6543991
Rubabel: wrapping open Babel with Ruby
BackgroundThe number and diversity of wrappers for chemoinformatic toolkits suggests the diverse needs of the chemoinformatic community. While existing chemoinformatics libraries provide a broad range of utilities, many chemoinformaticians find compiled language libraries intimidating, time-consuming, arcane, and verbose. Although high-level language wrappers have been implemented, more can be done to leverage the intuitiveness of object-orientation, the paradigms of high-level languages, and the extensibility of languages such as Ruby. We introduce Rubabel, an intuitive, object-oriented suite of functionality that substantially increases the accessibily of the tools in the Open Babel chemoinformatics library.ResultsRubabel requires fewer lines of code than any other actively developed wrapper, providing better object organization and navigation, and more intuitive object behavior than extant solutions. Moreover, Rubabel provides a convenient interface to the many extensions currently available in Ruby, greatly streamlining otherwise onerous tasks such as creating web applications that serve up Rubabel functionality.ConclusionsRubabel is powerful, intuitive, concise, freely available, cross-platform, and easy to install. We expect it to be a platform of choice for new users, Ruby users, and some users of current solutions.
2304899
Controlling for confounding variables in MS-omics protocol: why modularity matters
As the field of bioinformatics research continues to grow, more and more novel techniques are proposed to meet new challenges and improvements upon solutions to long-standing problems. These include data processing techniques and wet lab protocol techniques. Although the literature is consistently thorough in experimental detail and variable-controlling rigor for wet lab protocol techniques, bioinformatics techniques tend to be less described and less controlled. As the validation or rejection of hypotheses rests on the experiment's ability to isolate and measure a variable of interest, we urge the importance of reducing confounding variables in bioinformatics techniques during mass spectrometry experimentation.
27343241
Novel algorithms and the benefits of comparative validation
Contact: 2robsmith@gmail.com, jtprince@chem.byu.edu Bioinformatic research has produced a large volume of proposed algorithmic solutions to a host of problems. Whether presented as a processing step in a clinical experiment or treated in a stand-alone publication, novel bioinformatic algorithms are often not subjected to the thorough comparative evaluation endured by their counterparts in other closely related fields—such as computer science—where an algorithm unevaluated against extant methods is considered unpublishable. Two audiences are interested in algorithmic publications: the practitioner, who may use the algorithm, and the researcher, who will work to develop solutions superior to those extant. We argue that failure during the review/publication process to require comparative evaluation for novel algorithms is detrimental to both parties. To demonstrate the dilemma, we conducted a case study of novel LC-MS alignment algorithms. Of the 48 publications from 2001 to 2012 that present alignment algorithms of which we are aware, 60% include no comparison to other methods. Another 20%
15927414
LC-MS alignment in theory and practice: a comprehensive algorithmic review
Liquid chromatography-mass spectrometry is widely used for comparative replicate sample analysis in proteomics, lipidomics and metabolomics. Before statistical comparison, registration must be established to match corresponding analytes from run to run. Alignment, the most popular correspondence approach, consists of constructing a function that warps the content of runs to most closely match a given reference sample. To date, dozens of correspondence algorithms have been proposed, creating a daunting challenge for practitioners in algorithm selection. Yet, existing reviews have highlighted only a few approaches. In this review, we describe 50 correspondence algorithms to facilitate practical algorithm selection. We elucidate the motivation for correspondence and analyze the limitations of current approaches, which include prohibitive runtimes, numerous user parameters, model limitations and the need for reference samples. We suggest and describe a paradigm shift for overcoming current correspondence limitations by building on known liquid chromatography-mass spectrometry behavior.
13856154
Macroeconomic impact of pandemic influenza and associated policies in Thailand, South Africa and Uganda
BACKGROUND
Research has shown the value of conducting a macroeconomic analysis of the impact of influenza pandemics. However, previous modelling applications focus on high-income countries, and there is a lack of evidence concerning the potential impact of an influenza pandemic on lower- and middle-income countries.


OBJECTIVES
To estimate the macroeconomic impact of pandemic influenza in Thailand, South Africa and Uganda with particular reference to pandemic (H1N1) 2009.


METHODS
A single-country whole-economy Computable General Equilibrium (CGE) model was set up for each of the three countries in question and used to estimate the economic impact of declines in labour attributable to morbidity, mortality and school closure.


RESULTS
Overall GDP impacts were less than 1% of GDP for all countries and scenarios. Uganda's losses were proportionally larger than those of Thailand and South Africa. Labour-intensive sectors suffer the largest losses.


CONCLUSION
The economic cost of unavoidable absence in the event of an influenza pandemic could be proportionally larger for low-income countries. The cost of mild pandemics, such as pandemic (H1N1) 2009, appears to be small, but could increase for more severe pandemics and/or pandemics with greater behavioural change and avoidable absence.
15592441
Genomics knowledge and equity: a global public goods perspective of the patent system.
Genomics, the comprehensive examination of an organism's entire set of genes and their interactions, will have a major impact on the way disease is diagnosed, prevented and treated in the new millennium. Despite the tremendous potential it holds for improving global health, genomics challenges policy-makers to ensure that its benefits are harnessed equitably across populations and nations. The classification of genomics as a global public good and the inequity encountered in the development and application of genomics knowledge are outlined in this paper, We examine the effect of the current patent system on the distribution of costs and benefits relating to genomics knowledge between countries of different economic strength. The global public goods concept provides a normative economic rationale for the modification of certain aspects of the current patent system and for the creation of complementary mechanisms to respond to the health needs of low-income and middle-income countries.
205696369
Impact of HIV severity on cognitive and adaptive functioning during childhood and adolescence.
BACKGROUND
The influence of disease severity on cognitive and adaptive functioning in perinatally HIV-infected youth with (PHIV+/C) and without (PHIV+/NoC) a previous AIDS-defining illness (Centers for Disease Control and Prevention Class C event), compared with perinatally HIV-exposed but uninfected youth (PHEU) is not well understood.


METHODS
This was a cross-sectional analysis of cognitive and adaptive functioning in PHIV+/C (n = 88), PHIV+/NoC (n = 270) and PHEU (n = 200) youth aged 7-16 years, from a multisite prospective cohort study. Youth and caregivers completed the Wechsler Intelligence Scale for Children, Fourth Edition and the Adaptive Behavior Assessment System, Second Edition, respectively. We compared means and rates of impairment between groups, and examined associations with other psychosocial factors.


RESULTS
Overall mean scores on measures of cognitive and adaptive functioning were in the low average range for all 3 groups. After adjustment for covariates, mean full-scale intelligence quotient scores were significantly lower for the PHIV+/C group than the PHIV+/NoC and PHEU groups (mean = 77.8 versus 83.4 and 83.3, respectively), whereas no significant differences were observed between the PHEU and PHIV+/NoC groups in any domain. Lower cognitive performance for the PHIV+/C group was primarily attributable to a prior diagnosis of encephalopathy. No significant differences between groups were observed in adaptive functioning.


CONCLUSION
For long-term survivors, youth with HIV infection and a prior Centers for Disease Control and Prevention Class C event have higher risk for cognitive but not adaptive impairment regardless of current health status; this finding appears attributable to a previous diagnosis of encephalopathy. Early preventive therapy may be critical in reducing risk of later neurodevelopmental impairments.
11455466
Trade and health: an agenda for action
The processes of contemporary globalisation are creating ever-closer ties between individuals and populations across different countries. The health of a population, and the systems in place to deliver health care, are affected increasingly by factors beyond the population and health system. The Lancet's Series on trade and health has provided an overview of these links between international trade, trade liberalisation, and health, and raised the key issues that face the health community. In this final paper in the Series, we call for a substantial and sustained effort by those within the health profession to engage with issues of trade, to strengthen institutional capacity in this area, and to place health higher on the agenda of trade negotiations. The rapid rise of trade agreements and treaties, as well as trade that occurs beyond these institutional boundaries, means that further action is required by a range of actors, including WHO, the World Bank, the World Trade Organization (WTO), regional agencies, foundations, national governments, civil society, non-governmental organisations, and academics. The stewardship of a domestic health system in the 21st century requires a sophisticated understanding of how trade affects, and will affect, a country's health system and policy, to optimise opportunities to benefit health and health care while minimising the risks posed though the assertion of health goals in trade policy. To acheive this will place a premium on all those engaged in health to understand the importance of trade and to engage with their counterparts involved in trade and trade policy. We hope that this Series has prompted the reader to become involved in these efforts.
44367961
Recent advances in understanding the endocrinology of human birth
The timing of human birth has a crucial impact upon the survival of the fetus. New knowledge on the regulation of human birth includes the role of endogenous retroviruses in the formation of the syncytiotrophoblast cells and consequently the secretion of corticotrophin releasing hormone, a hormone linked to gestational length determination. miRNAs have been identified that mediate progesterone withdrawal at labor by suppressing progesterone-induced transcription factors. Progress has also been made in understanding how the contractile machinery of the uterine myocytes is activated at labor and the role of small heat-shock proteins in this process. From this work, new therapeutic targets have been identified that may be used to regulate the onset of labor and improve neonatal mortality.