Effects of Inorganic Nutrients and Dissolved Organic Carbon on Oxygen Demand in Select Rivers in Northern Utah

Sewage, agricultural runoff, and atmospheric deposition have greatly increased the amount of nutrients (largely nitrogen (N) and phosphorus (P)) in surface water nationwide. Excess nutrients are associated with algal blooms and dissolved oxygen depletion in many water bodies, but linkages between nutrients and dissolved oxygen have been largely correlative. Biochemical oxygen demand (BOD) is a regulated water quality parameter that is aimed at describing the amount of oxygen consumed during the decomposition of organic matter. Despite the awareness that excess nutrients are linked to dissolved oxygen in rivers, few studies in the nutrient criteria literature discuss BOD measurements or how nutrients may impact BOD. Accordingly, I used factorial experiments to test the effect of inorganic nutrients (as N, P and N+P) and dissolved organic carbon on BOD measurements in Utah streams. The study was carried out from January through summer baseflow in 2011, allowing me to evaluate the effects of spatial and temporal variation of ambient nutrient concentration on oxygen demand. The study design included measurements in streams above and below nutrient point-sources (publicly owned treatment works) and several reference sites. I used classification and regression trees to identify thresholds of TN and TP that separate BOD response to nutrients into statistically distinct groups. My results show that seasonal variation affected BOD levels. As temperatures rose and water levels increased during peak runoff, I observed the highest BOD response to nutrient additions. I also found a significant correlation between BOD and ambient nutrient concentrations during that time period. I identified potential nutrient-related thresholds that could be used to assign numeric criteria that would protect designated uses. The threshold values I found for TN and TP were 0.56 mg/L and 0.09 mg/L, respectively. My results suggest that BOD may be sensitive to nutrient inputs and my experimental approach could be used as one line of evidence to support nutrient criteria related to aquatic life uses

Advances in Functional Testing with SFF Parts

Functional testing of SFF parts represents an exciting area of research in solid freeform fabrication. One approach to functional testing is to use similitude techniques to correlate the behavior of an SFF model and a product. Previous research at UT Austin has resulted in development of an empirical similitude technique to correlate the behavior of parts of dissimilar materials and geometry. Advances in the empirical similitude technique are presented in this paper. Sources of coupling between material and geometry characteristics that produce errors in the current empirical similitude technique are outlined. A modified approach that corrects for such errors is presented. Numerical examples are used to illustrate both the current and the advanced empirical similitude methods.Mechanical Engineerin

A Study of Functional Testing with SFF Parts

A study of functional testing with SFF parts is presented. The study includes the use of traditional similitude methods as well as advanced similitude methods for predicting product performance through prototype testing. Cantilever beams created from the selective laser sintering process are used to predict the static deflection of both aluminum and polycarbonate beams. The results of 20 experiments using various geometric, loading, and material configurations are presented. Results of the study suggest that a coupling between geometry and material properties exists in SLS parts. Possible sources for the coupling are discussed. An approach for establishing the functional relationship between material and geometry is outlined.Mechanical Engineerin

Gut inflammation provides a respiratory electron acceptor for Salmonella.

Salmonella enterica serotype Typhimurium (S. Typhimurium) causes acute gut inflammation by using its virulence factors to invade the intestinal epithelium and survive in mucosal macrophages. The inflammatory response enhances the transmission success of S. Typhimurium by promoting its outgrowth in the gut lumen through unknown mechanisms. Here we show that reactive oxygen species generated during inflammation react with endogenous, luminal sulphur compounds (thiosulphate) to form a new respiratory electron acceptor, tetrathionate. The genes conferring the ability to use tetrathionate as an electron acceptor produce a growth advantage for S. Typhimurium over the competing microbiota in the lumen of the inflamed gut. We conclude that S. Typhimurium virulence factors induce host-driven production of a new electron acceptor that allows the pathogen to use respiration to compete with fermenting gut microbes. Thus the ability to trigger intestinal inflammation is crucial for the biology of this diarrhoeal pathogen

Sentinel Case of Candida auris in the Western United States Following Prolonged Occult Colonization in a Returned Traveler from India.

Candida auris is an emerging multidrug-resistant yeast with high mortality. We report the sentinel C. auris case on the United States West Coast in a patient who relocated from India. We identified close phylogenetic relatedness to the South Asia clade and ERG11 Y132F and FKS1 S639Y mutations potentially explaining antifungal resistance

Emission-Line Properties of the Optical Filaments of NGC 1275

Extended nebular filaments are seen at optical wavelengths in NGC 1275, the central galaxy in the Perseus cluster. The agents responsible for the excitation of these filaments remain poorly understood. In this paper we investigate possible mechanisms for powering the filaments, using measurements from an extensive spectroscopic data set acquired at the Lick Observatory 3-m Shane telescope. The results show that the filaments are in an extremely low ionization and excitation state. The high signal-to-noise ratio of the spectra allows us to measure or place sensitive upper limits on weak but important diagnostic lines. We compare the observed line intensity ratios to the predictions of various ionization models, including photoionization by an active galactic nucleus, shock heating, stellar photoionization, and photoionization by the intracluster medium. We also investigate possible roles for cluster extreme-ultraviolet emission, and filtering of cluster soft X-ray emission by an ionized screen, in the energetics of the filaments. None of these mechanisms provides an entirely satisfactory explanation for the physical state of the nebulae. Heating and ionization by reconnection of the intracluster magnetic field remains a potentially viable alternative, which merits further investigation through Faraday rotation studies.Comment: Accepted for publication in Ap

Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens.

The burden of meningitis in low-and-middle-income countries remains significant, but the infectious causes remain largely unknown, impeding institution of evidence-based treatment and prevention decisions. We conducted a validation and application study of unbiased metagenomic next-generation sequencing (mNGS) to elucidate etiologies of meningitis in Bangladesh. This RNA mNGS study was performed on cerebrospinal fluid (CSF) specimens from patients admitted in the largest pediatric hospital, a World Health Organization sentinel site, with known neurologic infections (n = 36), with idiopathic meningitis (n = 25), and with no infection (n = 30), and six environmental samples, collected between 2012 and 2018. We used the IDseq bioinformatics pipeline and machine learning to identify potentially pathogenic microbes, which we then confirmed orthogonally and followed up through phone/home visits. In samples with known etiology and without infections, there was 83% concordance between mNGS and conventional testing. In idiopathic cases, mNGS identified a potential bacterial or viral etiology in 40%. There were three instances of neuroinvasive Chikungunya virus (CHIKV), whose genomes were >99% identical to each other and to a Bangladeshi strain only previously recognized to cause febrile illness in 2017. CHIKV-specific qPCR of all remaining stored CSF samples from children who presented with idiopathic meningitis in 2017 (n = 472) revealed 17 additional CHIKV meningitis cases, exposing an unrecognized meningitis outbreak. Orthogonal molecular confirmation, case-based clinical data, and patient follow-up substantiated the findings. Case-control CSF mNGS surveys can complement conventional diagnostic methods to identify etiologies of meningitis, conduct surveillance, and predict outbreaks. The improved patient- and population-level data can inform evidence-based policy decisions.IMPORTANCE Globally, there are an estimated 10.6 million cases of meningitis and 288,000 deaths every year, with the vast majority occurring in low- and middle-income countries. In addition, many survivors suffer from long-term neurological sequelae. Most laboratories assay only for common bacterial etiologies using culture and directed PCR, and the majority of meningitis cases lack microbiological diagnoses, impeding institution of evidence-based treatment and prevention strategies. We report here the results of a validation and application study of using unbiased metagenomic sequencing to determine etiologies of idiopathic (of unknown cause) cases. This included CSF from patients with known neurologic infections, with idiopathic meningitis, and without infection admitted in the largest children's hospital of Bangladesh and environmental samples. Using mNGS and machine learning, we identified and confirmed an etiology (viral or bacterial) in 40% of idiopathic cases. We detected three instances of Chikungunya virus (CHIKV) that were >99% identical to each other and to a strain previously recognized to cause systemic illness only in 2017. CHIKV qPCR of all remaining stored 472 CSF samples from children who presented with idiopathic meningitis in 2017 at the same hospital uncovered an unrecognized CHIKV meningitis outbreak. CSF mNGS can complement conventional diagnostic methods to identify etiologies of meningitis, and the improved patient- and population-level data can inform better policy decisions

EBP-Colombia and the bioeconomy: Genomics in the service of biodiversity conservation and sustainable development

The 2016 Peace Agreement has increased access to Colombia’s unique ecosystems, which remain understudied and increasingly under threat. The Colombian government has recently announced its National Bioeconomic Strategy (NBS), founded on the sustainable characterization, management, and conservation of the nation's biodiversity as a means to achieve sustainability and peace. Molecular tools will accelerate such endeavors, but capacity remains limited in Colombia. The Earth Biogenome Project's (EBP) objective is to characterize the genomes of all eukaryotic life on Earth through networks of partner institutions focused on sequencing either specific taxa or eukaryotic communities at regional or national scales. Colombia’s immense biodiversity and emerging network of stakeholders have inspired the creation of the national partnership “EBP-Colombia.” Here, we discuss how this Colombian-driven collaboration between government, academia, and the private sector is integrating research with sustainable, environmentally focused strategies to develop Colombia’s postconflict bioeconomy and conserve biological and cultural diversity. EBP-Colombia will accelerate the uptake of technology and promote partnership and exchange of knowledge among Colombian stakeholders and the EBP’s global network of experts; assist with conservation strategies to preserve Colombia’s vast biological wealth; and promote innovative approaches among public and private institutions in sectors such as agriculture, tourism, recycling, and medicine. EBP-Colombia can thus support Colombia’s NBS with the objective of sustainable and inclusive development to address the many social, environmental, and economic challenges, including conflict, inequality, poverty, and low agricultural productivity, and so, offer an alternative model for economic development that similarly placed countries can adopt

Implantable Cardioverter Defibrillator Therapy in Patients with Cardiac Sarcoidosis

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/93643/1/j.1540-8167.2012.02350.x.pd

Pan-viral serology implicates enteroviruses in acute flaccid myelitis.

Since 2012, the United States of America has experienced a biennial spike in pediatric acute flaccid myelitis (AFM)1-6. Epidemiologic evidence suggests non-polio enteroviruses (EVs) are a potential etiology, yet EV RNA is rarely detected in cerebrospinal fluid (CSF)2. CSF from children with AFM (n = 42) and other pediatric neurologic disease controls (n = 58) were investigated for intrathecal antiviral antibodies, using a phage display library expressing 481,966 overlapping peptides derived from all known vertebrate and arboviruses (VirScan). Metagenomic next-generation sequencing (mNGS) of AFM CSF RNA (n = 20 cases) was also performed, both unbiased sequencing and with targeted enrichment for EVs. Using VirScan, the viral family significantly enriched by the CSF of AFM cases relative to controls was Picornaviridae, with the most enriched Picornaviridae peptides belonging to the genus Enterovirus (n = 29/42 cases versus 4/58 controls). EV VP1 ELISA confirmed this finding (n = 22/26 cases versus 7/50 controls). mNGS did not detect additional EV RNA. Despite rare detection of EV RNA, pan-viral serology frequently identified high levels of CSF EV-specific antibodies in AFM compared with controls, providing further evidence for a causal role of non-polio EVs in AFM