Comparison of real-time and droplet digital PCR to detect and quantify SARS-CoV-2 RNA in plasma.

BACKGROUND: The presence of SARS-CoV-2 RNA in plasma has been linked to disease severity and mortality. We compared RT-qPCR to droplet digital PCR (ddPCR) to detect SARS-CoV-2 RNA in plasma from COVID-19 patients (mild, moderate, and critical disease). METHODS: The presence/concentration of SARS-CoV-2 RNA in plasma was compared in three groups of COVID-19 patients (30 outpatients, 30 ward patients and 30 ICU patients) using both RT-qPCR and ddPCR. Plasma was obtained in the first 24h following admission, and RNA was extracted using eMAG. ddPCR was performed using Bio-Rad SARS-CoV-2 detection kit, and RT-qPCR was performed using GeneFinder™ COVID-19 Plus RealAmp Kit. Statistical analysis was performed using Statistical Package for the Social Science. RESULTS: SARS-CoV-2 RNA was detected, using ddPCR and RT-qPCR, in 91% and 87% of ICU patients, 27% and 23% of ward patients and 3% and 3% of outpatients. The concordance of the results obtained by both methods was excellent (Cohen's kappa index = 0.953). RT-qPCR was able to detect 34/36 (94.4%) patients positive for viral RNA in plasma by ddPCR. Viral RNA load was higher in ICU patients compared with the other groups (P < .001), by both ddPCR and RT-qPCR. AUC analysis revealed Ct values (RT-qPCR) and viral RNA load values (ddPCR) can similarly differentiate between patients admitted to wards and to the ICU (AUC of 0.90 and 0.89, respectively). CONCLUSION: Both methods yielded similar prevalence of RNAemia between groups, with ICU patients showing the highest (>85%). RT-qPCR was as useful as ddPCR to detect and quantify SARS-CoV-2 RNAemia in plasma.

Photoinduced Intermolecular Electron Transfer in Gas Phase Ion Pairs of the 1-Ethyl-3-methylimidazolium Cation and the Bis(trifluoromethylsulfonyl)imide Anion.

In this study, the UV photodissociation of gas phase ion pairs of the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [emim]+[tf2n]-, is shown to proceed primarily through radical intermediates. [emim]+[tf2n]- ion pairs have been shown previously to undergo two-photon-dependent dissociation, but the mechanisms of this have not been probed in detail. By employing a two-laser pump probe spectroscopy and time-dependent density functional theory (TD-DFT) calculations, we have illustrated that one of the major UV photodissociation pathways in [emim]+[tf2n]- ion pairs is an intermolecular electron transfer wherein the anion transfers an electron to the cation resulting in two neutral open-shelled products. These products were observable for at least 1.6 µs post photodissociation, the experimental limit, via detection of the [emim]+ cation. This data demonstrates that the likely photoproducts of [emim]+[tf2n]- UV photodissociation are two neutral species that separate spatially, demonstrated through lack of observed relaxation pathways such as electron recombination. TD-DFT and frontier molecular orbital analysis calculations at the MN15/6-311++G(d,p) level are employed to aid in identifying excited state characteristics and support the interpretations of the experimental data. The energetic onset of the intermolecular electron transfer is consistent with previously observed [emim]+[tf2n]- absorption spectra in the bulk and gas phases. The similarities between bulk and gas phase UV spectra imply that this electron-transfer pathway may be a major photodissociation channel in both phases.

Theoretical Investigation of the Reactivity of Sodium Dicyanamide with Nitric Acid.

There is a need to replace current hydrazine fuels with safer propellants, and dicyanamide (DCA-)-based systems have emerged as promising alternatives because they autoignite when mixed with some oxidizers. Previous studies of the hypergolic reaction mechanism have focused on the reaction between DCA- and the oxidizer HNO3; here, we compare the calculated pathway of DCA- + HNO3 with the reaction coordinate of the ion pair sodium dicyanamide with nitric acid, Na[DCA] + HNO3. Enthalpies and free energies are calculated in the gas phase and in solution using a quantum mechanical continuum solvation model, SMD-GIL. The barriers to the Na[DCA] + HNO3 reaction are dramatically lowered relative to those of the reaction with the bare anion, and an exothermic exit channel to produce NaNO3 and the reactive intermediate HDCA appears. These results suggest that Na[DCA] may accelerate the ignition reaction.

Hydroxyl Radical Fluorescence and Quantum Yield Following Lyman-α Photoexcitation of Water Vapor in a Room Temperature Cell and Cooled in a Supersonic Expansion.

Photoexcitation of water by Lyman-α (121.6 nm) induces a dissociation reaction that produces OH(A2Σ+) + H. Despite this reaction being part of numerous studies, a combined understanding of the product and fluorescence yields is still lacking. Here, the rotational and vibrational distributions of OH(A) are determined from dispersed fluorescence following photoexcitation of both room-temperature and jet-cooled water vapor, for the first time in the same experiment. This work compares new data of state-resolved fluorescence with literature molecular branching ratios and brings previous studies into agreement through careful consideration of OH(A) fluorescent and predissociation lifetimes and confirms a fluorescent quantum yield of 8%. Comparison of the room-temperature and jet-cooled OH(A) populations indicate the temperature of H2O prior to excitation has subtle effects on the OH(A) population distribution, such as altering the rotational distribution in the ν' = 0 population and affecting the population in the ν' = 1 state. These results indicate jet-cooled water vapor may have a 1% higher fluorescence quantum yield compared to room-temperature water vapor.

Identification of multiple conformers of the ionic liquid [emim][tf2n] in the gas phase using IR/UV action spectroscopy.

In this study we investigate the effect of deuteration and molecular beam temperature on the hydrogen bond in the ionic liquid [emim][tf2n]. Using IR/UV double resonance spectroscopy, we probe the microscopic structure of the [emim][tf2n] ion pair and its mono-deuterated, [emim-d1][tf2n], analog. Comparisons of the infrared absorption frequencies between these two species show that there are multiple conformers of the ion pair present in the gas phase and trapped through the molecular beam cooling process. Furthermore, each conformer has a characteristic red shift in the frequency of its C2-H group that reveals the variation in strength of a hydrogen bond between the cation and anion.

Further studies into the photodissociation pathways of 2-bromo-2-nitropropane and the dissociation channels of the 2-nitro-2-propyl radical intermediate.

These experiments investigate the decomposition mechanisms of geminal dinitro energetic materials by photolytically generating two key intermediates: 2-nitropropene and 2-nitro-2-propyl radicals. To characterize the unimolecular dissociation of each intermediate, we form them under collision-free conditions using the photodissociation of 2-bromo-2-nitropropane; the intermediates are formed at high internal energies and undergo a multitude of subsequent unimolecular dissociation events investigated herein. Complementing our prior work on this system, the new data obtained with a crossed-laser molecular beam scattering apparatus with VUV photoionization detection at Taiwan's National Synchrotron Radiation Research Center (NSRRC) and new velocity map imaging data better characterize two of the four primary 193 nm photodissociation channels. The C-Br photofission channel forming the 2-nitro-2-propyl radicals has a trimodal recoil kinetic energy distribution, P(ET), suggesting that the 2-nitro-2-propyl radicals are formed both in the ground electronic state and in two low-lying excited electronic states. The new data also revise the HBr photoelimination P(ET) forming the 2-nitropropene intermediate. We then resolved the multiple competing unimolecular dissociation channels of each photoproduct, confirming many of the channels detected in the prior study, but not all. The new data detected HONO product at m/e = 47 using 11.3 eV photoionization from both intermediates; analysis of the momentum-matched products allows us to establish that both 2-nitro-2-propyl → HONO + CH3CCH2 and 2-nitropropene → HONO + C3H4 occur. Photoionization at 9.5 eV allowed us to detect the mass 71 coproduct formed in OH loss from 2-nitro-2-propyl; a channel missed in our prior study. The dynamics of the highly exothermic 2-nitro-2-propyl → NO + acetone dissociation is also better characterized; it evidences a sideways scattered angular distribution. The detection of some stable 2-nitropropene photoproducts allows us to fit signal previously assigned to H loss from 2-nitro-2-propyl radicals. Overall, the data provide a comprehensive study of the unimolecular dissociation channels of these important nitro-containing intermediates.

Thermal decomposition pathways for 1,1-diamino-2,2-dinitroethene (FOX-7).

In this study, we computationally investigate the initial and subsequent steps in the chemical mechanism for the gas-phase thermal decomposition of 1,1-diamino-2,2-dinitroethene (FOX-7). We determine the key exothermic step in the gas-phase thermal decomposition of FOX-7 and explore the similarities and differences between FOX-7 and other geminal dinitro energetic materials. The calculations reveal a mechanism for NO loss involving a 3-member cyclic intermediate, rather than a nitro-nitrite isomerization, that occurs in the radical intermediates formed throughout the decomposition mechanism.

Elucidating the decomposition mechanism of energetic materials with geminal dinitro groups using 2-bromo-2-nitropropane photodissociation.

These experiments photolytically generate two key intermediates in the decomposition mechanisms of energetic materials with nitro substituents, 2-nitropropene, and 2-nitro-2-propyl radicals. These intermediates are produced at high internal energies and access a number of competing unimolecular dissociation channels investigated herein. We use a combination of crossed laser-molecular beam scattering and velocity map imaging to study the photodissociation of 2-bromo-2-nitropropane at 193 nm and the subsequent unimolecular dissociation of the intermediates above. Our results demonstrate that 2-bromo-2-nitropropane has four primary photodissociation pathways: C-Br bond fission yielding the 2-nitro-2-propyl radical, HBr elimination yielding 2-nitropropene, C-N bond fission yielding the 2-bromo-2-propyl radical, and HONO elimination yielding 2-bromopropene. The photofragments are formed with significant internal energy and undergo many secondary dissociation events, including the exothermic dissociation of 2-nitro-2-propyl radicals to NO + acetone. Calculations at the G4//B3LYP/6-311++g(3df,2p) level show that the presence of a radical at a nitroalkyl center changes the mechanism for and substantially lowers the barrier to NO loss. This mechanism involves an intermediate with a three-center ring rather than the intermediate formed during the traditional nitro-nitrite isomerization. The observed dissociation pathways of the 2-nitro-2-propyl radical and 2-nitropropene help elucidate the decomposition mechanism of larger energetic materials with geminal dinitro groups.

Ten-nanometer dense hole arrays generated by nanoparticle lithography.

Large area dense hole arrays with a feature size of ~10 nm were generated using self-assembled monolayers of nanoparticles as etch masks. To fabricate the hole arrays, monolayers of nanoparticles were irradiated by electron beam to turn surfactants into amorphous carbon, treated by acid to remove the nanoparticle cores, and then etched by CF(4) to deepen the holes. Evaporated gold films preferentially diffuse into the holes to generate gold nanoparticle arrays. However no obvious diffusion into holes was observed for a sputtered iron platinum film.

Characterizing the rovibrational distribution of CD2CD2OH radicals produced via the photodissociation of 2-bromoethanol-d4.

This work characterizes the internal energy distribution of the CD(2)CD(2)OH radical formed via photodissociation of 2-bromoethanol-d(4). The CD(2)CD(2)OH radical is the first radical adduct in the addition of the hydroxyl radical to C(2)D(4) and the product branching of the OH + C(2)D(4) reaction is dependent on the total internal energy of this adduct and how that energy is partitioned between rotation and vibration. Using a combination of a velocity map imaging apparatus and a crossed laser-molecular beam scattering apparatus, we photodissociate the BrCD(2)CD(2)OH precursor at 193 nm and measure the velocity distributions of the Br atoms, resolving the Br((2)P(1/2)) and Br((2)P(3/2)) states with [2 + 1] resonance enhanced multiphoton ionization (REMPI) on the imaging apparatus. We also detect the velocity distribution of the subset of the nascent momentum-matched CD(2)CD(2)OH cofragments that are formed stable to subsequent dissociation. Invoking conservation of momentum and conservation of energy and a recently developed impulsive model, we determine the vibrational energy distribution of the nascent CD(2)CD(2)OH radicals from the measured velocity distributions.

Heterologous immunization with Covishield and Pfizer vaccines against SARS-CoV-2 elicits a robust humoral immune response.

Understanding the efficacy and durability of heterologous immunization schedules against SARS-CoV-2 is critical, as supply demands and vaccine choices become significant issues in the global vaccination strategy. Here we characterize the neutralizing antibodies produced in two subjects who received combination immunizations against SARS-CoV-2, first with Covishield (Oxford-AstraZeneca) vaccine, followed 33 days later with a second dose (booster) shot of the Pfizer-BioNTech vaccine. Serum samples were collected 25 days following the primary vaccination and 13 days after the secondary Pfizer vaccination. Both subjects exhibited increased levels of isotype IgG and IgM antibodies directed against the entire spike protein following immunizations. These antibodies also exhibited increased reactivity with the receptor binding domain (RBD) in the spike protein and neutralized the infectivity of replicating vesicular stomatitis virus (VSV) that contains the COVID-19 coronavirus S protein gene in place of its normal G glycoprotein. This VSV pseudovirus also contains the reporter gene for enhanced green fluorescent protein (eGFP). Antibody titers against the spike protein and serum neutralization titers against the reporter virus are reported for the 2 heterologous vaccinated individuals and compared to a positive control derived from a convalescent patient and a negative control from an unexposed individual. The Pfizer-BioNTech vaccine increased antibody binding to the spike protein and RBD, and approached levels found in the convalescent positive control. Neutralizing antibodies against the VSV-S pseudovirus in the 2 subjects also approached levels in the convalescent sera. These results firmly validate the value of the Pfizer-BioNTech vaccine in boosting immunity following initial Covishield inoculation.

Centenarians and extremely old people living with frailty can elicit durable SARS-CoV-2 spike specific IgG antibodies with virus neutralization functions following virus infection as determined by serological study.

BACKGROUND: The SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2) has led to more than 165 million COVID-19 cases and >3.4 million deaths worldwide. Epidemiological analysis has revealed that the risk of developing severe COVID-19 increases with age. Despite a disproportionate number of older individuals and long-term care facilities being affected by SARS-CoV-2 and COVID-19, very little is understood about the immune responses and development of humoral immunity in the extremely old person after SARS-CoV-2 infection. Here we conducted a serological study to investigate the development of humoral immunity in centenarians following a SARS-CoV-2 outbreak in a long-term care facility. METHODS: Extreme aged individuals and centenarians who were residents in a long-term care facility and infected with or exposed to SARS-CoV-2 were investigated between April and June 2020 for the development of antibodies to SARS-CoV-2. Blood samples were collected from positive and bystander individuals 30 and 60 days after original diagnosis of SARS-CoV-2 infection. Plasma was used to quantify IgG, IgA, and IgM isotypes and subsequent subclasses of antibodies specific for SARS-CoV-2 spike protein. The function of anti-spike was then assessed by virus neutralization assays against the native SARS-CoV-2 virus. FINDINGS: Fifteen long-term care residents were investigated for SARS-CoV-2 infection. All individuals had a Clinical Frailty scale score ≥5 and were of extreme older age or were centenarians. Six women with a median age of 98.8 years tested positive for SARS-CoV-2. Anti-spike IgG antibody titers were the highest titers observed in our cohort with all IgG positive individuals having virus neutralization ability. Additionally, 5 out of the 6 positive participants had a robust IgA anti-SARS-CoV-2 response. In all 5, antibodies were detected after 60 days from initial diagnosis.

Origin of reduced magnetization and domain formation in small magnetite nanoparticles.

The structural, chemical, and magnetic properties of magnetite nanoparticles are compared. Aberration corrected scanning transmission electron microscopy reveals the prevalence of antiphase boundaries in nanoparticles that have significantly reduced magnetization, relative to the bulk. Atomistic magnetic modelling of nanoparticles with and without these defects reveals the origin of the reduced moment. Strong antiferromagnetic interactions across antiphase boundaries support multiple magnetic domains even in particles as small as 12-14 nm.

A Novel Mechanism for Nitric Oxide Production in Nitroalkyl Radicals that Circumvents Nitro-Nitrite Isomerization.

In this study, we present a novel mechanism for NO loss from nitroalkyl radicals that circumvents the traditional higher-energy nitro-nitrite isomerization. We characterize the intrinsic reaction coordinate at the B3LYP/6-311++g(3df,2p) level of theory and calculate the transition-state energies using the G4 composite method; the subsequent dynamics en route to the highly exothermic NO + acetone product channel proceeds through a three-membered ring intermediate. Crossed laser-molecular beam scattering experiments on the 2-nitro-2-propyl radical confirm the importance of this new mechanism in determining the product branching.

Hyaluronic acid N-deacetylase assay in whole skin.

Hyaluronic acid (HA) N-deacetylase(s) was quantified in whole skin, using a novel method that involved reaction of skin with exogenous HA as substrate. Acetyl (CH(3)CO-) moieties generated were converted chemically to MeOAc and quantified using gas chromatography/mass spectrometry. HA (1.7 mg) and skin (1.0 g) yielded 3.32 and 769.00 microg of MeOAc from the 69.0- and 76.5-year-old-patient samples, respectively. Without added HA, 194.00 microg of product was obtained from the 76.5-year-old-patient samples. With chondroitin as substrate, the yields were 2.89 and 818.04 microg of MeOAc from the 69.0- and 76.5-year-old-patient samples, respectively. The K5 (capsular, Escherichia coli polysaccharide) substrate yielded no detectable product, except for 170.02 microg from the 76.5-year-old-patient samples. This highly sensitive method was used to demonstrate that human-skin-HA N-deacetylase(s) was first detectable at 69 years of age, highly active at 76.5 years of age, and specific for N-acetyl moieties of d-GlcNAc and d-GalNAc where C(1) is beta-linked as in HA and CH.