Community-based interventions to prevent serious complications following spinal cord injury in Bangladesh:the CIVIC trial statistical analysis plan

Background: People who sustain spinal cord injuries in low- and middle-income countries are vulnerable to life-threatening complications after discharge. The aim of this trial is to determine the effect on all-cause mortality of a sustainable model of community-based care provided over the first 2 years after discharge. Methods and analysis: The CIVIC trial is a single centre, parallel group trial with concealed and stratified randomisation. The protocol has been previously published (BMJ Open 2016;6:e010350). This paper provides the accompanying detailed statistical plan. In total, 410 people with recent spinal cord injury who are wheelchair dependent and about to be discharged from the Centre for the Rehabilitation of the Paralysed in Bangladesh are randomised to intervention or control groups. Participants assigned to the intervention group receive a model of community-based care in which a case manager provides ongoing telephone-based support and visits participants in their homes over a 2-year period. Participants assigned to the control group receive usual care which may involve a follow-up phone call or a home visit. The primary outcome is all-cause mortality at 2 years as determined by a blinded assessor (Bangladesh does not have a death registry). The primary effectiveness analysis will compare Kaplan-Meier survival curves (time from allocation to death) in the intervention and control groups using the log-rank test (two-tailed α = 0.05). Participants will be censored at the time they were last known to be alive or at the time of the follow-up assessment. Recruitment finished in March 2018 and the last assessment will be conducted in March 2020. Discussion: The CIVIC trial will provide unbiased and precise estimates of the effectiveness of a model of community-based care for people with spinal cord injuries in Bangladesh. The results will have implications for provision of health services for people with spinal cord injuries and other conditions that cause serious disability in low-income and middle-income countries. Trial registration: ANZCTR, ACTRN12615000630516, U1111-1171-1876. Registered on 17 June 2015

Synthesis beyond limit

<p>Rice production needs to increase in the future in order to meet increasing demands. The development of new improved and higher yielding varieties more quickly will be needed to meet this demand. However, most rice breeding programmes in the world have not changed in several decades. In this article, we revisit the evidence in favour of using rapid generation advance (RGA) as a routine breeding method. We describe preliminary activities at the International Rice Research Institute (IRRI) to re-establish RGA on a large scale as the main breeding method for irrigated rice breeding. We also describe experiences from the early adoption at the Bangladesh Rice Research Institute. Evaluation of RGA breeding lines at IRRI for yield, flowering time and plant height indicated transgressive segregation for all traits. Some RGA lines were also higher yielding than the check varieties. The cost advantages of using RGA compared to the pedigree method were also empirically determined by performing an economic analysis. This indicated that RGA is several times more cost effective and advantages will be realized after 1 year even if facilities need to be built. Based on our experience, and previous independent research empirically testing the RGA method in rice, we recommend that this method should be implemented for routine rice breeding in order to improve breeding efficiency.</p

Community Integration and Life Satisfaction Among Individuals With Spinal Cord Injury Living in the Community After Receiving Institutional Care in Bangladesh

PURPOSE: This study reports level of community integration and life satisfaction among individuals who sustained traumatic spinal cord injuries, received institutional rehabilitation care services, and went back to live in the community in Bangladesh. It examines the impact of type of injury, demographic characteristics, socio-economic profile, and secondary health conditions on community integration and life satisfaction and explores the association between these two measures. METHOD: Individuals with spinal cord injury were telephone interviewed by the Centre for the Rehabilitation of the Paralysed, Bangladesh from February to June of 2014. Data were collected from the subjects on type of injury, demographic and socio-economic profile, and secondary health conditions. The outcome measures were determined by using two validated tools - Community Integration Questionnaire and Life Satisfaction 9 Questionnaire. RESULTS: Total community integration and life satisfaction scores were 15.09 and 3.69, respectively. A significant positive relationship between community integration and life satisfaction was revealed. Type of injury, gender, and age were found to be significant predictors of both community integration and life satisfaction scores. Higher education was significantly related to community integration and life satisfaction scores. CONCLUSION: Participants scored low in total community integration and life satisfaction, suggesting there is a great need to develop interventions by governmental and non-governmental organizations to better integrate individuals with spinal cord injury in the community. Implications for Rehabilitation Government and non-government organizations should offer disability friendly public transportation facilities for individuals with spinal cord injury so that they can return to education, resume employment, and involve in social activities. Entrepreneurs and businesses should develop assistive devices featuring low technology, considering the rural structure and housing conditions in Bangladesh. Innovations being made in assistive technology should be supported by subsidies and grants. They should also plan to offer injury appropriate employment opportunities for individuals who suffer major injuries like spinal cord injury in Bangladesh. Housing facilities with accessible bathrooms, kitchens and stairs should be designed and offered for this population to improve their ability to self-care and decrease the dependence on caregivers for household tasks such as - cooking meals and taking care of children

Genetic Mapping to Detect Stringent QTLs Using 1k-RiCA SNP Genotyping Platform from the New Landrace Associated with Salt Tolerance at the Seedling Stage in Rice

Rice is the world&rsquo;s most important food crop, providing the daily calorie intake for more than half of the world&rsquo;s population. Rice breeding has always been preoccupied with maximizing yield potential. However, numerous abiotic factors, such as salt, cold, drought, and heat, significantly reduce rice productivity. Salinity, one of the major abiotic stresses, reduces rice yield worldwide. This study was conducted to determine new quantitative trait loci (QTLs) that regulate salt tolerance in rice seedlings. One F2:3 mapping population was derived from a cross between BRRI dhan49 (a popular but sensitive rainfed rice variety) and Akundi (a salt-tolerant rice landrace in Bangladesh used as a donor parent). The 1k-Rice Custom Amplicon (1k-RiCA) single-nucleotide polymorphism (SNP) markers were used to genotype this mapping population. After removing segregation distortion and monomorphic markers, 884 SNPs generated a 1526.8 cM-long genetic linkage map with a mean marker density of 1.7 cM for the 12 linkage groups. By exploiting QGene and ICIM-ADD, a sum of 15 QTLs for nine traits was identified in salt stress on seven chromosomes. Four important genomic loci were identified (qSES1, qSL1, qSUR1 and qRL1) on chromosome 1. Out of these 15 QTLs, 14 QTLs are unique, as no other study has mapped in the same chromosomal location. We also detected 15 putative candidate genes and their functions. The ICIM-EPI approach identified 43 significant pairwise epistasis interactions between regions associated with and unassociated with QTLs. Apart from more well-known donors, Akundi serves as an important new donor source for global salt tolerance breeding initiatives, including Bangladesh. The introgression of the novel QTLs identified in this study will accelerate the development of new salt-tolerant varieties that are highly resistant to salt stress using marker-enabled breeding

SNP Based Trait Characterization Detects Genetically Important and Stable Multiple Stress Tolerance Rice Genotypes in Salt-Stress Environments

Soil salinity is a major constraint to rice production in coastal areas around the globe, and modern high-yielding rice cultivars are more sensitive to high salt stress, which limits rice productivity. Traditional breeding programs find it challenging to develop stable salt-tolerant rice cultivars with other stress-tolerant for the saline environment in Bangladesh due to large yield variations caused by excessive salinity fluctuations during the dry (boro) season. We examined trait characterization of 18 advanced breeding lines using SNP genotyping and among them, we found line G6 (BR9621-B-1-2-11) (single breeding line with multiple-stress-tolerant QTL/genes) possessed 9 useful QTLs/genes, and two lines (G4:BR9620-2-7-1-1 and G14: IR 103854-8-3-AJY1) carried 7 QTLs/genes that control the desirable traits. To evaluate yield efficiency and stability of 18 rice breeding lines, two years of field experiment data were analyzed using AMMI (additive main effect and multiplicative interaction) and GGE (Genotype, Genotype Environment) biplot analysis. The AMMI analysis of variance demonstrated significant genotype, environment, and their interaction, accounting for 14.48%, 62.38%, and 19.70% of the total variation, respectively, and revealed that among the genotypes G1, G13, G14, G17, and G18 were shown to some extent promising. Genotype G13 (IR 104002-CMU 28-CMU 1-CMU 3) was the most stable yield based on the AMMI stability value. The GGE biplot analysis indicates 76% of the total variation (PC1 48.5% and PC2 27.5%) which is performed for revealing genotype × environment interactions. In the GGE biplot analysis, genotypes were checked thoroughly in two mega-environments (ME). Genotype G14 (IR103854-8-3-AJY1) was the winning genotype in ME I, whereas G1 (BR9627-1-3-1-10) in ME II. Because of the salinity and stability factors, as well as the highest averages of grain yield, the GGE and AMMI biplot model can explain that G1 and G13 are the best genotypes. These (G1, G6, G13, G14, G17, and G18) improved multiple-stress-tolerant breeding lines with stable grain yield could be included in the variety release system in Bangladesh and be used as elite donor parents for the future breeding program as well as for commercial purposes with sustainable production

Revisiting rice breeding methods – evaluating the use of rapid generation advance (RGA) for routine rice breeding

Rice production needs to increase in the future in order to meet increasing demands. The development of new improved and higher yielding varieties more quickly will be needed to meet this demand. However, most rice breeding programmes in the world have not changed in several decades. In this article, we revisit the evidence in favour of using rapid generation advance (RGA) as a routine breeding method. We describe preliminary activities at the International Rice Research Institute (IRRI) to re-establish RGA on a large scale as the main breeding method for irrigated rice breeding. We also describe experiences from the early adoption at the Bangladesh Rice Research Institute. Evaluation of RGA breeding lines at IRRI for yield, flowering time and plant height indicated transgressive segregation for all traits. Some RGA lines were also higher yielding than the check varieties. The cost advantages of using RGA compared to the pedigree method were also empirically determined by performing an economic analysis. This indicated that RGA is several times more cost effective and advantages will be realized after 1 year even if facilities need to be built. Based on our experience, and previous independent research empirically testing the RGA method in rice, we recommend that this method should be implemented for routine rice breeding in order to improve breeding efficiency