increased from 23.9% to 45.0%.
What Do These Findings Mean?
These findings reveal a substantial improvement in access to maternal and reproductive health care in the study communities during the MOM project. However, because the study compared two independent groups of women before and after implementation of the MOM project rather than concurrently comparing groups of women who did and did not receive the services provided by the MOM project, this study does not prove that the MOM approach was the cause of the changes in the coverage of essential maternal health care. Nevertheless, these findings suggest that the type of approach used in the MOM project—the expansion of interventions (including components of emergency obstetric care) delivered outside healthcare facilities by community-based providers—might be an effective way to deliver maternal and reproductive health services in other parts of Burma and in other places where there are ongoing conflicts.
Additional Information
Please access these Web sites via the online version of this summary at
More information about the MOM project is available in previous publications by the researchers in PLoS Medicine, in Reproductive Health Matters, and in Social Science and Medicine
Additional resources are also available on the MOM Project
The Reproductive Health Response in Conflict Consortium provides information on how conflicts affect reproductive health
The World Health Organization provides information on all aspects of health in Burma (in several languages)
The Mae Tao clinic also provides general information about Burma and its health services
The Burma Campaign UK and Human Rights Watch both provide detailed information about human rights violations, including those that affect maternal health in Burma
The United Nations Population Fund provides information about safe motherhood and maternal and reproductive health during conflicts and among refugees (in several languages)
PMCID: PMC2914639  PMID: 20689805
7.  Access To Essential Maternal Health Interventions and Human Rights Violations among Vulnerable Communities in Eastern Burma 
PLoS Medicine  2008;5(12):e242.
Health indicators are poor and human rights violations are widespread in eastern Burma. Reproductive and maternal health indicators have not been measured in this setting but are necessary as part of an evaluation of a multi-ethnic pilot project exploring strategies to increase access to essential maternal health interventions. The goal of this study is to estimate coverage of maternal health services prior to this project and associations between exposure to human rights violations and access to such services.
Methods and Findings
Selected communities in the Shan, Mon, Karen, and Karenni regions of eastern Burma that were accessible to community-based organizations operating from Thailand were surveyed to estimate coverage of reproductive, maternal, and family planning services, and to assess exposure to household-level human rights violations within the pilot-project target population. Two-stage cluster sampling surveys among ever-married women of reproductive age (15–45 y) documented access to essential antenatal care interventions, skilled attendance at birth, postnatal care, and family planning services. Mid-upper arm circumference, hemoglobin by color scale, and Plasmodium falciparum parasitemia by rapid diagnostic dipstick were measured. Exposure to human rights violations in the prior 12 mo was recorded. Between September 2006 and January 2007, 2,914 surveys were conducted. Eighty-eight percent of women reported a home delivery for their last pregnancy (within previous 5 y). Skilled attendance at birth (5.1%), any (39.3%) or ≥ 4 (16.7%) antenatal visits, use of an insecticide-treated bed net (21.6%), and receipt of iron supplements (11.8%) were low. At the time of the survey, more than 60% of women had hemoglobin level estimates ≤ 11.0 g/dl and 7.2% were Pf positive. Unmet need for contraceptives exceeded 60%. Violations of rights were widely reported: 32.1% of Karenni households reported forced labor and 10% of Karen households had been forced to move. Among Karen households, odds of anemia were 1.51 (95% confidence interval [CI] 0.95–2.40) times higher among women reporting forced displacement, and 7.47 (95% CI 2.21–25.3) higher among those exposed to food security violations. The odds of receiving no antenatal care services were 5.94 (95% CI 2.23–15.8) times higher among those forcibly displaced.
Coverage of basic maternal health interventions is woefully inadequate in these selected populations and substantially lower than even the national estimates for Burma, among the lowest in the region. Considerable political, financial, and human resources are necessary to improve access to maternal health care in these communities.
Luke Mullany and colleagues examine access to essential maternal health interventions and human rights violations within vulnerable communities in eastern Burma.
Editors' Summary
After decades of military rule, Burma has one of the world's worst health-care systems and high levels of ill health. For example, maternal mortality (deaths among women from pregnancy-related causes) is around 360 per 100,000 live births in Burma, whereas in neighboring Thailand it is only 44 per 100,000 live births. Maternal health is even worse in the Shan, Karenni, Karen and Mon states in eastern Burma where ethnic conflicts and enforced village relocations have internally displaced more than half a million people. Here, maternal mortality is thought to be about 1000 per 100, 000 live births. In an effort to improve access to life-saving maternal health interventions in these states, Burmese community-based health organizations, the Johns Hopkins Center for Public Health and Human Rights and the Global Health Access Program in the USA, and the Mae Tao Clinic (a health-worker training center in Thailand) recently set up the Mobile Obstetric Maternal Health Workers (MOM) Project. In this pilot project, local health workers from 12 communities in eastern Burma received training in antenatal care, emergency obstetrics (the care of women during childbirth), blood transfusion, and family planning at the Mae Tao Clinic. Back in Burma, these maternal health workers trained additional local health workers and traditional birth attendants. All these individuals now provide maternal health care to their communities.
Why Was This Study Done?
The effectiveness of the MOM project can only be evaluated if accurate baseline information on women's access to maternal health-care services is available. This information is also needed to ensure the wise use of scarce health-care resources. However, very little is known about reproductive and maternal health in eastern Burma. In this study, the researchers analyze the information on women's access to reproductive and maternal health-care services that was collected during the initial field implementation stage of the MOM project. In addition, they analyze whether exposure to enforced village relocations and other human rights violations affect access to maternal health-care services.
What Did the Researchers Do and Find?
Trained survey workers asked nearly 3000 ever-married women of reproductive age in the selected communities about their access to antenatal and postnatal care, skilled birth attendants, and family planning. They measured each woman's mid-upper arm circumference (an indicator of nutritional status) and tested them for anemia (iron deficiency) and infection with malaria parasites (a common cause of anemia in tropical countries). Finally, they asked the women about any recent violations of their human rights such as forced labour or relocation. Nearly 90% of the women reported a home delivery for their last baby. A skilled attendant was present at only one in 20 births and only one in three women had any antenatal care. One third of the women received postnatal care and only a third said they had access to effective contraceptives. Few women had received iron supplements or had used insecticide-treated bednets to avoid malaria-carrying mosquitos. Consequently, more than half the women were anemic and 7.2% were infected with malaria parasites. Many women also showed signs of poor nutrition. Finally, human rights violations were widely reported by the women. In Karen, the region containing most of the study communities, forced relocation tripled the risk of women developing anemia and greatly decreased their chances of receiving any antenatal care.
What Do These Findings Mean?
These findings show that access to maternal health-care interventions is extremely limited and that poor nutrition, anemia, and malaria, all of which increase the risk of pregnancy complications, are widespread in the communities in the MOM project. Because these communities had some basic health services and access to training in Thailand before the project started, these results probably underestimate the lack of access to maternal health-care services in eastern Burma. Nevertheless, it is clear that considerable political, financial, and human resources will be needed to improve maternal health in this region. Finally, the findings also reveal a link between human rights violations and reduced access to maternal health-care services. Thus, the scale of human rights violations will need to be considered when evaluating programs designed to improve maternal health in Burma and in other places where there is ongoing conflict.
Additional Information.
Please access these Web sites via the online version of this summary at
This research article is further discussed in a PLoS Medicine Perspective by Macaya Douoguih
The World Health Organization provides information on all aspects of health in Burma (in several languages)
The Mae Tao Clinic also provides general information about Burma and its health services
More information about the MOM project is available in a previous publication by the researchers
The Burma Campaign UK and Human Rights Watch both provide detailed information about human rights violations in Burma
The United Nations Population Fund provides information about safe motherhood and ongoing efforts to save mothers' lives around the world
PMCID: PMC2605890  PMID: 19108601
8.  Annotation-based inference of transporter function 
Bioinformatics  2008;24(13):i259-i267.
Motivation: We present a method for inferring and constructing transport reactions for transporter proteins based primarily on the analysis of the names of individual proteins in the genome annotation of an organism. Transport reactions are declarative descriptions of transporter activities, and thus can be manipulated computationally, unlike free-text protein names. Once transporter activities are encoded as transport reactions, a number of computational analyses are possible including database queries by transporter activity; inclusion of transporters into an automatically generated metabolic-map diagram that can be painted with omics data to aid in their interpretation; detection of anomalies in the metabolic and transport networks, such as substrates that are transported into the cell but are not inputs to any metabolic reaction or pathway; and comparative analyses of the transport capabilities of different organisms.
Results: On randomly selected organisms, the method achieves precision and recall rates of 0.93 and 0.90, respectively in identifying transporter proteins by name within the complete genome. The method obtains 67.5% accuracy in predicting complete transport reactions; if allowance is made for predictions that are overly general yet not incorrect, reaction prediction accuracy is 82.5%.
Availability: The method is implemented as part of PathoLogic, the inference component of the Pathway Tools software. Pathway Tools is freely available to researchers at non-commercial institutions, including source code; a fee applies to commercial institutions.
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC2718656  PMID: 18586723
9.  Responding to infectious diseases in Burma and her border regions 
PMCID: PMC2374771  PMID: 18341693
10.  Prevalence of plasmodium falciparum in active conflict areas of eastern Burma: a summary of cross-sectional data 
Burma records the highest number of malaria deaths in southeast Asia and may represent a reservoir of infection for its neighbors, but the burden of disease and magnitude of transmission among border populations of Burma remains unknown.
Plasmodium falciparum (Pf) parasitemia was detected using a HRP-II antigen based rapid test (Paracheck-Pf®). Pf prevalence was estimated from screenings conducted in 49 villages participating in a malaria control program, and four retrospective mortality cluster surveys encompassing a sampling frame of more than 220,000. Crude odds ratios were calculated to evaluate Pf prevalence by age, sex, and dry vs. rainy season.
9,796 rapid tests were performed among 28,410 villagers in malaria program areas through four years (2003: 8.4%, 95% CI: 8.3 – 8.6; 2004: 7.1%, 95% CI: 6.9 – 7.3; 2005:10.5%, 95% CI: 9.3 – 11.8 and 2006: 9.3%, 95% CI: 8.2 – 10.6). Children under 5 (OR = 1.99; 95% CI: 1.93 – 2.06) and those 5 to 14 years (OR = 2.24, 95% CI: 2.18 – 2.29) were more likely to be positive than adults. Prevalence was slightly higher among females (OR = 1.04, 95% CI: 1.02 – 1.06) and in the rainy season (OR = 1.48, 95% CI: 1.16 – 1.88). Among 5,538 rapid tests conducted in four cluster surveys, 10.2% were positive (range 6.3%, 95% CI: 3.9 – 8.8; to 12.4%, 95% CI: 9.4 – 15.4).
Prevalence of plasmodium falciparum in conflict areas of eastern Burma is higher than rates reported among populations in neighboring Thailand, particularly among children. This population serves as a large reservoir of infection that contributes to a high disease burden within Burma and likely constitutes a source of infection for neighboring regions.
PMCID: PMC2034373  PMID: 17803819
11.  Responding to AIDS, Tuberculosis, Malaria, and Emerging Infectious Diseases in Burma: Dilemmas of Policy and Practice 
PLoS Medicine  2006;3(10):e393.
Beyrer and colleagues discuss infectious disease threats in Burma and suggest policy options for responding to them.
PMCID: PMC1592343  PMID: 17032061
12.  BioWarehouse: a bioinformatics database warehouse toolkit 
BMC Bioinformatics  2006;7:170.
This article addresses the problem of interoperation of heterogeneous bioinformatics databases.
We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research.
BioWarehouse embodies significant progress on the database integration problem for bioinformatics.
PMCID: PMC1444936  PMID: 16556315

Results 1-12 (12)