Parsimony and likelihood reconstruction of human segmental duplications

Motivation: Segmental duplications > 1 kb in length with ≥ 90% sequence identity between copies comprise nearly 5% of the human genome. They are frequently found in large, contiguous regions known as duplication blocks that can contain mosaic patterns of thousands of segmental duplications. Reconstructing the evolutionary history of these complex genomic regions is a non-trivial, but important task

Dynamic assessment of children with language impairments: A pilot study

This article describes the construction of a procedure for dynamic assessment of the expressive grammar of children already identified with language impairments. Few instruments exist for the dynamic assessment of language, and those that have been developed have been largely used to successfully differentiate language impaired from culturally different or typically developing populations. The emphasis in this study was on eliciting clinically useful information that may be used to inform intervention for children with specific language impairment (SLI). The method was piloted on three children with specific language impairments.The test—train—retest format made use of standardized administration of the CELF-3 (UK) before and after a designated training protocol. The training procedure required the children to formulate sentences from randomly presented words, assisted by mediation from the assessor. Results showed that the task used was valuable and appropriate for use as a dynamic measure, and elicited differentiated amounts of change in the children in response to the mediated training phase. Pre-test—post-test results were inconclusive, however, and the frameworks for summarizing information could benefit from revision

Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes

Background: Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics comprised of multiple duplicated fragments. This complex genomic organization complicates analysis of the evolutionary history of these sequences. One model proposed to explain this mosaic patterns is a model of repeated aggregation and subsequent duplication of genomic sequences. Results: We describe a polynomial-time exact algorithm to compute duplication distance, a genomic distance defined as the most parsimonious way to build a target string by repeatedly copying substrings of a fixed source string. This distance models the process of repeated aggregation and duplication. We also describe extensions of this distance to include certain types of substring deletions and inversions. Finally, we provide an description of a sequence of duplication events as a context-free grammar (CFG). Conclusion: These new genomic distances will permit more biologically realistic analyses of segmental duplications in genomes.

Who pays for home care? A study of nationally representative data on disabled older Americans

Background: We examine who pays for services that support disabled older Americans at home. We consider both personal sources (e.g., out-of-pocket payment, family members) and publicly funded programs (e.g., Medicaid) as sources of payment for services. We examine how the funding mix for home care services is related to older people’s economic resources, needs for care, and other socio-demographic characteristics. Methods: Our sample consists of 11,725 person-years from the 1989, 1994, 1999, and 2004 waves of the National Long-Term Care Survey. Two-part regression analyses were performed to model hours of care received from each payer. “Random effects” and “fixed effects” estimation yielded similar results. Results: About six in ten caregivers (63 %) providing home care services are paid by personal sources alone. By contrast, 28 % receive payment from publicly funded programs alone, and 9 % from a combination of personal and public program sources. Older people with family incomes over 75,000 dollars per year receive 8.5 more hours of home care overall than those in the lowest income category (less than 15,000 dollars). While the funding mix for home care services is strongly related to older people’s economic resources, in all income groups at least 65 % of services are provided by caregivers paid in whole or in part from personal sources. In fact, almost all (97 %) home care received by those with family incomes over 75,000 dollars per year are financed by personal sources alone. Conclusions: We outline the implications that heavy reliance on personally financed services and economic disparities in overall services use has for disabled older Americans and their families