Temperature-Dependent, Site-Specific Rate Coefficients for the Reaction of OH (OD) with Methyl Formate Isotopologues via Experimental and Theoretical Studies.

Methyl esters are an important component of combustion and atmospheric systems. Reaction with the OH radical plays an important role in the removal of the simplest methyl ester, methyl formate (MF, CH3OCHO). In this paper, the overall rate coefficients for the reactions of OH and OD with MF isotopologues, studied under pseudo-first-order conditions, are reported using two different laser flash photolysis systems with the decay of OH monitored by laser-induced fluorescence. The room-temperature rate coefficient for OH + MF, (1.95 ± 0.34) × 10-13 cm3 molecule-1 s-1, is in good agreement with the literature. The rate coefficient exhibits curved Arrhenius behavior, and our results bridge the gap between previous low-temperature and shock tube studies. In combination with the literature, the rate coefficient for the reaction of OH with MF between 230 and 1400 K can be parametrized as kOH+MF = (3.2 × 10-13) × (T/300 K)2.3 × exp(-141.4 K/T) cm3 molecule-1 s-1 with an overall estimated uncertainty of ∼30%. The reactions of OD with MF isotopologues show a small enhancement (inverse secondary isotope effect) compared to the respective OH reactions. The reaction of OH/OD with MF shows a normal primary isotope effect, a decrease in the rate coefficient when MF is partially or fully deuterated. Experimental studies have been supported by ab initio calculations at the CCSD(T)-F12/aug-cc-pVTZ//M06-2X/6-31+G** level of theory. The calculated, zero-point-corrected, barrier heights for abstraction at the methyl and formate sites are 1.3 and 6.0 kJ mol-1, respectively, and the ab initio predictions of kinetic isotope effects are in agreement with experiment. Fitting the experimental isotopologue data refines these barriers to 0.9 ± 0.6 and 4.1 ± 0.9 kJ mol-1. The branching ratio is approximately 50:50 at 300 K. Between 300 and 500 K, abstraction via the higher-energy, higher-entropy formate transition state becomes more favored (60:40). However, experiment and calculations suggest that as the temperature increases further, with higher energy, less constrained conformers of the methyl transition state become more significant. The implications of the experimental and theoretical results for the mechanisms of MF atmospheric oxidation and low-temperature combustion are discussed.

Impact of repeated sportive chokes on carotid intima media thickness and brain injury biomarkers in grappling athletes.

PURPOSE: Vascular neck compression techniques, referred to as 'chokes' in combat sports, reduce cerebral perfusion, causing loss of consciousness or voluntary submission by the choked athlete. Despite these chokes happening millions of times yearly around the world, there is scant research on their long-term effects. This pilot study evaluated whether repeated choking in submission grappling impacts the carotid intima media thickness (CIMT) and brain injury biomarkers (NFL, hGFAP, t-Tau, and UCH-L1). METHODS: Participants (n = 39, 29 male; ages 27-60 years) were assigned to one of two study arms: Grapplers (n = 20, 15 male) and 19 age/sex/body size matched controls. Grapplers had been exposed to >500 choke events while training for >5 years in a choke-inclusive sport. Exclusion criteria were recent TBI or deficits from a past TBI or stroke. Bilateral ultrasound measurement of the CIMT was performed, and blood was collected for quantitative analysis of four brain injury markers. Subgroup analyses were performed within the Grappler group to account for blunt head trauma as a possible confounder. RESULTS: There was no overall difference in CIMT measurements between Grapplers (mean 0.55 mm, SD 0.07) and Controls (mean 0.57 mm, SD 0.10) p = 0.498 [95% CI -0.04-0.08], nor were there CIMT differences between Grappler subgroups of blunt Trauma and No-Trauma. There were no significant differences in any biomarkers comparing Grapplers and Controls or comparing Grappler subgroups of Trauma and No-Trauma. CONCLUSION: This study found no significant difference in CIMT and serum brain injury biomarkers between controls and grapplers with extensive transient choke experience, nor between grapplers with extensive past blunt head trauma and those without.

Gene editing for latent herpes simplex virus infection reduces viral load and shedding in vivo.

Anti-HSV therapies are only suppressive because they do not eliminate latent HSV present in ganglionic neurons, the source of recurrent disease. We have developed a potentially curative approach against HSV infection, based on gene editing using HSV-specific meganucleases delivered by adeno-associated virus (AAV) vectors. Gene editing performed with two anti-HSV-1 meganucleases delivered by a combination of AAV9, AAV-Dj/8, and AAV-Rh10 can eliminate 90% or more of latent HSV DNA in mouse models of orofacial infection, and up to 97% of latent HSV DNA in mouse models of genital infection. Using a pharmacological approach to reactivate latent HSV-1, we demonstrate that ganglionic viral load reduction leads to a significant decrease of viral shedding in treated female mice. While therapy is well tolerated, in some instances, we observe hepatotoxicity at high doses and subtle histological evidence of neuronal injury without observable neurological signs or deficits. Simplification of the regimen through use of a single serotype (AAV9) delivering single meganuclease targeting a duplicated region of the HSV genome, dose reduction, and use of a neuron-specific promoter each results in improved tolerability while retaining efficacy. These results reinforce the curative potential of gene editing for HSV disease.

Kinetics of the Gas-Phase Reactions of syn- and anti-CH3CHOO Criegee Intermediate Conformers with SO2 as a Function of Temperature and Pressure.

Kinetics of reactions between SO2 and CH3CHOO Criegee intermediate conformers have been measured at temperatures between 242 and 353 K and pressures between 10 and 600 Torr using laser flash photolysis of CH3CHI2/O2/N2/SO2 gas mixtures coupled with time-resolved broadband UV absorption spectroscopy. The kinetics of syn-CH3CHOO + SO2 are pressure-dependent and exhibit a negative temperature dependence, with the observed pressure dependence reconciling apparent discrepancies between previous measurements performed at ∼298 K. Results indicate a rate coefficient of (4.80 ± 0.46) × 10-11 cm3 s-1 for the reaction of syn-CH3CHOO with SO2 at 298 K and 760 Torr. In contrast to the behavior of the syn-conformer, the kinetics of anti-CH3CHOO + SO2 display no significant dependence on temperature or pressure over the ranges investigated, with a mean rate coefficient of (1.18 ± 0.21) × 10-10 cm3 s-1 over all conditions studied in this work. Results indicate that the reaction of syn-CH3CHOO with SO2 competes with unimolecular decomposition and reaction with water vapor in areas with high SO2 concentration and low humidity, particularly at lower temperatures.

Effect of Viral Illness on Procalcitonin as a Predictor of Bacterial Infection in Febrile Infants.

OBJECTIVE: The impact of confirmed viral infections (CVI) on procalcitonin (PCT) levels in febrile infants aged 8-60 days with a bacterial illness (BI) is unknown. The objectives of the study were to (1) examine the association of CVI with PCT levels in patients with/without a concurrent BI, defined as bacteremia, meningitis, or urinary tract infection, and (2) assess PCT as a predictor of BI in infants with a concurrent CVI. METHODS: In this single-center, retrospective cohort study, we examined febrile infants aged 8-60 days presenting between January 1, 2018 and December 31, 2020. PCT levels were compared between groups, according to results of bacterial cultures and viral tests, using the Wilcoxon rank test. The prediction ability of PCT to detect BI with/without concurrent CVI was assessed by using area under the curve from logistic regression. RESULTS: Patients included: 404 BI-/CVI+, 73 BI+/CVI-, 48 BI+/CVI+, and 138 BI-/CVI-. Median PCT level in the BI+/CVI+ group was significantly lower when compared to BI+/CVI- (0.36 ng/mL vs 0.89 ng/mL), but significantly higher than the BI-/CVI- group (0.36 ng/mL vs 0.1 ng/mL). The presence of a CVI reduced the sensitivity of PCT in BI detection (68% vs 44%), with minimal impact specificity (93% vs 96%). CONCLUSIONS: In previously healthy febrile infants 8-60 days old, the presence of a CVI reduces the sensitivity of PCT BI detection without impacting its specificity. The impact of a CVI on PCT levels in febrile infants has implications for how this marker of infection should be considered when assessing risk of BI in infants.

SNAP-tagging live cells via chelation-assisted copper-catalyzed azide-alkyne cycloaddition.

SNAP-tag is a single-turnover enzyme that has become a powerful tool, hence a popular choice, of targeted cellular protein labeling. Three SNAP-tag substrates that carry the copper-chelating 2-picolyl azide moiety are prepared, one of which has an unconventional 5-pyridylmethyl-substituted guanine structure, rather than the usual benzylguanine that is optimized to be accepted by SNAP-tag. All three substrates are effective in transferring a 2-picolyl azide moiety to SNAP-tag in live cells under conventional labeling conditions (30-minute incubation of cells with labeling reagents at 37 °C under 5% CO2). Live cells that are decorated with chelating azido groups on the extracellular side of membranes undergo copper-catalyzed azide-alkyne cycloaddition (CuAAC) with an ethynyl-functionalized fluorophore to accomplish membrane protein labeling by a fluorescent dye. The chelation-assisted CuAAC labeling step is rapid (<1 minute) with a relatively low dose of the copper catalyst (20 µM), and consequently exerts no ill effect on the labeled cells. A SNAP-tag substrate that carries a non-chelating azide moiety, on the other hand, fails to produce satisfactory labeling under the same constraints. The rapid, live cell-compatible SNAP-tag/chelation-assisted CuAAC two-step method expands the utility of SNAP-tag in protein labeling applications.

Liver-Humanized NSG-PiZ Mice Support the Study of Chronic Hepatitis B Virus Infection and Antiviral Therapies.

Hepatitis B virus (HBV) is a pathogen of major public health importance that is largely incurable once a chronic infection is established. Only humans and great apes are fully permissive to HBV infection, and this species restriction has impacted HBV research by limiting the utility of small animal models. To combat HBV species restrictions and enable more in vivo studies, liver-humanized mouse models have been developed that are permissive to HBV infection and replication. Unfortunately, these models can be difficult to establish and are expensive commercially, which has limited their academic use. As an alternative mouse model to study HBV, we evaluated liver-humanized NSG-PiZ mice and showed that they are fully permissive to HBV. HBV selectively replicates in human hepatocytes within chimeric livers, and HBV-positive (HBV+) mice secrete infectious virions and hepatitis B surface antigen (HBsAg) into blood while also harboring covalently closed circular DNA (cccDNA). HBV+ mice develop chronic infections lasting at least 169 days, which should enable the study of new curative therapies targeting chronic HBV, and respond to entecavir therapy. Furthermore, HBV+ human hepatocytes in NSG-PiZ mice can be transduced by AAV3b and AAV.LK03 vectors, which should enable the study of gene therapies that target HBV. In summary, our data demonstrate that liver-humanized NSG-PiZ mice can be used as a robust and cost-effective alternative to existing chronic hepatitis B (CHB) models and may enable more academic research labs to study HBV disease pathogenesis and antiviral therapy. IMPORTANCE Liver-humanized mouse models have become the gold standard for the in vivo study of hepatitis B virus (HBV), yet their complexity and cost have prohibited widespread use of existing models in research. Here, we show that the NSG-PiZ liver-humanized mouse model, which is relatively inexpensive and simple to establish, can support chronic HBV infection. Infected mice are fully permissive to hepatitis B, supporting both active replication and spread, and can be used to study novel antiviral therapies. This model is a viable and cost-effective alternative to other liver-humanized mouse models that are used to study HBV.

Adeno-associated virus vectors and neurotoxicity-lessons from preclinical and human studies.

Over 15 years after hepatotoxicity was first observed following administration of an adeno-associated virus (AAV) vector during a hemophilia B clinical trial, recent reports of treatment-associated neurotoxicity in animals and humans have brought the potential impact of AAV-associated toxicity back to prominence. In both pre-clinical studies and clinical trials, systemic AAV administration has been associated with neurotoxicity in peripheral nerve ganglia and spinal cord. Neurological signs have also been seen following direct AAV injection into the brain, both in non-human primates and in a clinical trial for late infantile Batten disease. Neurotoxic events appear variable across species, and preclinical animal studies do not fully predict clinical observations. Accumulating data suggest that AAV-associated neurotoxicity may be underdiagnosed and may differ between species in terms of frequency and/or severity. In this review, we discuss the different animal models that have been used to demonstrate AAV-associated neurotoxicity, its potential causes and consequences, and potential approaches to blunt AAV-associated neurotoxicity.

A multiplexed barcode approach to simultaneously evaluate gene delivery by adeno-associated virus capsid variants in nonhuman primates.

BACKGROUND AND AIMS: Adeno-associated virus (AAV) vectors are widely used to deliver therapeutic transgenes to distinct tissues, including the liver. Vectors based on naturally occurring AAV serotypes as well as vectors using engineered capsids have shown variations in tissue tropism and level of transduction between different mouse models. Moreover, results obtained in rodents frequently lack translatability into large animal studies. In light of the increasing interest in AAV vectors for human gene therapy, an increasing number of studies are being performed in nonhuman primates. To keep animal numbers to a minimum and thus optimize the process of AAV capsid selection, we developed a multiplex barcoding approach to simultaneously evaluate the in vivo vector performance for a set of serotypes and capsid-engineered AAV vectors across multiple organs. APPROACH AND RESULTS: Vector biodistribution and transgene expression were assessed by quantitative PCR, quantitative reverse transcription PCR, vector DNA amplicon Illumina sequencing and vRNAseq in male and female rhesus macaques simultaneously dosed with a mixture of barcoded naturally occurring or engineered AAV vectors encoding the same transgene. As expected, our findings show animal-to-animal variation in both the biodistribution and tissue transduction pattern, which was partly influenced by each animal's distinctive serological status. CONCLUSIONS: This method offers a robust approach to AAV vector optimization that can be used to identify and validate AAV vectors for gene delivery to potentially any anatomical site or cell type.

Examining the Effectiveness of an Intensive Telemental Health Treatment for Pediatric Anxiety and OCD During the COVID-19 Pandemic and Pediatric Mental Health Crisis.

Despite research supporting the efficacy of weekly outpatient videoconferencing-based cognitive behavioral therapy (VCBT), limited evidence exists about the benefits of leveraging VCBT for brief intensive formats. We examined the effectiveness of an intensive outpatient VCBT targeting pediatric anxiety and OCD. Quasi-experimental design was used to compare outcomes of intensive, in-person, group-based cognitive-behavioral therapy with medication management and caregiver guidance pre-pandemic, to a similar VCBT peri-pandemic (n = 130). Pretreatment and posttreatment assessments included patient- and caregiver-report of anxiety and functional impairment. Analyses of covariance were conducted, examining changes in anxiety and impairment between treatment groups, controlling for admission levels. No significant differences in posttreatment anxiety or impairment were observed between conditions. This study illustrates that intensive, group-based treatment for pediatric anxiety and OCD using VCBT is associated with comparable reductions in anxiety and impairment. It marks a crucial step toward providing broader access to quality care for youth in need.

Prediction of left ventricular ejection fraction changes in heart failure patients using machine learning and electronic health records: a multi-site study.

Left ventricular ejection fraction (EF) is a key measure in the diagnosis and treatment of heart failure (HF) and many patients experience changes in EF overtime. Large-scale analysis of longitudinal changes in EF using electronic health records (EHRs) is limited. In a multi-site retrospective study using EHR data from three academic medical centers, we investigated longitudinal changes in EF measurements in patients diagnosed with HF. We observed significant variations in baseline characteristics and longitudinal EF change behavior of the HF cohorts from a previous study that is based on HF registry data. Data gathered from this longitudinal study were used to develop multiple machine learning models to predict changes in ejection fraction measurements in HF patients. Across all three sites, we observed higher performance in predicting EF increase over a 1-year duration, with similarly higher performance predicting an EF increase of 30% from baseline compared to lower percentage increases. In predicting EF decrease we found moderate to high performance with low confidence for various models. Among various machine learning models, XGBoost was the best performing model for predicting EF changes. Across the three sites, the XGBoost model had an F1-score of 87.2, 89.9, and 88.6 and AUC of 0.83, 0.87, and 0.90 in predicting a 30% increase in EF, and had an F1-score of 95.0, 90.6, 90.1 and AUC of 0.54, 0.56, 0.68 in predicting a 30% decrease in EF. Among features that contribute to predicting EF changes, baseline ejection fraction measurement, age, gender, and heart diseases were found to be statistically significant.

Extensive field evidence for the release of HONO from the photolysis of nitrate aerosols.

Particulate nitrate ([Formula: see text]) has long been considered a permanent sink for NOx (NO and NO2), removing a gaseous pollutant that is central to air quality and that influences the global self-cleansing capacity of the atmosphere. Evidence is emerging that photolysis of [Formula: see text] can recycle HONO and NOx back to the gas phase with potentially important implications for tropospheric ozone and OH budgets; however, there are substantial discrepancies in "renoxification" photolysis rate constants. Using aircraft and ground-based HONO observations in the remote Atlantic troposphere, we show evidence for renoxification occurring on mixed marine aerosols with an efficiency that increases with relative humidity and decreases with the concentration of [Formula: see text], thus largely reconciling the very large discrepancies in renoxification photolysis rate constants found across multiple laboratory and field studies. Active release of HONO from aerosol has important implications for atmospheric oxidants such as OH and O3 in both polluted and clean environments.

Unimolecular Kinetics of Stabilized CH3CHOO Criegee Intermediates: syn-CH3CHOO Decomposition and anti-CH3CHOO Isomerization.

The kinetics of the unimolecular decomposition of the stabilized Criegee intermediate syn-CH3CHOO has been investigated at temperatures between 297 and 331 K and pressures between 12 and 300 Torr using laser flash photolysis of CH3CHI2/O2/N2 gas mixtures coupled with time-resolved broadband UV absorption spectroscopy. Fits to experimental results using the Master Equation Solver for Multi-Energy well Reactions (MESMER) indicate that the barrier height to decomposition is 67.2 ± 1.3 kJ mol-1 and that there is a strong tunneling component to the decomposition reaction under atmospheric conditions. At 298 K and 760 Torr, MESMER simulations indicate a rate coefficient of 150-81+176 s-1 when tunneling effects are included but only 5-2+3 s-1 when tunneling is not considered in the model. MESMER simulations were also performed for the unimolecular isomerization of the stabilized Criegee intermediate anti-CH3CHOO to methyldioxirane, indicating a rate coefficient of 54-21+34 s-1 at 298 K and 760 Torr, which is not impacted by tunneling effects. Expressions to describe the unimolecular kinetics of syn- and anti-CH3CHOO are provided for use in atmospheric models, and atmospheric implications are discussed.

Design and validation of a FHIR-based EHR-driven phenotyping toolbox.

OBJECTIVES: To develop and validate a standards-based phenotyping tool to author electronic health record (EHR)-based phenotype definitions and demonstrate execution of the definitions against heterogeneous clinical research data platforms. MATERIALS AND METHODS: We developed an open-source, standards-compliant phenotyping tool known as the PhEMA Workbench that enables a phenotype representation using the Fast Healthcare Interoperability Resources (FHIR) and Clinical Quality Language (CQL) standards. We then demonstrated how this tool can be used to conduct EHR-based phenotyping, including phenotype authoring, execution, and validation. We validated the performance of the tool by executing a thrombotic event phenotype definition at 3 sites, Mayo Clinic (MC), Northwestern Medicine (NM), and Weill Cornell Medicine (WCM), and used manual review to determine precision and recall. RESULTS: An initial version of the PhEMA Workbench has been released, which supports phenotype authoring, execution, and publishing to a shared phenotype definition repository. The resulting thrombotic event phenotype definition consisted of 11 CQL statements, and 24 value sets containing a total of 834 codes. Technical validation showed satisfactory performance (both NM and MC had 100% precision and recall and WCM had a precision of 95% and a recall of 84%). CONCLUSIONS: We demonstrate that the PhEMA Workbench can facilitate EHR-driven phenotype definition, execution, and phenotype sharing in heterogeneous clinical research data environments. A phenotype definition that integrates with existing standards-compliant systems, and the use of a formal representation facilitates automation and can decrease potential for human error.

Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration.

OBJECTIVE: The large-scale collection of observational data and digital technologies could help curb the COVID-19 pandemic. However, the coexistence of multiple Common Data Models (CDMs) and the lack of data extract, transform, and load (ETL) tool between different CDMs causes potential interoperability issue between different data systems. The objective of this study is to design, develop, and evaluate an ETL tool that transforms the PCORnet CDM format data into the OMOP CDM. METHODS: We developed an open-source ETL tool to facilitate the data conversion from the PCORnet CDM and the OMOP CDM. The ETL tool was evaluated using a dataset with 1000 patients randomly selected from the PCORnet CDM at Mayo Clinic. Information loss, data mapping accuracy, and gap analysis approaches were conducted to assess the performance of the ETL tool. We designed an experiment to conduct a real-world COVID-19 surveillance task to assess the feasibility of the ETL tool. We also assessed the capacity of the ETL tool for the COVID-19 data surveillance using data collection criteria of the MN EHR Consortium COVID-19 project. RESULTS: After the ETL process, all the records of 1000 patients from 18 PCORnet CDM tables were successfully transformed into 12 OMOP CDM tables. The information loss for all the concept mapping was less than 0.61%. The string mapping process for the unit concepts lost 2.84% records. Almost all the fields in the manual mapping process achieved 0% information loss, except the specialty concept mapping. Moreover, the mapping accuracy for all the fields were 100%. The COVID-19 surveillance task collected almost the same set of cases (99.3% overlaps) from the original PCORnet CDM and target OMOP CDM separately. Finally, all the data elements for MN EHR Consortium COVID-19 project could be captured from both the PCORnet CDM and the OMOP CDM. CONCLUSION: We demonstrated that our ETL tool could satisfy the data conversion requirements between the PCORnet CDM and the OMOP CDM. The outcome of the work would facilitate the data retrieval, communication, sharing, and analysis between different institutions for not only COVID-19 related project, but also other real-world evidence-based observational studies.

Kinetics of the gas phase reaction of the Criegee intermediate CH2OO with SO2 as a function of temperature.

The kinetics of the gas phase reaction of the Criegee intermediate CH2OO with SO2 have been studied as a function of temperature in the range 223-344 K at 85 Torr using flash photolysis of CH2I2/O2/SO2/N2 mixtures at 248 nm coupled to time-resolved broadband UV absorption spectroscopy. Measurements were performed under pseudo-first-order conditions with respect to SO2, revealing a negative temperature dependence. Analysis of experimental results using the Master Equation Solver for Multi-Energy well Reactions (MESMER) indicates that the observed temperature dependence, combined with the reported lack of a pressure dependence in the range 1.5-760 Torr, can be described by a reaction mechanism consisting of the formation of a pre-reaction complex leading to a cyclic secondary ozonide which subsequently decomposes to produce HCHO + SO3. The temperature dependence can be characterised by kCH2OO+SO2 = (3.72 ± 0.13) × 10-11 (T/298)(-2.05±0.38) cm3 molecule-1 s-1. The observed negative temperature dependence for the title reaction in conjunction with the decrease in water dimer (the main competitor for the Criegee intermediate) concentration at lower temperatures means that Criegee intermediate chemistry can play an enhanced role in SO2 oxidation in the atmosphere at lower temperatures.

Integration of NLP2FHIR Representation with Deep Learning Models for EHR Phenotyping: A Pilot Study on Obesity Datasets.

HL7 Fast Healthcare Interoperability Resources (FHIR) is one of the current data standards for enabling electronic healthcare information exchange. Previous studies have shown that FHIR is capable of modeling both structured and unstructured data from electronic health records (EHRs). However, the capability of FHIR in enabling clinical data analytics has not been well investigated. The objective of the study is to demonstrate how FHIR-based representation of unstructured EHR data can be ported to deep learning models for text classification in clinical phenotyping. We leverage and extend the NLP2FHIR clinical data normalization pipeline and conduct a case study with two obesity datasets. We tested several deep learning-based text classifiers such as convolutional neural networks, gated recurrent unit, and text graph convolutional networks on both raw text and NLP2FHIR inputs. We found that the combination of NLP2FHIR input and text graph convolutional networks has the highest F1 score. Therefore, FHIR-based deep learning methods has the potential to be leveraged in supporting EHR phenotyping, making the phenotyping algorithms more portable across EHR systems and institutions.