Gene Context Analysis in the Integrated Microbial Genomes (IMG) Data Management System

Computational methods for determining the function of genes in newly sequenced genomes have been traditionally based on sequence similarity to genes whose function has been identified experimentally. Function prediction methods can be extended using gene context analysis approaches such as examining the conservation of chromosomal gene clusters, gene fusion events and co-occurrence profiles across genomes. Context analysis is based on the observation that functionally related genes are often having similar gene context and relies on the identification of such events across phylogenetically diverse collection of genomes. We have used the data management system of the Integrated Microbial Genomes (IMG) as the framework to implement and explore the power of gene context analysis methods because it provides one of the largest available genome integrations. Visualization and search tools to facilitate gene context analysis have been developed and applied across all publicly available archaeal and bacterial genomes in IMG. These computations are now maintained as part of IMG''s regular genome content update cycle. IMG is available at: http://img.jgi.doe.gov.     

The Cultural Context of Health, Illness, and Medicine

The Cultural Context of Health, Illness, and Medicine. Martha O. Loustaunau and Elisa J. Sobo. Westport, CT: Begin & Garvey, 1997. 222 pp.     

Cost Effectiveness of Implementing Integrated Management of Neonatal and Childhood Illnesses Program in District Faridabad,India

Introduction

Despite the evidence for preventing childhood morbidity and mortality, financial resources are cited as a constraint for Governments to scale up the key health interventions in some countries. We evaluate the cost effectiveness of implementing IMNCI program in India from a health system and societal perspective.

Methods

We parameterized a decision analytic model to assess incremental cost effectiveness of IMNCI program as against routine child health services for infant population at district level in India. Using a 15-years time horizon from 2007 to 2022, we populated the model using data on costs and effects as found from a cluster-randomized trial to assess effectiveness of IMNCI program in Haryana state. Effectiveness was estimated as reduction in infant illness episodes, deaths and disability adjusted life years (DALY). Incremental cost per DALY averted was used to estimate cost effectiveness of IMNCI. Future costs and effects were discounted at a rate of 3%. Probabilistic sensitivity analysis was undertaken to estimate the probability of IMNCI to be cost effective at varying willingness to pay thresholds.

Results

Implementation of IMNCI results in a cumulative reduction of 57384 illness episodes, 2369 deaths and 76158 DALYs among infants at district level from 2007 to 2022. Overall, from a health system perspective, IMNCI program incurs an incremental cost of USD 34.5 (INR 1554) per DALY averted, USD 34.5 (INR 1554) per life year gained, USD 1110 (INR 49963) per infant death averted. There is 90% probability for ICER to be cost effective at INR 2300 willingness to pay, which is 5.5% of India’s GDP per capita. From a societal perspective, IMNCI program incurs an additional cost of USD 24.1 (INR 1082) per DALY averted, USD 773 (INR 34799) per infant death averted and USD 26.3 (INR 1183) per illness averted in during infancy.

Conclusion

IMNCI program in Indian context is very cost effective and should be scaled-up as a major child survival strategy.     

Influenza Illness among Case-Patients Hospitalized for Suspected Dengue,El Salvador, 2012

We estimate the proportion of patients hospitalized for suspected dengue that tested positive for influenza virus in El Salvador during the 2012 influenza season. We tested specimens from 321 hospitalized patients: 198 patients with SARI and 123 patients with suspected dengue. Among 121 hospitalized suspected dengue (two co-infected excluded) patients, 28% tested positive for dengue and 19% positive for influenza; among 35 with suspected dengue and respiratory symptoms, 14% were positive for dengue and 39% positive for influenza. One percent presented co-infection between influenza and dengue. Clinicians should consider the diagnosis of influenza among patients with suspected dengue during the influenza season.     

Day-to-Day Population Movement and the Management of Dengue Epidemics

Dengue is a growing public health problem in tropical and subtropical cities. It is transmitted by mosquitoes, and the main strategy for epidemic prevention and control is insecticide fumigation. Effective management is, however, proving elusive. People’s day-to-day movement about the city is believed to be an important factor in the epidemiological dynamics. We use a simple model to examine the fundamental roles of broad demographic and spatial structures in epidemic initiation, growth and control. We show that the key factors are local dilution, characterised by the vector–host ratio, and spatial connectivity, characterised by the extent of habitually variable movement patterns. Epidemic risk in the population is driven by the demographic groups that frequent the areas with the highest vector–host ratio, even if they only spend some of their time there. Synchronisation of epidemic trajectories in different demographic groups is governed by the vector–host ratios to which they are exposed and the strength of connectivity. Strategies for epidemic prevention and management may be made more effective if they take into account the fluctuating landscape of transmission intensity associated with spatial heterogeneity in the vector–host ratio and people’s day-to-day movement patterns.     

Community Involvement in Dengue Outbreak Control: An Integrated Rigorous Intervention Strategy

BackgroundAn explosive outbreak of dengue fever occurred in Guangdong Province, China in 2014. A community-based integrated intervention was applied to control this outbreak in the capital city Guangzhou, where dengue epidemic was mainly caused by imported cases.ConclusionsThis study suggests that an integrated dengue intervention program has significant effects to control a dengue outbreak in areas where dengue epidemic was mainly caused by imported dengue cases.     

Management of Ingested Foreign Bodies in Childhood

A total of 660 patients with ingested foreign bodies admitted to the general surgical services in two children''s hospitals in Liverpool are reviewed. Endoscopic removal (205 cases) is recommended for all foreign objects impacted in the oesophagus, with the exception of rounded or blunt objects in the lower third, which should be observed for a maximum of 12 hours. The indications for laparotomy for removal of a foreign body (43 cases, 6·5%) are the danger of perforation and failure of progression. The ingestion of a long slender object—for example a hair-grip—in a child under 2 years of age, is an absolute indication for prophylactic operative removal owing to the high incidence of impaction and perforation of the duodenum.     

Associations of Different Phenotypes of Wheezing Illness in Early Childhood with Environmental Variables Implicated in the Aetiology of Asthma

Rationale

Asthma is a complex heterogeneous disease that has increased in prevalence in many industrialised countries. However, the causes of asthma inception remain elusive. Consideration of sub-phenotypes of wheezing may reveal important clues to aetiological risk factors.

Methods

Longitudinal phenotypes capturing population heterogeneity in wheezing reports from birth to 7 years were derived using latent class analysis in the Avon Longitudinal Study of Parents and Children (ALSPAC). Probability of class membership was used to examine the association between five wheezing phenotypes (transient early, prolonged early, intermediate-onset, late-onset, persistent) and early life risk factors for asthma.

Results

Phenotypes had similar patterns and strengths of associations with early environmental factors. Comparing transient early with prolonged early wheezing showed a similar pattern of association with most exposure variables considered in terms of the direction of the effect estimates but with prolonged early wheezing tending to have stronger associations than transient early wheezing except for parity and day care attendance.

Conclusions

Associations with early life risk factors suggested that prolonged early wheeze might be a severe form of transient early wheezing. Although differences were found in the associations of early life risk factors with individual phenotypes, these did not point to novel aetiological pathways. Persistent wheezing phenotype has features suggesting overlap of early and late-onset phenotypes.     

Ecosystem Management in the Context of Large, Infrequent Disturbances

Large, infrequent disturbances (LIDs) can have significant impacts yet seldom are included in management plans. Although this neglect may stem from relative unfamiliarity with a kind of event that rarely occurs in the experience or jurisdiction of individual managers, it may also reflect the assumption that LIDs are so large and powerful as to be beyond the ability of managers to affect. However, some LIDs can be affected by management, and for many of those that cannot be affected, the resilience or recovery of the system disrupted by the disturbance can be influenced to meet management goals. Such results can be achieved through advanced planning that allows for LIDs, whether caused by natural events, human activities, or a combination of the two. Management plans for LIDs may adopt a variety of goals, depending on the nature of the system and the nature of the anticipated disturbance regime. Managers can choose to influence (a) the system prior to the disturbance, (b) the disturbance itself, (c) the system after the disturbance, or (d) the recovery process. Prior to the disturbance, the system can be managed in ways that alter its vulnerability or change how it will respond to a disturbance. The disturbance can be managed through no action, preventive measures, or manipulations that can affect the intensity or frequency of the disturbance. Recovery efforts can focus on either managing the state of the system immediately after the disturbance or managing the ongoing process of recovery. This review of the management implications of LIDs suggests that management actions should be tailored to particular disturbance characteristics and management goals. Management actions should foster survival of residuals and spatial heterogeneity that promote the desired recovery pattern and process. Most importantly, however, management plans need to recognize LIDs and include the potential for such disturbances to occur. Received 14 July 1998; accepted 16 September 1998     

Nation-Wide,Web-Based,Geographic Information System for the Integrated Surveillance and Control of Dengue Fever in Mexico

Dengue fever incidence and its geographical distribution are increasing throughout the world. Quality and timely information is essential for its prevention and control. A web based, geographically enabled, dengue integral surveillance system (Dengue-GIS) was developed for the nation-wide collection, integration, analysis and reporting of geo-referenced epidemiologic, entomologic, and control interventions data. Consensus in the design and practical operation of the system was a key factor for its acceptance. Working with information systems already implemented as a starting point facilitated its acceptance by officials and operative personnel. Dengue-GIS provides the geographical detail needed to plan, asses and evaluate the impact of control activities. The system is beginning to be adopted as a knowledge base by vector control programs. It is used to generate evidence on impact and cost-effectiveness of control activities, promoting the use of information for decision making at all levels of the vector control program. Dengue-GIS has also been used as a hypothesis generator for the academic community. This GIS-based model system for dengue surveillance and the experience gathered during its development and implementation could be useful in other dengue endemic countries and extended to other infectious or chronic diseases.     

Sustained Reduction of the Dengue Vector Population Resulting from an Integrated Control Strategy Applied in Two Brazilian Cities

Aedes aegypti has developed evolution-driven adaptations for surviving in the domestic human habitat. Several trap models have been designed considering these strategies and tested for monitoring this efficient vector of Dengue. Here, we report a real-scale evaluation of a system for monitoring and controlling mosquito populations based on egg sampling coupled with geographic information systems technology. The SMCP-Aedes, a system based on open technology and open data standards, was set up from March/2008 to October/2011 as a pilot trial in two sites of Pernambuco -Brazil: Ipojuca (10,000 residents) and Santa Cruz (83,000), in a joint effort of health authorities and staff, and a network of scientists providing scientific support. A widespread infestation by Aedes was found in both sites in 2008–2009, with 96.8%–100% trap positivity. Egg densities were markedly higher in SCC than in Ipojuca. A 90% decrease in egg density was recorded in SCC after two years of sustained control pressure imposed by suppression of >7,500,000 eggs and >3,200 adults, plus larval control by adding fishes to cisterns. In Ipojuca, 1.1 million mosquito eggs were suppressed and a 77% reduction in egg density was achieved. This study aimed at assessing the applicability of a system using GIS and spatial statistic analysis tools for quantitative assessment of mosquito populations. It also provided useful information on the requirements for reducing well-established mosquito populations. Results from two cities led us to conclude that the success in markedly reducing an Aedes population required the appropriate choice of control measures for sustained mass elimination guided by a user-friendly mosquito surveillance system. The system was able to support interventional decisions and to assess the program’s success. Additionally, it created a stimulating environment for health staff and residents, which had a positive impact on their commitment to the dengue control program.     

The Recognition of and Care Seeking Behaviour for Childhood Illness in Developing Countries: A Systematic Review

Background

Pneumonia, diarrhoea, and malaria are among the leading causes of death in children. These deaths are largely preventable if appropriate care is sought early. This review aimed to determine the percentage of caregivers in low- and middle-income countries (LMICs) with a child less than 5 years who were able to recognise illness in their child and subsequently sought care from different types of healthcare providers.

Methods and Findings

We conducted a systematic literature review of studies that reported recognition of, and/or care seeking for episodes of diarrhoea, pneumonia or malaria in LMICs. The review is registered with PROSPERO (registration number: CRD42011001654). Ninety-one studies met the inclusion criteria. Eighteen studies reported data on caregiver recognition of disease and seventy-seven studies on care seeking. The median sensitivity of recognition of diarrhoea, malaria and pneumonia was low (36.0%, 37.4%, and 45.8%, respectively). A median of 73.0% of caregivers sought care outside the home. Care seeking from community health workers (median: 5.4% for diarrhoea, 4.2% for pneumonia, and 1.3% for malaria) and the use of oral rehydration therapy (median: 34%) was low.

Conclusions

Given the importance of this topic to child survival programmes there are few published studies. Recognition of diarrhoea, malaria and pneumonia by caregivers is generally poor and represents a key factor to address in attempts to improve health care utilisation. In addition, considering that oral rehydration therapy has been widely recommended for over forty years, its use remains disappointingly low. Similarly, the reported levels of care seeking from community health workers in the included studies are low even though global action plans to address these illnesses promote community case management. Giving greater priority to research on care seeking could provide crucial evidence to inform child mortality programmes.     

Environmental Risk Management Decision-Making in a Societal Context

Recent studies point to the need for improved understanding of environmental management frameworks designed to combine qualitative public and quantitative technical inputs in decision-making processes. Flux in public perception and concern about risks imply frameworks must be iterative in nature and incorporate a variety of assessment triggers in the form of decision points. A conceptual model is proposed here to explain the de facto operation of standard risk analytic frameworks within the broader sociopolitical milieu of public policy. The model is presented as a decision flow diagram that emphasizes setting environmental management goals based on societal input and the formulation of decision criteria for selecting management actions to achieve those goals. Prospective and retrospective decision control points operate to select management options that, respectively, avoid or reduce actual or predicted effects. Feedback loops that modify risk management outcomes are identified. Technical and scientific inputs (i.e., risk analysis) are assigned an essential information role within the framework and are responsible for informing the management process with the results of appropriately conducted and reviewed investigations. The proposed model is intended primarily to indicate how environmental risk management decision-making and associated technical assessments may be influenced by social pressures. It is hoped this understanding will lead to analytical transparency and better public communication of the environmental implications of policy options.