Assessment of cognitive abilities in multiethnic countries: The case of the Wolof and Mandinka in the Gambia

Background: The use of cognitive tests is increasing in Africa but little is known about how such tests are affected by the great ethnic and linguistic diversity on the continent. Aim: To assess ethnic and linguistic group differences in cognitive test performance in the West African country of the Gambia and to investigate the sources of these differences. Samples: Study 1 included 579 participants aged 14–19 years from the Wolof and Mandinka ethnic groups of the Gambia. Study 2 included 41 participants aged 12–18 years from the two ethnic groups. Methods: Study 1 assessed performance on six cognitive tests. Participants were also asked about their history of education, residence in the city, parental education, and family socio-economic status. Study 2 assessed performance on two versions of the digit span test. Recall of the numbers 1–5 were compared with recall of numbers 1–9 for both the Wolof (who count in base 5) and the Mandinka (who count in base 10). Results: Study 1 established that Wolof performance was lower than that of the Mandinka on five out of six cognitive tests. In four of these tests, group differences were partially mediated by participation in primary school and migration to the city. Group differences were substantial for the digit span test and were not attenuated by mediating variables. Study 2 found that digit span among the Wolof was shorter than that of the Mandinka for numbers 1–9 but not for numbers 1–5. Conclusions: Several suggestions are made on how to consider the ethnicity, language, education, and residence (urban vs. rural) of groups when conducting comparative cognitive assessments or collecting normative data

“Respect is an Investment”: Community Perceptions of Social and Emotional Competencies in Early Childhood from Mtwara, Tanzania

Education programs in Africa increasingly aim to develop and measure social and emotional competencies. However, assessments are typically adapted from those developed in other continents and are not derived from local perspectives. In the current study, we conducted focus groups and individual interviews with teachers, parents and students in 4 randomly selected rural primary schools from Mtwara region in Tanzania, 3 of which had recently begun participation in a pre-primary education program. The aim was to understand the social and emotional competencies in early childhood that participants viewed as important for school and for life in general. Compared to existing frameworks of social and emotional competencies, participants placed more emphasis on aspects of social responsibility, for example respect, obedience and being an attentive listener. Individual competencies such as curiosity, self-direction and self-belief were valued more by teachers than parents and seen as most important for success at school. In general, most social and emotional competencies – even individual competencies - were discussed in terms of social relationships. Findings have implications for how cultural values are taken into account in assessment, curriculum design and parent and community engagement around pre-school education

Maximum principle and mutation thresholds for four-letter sequence evolution

A four-state mutation-selection model for the evolution of populations of DNA-sequences is investigated with particular interest in the phenomenon of error thresholds. The mutation model considered is the Kimura 3ST mutation scheme, fitness functions, which determine the selection process, come from the permutation-invariant class. Error thresholds can be found for various fitness functions, the phase diagrams are more interesting than for equivalent two-state models. Results for (small) finite sequence lengths are compared with those for infinite sequence length, obtained via a maximum principle that is equivalent to the principle of minimal free energy in physics.Comment: 25 pages, 16 figure

Nocardia kroppenstedtii sp. nov., a novel actinomycete isolated from a lung transplant patient with a pulmonary infection

An actinomycete, strain N1286T, isolated from a lung transplant patient with a pulmonary infection, was provisionally assigned to the genus Nocardia. The strain had chemotaxonomic and morphological properties typical of members of the genus Nocardia and formed a distinct phyletic line in the Nocardia 16S rRNA gene tree. It was most closely related to Nocardia farcinica DSM 43665T (99.8% gene similarity) but was distinguished from the latter by a low level of DNA:DNA relatedness. These strains were also distinguished by a broad range of phenotypic properties. On the basis of these data, it is proposed that isolate N1286T (=DSM 45810T = NCTC 13617T) should be classified as the type strain of a new Nocardia species for which the name Nocardia kroppenstedtii is proposed

Impact of intermittent screening and treatment for malaria among school children in Kenya: a cluster randomised trial.

BACKGROUND: Improving the health of school-aged children can yield substantial benefits for cognitive development and educational achievement. However, there is limited experimental evidence of the benefits of alternative school-based malaria interventions or how the impacts of interventions vary according to intensity of malaria transmission. We investigated the effect of intermittent screening and treatment (IST) for malaria on the health and education of school children in an area of low to moderate malaria transmission. METHODS AND FINDINGS: A cluster randomised trial was implemented with 5,233 children in 101 government primary schools on the south coast of Kenya in 2010-2012. The intervention was delivered to children randomly selected from classes 1 and 5 who were followed up for 24 months. Once a school term, children were screened by public health workers using malaria rapid diagnostic tests (RDTs), and children (with or without malaria symptoms) found to be RDT-positive were treated with a six dose regimen of artemether-lumefantrine (AL). Given the nature of the intervention, the trial was not blinded. The primary outcomes were anaemia and sustained attention. Secondary outcomes were malaria parasitaemia and educational achievement. Data were analysed on an intention-to-treat basis. During the intervention period, an average of 88.3% children in intervention schools were screened at each round, of whom 17.5% were RDT-positive. 80.3% of children in the control and 80.2% in the intervention group were followed-up at 24 months. No impact of the malaria IST intervention was observed for prevalence of anaemia at either 12 or 24 months (adjusted risk ratio [Adj.RR]: 1.03, 95% CI 0.93-1.13, p = 0.621 and Adj.RR: 1.00, 95% CI 0.90-1.11, p = 0.953) respectively, or on prevalence of P. falciparum infection or scores of classroom attention. No effect of IST was observed on educational achievement in the older class, but an apparent negative effect was seen on spelling scores in the younger class at 9 and 24 months and on arithmetic scores at 24 months. CONCLUSION: In this setting in Kenya, IST as implemented in this study is not effective in improving the health or education of school children. Possible reasons for the absence of an impact are the marked geographical heterogeneity in transmission, the rapid rate of reinfection following AL treatment, the variable reliability of RDTs, and the relative contribution of malaria to the aetiology of anaemia in this setting. TRIAL REGISTRATION: www.ClinicalTrials.gov NCT00878007

Stops making sense: translational trade-offs and stop codon reassignment

Background Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codons in the genetic code. Although genetic codes are highly constrained, stop codon number appears to be their most volatile feature. Results In the human genome, codons readily mutable to stops are underrepresented in coding sequences. We construct a simple mathematical model based on the relative likelihoods of premature termination and readthrough. When readthrough occurs, the resultant protein has a tail of amino acid residues incorrectly added to the C-terminus. Our results depend strongly on the number of stop codons in the genetic code. When the code has more stop codons, premature termination is relatively more likely, particularly for longer genes. When the code has fewer stop codons, the length of the tail added by readthrough will, on average, be longer, and thus more deleterious. Comparative analysis of taxa with a range of stop codon numbers suggests that genomes whose code includes more stop codons have shorter coding sequences. Conclusions We suggest that the differing trade-offs presented by alternative genetic codes may result in differences in genome structure. More speculatively, multiple stop codons may mitigate readthrough, counteracting the disadvantage of a higher rate of nonsense mutation. This could help explain the puzzling overrepresentation of stop codons in the canonical genetic code and most variants

Active flow control systems architectures for civil transport aircraft

Copyright @ 2010 American Institute of Aeronautics and AstronauticsThis paper considers the effect of choice of actuator technology and associated power systems architecture on the mass cost and power consumption of implementing active flow control systems on civil transport aircraft. The research method is based on the use of a mass model that includes a mass due to systems hardware and a mass due to the system energy usage. An Airbus A320 aircraft wing is used as a case-study application. The mass model parameters are based on first-principle physical analysis of electric and pneumatic power systems combined with empirical data on system hardware from existing equipment suppliers. Flow control methods include direct fluidic, electromechanical-fluidic, and electrofluidic actuator technologies. The mass cost of electrical power distribution is shown to be considerably less than that for pneumatic systems; however, this advantage is reduced by the requirement for relatively heavy electrical power management and conversion systems. A tradeoff exists between system power efficiency and the system hardware mass required to achieve this efficiency. For short-duration operation the flow control solution is driven toward lighter but less power-efficient systems, whereas for long-duration operation there is benefit in considering heavier but more efficient systems. It is estimated that a practical electromechanical-fluidic system for flow separation control may have a mass up to 40% of the slat mass for a leading-edge application and 5% of flap mass for a trailing-edge application.This work is funded by the Sixth European Union Framework Programme as part of the AVERT project (Contract No. AST5-CT-2006-030914

Developing and applying heterogeneous phylogenetic models with XRate

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART .Comment: 34 pages, 3 figures, glossary of XRate model terminolog

Fast computation of distance estimators

BACKGROUND: Some distance methods are among the most commonly used methods for reconstructing phylogenetic trees from sequence data. The input to a distance method is a distance matrix, containing estimated pairwise distances between all pairs of taxa. Distance methods themselves are often fast, e.g., the famous and popular Neighbor Joining (NJ) algorithm reconstructs a phylogeny of n taxa in time O(n(3)). Unfortunately, the fastest practical algorithms known for Computing the distance matrix, from n sequences of length l, takes time proportional to l·n(2). Since the sequence length typically is much larger than the number of taxa, the distance estimation is the bottleneck in phylogeny reconstruction. This bottleneck is especially apparent in reconstruction of large phylogenies or in applications where many trees have to be reconstructed, e.g., bootstrapping and genome wide applications. RESULTS: We give an advanced algorithm for Computing the number of mutational events between DNA sequences which is significantly faster than both Phylip and Paup. Moreover, we give a new method for estimating pairwise distances between sequences which contain ambiguity Symbols. This new method is shown to be more accurate as well as faster than earlier methods. CONCLUSION: Our novel algorithm for Computing distance estimators provides a valuable tool in phylogeny reconstruction. Since the running time of our distance estimation algorithm is comparable to that of most distance methods, the previous bottleneck is removed. All distance methods, such as NJ, require a distance matrix as input and, hence, our novel algorithm significantly improves the overall running time of all distance methods. In particular, we show for real world biological applications how the running time of phylogeny reconstruction using NJ is improved from a matter of hours to a matter of seconds

Factors Associated with Access to Immunotherapy and Its Impact on Survival in Mucosal Melanoma

Mucosal melanoma is rare, comprising only 1.4% of all melanomas in the United States. Yet it is associated with a worse prognosis compared to cutaneous melanoma due to aggressive biology and advanced stage at diagnosis with a reported 5-year survival rate of less than 30%. Although there are no established guidelines for the treatment of mucosal melanoma, immunotherapy has been increasingly used for the management of advanced mucosal melanoma