Updating RNA-Seq analyses after re-annotation

The estimation of isoform abundances from RNA-Seq data requires a time-intensive step of mapping reads to either an assembled or previously annotated transcriptome, followed by an optimization procedure for deconvolution of multi-mapping reads. These procedures are essential for downstream analysis such as differential expression. In cases where it is desirable to adjust the underlying annotation, for example, on the discovery of novel isoforms or errors in existing annotations, current pipelines must be rerun from scratch. This makes it difficult to update abundance estimates after re-annotation, or to explore the effect of changes in the transcriptome on analyses. We present a novel efficient algorithm for updating abundance estimates from RNA-Seq experiments on re-annotation that does not require re-analysis of the entire dataset. Our approach is based on a fast partitioning algorithm for identifying transcripts whose abundances may depend on the added or deleted isoforms, and on a fast follow-up approach to re-estimating abundances for all transcripts. We demonstrate the effectiveness of our methods by showing how to synchronize RNA-Seq abundance estimates with the daily RefSeq incremental updates. Thus, we provide a practical approach to maintaining relevant databases of RNA-Seq derived abundance estimates even as annotations are being constantly revised

Restoring Health to Health Reform: Integrating Medicine and Public Health to Advance the Population\u27s Wellbeing

The Patient Protection and Affordable Care Act is a major achievement in improving access to health care services. However, evidence indicates that the nation could achieve greater improvements in health outcomes, at a lower cost, by shifting its focus to public health. By focusing nearly exclusively on health care, policy makers have chronically starved public health of adequate and stable funding and political support. The lack of support for public health is exacerbated by the fact that health care and public health are generally conceptualized, organized, and funded as two separate systems. In order to maximize gains in health status and to spend scarce health resources most effectively, health care and public health should be treated as two interactive parts of a single, unified health system. The core purpose of health reform ought to be the improvement of the population’s health. We propose five criteria that would significantly advance this goal: prevention and wellness, human resources, a strong and sustainable health infrastructure, robust performance measurement, and reduction of health disparities. Although the Patient Protection and Affordable Care Act includes provisions addressing these criteria, population health is not a central focus of the reform. In order to guide health reform implementation and to inform future health reform efforts, we offer three major policy reforms: changing the environment to incentivize healthy behavioral choices, strengthening the public health infrastructure at the state and local levels, and developing a health-in-all policies strategy that would engage multiple agencies in improving health incomes. Adopting these reforms would facilitate integration and dramatically improve the population’s health, particularly when compared to the health gains likely to be realized from a continued focus on access to health care services

THE INTERPLAY OF INTRAHOUSEHOLD DYNAMICS AND CHILDREN’S PROCESSES OF RESILIENCE IN RURAL HONDURAS

This study examined the relationship between resilience and intrahousehold dynamics among rural Honduran children. The aim was to identify coping methods among children facing adversity and the mechanisms through which the household influenced these processes. A social ecological systems model of resilience was applied to identify children’s protective processes, while household relationships, activities, and role expectations were examined to illuminate intrahousehold dynamics. Using mixed methods, three research phases were employed. Phase one explored childhood adversities through focus groups. Findings indicated that children faced multiple, co-occurring risks inclusive of poverty and parental absence, among others. Phase two assessed resilience using the Child and Youth Resilience Measure (CYRM-28). Survey results revealed that children’s resilience was predominately relationally-centred, indicating that social networks facilitated key protective resources. Logistic regressions identified four contextually-relevant protective resources: three facets of intrahousehold dynamics (allocated time to complete schoolwork, availability of academic resources, and adult presence in the household) and one community element (perceived safety). Phase three employed case studies to investigate the dynamics of nine households. Case studies illuminated the influences of contextual factors—specifically, familism cultural values and community resources—on intrahousehold dynamics, which created discernible variations in household quality. Data integration elucidated how adaptations of familism values and variations in the availability/accessibility of community resources led to unique intrahousehold dynamics, thus influencing the extent to which protective resources operant in this setting were present in children’s lives—resulting in a plurality of resilient outcomes. The findings point to the complex contextual influences on intrahousehold dynamics, and the highly variable ways in which intrahousehold dynamics manifest protective resources in children’s lives. Findings show that resilience is a quality of the child-environment interaction influenced by a broad range of interconnected structural, cultural, and social factors, including the structural impediments of poverty, adherence to familism values, and the quality of relationships. This study provides empirical evidence of the reciprocal systemic processes associated with positive development under stress and underscores the importance of targeting interventions at multiple socioecological levels to bolster children’s resilience-enhancing potential. Key words: Children, resilience, social ecological systems model, household dynamics, familism, mixed methods research, Honduras, middle childhood, culture, protective factors, risk factors, poverty, Child and Youth Resilience Measure (CYRM-28

Assessment strategy framework for the National Diploma : fashion course at one Eastern Cape Comprehensive University

The purpose of the study was born out of a perceived need to establish an assessment strategy framework for the fashion programme of one Eastern Cape comprehensive university. The study focused on one Eastern Cape comprehensive university. The programme, National Diploma: Fashion, is offered by the university at two campuses (120km apart). Although this programme is currently offered at both of the sites under the auspices of the university, disparity exists in many of the academic functions within the programme. The most challenging is assessment and the implications of a non-existent standard framework for assessment across both campuses. This research undertook to identify a framework that would best serve the Fashion programme of the researched university. Assessment in the context of this study referred to the process of both gathering evidence of student learning as well as assigning grades to that learning. The lack of an assessment framework affects the quality of assessment. Consistency in the assessment process across both campuses is important. At present assessment is not consistent as it is done independently on each campus. This lack of consistency could prove to favour students at the one campus while marginalizing students at the other campus and vice versa. Inconsistency arises from staff having no common assessment framework to refer to when assessment takes place. This study was a case study. Interviews were conducted with a sample of lecturers and students from both sites. A document analysis of relevant policies was done. The documents included the Higher Education Quality Committee document Criteria for Programme Accreditation, 2004, the South African Qualification Authority document Criteria and Guidelines for Assessment of NQF Registered Unit Standards and Qualifications, 2001, and the South African Qualification Authority document Guidelines for Integrated Assessment, 2005. University policy documents pertaining to assessment were also included in the research.The findings of this study lead to the conclusion that there is no clear assessment framework currently in place for the National Diploma: Fashion at one Eastern Cape comprehensive university. The assessment methods currently in use are not fully understood and comprehended by lecturers or students. The assessment types are limited with little or no variety as to how assessment is practiced. Although continuous assessment is advocated in the department, a lack of understanding by lecturers and students as to the true practice of continuous assessment is evident. Much of the assessment is done at the end of a teaching module, rather than embedded in the teaching module. This means that assessment is done of learning rather than for learning

Landscape of transcription in human cells

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell’s regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene