Nationwide Trends in COVID-19 Cases and SARS-CoV-2 RNA Wastewater Concentrations in the United States.

Wastewater-based epidemiology has emerged as a promising technology for population-level surveillance of COVID-19. In this study, we present results of a large nationwide SARS-CoV-2 wastewater monitoring system in the United States. We profile 55 locations with at least six months of sampling from April 2020 to May 2021. These locations represent more than 12 million individuals across 19 states. Samples were collected approximately weekly by wastewater treatment utilities as part of a regular wastewater surveillance service and analyzed for SARS-CoV-2 RNA concentrations. SARS-CoV-2 RNA concentrations were normalized to pepper mild mottle virus, an indicator of fecal matter in wastewater. We show that wastewater data reflect temporal and geographic trends in clinical COVID-19 cases and investigate the impact of normalization on correlations with case data within and across locations. We also provide key lessons learned from our broad-scale implementation of wastewater-based epidemiology, which can be used to inform wastewater-based epidemiology approaches for future emerging diseases. This work demonstrates that wastewater surveillance is a feasible approach for nationwide population-level monitoring of COVID-19 disease. With an evolving epidemic and effective vaccines against SARS-CoV-2, wastewater-based epidemiology can serve as a passive surveillance approach for detecting changing dynamics or resurgences of the virus.

Appraising Virtual Technologies' Impact on Older Citizens' Mental Health-A Comparative between 360° Video and Virtual Reality.

Aging populations across the world are facing a number of challenges in the context of health and healthcare. These challenges are driven by the aging process and the illnesses associated with aging. Healthcare for older people has become a point of concern with most health organizations, and this is particularly the case with palliative care. In this instance, the movement of the patient may be restricted to a room with no or limited access to the outdoors. This research focuses on the active integration of immersive technologies with healthcare. By addressing the problem of providing patients with the experience of being present in an outdoors space, the associated psychological and physiological benefits can be identified. In this mixed methods research paper, the impact of a crossover study to discern technology preferences in relation to immersive technologies among a sample of older people is reported. In addition, the study highlights factors that contribute to a meaningful immersive experience that can improve psychological and physiological wellbeing. The study identifies that there are two significant categorical aspects that contribute to such immersive experiences, technological aspects (including, for example, the weight of headsets, visual impairment, pixelation, and gamification) and emotive aspects (for example, joy, anger, and fear). The study suggests that older people prefer immersive Virtual Reality (VR) environments rather than 360 video experiences. This can be attributed to the greater flexibility in the provision of interactivity in virtual reality systems.

Development of Melioidosis Subunit Vaccines Using an Enzymatically Inactive Burkholderia pseudomallei AhpC.

Burkholderia pseudomallei, the causative agent of melioidosis, is a facultative intracellular, Gram-negative pathogen that is highly infectious via the respiratory route and can cause severe, debilitating, and often fatal diseases in humans and animals. At present, no licensed vaccines for immunization against this CDC Tier 1 select agent exist. Studies in our lab have previously demonstrated that subunit vaccine formulations consisting of a B. pseudomallei capsular polysaccharide (CPS)-based glycoconjugate (CPS-CRM197) combined with hemolysin-coregulated protein (Hcp1) provided C57BL/6 mice with high-level protection against an acute inhalational challenge of B. pseudomallei. In this study, we evaluated the immunogenicity and protective capacity of B. pseudomallei alkyl hydroperoxide reductase subunit C (AhpC) in combination with CPS-CRM197. AhpC is a peroxiredoxin involved in oxidative stress reduction and is a potential protective antigen. To facilitate our studies and maximize safety in animals, recombinant B. pseudomallei AhpC harboring an active site mutation (AhpCC57G) was expressed in Escherichia coli and purified using tandem nickel-cobalt affinity chromatography. Immunization of C57BL/6 mice with CPS-CRM197 combined with AhpCC57G stimulated high-titer IgG responses against the CPS component of the glycoconjugate as well as stimulated high-titer IgG and robust interferon gamma (IFN-γ)-, interleukin-5 (IL-5)-, and IL-17-secreting T cell responses against AhpCC57G. When challenged via an inhalational route with a high dose (~27 50% lethal doses [LD50s]) of B. pseudomallei, 70% of the immunized mice survived 35 days postchallenge. Collectively, our findings demonstrate that AhpCC57G is a potent activator of cellular and humoral immune responses and may be a promising candidate to include in future melioidosis subunit vaccines.

Establishing Task-Relevant MVC Protocols for Modelling Sustained Isometric Force Variability: A Manual Control Study.

The present study examined how prevalent methods for determining maximal voluntary contraction (MVC) impact the experimentally derived functions of graded force-force variability. Thirty-two young healthy subjects performed continuous isometric force tracking (20 s trials) at 10 target percentages (5-95% MVC) normalized to a conventional discrete-point (n = 16), or sustained (n = 16) MVC calculation. Distinct rates and magnitudes of change were observed for absolute variability (standard deviation (SD), root mean squared error (RMSE)), tracking error (RMSE, constant error (CE)), and complexity (detrended fluctuation analysis (DFA)) (all p < 0.05) of graded force fluctuations between the MVC groups. Differential performance strategies were observed beyond ~65% MVC, with the discrete-point group minimizing their SD at force values below that of the criterion target (higher CE/RMSE). Moreover, the sustained group's capacity to minimize SD/RMSE/CE corresponded to a more complex structure in their force fluctuations. These findings reveal that the time component of MVC estimation has a direct influence on the corrective strategies supporting near-maximal manual force control. While discrete MVC protocols predominate in the study of manual strength/endurance/precision, a 1:1 MVC-task mapping appears more to be ecologically valid if visuo-motor precision outcomes are of central importance.

Predicting toxins found in toxin-antitoxin systems with a role in host-induced Burkholderia pseudomallei persistence.

Burkholderia pseudomallei (Bpm) is a bacterial pathogen that causes Melioidosis, a disease with up to 40% mortality and an infection relapse of 15-23% despite antibiotic treatment. Ineffective clearance of Bpm by antibiotics is believed to be due to persistence, a hibernation-like survival mechanism modulated, in part, by toxin-antitoxin systems (TAS). Several organisms possess a repertoire of TASs but defining environmental cues eliciting their activity is hindered by laborious in vitro experiments, especially when there are many toxins with redundant function. Here, we identified which of 103 proteins in Bpm that share features found in toxins of the TAS and repurposed transcriptional data to identify which ones play a role in surviving intracellular host defenses. Putative toxins with the strongest transcriptional response were found to have low conservation between Bpm strains, while toxins that were constitutively expressed were highly conserved. Further examination of highly conserved toxins BPSS0899, BPSS1321, and BPSL1494 showed that they were functional, and their mutation led to reduce survival within macrophages and reduced in vivo persistence-associated pathology (abscesses) during treatment, but did not affect macrophages persistence. These findings highlight the utility of a data-driven approach to select putative toxins and suggests a selective role for some TAS in host survival.

Neurogaming With Motion-Onset Visual Evoked Potentials (mVEPs): Adults Versus Teenagers.

Motion-onset visually evoked potentials (mVEPs) are neural potentials that are time-locked to the onset of motion of evoking stimuli. Due to their visually elegant properties, mVEP stimuli may be suited to video game control given gaming's inherent demand on the users' visual attention and the requirement to process rapidly changing visual information. Here, we investigate mVEPs associated with five different stimuli to control the position of a car in a visually rich 3D racing game in a group of 15 BCI naïve teenagers and compared with 19 BCI naive adults. Results from an additional 14 BCI experienced adults were compared with BCI naïve adults. Our results demonstrate that the game control accuracy is related to the number of trials used to make a decision on the users' chosen button/stimulus (76%, 62%, and 35% for 5, 3, and 1 trials, respectively) and information transfer rate (ITR) (13.4, 13.9, and 6.6 bits per minute (BPM)), although, even though accuracy decreases when using three compared to the commonly used five trial repetitions, ITR is maintained. A Kruskal-Wallis test suggests that BCI naïve adults do not outperform BCI naïve teenagers in the 3D racing game in the first and seconds laps (p > 0.05), but do outperform in the third lap (p < 0.05). A comparison between BCI naïve and BCI experienced adults indicates BCI experienced adults do not perform better than BCI naïve adults (p > 0.05).

Developing Cancer Informatics Applications and Tools Using the NCI Genomic Data Commons API.

The NCI Genomic Data Commons (GDC) was launched in 2016 and makes available over 4 petabytes (PB) of cancer genomic and associated clinical data to the research community. This dataset continues to grow and currently includes over 14,500 patients. The GDC is an example of a biomedical data commons, which collocates biomedical data with storage and computing infrastructure and commonly used web services, software applications, and tools to create a secure, interoperable, and extensible resource for researchers. The GDC is (i) a data repository for downloading data that have been submitted to it, and also a system that (ii) applies a common set of bioinformatics pipelines to submitted data; (iii) reanalyzes existing data when new pipelines are developed; and (iv) allows users to build their own applications and systems that interoperate with the GDC using the GDC Application Programming Interface (API). We describe the GDC API and how it has been used both by the GDC itself and by third parties. Cancer Res; 77(21); e15-18. ©2017 AACR.

Community Partnership Designed to Promote Lyme Disease Prevention and Engagement in Citizen Science.

The goal of this project is to promote Lyme disease prevention and to cultivate an interest in science through a citizen-science project coordinated by researchers at a public university and teachers at rural high schools. The lesson plan is designed to increase student interest in pursuing a science career through participation in an authentic research experience, utilizing a topic that has implications on the health of the surrounding community. Students are introduced in the classroom to zoonotic diseases transmitted by the Ixodes tick, the health risks of Lyme disease, and disease prevention strategies. Students then participate in a research experience collecting field data and ticks from their community, which are used in university research. To measure changes in student knowledge and attitudes toward Lyme disease and science careers, students completed surveys related to the learning objectives associated with the experience. We found participation in the activity increased student confidence and ability to correctly differentiate a deer tick from a wood tick and to recognize the symptoms of Lyme disease. In addition, students reported increased interest in pursuing a science degree in college or graduate school. Authentic research experience related to a disease relevant to the local community is effective at enhancing high school student engagement in science.

CaPSID: a bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes.

BACKGROUND: It is now well established that nearly 20% of human cancers are caused by infectious agents, and the list of human oncogenic pathogens will grow in the future for a variety of cancer types. Whole tumor transcriptome and genome sequencing by next-generation sequencing technologies presents an unparalleled opportunity for pathogen detection and discovery in human tissues but requires development of new genome-wide bioinformatics tools. RESULTS: Here we present CaPSID (Computational Pathogen Sequence IDentification), a comprehensive bioinformatics platform for identifying, querying and visualizing both exogenous and endogenous pathogen nucleotide sequences in tumor genomes and transcriptomes. CaPSID includes a scalable, high performance database for data storage and a web application that integrates the genome browser JBrowse. CaPSID also provides useful metrics for sequence analysis of pre-aligned BAM files, such as gene and genome coverage, and is optimized to run efficiently on multiprocessor computers with low memory usage. CONCLUSIONS: To demonstrate the usefulness and efficiency of CaPSID, we carried out a comprehensive analysis of both a simulated dataset and transcriptome samples from ovarian cancer. CaPSID correctly identified all of the human and pathogen sequences in the simulated dataset, while in the ovarian dataset CaPSID's predictions were successfully validated in vitro.