Browsing by Author "Barnett, R. Matthew"

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    Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting
    (Oxford University Press, on behalf of the Society of Systematic Biologists, 2013) Yu, Yun; Barnett, R. Matthew; Nakhleh, Luay
    Hybridization plays an important evolutionary role in several groups of organisms. A phylogenetic approach to detect hybridization entails sequencing multiple loci across the genomes of a group of species of interest, reconstructing their gene trees, and taking their differences as indicators of hybridization. However, methods that follow this approach mostly ignore population effects, such as incomplete lineage sorting (ILS). Given that hybridization occurs between closely related organisms, ILS may very well be at play and, hence, must be accounted for in the analysis framework. To address this issue, we present a parsimony criterion for reconciling gene trees within the branches of a phylogenetic network, and a local search heuristic for inferring phylogenetic networks from collections of gene-tree topologies under this criterion. This framework enables phylogenetic analyses while accounting for both hybridization and ILS. Further, we propose two techniques for incorporating information about uncertainty in gene-tree estimates. Our simulation studies demonstrate the good performance of our framework in terms of identifying the location of hybridization events, as well as estimating the proportions of genes that underwent hybridization. Also, our framework shows good performance in terms of efficiency on handling large data sets in our experiments. Further, in analyzing a yeast data set, we demonstrate issues that arise when analyzing real data sets. While a probabilistic approach was recently introduced for this problem, and while parsimonious reconciliations have accuracy issues under certain settings, our parsimony framework provides a much more computationally efficient technique for this type of analysis. Our framework now allows for genome-wide scans for hybridization, while also accounting for ILS.
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    The Family Level Assessment of Screen Use–Mobile Approach: Development of an Approach to Measure Children’s Mobile Device Use
    (JMIR, 2022) Perez, Oriana; Vadathya, Anil Kumar; Beltran, Alicia; Barnett, R. Matthew; Hindera, Olivia; Garza, Tatyana; Musaad, Salma M.; Baranowski, Tom; Hughes, Sheryl O.; Mendoza, Jason A.; Sabharwal, Ashutosh; Veeraraghavan, Ashok; O'Connor, Teresia M.
    Background: There is a strong association between increased mobile device use and worse dietary habits, worse sleep outcomes, and poor academic performance in children. Self-report or parent-proxy report of children’s screen time has been the most common method of measuring screen time, which may be imprecise or biased. Objective: The objective of this study was to assess the feasibility of measuring the screen time of children on mobile devices using the Family Level Assessment of Screen Use (FLASH)–mobile approach, an innovative method that leverages the existing features of the Android platform. Methods: This pilot study consisted of 2 laboratory-based observational feasibility studies and 2 home-based feasibility studies in the United States. A total of 48 parent-child dyads consisting of a parent and child aged 6 to 11 years participated in the pilot study. The children had to have their own or shared Android device. The laboratory-based studies included a standardized series of tasks while using the mobile device or watching television, which were video recorded. Video recordings were coded by staff for a gold standard comparison. The home-based studies instructed the parent-child dyads to use their mobile device as they typically use it over 3 days. Parents received a copy of the use logs at the end of the study and completed an exit interview in which they were asked to review their logs and share their perceptions and suggestions for the improvement of the FLASH-mobile approach. Results: The final version of the FLASH-mobile approach resulted in user identification compliance rates of >90% for smartphones and >80% for tablets. For laboratory-based studies, a mean agreement of 73.6% (SD 16.15%) was achieved compared with the gold standard (human coding of video recordings) in capturing the target child’s mobile use. Qualitative feedback from parents and children revealed that parents found the FLASH-mobile approach useful for tracking how much time their child spends using the mobile device as well as tracking the apps they used. Some parents revealed concerns over privacy and provided suggestions for improving the FLASH-mobile approach. Conclusions: The FLASH-mobile approach offers an important new research approach to measure children’s use of mobile devices more accurately across several days, even when the child shares the device with other family members. With additional enhancement and validation studies, this approach can significantly advance the measurement of mobile device use among young children.