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1. Using functional principal component analysis (FPCA) to quantify sitting patterns derived from wearable sensors

   https://doi.org/10.1186/s12966-024-01585-8  

   Zablocki, Rong W ; Hartman, Sheri J ; Di, Chongzhi ; Zou, Jingjing ; Carlson, Jordan A ; Hibbing, Paul R ; Rosenberg, Dori E ; Greenwood-Hickman, Mikael Anne ; Dillon, Lindsay ; LaCroix, Andrea Z ; et al ( December 2024 , International Journal of Behavioral Nutrition and Physical Activity)

   Sedentary behavior (SB) is a recognized risk factor for many chronic diseases. ActiGraph and activPAL are two commonly used wearable accelerometers in SB research. The former measures body movement and the latter measures body posture. The goal of the current study is to quantify the pattern and variation of movement (by ActiGraph activity counts) during activPAL-identified sitting events, and examine associations between patterns and health-related outcomes, such as systolic and diastolic blood pressure (SBP and DBP).

   The current study included 314 overweight postmenopausal women, who were instructed to wear an activPAL (at thigh) and ActiGraph (at waist) simultaneously for 24 hours a day for a week under free-living conditions. ActiGraph and activPAL data were processed to obtain minute-level time-series outputs. Multilevel functional principal component analysis (MFPCA) was applied to minute-level ActiGraph activity counts within activPAL-identified sitting bouts to investigate variation in movement while sitting across subjects and days. The multilevel approach accounted for the nesting of days within subjects.

   At least 90% of the overall variation of activity counts was explained by two subject-level principal components (PC) and six day-level PCs, hence dramatically reducing the dimensions from the original minute-level scale. The first subject-level PC captured patterns of fluctuation in movement during sitting, whereas the second subject-level PC delineated variation in movement during different lengths of sitting bouts: shorter (< 30 minutes), medium (30 -39 minutes) or longer (> 39 minute). The first subject-level PC scores showed positive association with DBP (standardized$$\hat{\beta }$$$\hat{\beta }$: 2.041, standard error: 0.607, adjustedp= 0.007), which implied that lower activity counts (during sitting) were associated with higher DBP.

   In this work we implemented MFPCA to identify variation in movement patterns during sitting bouts, and showed that these patterns were associated with cardiovascular health. Unlike existing methods, MFPCA does not require pre-specified cut-points to define activity intensity, and thus offers a novel powerful statistical tool to elucidate variation in SB patterns and health.

   ClinicalTrials.gov NCT03473145; Registered 22 March 2018;https://clinicaltrials.gov/ct2/show/NCT03473145; International Registered Report Identifier (IRRID): DERR1-10.2196/28684

    

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2. At-Home use of App-Based Mindfulness for Children: A Randomized Active-Controlled Trial

   https://doi.org/10.1007/s12671-023-02231-3  

   Treves, Isaac N. ; Olson, Halie A. ; Ozernov-Palchik, Ola ; Li, Cindy E. ; Wang, Kimberly L. ; Arechiga, Xochitl M. ; Goldberg, Simon B. ; Gabrieli, John D. E. ( October 2023 , Mindfulness)

   School-based mindfulness interventions in children have shown benefits to child well-being. Here, we investigated the effectiveness of a remote, app-based mindfulness intervention for promoting well-being in children.

   We conducted a randomized controlled trial (RCT) with two control groups to examine the effects of an 8-week mindfulness intervention in U.S. children ages 8–10. We compared pre-post effects between a mindfulness intervention using theInner Explorerapp, and two audiobook control interventions. The 279 children who participated in the interventions were assessed on self-report measures of anxiety and depression symptoms, perceived stress and trait mindfulness and we also collected parental reports.

   Over 80% of children completed the intervention in each condition. There was evidence for reduced self-perceived stress in children and reduced negative affect in children by parental reports using the mindfulness app, but no significant reduction for anxiety or depression symptoms. In general, between-group effect sizes were small (d < 0.45). Regular use, defined as at least 30 days of mindfulness practice within the study period, was associated with reduced child negative affect by parental reports, as well as reduced parental stress and child self-perceived stress.

   These findings suggest that home use of a mindfulness app in young children can have a positive impact on children’s emotional well-being if the app is used regularly, specifically for at least 30 days in the 8-week study period. Strategies aimed at promoting regular use of the mindfulness app at home could lead to even better outcomes for children.

   Preregistered on OSF athttps://osf.io/23vax

    

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3. dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra

   https://doi.org/10.1101/2023.06.15.545182  

   Huang, Xin ; Struck, Travis J ; Davey, Sean W ; Gutenkunst, Ryan N ( June 2023 , bioRxiv)

   dadi is a popular software package for inferring models of demographic history and natural selection from population genomic data. But using dadi requires Python scripting and manual parallelization of optimization jobs. We developed dadi-cli to simplify dadi usage and also enable straighforward distributed computing.

   dadi-cli is implemented in Python and released under the Apache License 2.0. The source code is available athttps://github.com/xin-huang/dadi-cli. dadi-cli can be installed via PyPI and conda, and is also available through Cacao on Jetstream2https://cacao.jetstream-cloud.org/.

    

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4. Progesterone for Neurodevelopment in Fetuses With Congenital Heart Defects: A Randomized Clinical Trial

   https://doi.org/10.1001/jamanetworkopen.2024.12291  

   Gaynor, J William ; Moldenhauer, Julie S ; Zullo, Erin E ; Burnham, Nancy B ; Gerdes, Marsha ; Bernbaum, Judy C ; D’Agostino, Jo Ann ; Linn, Rebecca L ; Klepczynski, Brenna ; Randazzo, Isabel ; et al ( May 2024 , JAMA Network Open)

   Neurodevelopmental outcomes for children with congenital heart defects (CHD) have improved minimally over the past 20 years.

   To assess the feasibility and tolerability of maternal progesterone therapy as well as the magnitude of the effect on neurodevelopment for fetuses with CHD.

   This double-blinded individually randomized parallel-group clinical trial of vaginal natural progesterone therapy vs placebo in participants carrying fetuses with CHD was conducted between July 2014 and November 2021 at a quaternary care children’s hospital. Participants included maternal-fetal dyads where the fetus had CHD identified before 28 weeks’ gestational age and was likely to need surgery with cardiopulmonary bypass in the neonatal period. Exclusion criteria included a major genetic or extracardiac anomaly other than 22q11 deletion syndrome and known contraindication to progesterone. Statistical analysis was performed June 2022 to April 2024.

   Participants were 1:1 block-randomized to vaginal progesterone or placebo by diagnosis: hypoplastic left heart syndrome (HLHS), transposition of the great arteries (TGA), and other CHD diagnoses. Treatment was administered twice daily between 28 and up to 39 weeks’ gestational age.

   The primary outcome was the motor score of the Bayley Scales of Infant and Toddler Development-III; secondary outcomes included language and cognitive scales. Exploratory prespecified subgroups included cardiac diagnosis, fetal sex, genetic profile, and maternal fetal environment.

   The 102 enrolled fetuses primarily had HLHS (n = 52 [50.9%]) and TGA (n = 38 [37.3%]), were more frequently male (n = 67 [65.7%]), and without genetic anomalies (n = 61 [59.8%]). The mean motor score differed by 2.5 units (90% CI, −1.9 to 6.9 units;P = .34) for progesterone compared with placebo, a value not statistically different from 0. Exploratory subgroup analyses suggested treatment heterogeneity for the motor score for cardiac diagnosis (Pfor interaction = .03) and fetal sex (Pfor interaction = .04), but not genetic profile (Pfor interaction = .16) or maternal-fetal environment (Pfor interaction = .70).

   In this randomized clinical trial of maternal progesterone therapy, the overall effect was not statistically different from 0. Subgroup analyses suggest heterogeneity of the response to progesterone among CHD diagnosis and fetal sex.

   ClinicalTrials.gov Identifier:NCT02133573

    

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5. Reference-agnostic representation and visualization of pan-genomes

   https://doi.org/10.1186/s12859-021-04424-w  

   Liang, Qihua ; Lonardi, Stefano ( October 2021 , BMC Bioinformatics)

   The pan-genome of a species is the union of the genes and non-coding sequences present in all individuals (cultivar, accessions, or strains) within that species.

   Here we introduce PGV, a reference-agnostic representation of the pan-genome of a species based on the notion of consensus ordering. Our experimental results demonstrate that PGV enables an intuitive, effective and interactive visualization of a pan-genome by providing a genome browser that can elucidate complex structural genomic variations.

   The PGV software can be installed via conda or downloaded fromhttps://github.com/ucrbioinfo/PGV. The companion PGV browser athttp://pgv.cs.ucr.educan be tested using example bed tracks available from the GitHub page.

    

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