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The human microbiome plays an important role in our health and identifying factors associated with microbiome composition provides insights into inherent disease mechanisms. By amplifying and sequencing the marker genes in high-throughput sequencing, with highly similar sequences binned together, we obtain operational taxonomic units (OTUs) profiles for each subject. Due to the high-dimensionality and nonnormality features of the OTUs, the measure of diversity is introduced as a summarization at the microbial community level, including the distance-based beta-diversity between individuals. Analyses of such between-subject attributes are not amenable to the predominant within-subject-based statistical paradigm, such as t-tests and linear regression. In this paper, we propose a new approach to model beta-diversity as a response within a regression setting by utilizing the functional response models (FRMs), a class of semiparametric models for between- as well as within-subject attributes. The new approach not only addresses limitations of current methods for beta-diversity with cross-sectional data, but also provides a premise for extending the approach to longitudinal and other clustered data in the future. The proposed approach is illustrated with both real and simulated data.

Case presentation: A 32-year-old man with a history of hemophilia A presented to the emergency department with right shoulder pain, swelling, and decreased range of motion.Discussion: Emergency physicians can use ultrasound to quickly and accurately identify hemarthrosis at the bedside.

Airborne electromagnetic (AEM) data can be inverted to recover models of the electrical resistivity of the subsurface; these, in turn, can be transformed to obtain models of sediment type. AEM data were acquired in Butte and Glenn Counties, California, USA to improve the understanding of the aquifer system. Around 800 line-kilometers of high-quality data were acquired, imaging to a depth of ∼300 m. We developed a workflow designed to obtain, from the AEM data, information about the large-scale structure and heterogeneity of the aquifer system to better understand the vertical connectivity. Using six different inversions incorporating various forms of available information and posterior sampling of the recovered resistivity models, we produced 6,006 resistivity models. These models were transformed to models of sediment type and estimates of percentage of sand/gravel. Exploring the model space, containing the resistivity models and the derived models, allowed us to delineate the large-scale structure of the aquifer system in a way that captures and communicates the uncertainty in the identified sediment type. The uncertainty increased, as expected, with depth, but also served to indicate, as areas of high uncertainty in sediment type, the location of both large-scale and small-scale interfaces between sediment types. A plan view map of the integrated percentage of sand/gravel, when compared to existing hydrographs, revealed the extent of lateral changes in vertical connectivity within the aquifer system throughout the study area.

Nonalcoholic fatty liver disease (NALFD) is now a leading cause of chronic liver disease worldwide, in part, as a consequence of rapidly rising levels of obesity and metabolic syndrome and is a major risk factor for cirrhosis, hepatocellular carcinoma, and liver-related mortality. From NAFLD stems a myriad of clinical challenges related to both diagnosis and management. A growing body of evidence suggests an intricate linkage between the gut microbiome and the pathogenesis of NAFLD. We highlight how our current knowledge of the gut-liver axis in NAFLD may be leveraged to develop gut microbiome-based personalized approaches for disease management, including its use as a non-invasive biomarker for diagnosis and staging, as a target for therapeutic modulation, and as a marker of drug response. We will also discuss current limitations of these microbiome-based approaches. Ultimately, a better understanding of microbiota-host interactions in NAFLD will inform the development of novel preventative strategies and precise therapeutic targets.

The vitamin D receptor is highly expressed in the gastrointestinal tract where it transacts gene expression. With current limited understanding of the interactions between the gut microbiome and vitamin D, we conduct a cross-sectional analysis of 567 older men quantifying serum vitamin D metabolites using LC-MSMS and defining stool sub-Operational Taxonomic Units from16S ribosomal RNA gene sequencing data. Faith’s Phylogenetic Diversity and non-redundant covariate analyses reveal that the serum 1,25(OH)2D level explains 5% of variance in α-diversity. In β-diversity analyses using unweighted UniFrac, 1,25(OH)2D is the strongest factor assessed, explaining 2% of variance. Random forest analyses identify 12 taxa, 11 in the phylum Firmicutes, eight of which are positively associated with either 1,25(OH)2D and/or the hormone-to-prohormone [1,25(OH)2D/25(OH)D] “activation ratio.” Men with higher levels of 1,25(OH)2D and higher activation ratios, but not 25(OH)D itself, are more likely to possess butyrate producing bacteria that are associated with better gut microbial health.

Microbial communities along mucosal surfaces throughout the digestive tract are hypothesized as risk factors for impaired glucose regulation and the development of clinical cardiometabolic disease. We investigated whether baseline measures of subgingival microbiota predicted fasting plasma glucose (FPG) longitudinally. The Oral Infections, Glucose Intolerance and Insulin Resistance Study (ORIGINS) enrolled 230 diabetes-free adults (77% female) aged 20 to 55 y (mean ± SD, 34 ± 10 y) from whom baseline subgingival plaque and longitudinal FPG were measured. DNA was extracted from subgingival plaque, and V3 to V4 regions of the 16S rRNA gene were sequenced. FPG was measured at baseline and again at 2 y; glucose change was defined as follow-up minus baseline. Multivariable linear models regressed 2-y glucose change onto baseline measures of community diversity and abundances of 369 individual taxa. A microbial dysbiosis index (MDI) summarizing top individual taxa associated with glucose change was calculated and used in regression models. Models were adjusted for age, sex, race/ethnicity, education, smoking status, body mass index, and baseline glucose levels. Statistical significance was based on the false discovery rate (FDR;

Background: Studies of the cystic fibrosis (CF) lung microbiome have consistently shown that lung function decline is associated with decreased microbial diversity due to the dominance of opportunistic pathogens. However, how this phenomenon is reflected in the metabolites and chemical environment of lung secretions remains poorly understood. Methods: Here we investigated the microbial and molecular composition of CF sputum samples using 16S rRNA gene amplicon sequencing and untargeted tandem mass spectrometry to determine their interrelationships and associations with clinical measures of disease severity. Results: The CF metabolome was found to exist in two states: one from patients with more severe disease that had higher molecular diversity and more Pseudomonas aeruginosa and the other from patients with better lung function having lower metabolite diversity and fewer pathogenic bacteria. The two molecular states were differentiated by the abundance and diversity of peptides and amino acids. Patients with severe disease and more pathogenic bacteria had higher levels of peptides. Analysis of the carboxyl terminal residues of these peptides indicated that neutrophil elastase and cathepsin G were responsible for their generation, and accordingly, these patients had higher levels of proteolytic activity from these enzymes in their sputum. The CF pathogen Pseudomonas aeruginosa was correlated with the abundance of amino acids and is known to primarily feed on them in the lung. Conclusions: In cases of severe CF lung disease, proteolysis by host enzymes creates an amino acid-rich environment that P. aeruginosa comes to dominate, which may contribute to the pathogen's persistence by providing its preferred carbon source.

The immune system responds vigorously to microbial infection while permitting lifelong colonization by the microbiome. Mechanisms that facilitate the establishment and stability of the gut microbiota remain poorly described. We found that a regulatory system in the prominent human commensal Bacteroides fragilis modulates its surface architecture to invite binding of immunoglobulin A (IgA) in mice. Specific immune recognition facilitated bacterial adherence to cultured intestinal epithelial cells and intimate association with the gut mucosal surface in vivo. The IgA response was required for B. fragilis (and other commensal species) to occupy a defined mucosal niche that mediates stable colonization of the gut through exclusion of exogenous competitors. Therefore, in addition to its role in pathogen clearance, we propose that IgA responses can be co-opted by the microbiome to engender robust host-microbial symbiosis.

Background: Studies of the cystic fibrosis (CF) lung microbiome have consistently shown that lung function decline is associated with decreased microbial diversity due to the dominance of opportunistic pathogens. However, how this phenomenon is reflected in the metabolites and chemical environment of lung secretions remains poorly understood. Methods: Here we investigated the microbial and molecular composition of CF sputum samples using 16S rRNA gene amplicon sequencing and untargeted tandem mass spectrometry to determine their interrelationships and associations with clinical measures of disease severity. Results: The CF metabolome was found to exist in two states: one from patients with more severe disease that had higher molecular diversity and more Pseudomonas aeruginosa and the other from patients with better lung function having lower metabolite diversity and fewer pathogenic bacteria. The two molecular states were differentiated by the abundance and diversity of peptides and amino acids. Patients with severe disease and more pathogenic bacteria had higher levels of peptides. Analysis of the carboxyl terminal residues of these peptides indicated that neutrophil elastase and cathepsin G were responsible for their generation, and accordingly, these patients had higher levels of proteolytic activity from these enzymes in their sputum. The CF pathogen Pseudomonas aeruginosa was correlated with the abundance of amino acids and is known to primarily feed on them in the lung. Conclusions: In cases of severe CF lung disease, proteolysis by host enzymes creates an amino acid-rich environment that P. aeruginosa comes to dominate, which may contribute to the pathogen's persistence by providing its preferred carbon source.

The HOMEChem (House Observations of Microbial and Environmental Chemistry) is a collaborative indoor air chemistry field study to be performed in June 2018 at the UTest House, a manufactured research house located in the University of Texas at Austin's research campus. The HOMEChem experiment investigates the effects of building occupants and their activities, such as cooking and cleaning, on the chemistry of the gas phase, particle phase, and surfaces in a simulated home environment. Specifically, this study focuses on the presence of organic species, chemical oxidants, and reactive nitrogen species indoors compared to outdoor levels. This study incorporates state-of the art atmospheric chemistry instrumentation from multiple research groups to build a shared dataset from those measurements.

The National Ignition Facility uses a soft x-ray opacity spectrometer for x-ray spectral imaging in high-energy-density experiments. The increased demand for a better spectral resolution prompted the investigation into the Agfa D4 film. Characterization is already under way for the film. A Manson x-ray source using six different anodes was used to expose film to the linear optical density (OD) region. This is a continuation of the previous work, and the updated analysis process is communicated here. The identified uncertainties have been reduced with the updated steps that improve the results of the characterization process. When the Stanford Synchrotron Radiation Lightsource Beamline 16-2 was operational, the film was characterized at that source. Its beam offered a higher fluency with a lower exposure time needed to reach saturation. Results for both sources are compared in this paper. [ABSTRACT FROM AUTHOR]

The ability to notice and reflect on distressing internal experiences from an objective perspective, often called psychological decentering, has been posited to be protective against mental health difficulties. However, little is known about how this skill relates to age across adolescence, its relationship with mental health, and how it may impact key domains such as affective executive control and social cognition. This study analysed a pre-existing dataset including mental health measures and cognitive tasks, administered to adolescents in Greater London and Cambridge (mean age (SD) = 14.4 (1.77) years, N = 553). A self-report index of decentering based on available questionnaire items in the dataset was developed. Multiple linear regression was used to examine associations between decentering and mental health, affective executive control (measured using an affective Stroop Task, affective Working Memory Task, and affective Sustained Attention to Response Task) and social cognition. Higher decentering was significantly associated with lower depression and anxiety scores and higher psychological wellbeing. Results did not indicate significant relationships between decentering, affective executive control and social cognition. Further research is needed to discover cognitive mechanisms associated with this process, which could allow for optimisation of existing psychological therapy and reveal new avenues of intervention. [ABSTRACT FROM AUTHOR]

Opacity measurements are being carried out at the Z-facility at Sandia National Laboratories and at the National Ignition Facility (NIF) at Lawrence Livermore National Laboratory. The current soft x-ray Opacity Spectrometer (OpSpec) used on the NIF uses two elliptically bent crystals in time-integrated mode on either an image plate or a film. Plans are under way to expand these opacity measurements into a mode of time-resolved detection, called OpSpecTR. Previously, considerations for the available hCMOS detector size and photometrics led to a crystal geometry redesign and the use of a grazing angle x-ray mirror. The mirror acts as a low-pass x-ray energy filter, reducing the contribution of higher energy x rays. The first tests of the mirror and the crystal for OpSpecTR are presented here. The size of the mirror reflection and the reflectivity is tested using a Manson x-ray source. The mirror coupled with the new elliptical crystal shape demonstrates OpSpecTR's spectral coverage. The results from the x-ray optics performance testing are shown along with the intended design. [ABSTRACT FROM AUTHOR]

Metagenomics is increasingly used not just to show patterns of microbial diversity but also as a culture-independent method to detect individual organisms of intense clinical, epidemiological, conservation, forensic, or regulatory interest. A widely reported metagenomic study of the New York subway suggested that the pathogens Yersinia pestis and Bacillus anthracis were part of the "normal subway microbiome." In their article in mSystems, Hsu and collaborators (mSystems 1(3):e00018-16, 2016, http://dx.doi.org/10.1128/mSystems.00018-16) showed that microbial communities on transit surfaces in the Boston subway system are maintained from a metapopulation of human skin commensals and environmental generalists and that reanalysis of the New York subway data with appropriate methods did not detect the pathogens. We note that commonly used software pipelines can produce results that lack prima facie validity (e.g., reporting widespread distribution of notorious endemic species such as the platypus or the presence of pathogens) but that appropriate use of inclusion and exclusion sets can avoid this issue.

Quantitative real-time PCR (qPCR) assays that target the human-associated HF183 bacterial cluster within members of the genus Bacteroides are among the most widely used methods for the characterization of human fecal pollution in ambient surface waters. In this study, we show that a current TaqMan HF183 qPCR assay (HF183/BFDrev) routinely forms nonspecific amplification products and introduce a modified TaqMan assay (HF183/BacR287) that alleviates this problem. The performance of each qPCR assay was compared in head-to-head experiments investigating limits of detection, analytical precision, predicted hybridization to 16S rRNA gene sequences from a reference database, and relative marker concentrations in fecal and sewage samples. The performance of the modified HF183/BacR287 assay is equal to or improves upon that of the original HF183/BFDrev assay. In addition, a qPCR chemistry designed to combat amplification inhibition and a multiplexed internal amplification control are included. In light of the expanding use of PCR-based methods that rely on the detection of extremely low concentrations of DNA template, such as qPCR and digital PCR, the new TaqMan HF183/BacR287 assay should provide more accurate estimations of human-derived fecal contaminants in ambient surface waters.

A new time-resolved opacity spectrometer (OpSpecTR) is currently under development for the National Ignition Facility (NIF) opacity campaign. The spectrometer utilizes Icarus version 2 (IV2) hybridized complementary metal–oxide–semiconductor sensors to collect gated data at the time of the opacity transmission signal, unlocking the ability to collect higher-temperature measurements on NIF. Experimental conditions to achieve higher temperatures are feasible; however, backgrounds will dominate the data collected by the current time-integrating opacity spectrometer. The shortest available OpSpecTR integration time of ∼2 ns is predicted to reduce self-emission and other late-time backgrounds by up to 80%. Initially, three Icarus sensors will be used to collect data in the self-emission, backlighter, and absorption regions of the transmission spectrum, with plans to upgrade to five Daedalus sensors in future implementations with integration times of ∼1.3 ns. We present the details of the diagnostic design along with recent characterization results of the IV2 sensors. [ABSTRACT FROM AUTHOR]

Due to the significantly high levels of comorbid substance use and mental health diagnosis among urban poor populations, examining the intersection of drug policy and place requires a consideration of the role of housing in drug user mental health. In San Francisco, geographic boundedness and progressive health and housing polices have coalesced to make single room occupancy hotels (SROs) a key urban built environment used to house poor populations with co-occurring drug use and mental health issues. Unstably housed women who use illicit drugs have high rates of lifetime and current trauma, which manifests in disproportionately high rates of post-traumatic stress disorder (PTSD), anxiety, and depression when compared to stably housed women. We report data from a qualitative interview study (n=30) and four years of ethnography conducted with housing policy makers and unstably housed women who use drugs and live in SROs. Women in the study lived in a range of SRO built environments, from publicly-funded, newly built SROs to privately-owned, dilapidated buildings, which presented a rich opportunity for ethnographic comparison. Applying Rhodes et al.’s framework of socio-structural vulnerability, we explore how SROs can operate as “mental health risk environments” in which macro-structural factors (housing policies shaping the built environment) interact with meso-level factors (social relations within SROs) and micro-level, behavioral coping strategies to impact women’s mental health. The degree to which SRO built environments were “trauma-sensitive” at the macro level significantly influenced women’s mental health at meso- and micro- levels. Women who were living in SROs which exacerbated fear and anxiety attempted, with limited success, to deploy strategies on the meso- and micro- level to manage their mental health symptoms. Study findings underscore the importance of housing polices which consider substance use in the context of current and cumulative trauma experiences in order to improve quality of life and mental health for unstably housed women.