ALBERT

Description: Background Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades. Results Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation. Conclusions We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.

Description: Physical activity is important for health. However, there is a lack of literature related to the physical activity levels of adults living in urban villagers, which is a vulnerable population in China. The aim of this study is to compare the physical activity and sedentary behavior engagements between urban villagers and non-urban villagers using the 2019 Luohu Shenzhen, China Community Diagnosis Questionnaire. A total of 1205 adults living in urban villages and non-urban villages were included in the analysis. Unadjusted and multiple multivariate logistic regression were conducted for the dependent variable of engagement in recreational physical activity, frequency of recreational physical activity per week, and hours spent in sedentary behaviors per day. Descriptive analysis was conducted to identify the reasons for not engaging in physical activity among urban villagers and non-urban villagers. Across the included sample, 29.05% were urban villagers and 70.95% were non-urban villagers. The results suggested that urban villagers are more likely to engage in physical activity than non-urban villager (OR = 1.90, 95% CI [1.40, 2.59], p 〈 0.001). However, it was also found that urban village status had no significant association for frequency in engaging in physical activity and average hours spent in sedentary behaviors. Both urban villagers and non-urban villages indicated that lack of time, lack of safe and appropriate environment, and working in labor intensive occupations as some of the reasons for not engaging in physical activity. There is a need for tailed interventions and policies for promoting physical activity among urban villagers and non-urban villagers. Additional studies are needed to further our understanding of the physical activity behaviors among urban villagers in China.

Description: Adherent-invasive Escherichia coli (AIEC) is a pathovar linked to inflammatory bowel diseases (IBD), especially Crohn’s disease, and colorectal cancer. AIEC are genetically diverse, and in the absence of a universal molecular signature, are defined by in vitro functional attributes. The relative ability of difference AIEC strains to colonize, persist, and induce inflammation in an IBD-susceptible host is unresolved. To evaluate strain-level variation among tissue-associated E. coli in the intestines, we develop a long-read sequencing approach to identify AIEC by strain that excludes host DNA. We use this approach to distinguish genetically similar strains and assess their fitness in colonizing the intestine. Here we have assembled complete genomes using long-read nanopore sequencing for a model AIEC strain, NC101, and seven strains isolated from the intestinal mucosa of Crohn’s disease and non-Crohn’s tissues. We show these strains can colonize the intestine of IBD susceptible mice and induce inflammatory cytokines from cultured macrophages. We demonstrate that these strains can be quantified and distinguished in the presence of 99.5% mammalian DNA and from within a fecal population. Analysis of global genomic structure and specific sequence variation within the ribosomal RNA operon provides a framework for efficiently tracking strain-level variation of closely-related E. coli and likely other commensal/pathogenic bacteria impacting intestinal inflammation in experimental settings and IBD patients.

Description: Gene Set Enrichment Analysis (GSEA) is a powerful algorithm to determine biased pathways between groups based on expression profiling. However, for fruit fly, a popular animal model, gene matrixes for GSEA are unavailable. This study provides the pathway-targeting gene matrixes based on Reactome and KEGG database for fruit fly. An expression profiling containing neurons or glia of fruit fly was used to validate the feasibility of the generated gene matrixes. We validated the gene matrixes and identified characteristic neuronal and glial pathways, including mRNA splicing and endocytosis. In conclusion, we generated and validated the feasibility of Reactome and KEGG gene matrix files, which may benefit future profiling studies using Drosophila.

Description: This paper establishes a compartment model describing the propagation of injurious information among a well-mixed population. We define the information’s injuriousness as the people practicing the information being injured and leaving the system. Some informed people practice the information and are active, while others do not practice and are inactive. With the recovery resources fixed, the two groups of informed people’s recovering rates are normalized considering the information features. The stability of the nonlinear system is thoroughly studied. Analyzing the reproduction number of the injurious information, we find that in general parameter space, when there are people in an informed compartment, it is not always necessary to consider their recovery resource allocation. Instead, only when their proportion reaches a critical point should it be allocated. Unless the people in an informed compartment form a certain proportion, we can take a laissez-faire attitude towards them. In a more realistic parameter space, once inactive informed people exist, they should be allocated recovery resources. On the one hand, when the recovering rate rises, the focus on both groups of informed people is necessary for more situations. On the other hand, when the rate of active informed people leaving the system rises, ignoring active informed people benefits removing the injurious information in more cases. The model provides qualitative ways in the scenarios of removing injurious information.

Description: Homozygous nonsense mutations in CEP55 are associated with several congenital malformations that lead to perinatal lethality suggesting that it plays a critical role in regulation of embryonic development. CEP55 has previously been studied as a crucial regulator of cytokinesis, predominantly in transformed cells, and its dysregulation is linked to carcinogenesis. However, its molecular functions during embryonic development in mammals require further investigation. We have generated a Cep55 knockout (Cep55-/-) mouse model which demonstrated preweaning lethality associated with a wide range of neural defects. Focusing our analysis on the neocortex, we show that Cep55-/- embryos exhibited depleted neural stem/progenitor cells in the ventricular zone as a result of significantly increased cellular apoptosis. Mechanistically, we demonstrated that Cep55-loss downregulates the pGsk3β/β-Catenin/Myc axis in an Akt-dependent manner. The elevated apoptosis of neural stem/progenitors was recapitulated using Cep55-deficient human cerebral organoids and we could rescue the phenotype by inhibiting active Gsk3β. Additionally, we show that Cep55-loss leads to a significant reduction of ciliated cells, highlighting a novel role in regulating ciliogenesis. Collectively, our findings demonstrate a critical role of Cep55 during brain development and provide mechanistic insights that may have important implications for genetic syndromes associated with Cep55-loss.

Description: Objective To examine the main and interactive effects of the amount of daily television exposure and frequency of parent conversation during shared television viewing on parent ratings of curiosity at kindergarten, and to test for moderation by socioeconomic status (SES). Study design Sample included 5100 children from the Early Childhood Longitudinal Study, Birth Cohort. Hours of daily television exposure and frequency of parent screen-time conversation were assessed from a parent interview at preschool, and the outcome of early childhood curiosity was derived from a child behavior questionnaire at kindergarten. Multivariate linear regression examined the main and interactive effects of television exposure and parent screen-time conversation on kindergarten curiosity and tested for moderation by SES. Results In adjusted models, greater number of hours of daily television viewing at preschool was associated with lower curiosity at kindergarten (B = -0.14, p = .008). More frequent parent conversation during shared screen-time was associated with higher parent-reported curiosity at kindergarten with evidence of moderation by SES. The magnitude of association between frequency of parent conversation during television viewing and curiosity was greater for children from low SES environments, compared to children from high SES environments: (SES ≤ median): B = 0.29, p 〈 .001; (SES 〉 median): B = 0.11, p 〈 .001. Conclusions Higher curiosity at kindergarten was associated with greater frequency of parent conversation during shared television viewing, with a greater magnitude of association in low-SES families. While the study could not include measures of television program content, digital media use and non-screen time conversation, our results suggest the importance of parent conversation to promote early childhood curiosity, especially for children with socioeconomic disadvantage.

Description: Background The Substance Abuse and Mental Health Administration awarded State Targeted Response grants to support states’ efforts to address the opioid epidemic. In Nevada, one component of this grant was mobile recovery outreach teams (MROTs) that utilized peer recovery support specialists to provide care for qualifying patients in emergency departments (EDs). The Mobile Emergency Recovery Intervention Trial (MERIT) is a mixed methods study to assess the feasibility/acceptability and effectiveness of the MROT intervention. This protocol mainly describes the R33 research activities and outcomes. The full protocol can be found protocols.io. Methods Data will be derived from state-level data sets containing de-identified emergency department visits, substance use disorder treatment records, and mortality files; in-person mixed methods interviews; participant observation; and self-report process evaluation forms. Primary outcomes include Medication Assisted Treatment (MAT) initiation and non-fatal overdose; secondary outcomes include MAT retention and fatal overdose. Quantitative hypotheses will be tested using generalized linear mixed effects models, Bayesian hierarchical models, and marginal Cox models. Qualitative interview data will be analyzed using an inductive thematic analysis procedure. Discussion It is impossible to conduct a randomized controlled trial of the effectiveness of the MROTs, given the ethical and logistical considerations of this intervention. This study’s innovative design employs a mixed methods formative phase to examine feasibility and acceptability, and a quasi-experimental outcomes evaluation phase employing advanced statistical methods to mitigate bias and suggest causal inference regarding the effectiveness of the MROTs. Innovative interventions have been deployed in many states; evidence regarding their effectiveness is lacking, but critical to informing an effective public health response to the opioid epidemic.

Description: Stay-at-home orders and shutdowns of non-essential businesses are powerful, but socially costly, tools to control the pandemic spread of SARS-CoV-2. Mass testing strategies, which rely on widely administered frequent and rapid diagnostics to identify and isolate infected individuals, could be a potentially less disruptive management strategy, particularly where vaccine access is limited. In this paper, we assess the extent to which mass testing and isolation strategies can reduce reliance on socially costly non-pharmaceutical interventions, such as distancing and shutdowns. We develop a multi-compartmental model of SARS-CoV-2 transmission incorporating both preventative non-pharmaceutical interventions (NPIs) and testing and isolation to evaluate their combined effect on public health outcomes. Our model is designed to be a policy-guiding tool that captures important realities of the testing system, including constraints on test administration and non-random testing allocation. We show how strategic changes in the characteristics of the testing system, including test administration, test delays, and test sensitivity, can reduce reliance on preventative NPIs without compromising public health outcomes in the future. The lowest NPI levels are possible only when many tests are administered and test delays are short, given limited immunity in the population. Reducing reliance on NPIs is highly dependent on the ability of a testing program to identify and isolate unreported, asymptomatic infections. Changes in NPIs, including the intensity of lockdowns and stay at home orders, should be coordinated with increases in testing to ensure epidemic control; otherwise small additional lifting of these NPIs can lead to dramatic increases in infections, hospitalizations and deaths. Importantly, our results can be used to guide ramp-up of testing capacity in outbreak settings, allow for the flexible design of combined interventions based on social context, and inform future cost-benefit analyses to identify efficient pandemic management strategies.