Antigenic cartography using hamster sera identifies SARS-CoV-2 JN.1 evasion seen in human XBB.1.5 booster sera

Antigenic assessments of SARS-CoV-2 variants inform decisions to update COVID-19 vaccines. Primary infection sera are often used for assessments, but such sera are rare due to population immunity from SARS-CoV-2 infections and COVID-19 vaccinations. Here, we show that neutralization titers and breadth of matched human and hamster pre-Omicron variant primary infection sera correlate well and generate similar antigenic maps. The hamster antigenic map shows modest antigenic drift among XBB sub-lineage variants, with JN.1 and BA.4/BA.5 variants within the XBB cluster, but with five to six-fold antigenic differences between these variants and XBB.1.5. Compared to sera following only ancestral or bivalent COVID-19 vaccinations, or with post-vaccination infections, XBB.1.5 booster sera had the broadest neutralization against XBB sub-lineage variants, although a five-fold titer difference was still observed between JN.1 and XBB.1.5 variants. These findings suggest that antibody coverage of antigenically divergent JN.1 could be improved with a matched vaccine antigen.

Comparative Analysis of SARS-CoV-2 Antigenicity across Assays and in Human and Animal Model Sera

The antigenic evolution of SARS-CoV-2 requires ongoing monitoring to judge the immune escape of newly arising variants. A surveillance system necessitates an understanding of differences in neutralization titers measured in different assays and using human and animal sera. We compared 18 datasets generated using human, hamster, and mouse sera, and six different neutralization assays. Titer magnitude was lowest in human, intermediate in hamster, and highest in mouse sera. Fold change, immunodominance patterns and antigenic maps were similar among sera. Most assays yielded similar results, except for differences in fold change in cytopathic effect assays. Not enough data was available for conclusively judging mouse sera, but hamster sera were a consistent surrogate for human first-infection sera.

Low-Cost Sensor Performance Intercomparison, Correction Factor Development, and 2+ Years of Ambient PM2.5 Monitoring in Accra, Ghana

Particulate matter air pollution is a leading cause of global mortality, particularly in Asia and Africa. Addressing the high and wide-ranging air pollution levels requires ambient monitoring, but many low- and middle-income countries (LMICs) remain scarcely monitored. To address these data gaps, recent studies have utilized low-cost sensors. These sensors have varied performance, and little literature exists about sensor intercomparison in Africa. By colocating 2 QuantAQ Modulair-PM, 2 PurpleAir PA-II SD, and 16 Clarity Node-S Generation II monitors with a reference-grade Teledyne monitor in Accra, Ghana, we present the first intercomparisons of different brands of low-cost sensors in Africa, demonstrating that each type of low-cost sensor PM2.5 is strongly correlated with reference PM2.5, but biased high for ambient mixture of sources found in Accra. When compared to a reference monitor, the QuantAQ Modulair-PM has the lowest mean absolute error at 3.04 μg/m3, followed by PurpleAir PA-II (4.54 μg/m3) and Clarity Node-S (13.68 μg/m3). We also compare the usage of 4 statistical or machine learning models (Multiple Linear Regression, Random Forest, Gaussian Mixture Regression, and XGBoost) to correct low-cost sensors data, and find that XGBoost performs the best in testing (R2: 0.97, 0.94, 0.96; mean absolute error: 0.56, 0.80, and 0.68 μg/m3 for PurpleAir PA-II, Clarity Node-S, and Modulair-PM, respectively), but tree-based models do not perform well when correcting data outside the range of the colocation training. Therefore, we used Gaussian Mixture Regression to correct data from the network of 17 Clarity Node-S monitors deployed around Accra, Ghana, from 2018 to 2021. We find that the network daily average PM2.5 concentration in Accra is 23.4 μg/m3, which is 1.6 times the World Health Organization Daily PM2.5 guideline of 15 μg/m3. While this level is lower than those seen in some larger African cities (such as Kinshasa, Democratic Republic of the Congo), mitigation strategies should be developed soon to prevent further impairment to air quality as Accra, and Ghana as a whole, rapidly grow.

Antigenic cartography of well-characterized human sera shows SARS-CoV-2 neutralization differences based on infection and vaccination history

The rapid emergence of SARS-CoV-2 variants challenges vaccination strategies. Here, we collected 201 serum samples from persons with a single infection or multiple vaccine exposures, or both. We measured their neutralization titers against 15 natural variants and 7 variants with engineered spike mutations and analyzed antigenic diversity. Antigenic maps of primary infection sera showed that Omicron sublineages BA.2, BA.4/BA.5, and BA.2.12.1 are distinct from BA.1 and more similar to Beta/Gamma/Mu variants. Three mRNA COVID-19 vaccinations increased neutralization of BA.1 more than BA.4/BA.5 or BA.2.12.1. BA.1 post-vaccination infection elicited higher neutralization titers to all variants than three vaccinations alone, although with less neutralization to BA.2.12.1 and BA.4/BA.5. Those with BA.1 infection after two or three vaccinations had similar neutralization titer magnitude and antigenic recognition. Accounting for antigenic differences among variants when interpreting neutralization titers can aid the understanding of complex patterns in humoral immunity that informs the selection of future COVID-19 vaccine strains.

Effect of feed particle size and solvent flow rate on soybean oil extraction in a percolation type extractor

The influence of particle size and solvent flow rate on the kinetics of oil extraction from soybean (eight fractions from 0.433 to 0.122 mm) was studied using hexane, simulating commercial percolation type extractor. The reduction in particle size from 0.433 mm to 0.141 mm showed an increase in the oil yield. However, further reduction to 0.129 mm and 0.122 mm affected the yield due to bed compaction, reducing porosity and contact area. The yield (21.5%) of the ground mass was similar to the major mass fractions (0.239-0.353 mm). The rate of extraction increased drastically with the solvent flow rate. The highest flow rate (9.67 mL/min) exhibited the highest mass transfer coefficient (km) 1.62 × 10-3 s-1 and the diffusion coefficient (De) 1.77 × 10-12 m2/s. At 7.33 mL/min, the yield and the rate of extraction were optimal and no potential benefits were obtained at higher flow rates.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-022-05554-6.

A novel approach to improve network validity using various soft computing techniques

Mobile Adhoc Networks (MANET) in modern research have many optimal energy conservation mechanisms that can be deployed easily and in a faster manner. The routing approaches associated with energy consumption play a dominant role in routing the data packets between the mobile sensor nodes within the range of optimization. However, major challenges associated with energy consumption in MANETs include reduced lifetime of sensor nodes, poor coverage, and throughput. Most methods tend to reduce the interference of data while traversing between the sensor nodes and increase the capacity of the network. This results in delays while transmitting the packets across the network, and this may result in failure of packets being transmitted. To resolve this issue, in this paper, we propose an ant colony optimization combined with a flower pollination algorithm for minimal energy consumption and throughput maximisation in MANETs. This hybrid meta-heuristic model resolves the issues, including delays, poor coverage, and reduced network lifetime. This hybrid model uses the estimation of neighbourhood distance among the nodes for optimal placement of nodes for effective location. The estimation of location is found using a flower pollination algorithm with a levy flight mechanism. The estimation is carried out in a hyper sphere model that helps in finding the coverage area of the sensor nodes. Depending upon the estimation of neighbourhood distance among the sensor nodes, the consumption of energy among the sensor nodes in MANETs is reduced. The simulation was conducted between the proposed hybrid approach and conventional soft computing heuristics, where the results show that the proposed model achieves a higher rate of energy conservation and reduces delay than other methods.

Using patching asymmetric regions to assess ischemic stroke lesion in neuro imaging

Ischemic stroke is a universal ailment that endangers the life of patients and makes them bedridden until death. Over a decade, doctors and radiologists have been dissecting patient status straightforwardly from the printouts of the slice images delivered by different diagnostic imaging modalities. Computed Tomography (CT) is a frequently used imaging strategy for therapeutic analysis and neuroanatomical investigations. The main objective of the paper is to develop a simple technique with less architectural complication and power consumption. The proposed work is to section the ischemic stroke lesion more efficiently from multi-succession CT images using patching the asymmetric region. The Hough transform segment and extracts the features from the asymmetric region of the CT image and finally, the random forest is implemented to classify the unusual tissues from the CT image dependent on their pathological properties. RF classifier has been trained for different parts of the cerebrum for fragmenting the stroke lesion. The acquired outcomes produce better segmentation accuracy when compared with different strategies. The overall efficiency of the proposed method determines the Ischemic stroke with an accuracy of 95% with an RF classifier. Hence this method can be used in the segmentation process of stroke lesions.

Using a recurrent neural network with S2 characteristics, efficient identification of localised cortical dysplasia

Focal cortical dysplasia (FCD) is an inborn anomaly in brain growth and morphological deformation in lesions of the brain which induces focal seizures. Neurosurgical therapies were performed for the detection of FCD. Furthermore, it can be overcome through the presurgical evaluation of epilepsy. The surgical result is attained basically through the output of the presurgical output. In preprocessing the process of increasing true positives with the decrease in false negatives occurs which results in an effective outcome. MRI (Magnetic Resonance Imaging) outputs are efficient to predict the FCD lesions through T1- MPRAGE and T2- FLAIR efficient output can be obtained. In our proposed work we extract the S2 features through the testing of T1, T2 images. Using RNN-LSTM (Recurrent neural network-Long short-term memory) test images were trained and the FCD lesions were segmented. The output of our work is compared with the proposed work yields better results compared to the existing system such as artificial neural network (ANN), support vector machine (SVM), and convolution neural network (CNN). This approach obtained an accuracy rate of 0.195% (ANN), 0.20% (SVM), 0.14% (CNN), specificity rate of 0.23% (ANN), 0.15% (SVM), 0.13% (CNN) and sensitivity rate of 0.22% (ANN), 0.14% (SVM), 0.08% (CNN) respectively in comparison with RNN-LSTM.

Characterizing the Aging of Alphasense NO2 Sensors in Long-Term Field Deployments

Low-cost NO₂ sensors have been widely deployed for atmospheric sampling. While their initial performance has been characterized, few studies have examined their long-term degradation. This study focused on the performance of Alphasense low-cost NO₂ sensors (NO2-B42F and NO2-B43F) over 4 years (2016-2020). A total of 29 NO₂ sensors from 10 batches were collocated 78 times at two sites with reference instruments. Raw signals from "functional" NO₂ sensors correlated linearly with reference NO₂ concentrations. After long-term deployment, sensor raw signals started to deviate from reference NO₂ concentrations due to sensor aging, an accumulated effect after sensor unpacking. Several sensors eventually became "non-functional" as sensor raw signals showed no correlation with reference NO₂ concentrations. Sensor aging and non-functionality may be primarily caused by expiration of the ozone (O₃) scrubber built into these sensors so that sensors responded to both ambient NO₂ and O₃. The influence of O₃ on sensor response is quantified through the permutation importance method. Most of the sensors are non-functional after approximately 200-400 days of deployment, and no sensor was functional after 400 days of deployment. This result agrees well with the estimated lifetime of the built-in ozone scrubbers considering the ambient ozone concentration in the Pittsburgh area where these sensors were deployed. To ensure reliable data quality in long-term field deployments, we recommend collocating NO₂ sensors with reference instruments regularly after 200-400 days of deployment to identify and replace non-functional sensors in a timely manner.

843 Improving Practical Skills Training with In-Situ Trauma Simulation

Introduction

Safe and effective management of trauma patients requires numerous practical skills. Our in-situ trauma simulation identified key areas requiring increased training and exposure. This enabled improvement to education, patient safety and efficiency when managing these emergencies.

Method

We carried out a simulated trauma call according to ATLS principles, recording the time and person completing each task. Key areas for improvement were identified; most notably the application of Femoral Traction Splints (FTS). 0/7 doctors present were not able to do this. Subsequently, a formal training day was delivered, with 38 attendees across specialties, assessing confidence before and after the session.

Results

Prior to the training session, 52.6% of attendees did not have formal teaching using FTS and 65.8% had never used one. Confidence with FTS application was measured on a scale of 1 (not confident) to 5 (very confident), with an average score of 2.6/5.

After training, the average confidence score was 4.7/5 (p < 0.01). 100% of participants found the session very useful.

Conclusions

In-situ simulation allows identification of key areas for improvement in training of practical skills. Essential tailored teaching can then be delivered to increase exposure and confidence for these necessary practical skills.

Quantifying asymptomatic infection and transmission of COVID-19 in New York City using observed cases, serology, and testing capacity

The contributions of asymptomatic infections to herd immunity and community transmission are key to the resurgence and control of COVID-19, but are difficult to estimate using current models that ignore changes in testing capacity. Using a model that incorporates daily testing information fit to the case and serology data from New York City, we show that the proportion of symptomatic cases is low, ranging from 13 to 18%, and that the reproductive number may be larger than often assumed. Asymptomatic infections contribute substantially to herd immunity, and to community transmission together with presymptomatic ones. If asymptomatic infections transmit at similar rates as symptomatic ones, the overall reproductive number across all classes is larger than often assumed, with estimates ranging from 3.2 to 4.4. If they transmit poorly, then symptomatic cases have a larger reproductive number ranging from 3.9 to 8.1. Even in this regime, presymptomatic and asymptomatic cases together comprise at least 50% of the force of infection at the outbreak peak. We find no regimes in which all infection subpopulations have reproductive numbers lower than three. These findings elucidate the uncertainty that current case and serology data cannot resolve, despite consideration of different model structures. They also emphasize how temporal data on testing can reduce and better define this uncertainty, as we move forward through longer surveillance and second epidemic waves. Complementary information is required to determine the transmissibility of asymptomatic cases, which we discuss. Regardless, current assumptions about the basic reproductive number of severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) should be reconsidered.

Using a network of lower-cost monitors to identify the influence of modifiable factors driving spatial patterns in fine particulate matter concentrations in an urban environment

BACKGROUND

There is substantial interest in using networks of lower-cost air quality sensors to characterize urban population exposure to fine particulate matter mass (PM_2.5). However, sensor uncertainty is a concern with these monitors.

OBJECTIVES

(1) Quantify the uncertainty of lower-cost PM_2.5 sensors; (2) Use the high spatiotemporal resolution of a lower-cost sensor network to quantify the contribution of different modifiable and non-modifiable factors to urban PM_2.5.

METHODS

A network of 64 lower-cost monitors was deployed across Pittsburgh, PA, USA. Measurement and sampling uncertainties were quantified by comparison to local reference monitors. Data were sorted by land-use characteristics, time of day, and wind direction.

RESULTS

Careful calibration, temporal averaging, and reference site corrections reduced sensor uncertainty to 1 μg/m³, ~10% of typical long-term average PM_2.5 concentrations in Pittsburgh. Episodic and long-term enhancements to urban PM_2.5 due to a nearby large metallurgical coke manufacturing facility were 1.6 ± 0.36 μg/m³ and 0.3 ± 0.2 μg/m³, respectively. Daytime land-use regression models identified restaurants as an important local contributor to urban PM_2.5. PM_2.5 above EPA and WHO daily health standards was observed at several sites across the city.

SIGNIFICANCE

With proper management, a large network of lower-cost sensors can identify statistically significant trends and factors in urban exposure.

Predicting re-emergence times of dengue epidemics at low reproductive numbers: DENV1 in Rio de Janeiro, 1986-1990

Predicting arbovirus re-emergence remains challenging in regions with limited off-season transmission and intermittent epidemics. Current mathematical models treat the depletion and replenishment of susceptible (non-immune) hosts as the principal drivers of re-emergence, based on established understanding of highly transmissible childhood diseases with frequent epidemics. We extend an analytical approach to determine the number of ‘skip’ years preceding re-emergence for diseases with continuous seasonal transmission, population growth and under-reporting. Re-emergence times are shown to be highly sensitive to small changes in low R₀ (secondary cases produced from a primary infection in a fully susceptible population). We then fit a stochastic Susceptible–Infected–Recovered (SIR) model to observed case data for the emergence of dengue serotype DENV1 in Rio de Janeiro. This aggregated city-level model substantially over-estimates observed re-emergence times either in terms of skips or outbreak probability under forward simulation. The inability of susceptible depletion and replenishment to explain re-emergence under ‘well-mixed’ conditions at a city-wide scale demonstrates a key limitation of SIR aggregated models, including those applied to other arboviruses. The predictive uncertainty and high skip sensitivity to epidemiological parameters suggest a need to investigate the relevant spatial scales of susceptible depletion and the scaling of microscale transmission dynamics to formulate simpler models that apply at coarse resolutions.

0155 SUVN-G3031, A Potent and Selective Histamine H3 Receptor Inverse Agonist - Differentiating Features Over Current Treatments of Narcolepsy

Introduction

Majority of pharmacological agents used in the treatment of narcolepsy have several limitations. Both nonclinical and clinical evidences suggest usefulness of the histamine H3 receptor (H3R) inverse agonists for the treatment of narcolepsy and addressing several of the current limitations.

Methods

Extensive nonclinical studies were carried out for SUVN-G3031 and other pharmacological agents that are currently being used for the treatment of narcolepsy. Nonclinical parameters like inter-species binding affinity, selectivity profile, in vivo and in vitro ADME features, nonclinical efficacy, neurochemistry and safety were compared.

Results

SUVN-G3031 has no inter-species variation in binding affinity at H3R with less than 50% inhibition at 1 µM against 70 other targets. Unlike pitolisant, SUVN-G3031 has no significant binding affinity at sigma 1 and 2 receptor. SUVN-G3031 has no inhibition and induction liability towards major CYP enzymes and transporters. Pitolisant is reported to be a CYP3A4, CYP2B6, and CYP1A2 inducer and a CYP2D6 and OCT1 inhibitor. SUVN-G3031 has robust wake promoting effects. SUVN-G3031 showed negligible affinity towards hERG channel with IC50 > 10 µM and had no effects on any ECG parameters in dog telemetry study. SUVN-G3031 did not show convulsion in rats up to the tested dose of 100 mg/kg, p.o. Most of the pharmacological agents used for the treatment of narcolepsy have abuse liability; SUVN-G3031 produced no change in the striatal and accumbal dopamine levels in rats suggesting no propensity to induce abuse liability. Unlike competing H3R inverse agonists, SUVN-G3031 has no effects on fertility and embryo-fetal development up to the highest tested doses.

Conclusion

Nonclinical studies demonstrate superiority of SUVN-G3031 over pharmacological agents currently used in the treatment of narcolepsy. SUVN-G3031 is being evaluated in a Phase 2 study as monotherapy for the treatment of narcolepsy with and without cataplexy (ClinicalTrials.gov Identifier: NCT04072380).

Support

None

0072 Preclinical Characterization of SUVN-G3031, a Histamine H3 Receptor Inverse Agonist for the Treatment of Narcolepsy

Introduction

Narcolepsy is a chronic sleep disorder characterized by overwhelming daytime drowsiness, sudden attacks of sleep and sometimes accompanied by cataplexy. Although the orexin deficiency is considered to be the primary cause of this disorder, lot of attention has been focused recently on targeting histaminergic neurotransmission by blockade of histamine H3 receptor (H3R). SUVN-G3031 is one of the potent and selective H3R inverse agonist currently being evaluated in a Phase 2 study as monotherapy for the treatment of narcolepsy with and without cataplexy (ClinicalTrials.gov Identifier: NCT04072380).

Methods

Binding of SUVN-G3031 in human and rat histamine H3R was evaluated in in vitro radioligand binding assay and functionality was assessed in GTPγS assay. Pharmacokinetic properties were evaluated after oral administration in rat and dog. Neurotransmitters like histamine, dopamine and norepinephrine were estimated in rat cortex using microdialysis.

Results

SUVN-G3031 is an inverse agonist at histamine H3R with hKi of 8.7 nM and showed minimal binding against over 70 target sites. SUVN-G3031 exhibited desired pharmacokinetic properties in rat and dog with excellent brain penetration in rats. SUVN-G3031 produced significant increase in histamine, dopamine and norepinephrine levels in cortex. SUVN-G3031 produced no change in the striatal and accumbal dopamine levels in rats, suggesting no propensity to induce abuse liability. SUVN-G3031 blocked R-α-methylhistamine induced water intake and produced dose dependent increase in tele-methylhistamine levels in various brain regions and in cerebrospinal fluid of male Wistar rats.

Conclusion

SUVN-G3031 is an inverse agonist at histamine H3 receptor and results from the preclinical studies presented here provide a strong evidence for the potential utility of SUVN-G3031 in the treatment of narcolepsy with and without cataplexy.

Support

None

0008 SUVN-G3031, A Histamine H3 Receptor Inverse Agonist Produces Robust Wake Promoting and Anticataplectic Activity in Orexin Knockout Mice

Introduction

Narcolepsy is a sleep disorder characterized by excessive daytime sleepiness, sleep paralysis, hallucinations, and in some cases episodes of cataplexy. Results from animal studies indicate the involvement of deficient orexin transmission in narcolepsy which can be circumvented by the activation of histaminergic neurons. SUVN-G3031 is a potent and selective histamine H3 receptor inverse agonist with hKi of 8.7 nM and shows less than 50% inhibition at 1 µM against 70 other targets. SUVN-G3031 exhibited excellent pharmacokinetic properties and brain penetration in preclinical species. Oral administration of SUVN-G3031 produces significant increase in histamine, dopamine and norepinephrine levels in the rat cortex. Long-term safety studies in animals have been successfully completed without any concern for further development of SUVN-G3031. In the present study, the effects of SUVN-G3031 were evaluated in orexin knockout mice, a reliable animal model of narcolepsy as a proof-of-concept study for the treatment of narcolepsy with and without cataplexy.

Methods

Male orexin knockout mice (10 - 15 weeks old, 25 - 35 g at the time of surgery) were implanted with telemetric device for simultaneous monitoring of electroencephalography (EEG) and electromyography. Animals were allowed surgical recovery of 3 weeks prior to EEG recording. Effects of SUVN-G3031 (3 and 10 mg/kg, p.o.) were evaluated during active period of animals.

Results

SUVN-G3031 produced significant increase in wakefulness with concomitant decrease in non-rapid eye movement sleep in orexin knockout mice. SUVN-G3031 also significantly decreased the number of cataplectic episodes in orexin knockout mice.

Conclusion

Results from the current preclinical study provide a strong basis for the utility of SUVN-G3031 for the treatment of narcolepsy with and without cataplexy. SUVN-G3031 is currently being evaluated in a Phase 2 study as monotherapy for the treatment of narcolepsy with and without cataplexy (ClinicalTrials.gov Identifier: NCT04072380).

Support

None

Demonstration of a Low-Cost Multi-Pollutant Network to Quantify Intra-Urban Spatial Variations in Air Pollutant Source Impacts and to Evaluate Environmental Justice

Air quality monitoring has traditionally been conducted using sparsely distributed, expensive reference monitors. To understand variations in PM_2.5 on a finely resolved spatiotemporal scale a dense network of over 40 low-cost monitors was deployed throughout and around Pittsburgh, Pennsylvania, USA. Monitor locations covered a wide range of site types with varying traffic and restaurant density, varying influences from local sources, and varying socioeconomic (environmental justice, EJ) characteristics. Variability between and within site groupings was observed. Concentrations were higher near the source-influenced sites than the Urban or Suburban Residential sites. Gaseous pollutants (NO₂ and SO₂) were used to differentiate between traffic (higher NO₂ concentrations) and industrial (higher SO₂ concentrations) sources of PM_2.5. Statistical analysis proved these differences to be significant (coefficient of divergence > 0.2). The highest mean PM_2.5 concentrations were measured downwind (east) of the two industrial facilities while background level PM_2.5 concentrations were measured at similar distances upwind (west) of the point sources. Socioeconomic factors, including the fraction of non-white population and fraction of population living under the poverty line, were not correlated with increases in PM_2.5 or NO₂ concentration. The analysis conducted here highlights differences in PM_2.5 concentration within site groupings that have similar land use thus demonstrating the utility of a dense sensor network. Our network captures temporospatial pollutant patterns that sparse regulatory networks cannot.

Deliberating performance targets workshop: Potential paths for emerging PM2.5 and O3 air sensor progress

The United States Environmental Protection Agency held an international two-day workshop in June 2018 to deliberate possible performance targets for non-regulatory fine particulate matter (PM_2.5) and ozone (O₃) air sensors. The need for a workshop arose from the lack of any market-wide manufacturer requirement for Ozone documented sensor performance evaluations, the lack of any independent third party or government-based sensor performance certification program, and uncertainty among all users as to the general usability of air sensor data. A multi-sector subject matter expert panel was assembled to facilitate an open discussion on these issues with multiple stakeholders. This summary provides an overview of the workshop purpose, key findings from the deliberations, and considerations for future actions specific to sensors. Important findings concerning PM_2.5 and O₃ sensors included the lack of consistent performance indicators and statistical metrics as well as highly variable data quality requirements depending on the intended use. While the workshop did not attempt to yield consensus on any topic, a key message was that a number of possible future actions would be beneficial to all stakeholders regarding sensor technologies. These included documentation of best practices, sharing quality assurance results along with sensor data, and the development of a common performance target lexicon, performance targets, and test protocols.

Quantifying high-resolution spatial variations and local source impacts of urban ultrafine particle concentrations

To quantify the fine-scale spatial variations and local source impacts of urban ultrafine particle (UFP) concentrations, we conducted 3-6 weeks of continuous measurements of particle number (a proxy for UFP) and other air pollutant (CO, NO₂, and PM_2.5) concentrations at 32 sites in Pittsburgh, Pennsylvania during the winters of 2017 and 2018. Sites were selected to span a range of urban land use attributes, including urban background, near local and arterial roads, traffic intersections, urban street canyon, near-highway, near large industrial source, and restaurant density. The spatial variations in urban particle number concentrations varied by about a factor of three. Particle number concentrations are 2-3 times more spatially heterogeneous than PM_2.5 mass. The observed order of spatial heterogeneity is UFP > NO₂ > CO > PM_2.5. On average, particle number concentrations near local roads with a cluster of restaurants and near arterial roads are roughly two times higher than the urban background. Particle number concentrations in the urban street canyon, downwind of a major highway, and near large industrial sources are 2-4 times higher than background concentrations. While traffic is known as an important contributor to particle number concentrations, restaurants and industrial emissions also contribute significantly to spatial variations in Pittsburgh. Particle size distribution measurements using a mobile laboratory show that the local spatial variations in particle number concentrations are dictated by concentrations of particles smaller than 50 nm. A large fraction of urban residents (e.g., ~50%) in Pittsburgh live near local sources and are therefore exposed to 50%-300% higher particle number concentrations than urban background location. These locally emitted particles may have greater health effects than background particles.

Aerosol Optical Properties and Climate Implications of Emissions from Traditional and Improved Cookstoves

Cookstove emissions are a major global source of black carbon but their impact on climate is uncertain because of limited understanding of their optical properties. We measured optical properties of fresh aerosol emissions from 32 different stove/fuel combinations, ranging from simple open fires to high-performing forced-draft stoves. Stoves were tested in the laboratory using the firepower sweep protocol, which measures emissions across the entire range of functional firepower. There is large variability in measured optical properties across the entire range of firepower. This variability is strongly correlated with black carbon-to-particulate matter mass ratio (BC/PM). In comparison, stove type, fuel, and operational metrics were poor predictors of optical properties. We developed parametrizations of the mass absorption cross-section, the absorption angstrom exponent, and the single scattering albedo of fresh emissions as a function of BC/PM. These parametrizations, derived from laboratory data, also reproduce previously reported field measurements of optical properties of real-world cooking emissions. We combined our new parametrizations of intensive optical properties with published emissions data to estimate the direct radiative effect of emissions for different stove technologies. Our data suggest that so-called "improved" stove reduce CO₂ equivalent emission (i.e., climate benefits) by 20-30% compared to traditional stoves.

Methane Emissions from Natural Gas Production Sites in the United States: Data Synthesis and National Estimate

We used site-level methane (CH₄) emissions data from over 1000 natural gas (NG) production sites in eight basins, including 92 new site-level CH₄ measurements in the Uinta, northeastern Marcellus, and Denver-Julesburg basins, to investigate CH₄ emissions characteristics and develop a new national CH₄ emission estimate for the NG production sector. The distribution of site-level emissions is highly skewed, with the top 5% of sites accounting for 50% of cumulative emissions. High emitting sites are predominantly also high producing (>10 Mcfd). However, low NG production sites emit a larger fraction of their CH₄ production. When combined with activity data, we predict that this creates substantial variability in the basin-level CH₄ emissions which, as a fraction of basin-level CH₄ production, range from 0.90% for the Appalachian and Greater Green River to >4.5% in the San Juan and San Joaquin. This suggests that much of the basin-level differences in production-normalized CH₄ emissions reported by aircraft studies can be explained by differences in site size and distribution of site-level production rates. We estimate that NG production sites emit total CH₄ emissions of 830 Mg/h (95% CI: 530-1200), 63% of which come from the sites producing <100 Mcfd that account for only 10% of total NG production. Our total CH₄ emissions estimate is 2.3 times higher than the U.S. Environmental Protection Agency's estimate and likely attributable to the disproportionate influence of high emitting sites.

The Firepower Sweep Test: A novel approach to cookstove laboratory testing

Emissions from solid-fuel cookstoves have been linked to indoor and outdoor air pollution, climate forcing, and human disease. Although task-based laboratory protocols, such as the Water Boiling Test (WBT), overestimate the ability of improved stoves to lower emissions, WBT emissions data are commonly used to benchmark cookstove performance, estimate indoor and outdoor air pollution concentrations, estimate impacts of stove intervention projects, and select stoves for large-scale control trials. Multiple-firepower testing has been proposed as an alternative to the WBT and is the basis for a new standardized protocol (ISO 19867-1:2018); however, data are needed to assess the value of this approach. In this work, we (a) developed a Firepower Sweep Test [FST], (b) compared emissions from the FST, WBT, and in-home cooking, and (c) quantified the relationship between firepower and emissions using correlation analysis and linear model selection. Twenty-three stove-fuel combinations were evaluated. The FST reproduced the range of PM_2.5 and CO emissions observed in the field, including high emissions events not typically observed under the WBT. Firepower was modestly correlated with emissions, although the relationship varied between stove-fuel combinations. Our results justify incorporating multiple-firepower testing into laboratory-based protocols but demonstrate that firepower alone cannot explain the observed variability in cookstove emissions.

Influence of milling on the nutritional composition of bran from different rice varieties

The nutritional composition of bran from four rice varieties namely, Jyothi/IR64, Basmati and Agonibora representing high amylose, intermediate amylose and waxy, respectively were evaluated with friction and abrasive mills at different degrees of milling (DOM). Fat and protein content of the bran inversely correlated to amylose content of rice variety. The fat and fibre contents reduced with increased DOM due to increasing starch influx from the endosperm. Abrasive milling produced bran with higher protein content and total dietary fibre, resulting in superior quality bran, while friction milling led to higher fat. Agonibora bran was found to be superior in terms of nutritional quality. Industrial milling resulted in higher protein content in bran, and Jyothi variety had a better amino acid profile.

Comorbidities and related factors in rheumatoid arthritis patients of south India- Karnataka Rheumatoid Arthritis Comorbidity (KRAC) study

The aim was to study the prevalence of comorbidities in rheumatoid arthritis (RA) patients in everyday clinical practice and their association with disease-specific and demographic factors. The multi-center study recruited 3,247 (at 14 centers, and 265) were excluded due to incomplete data. The number of subjects considered for the analysis was 2982. The mean (±standard deviation) age was 48.98±12.64 years and the male-to-female ratio was 1:5. The data was collected based on a pre-structured pro forma by trained clinical research associates through interview and verification of charts and reports available in the patient records. The following comorbidities were studied: cardiovascular disease, hypertension, diabetes mellitus, hypercholesterolemia, thyroid disease, psychiatric diseases like depression, and pulmonary disease. Hypertension (20.7%), diabetes mellitus (14.4%) and thyroid disease (18.3%) were the most prevalent comorbidities. Hypercholesterolemia (5.3%), pulmonary diseases (2.1%), cardiovascular diseases (0.2%) and depression (0.03%) were prevalent in ≤5% of the study population. The overall presence of comorbidity increased with age and reduced with the duration of illness prior (DOIP). The age, gender, and DOIP differed significantly between groups with and without hypercholesterolemia. Females had a statistically increased prevalence of thyroid disease. The prevalence of comorbidities in RA patients from south India is around 40% and the incidence of comorbidity increased with age. As per the literature evidence, the prevalence in the current study subjects was higher when compared to prevalence of similar diseases occurring in the general south Indian population.

Comparison of Post-Liver Transplantation Outcomes in Portopulmonary Hypertension and Pulmonary Venous Hypertension: A Single-Center Experience

BACKGROUND

In potential liver transplant candidates, pulmonary vascular diseases, including portopulmonary hypertension (PoPH) and pulmonary venous hypertension (PVH), can be associated with high morbidity and mortality. Although there are clear guidelines regarding management and transplant listing criteria for patients with PoPH, the listing criteria for PVH are not well defined.

OBJECTIVE

The aim of this study was to describe and compare the perioperative and postoperative morbidity and mortality associated with PoPH and PVH in patients undergoing liver transplantation.

METHODS

We conducted a retrospective observational study of all patients referred for liver transplantation to our center between 2005 and 2015 who underwent a right heart catheterization (RHC) for screening for pulmonary hypertension as suggested by initial echocardiography. Based on the RHC data, the patients were grouped into no pulmonary hypertension (No PH), PoPH, and PVH categories. In patients who underwent liver transplantation, we recorded vital status intraoperatively and at 30 days and 1-year post-transplant, and we recorded the incidence of postoperative cardiopulmonary and renal complications.

RESULTS

Of the 134 patients who underwent RHC as part of the initial transplant evaluation, 50 patients were successfully transplanted. There was 1 intraoperative death in the PoPH group. No significant difference in mortality was noted between the No PH, PoPH, and PVH groups intraoperatively and 30 days after liver transplantation. At 1 year, the survival rates were 100%, 69.2%, and 94.1% in the No PH, PoPH, and PVH groups, respectively. With respect to cardiopulmonary and renal complications, no statistically significant difference was noted among the groups, though there was a trend toward increased post-transplant reversible pulmonary complications in the PVH group.

CONCLUSION

Our findings suggest that the post-transplant outcomes of patients with PoPH and PVH are similar. In light of the growing recognition of diastolic dysfunction and cirrhotic cardiomyopathy in decompensated cirrhotic patients at the time of transplant, the issue of pulmonary hypertension related to PVH will gain increasing importance as we assess these patients for transplantation. Therefore, future studies are needed to define evidence based guidelines to determine candidacy for liver transplantation in the context of PVH.

Abstract P1-07-15: Detection of molecular alterations in breast cancer through next generation sequencing of both tumor tissue and circulating tumor DNA: The UC San Diego Moores Cancer Center experience

Background: Next generation sequencing (NGS) analysis of actionable molecular alterations has the potential to guide cancer treatment, especially for patients with advanced cancer who have progressed on standard treatment. In this study, we analyzed tumor biopsies and peripheral blood from 62 patients with advanced breast cancer by two different NGS clinical-grade assays for molecular alterations in tumor tissue or in circulating tumor DNA (ctDNA). We used these results to determine if these specimens have potentially “actionable” alterations that could guide cancer therapy.

Methods: From 2014 to 2016, 62 patients with advanced breast cancer had plasma sent for ctDNA analysis (Guardant360 assay; 54 to 70 genes) Thirty-eight of these patients (61%) also had tumor biopsies evaluated by NGS (FoundationOne®; 182 to 315 genes). Alterations were defined as mutations, insertions, deletions, truncations, or rearrangements or amplifications/copy number variations. Patients that harbored multiple alterations in the same gene were not counted as having separate alterations; however, if a gene amplification and an alteration were found in the same gene these were counted as separate events. Variants of unknown significance (VUS) and synonymous mutations were excluded from both assays. Data were collected and analyzed according to a UCSD Institutional Review Board approved protocol.

Results: The median age of our patients at the time of ctDNA analysis was 55 years (range, 44 to 84 years); the median age at the time of tissue biopsy for NGS was 52 years (range, 39 to 82 years). One patient was male. The most common receptor status was estrogen receptor (ER) and progesterone receptor (PR) positive, human epidermal growth factor receptor 2 (HER2) non-amplified or negative (neg)(N=44; 71%), followed by triple negative breast cancer (ERnegPRnegHer2neg) (N=10, 16%), triple positive (N=6, 1%) and finally ERnegPRnegHER2positive (N=2, 0.03%). One patient of 38 (2%) had no tumor alteration detected and 19 of 62 had no ctDNA alterations (31%). In 38 breast cancer patients with tumor NGS results, alterations were detected in 79 unique genes, with the most frequent being TP53 (37% of patients), PIK3CA (24%) and GATA3 (24%) genes. In the 62 patients with ctDNA analysis, 31 unique genes had at least one alteration, with the most frequent being TP53 (36% of patients) and PIK3CA (23%) and EGFR amplification (11%) (GATA3 was not analyzed in the ctDNA assay). Both assays had a high rate of detection for potentially actionable mutations: 41 out of 62 patients (66%) by ctDNA and 34 out of 38 (89%) by tumor NGS. No two patients harbored identical genomic profiles by either tumor NGS or plasma ctDNA analysis except for 1 patient who had no alterations detected by either assay.

Conclusions: Plasma and tissue NGS analysis appear to be complementary assays that yield a high percentage of potentially actionable alterations in patients with advanced breast cancer. Studies of the clinical impact of NGS-guided therapy in breast cancer are warranted.

Citation Format: Shatsky RA, Parker BA, Schwab R, Helsten T, Boles SG, Subramanian R, Piccioni D, Kurzrock R. Detection of molecular alterations in breast cancer through next generation sequencing of both tumor tissue and circulating tumor DNA: The UC San Diego Moores Cancer Center experience [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-07-15.