Projection Package Research Articles

POINCARÉ CODE: A package of open-source implements for normalization and computer algebra reduction near equilibria of coupled ordinary differential equations

Abstract The Poincare code is a Maple project package that aims to gather significant computer algebra normal form (and subsequent reduction) methods for handling nonlinear ordinary differential equations. As a first version, a set of fourteen easy-to-use Maple commands is introduced for symbolic creation of (improved variants of Poincare’s) normal forms as well as their associated normalizing transformations. The software is the implementation by the authors of carefully studied and followed up selected normal form procedures from the literature, including some authors’ contributions to the subject. As can be seen, joint-normal-form programs involving Lie-point symmetries are of special interest and are published in CPC Program Library for the first time, Hamiltonian variants being also very useful as they lead to encouraging results when applied, for example, to models from computational physics like Henon–Heiles. Program summary Program title: POINCARE Catalogue identifier: AEPJ_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEPJ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 7694 No. of bytes in distributed program, including test data, etc.: 597943 Distribution format: tar.gz Programming language: Maple V11. Computer: See specifications for running Maple V11 or above. Operating system: MS Windows. Classification: 4.3, 5, 16.9. Nature of problem: Computing structure-preserving normal forms near the origin for nonlinear vector fields. Solution method: 14 Maple commands are designed to compute various normal forms as well as their generating functions and associated normalizing transformations for nonlinear systems of ordinary differential equations, including Hamiltonian ones. Further reduction of these normal forms–in the presence of Lie-point symmetries–is also considered. All algorithms are based on Lie transform, thus leading to the structure-preserving normal forms in the sense that all properties that can be formulated in terms of graded Lie algebras are preserved. Restrictions: The semisimple part of the leading matrix about the origin (resp. the quadratic part in the Hamiltonian case) is assumed to be already taken into diagonal form (resp. canonical form) via a linear change of variables. In other words, the eigenvalues must be explicitly known. Unusual features: Further reduction of Poincare–Dulac normal form via the joint normal form commands, taking profitably Lie-point symmetries, is perhaps the main feature of the software. Besides, to the best of our knowledge, and except the Hamiltonian case, it seems that there is no CPC programs for computation of (structure-preserving) normal forms in the general case. Running time: Depends on the input data, mainly on system size, type of the leading matrix (semisimple or not), type of resonances, order of normalization and required options. Instantaneous for the provided examples.

Applications of the InChI in cheminformatics with the CDK and Bioclipse

BackgroundThe InChI algorithms are written in C++ and not available as Java library. Integration into software written in Java therefore requires a bridge between C and Java libraries, provided by the Java Native Interface (JNI) technology.ResultsWe here describe how the InChI library is used in the Bioclipse workbench and the Chemistry Development Kit (CDK) cheminformatics library. To make this possible, a JNI bridge to the InChI library was developed, JNI-InChI, allowing Java software to access the InChI algorithms. By using this bridge, the CDK project packages the InChI binaries in a module and offers easy access from Java using the CDK API. The Bioclipse project packages and offers InChI as a dynamic OSGi bundle that can easily be used by any OSGi-compliant software, in addition to the regular Java Archive and Maven bundles. Bioclipse itself uses the InChI as a key component and calculates it on the fly when visualizing and editing chemical structures. We demonstrate the utility of InChI with various applications in CDK and Bioclipse, such as decision support for chemical liability assessment, tautomer generation, and for knowledge aggregation using a linked data approach.ConclusionsThese results show that the InChI library can be used in a variety of Java library dependency solutions, making the functionality easily accessible by Java software, such as in the CDK. The applications show various ways the InChI has been used in Bioclipse, to enrich its functionality.

Projection of Human Immunodeficiency Virus among High-Risk Groups in Malaysia

Human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) presents a serious healthcare threat to young individuals in Malaysia and worldwide. This study aimed to identify trends in HIV-related risk behaviors among recognized high-risk groups and to estimate HIV transmission up to the year 2015. Data and necessary information were obtained from the Ministry of Health Malaysia, published reports from the World Health Organization and United Nations Program on HIV/AIDS, and other articles. The Estimation and Projection Package was used to estimate HIV transmission. The results of the present study revealed that within the high-risk groups, intravenous drug users (IDUs) had the highest prevalence rate of HIV transmission, followed by patients with sexually transmitted infections (STIs), female sex workers (SWs), and men who have sex with men (MSM). Within these at-risk populations, patients with STIs have the highest prevalence of HIV, followed by IDUs, MSM, and SWs. If the transmission rate continues to increase, the situation will worsen; therefore, there is an urgent need for a comprehensive prevention program to control HIV transmission in Malaysia.

Updates to the Spectrum/Estimation and Projection Package (EPP) model to estimate HIV trends for adults and children

BackgroundThe Spectrum and Estimation and Projection Package (EPP) programs are used to estimate key HIV indicators based on HIV surveillance and surveys, programme statistics and epidemic patterns. These indicators include...

Spline-based modelling of trends in the force of HIV infection, with application to the UNAIDS Estimation and Projection Package

ObjectiveWe previously developed a flexible specification of the UNAIDS Estimation and Projection Package (EPP) that relied on splines to generate time-varying values for the force of infection parameter. Here, we...

Multi-strategy budget allocation decision support system for seismic rehabilitation of road infrastructure

Economic efficiency is an important factor in seismic rehabilitation of road infrastructures. An inventory of structures is screened to identify seismically deficient parts and prioritise them in the order of need for rehabilitation purposes. In most cases, the financial resources for road infrastructure rehabilitation projects are limited. Therefore, there is a need to efficiently allocate resources to various projects. This article presents a multi-strategy decision support system (DSS) for seismic rehabilitation budget allocation across existing road infrastructures. This DSS employs a multi-criteria assessment module that takes into account different criteria to estimate the financial needs for rehabilitation and to establish an allocation methodology based on the available budget in a fiscal year. To select the optimal package of projects, a genetic algorithm (GA) optimisation module is developed. Multi-objective decision-making is conducted under a specific decision strategy (DS) by solving a (0–1) Knapsack problem. To demonstrate the applicability of the GA-based approach, a hypothetical decision-making problem is presented. The results reveal that the optimal package is more sensitive to the available budget and DS than to the weights of criteria and project scores. Using this system, managers can compare their decisions for different strategies and significantly improve management efficiency.

A new infectious disease model for estimating and projecting HIV/AIDS epidemics

ObjectivesAs the global HIV pandemic enters its fourth decade, countries have collected longer time series of surveillance data, and the AIDS-specific mortality has been substantially reduced by the increasing availability...

Modelling national HIV/AIDS epidemics: revised approach in the UNAIDS Estimation and Projection Package 2011

ObjectiveUnited Nations Programme on HIV/AIDS reports regularly on estimated levels and trends in HIV/AIDS epidemics, which are evaluated using an epidemiological model within the Estimation and Projection Package (EPP). The relatively simple four-parameter model of HIV incidence used in EPP through the previous round of estimates has encountered challenges when attempting to fit certain data series on prevalence over time, particularly in settings with long running epidemics where prevalence has increased recently. To address this, the most recent version of the modelling package (EPP 2011) includes a more flexible epidemiological model that allows HIV infection risk to vary over time. This paper describes the technical details of this flexible approach to modelling HIV transmission dynamics within EPP 2011.MethodologyFor the flexible modelling approach, the force of infection parameter, r, is allowed to vary over time through a random walk formulation, and an informative prior distribution is used to improve short-term projections beyond the last year of data. Model parameters are estimated using a Bayesian estimation approach in which models are fit to HIV seroprevalence data from surveillance sites.ResultsThis flexible model can yield better estimates of HIV prevalence over time in situations where the classic EPP model has difficulties, such as in Uganda, where prevalence is no longer falling. Based on formal out-of-sample projection tests, the flexible modelling approach also improves predictions and CIs for extrapolations beyond the last observed data point.ConclusionsWe recommend use of a flexible modelling approach where data are sufficient (eg, where at least 5 years of observations are available), and particularly where an epidemic is beyond its peak.

D6 Estimation and Projection of HIV Epidemic Among High-Risk Populations in Jilin Province, China

Background National HIV estimates for China are conflicting. Current estimates are 0.057% (Chinese government), 0.1% (UNAIDS). Objective: To estimate the number of people living with HIV/AIDS (PLWHA) in Jilin province, China, in 2009 and to analyze and project the HIV epidemic trend in the next five years (2010–2015), thereby providing evidence for targeted HIV prevention and control measures. Method Workbook method, Estimation and Projection Package and Asia Epidemic Model were used to estimate the number of individuals with HIV/AIDS and to project the HIV epidemic trend from 2010 to 2015 using data from sentinel surveillance, case reports, epidemiological surveys and scientific lectures. Results By the end of 2009, there were 4388 PLWHA in Jilin Province, with a provincial HIV prevalence rate of 0.024%. Over 50% of PLWHA were men who have sex with men (MSM). From 2010 to 2015, the HIV epidemic will rise markedly among MSM [from 2.96% (2010) to 7.45 (2015)], relatively rise slowly among injecting drug users (IDU) [4.75% (2010) to 6.40 (2015)], and slow down among female sex workers (FSW) [0.66% (2010) to 1.62 (2015)] and their clients [1.05% (2010) to 2.62 (2015)]. Conclusions The number of PLWHA in Jilin province (and China) will rise quickly in the next five years if intervention efforts are not intensified to thwart the spread of HIV and if stigma and discrimination against MSM is not stopped. There is need for targeted preventive interventions. There is need to sensitize health care workers and health care administrators on the importance of accurate reporting of HIV cases.

Application of Estimation and Projection Package and Spectrum to the Context of Australia’s HIV Epidemic

Objectives: Understanding and monitoring the HIV epidemic is essential for developing and evaluating public health responses. The Joint United Nations Programme on AIDS (UNAIDS) Estimation and Projection Package (EPP) and Spectrum have become a standard tool to interpret HIV surveillance systems in many settings, particularly in low- and middle-income countries where surveillance data is often based on serial cross-sectional prevalence studies and not on notifications. EPP has not previously been used to evaluate the HIV epidemic in Australia. We derived best HIV estimates using EPP and assumptions that reflect the current understanding of HIV epidemiology in Australia and compared derived estimates with independent estimates and estimates from mathematical models using backprojections method. Methods: The epidemic curves for different population groups (i.e., men who have sex with men, injecting drug users, and low-risk population) generated by EPP were combined with antiretroviral therapy (ART) data into a demographic projection model, Spectrum to determine the consequences of the HIV epidemic in Australia. Results: The overall pattern of the HIV epidemic was consistent with both independent estimates and backprojection modelling estimates. However, the number of HIV-infected females, AIDS-related deaths, and the number in need of ART estimated by EPP were approximately 3.7 times, 20 times, and 6.3 times, respectively higher than independent estimates based on our current surveillance system. EPP estimates of new HIV infections were, however, half the number of independent and back-projection estimates. Conclusions: These findings suggest that customized tools that are tailored to the unique epidemiology and surveillance mechanisms in each setting are required to enable effective programmatic response and policy.

Estimation and Projection of the HIV Epidemic Trend among the Migrant Population in China

The migrant population is a vulnerable group for HIV infection in China. Understanding potential epidemic trends among migrants is critical for developing HIV preventative measures in this population. The Estimation and Projection Package (EPP) model was used to process prefecture and county-level surveillance data to generate HIV prevalence and epidemic trends for migrant populations in China. The prevalence of HIV among migrants in 2009 was estimated at 0.075% (95% CI: 0.042%, 0.108%) in China. The HIV epidemic among migrants is likely to increase over the next 5 years, with the prevalence expected to reach 0.110% (95% CI: 0.070%, 0.150%) by 2015. Although the 2009 estimates for the HIV/AIDS epidemic in China indicate a slower rate of increase compared with the national HIV/AIDS epidemic, it is estimated to persistently increase among migrants over the next 5 years. Migrants will have a strong impact on the overall future of the HIV epidemic trend in China and evidence-based prevention and monitoring efforts should be expanded for this vulnerable population.

When does rigorous impact evaluation make a difference? The case of the Millennium Villages

When is the rigorous impact evaluation of development projects a luxury, and when a necessity? The authors study one high-profile case: the Millennium Villages Project (MVP), an experimental and intensive package intervention to spark sustained local economic development in rural Africa. They illustrate the benefits of rigorous impact evaluation in this setting by showing that estimates of the project's effects depend heavily on the evaluation method. Comparing trends at the MVP intervention sites in Kenya, Ghana, and Nigeria with trends in the surrounding areas yields much more modest estimates of the project's effects than the before-versus-after comparisons published thus far by the MVP. Neither approach constitutes a rigorous impact evaluation of the MVP, which is impossible to perform due to weaknesses in the evaluation design of the project's initial phase. These weaknesses include the subjective choice of intervention sites, the subjective choice of comparison sites, the lack of baseline data on comparison sites, the small sample size, and the short time horizon. The authors describe one of many ways that the next wave of the intervention could be designed to allow proper evaluation of the MVP's impact at little additional cost.

National estimate of HIV prevalence in the Netherlands: comparison and applicability of different estimation tools

to determine limitations and strengths of three methodologies developed to estimate HIV prevalence and the number of people living with HIV/AIDS (PLWHA). the UNAIDS/WHO Workbook method; the Multiparameter Evidence Synthesis (MPES) adopted by the Health Protection Agency; and the UNAIDS/WHO Estimation and Projection Package (EPP) and Spectrum method were used and their applicability and feasibility were assessed. All methods estimate the number infected in mutually exclusive risk groups among 15-70-year-olds. using data from the Netherlands, the Workbook method estimated 23 969 PLWHA as of January 2008. MPES estimated 21 444 PLWHA, with a 95% credible interval (CrI) of 17 204-28 694. Adult HIV prevalence was estimated at 0.2% (95% CrI 0.15-0.24%) and 40% (95% CrI 25-55%) were undiagnosed. Spectrum applied gender-specific mortality, resulting in a projected estimate of 19 115 PLWHA. although outcomes differed between the methods, they broadly concurred. An advantage of MPES is that the proportion diagnosed can be estimated by risk group, which is important for policy guidance. However, before MPES can be used on a larger scale, it should be made more easily applicable. If the aim is not only to obtain annual estimates, but also short-term projections, then EPP and Spectrum are more suitable. Research into developing and refining analytical tools, which make use of all available information, is recommended, especially HIV diagnosed cases, as this information is becoming routinely collected in most countries with concentrated HIV epidemics.

Institutional Actors, Learning and Agency

This article argues that conventional approaches to infrastructure reform in developing countries underestimate the agency of local actors and organisations in assisting small and medium-scale enterprises (SMEs) to surmount problems. It uses case study material based on Sialkot’s City Package Project to illustrate how state initiatives combined with SMEs’ efforts engendered a group-based coordination process for an endogenous solution to upgrade infrastructure. This process generated social benefits for the entire industrial district. By using ideas from the learning-centred approach, this article analyses the micro-processes and institutional arrangements of building state–SME relations for solving infrastructure problems. It concludes by reflecting on the need to rethink the strategic role of actors and institutions for SMEs’ infrastructure needs in industrial and regional development.

Using Estimation and Projection Package and Spectrum for Jamaica's national HIV estimates and targets

BackgroundAdequate coverage of target populations ensures that desired outcomes, such as increased survival of people living with HIV, are achieved. However, estimates of coverage and impact of HIV programmes using...

A stochastic infection rate model for estimating and projecting national HIV prevalence rates

BackgroundEvery 2 years, the Joint United Nations Programme on HIV/AIDS (UNAIDS) produces probabilistic estimates and projections of HIV prevalence rates for countries with generalised HIV/AIDS epidemics. To do this they...

The 2009 HIV and AIDS estimates and projections: methods, tools and analyses

Since 2004 we have provided detailed descriptions of the tools and assumptions used in generating HIV and AIDS estimates, as well as the data and analyses underpinning them.1–3 The UNAIDS...

The Spectrum projection package: improvements in estimating incidence by age and sex, mother-to-child transmission, HIV progression in children and double orphans

BackgroundThe Spectrum program is used to estimate key HIV indicators from the trends in incidence and prevalence estimated by the Estimation and Projection Package or the Workbook. These indicators include the number of people living with HIV, new infections, AIDS deaths, AIDS orphans, the number of adults and children needing treatment, the need for prevention of mother-to-child transmission and the impact of antiretroviral treatment on survival. The UNAIDS Reference Group on Estimates, Models and Projections regularly reviews new data and information needs, and recommends updates to the methodology and assumptions used in Spectrum.MethodsThe latest update to Spectrum was used in the 2009 round of global estimates. This update contains new procedures for estimating: the age and sex distribution of adult incidence, new child infections occurring around delivery or through breastfeeding, the survival of children by timing of infection and the number of double orphans.

Flexible epidemiological model for estimates and short-term projections in generalised HIV/AIDS epidemics

ObjectiveUNAIDS and country analysts use a simple infectious disease model, embedded in the Estimation and Projection Package (EPP), to generate annual updates on the global HIV/AIDS epidemic. Our objective was...

Derivation of parameters used in Spectrum for eligibility for antiretroviral therapy and survival on antiretroviral therapy

BackgroundThe Spectrum projection package uses estimates of national HIV incidence, demographic data and other assumptions to describe the consequences of the HIV epidemic in low and middle-income countries. The default...