Publications by authors named "Alexis Sullivan"

Understanding the process of genetic adaptation in response to human-mediated ecological change will help elucidate the eco-evolutionary impacts of human activity. In the 1930s red imported fire ants (Solenopsis invicta) were accidently introduced to the Southeastern USA, where today they are both venomous predators and toxic prey to native eastern fence lizards (Sceloporus undulatus). Here, we investigate potential lizard adaptation to invasive fire ants by generating whole-genome sequences from 420 lizards across three populations: one with long exposure to fire ants, and two unexposed populations.

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Politics as the exercise of power always influence public policies-which reflects the multifaceted nature of decision-making-but "using politics" as a motivation for self-serving interests of government leaders and their allies poses problems. This article reviews the impacts of COVID-19 on health systems of the Latin American and Caribbean region from a political lens. We highlight the overriding influence of politics in health policies, weak governance structures that became compromised, exacerbation of corruption, and breakdowns in the communication and trust between governments and their citizens.

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  • Intestinal microbiota plays a crucial role in various diseases, and understanding diet's impact on it is essential for developing targeted therapies.
  • A study analyzing meals and stool samples from 173 hospitalized patients found that higher caloric intake is linked to greater fecal microbiota diversity.
  • The research indicates that consuming sweets or sugars while on antibiotics may disrupt the microbiome, suggesting that reducing sugar intake during such treatment could help protect gut health.
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Antibiotic-induced microbiome injury, defined as a reduction of ecological diversity and obligate anaerobe taxa, is associated with negative health outcomes in hospitalized patients, and healthy individuals who received antibiotics in the past are at higher risk for autoimmune diseases. No interventions are currently available that effectively target the microbial ecosystem in the gut to prevent this negative collateral damage of antibiotics. Here, we present the results from a single-center, randomized placebo-controlled trial involving 32 patients who received an oral, fermentation-derived postbiotic alongside oral antibiotic therapy for gastrointestinal (GI)-unrelated infections.

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  • Executive functions, crucial for problem-solving and planning, develop rapidly in childhood, but prenatal exposure to environmental toxicants like polycyclic aromatic hydrocarbons (PAHs) may hinder this development.
  • The study analyzed 814 children from non-smoking mothers, measuring urine levels of PAH metabolites during pregnancy and evaluating their executive functions at age 8-9, focusing on cognitive flexibility, working memory, and inhibitory control.
  • Results showed mostly null associations between PAH exposure and executive functions, although some interactions between specific PAH metabolites and working memory were observed, highlighting the need for further research in this area.
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  • The study investigates the impact of early childhood air pollution on executive function in school-aged children, using data from 1235 participants across three US pregnancy cohorts.
  • It examines the effects of pollutants like PM 2.5, nitrogen dioxide (NO2), and ozone (O3) during the ages of 0-4, assessing various cognitive abilities such as working memory and cognitive flexibility.
  • Results suggest that air pollution exposure, particularly NO2, negatively affects executive function, with stronger effects observed in areas with higher educational opportunities; further research is needed to deepen understanding of these environmental influences on child development.
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The human gut microbiome is a promising therapeutic target, but interventions are hampered by our limited understanding of microbial ecosystems. Here, we present a platform to develop, evaluate, and score approaches to learn ecological interactions from microbiome time series data. The microbiome time series inference standardized test (MTIST) comprises: a simulation framework for the generation of microbiome study data akin to what is obtained with quantitative next-generation sequencing approaches, a compilation of a large curated data set generated by the simulation framework representing 648 simulated microbiome studies containing 18,360 time series, with a total of 2,182,800 species abundance measurements, and a scoring method to rank ecological inference algorithms.

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Background: Research and clinical practice rely heavily on caregiver-report measures, such as the Child Behavior Checklist 1.5-5 (CBCL/1.5-5), to gather information about early childhood behavior problems and to screen for child psychopathology.

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Background: Previous work suggests that proprioceptive information from ankle and hip are crucial in maintaining balance during upright standing; however, the contribution of these proprioceptive information during stepping balance recovery in not clear. The goal of the current study was to assess the role of ankle and hip proprioceptive information on balance recovery performance by manipulating type 1a afferent in muscle spindles using vibratory stimulation.

Methods: Twenty healthy young participants were recruited (age = 22.

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Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation.

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Global health research has traditionally been rooted in colonialism, with some investigators in high-income countries leading and managing research and investigators in low- and middle-income countries serving as implementing partners. The Community Health Worker-Led Intervention for Vaccine Information and Confidence (CIVIC) Project, conducted in India and led jointly by India- and US-based investigators, leveraged web-based platforms to facilitate a more horizontal, inclusive, and balanced approach to partnerships between researchers and the community. Using web-based platforms to conduct research was found to be an effective strategy to engage researchers at all levels and combat systemic barriers associated with in-person activities such as power, economic, social, and gender dynamics.

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  • A study analyzed how different factors affected children's and caregivers' experiences during the COVID-19 pandemic using data from a large, diverse group of participants across the US and Puerto Rico.
  • The research looked at variables like caregiver education level, child age, and whether families lived in urban or rural areas, examining outcomes related to COVID-19 infections, school and healthcare disruptions, financial struggles, and remote work.
  • Results showed that caregivers with less education faced more difficulties with accessing tests, lower chances of working remotely, and greater food access issues compared to those with higher education levels.
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Women's social experiences can have long-term implications for their offspring's health, but little is known about the potential independent contributions of multiple periods of stress exposures over time. This study examined associations of maternal exposure to adversity in childhood and pregnancy with children's anxiety and depression symptoms in a large, sociodemographically diverse sample. Participants were 1389 mother-child dyads (child age M = 8.

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  • The study aimed to investigate the relationship between prenatal exposure to polycyclic aromatic hydrocarbons (PAHs) and childhood behavior in a diverse group of children aged 4-6 years.
  • It pooled data from 1118 mother-child pairs across six U.S. cities, measuring PAH levels in prenatal urine and assessing children's behavior using the Child Behavior Checklist.
  • Results indicated that higher levels of one specific PAH metabolite, 2-hydroxynaphthalene, were linked to fewer behavioral problems, especially in boys and in children breastfed for six months or more, although overall findings did not support significant effects of PAH mixtures or other metabolites.
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  • Gut microbiome dysbiosis is linked to COVID-19 severity, but a direct causal relationship has not been proven yet.
  • Research shows that SARS-CoV-2 infection leads to changes in gut bacteria in mice, which could compromise gut barrier function and increase infection risk.
  • Analysis of samples from 96 COVID-19 patients indicates that altered gut bacteria can enter the bloodstream, potentially causing severe secondary infections in these patients.
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Purpose: Exposures early in life, beginning in utero, have long-term impacts on mental and physical health. The ECHO prenatal and early childhood pathways to health consortium (ECHO-PATHWAYS) was established to examine the independent and combined impact of pregnancy and childhood chemical exposures and psychosocial stressors on child neurodevelopment and airway health, as well as the placental mechanisms underlying these associations.

Participants: The ECHO-PATHWAYS consortium harmonises extant data from 2684 mother-child dyads in three pregnancy cohort studies (CANDLE [Conditions Affecting Neurocognitive Development and Learning in Early Childhood], TIDES [The Infant Development and Environment Study] and GAPPS [Global Alliance to Prevent Prematurity and Stillbirth]) and collects prospective data under a unified protocol.

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Introduction: Religious faith is a key marker of identity and shapes community perspectives and trust. Faith leader involvement in vaccine campaigns in India have been beneficial to counter misinformation regarding infectious diseases such as polio. Faith leaders are influential stakeholders who bear potential to enhance public confidence in vaccine campaigns.

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  • * Research using a mouse model shows that SARS-CoV-2 infection disrupts the gut microbiome and affects gut cell function, mirroring findings in human patients.
  • * The study found that hospitalized COVID-19 patients have an overgrowth of harmful bacteria, including antibiotic-resistant strains, which are associated with secondary infections that may originate from the gut.
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Background: Animal and epidemiological studies suggest that prenatal exposure to polycyclic aromatic hydrocarbons (PAHs) may negatively impact toddler neurodevelopment.

Methods: We investigated this association in 835 mother-child pairs from CANDLE, a diverse pregnancy cohort in the mid-South region of the U.S.

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  • A high-quality genomic reference assembly named SceUnd1.0 was created for the eastern fence lizard (Sceloporus undulatus), leveraging advanced sequencing technologies.
  • *The study explored chromosome evolution in lizards and snakes, revealing key changes like the fusion of chromosomes, and this genomic resource also supports improved references for 34 related Sceloporus species.
  • *Findings indicate that while the initial Supernova Assembly is effective for various analyses, incorporating additional data (HiC and PacBio) significantly improves structural genome insights, enhancing the utility for physiological and evolutionary research.*
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  • The gut microbiome has been linked to the severity of COVID-19, but a direct causal relationship had not been clearly established before this study.
  • This research demonstrates that dysbiosis (imbalance) in the gut microbiome can lead to harmful bacteria entering the bloodstream during COVID-19, potentially causing serious infections.
  • Analysis of stool samples from COVID-19 patients showed significant microbiome imbalances, including an increase in harmful bacteria, which aligns with findings from a mouse model that confirms viral infection adversely affects gut health.
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Although protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.

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Understanding the origin and distribution of genetic diversity across landscapes is critical for predicting the future of organisms in changing climates. This study investigated how adaptive and demographic forces have shaped diversity and population structure in Pinus densata, a keystone species on Qinghai-Tibetan Plateau (QTP). We examined the distribution of genomic diversity across the range of P.

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Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies).

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Noninvasive sampling is an important development in population genetic monitoring of wild animals. Particularly, the collection of environmental DNA (eDNA) which can be collected without needing to encounter the target animal facilitates the genetic analysis of endangered species. One method that has been applied to these sample types is target capture and enrichment which overcomes the issue of high proportions of exogenous (nonhost) DNA from these lower quality samples.

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