Integrated Detection of Pathogens and Host Biomarkers for Wounds

The increasing incidence and complications arising from combat wounds has necessitated a reassessment of methods for effective treatment. Infection, excessive inflammation, and incidence of drug-resistant organisms all contribute toward negative outcomes for afflicted individuals. The organisms and host processes involved in wound progression, however, are incompletely understood. We therefore set out, using our unique technical resources, to construct a profile of combat wounds which did or did not successfully resolve. We employed the Lawrence Livermore Microbial Detection Array and identified a number of nosocomial pathogens present in wound samples. Some of these identities corresponded with bacterial isolates previously cultured, while others were not obtained via standard microbiology. Further, we optimized proteomics protocols for the identification of host biomarkers indicative of various stages in wound progression. In combination with our pathogen data, our biomarker discovery efforts will provide a profile corresponding to wound complications, and will assist significantly in treatment of these complex cases

Mapping Inequalities in Activity-based Carbon Footprints of Urban Dwellers using Fine-grained Human Trajectory Data

Effective climate mitigation strategies in cities rely on understanding and mapping urban carbon footprints. One significant source of carbon is a product of lifestyle choices and travel behaviors of urban residents. Although previous research addressed consumption- and home-related footprints, activity-based footprints of urban dwellers have garnered less attention. This study relies on deidentified human trajectory data from 5 million devices to examine the activity-based carbon footprint in Harris County, Texas. Our analysis of the heterogeneity of footprints based on places visited and distance traveled reveals significant inequality: 10% of users account for 88% of visitation-based footprints and 71% of distance-traveled footprints. We also identify the influence of income on activity-based carbon footprint gap of users related to their travel behavior and lifestyle choices, with high-income users having larger footprints due to lifestyle choices, while low- to medium-income users' footprints are due to limited access. Our findings underscore the need for urban design adjustments to reduce carbon-intensive behaviors and to improve facility distribution. Our conclusions highlight the importance of addressing urban design parameters that shape carbon-intensive lifestyle choices and facility distribution, decisions which have implications for developing interventions to reduce carbon footprints caused by human activities.Comment: 15 pages, 6 figures, 1 tabl

Emergency Department Closures: The Critical Case of Reduced Care AccessWithin Rural Populations

In this paper, the researchers analyzed the effects of overcrowding and financial difficulties faced by rural emergency departments, which can lead to closures. To achieve this goal, we relied on a systematic analysis of the rural emergency department system, including the financial aspects, ethical considerations, and patient demographics. The researchers also utilized past evaluated interventions in order to determine methods of creating an efficient emergency department. We found that while there was an increase in emergency department patients, finances have not increased to accommodate overcrowding. This paper contributes to emergency department and rural health literature, as the researchers propose an evidence-based intervention that will minimize overcrowding and utilize finances effectively, while taking into account patient medical knowledge and scheduling

Report for the NGFA-5 project.

The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, TaqMan PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. To effectively compare the sensitivity and specificity of the different genomic technologies, we used SNP TaqMan PCR, MLVA, microarray and high-throughput illumine and 454 sequencing to test various strains from B. anthracis, B. thuringiensis, BioWatch aerosol filter extracts or soil samples that were spiked with B. anthracis, and samples that were previously collected during DHS and EPA environmental release exercises that were known to contain B. thuringiensis spores. The results of all the samples against the various assays are discussed in this report

A microbial detection array (MDA) for viral and bacterial detection

BACKGROUND: Identifying the bacteria and viruses present in a complex sample is useful in disease diagnostics, product safety, environmental characterization, and research. Array-based methods have proven utility to detect in a single assay at a reasonable cost any microbe from the thousands that have been sequenced. METHODS: We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phages), bacteria and plasmids and developed a novel statistical analysis method to identify mixtures of organisms from complex samples hybridized to the array. The array has broader coverage of bacterial and viral targets and is based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms, and to have no significant matches to the human genome sequence. RESULTS: In blinded testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR. CONCLUSIONS: The MDA can be used to identify the suite of viruses and bacteria present in complex samples

Evaluation of co-circulating pathogens and microbiome from COVID-19 infections.

Co-infections or secondary infections with SARS-CoV-2 have the potential to affect disease severity and morbidity. Additionally, the potential influence of the nasal microbiome on COVID-19 illness is not well understood. In this study, we analyzed 203 residual samples, originally submitted for SARS-CoV-2 testing, for the presence of viral, bacterial, and fungal pathogens and non-pathogens using a comprehensive microarray technology, the Lawrence Livermore Microbial Detection Array (LLMDA). Eighty-seven percent of the samples were nasopharyngeal samples, and 23% of the samples were oral, nasal and oral pharyngeal swabs. We conducted bioinformatics analyses to examine differences in microbial populations of these samples, as a proxy for the nasal and oral microbiome, from SARS-CoV-2 positive and negative specimens. We found 91% concordance with the LLMDA relative to a diagnostic RT-qPCR assay for detection of SARS-CoV-2. Sixteen percent of all the samples (32/203) revealed the presence of an opportunistic bacterial or frank viral pathogen with the potential to cause co-infections. The two most detected bacteria, Streptococcus pyogenes and Streptococcus pneumoniae, were present in both SARS-CoV-2 positive and negative samples. Human metapneumovirus was the most prevalent viral pathogen in the SARS-CoV-2 negative samples. Sequence analysis of 16S rRNA was also conducted to evaluate bacterial diversity and confirm LLMDA results

Pontine Primitive Neuroectodermal Tumor With Spinal Metastasis in a 10-year-old Girl

AbstractBrain tumors are the most common type of solid cancer in children. Approximately 20% of pediatric brain tumors originate from the brain stem, and most are comprised of gliomas. However, metastasis of brain stem gliomas along the neuraxis is rare. Brain stem primitive neuroectodermal tumors (PNETs) are also rare and are prone to leptomeningeal metastasis. We describe here a 10-year-old girl with a pontine tumor. Initially, she was diagnosed with a glioma because of the clinical presentation, but later pathology of a metastatic tumor in the spinal cord showed PNET. The tumor response to radiotherapy was poor and she died 6 months after diagnosis. Since biopsy of brain stem tumors is not always feasible, diagnoses other than glioma should be considered if the patient's clinical presentation is unusual

Report for Evaluation of Canonical SNP Taqman Assays to Detect Biothreat Agents and Environmental Samples for DHS

Abstract not provide

Nonstructural proteins nsp2TF and nsp2N of porcine reproductive and respiratory syndrome virus (PRRSV) play important roles in suppressing host innate immune responses.

Recently, we identified a unique -2/-1 ribosomal frameshift mechanism in PRRSV, which yields two truncated forms of nonstructural protein (nsp) 2 variants, nsp2TF and nsp2N. Here, in vitro expression of individual PRRSV nsp2TF and nsp2N demonstrated their ability to suppress cellular innate immune responses in transfected cells. Two recombinant viruses were further analyzed, in which either nsp2TF was C-terminally truncated (vKO1) or expression of both nsp2TF and nsp2N was knocked out (vKO2). Host cellular mRNA profiling showed that a panel of cellular immune genes, in particular those involved in innate immunity, was upregulated in cells infected with vKO1 and vKO2. Compared to the wild-type virus, vKO1 and vKO2 expedited the IFN-α response and increased NK cell cytotoxicity, and subsequently enhanced T cell immune responses in infected pigs. Our data strongly implicate nsp2TF/nsp2N in arteriviral immune evasion and demonstrate that nsp2TF/nsp2N-deficient PRRSV is less capable of counteracting host innate immune responses