Insights from a workplace SARS-CoV-2 specimen collection program, with genomes placed into global sequence phylogeny.

In 2020, the Department of Energy established the National Virtual Biotechnology Laboratory (NVBL) to address key challenges associated with COVID-19. As part of that effort, Pacific Northwest National Laboratory (PNNL) established a capability to collect and analyze specimens from employees who self-reported symptoms consistent with the disease. During the spring and fall of 2021, 688 specimens were screened for SARS-CoV-2, with 64 (9.3%) testing positive using reverse-transcriptase quantitative PCR (RT-qPCR). Of these, 36 samples were released for research. All 36 positive samples released for research were sequenced and genotyped. Here, the relationship between patient age and viral load as measured by Ct values was measured and determined to be only weakly significant. Consensus sequences for each sample were placed into a global phylogeny and transmission dynamics were investigated, revealing that the closest relative for many samples was from outside of Washington state, indicating mixing of viral pools within geographic regions.

Nucleated red blood cells as a biomarker for mortality in neonates following cardiac surgery.

INTRODUCTION: Nucleated red blood cells (NRBCs) are immature red cells that under normal conditions are not present in the peripheral circulation. Several studies have suggested an association between elevated NRBC and poor outcome in critically ill adults and neonates. We sought to determine if elevations in NRBC value following cardiac surgery and following clinical events during the hospital stay can be used as a biomarker to monitor for mortality risk in neonates post-cardiac surgery. MATERIALS AND METHODS: We constructed a retrospective study of 264 neonates who underwent cardiac surgery at Children's Hospital, New Orleans between 2011 and 2020. Variables included mortality and NRBC value were recorded following cardiac surgery and following peri-operative clinical events. The study was approved by LSU Health IRB. Sensitivity, specificity, receiver operating characteristic (ROC) curves with area under the curve (AUC) and logistic regression analysis were performed. RESULTS: Thirty-six patients (13.6%) died, of which 32 had an NRBC value ≥10/100 white blood cell (WBC) during hospitalisation. Multi-variable analysis found extracorporeal membrane oxygenation use (OR 10, 95% CI 2.9-33, p=<0.001), NRBC ≥10/100 WBC (OR 16.1, CI 4.1-62.5, p ≤ 0.001) and peak NRBC in the 14-day period post-cardiac surgery (continuous variable, OR 1.05, 95% CI 1.0-1.09, p = 0.03), to be independently associated with mortality. Using a cut-off NRBC value of 10/100 WBC, there was an 88.9% sensitivity and a 90.8% specificity, with ROC curve showing an AUC of 0.9 and 0.914 for peak NRBC value in 14 days post-surgery and entire hospitalisation, respectively. CONCLUSIONS: NRBC ≥10/100 WBC post-cardiac surgery is strongly associated with mortality. Additionally, NRBC trend appears to show promise as an accurate biomarker for mortality.

Effect of Increasing Pulse Phase Duration on Neural Responsiveness of the Electrically Stimulated Cochlear Nerve.

OBJECTIVES: The aim of this study is to (1) investigate the effects of increasing the pulse phase duration (PPD) on the neural response of the electrically stimulated cochlear nerve (CN) in children with CN deficiency (CND) and (2) compare the results from the CND population to those measured in children with normal-sized CNs. DESIGN: Study participants included 30 children with CND and 30 children with normal-sized CNs. All participants used a Cochlear Nucleus device in the test ear. For each subject, electrically evoked compound action potential (eCAP) input/output (I/O) functions evoked by single biphasic pulses with different PPDs were recorded at three electrode locations across the electrode array. PPD durations tested in this study included 50, 62, 75, and 88 µsec/phase. For each electrode tested for each study participant, the amount of electrical charge corresponding to the maximum comfortable level measured for the 88 µsec PPD was used as the upper limit of stimulation. The eCAP amplitude measured at the highest electrical charge level, the eCAP threshold (i.e., the lowest level that evoked an eCAP), and the slope of the eCAP I/O function were measured. Generalized linear mixed effect models with study group, electrode location, and PPD as the fixed effects and subject as the random effect were used to compare these dependent variables measured at different electrode locations and PPDs between children with CND and children with normal-sized CNs. RESULTS: Children with CND had smaller eCAP amplitudes, higher eCAP thresholds, and smaller slopes of the eCAP I/O function than children with normal-sized CNs. Children with CND who had fewer electrodes with a measurable eCAP showed smaller eCAP amplitudes and flatter eCAP I/O functions than children with CND who had more electrodes with eCAPs. Increasing the PPD did not show a statistically significant effect on any of these three eCAP parameters in the two subject groups tested in this study. CONCLUSIONS: For the same amount of electrical charge, increasing the PPD from 50 to 88 µsec for a biphasic pulse with a 7 µsec interphase gap did not significantly affect CN responsiveness to electrical stimulation in human cochlear implant users. Further studies with different electrical pulse configurations are warranted to determine whether evaluating the eCAP sensitivity to changes in the PPD can be used as a testing paradigm to estimate neural survival of the CN for individual cochlear implant users.

Recommendations for Measuring the Electrically Evoked Compound Action Potential in Children With Cochlear Nerve Deficiency.

OBJECTIVES: This study reports a method for measuring the electrically evoked compound action potential (eCAP) in children with cochlear nerve deficiency (CND). DESIGN: This method was developed based on experience with 50 children with CND who were Cochlear Nucleus cochlear implant users. RESULTS: This method includes three recommended steps conducted with recommended stimulating and recording parameters: initial screen, pulse phase duration optimization, and eCAP threshold determination (i.e., identifying the lowest stimulation level that can evoke an eCAP). Compared with the manufacturer-default parameters, the recommended parameters used in this method yielded a higher success rate for measuring the eCAP in children with CND. CONCLUSIONS: The eCAP can be measured successfully in children with CND using recommended parameters. This specific method is suitable for measuring the eCAP in children with CND in clinical settings. However, it is not suitable for intraoperative eCAP recordings due to the extensive testing time required.

Polysaccharide-based liquid storage and transport media for non-refrigerated preservation of bacterial pathogens.

The preservation of biological samples for an extended time period of days to weeks after initial collection is important for the identification, screening, and characterization of bacterial pathogens. Traditionally, preservation relies on cold-chain infrastructure; however, in many situations this is impractical or not possible. Thus, our goal was to develop alternative bacterial sample preservation and transport media that are effective without refrigeration or external instrumentation. The viability, nucleic acid stability, and protein stability of Bacillus anthracis Sterne 34F2, Francisella novicida U112, Staphylococcus aureus ATCC 43300, and Yersinia pestis KIM D27 (pgm-) was assessed for up to 28 days. Xanthan gum (XG) prepared in PBS with L-cysteine maintained more viable F. novicida U112 cells at elevated temperature (40°C) compared to commercial reagents and buffers. Viability was maintained for all four bacteria in XG with 0.9 mM L-cysteine across a temperature range of 22-40°C. Interestingly, increasing the concentration to 9 mM L-cysteine resulted in the rapid death of S. aureus. This could be advantageous when collecting samples in the built environment where there is the potential for Staphylococcus collection and stabilization rather than other organisms of interest. F. novicida and S. aureus DNA were stable for up to 45 days upon storage at 22°C or 40°C, and direct analysis by real-time qPCR, without DNA extraction, was possible in the XG formulations. XG was not compatible with proteomic analysis via LC-MS/MS due to the high amount of residual Xanthomonas campestris proteins present in XG. Our results demonstrate that polysaccharide-based formulations, specifically XG with L-cysteine, maintain bacterial viability and nucleic acid integrity for an array of both Gram-negative and Gram-positive bacteria across ambient and elevated temperatures.

Magnetic iron oxide and manganese-doped iron oxide nanoparticles for the collection of alpha-emitting radionuclides from aqueous solutions.

Magnetic nanoparticles are well known to possess chemically active surfaces and large surface areas that can be employed to extract a range of ions from aqueous solutions. Additionally, their superparamagnetic properties provide a convenient means for bulk collection of the material from solution after the targeted ions have been adsorbed. Herein, two nanoscale amphoteric metal oxides, each possessing useful magnetic attributes, were evaluated for their ability to collect trace levels of a chemically diverse range of alpha emitting radioactive isotopes (polonium (Po), radium (Ra), uranium (U), and americium (Am)) from a wide range of aqueous solutions. The nanomaterials include commercially available magnetite (Fe3O4) and magnetite modified to incorporate manganese (Mn) into the crystal structure. The chemical stability of these nanomaterials was evaluated in Hanford Site, WA ground water between the natural pH (~8) and pH 1. Whereas the magnetite was observed to have good stability over the pH range, the Mn-doped material was observed to leach Mn at low pH. The materials were evaluated in parallel to characterize their uptake performance of the alpha-emitting radionuclide spikes from ground water across a range of pH (from ~8 down to 2). In addition, radiotracer uptake experiments were performed on Columbia River water, seawater, and human urine at their natural pH and at pH 2. Despite the observed leaching of Mn from the Mn-doped nanomaterial in the lower pH range, it exhibited generally superior analyte extraction performance compared to the magnetite, and analyte uptake was observed across a broader pH range. We show that the uptake behavior of the various radiotracers on these two materials at different pH levels can generally be explained by the amphoteric nature of the nanoparticle surfaces. Finally, the rate of sorption of the radiotracers on the two materials in unacidified ground water was evaluated. The uptake curves generally indicate that equilibrium is obtained within a few minutes, which is attributed to the high surface areas of the nanomaterials and the high level of dispersion in the liquids. Overall, the results indicate that these nanomaterials may have the potential to be employed for a range of applications to extract radionuclides from aqueous solutions.

Manganese doping of magnetic iron oxide nanoparticles: tailoring surface reactivity for a regenerable heavy metal sorbent.

A method for tuning the analyte affinity of magnetic, inorganic nanostructured sorbents for heavy metal contaminants is described. The manganese-doped iron oxide nanoparticle sorbents have a remarkably high affinity compared to the precursor material. Sorbent affinity can be tuned toward an analyte of interest simply by adjustment of the dopant quantity. The results show that following the Mn doping process there is a large increase in affinity and capacity for heavy metals (i.e., Co, Ni, Zn, As, Ag, Cd, Hg, and Tl). Capacity measurements were carried out for the removal of cadmium from river water and showed significantly higher loading than the relevant commercial sorbents tested for comparison. The reduction in Cd concentration from 100 ppb spiked river water to 1 ppb (less than the EPA drinking water limit of 5 ppb for Cd) was achieved following treatment with the Mn-doped iron oxide nanoparticles. The Mn-doped iron oxide nanoparticles were able to load ~1 ppm of Cd followed by complete stripping and recovery of the Cd with a mild acid wash. The Cd loading and stripping is shown to be consistent through multiple cycles with no loss of sorbent performance.

Investigation of magnetic nanoparticles for the rapid extraction and assay of alpha-emitting radionuclides from urine: demonstration of a novel radiobioassay method.

In the event of an accidental or intentional release of radionuclides into a populated area, massive numbers of people may require radiobioassay screening as triage for dose-reduction therapy or identification for longer-term follow-up. If the event released significant levels of beta- or alpha-emitting radionuclides, in vivo assays would be ineffective. Therefore, highly efficient and rapid analytical methods for radionuclide detection from submitted spot urine samples (≤50 mL) would be required. At present, the quantitative determination of alpha-emitting radionuclides from urine samples is highly labor intensive and requires significant time to prepare and analyze samples. Sorbent materials that provide effective collection and enable rapid assay could significantly streamline the radioanalytical process. The authors have demonstrated the use of magnetic nanoparticles as a novel method of extracting media for four alpha-emitting radionuclides of concern (polonium, radium, uranium and americium) from chemically-unmodified and pH-2 human urine. Herein, the initial experimental sorption results are presented along with a novel method that uses magnetic nanoparticles to extract radionuclides from unmodified human urine and then collect the magnetic field-induced particles for subsequent alpha-counting-source preparation. Additionally, a versatile human dose model is constructed that determines the detector count times required to estimate dose at specific protective-action thresholds. The model provides a means to assess a method's detection capabilities and uses fundamental health physics parameters and actual experimental data as core variables. The modeling shows that, with effective sorbent materials, rapid screening for alpha-emitters is possible with a 50-mL urine sample collected within 1 wk of exposure/intake.

Functionalized nanoporous silica for the removal of heavy metals from biological systems: adsorption and application.

Surface-functionalized nanoporous silica, often referred to as self-assembled monolayers on mesoporous supports (SAMMS), has previously demonstrated the ability to serve as very effective heavy metal sorbents in a range of aquatic and environmental systems, suggesting that they may be advantageously utilized for biomedical applications such as chelation therapy. Herein we evaluate surface chemistries for heavy metal capture from biological fluids, various facets of the materials' biocompatibility, and the suitability of these materials as potential therapeutics. Of the materials tested, thiol-functionalized SAMMS proved most capable of removing selected heavy metals from biological solutions (i.e., blood, urine, etc.) Consequentially, thiol-functionalized SAMMS was further analyzed to assess the material's performance under a number of different biologically relevant conditions (i.e., variable pH and ionic strength) to gauge any potentially negative effects resulting from interaction with the sorbent, such as cellular toxicity or the removal of essential minerals. Additionally, cellular uptake studies demonstrated no cell membrane permeation by the silica-based materials generally highlighting their ability to remain cellularly inert and thus nontoxic. The results show that organic ligand functionalized nanoporous silica could be a valuable material for a range of detoxification therapies and potentially other biomedical applications.

Thiol-ene induced diphosphonic acid functionalization of superparamagnetic iron oxide nanoparticles.

Multifunctional organic molecules represent an interesting challenge for nanoparticle functionalization due to the potential for undesirable interactions between the substrate material and the variable functionalities, making it difficult to control the final orientation of the ligand. In the present study, UV-induced thiol-ene click chemistry has been utilized as a means of directed functionalization of bifunctional ligands on an iron oxide nanoparticle surface. Allyl diphosphonic acid ligand was covalently deposited on the surface of thiol-presenting iron oxide nanoparticles via the formation of a UV-induced thioether. This method of thiol-ene click chemistry offers a set of reaction conditions capable of controlling the ligand deposition and circumventing the natural affinity exhibited by the phosphonic acid moiety for the iron oxide surface. These claims are supported via a multimodal characterization platform which includes thermogravimetric analysis, X-ray photoelectron spectroscopy, and metal contact analysis and are consistent with a properly oriented, highly active ligand on the nanoparticle surface. These experiments suggest thiol-ene click chemistry as both a practical and generally applicable strategy for the directed deposition of multifunctional ligands on metal oxide nanoparticle surfaces.

High-performance, superparamagnetic, nanoparticle-based heavy metal sorbents for removal of contaminants from natural waters.

We describe the synthesis and characterization of high-performance, superparamagnetic, iron oxide nanoparticle-based, heavy metal sorbents, which demonstrate excellent affinity for the separation of heavy metals in contaminated water systems (i.e., spiked Columbia River water). The magnetic nanoparticle sorbents were prepared from an easy-to-synthesize iron oxide precursor, followed by a simple, one-step ligand exchange reaction to introduce an affinity ligand to the nanoparticle surface that is specific to a heavy metal or class of heavy metal contaminants. The engineered magnetic nanoparticle sorbents have inherently high active surface areas, allowing for increased binding capacities. To demonstrate the performance of the nanoparticle sorbents, river water was spiked with specific metals and exposed to low concentrations of the functionalized nanoparticles. In almost all cases, the nanoparticles were found to be superior to commercially available sorbent materials as well as the unfunctionalized iron oxide nanoparticles.

Same-visit HIV testing in Trinidad and Tobago.

BACKGROUND: The Ministry of Health (hereafter, Ministry) of Trinidad and Tobago is responsible for delivery of all health services in the country. The Ministry takes responsibility for direct delivery of care in the public sector and has initiated a process whereby those seeking HIV test results could obtain confidential reports during a single-visit to a testing location. The Ministry requested technical assistance with this process from the Caribbean Epidemiology Centre (CAREC). The United States Centers for Disease Control and Prevention (CDC) played an important role in this process through its partnership with CAREC. METHODS: Under the technical guidance of CAREC and CDC, the Ministry organized a technical working group which included representatives from key national HIV program services and technical assistance partners. This working group reviewed internationally-recognized best practices for HIV rapid testing and proposed a program that could be integrated into the national HIV programs of Trinidad and Tobago. The working group wrote a consensus protocol, defined certification criteria, prepared training materials and oversaw implementation of "same-visit" HIV testing at two pilot sites. RESULTS: A Ministry-of-Health-supported program of "same-visit" HIV testing has been established in Trinidad and Tobago. This program provides confidential testing that is independent of laboratory confirmation. The program allows clients who want to know their HIV status to obtain this information during a single-visit to a testing location. Testers who are certified to provide testing on behalf of the Ministry are also counselors. Non-laboratory personnel have been trained to provide HIV testing in non-laboratory locations. The program includes procedures to assure uniform quality of testing across multiple testing sites. Several procedural and training documents were developed during implementation of this program. This report contains links to those documents. CONCLUSIONS: The Ministry of Health has implemented a program of "same-visit" HIV testing in Trinidad and Tobago. This program provides clients confidential HIV test reports during a single visit to a testing location. The program is staffed by non-laboratory personnel who are trained to provide both testing and counseling in decentralized (non-laboratory) settings. This approach may serve as a model for other small countries.

Same-visit HIV testing in Trinidad and Tobago

BACKGROUND: The Ministry of Health (hereafter, Ministry) of Trinidad and Tobago is responsible for delivery of all health services in the country. The Ministry takes responsibility for direct delivery of care in the public sector and has initiated a process whereby those seeking HIV test results could obtain confidential reports during a single-visit to a testing location. The Ministry requested technical assistance with this process from the Caribbean Epidemiology Centre (CAREC). The United States Centers for Disease Control and Prevention (CDC) played an important role in this process through its partnership with CAREC. METHODS: Under the technical guidance of CAREC and CDC, the Ministry organized a technical working group which included representatives from key national HIV program services and technical assistance partners. This working group reviewed internationally-recognized best practices for HIV rapid testing and proposed a program that could be integrated into the national HIV programs of Trinidad and Tobago. The working group wrote a consensus protocol, defined certification criteria, prepared training materials and oversaw implementation of "same-visit" HIV testing at two pilot sites. RESULTS: A Ministry-of-Health-supported program of "same-visit" HIV testing has been established in Trinidad and Tobago. This program provides confidential testing that is independent of laboratory confirmation. The program allows clients who want to know their HIV status to obtain this information during a single-visit to a testing location. Testers who are certified to provide testing on behalf of the Ministry are also counselors. Non-laboratory personnel have been trained to provide HIV testing in non-laboratory locations. The program includes procedures to assure uniform quality of testing across multiple testing sites. Several procedural and training documents were developed during implementation of this program. This report contains links to those documents. CONCLUSIONS: The Ministry of Health has implemented a program of "same-visit" HIV testing in Trinidad and Tobago. This program provides clients confidential HIV test reports during a single visit to a testing location. The program is staffed by non-laboratory personnel who are trained to provide both testing and counseling in decentralized (non-laboratory) settings. This approach may serve as a model for other small countries.

Direct detection of Pb in urine and Cd, Pb, Cu, and Ag in natural waters using electrochemical sensors immobilized with DMSA functionalized magnetic nanoparticles.

Urine is universally recognized as one of the best non-invasive matrices for biomonitoring exposure to a broad range of xenobiotics, including toxic metals. Detection of metal ions in urine has been problematic due to the protein competition and electrode fouling. For direct, simple, and field-deployable monitoring of urinary Pb, electrochemical sensors employing superparamagnetic iron oxide (Fe3O4) nanoparticles with a surface functionalization of dimercaptosuccinic acid (DMSA) has been developed. The metal detection involves rapid collection of dispersed metal-bound nanoparticles from a sample solution at a magnetic or electromagnetic electrode, followed by the stripping voltammetry of the metal in acidic medium. The sensors were evaluated as a function of solution pH, the binding affinity of Pb to DMSA-Fe3O4, the ratio of nanoparticles per sample volume, preconcentration time, and Pb concentrations. The effect of binding competitions between the DMSA-Fe3O4 and urine constituents for Pb on the sensor responses was studied. After 90 s of preconcentration in samples containing 25 vol.% of rat urine and 0.1 g L(-1) of DMSA-Fe3O4, the sensor could detect background level of Pb (0.5 ppb) and yielded linear responses from 0 to 50 ppb of Pb, excellent reproducibility (%RSD of 5.3 for seven measurements of 30 ppb Pb), and Pb concentrations comparable to those measured by ICP-MS. The sensor could also simultaneously detect background levels (<1 ppb) of Cd, Pb, Cu, and Ag in river and seawater.

A simple method for the prevention of non-specific adsorption by nanocrystals onto surfaces.

In this work we introduce an efficient method for averting non-specific adsorption of various nanoparticles to typical oxide surfaces, such as glass, quartz, and sapphire, through the attachment of a fluorinated self-assembled monolayer (SAM) that minimizes the interactions between stabilized nanoparticles and these surfaces. This surface treatment is shown to be effective for a variety of nanoparticles in a range of solvent systems. As a result, monitoring and characterization of nanoparticles and their surface chemistry is allowed, while simultaneously preventing loss of expensive nanomaterials to the various surfaces inherent in laboratory apparatus.

Removal of heavy metals from aqueous systems with thiol functionalized superparamagnetic nanoparticles.

We have shown that superparamagnetic iron oxide (Fe3O4) nanoparticles with a surface functionalization of dimercaptosuccinic acid (DMSA) are an effective sorbent material for toxic soft metals such as Hg, Ag, Pb, Cd, and Tl, which effectively bind to the DMSA ligands and for As, which binds to the iron oxide lattices. The nanoparticles are highly dispersible and stable in solutions, have a large surface area (114 m2/g), and have a high functional group content (1.8 mmol thiols/g). They are attracted to a magnetic field and can be separated from solution within a minute with a 1.2 T magnet. The chemical affinity, capacity, kinetics, and stability of the magnetic nanoparticles were compared to those of conventional resin based sorbents (GT-73), activated carbon, and nanoporous silica (SAMMS) of similar surface chemistries in river water, groundwater, seawater, and human blood and plasma. DMSA-Fe3O4 had a capacity of 227 mg of Hg/g, a 30-fold larger value than GT-73. The nanoparticles removed 99 wt% of 1 mg/L Pb within a minute, while it took over 10 and 120 min for Chelex-100 and GT-73 to remove 96% of Pb.