Search

Volatile organic compounds (VOCs) have diverse functionality, emission sources, and environmental fates. Speciated measurements of their spatiotemporal variability are thus key to understanding their impacts on air quality, health, and climate. Networks of passive samplers can be used to map VOC concentrations, or in situ instruments can be deployed on mobile platforms. Limitations of existing in situ instruments include high cost, identification of non-target species, differentiation of isomeric species, and low time resolution, which limits how quickly an area can be spatially mapped with mobile measurements. This work describes the development of the Multichannel Organics In situ enviRonmental Analyzer (MOIRA), which has been designed for in situ mobile measurements of target and non-target VOCs from the cargo area of a hybrid hatchback wagon vehicle. Staggered sample collection and analysis by four thermal desorption collectors, four miniature gas chromatography (GC) heaters, and two compact residual gas analyzer (RGA) mass spectrometer (MS) detectors enable continuous measurements at a 10 min time resolution. Non-target species and structural isomers can be identified with electron ionization (EI), and species detected include alkanes (from pentane to pentadecane) and aromatics, as well as more oxidized species such as aldehydes, esters, and carboxylic acids. The instrument is characterized in the laboratory under different environmental conditions and in two pilot field studies of indoor air in a single-family residence and of ambient air during a mobile deployment.

Summary: The COVID-19 pandemic has exposed and exacerbated the persistent racial and ethnic health disparities in the United States. The pandemic has also had profound spillover effects on other aspects of health and wellbeing, such as mental health, chronic diseases, education, and income, for marginalized groups. In this article, we provide a thorough analysis of the pandemic’s impact on racial and ethnic health disproportionalities, highlighting the multifaceted and interrelated factors that contribute to these inequities. We also argue for a renewed focus on health equity in healthcare policy and practice, emphasizing the need for systemic changes that address both the immediate and long-term consequences of these imbalances. We propose a framework for achieving health equity that involves creating equitable systems, care, and outcomes for all individuals, regardless of their race or ethnicity.

Abstract Amidst the backdrop of the COVID-19 pandemic, vaccine innovation has garnered significant attention, but this field was already on the cusp of a groundbreaking renaissance. Propelling these advancements are scientific and technological breakthroughs, alongside a growing understanding of the societal and economic boons vaccines offer, particularly for non-pediatric populations like adults and the immunocompromised. In a departure from previous decades where vaccine launches could be seamlessly integrated into existing processes, we anticipate potentially than 100 novel, risk-adjusted product launches over the next 10 years in the adult vaccine market, primarily addressing new indications. However, this segment is infamous for its challenges: low uptake, funding shortfalls, and operational hurdles linked to delivery and administration. To unlock the societal benefits of this burgeoning expansion, we need to adopt a fresh perspective to steer through the dynamics sparked by the rapid growth of the global adult vaccine market. This article aims to provide that fresh perspective, offering a detailed analysis of the anticipated number of adult vaccine approvals by category and exploring how our understanding of barriers to adult vaccine uptake might evolve. We incorporated pertinent insights from external stakeholder interviews, spotlighting shifting preferences, perceptions, priorities, and decision-making criteria. Consequently, this article aspires to serve as a pivotal starting point for industry participants, equipping them with the knowledge to skillfully navigate the anticipated surge in both volume and complexity.

Abstract Dysregulation of the alternative pathway (AP) of the complement system is a significant contributor to age-related macular degeneration (AMD), a primary cause of irreversible vision loss worldwide. Here, we assess the contribution of the liver-produced complement factor H-related 4 protein (FHR-4) to AMD initiation and course of progression. We show that FHR-4 variation in plasma and at the primary location of AMD-associated pathology, the retinal pigment epithelium/Bruch’s membrane/choroid interface, is entirely explained by three independent quantitative trait loci (QTL). Using two distinct cohorts composed of a combined 14,965 controls and 20,741 cases, we ascertain that independent QTLs for FHR-4 are distinct from variants causally associated with AMD, and that FHR-4 variation is not independently associated with disease. Additionally, FHR-4 does not appear to influence AMD progression course among patients with disease driven predominantly by AP dysregulation. Modulation of FHR-4 is therefore unlikely to be an effective therapeutic strategy for AMD.

The Aerodyne Aerosol Mass Spectrometer (AMS) and Aerosol Chemical Speciation Monitor (ACSM) are the most widely applied tools for in situ chemical analysis of the non-refractory bulk composition of fine atmospheric particles. The mass spectra (MS) of many AMS and ACSM observations from field and laboratory studies have been reported in peer-reviewed literature and many of these MS have been submitted to an open-access website. With the increased reporting of such datasets, the database interface requires revisions to meet new demands and applications. One major limitation of the web-based database is the inability to automatically search the database and compare previous MS with the researcher's own data. In this study, a searchable database tool for the AMS and ACSM mass spectral dataset was built to improve the efficiency of data analysis using Igor Pro, consistent with existing AMS and ACSM software. The database tool incorporates the published MS and sample information uploaded on the website. This tool allows the comparison of a target mass spectrum with the reference MS in the database, calculating cosine similarity, and provides a range of MS comparison plots, reweighting, and mass spectrum filtering options. The aim of this work is to help AMS and ACSM users efficiently analyze their own data for possible source or atmospheric processing features by comparison to previous studies, enhancing information gained from past and current global research on atmospheric aerosol.

Abstract The COVID-19 pandemic was met with rapid, unprecedented global collaboration and action. Even still, the public health, societal, and economic impact may be felt for years to come. The risk of another pandemic occurring in the next few decades is ever-present and potentially increasing due to trends such as urbanization and climate change. While it is difficult to predict the next pandemic pathogen threat, making reasonable assumptions today and evaluating prior efforts to plan for and respond to disease outbreaks and pandemics may enable a more proactive, effective response in the future. Lessons from the COVID-19 response and pandemic influenza preparedness underscore the importance of strengthening surveillance systems, investing in early-stage research on pandemic pathogens and development of platform technologies, and diversifying response plans across a range of tactics to enable earlier access to safe and effective interventions in the next pandemic. Further, sustaining the robust vaccine manufacturing capacity built because of COVID-19 will keep it ready for rapid response in the future. These actions will not be successful without improved global coordination and collaboration. Everyone, including the biopharmaceutical industry, has a role to play in pandemic preparedness, and working together will ensure that the most lives are saved in the next pandemic.

ABSTRACT Assuring that cell therapy products are safe before releasing them for use in patients is critical. Currently, compendial sterility testing for bacteria and fungi can take 7–14 days. The goal of this work was to develop a rapid untargeted approach for the sensitive detection of microbial contaminants at low abundance from low volume samples during the manufacturing process of cell therapies. We developed a long-read sequencing methodology using Oxford Nanopore Technologies MinION platform with 16S and 18S amplicon sequencing to detect USP organisms and other microbial species. Reads are classified metagenomically to predict the microbial species. We used an extreme gradient boosting machine learning algorithm (XGBoost) to first assess if a sample is contaminated, and second, determine whether the predicted contaminant is correctly classified or misclassified. The model was used to make a final decision on the sterility status of the input sample. An optimized experimental and bioinformatics pipeline starting from spiked species through to sequenced reads allowed for the detection of microbial samples at 10 colony-forming units (CFU)/mL using metagenomic classification. Machine learning can be coupled with long-read sequencing to detect and identify sample sterility status and microbial species present in T-cell cultures, including the USP organisms to 10 CFU/mL. IMPORTANCE This research presents a novel method for rapidly and accurately detecting microbial contaminants in cell therapy products, which is essential for ensuring patient safety. Traditional testing methods are time-consuming, taking 7–14 days, while our approach can significantly reduce this time. By combining advanced long-read nanopore sequencing techniques and machine learning, we can effectively identify the presence and types of microbial contaminants at low abundance levels. This breakthrough has the potential to improve the safety and efficiency of cell therapy manufacturing, leading to better patient outcomes and a more streamlined production process.

Abstract Background More than 4 billion doses of the Coronavirus disease (COVID-19) vaccine have been administered worldwide but the relationship between the different vaccines and the development of renal disease is unknown. We present a case of tubulointerstitial nephritis following administration of the Oxford-AstraZeneca COVID-19 vaccine. Case presentation A previously fit and well 51-year-old female presented on 27th May 2021 with a one-month history of weight loss, fatigue, nausea, and a metallic taste. She had an acute kidney injury with a creatinine of 484 umol/L. She was on no regular medications and denied taking any over-the-counter or alternative medicines. She had received her first dose of the Oxford-AstraZeneca vaccine on 23rd March 2021 and her second dose on 20th May 2021. A renal biopsy was performed the following day. The 19 glomeruli appeared normal to light microscopy but the tubulointerstitial compartment contained a dense inflammatory infiltrate including many eosinophils. There was widespread acute tubular injury with tubulitis, but no established or longstanding atrophy. A diagnosis was made of an acute tubulointerstitial nephritis. She was commenced on oral prednisolone and her renal function improved. She did not require renal replacement therapy at any time. Conclusions To our knowledge, this was the first described case of acute tubulointerstitial nephritis following administration of the Oxford-AstraZeneca COVID-19 vaccine, although a number of cases have emerged more recently. In our case the patient was very fit and well, had no previous past medical history and had not taken any recent prescribed, over-the-counter or alternative medications. The absence of these provoking factors in our case makes the vaccine the most likely explanation for the development of tubulointerstitial nephritis although the pathophysiology behind this remains unknown. Given the unprecedented number of vaccinations being delivered around the world, nephrologists should be aware of this possible link although more research into the topic is required.

Abstract Conventional nitrogen removal in wastewater treatment requires a high oxygen and energy input. Anaerobic ammonium oxidation (anammox), the single-step conversion of ammonium and nitrite to nitrogen gas, is a more energy and cost effective alternative applied extensively to sidestream wastewater treatment. It would also be a mainstream treatment option if species diversity and physiology were better understood. Anammox bacteria were enriched up to 80%, 90% and 50% relative abundance, from a single inoculum, under standard enrichment conditions with either stepwise-nitrite and ammonia concentration increases (R1), nitric oxide supplementation (R2), or complex organic carbon from mainstream wastewater (R3), respectively. Candidatus Brocadia caroliniensis predominated in all reactors, but a shift towards Ca. Brocadia sinica occurred at ammonium and nitrite concentrations > 270 mg NH4–N L−1 and 340 mg NO2–N L−1 respectively. With NO present, heterotrophic growth was inhibited, and Ca. Jettenia coexisted with Ca. B. caroliniensis before diminishing as nitrite increased to 160 mg NO2–N L−1. Organic carbon supplementation led to the emergence of heterotrophic communities that coevolved with Ca. B. caroliniensis. Ca. B. caroliniensis and Ca. Jettenia preferentially formed biofilms on surfaces, whereas Ca. Brocadia sinica formed granules in suspension. Our results indicate that multiple anammox bacteria species co-exist and occupy sub-niches in anammox reactors, and that the dominant population can be reversibly shifted by, for example, changing nitrogen load (i.e. high nitrite concentration favors Ca. Brocadia caroliniensis). Speciation has implications for wastewater process design, where the optimum cell immobilization strategy (i.e. carriers vs granules) depends on which species dominates.

Background Clinically relevant aortic dilatation (>40 mm) and increased cardiovascular risk are common among retired professional American‐style football athletes. Among younger athletes, the effect of American‐style football participation on aortic size is incompletely understood. We sought to determine changes in aortic root (AR) size and associated cardiovascular phenotypes across the collegiate career. Methods and Results This was a multicenter, longitudinal repeated‐measures observational cohort study of athletes across 3 years of elite collegiate American‐style football participation. A total of 247 athletes (119 [48%] Black, 126 [51%] White, 2 [1%] Latino; 91 [37%] linemen, 156 [63%] non‐linemen) were enrolled as freshmen and studied at pre‐ and postseason year 1, postseason year 2 (N=140 athletes), and postseason year 3 (N=82 athletes). AR size was measured with transthoracic echocardiography. AR diameter increased over the study period from 31.7 (95% CI, 31.4–32.0) to 33.5 mm (95% CI, 33.1–33.8; P

The ocular surface microbiome has implications for ocular surface inflammation and immunology. Previous shotgun metagenomics analyses were performed in China, showing results that differed according to environment and age. Patients with Sjogren’s syndrome were reported to have altered conjunctival microbiome, but such studies have not been done in milder dry eye. The aim of this study is to describe the conjunctival microbiome in people with mild dry eye in Singapore. Samples were collected from 14 participants with mild dry eye and 10 age-matched comparison participants recruited from Singapore National Eye Centre (SNEC) clinics. Shotgun metagenomic sequencing analysis was employed to evaluate the conjunctival microbiome composition. Proteobacteria formed the predominant phylum in the conjunctiva. As in a study from a coastal city in China, Achromobacter spp. was numerically most abundant. Compared to age-matched controls, the conjunctival microbial composition in mild dry eye was similar. Several microorganisms, including Streptococcus spp. increased in representation with age, and the abundance of Staphylococcus correlated with Schirmer readings. In addition, when cultured corneal epithelial cells were exposed to three strains of Achromobacter xylosoxidans, cytokines such as TNF-α and IL-6 were upregulated in the cell lysates and supernatants. Ourresults suggest that age is an important factor that affects composition of the conjunctival microbiome, and relative abundance of specific microorganism may vary according to the environment of the human host.

Abstract This study aimed to characterize the alteration of the fecal microbiome and antimicrobial resistance (AMR) determinants in 24 piglets at day 3 pre-weaning (D. − 3), weaning day (D.0), days 3 (D.3) and 8 post-weaning (D.8), using whole-genome shotgun sequencing. Distinct clusters of microbiomes and AMR determinants were observed at D.8 when Prevotella (20.9%) was the major genus, whereas at D. − 3–D.3, Alistipes (6.9–12.7%) and Bacteroides (5.2–8.5%) were the major genera. Lactobacillus and Escherichia were notably observed at D. − 3 (1.2%) and D. − 3–D.3 (0.2–0.4%), respectively. For AMR, a distinct cluster of AMR determinants was observed at D.8, mainly conferring resistance to macrolide–lincosamide–streptogramin (mefA), β-lactam (cfxA6 and aci1) and phenicol (rlmN). In contrast, at D. − 3–D.3, a high abundance of determinants with aminoglycoside (AMG) (sat, aac(6')-aph(2''), aadA and acrF), β-lactam (fus-1, cepA and mrdA), multidrug resistance (MDR) (gadW, mdtE, emrA, evgS, tolC and mdtB), phenicol (catB4 and cmlA4), and sulfonamide patterns (sul3) was observed. Canonical correlation analysis (CCA) plot associated Escherichia coli with aac(6')-aph(2''), emrA, mdtB, catB4 and cmlA4 at D. − 3, D.0 and/or D.3 whereas at D.8 associations between Prevotella and mefA, cfxA6 and aci1 were identified. The weaning age and diet factor played an important role in the microbial community composition.

Abstract Background Cylindrospermopsin is a highly persistent cyanobacterial secondary metabolite toxic to humans and other living organisms. Strain OF001 and A210 are manganese-oxidizing bacteria (MOB) able to transform cylindrospermopsin during the oxidation of Mn2+. So far, the enzymes involved in manganese oxidation in strain OF001 and A210 are unknown. Therefore, we analyze the genomes of two cylindrospermopsin-transforming MOB, Pseudomonas sp. OF001 and Rubrivivax sp. A210, to identify enzymes that could catalyze the oxidation of Mn2+. We also investigated specific metabolic features related to pollutant degradation and explored the metabolic potential of these two MOB with respect to the role they may play in biotechnological applications and/or in the environment. Results Strain OF001 encodes two multicopper oxidases and one haem peroxidase potentially involved in Mn2+ oxidation, with a high similarity to manganese-oxidizing enzymes described for Pseudomonas putida GB-1 (80, 83 and 42% respectively). Strain A210 encodes one multicopper oxidase potentially involved in Mn2+ oxidation, with a high similarity (59%) to the manganese-oxidizing multicopper oxidase in Leptothrix discophora SS-1. Strain OF001 and A210 have genes that might confer them the ability to remove aromatic compounds via the catechol meta- and ortho-cleavage pathway, respectively. Based on the genomic content, both strains may grow over a wide range of O2 concentrations, including microaerophilic conditions, fix nitrogen, and reduce nitrate and sulfate in an assimilatory fashion. Moreover, the strain A210 encodes genes which may convey the ability to reduce nitrate in a dissimilatory manner, and fix carbon via the Calvin cycle. Both MOB encode CRISPR-Cas systems, several predicted genomic islands, and phage proteins, which likely contribute to their genome plasticity. Conclusions The genomes of Pseudomonas sp. OF001 and Rubrivivax sp. A210 encode sequences with high similarity to already described MCOs which may catalyze manganese oxidation required for cylindrospermopsin transformation. Furthermore, the analysis of the general metabolism of two MOB strains may contribute to a better understanding of the niches of cylindrospermopsin-removing MOB in natural habitats and their implementation in biotechnological applications to treat water.

Abstract New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read data (ONT MinION) obtained from an ensemble of activated sludge enrichment bioreactors we recover 22 closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses, specifically microbes known to exhibit the polyphosphate- and glycogen-accumulating organism phenotypes (namely Candidatus Accumulibacter and Dechloromonas, and Micropruina, Defluviicoccus and Candidatus Contendobacter, respectively), and filamentous bacteria (Thiothrix) associated with the formation and stability of activated sludge flocs. Additionally we demonstrate the recovery of close to 100 circularised plasmids, phages and small microbial genomes from these microbial communities using long read assembled sequence. We describe methods for validating long read assembled genomes using their counterpart short read metagenome-assembled genomes, and assess the influence of different correction procedures on genome quality and predicted gene quality. Our findings establish the feasibility of performing long read metagenome-assembled genome recovery for both chromosomal and non-chromosomal replicons, and demonstrate the value of parallel sampling of moderately complex enrichment communities to obtaining high quality reference genomes of key functional species relevant for wastewater bioprocesses.

The NOD-like receptor protein 3 (NLRP3) inflammasome is a multi-protein signalling complex integral to the chronic inflammatory response, activated in response to sterile and non-sterile cellular damage. The assembly and activation of the NLRP3 inflammasome comprise a two-step process involving nuclear factor kappa B (NFkB)-mediated priming, followed by canonical, non-canonical or alternative signalling pathways. These result in the maturation and release of inflammatory cytokines interleukin 1 beta (IL1ß) and interleukin-18 (IL18), which are associated with chronic inflammatory conditions including diabetic kidney disease. Diabetic nephropathy is a condition affecting ∼40% of people with diabetes, the key underlying pathology of which is tubulointerstitial inflammation and fibrosis. There is growing evidence to suggest the involvement of the NLRP3 inflammasome in this chronic inflammation. Early deterioration of kidney function begins in the glomerulus, with tubular inflammation dictating the progression of late-stage disease. Priming and activation of the NLRP3 inflammasome have been linked to several clinical markers of nephropathy including proteinuria and albuminuria, in addition to morphological changes including mesangial expansion. Treatment options for diabetic nephropathy are limited, and research that examines the impact of directly targeting the NLRP3 inflammasome, or associated downstream components are beginning to gain favour, with several agents currently in clinical trials. This review will explore a role for NLRP3 inflammasome activation and signalling in mediating inflammation in diabetic nephropathy, specifically in the glomerulus and proximal tubule, before briefly describing the current position of therapeutic research in this field.

The analysis of metagenome data based on the recovery of draft genomes (so called metagenome-assembled genomes, or MAG) has assumed an increasingly central role in microbiome research in recent years. Microbial communities underpinning the operation of wastewater treatment plants are particularly challenging targets for MAG analysis due to their high ecological complexity, and remain important, albeit understudied, microbial communities that play ssa key role in mediating interactions between human and natural ecosystems. Here we consider strategies for recovery of MAG sequence from time series metagenome surveys of full-scale activated sludge microbial communities. We generate MAG catalogs from this set of data using several different strategies, including the use of multiple individual sample assemblies, two variations on multi-sample co-assembly and a recently published MAG recovery workflow using deep learning. We obtain a total of just under 9,100 draft genomes, which collapse to around 3,100 non-redundant genomic clusters. We examine the strengths and weaknesses of these approaches in relation to MAG yield and quality, showing that co-assembly may offer advantages over single-sample assembly in the case of metagenome data obtained from closely sampled longitudinal study designs. Around 1,000 MAGs were candidates for being considered high quality, based on single-copy marker gene occurrence statistics, however only 58 MAG formally meet the MIMAG criteria for being high quality draft genomes. These findings carry broader broader implications for performing genome-resolved metagenomics on highly complex communities, the design and implementation of genome recoverability strategies, MAG decontamination and the search for better binning methodology.

Members of the genus Defluviicoccus occur often at high abundances in activated sludge wastewater treatment plants designed to remove phosphorus, where biomass is subjected to alternating anaerobic feed/aerobic famine conditions, believed to favor the proliferation of organisms like Ca. Accumulibacter and other phosphate-accumulating organisms (PAO), and Defluviicoccus. All have a capacity to assimilate readily metabolizable substrates and store them intracellularly during the anaerobic feed stage so that under the subsequent famine aerobic stage, these can be used to synthesize polyphosphate reserves by the PAO and glycogen by Defluviicoccus. Consequently, Defluviicoccus is described as a glycogen-accumulating organism or GAO. Because they share a similar anaerobic phenotype, it has been proposed that at high Defluviicoccus abundance, the PAO are out-competed for assimilable metabolites anaerobically, and hence aerobic P removal capacity is reduced. Several Defluviicoccus whole genome sequences have been published (Ca. Defluviicoccus tetraformis, Defluviicoccus GAO-HK, and Ca. Defluviicoccus seviourii). The available genomic data of these suggest marked metabolic differences between them, some of which have ecophysiological implications. Here, we describe the whole genome sequence of the type strain Defluviicoccus vanusT, the only cultured member of this genus, and a detailed comparative re-examination of all extant Defluviicoccus genomes. Each, with one exception, which appears not to be a member of this genus, contains the genes expected of GAO members, in possessing multiple copies of those for glycogen biosynthesis and catabolism, and anaerobic polyhydroxyalkanoate (PHA) synthesis. Both 16S rRNA and genome sequence data suggest that the current recognition of four clades is insufficient to embrace their phylogenetic biodiversity, but do not support the view that they should be re-classified into families other than their existing location in the Rhodospirillaceae. As expected, considerable variations were seen in the presence and numbers of genes encoding properties associated with key substrate assimilation and metabolic pathways. Two genomes also carried the pit gene for synthesis of the low-affinity phosphate transport protein, pit, considered by many to distinguish all PAO from GAO. The data re-emphasize the risks associated with extrapolating the data generated from a single Defluviicoccus population to embrace all members of that genus.

Herold et al. present an integrated meta-omics framework to investigate how mixed microbial communities, such as oleaginous bacterial populations in biological wastewater treatment plants, respond with distinct adaptation strategies to disturbances. They show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity.

The geosciences are one of the least diverse disciplines in the United States, despite the field's relevance to livelihoods and local and global economies. Bias, discrimination, and harassment present serious hurdles to diversifying the field. These behaviors persist due to historical structures of exclusion, severe power imbalances, unique challenges associated with geoscientist stereotypes, and a culture of impunity that tolerates exclusionary behaviors and marginalization of scholars from underserved groups. We summarize recent research on exclusionary behaviors that create hostile climates and contribute to persistent low retention of diverse groups in the geosciences and other science, technology, engineering, and mathematics (STEM) fields. We then discuss recent initiatives in the US by geoscience professional societies and organizations, including the National Science Foundation-supported ADVANCEGeo Partnership, to improve diversity, equity, and inclusion by improving workplace climate. Social networks and professional organizations can transform scientific culture through providing opportunities for mentorship and community building and counteracting professional isolation that can result from experiencing hostile behaviors, codifying ethical practice, and advocating for policy change. We conclude with a call for a reexamination of current institutional structures, processes, and practices for a transformational and equitable scientific enterprise. To be truly successful, cultural and behavioral changes need to be accompanied by reeducation about the historical political structures of academic institutions to start conversations about the real change that has to happen for a transformational and equitable scientific enterprise.

Background Ventricular–arterial (VA) coupling is defined as the ratio between arterial elastance (EA) and left ventricular elastance (ELV). VA uncoupling, as occurs in hypertensive heart disease, is associated with adverse outcomes. This study sought to determine the relationship between American football (AF)–associated hypertension and VA uncoupling. Methods and Results This was a multicenter, longitudinal, and repeated measures observational study of collegiate AF athletes across 3 years of AF participation. Of 200 freshman athletes initially enrolled, 142 (67 Black [47%]/75 White [53%], 58 linemen [41%]/84 nonlinemen [59%]) were prospectively studied with echocardiography and applanation tonometry. Primary echocardiographic VA coupling outcome measures were EA/ELV and ΔEA/ELV, with increased EA/ELV indicating VA uncoupling. Adjusting for race and player position, AF athletes demonstrated increased EA/ELV (mean [95% CI]Δ, 0.10 [0.04–0.15]; P=0.001) and systolic blood pressure (SBP) (mean [95% CI]Δ, 11.4 [8.3–14.5] mm Hg, P

Equine theileriosis, caused by Theileria haneyi and Theileria equi, leads to anemia, exercise intolerance, and occasionally, death. Theileriosis-free countries prohibit the importation of infected horses, resulting in significant costs for the equine industry. Imidocarb dipropionate is the only treatment for T. equi in the United States, but lacks efficacy against T. haneyi. The goal of this study was to assess the in vivo efficacy of tulathromycin and diclazuril against T. haneyi. Fourteen T. haneyi-infected horses were utilized. Six were treated with eight weekly 2.5 mg/kg doses of tulathromycin. Three were treated daily for eight weeks with 2.5 mg/kg diclazuril. Three were pre-treated with 0.5 mg/kg diclazuril daily for one month to determine whether low-dose diclazuril prevents infection. Following infection, the dose was increased to 2.5 mg/kg for eight weeks. Two infected horses remained untreated as controls. The horses were assessed via nested PCR, physical exams, complete blood counts, serum chemistry panels, and cytology. Tulathromycin and diclazuril failed to clear T. haneyi and the treated and control groups exhibited similar parasitemia and packed cell volume declines. To obtain additional safety data on tulathromycin use in adult horses, necropsy and histopathology were performed on tulathromycin-treated horses. No significant lesions were detected.

In this paper we present an overview of measurements conducted during the WADIS-2 rocket campaign. We investigate the effect of small-scale processes like gravity waves and turbulence on the distribution of atomic oxygen and other species in the mesosphere–lower thermosphere (MLT) region. Our analysis suggests that density fluctuations of atomic oxygen are coupled to fluctuations of other constituents, i.e., plasma and neutrals. Our measurements show that all measured quantities, including winds, densities, and temperatures, reveal signatures of both waves and turbulence. We show observations of gravity wave saturation and breakdown together with simultaneous measurements of generated turbulence. Atomic oxygen inside turbulence layers shows two different spectral behaviors, which might imply a change in its diffusion properties.

Abstract Background Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible. Results We demonstrate that whole bacterial chromosomes can be obtained from an enriched community, by application of MinION sequencing to a sample from an EBPR bioreactor, producing 6 Gb of sequence that assembles into multiple closed bacterial chromosomes. We provide a simple pipeline for processing such data, which includes a new approach to correcting erroneous frame-shifts. Conclusions Advances in long-read sequencing technology and corresponding algorithms will allow the routine extraction of whole chromosomes from environmental samples, providing a more detailed picture of individual members of a microbiome.

Abstract NRLMSIS® 2.0 is an empirical atmospheric model that extends from the ground to the exobase and describes the average observed behavior of temperature, eight species densities, and mass density via a parametric analytic formulation. The model inputs are location, day of year, time of day, solar activity, and geomagnetic activity. NRLMSIS 2.0 is a major, reformulated upgrade of the previous version, NRLMSISE‐00. The model now couples thermospheric species densities to the entire column, via an effective mass profile that transitions each species from the fully mixed region below ~70 km altitude to the diffusively separated region above ~200 km. Other changes include the extension of atomic oxygen down to 50 km and the use of geopotential height as the internal vertical coordinate. We assimilated extensive new lower and middle atmosphere temperature, O, and H data, along with global average thermospheric mass density derived from satellite orbits, and we validated the model against independent samples of these data. In the mesosphere and below, residual biases and standard deviations are considerably lower than NRLMSISE‐00. The new model is warmer in the upper troposphere and cooler in the stratosphere and mesosphere. In the thermosphere, N2 and O densities are lower in NRLMSIS 2.0; otherwise, the NRLMSISE‐00 thermosphere is largely retained. Future advances in thermospheric specification will likely require new in situ mass spectrometer measurements, new techniques for species density measurement between 100 and 200 km, and the reconciliation of systematic biases among thermospheric temperature and composition data sets, including biases attributable to long‐term changes.

Bulk production of medium-chain carboxylates (MCCs) with 6–12 carbon atoms is of great interest to biotechnology. Open cultures (e.g., reactor microbiomes) have been utilized to generate MCCs in bioreactors. When in-line MCC extraction and prevention of product inhibition is required, the bioreactors have been operated at mildly acidic pH (5.0–5.5). However, model chain-elongating bacteria grow optimally at neutral pH values. Here, we isolated a chain-elongating bacterium (strain 7D4C2) that grows at mildly acidic pH. We studied its metabolism and compared its whole genome and the reverse β-oxidation (rBOX) genes to other bacteria. Strain 7D4C2 produces lactate, acetate, n-butyrate, n-caproate, biomass, and H2/CO2 from hexoses. With only fructose as substrate (pH 5.5), the maximum n-caproate specificity (i.e., products per other carboxylates produced) was 60.9 ± 1.5%. However, this was considerably higher at 83.1 ± 0.44% when both fructose and n-butyrate (electron acceptor) were combined as a substrate. A comparison of 7D4C2 cultures with fructose and n-butyrate with an increasing pH value from 4.5 to 9.0 showed a decreasing n-caproate specificity from ∼92% at mildly acidic pH (pH 4.5-5.0) to ∼24% at alkaline pH (pH 9.0). Moreover, when carboxylates were extracted from the broth (undissociated n-caproic acid was ∼0.3 mM), the n-caproate selectivity (i.e., product per substrate fed) was 42.6 ± 19.0% higher compared to 7D4C2 cultures without extraction. Based on the 16S rRNA gene sequence, strain 7D4C2 is most closely related to the isolates Caproicibacter fermentans (99.5%) and Caproiciproducens galactitolivorans (94.7%), which are chain-elongating bacteria that are also capable of lactate production. Whole-genome analyses indicate that strain 7D4C2, C. fermentans, and C. galactitolivorans belong to the same genus of Caproiciproducens. Their rBOX genes are conserved and located next to each other, forming a gene cluster, which is different than for other chain-elongating bacteria such as Megasphaera spp. In conclusion, Caproiciproducens spp., comprising strain 7D4C2, C. fermentans, C. galactitolivorans, and several unclassified strains, are chain-elongating bacteria that encode a highly conserved rBOX gene cluster. Caproiciproducens sp. 7D4C2 (DSM 110548) was studied here to understand n-caproate production better at mildly acidic pH within microbiomes and has the additional potential as a pure-culture production strain to convert sugars into n-caproate.

ABSTRACT This study describes the first direct functional assignment of a highly abundant extracellular protein from a key environmental and biotechnological biofilm performing an anaerobic ammonium oxidation (anammox) process. Expression levels of Brosi_A1236, belonging to a class of proteins previously suggested to be cell surface associated, were in the top one percentile of all genes in the “Candidatus Brocadia sinica”-enriched biofilm. The Brosi_A1236 structure was computationally predicted to consist of immunoglobulin-like anti-parallel β-strands, and circular dichroism conducted on the isolated surface protein indicated that β-strands are the dominant higher-order structure. The isolated protein was stained positively by the β-sheet-specific stain thioflavin T, along with cell surface- and matrix-associated regions of the biofilm. The surface protein has a large unstructured content, including two highly disordered domains at its C terminus. The disordered domains bound to the substratum and thereby facilitated the adhesion of negatively charged latex microspheres, which were used as a proxy for cells. The disordered domains and isolated whole surface protein also underwent liquid-liquid phase separation to form liquid droplets in suspension. Liquid droplets of disordered protein wet the surfaces of microspheres and bacterial cells and facilitated their coalescence. Furthermore, the surface layer protein formed gels as well as ordered crystalline structures. These observations suggest that biophysical remodeling through phase transitions promotes aggregation and biofilm formation. IMPORTANCE By employing biophysical and liquid-liquid phase separation concepts, this study revealed how a highly abundant extracellular protein enhances the key environmental and industrial bioprocess of anaerobic ammonium oxidation (anammox). Extracellular proteins of environmental biofilms are understudied and poorly annotated in public databases. Understanding the function of extracellular proteins is also increasingly important for improving bioprocesses and resource recovery. Here, protein functions were assessed based on theoretical predictions of intrinsically disordered domains, known to promote adhesion and liquid-liquid phase separation, and available surface layer protein properties. A model is thus proposed to explain how the protein promotes aggregation and biofilm formation by extracellular matrix remodeling and phase transitions. This work provides a strong foundation for functional investigations of extracellular proteins involved in biofilm development.

Abstract Background There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing, and there is a need to adapt short read tools to long read datasets. Methods We describe a new LCA-based algorithm for taxonomic binning, and an interval-tree based algorithm for functional binning, that are explicitly designed for long reads and assembled contigs. We provide a new interactive tool for investigating the alignment of long reads against reference sequences. For taxonomic and functional binning, we propose to use LAST to compare long reads against the NCBI-nr protein reference database so as to obtain frame-shift aware alignments, and then to process the results using our new methods. Results All presented methods are implemented in the open source edition of MEGAN, and we refer to this new extension as MEGAN-LR (MEGAN long read). We evaluate the LAST+MEGAN-LR approach in a simulation study, and on a number of mock community datasets consisting of Nanopore reads, PacBio reads and assembled PacBio reads. We also illustrate the practical application on a Nanopore dataset that we sequenced from an anammox bio-rector community. Reviewers This article was reviewed by Nicola Segata together with Moreno Zolfo, Pete James Lockhart and Serghei Mangul. Conclusion This work extends the applicability of the widely-used metagenomic analysis software MEGAN to long reads. Our study suggests that the presented LAST+MEGAN-LR pipeline is sufficiently fast and accurate.

Oxidation flow reactors (OFRs) have been developed to achieve high degrees of oxidant exposures over relatively short space times (defined as the ratio of reactor volume to the volumetric flow rate). While, due to their increased use, attention has been paid to their ability to replicate realistic tropospheric reactions by modeling the chemistry inside the reactor, there is a desire to customize flow patterns. This work demonstrates the importance of decoupling tracer signal of the reactor from that of the tubing when experimentally obtaining these flow patterns. We modeled the residence time distributions (RTDs) inside the Washington University Potential Aerosol Mass (WU-PAM) reactor, an OFR, for a simple set of configurations by applying the tank-in-series (TIS) model, a one-parameter model, to a deconvolution algorithm. The value of the parameter, N, is close to unity for every case except one having the highest space time. Combined, the results suggest that volumetric flow rate affects mixing patterns more than use of our internals. We selected results from the simplest case, at 78 s space time with one inlet and one outlet, absent of baffles and spargers, and compared the experimental F curve to that of a computational fluid dynamics (CFD) simulation. The F curves, which represent the cumulative time spent in the reactor by flowing material, match reasonably well. We value that the use of a small aspect ratio reactor such as the WU-PAM reduces wall interactions; however sudden apertures introduce disturbances in the flow, and suggest applying the methodology of tracer testing described in this work to investigate RTDs in OFRs to observe the effect of modified inlets, outlets and use of internals prior to application (e.g., field deployment vs. laboratory study).

The chemical complexity of biomass burning organic aerosol (BBOA) greatly increases with photochemical aging in the atmosphere, necessitating controlled laboratory studies to inform field observations. In these experiments, BBOA from American white oak (Quercus alba) leaf and heartwood samples was generated in a custom-built emissions and combustion chamber and photochemically aged in a potential aerosol mass (PAM) flow reactor. A thermal desorption aerosol gas chromatograph (TAG) was used in parallel with a high-resolution time-of-flight aerosol mass spectrometer (AMS) to analyze BBOA chemical composition at different levels of photochemical aging. Individual compounds were identified and integrated to obtain relative decay rates for key molecules. A recently developed chromatogram binning positive matrix factorization (PMF) technique was used to obtain mass spectral profiles for factors in TAG BBOA chromatograms, improving analysis efficiency and providing a more complete determination of unresolved complex mixture (UCM) components. Additionally, the recently characterized TAG decomposition window was used to track molecular fragments created by the decomposition of thermally labile BBOA during sample desorption. We demonstrate that although most primary (freshly emitted) BBOA compounds deplete with photochemical aging, certain components eluting within the TAG thermal decomposition window are instead enhanced. Specifically, the increasing trend in the decomposition m∕z 44 signal (CO2+) indicates formation of secondary organic aerosol (SOA) in the PAM reactor. Sources of m∕z 60 (C2H4O2+), typically attributed to freshly emitted BBOA in AMS field measurements, were also investigated. From the TAG chemical speciation and decomposition window data, we observed a decrease in m∕z 60 with photochemical aging due to the decay of anhydrosugars (including levoglucosan) and other compounds, as well as an increase in m∕z 60 due to the formation of thermally labile organic acids within the PAM reactor, which decompose during TAG sample desorption. When aging both types of BBOA (leaf and heartwood), the AMS data exhibit a combination of these two contributing effects, causing limited change to the overall m∕z 60 signal. Our observations demonstrate the importance of chemically speciated data in fully understanding bulk aerosol measurements provided by the AMS in both laboratory and field studies.

Single-step inkjet printing infiltration with doped ceria Ce0.9Ye0.1O1.95 (YDC) and cobalt oxide (CoxOy) precursor inks was performed in order to modify the properties of the doped ceria interlayer in commercial (50 × 50 × 0.5 mm3 size) anode-supported SOFCs. The penetration of the inks throughout the La0.8Sr0.2Co0.5Fe0.5O3−δ porous cathode to the Gd0.1Ce0.9O2 (GDC) interlayer was achieved by optimisation of the inks’ rheology jetting parameters. The low-temperature calcination (750 °C) resulted in densification of the Gd-doped ceria porous interlayer as well as decoration of the cathode scaffold with nanoparticles (~20–50 nm in size). The I–V testing in pure hydrogen showed a maximum power density gain of ~20% at 700 °C and ~97% at 800 °C for the infiltrated cells. The latter effect was largely assigned to the improvement in the interfacial Ohmic resistance due to the densification of the interlayer. The EIS study of the polarisation losses of the reference and infiltrated cells revealed a reduction in the activation polarisations losses at 700 °C due to the nano-decoration of the La0.8Sr0.2Co0.5Fe0.5O3−δ scaffold surface. Such was not the case at 800 °C, where the drop in Ohmic losses was dominant. This work demonstrated that single-step inkjet printing infiltration, a non-disruptive, low-cost technique, can produce significant and scalable performance enhancements in commercial anode-supported SOFCs.

Abstract Commercially available anode supported solid oxide fuel cells (NiO-8YSZ/8YSZ/LSCF- 20 mm in diameter) were anode infiltrated with gadolinium doped ceria (CGO) using a scalable drop-on-demand inkjet printing process. Cells were infiltrated with two different precursor solutions—water based or propionic acid based. The saturation limit of the 0.5 μm thick anode supports sintered at 1400 °C was found to be approximately 1wt%. No significant enhancement in power output was recorded at practical voltage levels. Microstructural characterisation was carried out after electrochemical performance testing using high resolution scanning electron microscopy. This work demonstrates that despite the feasibility of achieving CGO nanoparticle infiltration into thick, commercial SOFC anodes with a simple, low-cost and industrially scalable procedure other loss mechanisms were dominant. Infiltration of model symmetric anode cells with the propionic acid based ink demonstrated that significant reductions in polarisation resistance were possible.

Oxidation of biogenic volatile organic compounds (BVOC) by the nitrate radical (NO3) represents one of the important interactions between anthropogenic emissions related to combustion and natural emissions from the biosphere. This interaction has been recognized for more than 3 decades, during which time a large body of research has emerged from laboratory, field, and modeling studies. NO3-BVOC reactions influence air quality, climate and visibility through regional and global budgets for reactive nitrogen (particularly organic nitrates), ozone, and organic aerosol. Despite its long history of research and the significance of this topic in atmospheric chemistry, a number of important uncertainties remain. These include an incomplete understanding of the rates, mechanisms, and organic aerosol yields for NO3-BVOC reactions, lack of constraints on the role of heterogeneous oxidative processes associated with the NO3 radical, the difficulty of characterizing the spatial distributions of BVOC and NO3 within the poorly mixed nocturnal atmosphere, and the challenge of constructing appropriate boundary layer schemes and non-photochemical mechanisms for use in state-of-the-art chemical transport and chemistry–climate models. This review is the result of a workshop of the same title held at the Georgia Institute of Technology in June 2015. The first half of the review summarizes the current literature on NO3-BVOC chemistry, with a particular focus on recent advances in instrumentation and models, and in organic nitrate and secondary organic aerosol (SOA) formation chemistry. Building on this current understanding, the second half of the review outlines impacts of NO3-BVOC chemistry on air quality and climate, and suggests critical research needs to better constrain this interaction to improve the predictive capabilities of atmospheric models.

Recombinant herpesvirus vaccine vectors offer distinct advantages in next-generation vaccine development, primarily due to the ability to establish persistent infections to provide sustainable antigen responses in the host. Recombinant bovine herpesvirus-4 (BoHV-4) has been previously shown to elicit protective immunity in model laboratory animal species against a variety of pathogens. For the first time, we describe the induction of antigen-specific immune responses to two delivered antigens in the host species after intranasal nebulization of recombinant BoHV-4 expressing the chimeric peptide containing the bovine viral diarrhea virus (BVDV) glycoprotein E2 and the bovine herpesvirus 1 (BoHV-1) glycoprotein D (BoHV-4-A-CMV-IgK-gE2gD-TM). In this study, four cattle were immunized via intranasal nebulization with the recombinant BoHV-4 construct. Two of the cattle were previously infected with wild-type BoHV-4, and both developed detectable serologic responses to BVDV and BoHV-1. All four immunized cattle developed detectable viral neutralizing antibody responses to BVDV, and one steer developed a transient viral neutralizing response to BoHV-1. Approximately one year after immunization, immunosuppressive doses of the glucocorticoid dexamethasone were administered intravenously to all four cattle. Within two weeks of immunosuppression, all animals developed viral neutralizing antibody responses to BoHV-1, and all animals maintained BVDV viral neutralizing capacity. Overall, nebulization of BoHV-4-A-CMV-IgK-gE2gD-TM persistently infects cattle, is capable of eliciting antigen-specific immunity following immunization, including in the presence of pre-existing BoHV-4 immunity, and recrudescence of the virus boosts the immune response to BoHV-4-vectored antigens. These results indicate that BoHV-4 is a viable and attractive vaccine delivery platform for use in cattle.

Metabolome profiling is becoming more commonly used in the study of complex microbial communities and microbiomes; however, to date, little information is available concerning appropriate extraction procedures. We studied the influence of different extraction solvent mixtures on untargeted metabolomics analysis of two continuous culture enrichment communities performing enhanced biological phosphate removal (EBPR), with each enrichment targeting distinct populations of polyphosphate-accumulating organisms (PAOs). We employed one non-polar solvent and up to four polar solvents for extracting metabolites from biomass. In one of the reactor microbial communities, we surveyed both intracellular and extracellular metabolites using the same set of solvents. All samples were analysed using ultra-performance liquid chromatography mass spectrometry (UPLC-MS). UPLC-MS data obtained from polar and non-polar solvents were analysed separately and evaluated using extent of repeatability, overall extraction capacity and the extent of differential abundance between physiological states. Despite both reactors demonstrating the same bioprocess phenotype, the most appropriate extraction method was biomass specific, with methanol: water (50:50 v/v) and methanol: chloroform: water (40:40:20 v/v/v) being chosen as the most appropriate for each of the two different bioreactors, respectively. Our approach provides new data on the influence of solvent choice on the untargeted surveys of the metabolome of PAO enriched EBPR communities and suggests that metabolome extraction methods need to be carefully tailored to the specific complex microbial community under study.

We present a rapid method for apportioning the sources of atmospheric organic aerosol composition measured by gas chromatography–mass spectrometry methods. Here, we specifically apply this new analysis method to data acquired on a thermal desorption aerosol gas chromatograph (TAG) system. Gas chromatograms are divided by retention time into evenly spaced bins, within which the mass spectra are summed. A previous chromatogram binning method was introduced for the purpose of chromatogram structure deconvolution (e.g., major compound classes) (Zhang et al., 2014). Here we extend the method development for the specific purpose of determining aerosol samples' sources. Chromatogram bins are arranged into an input data matrix for positive matrix factorization (PMF), where the sample number is the row dimension and the mass-spectra-resolved eluting time intervals (bins) are the column dimension. Then two-dimensional PMF can effectively do three-dimensional factorization on the three-dimensional TAG mass spectra data. The retention time shift of the chromatogram is corrected by applying the median values of the different peaks' shifts. Bin width affects chemical resolution but does not affect PMF retrieval of the sources' time variations for low-factor solutions. A bin width smaller than the maximum retention shift among all samples requires retention time shift correction. A six-factor PMF comparison among aerosol mass spectrometry (AMS), TAG binning, and conventional TAG compound integration methods shows that the TAG binning method performs similarly to the integration method. However, the new binning method incorporates the entirety of the data set and requires significantly less pre-processing of the data than conventional single compound identification and integration. In addition, while a fraction of the most oxygenated aerosol does not elute through an underivatized TAG analysis, the TAG binning method does have the ability to achieve molecular level resolution on other bulk aerosol components commonly observed by the AMS.

Atmospheric aerosol composition is often analyzed using thermal desorption techniques to evaporate samples and deliver organic or inorganic molecules to various designs of detectors for identification and quantification. The organic aerosol (OA) fraction is composed of thousands of individual compounds, some with nitrogen- and sulfur-containing functionality and, often contains oligomeric material, much of which may be susceptible to decomposition upon heating. Here we analyze thermal decomposition products as measured by a thermal desorption aerosol gas chromatograph (TAG) capable of separating thermal decomposition products from thermally stable molecules. The TAG impacts particles onto a collection and thermal desorption (CTD) cell, and upon completion of sample collection, heats and transfers the sample in a helium flow up to 310 °C. Desorbed molecules are refocused at the head of a gas chromatography column that is held at 45 °C and any volatile decomposition products pass directly through the column and into an electron impact quadrupole mass spectrometer. Analysis of the sample introduction (thermal decomposition) period reveals contributions of NO+ (m/z 30), NO2+ (m/z 46), SO+ (m/z 48), and SO2+ (m/z 64), derived from either inorganic or organic particle-phase nitrate and sulfate. CO2+ (m/z 44) makes up a major component of the decomposition signal, along with smaller contributions from other organic components that vary with the type of aerosol contributing to the signal (e.g., m/z 53, 82 observed here for isoprene-derived secondary OA). All of these ions are important for ambient aerosol analyzed with the aerosol mass spectrometer (AMS), suggesting similarity of the thermal desorption processes in both instruments. Ambient observations of these decomposition products compared to organic, nitrate, and sulfate mass concentrations measured by an AMS reveal good correlation, with improved correlations for OA when compared to the AMS oxygenated OA (OOA) component. TAG signal found in the traditional compound elution time period reveals higher correlations with AMS hydrocarbon-like OA (HOA) combined with the fraction of OOA that is less oxygenated. Potential to quantify nitrate and sulfate aerosol mass concentrations using the TAG system is explored through analysis of ammonium sulfate and ammonium nitrate standards. While chemical standards display a linear response in the TAG system, redesorptions of the CTD cell following ambient sample analysis show some signal carryover on sulfate and organics, and new desorption methods should be developed to improve throughput. Future standards should be composed of complex organic/inorganic mixtures, similar to what is found in the atmosphere, and perhaps will more accurately account for any aerosol mixture effects on compositional quantification.