HARVESTMAN: a framework for hierarchical feature learning and selection from whole genome sequencing data.

BACKGROUND: Supervised learning from high-throughput sequencing data presents many challenges. For one, the curse of dimensionality often leads to overfitting as well as issues with scalability. This can bring about inaccurate models or those that require extensive compute time and resources. Additionally, variant calls may not be the optimal encoding for a given learning task, which also contributes to poor predictive capabilities. To address these issues, we present HARVESTMAN, a method that takes advantage of hierarchical relationships among the possible biological interpretations and representations of genomic variants to perform automatic feature learning, feature selection, and model building. RESULTS: We demonstrate that HARVESTMAN scales to thousands of genomes comprising more than 84 million variants by processing phase 3 data from the 1000 Genomes Project, one of the largest publicly available collection of whole genome sequences. Using breast cancer data from The Cancer Genome Atlas, we show that HARVESTMAN selects a rich combination of representations that are adapted to the learning task, and performs better than a binary representation of SNPs alone. We compare HARVESTMAN to existing feature selection methods and demonstrate that our method is more parsimonious-it selects smaller and less redundant feature subsets while maintaining accuracy of the resulting classifier. CONCLUSION: HARVESTMAN is a hierarchical feature selection approach for supervised model building from variant call data. By building a knowledge graph over genomic variants and solving an integer linear program , HARVESTMAN automatically and optimally finds the right encoding for genomic variants. Compared to other hierarchical feature selection methods, HARVESTMAN is faster and selects features more parsimoniously.

How countries can reduce child stunting at scale: lessons from exemplar countries.

BACKGROUND: Child stunting and linear growth faltering have declined over the past few decades and several countries have made exemplary progress. OBJECTIVES: To synthesize findings from mixed methods studies of exemplar countries to provide guidance on how to accelerate reduction in child stunting. METHODS: We did a qualitative and quantitative synthesis of findings from existing literature and 5 exemplar country studies (Nepal, Ethiopia, Peru, Kyrgyz Republic, Senegal). Methodology included 4 broad research activities: 1) a series of descriptive analyses of cross-sectional data from demographic and health surveys and multiple indicator cluster surveys; 2) multivariable analysis of quantitative drivers of change in linear growth; 3) interviews and focus groups with national experts and community stakeholders and mothers; and 4) a review of policy and program evolution related to nutrition. RESULTS: Several countries have dramatically reduced child stunting prevalence, with or without closing geographical, economic, and other population inequalities. Countries made progress through interventions from within and outside the health sector, and despite significant heterogeneity and differences in context, contributions were comparable from health and nutrition sectors (40% of change) and other sectors (50%), previously called nutrition-specific and -sensitive strategies. Improvements in maternal education, maternal nutrition, maternal and newborn care, and reductions in fertility/reduced interpregnancy intervals were strong contributors to change. A roadmap to reducing child stunting at scale includes several steps related to diagnostics, stakeholder consultations, and implementing direct and indirect nutrition interventions related to the health sector and nonhealth sector . CONCLUSIONS: Our results show that child stunting reduction is possible even in diverse and challenging contexts. We propose that our framework of organizing nutrition interventions as direct/indirect and inside/outside the health sector should be considered when mapping causal pathways of child stunting and planning interventions and strategies to accelerate stunting reduction to achieve the 2030 Sustainable Development Goals.

Thermochromic Polymer Film Sensors for Detection of Incipient Thermal Damage in Carbon Fiber⁻Epoxy Composites.

Carbon fiber⁻epoxy composites have become prevalent in the aerospace industry where mechanical properties and light weight are at a premium. The significant non-destructive evaluation challenges of composites require new solutions, especially in detecting early-stage, or incipient, thermal damage. The initial stages of thermal damage are chemical rather than physical, and can cause significant reduction in mechanical properties well before physical damage becomes detectable in ultrasonic testing. Thermochromic fluorescent probe molecules have the potential to sense incipient thermal damage more accurately than traditional inspection methods. We have designed a molecule which transitions from a colorless, non-fluorescent state to a colorful, highly fluorescent state when exposed to temperature⁻time combinations that can cause damage in composites. Moreover, this molecule can be dispersed in a polymer film and attached to composite parts as a removable sensor. This work presents an evaluation of the sensor performance of this thermochromic film in comparison to ultrasonic C-scan as a method to detect incipient thermal damage in one of the most widely used carbon fiber⁻epoxy composite systems. Composite samples exposed to varying thermal exposures were used to evaluate the fluorescent thermal sensor films, and the results are compared to the results of ultrasonic imaging and short-beam shear tests for interlaminar shear strength.

Coverage and Utilization in Food Fortification Programs: Critical and Neglected Areas of Evaluation.

The need for evidence to inform nutrition program design and implementation has long been recognized, yet the generation and use of evidence for program decision making has lagged. The results of the coverage surveys reported in this supplement highlight some of the strengths and areas for improvement of current population-based (i.e., staple foods and condiments) and targeted (e.g., foods for infants and young children) fortification programs. Among other topics, the results identify a few striking successful fortification programs whereby the majority of the food vehicle used is fortifiable and fortified, and coverage is equitable among those classified as vulnerable and not. Other programs have great potential based on very high use of a fortifiable food vehicle, including in most cases among the vulnerable, but that potential is not currently reached because of low compliance with fortification requirements. Programs were also identified whereby the food vehicle has limited potential to make public health contributions to micronutrient intake, given the low proportions of the population who consume the food vehicle in general or who consume the fortifiable food vehicle. Four key lessons were learned: 1) the potential for impact of food fortification depends on the appropriate choice of food fortification vehicle but also on the proportion of the food vehicle consumed that is fortifiable; 2) the design of fortification programs should be informed by the magnitude and distribution of inadequate intake and deficiency and consumption of fortifiable foods, and part of micronutrient deficiency control strategies to ensure coordination with other programs; 3) effective quality control of fortification levels in foods urgently needs strengthening, including the many governance and other policy factors that influence the capacity, resources, and commitment to do this; 4) periodic review of the assumptions related to dietary patterns that underpin food fortification is needed to ensure continual safe and impactful programs.

Safety and Mortality Benefits of Delivering Vitamin A Supplementation at 6 Months of Age in Sub-Saharan Africa.

BACKGROUND: Vitamin A supplementation (VAS) among children 6 to 59 months of age reduces vitamin A deficiency (VAD)-related mortality. Child health days (CHDs) only reach an estimated 16.7% of children at exactly 6 months, leaving uncovered children at risk of VAD-related mortality; similarly, VAS provided at 9 months of age with measles-containing vaccine leaves infants unprotected for 3 months. OBJECTIVE: Using data from sub-Saharan Africa, we estimated the mortality benefits and safety of providing VAS at age 6 months, compared to delivery through CHDs and at 9 months. METHODS: We modeled VAS-preventable mortality benefits at 6 months as a function of published VAS effect sizes, intervention coverage, and proportion of infant deaths occurring between 6 and 11 months. To evaluate safety, we modeled the effect of different VAS coverage scenarios on maximum hepatic vitamin A concentrations (HVACs). RESULTS: VAS linked to a 6-month visit could reduce infant mortality by an additional 1.95 (95% confidence interval [CI]: 1.38-2.52) and 1.63 (95% CI: 1.15-2.11) percentage points compared to VAS through CHDs and at 9 months, respectively. The HVAC models indicate that VAS at 6 months is safe even in the presence of a second VAS dose 1 month later and other food-based vitamin A control strategies. CONCLUSION: Advancing the first VAS dose to 6 months should be considered in settings where VAS is currently given first at 9 months. A 6-month VAS dose should also be considered in settings where VAS is delivered through CHDs. VAS delivery at 6 months could also serve as a platform to deliver other high-impact interventions.

An alternative approach to prescribing sternal precautions after median sternotomy, "Keep Your Move in the Tube".

Traditional sternal precautions, given to sternotomy patients as part of their discharge education, are intended to help prevent sternal wound complications. They vary widely but generally include arbitrary load and time restrictions (lifting no more than a specified weight for up to 12 weeks) and may prohibit common shoulder joint and shoulder girdle movements. Having observed the negative effects of restrictive sternal precautions for many years, our research team performed a series of studies that measured the forces exerted during various common activities and their relationship to the sternum. The results, though informative, led us to realize that the goal of identifying "the" appropriate load restriction to prescribe for sternotomy patients was futile. The alternative approach that we introduce applies standard kinesiological principles and teaches patients how to perform load-bearing movements in a way that avoids excessive stress to the sternum.

University-level nutrition training in West Africa: cost and financing issues.

BACKGROUND: There is a serious shortage of skilled nutrition professionals in West Africa. Investing in nutrition training is one of the strategies for strengthening the human resource base in nutrition. However, little is known about how nutrition training in the region is financed and the levels of tuition fees charged. The purpose of this study was to provide a comprehensive assessment about the levels of tuition fees charged for nutrition training in the West Africa region and to determine to what extent this is of reach to the average student. METHODOLOGY: The data for this study were obtained from 74 nutrition degree programs operating in nine West African countries in 2013 through semi-structured interviews during on-site visits or through self-administered questionnaires. They included the age of the programs, school ownership, tuition fees, financial assistance, and main sources of funding. Tuition fees (in 2013 US$) were expressed per program to enable uniformity and comparability. Simple descriptive and bivariate analyses were performed. RESULTS: Results from 74 nutrition training programs in nine countries showed a wide variation in tuition fees within and between countries. The tuition fees for bachelor's, master's, and doctoral programs, respectively, ranged from 372 to 4,325 (mean: 2,353); 162 to 7,678 (mean: 2,232); and 369 to 5,600 (mean: 2,208). The tuition fees were significantly higher (p<0.05) in private institutions than in public institutions (mean: US$3,079 vs. US$2,029 for bachelor's programs; US$5,118 vs. US$1,820 for master's programs; and US$3,076 vs. US$1,815 for doctoral programs). The difference in the tuition fees between Francophone and Anglophone countries was not statistically significant (mean: US$2,570 vs. US$2,216 for bachelor's programs; US$2,417 vs. US$2,147 for master's programs; US$3,285 vs. US$2,055 for doctoral programs). In most countries, the tuition fees appeared to be out of reach of the average student. Recent master's programs appeared to charge higher fees than older ones. We found a significant negative correlation between tuition fees and the age of the program, after controlling for school ownership (r=-0.33, p<0.001). CONCLUSIONS: Our findings underscore the urgent need for national governments in the region to establish benchmarks and regulate nutrition training costs. In a region where the average annual gross national income (GNI) per capita is barely 890$, the rising cost of tuition fees is likely to hinder access of students from poor background to nutrition training. Governments should institute financing mechanisms such as scholarships, public-private partnerships, credit facilities, and donor funding to facilitate access to tertiary-level nutrition training in the region.

Integrating Vitamin A Supplementation at 6 months into the Expanded Program of Immunization in Sierra Leone.

Since 2004, twice-yearly mass vitamin A supplementation (VAS) has equitably reached over 85% of children 6-59 months old in Sierra Leone. However infants who turn 6 months after the event may wait until they are 11 months old to receive their first dose. The effectiveness of integrating VAS at 6 months into the Expanded Program of Immunization (EPI) in a revised child health card was studied. Health facilities matched according to staff cadre and work load were assigned to provide either a 'mini package' of VAS and infant and young child feeding (IYCF), a 'full package' of VAS, IYCF and family planning (FP), or 'child health card' only. 400 neonates were enrolled into each group, caregivers given the new child health card and followed until they were 12 months old. More infants in the full: 74.5% and mini: 71.7% group received VAS between 6 and 7 months of age compared with the new CH card only group: 60.2% (p = 0.002, p < 0.001 respectively). FP commodities were provided to 44.5% of caregivers in the full compared with <2.5% in the mini and new child health card only groups (p < 0.0001). Integration of VAS within the EPI schedule achieved >60% coverage for infants between 6 and 7 months of age. Provision of FP and/or IYCF further improved coverage. Funding was provided by the Canadian Department of Foreign Affairs, Trade and Development who had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Nutrition training in medical and other health professional schools in West Africa: the need to improve current approaches and enhance training effectiveness.

BACKGROUND: Health professionals play a key role in the delivery of nutrition interventions. Improving the quality of nutrition training in health professional schools is vital for building the necessary human resource capacity to implement effective interventions for reducing malnutrition in West Africa. This study was undertaken to assess the current status of nutrition training in medical, nursing and midwifery schools in West Africa. DESIGN: Data were collected from 127 training programs organized by 52 medical, nursing, and midwifery schools. Using a semi-structured questionnaire, we collected information on the content and distribution of nutrition instruction throughout the curriculum, the number of hours devoted to nutrition, the years of the curriculum in which nutrition was taught, and the prevailing teaching methods. Simple descriptive and bivariate analyses were performed. RESULTS: Nutrition instruction occurred mostly during the first 2 years for the nursing (84%), midwifery (87%), and nursing assistant (77%) programs and clinical years in medical schools (64%). The total amount of time devoted to nutrition was on average 57, 56, 48, and 28 hours in the medical, nursing, midwifery, and nursing assistant programs, respectively. Nutrition instruction was mostly provided within the framework of a dedicated nutrition course in nursing (78%), midwifery (87%), and nursing assistant programs (100%), whereas it was mainly embedded in other courses in medical schools (46%). Training content was heavily weighted to basic nutrition in the nursing (69%), midwifery (77%), and nursing assistant (100%) programs, while it was oriented toward clinical practice in the medical programs (64%). For all the programs, there was little focus (<6 hours contact time) on public health nutrition. The teaching methods on nutrition training were mostly didactic in all the surveyed schools; however, we found an integrated model in some medical schools (12%). None of the surveyed institutions had a dedicated nutrition faculty. The majority (55%) of the respondents rated nutrition instruction in their institutions as insufficient. CONCLUSIONS: The results of our study reveal important gaps in current approaches to nutrition training in health professional schools in West Africa. Addressing these gaps is critical for the development of a skilled nutrition workforce in the region. Nutrition curricula that provide opportunities to obtain more insights about the basic principles of human nutrition and their application to public health and clinical practice are recommended.

A systematic assessment of the current capacity to act in nutrition in West Africa: cross-country similarities and differences.

BACKGROUND: Although it is widely accepted that lack of capacity is one of the barriers to scaling up nutrition in West Africa, there is a paucity of information about what capacities exist and the capacities that need to be developed to accelerate progress toward improved nutrition outcomes in the region. OBJECTIVE: To systematically assess the current capacity to act in nutrition in the West Africa region and explore cross-country similarities and differences. DESIGN: Data were collected from 13 West African countries through interviews with government officials, key development partners, tertiary-level training institutions, and health professional schools. The assessment was based on a conceptual framework of four interdependent levels (tools; skills; staff and infrastructure; and structures, systems and roles). In each of the surveyed countries, we assessed capacity assets and gaps at individual, organizational, and systemic levels. RESULTS: Important similarities and differences in capacity assets and gaps emerged across all the surveyed countries. There was strong momentum to improve nutrition in nearly all the surveyed countries. Most of the countries had a set of policies on nutrition in place and had set up multisectoral, multi-stakeholder platforms to coordinate nutrition activities, although much remained to be done to improve the effectiveness of these platforms. Many initiatives aimed to reduce undernutrition were ongoing in the region, but there did not seem to be clear coordination between them. Insufficient financial resources to implement nutrition activities were a major problem in all countries. The bulk of financial allocations for nutrition was provided by development partners, even though some countries, such as Niger, Nigeria, and Senegal, had a national budget line for nutrition. Sporadic stock-outs of nutrition supplies were reported in most of the countries as a result of a weak logistic and supply chain system. They also had a critical shortage of skilled nutrition professionals. There was limited supervision of nutrition activities, especially at lower levels. Nigeria and Ghana emerged as the countries with the greatest capacities to support the expansion of a nutrition workforce, although a significant proportion of their trained nutritionists were not employed in the nutrition sector. None of the countries had in place a unified nutrition information system that could guide decision-making processes across the different sectors. CONCLUSIONS: There is an urgent need for a shift toward wider reforms for nutrition capacity development in the West Africa region. Addressing these unmet needs is a critical first step toward improved capacity for action in nutrition in the region.

Region-wide assessment of the capacity for human nutrition training in West Africa: current situation, challenges, and way forward.

BACKGROUND: There is a dearth of information on existing nutrition training programs in West Africa. A preliminary step in the process of developing a comprehensive framework to strengthen human capacity for nutrition is to conduct an inventory of existing training programs. OBJECTIVE: This study was conducted to provide baseline data on university-level nutrition training programs that exist in the 16 countries in West Africa. It also aimed to identify existing gaps in nutrition training and propose solutions to address them. DESIGN: Participating institutions were identified based on information provided by in-country key informants, UNICEF offices or through internet searches. Data were collected through semi-structured interviews during on-site visits or through self-administered questionnaires. Simple descriptive and bivariate analyses were performed. RESULTS: In total, 83 nutrition degree programs comprising 32 B.Sc. programs, 34 M.Sc. programs, and 17 Ph.D. programs were identified in the region. More than half of these programs were in Nigeria. Six countries (Cape Verde, Guinea-Bissau, Liberia, Mali, The Gambia, and Togo) offered no nutrition degree program. The programs in francophone countries were generally established more recently than those in anglophone countries (age: 3.5 years vs. 21.4 years). Programs were predominantly (78%) run by government-supported institutions. They did not provide a comprehensive coverage of all essential aspects of human nutrition. They were heavily oriented to food science (46%), with little emphasis on public health nutrition (24%) or overnutrition (2%). Annual student intakes per program in 2013 ranged from 3 to 262; 7 to 40; and 3 to 10, respectively, for bachelor's, master's, and doctoral programs while the number of graduates produced annually per country ranged from 6 to 271; 3 to 64; and 1 to 18, respectively. External collaboration only existed in 15% of the programs. In-service training programs on nutrition existed in less than half of the countries. The most important needs for improving the quality of existing training programs reported were teaching materials, equipment and infrastructures, funding, libraries and access to advanced technology resources. CONCLUSIONS: There are critical gaps in nutrition training in the West Africa region. The results of the present study underscore the urgent need to invest in nutrition training in West Africa. An expanded set of knowledge, skills, and competencies must be integrated into existing nutrition training curricula. Our study provides a basis for the development of a regional strategy to strengthen human capacity for nutrition across the region.

'FAN the SUN brighter': fortifying Africa nutritionally (FAN) - the role of public private partnership in scaling up nutrition (SUN) in West Africa.

The scaling up nutrition (SUN) policy framework requires extensive public­private partnership (PPP). Malnutrition is multi-dimensional and should engage multi-sectoral platforms. The SUN policy however did not fully embrace the dynamics of harnessing PPP. The objectives of the present paper are to highlight the reasons for the apprehension around PPP and illustrate how effective coordination of PPP in West Africa has contributed to implementing large-scale food fortification with micronutrients as a complementary nutrition intervention. The experience of Helen Keller International (HKI) in scaling up food fortification was emphasised with understanding of the factors contributing to indifference by the international community to private sector contribution to SUN. The roles of different stakeholders in a PPP are elucidated and the process linked to who, why and how to engage. The private sector provides direct nutrition services while the public sector creates the enabling environment for the private sector to thrive on social values. Through this approach fortified vegetable oil and wheat flour are now reaching over 70% of the population in West Africa. As a neutral broker HKI coordinated and facilitated dialogue among the different stakeholders. The core competencies of each stakeholder were harnessed and each partner was held accountable. It concludes that multi-sectoral relationship must be transparent, equitable and based on shared mutual interests. The rules and values of PPP offer opportunities for SUN.

Comparison of the estimated cost-effectiveness of preventive and therapeutic zinc supplementation strategies for reducing child morbidity and mortality in sub-Saharan Africa.

BACKGROUND: Zinc supplementation of young children in lower-income countries reduces morbidity from diarrhea and pneumonia and all-cause mortality, but the most cost-effective approach for distributing zinc supplements is unknown. OBJECTIVE: To examine the potential impact of four possible strategies for delivering zinc supplements on disease prevention and deaths averted among children 6 to 59 months of age in sub-Saharan Africa. METHODS: We analyzed different zinc supplementation strategies to assess their likely impact on morbidity and mortality of preschool children in sub-Saharan Africa and to estimate their possible costs. RESULTS: Preventive zinc supplementation reduces diarrhea incidence by 27% among children 12 to 59 months of age, pneumonia incidence by 21% among children 6 to 59 months of age, and all-cause mortality by 18% among children 12 to 59 months of age. The likely average total program costs of zinc supplementation programs were estimated from the outlays of existing service delivery platforms, such as child health days, community-based nutrition programs, and clinic-based treatment of diarrhea, assuming different levels of coverage and target age ranges of children. CONCLUSIONS: We found that the average total costs per life saved ranged from approximately US$462 to US$3,111, and the most cost-effective interventions were weekly or intermittent preventive zinc supplementation, because of the possibility of high coverage and fewer supplements required. Empirical data from zinc supplementation programs will be needed to confirm these estimates.

Urgent ultrasound guided hemodynamic assessments by a pediatric medical emergency team: a pilot study.

PURPOSE: To determine the feasibility of using the Ultrasound Cardiac Output Monitor (USCOM) as an adjunct during hemodynamic assessments by a pediatric medical emergency team (PMET). METHODS: Pediatric in-patients at McMaster Children's Hospital aged under 18 years requiring urgent PMET consultation, were eligible. Patients with known cardiac outflow valve defects, Pediatric Critical Care Unit in-patients, and those in cardiorespiratory arrest, were excluded. The primary outcome was feasibility, and the ease of USCOM transport and application as assessed by a self-administered user questionnaire. Secondary outcomes included the quality of USCOM measurements, and agreement in clinical versus USCOM-derived assessments. RESULTS: Forty-one patients from 85 eligible PMET consultations were enrolled between March and August 2011. A total of 55 USCOM assessments were performed on 36 of 41 (87.8%) participants. USCOM could not be completed in 5 (12.2%) participants due to patient agitation (n = 4) and emergent care (n = 1). USCOM was reported as easy to transport and apply by 97.4% and 94.7% of respondents respectively, not obstructive to patient care by 94.7%, and yielded timely measurements by 84.2% respondents. USCOM tracings were of good quality in 41 (75.9%) assessments. Agreement between clinical and USCOM-derived hemodynamic assessments by two independent raters was poor (Rater 1: κ = 0.094; Rater 2: κ = 0.146). CONCLUSION: USCOM can be applied by a PMET during urgent hemodynamic assessments in children. While USCOM has been validated in stable children, its role in guiding hemodynamic resuscitation and informing therapeutic goals in a hemodynamically unstable pediatric population requires further investigation.

Results of Fortification Rapid Assessment Tool (FRAT) surveys in sub-Saharan Africa and suggestions for future modifications of the survey instrument.

BACKGROUND: Food fortification has been increasingly recognized as a promising approach to prevent micronutrient deficiencies. The Fortification Rapid Assessment Tool (FRAT) was developed to assist public health program managers to acquire the information needed to implement an effective mass food fortification program. Multiple countries have conducted FRAT surveys, but information on results and experiences with the FRAT tool has been available only at the national level. OBJECTIVE: To summarize the findings of the FRAT surveys previously conducted in sub-Saharan Africa. METHODS: Surveys from 12 sub-Saharan African countries (Burkina Faso, Cameroon, Congo, Guinea, Malawi, Mali, Mauritania, Mozambique, Niger, Rwanda, Senegal, Uganda) were identified. Information on consumption patterns for wheat flour, vegetable oil, sugar, and bouillon cubes was reviewed and summarized. RESULTS: Most surveys found that a moderate to high proportion of women reported consuming wheat flour (48% to 93%), vegetable oil (44% to 98%), sugar (55% to 99%), and bouillon cubes (79% to 99%) in the past 7 days, although consumption was more common and more frequent in urban areas than in rural areas. Similarly, the reported amounts consumed during the previous 24 hours were generally higher in urban settings. CONCLUSIONS: The FRAT instrument has been successfully used in multiple countries, and the results obtained have helped in planning national food fortification programs. However, the recommended sampling scheme may need to be reconsidered, and the guidelines should be revised to clarify important aspects of fieldworker training, implementation, data analysis and interpretation, and reporting of the results.