Tests will be conducted on the same day as, and immediately before, assessments of parasitaemia and anemia. This will allow an analysis of the covariance between these biological indicators and ability to concentrate.

_Educational covariates_ : Recent analyses of large school-based cluster controlled trials (Raudenbush et al., 2007) demonstrates that power can be increased considerably through the assessment of an extensive range of covariates, including teacher and school characteristics and classroom behavior. These will be assessed in the current study as part of the behavioral and educational assessment battery. We will assess parental education and support for their children’s education, teacher’s levels of training, provision of textbooks, desks and other materials in the schools, and other socioeconomic covariates (Appendix 7). A subset of families will be selected to conduct further interviews about how literacy development is supported in the home.

# _Classroom Visits:_

The evaluation is interested in differences between teachers’ instructional behaviors that lead to better reading outcomes. With the teacher’s permission, we will video their classroom instruction while simultaneously observing. Each teacher will be observed several times with two instruments. The Stalling (Stallings, 1980) instrument codes the activities engaged in and materials used at multiple time points within one class period. The second instrument, the CLASSIC (Scanlon et al., 2003), assesses specific methods for literacy instruction. Following the lesson, the observer will meet with the teacher for about 30 minutes for a structured interview. The observations, videos, and interviews will support a more detailed analysis of how teachers’ behaviors differ and help our understanding of the ways teachers can influence their pupils’ reading acquisition.

_Cost benefit and effectiveness analysis:_ The evaluation will also examine the costs, cost-benefits and cost-effectiveness of IST in improving educational and health outcomes. The costs of IST will be assessed from both a provider’s and societal perspective. Both financial and opportunity costs will be evaluated using standardized methodologies **(** Drummond et al., 2005). In addition to estimating the rate of return to education, cost-benefit analysis will incorporate improved cognition and learning into the benefit streams (Jimenez & Patrinos, 2008). A comparison of and benefits of other education interventions in Kenya (e.g. Miguel & Kremer, 2004; Glewwe et al., 2004; Glewwe & Kremer, 2006) will also be undertaken. Cost per case of anemia will also be assessed.

_Process evaluation_ : This will aim to (i) investigate community acceptability of malaria intermittent screening and treatment; and (ii) document factors external to the intervention which might impact upon both its implementation and its effectiveness. Such an evaluation will help the interpretation of results and help inform future large-scale implementation of the intervention.

First, a modified stakeholder analysis approach will be adopted to identify and assess the importance of key people, or groups of people who are likely to affect the implementation and longer-term sustainability of the program (Steckler & Linnan, 2004; Varvasovszky & Brugha, 2000). Key stakeholders are likely to include: teachers, parents, children, community leaders, local health workers and education officers as well as individuals at provincial and central levels in the Ministries of Education and Health. Stakeholders from both intervention and control schools will be included in order to obtain views on the intervention, but also the acceptability of not immediately receiving the intervention. An assessment will be made of their importance to the success and sustainability of the program and data on their views about the program (e.g., expectations of the intervention, experiences of the intervention, acceptability of the approach, value to individuals & communities, impact on workload) will be collected through a series of focus group discussions as well as semi-structured interviews with people identified as key informants (Bernard, 2006). Discussions and interviews will be transcribed and translated, and content analysis using Nvivo 8 (QSR International, Melbourne, Australia) will be undertaken to identify themes based on people’s experience and involvement in the intervention.

Second, an analysis will be undertaken of the structural, organizational and management factors that enhance or constrain effective implementation of this and other school-based screening and treatment programs, for example, deworming and vitamin A, by staff from the Ministries of Health and Education. In addition to identifying and mapping these stakeholders through the stakeholder analysis, interviews will be conducted with purposefully selected key stakeholders in order to assess the organization and managerial capacities of the government at national and local levels (Jones et al., 2008). These data will be analyzed and interpreted iteratively based on implementation and organizational management theories (Damschroder et al. 2009) and the developed stakeholder analysis framework.

**x) Laboratory procedures**

Thick and thin blood smears will be stained with 2% Giemsa for 30 minutes and read by experienced laboratory technicians. Parasite densities will be calculated by counting the number of asexual parasites per 200 leukocytes (or per 500 leukocytes, if the count is <10 asexual parasites/200 leukocytes), assuming a leukocyte count of 8000/μl. A blood smear will be considered negative when the examination of 200 high power fields does not reveal asexual parasites. Thin smears will also be made for counting high parasitaemias. For quality control, all slides will be read by a second microscopist and a third reviewer will settle any discrepant readings.

Hemoglobin levels will be measured using a portable HemoCue photometer (HemoCue, Angelhom, Sweden).

Stool examinations will be conducted to determine the prevalence and intensity of intestinal nematodes, using the Kato-Katz method. Urine examinations will also be conducted to determine the prevalence and intensity of _Schistosoma haematobium_ , using the urine filtration method.

**xi) Sponsor** The sponsor of the study will be the London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.

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