Knowledge and Instance Mapping: architecture for premeditated interoperability of disparate data for materials

Predicting and elucidating the impacts of materials on human health and the environment is an unending task that has taken on special significance in the context of nanomaterials research over the last two decades. The properties of materials in environmental and physiological media are dynamic, reflecting the complex interactions between materials and these media. This dynamic behavior requires special consideration in the design of databases and data curation that allow for subsequent comparability and interrogation of the data from potentially diverse sources. We present two data processing methods that can be integrated into the experimental process to encourage pre-mediated interoperability of disparate material data: Knowledge Mapping and Instance Mapping. Originally developed as a framework for the NanoInformatics Knowledge Commons (NIKC) database, this architecture and associated methods can be used independently of the NIKC and applied across multiple subfields of nanotechnology and material science.

Multidimensional well-being of US households at a fine spatial scale using fused household surveys

Social science often relies on surveys of households and individuals. Dozens of such surveys are regularly administered by the U.S. government. However, they field independent, unconnected samples with specialized questions, limiting research questions to those that can be answered by a single survey. The presented data comprise the fusion onto the American Community Survey (ACS) microdata of select donor variables from the Residential Energy Consumption Survey (RECS) of 2015, the National Household Travel Survey (NHTS) of 2017, the American Housing Survey (AHS) of 2019, and the Consumer Expenditure Survey - Interview (CEI) for the years 2015-2019. This results in an integrated microdataset of household attributes and well-being dimensions that can be analyzed to address research questions in ways that are not currently possible. The underlying statistical techniques, designed under the fusionACS project, are included in an open-source R package, fusionModel, that provides generic tools for the creation, analysis, and validation of fused microdata.

Remotely sensed above-ground storage tank dataset for object detection and infrastructure assessment

Remotely sensed imagery has increased dramatically in quantity and public availability. However, automated, large-scale analysis of such imagery is hindered by a lack of the annotations necessary to train and test machine learning algorithms. In this study, we address this shortcoming with respect to above-ground storage tanks (ASTs) that are used in a wide variety of industries. We annotated available high-resolution, remotely sensed imagery to develop an original, publicly available multi-class dataset of ASTs. This dataset includes geospatial coordinates, border vertices, diameters, and orthorectified imagery for over 130,000 ASTs from five labeled classes (external floating roof tanks, closed roof tanks, spherical pressure tanks, sedimentation tanks, and water towers) across the contiguous United States. This dataset can be used directly or to train machine learning algorithms for large-scale risk and hazard assessment, production and capacity estimation, and infrastructure evaluation.

A Pregnancy and Childhood Epigenetics Consortium (PACE) meta-analysis highlights potential relationships between birth order and neonatal blood DNA methylation

Higher birth order is associated with altered risk of many disease states. Changes in placentation and exposures to in utero growth factors with successive pregnancies may impact later life disease risk via persistent DNA methylation alterations. We investigated birth order with Illumina DNA methylation array data in each of 16 birth cohorts (8164 newborns) with European, African, and Latino ancestries from the Pregnancy and Childhood Epigenetics Consortium. Meta-analyzed data demonstrated systematic DNA methylation variation in 341 CpGs (FDR adjusted P < 0.05) and 1107 regions. Forty CpGs were located within known quantitative trait loci for gene expression traits in blood, and trait enrichment analysis suggested a strong association with immune-related, transcriptional control, and blood pressure regulation phenotypes. Decreasing fertility rates worldwide with the concomitant increased proportion of first-born children highlights a potential reflection of birth order-related epigenomic states on changing disease incidence trends.

Air quality related equity implications of U.S. decarbonization policy

Climate policies that target greenhouse gas emissions can improve air quality by reducing co-emitted air pollutant emissions. However, the extent to which climate policy could contribute to the targets of reducing existing pollution disparities across different populations remains largely unknown. We quantify potential air pollution exposure reductions under U.S. federal carbon policy, considering implications of resulting health benefits for exposure disparities across U.S. racial/ethnic groups. We focus on policy cases that achieve reductions of 40-60% in 2030 economy-wide carbon dioxide (CO2) emissions, when compared with 2005 emissions. The 50% CO2 reduction policy case reduces average fine particulate matter (PM2.5) exposure across racial/ethnic groups, with greatest benefit for non-Hispanic Black (-0.44 μg/m3) and white populations (-0.37 μg/m3). The average exposure disparity for racial/ethnic minorities rises from 12.4% to 13.1%. Applying an optimization approach to multiple emissions reduction scenarios, we find that no alternate combination of reductions from different CO2 sources would substantially mitigate exposure disparities. Results suggest that CO2-based strategies for this range of reductions are insufficient for fully mitigating PM2.5 exposure disparities between white and racial/ethnic minority populations; addressing disparities may require larger-scale structural changes.

Unequal airborne exposure to toxic metals associated with race, ethnicity, and segregation in the USA

Persons of color have been exposed to a disproportionate burden of air pollution across the United States for decades. Yet, the inequality in exposure to known toxic elements of air pollution is unclear. Here, we find that populations living in racially segregated communities are exposed to a form of fine particulate matter with over three times higher mass proportions of known toxic and carcinogenic metals. While concentrations of total fine particulate matter are two times higher in racially segregated communities, concentrations of metals from anthropogenic sources are nearly ten times higher. Populations living in racially segregated communities have been disproportionately exposed to these environmental stressors throughout the past decade. We find evidence, however, that these disproportionate exposures may be abated though targeted regulatory action. For example, recent regulations on marine fuel oil not only reduced vanadium concentrations in coastal cities, but also sharply lessened differences in vanadium exposure by segregation.

Functionally diverse microbial communities show resilience in response to a record-breaking rain event

Estuaries provide many ecosystem services and host a majority of the world's population. Here, the response of microbial communities after a record-breaking flood event in a highly urbanized estuary was followed. Hurricane Harvey (hereafter Harvey) was a category 4 hurricane that made landfall on the Texas coast in 2017 and lashed the Houston area with 1.4-1.7 × 1010 m3 of rainfall, disrupting the natural gradients of nutrients and salinity. Here, we utilized metagenomics to analyze how Harvey altered the microbial community of Galveston Bay over five weeks following the storm. We hypothesized that the community would shift from a marine dominated community to that of a terrestrial and freshwater origin. We found that following the storm there were changes in the distribution of species with specific metabolic capacities, such as Cyanobacteria, enriched in oxygenic photosynthesis and nitrogen fixation genes, as well as Verrucomicrobia and Betaproteobacteria, with high prevalence of the SOX complex and anoxygenic photosynthesis genes. On the other hand, dominant members of the community with more diverse metabolic capabilities showed less fluctuations in their distribution. Our results highlight how massive precipitation disturbances can alter microbial communities and how the coalescence of diverse microorganisms creates a resilient community able to maintain ecosystem services even when the system is in an altered state.

The relationship between the gut microbiome and the risk of respiratory infections among newborns

Background

Emerging evidence points to a critical role of the developing gut microbiome in immune maturation and infant health; however, prospective studies are lacking.

Methods

We examined the occurrence of infections and associated symptoms during the first year of life in relation to the infant gut microbiome at six weeks of age using bacterial 16S rRNA V4-V5 gene sequencing (N = 465) and shotgun metagenomics (N = 185). We used generalized estimating equations to assess the associations between longitudinal outcomes and 16S alpha diversity and metagenomics species.

Results

Here we show higher infant gut microbiota alpha diversity was associated with an increased risk of infections or respiratory symptoms treated with a prescription medicine, and specifically upper respiratory tract infections. Among vaginally delivered infants, a higher alpha diversity was associated with an increased risk of all-cause wheezing treated with a prescription medicine and diarrhea involving a visit to a health care provider. Positive associations were specifically observed with Veillonella species among all deliveries and Haemophilus influenzae among cesarean-delivered infants.

Conclusion

Our findings suggest that intestinal microbial diversity and the relative abundance of key taxa in early infancy may influence susceptibility to respiratory infection, wheezing, and diarrhea.

Genetically stable CRISPR-based kill switches for engineered microbes

Microbial biocontainment is an essential goal for engineering safe, next-generation living therapeutics. However, the genetic stability of biocontainment circuits, including kill switches, is a challenge that must be addressed. Kill switches are among the most difficult circuits to maintain due to the strong selection pressure they impart, leading to high potential for evolution of escape mutant populations. Here we engineer two CRISPR-based kill switches in the probiotic Escherichia coli Nissle 1917, a single-input chemical-responsive switch and a 2-input chemical- and temperature-responsive switch. We employ parallel strategies to address kill switch stability, including functional redundancy within the circuit, modulation of the SOS response, antibiotic-independent plasmid maintenance, and provision of intra-niche competition by a closely related strain. We demonstrate that strains harboring either kill switch can be selectively and efficiently killed inside the murine gut, while strains harboring the 2-input switch are additionally killed upon excretion. Leveraging redundant strategies, we demonstrate robust biocontainment of our kill switch strains and provide a template for future kill switch development.

Wildland fire smoke alters the composition, diversity, and potential atmospheric function of microbial life in the aerobiome

The atmosphere contains a diverse reservoir of microbes but the sources and factors contributing to microbial aerosol variability are not well constrained. To advance understanding of microbial emissions in wildfire smoke, we used unmanned aircraft systems to analyze the aerosols above high-intensity forest fires in the western United States. Our results show that samples of the smoke contained ~four-fold higher concentrations of cells (1.02 ± 0.26 × 105 m-3) compared to background air, with 78% of microbes in smoke inferred to be viable. Fivefold higher taxon richness and ~threefold enrichment of ice nucleating particle concentrations in smoke implies that wildfires are an important source of diverse bacteria and fungi as well as meteorologically relevant aerosols. We estimate that such fires emit 3.71 × 1014 microbial cells ha-1 under typical wildfire conditions in western US forests and demonstrate that wildland biomass combustion has a large-scale influence on the local atmospheric microbial assemblages. Given the long-range transport of wildfire smoke emissions, these results expand the concept of a wildfire's perimeter of biological impact and have implications to biogeography, gene flow, the dispersal of plant, animal, and human pathogens, and meteorology.

Secondary organic aerosol association with cardiorespiratory disease mortality in the United States

Fine particle pollution, PM2.5, is associated with increased risk of death from cardiorespiratory diseases. A multidecadal shift in the United States (U.S.) PM2.5 composition towards organic aerosol as well as advances in predictive algorithms for secondary organic aerosol (SOA) allows for novel examinations of the role of PM2.5 components on mortality. Here we show SOA is strongly associated with county-level cardiorespiratory death rates in the U.S. independent of the total PM2.5 mass association with the largest associations located in the southeastern U.S. Compared to PM2.5, county-level variability in SOA across the U.S. is associated with 3.5× greater per capita county-level cardiorespiratory mortality. On a per mass basis, SOA is associated with a 6.5× higher rate of mortality than PM2.5, and biogenic and anthropogenic carbon sources both play a role in the overall SOA association with mortality. Our results suggest reducing the health impacts of PM2.5 requires consideration of SOA.

High-throughput toxicogenomic screening of chemicals in the environment using metabolically competent hepatic cell cultures

The ToxCast in vitro screening program has provided concentration-response bioactivity data across more than a thousand assay endpoints for thousands of chemicals found in our environment and commerce. However, most ToxCast screening assays have evaluated individual biological targets in cancer cell lines lacking integrated physiological functionality (such as receptor signaling, metabolism). We evaluated differentiated HepaRGTM cells, a human liver-derived cell model understood to effectively model physiologically relevant hepatic signaling. Expression of 93 gene transcripts was measured by quantitative polymerase chain reaction using Fluidigm 96.96 dynamic arrays in response to 1060 chemicals tested in eight-point concentration-response. A Bayesian framework quantitatively modeled chemical-induced changes in gene expression via six transcription factors including: aryl hydrocarbon receptor, constitutive androstane receptor, pregnane X receptor, farnesoid X receptor, androgen receptor, and peroxisome proliferator-activated receptor alpha. For these chemicals the network model translates transcriptomic data into Bayesian inferences about molecular targets known to activate toxicological adverse outcome pathways. These data also provide new insights into the molecular signaling network of HepaRGTM cell cultures.

Combining expert and crowd-sourced training data to map urban form and functions for the continental US

Although continental urban areas are relatively small, they are major drivers of environmental change at local, regional and global scales. Moreover, they are especially vulnerable to these changes owing to the concentration of population and their exposure to a range of hydro-meteorological hazards, emphasizing the need for spatially detailed information on urbanized landscapes. These data need to be consistent in content and scale and provide a holistic description of urban layouts to address different user needs. Here, we map the continental United States into Local Climate Zone (LCZ) types at a 100 m spatial resolution using expert and crowd-sourced information. There are 10 urban LCZ types, each associated with a set of relevant variables such that the map represents a valuable database of urban properties. These data are benchmarked against continental-wide existing and novel geographic databases on urban form. We anticipate the dataset provided here will be useful for researchers and practitioners to assess how the configuration, size, and shape of cities impact the important human and environmental outcomes.

Germline-dependent transmission of male reproductive traits induced by an endocrine disruptor, di-2-ethylhexyl phthalate, in future generations

In males, defective reproductive traits induced by an exposure to an endocrine disruptor are transmitted to future generations via epigenetic modification of the germ cells. Interestingly, the impacted future generations display a wide range of heterogeneity in their reproductive traits. In this study, the role that the Y chromosome plays in creating such heterogeneity is explored by testing the hypothesis that the Y chromosome serves as a carrier of the exposure impact to future generations. This hypothesis implies that a male who has a Y chromosome that is from a male that was exposed to an endocrine disruptor will display a more severe reproductive phenotype than a male whose Y chromosome is from an unexposed male. To test this hypothesis, we used a mouse model in which F1 generation animals were exposed prenatally to an endocrine disruptor, di-2-ethylhexyl phthalate (DEHP), and the severity of impacted reproductive traits was compared between the F3 generation males that were descendants of F1 males (paternal lineage) and those from F1 females (maternal lineage). Pregnant dams (F0 generation) were exposed to the vehicle or 20 or 200 μg/kg/day of DEHP from gestation day 11 until birth. Paternal lineage F3 DEHP males exhibited decreased fertility, testicular steroidogenic capacity, and spermatogenesis that were more severely impaired than those of maternal lineage males. Indeed, testicular transcriptome analysis found that a number of Y chromosomal genes had altered expression patterns in the paternal lineage males. This transgenerational difference in the DEHP impact can be attributed specifically to the Y chromosome.

Air pollution control strategies directly limiting national health damages in the US

Exposure to fine particulate matter (PM2.5) from fuel combustion significantly contributes to global and US mortality. Traditional control strategies typically reduce emissions for specific air pollutants and sectors to maintain pollutant concentrations below standards. Here we directly set national PM2.5 mortality cost reduction targets within a global human-earth system model with US state-level energy systems, in scenarios to 2050, to identify endogenously the control actions, sectors, and locations that most cost-effectively reduce PM2.5 mortality. We show that substantial health benefits can be cost-effectively achieved by electrifying sources with high primary PM2.5 emission intensities, including industrial coal, building biomass, and industrial liquids. More stringent PM2.5 reduction targets expedite the phaseout of high emission intensity sources, leading to larger declines in major pollutant emissions, but very limited co-benefits in reducing CO2 emissions. Control strategies limiting health damages achieve the greatest emission reductions in the East North Central and Middle Atlantic states.

Anomalously warm temperatures are associated with increased injury deaths

Temperatures that deviate from the long-term local norm affect human health, and are projected to become more frequent as the global climate changes1. There are limited data on how such anomalies affect deaths from injuries. In the present study, we used data on mortality and temperature over 38 years (1980-2017) in the contiguous USA and formulated a Bayesian spatio-temporal model to quantify how anomalous temperatures, defined as deviations of monthly temperature from the local average monthly temperature over the entire analysis period, affect deaths from unintentional (transport, falls and drownings) and intentional (assault and suicide) injuries, by age group and sex. We found that a 1.5 °C anomalously warm year, as envisioned under the Paris Climate Agreement2, would be associated with an estimated 1,601 (95% credible interval 1,430-1,776) additional injury deaths. Of these additional deaths, 84% would occur in males, mostly in adolescence to middle age. These would comprise increases in deaths from drownings, transport, assault and suicide, offset partly by a decline in deaths from falls in older ages. The findings demonstrate the need for targeted interventions against injuries during periods of anomalously warm temperatures, especially as these episodes are likely to increase with global climate change.

Measuring the shape of the biodiversity-disease relationship across systems reveals new findings and key gaps

Diverse host communities commonly inhibit the spread of parasites at small scales. However, the generality of this effect remains controversial. Here, we present the analysis of 205 biodiversity-disease relationships on 67 parasite species to test whether biodiversity-disease relationships are generally nonlinear, moderated by spatial scale, and sensitive to underrepresentation in the literature. Our analysis of the published literature reveals that biodiversity-disease relationships are generally hump-shaped (i.e., nonlinear) and biodiversity generally inhibits disease at local scales, but this effect weakens as spatial scale increases. Spatial scale is, however, related to study design and parasite type, highlighting the need for additional multiscale research. Few studies are unrepresentative of communities at low diversity, but missing data at low diversity from field studies could result in underreporting of amplification effects. Experiments appear to underrepresent high-diversity communities, which could result in underreporting of dilution effects. Despite context dependence, biodiversity loss at local scales appears to increase disease, suggesting that at local scales, biodiversity loss could negatively impact human and wildlife populations.

Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network

Blooms of planktonic cyanobacteria have long been of concern in lakes, but more recently, harmful impacts of riverine benthic cyanobacterial mats been recognized. As yet, we know little about how various benthic cyanobacteria are distributed in river networks, or how environmental conditions or other associated microbes in their consortia affect their biosynthetic capacities. We performed metagenomic sequencing for 22 Oscillatoriales-dominated (Cyanobacteria) microbial mats collected across the Eel River network in Northern California and investigated factors associated with anatoxin-a producing cyanobacteria. All microbial communities were dominated by one or two cyanobacterial species, so the key mat metabolisms involve oxygenic photosynthesis and carbon oxidation. Only a few metabolisms fueled the growth of the mat communities, with little evidence for anaerobic metabolic pathways. We genomically defined four cyanobacterial species, all which shared <96% average nucleotide identity with reference Oscillatoriales genomes and are potentially novel species in the genus Microcoleus. One of the Microcoleus species contained the anatoxin-a biosynthesis genes, and we describe the first anatoxin-a gene cluster from the Microcoleus clade within Oscillatoriales. Occurrence of these four Microcoleus species in the watershed was correlated with total dissolved nitrogen and phosphorus concentrations, and the species that contains the anatoxin-a gene cluster was found in sites with higher nitrogen concentrations. Microbial assemblages in mat samples with the anatoxin-a gene cluster consistently had a lower abundance of Burkholderiales (Betaproteobacteria) species than did mats without the anatoxin-producing genes. The associations of water nutrient concentrations and certain co-occurring microbes with anatoxin-a producing Microcoleus motivate further exploration for their roles as potential controls on the distributions of toxigenic benthic cyanobacteria in river networks.