Publications by authors named "David R Johnson"

Surface-associated microbial systems are hotspots for the spread of plasmid-encoded antibiotic resistance, but how surface association affects plasmid transfer and proliferation remains unclear. Surface association enables prolonged spatial proximities between different populations, which promotes plasmid transfer between them. However, surface association also fosters strong metabolic interactions between different populations, which can direct their spatial self-organization with consequences for plasmid transfer and proliferation.

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This study used data from the National Longitudinal Transition Study 2012 (NLTS 2012) to explore the future goal aspirations of students with extensive support needs who participate in alternate assessments, compared to other students with extensive support needs and to students with other disabilities. We examined students' individualized education program (IEP)/transition planning meeting experiences and postschool goals in relation to their functional, communication, and self-advocacy skills, as well as their school/community support. Students with other disabilities held higher expectations than all students with extensive support needs for future participation in postsecondary education, employment, independent living, and financial independence.

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Phage predation is generally assumed to reduce microbial proliferation while not contributing to the spread of antibiotic resistance. However, this assumption does not consider the effect of phage predation on the spatial organization of different microbial populations. Here, we show that phage predation can increase the spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth by reshaping spatial organization.

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Objectives: To assess whether increasing levels of hospital stress-measured by intensive care unit (ICU) bed occupancy (primary), ventilators in use and emergency department (ED) overflow-were associated with decreasing COVID-19 ICU patient survival in Colorado ICUs during the pre-Delta, Delta and Omicron variant eras.

Design: A retrospective cohort study using discrete-time survival models, fit with generalised estimating equations.

Setting: 34 hospital systems in Colorado, USA, with the highest patient volume ICUs during the COVID-19 pandemic.

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Using National Longitudinal Transition Study 2012 data, this study explored parent and youth expectations in the areas of postsecondary education, employment, independent living, and financial independence. Compared to youth with other disabilities, youth with intellectual and developmental disabilities and their parents had much lower expectations for the four postschool goals, and parent expectations were much lower than youth's own expectations. Also, youth's race, along with their daily living skills and functional abilities, were positively associated with parent and youth expectations in several future goal areas.

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Background: Exercise-based swallowing training (EBST) and transcutaneous neuromuscular electrical stimulation (TNMES) are common modalities used to treat late dysphagia after radiotherapy for nasopharyngeal carcinoma (NPC). We aimed to investigate and compare the efficacies of EBST and TNMES as proactive treatments administered early after radiotherapy.

Methods: Patients with early post-radiotherapy NPC ( = 120) underwent either TNMES or EBST.

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Article Synopsis
  • * Laboratory experiments with Paracoccus denitrificans showed that denitrification in low oxic conditions leads to increased levels of harmful nitrogen oxide intermediates like nitrite and nitric oxide.
  • * This accumulation of intermediates negatively affects growth at low pH, promoting surface growth behaviors that increase genetic diversity, which enhances the evolutionary potential of these microorganisms.
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Biodegradation holds promise as an effective and sustainable process for the removal of synthetic chemical pollutants. Nevertheless, rational engineering of biodegradation for pollutant remediation remains an unfulfilled goal, while chemical pollution of waters and soils continues to advance. Efforts to (i) identify functional bacteria from aquatic and soil microbiomes, (ii) assemble them into biodegrading consortia, and (iii) identify maintenance and performance determinants, are challenged by large number of pollutants and the complexity in the enzymology and ecology of pollutant biodegradation.

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We utilize a coupled economy-agroecology-hydrology modeling framework to capture the cascading impacts of climate change mitigation policy on agriculture and the resulting water quality cobenefits. We analyze a policy that assigns a range of United States government's social cost of carbon estimates ($51, $76, and $152/ton of CO-equivalents) to fossil fuel-based CO emissions. This policy raises energy costs and, importantly for agriculture, boosts the price of nitrogen fertilizer production.

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Metabolic cross-feeding is a pervasive microbial interaction type that affects community stability and functioning and directs carbon and energy flows. The mechanisms that underlie these interactions and their association with metal/metalloid biogeochemistry, however, remain poorly understood. Here, we identified two soil bacteria, Bacillus sp.

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Vaccination in pregnancy using a tetanus toxoid, reduced dose diphtheria toxoid, and reduced dose acellular pertussis (Tdap) vaccine is important for prevention of severe pertussis disease in young infants. The objectives of this systematic literature review were to search for original research studies evaluating the vaccine effectiveness, immunogenicity, and safety of Adacel/Adacel-Polio used during pregnancy to prevent pertussis disease in young infants. Medical databases used included EMBASE, BIOSIS Previews, and Chemical Abstracts, with search terms related to pregnancy, vaccines/immunization, safety, pertussis, effectiveness/efficacy, and immune response; other potentially eligible reports were included where applicable.

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Droplet evaporation is a general process in unsaturated environments that results in micro-scale hydrodynamic flows which in turn determine the spatial distributions of microbial cells across surfaces. These spatial distributions can have significant effects on the development and functioning of surface-associated microbial communities, with consequences for important processes such as the spread of plasmids. Here, we experimentally quantified how evaporation-induced hydrodynamic processes modulate the initial deposition patterns of microbial cells (via the coffee ring effect and Marangoni convection) and how these patterns control the spread of an antibiotic resistance-encoding plasmid during surface-associated growth.

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Plasmids are the main vector by which antibiotic resistance is transferred between bacterial cells within surface-associated communities. In this study, we ask whether there is an optimal time to administer antibiotics to minimize plasmid spread in new bacterial genotypes during community expansion across surfaces. We address this question using consortia of Pseudomonas stutzeri strains, where one is an antibiotic resistance-encoding plasmid donor and the other a potential recipient.

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Objective: To evaluate the effectiveness of the tetanus, diphtheria, and acellular pertussis (Tdap) vaccine containing five pertussis components (Tdap5; Adacel®, Sanofi) when given during pregnancy at preventing pertussis in infants less than 2 months of age.

Methods: The US Centers for Disease Control and Prevention (CDC), in collaboration with the Emerging Infections Program (EIP) Network, undertook a case-control study evaluating the effectiveness of Tdap vaccination in pregnancy against pertussis in infants less than 2 months of age based on data collected by the EIP Network from 2011 through 2014. The dataset from the CDC/EIP Network study was used to conduct this product-specific vaccine effectiveness analysis of Tdap5 vaccination in pregnancy to prevent disease in young infants.

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Direct policy search (DPS) is a method for identifying optimal policies (i.e., rules) for managing a system in response to changing conditions.

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Given the differential risk of type 1 diabetes (T1D) in offspring of affected fathers versus affected mothers and our observation that T1D cases have differential DNA methylation near the imprinted gene compared to controls, we examined whether methylation near mediates the association between T1D family history and T1D risk. In a nested case-control study of 87 T1D cases and 87 controls from the Diabetes Autoimmunity Study in the Young, we conducted causal mediation analyses at 12 region CpGs to decompose the effect of family history on T1D risk into indirect and direct effects. These effects were estimated from two regression models adjusted for the human leukocyte antigen DR3/4 genotype: a linear regression of family history on methylation (mediator model) and a logistic regression of family history and methylation on T1D (outcome model).

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The amount of bacterial diversity present on many surfaces is enormous; however, how these levels of diversity persist in the face of the purifying processes that occur as bacterial communities expand across space (referred to here as range expansion) remains enigmatic. We shed light on this apparent paradox by providing mechanistic evidence for a strong role of fungal hyphae-mediated dispersal on regulating bacterial diversity during range expansion. Using pairs of fluorescently labeled bacterial strains and a hyphae-forming fungal strain that expand together across a nutrient-amended surface, we show that a hyphal network increases the spatial intermixing and extent of range expansion of the bacterial strains.

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Multi-step substrate consumption pathways can promote microbial biodiversity via cross-feeding. If one cell type preferentially consumes a primary substrate rather than the subsequently formed intermediates, then other cell types can specialize in consuming the intermediates. While this mechanism for promoting biodiversity is established, predicting the long-term persistence of such cross-feeding interactions remains challenging.

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Vaccination against hepatitis B (HepB) provides long-term protection against infection. This is despite a reduction in HepB surface antibody (anti-HBs) concentrations over time to levels below the well-accepted correlate of protection of ≥10 mIU/mL. Continued evidence of immune memory and protection despite declined anti-HBs concentrations can be demonstrated by HepB virus surface antigen challenge studies.

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Microbes are social organisms that commonly live in sessile biofilms. Spatial patterns of populations within biofilms can be important determinants of community-level properties. Spatial intermixing emerging from microbial interaction is one of the best-studied characteristics of spatial patterns.

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Spatial self-organization is a hallmark of surface-associated microbial communities that is governed by local environmental conditions and further modified by interspecific interactions. Here, we hypothesize that spatial patterns of microbial cell-types can stabilize the composition of cross-feeding microbial communities under fluctuating environmental conditions. We tested this hypothesis by studying the growth and spatial self-organization of microbial co-cultures consisting of two metabolically interacting strains of the bacterium Pseudomonas stutzeri.

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Microalgal cell attaching and biofilm formation are critical in the application of microalgal biocathode, which severs as one of the hopeful candidates to an original cathode in bioelectrochemical systems. Many efforts have been put in biofilm formation and bioelectrochemical systems for years, but the predominant factors shaping microalgal biocathode formation are sketchy. We launched a pair of researches to investigate microalgal attachment and biofilm formation in the presence/absence of applied voltages using as a model unicellular motile microalga.

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Cell attachment onto electrode-forming biocathodes is a promising alternative to expensive catalysts used for electricity production in bioelectrochemical systems (BESs). Though BESs have been extensively studied for decades, the processes, underlying mechanisms, and determinant driving forces of microalgal biocathode formation remain largely unknown. In this study, we employed a model unicellular motile microalga, Chlamydomonas microsphaera, to investigate the microalgal attachment processes onto the electrode surface of a BES and to identify the determinant factors.

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Conjugative plasmids bestow important traits to microbial communities, such as virulence, antibiotic resistance, pollutant biotransformation, and biotechnology-relevant functions. While the biological mechanisms and determinants of plasmid conjugation are well established, the underlying physical and ecological driving forces remain unclear. Microbial communities often inhabit unsaturated environments, such as soils and host surfaces (e.

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Background: Hypotonic-hyporesponsive episode (HHE) after whole cell pertussis vaccination is a known adverse event. Less is known about the risk of HHE after administration of acellular pertussis vaccines.

Methods: Using parental interviews, this study actively surveyed for HHE among infants after doses 1 and 2 of acellular pertussis vaccine.

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