OBJECTIVES/GOALS: Whole-genome viral sequencing is vital to inform public health and study evolution. Arboviruses evolve in vectors, reservoir hosts, and humans, and require surveillance at all points. We developed a new rigorous method of sequencing that captures whole viral genomes in field-collected and clinical samples. METHODS/STUDY POPULATION: ClickSeq is a novel method of Next Generation Sequencing (NGS) library synthesis using azido-nucleotides to terminate reverse transcription. The cDNA generated can be ligated to sequencing and indexing primers at room temperature using copper (Cu I) and vitamin C. With this approach, we designed primers located ~250 bp apart along the genomes of the arboviruses Chikungunya 37797, Zika Dakar, Yellow Fever Asibi, Dengue serotype 2, West Nile 385-99, and St. Louis Encephalitis Virus (SLEV) clade II. We tested this method with varying viral titers: lab-infected mosquito pools, field-collected mosquito pools from a Texas West Nile and SLEV outbreak, and patient isolates from a Pakistani CHIKV outbreak. The cDNA was sequenced in the UTMB NGS Core and aligned using bowtie. RESULTS/ANTICIPATED RESULTS: The use of a single protocol to capture whole viral genomes including UTRs for multiple viruses from different sample collection styles is ideal for arboviruses. Primers for multiple viruses were pooled and used to sequence mosquito pools. The Tiled ClickSeq method captured whole viral genomes without the need for host depletion. UTRs were captured even when the viral strain used for primer design differed from the resulting strain. Discreet variants were captured in both the hypervariable nsP3 region and the UTR in the patient isolates from the CHIKV outbreak compared to the 2017 outbreak. Texas WNV and SLEV outbreaks are now defined from the 2020 outbreak and can be further tracked to update public health measures and understand viral evolution. DISCUSSION/SIGNIFICANCE: UTRs impact both human and mosquito fitness, leading to further outbreaks. Tiled ClickSeq aims to capture whole viral genomes with a method and cost that can be implemented by public health researchers to understand disease evolution as it happens to update both public health and basic virology to the effects of evolution on arboviruses.

A shock-induced separation loss reduction method, using local blade suction surface shape modification (smooth ramp structure) with constant adverse pressure gradient with the consideration of radial equilibrium effect to split a single shock foot into multiple weaker shock wave configuration, is investigated on the NASA Rotor 37 for promoting aerodynamic performance of a transonic compressor rotor. Numerical investigation on baseline blade and improved one with blade modification on suction side has been conducted employing the Reynolds-averaged Navier–Stokes method to reveal flow physics of ramp structure. The results indicate that the passage shock foot of baseline is replaced with a family of compression waves and a weaker shock foot generating moderate adverse pressure gradient on ramp profile, which is beneficial for mitigating the shock foot and shrinking flow separation region as well. In addition, the radial secondary flow of low-momentum fluids within boundary layer is decreased significantly in the region of passage shock-wave/boundary-layer interaction on blade suction side, which mitigates the mass flow and mixing intensity of tip leakage flow. With the reduction of flow separation loss induced by passage shock, the adiabatic efficiency and total pressure ratio of improved rotor are superior to baseline model. This study herein implies a potential application of ramp profile in design method of transonic and supersonic compressors.

Accurate geometrical calibration between the scan coordinates and the camera coordinates is critical in four-dimensional scanning transmission electron microscopy (4D-STEM) for both quantitative imaging and ptychographic reconstructions. For atomic-resolved, in-focus 4D-STEM datasets, we propose a hybrid method incorporating two sub-routines, namely a J-matrix method and a Fourier method, which can calibrate the uniform affine transformation between the scan-camera coordinates using raw data, without a priori knowledge of the crystal structure of the specimen. The hybrid method is found robust against scan distortions and residual probe aberrations. It is also effective even when defects are present in the specimen, or the specimen becomes relatively thick. We will demonstrate that a successful geometrical calibration with the hybrid method will lead to a more reliable recovery of both the specimen and the electron probe in a ptychographic reconstruction. We will also show that, although the elimination of local scan position errors still requires an iterative approach, the rate of convergence can be improved, and the residual errors can be further reduced if the hybrid method can be firstly applied for initial calibration. The code is made available as a simple-to-use tool to correct affine transformations of the scan-camera coordinates in 4D-STEM experiments.

To investigate the downstream rim seal gas ingestion characteristics of a 1.5-stage turbine, the URANS equations were solved numerically using the SST turbulence model. The effects of different purge flow rates and the second vane on the ingestion characteristics of the aft cavity and the nonuniform fluctuations of the main gas path pressure are analysed. The results showed that the aft cavity is affected by the combined effects of the blade and the second vane, and the potential field at the leading edge of the second vane greatly influence the airflow variation in the aft cavity, which enhances the ingress of the mainstream into the wheel-space. The front purge flow weakens the egress between the suction side of the blade and the suction side of the second vane. The potential field at the leading edge of the second vane suppresses the nonuniform distribution of airflow in the aft cavity caused by the rotational effect of the blade.

Schistosomiasis has been subjected to extensive control efforts in the People's Republic of China (China) which aims to eliminate the disease by 2030. We describe baseline results of a longitudinal cohort study undertaken in the Dongting and Poyang lakes areas of central China designed to determine the prevalence of Schistosoma japonicum in humans, animals (goats and bovines) and Oncomelania snails utilizing molecular diagnostics procedures. Data from the Chinese National Schistosomiasis Control Programme (CNSCP) were compared with the molecular results obtained.

Sixteen villages from Hunan and Jiangxi provinces were surveyed; animals were only found in Hunan. The prevalence of schistosomiasis in humans was 1.8% in Jiangxi and 8.0% in Hunan determined by real-time polymerase chain reaction (PCR), while 18.3% of animals were positive by digital droplet PCR. The CNSCP data indicated that all villages harboured S. japonicum-infected individuals, detected serologically by indirect haemagglutination assay (IHA), but very few, if any, of these were subsequently positive by Kato-Katz (KK).

Based on the outcome of the IHA and KK results, the CNSCP incorporates targeted human praziquantel chemotherapy but this approach can miss some infections as evidenced by the results reported here. Sensitive molecular diagnostics can play a key role in the elimination of schistosomiasis in China and inform control measures allowing for a more systematic approach to treatment.

Background: Phase 3 COMET trial (NCT02782741) compares avalglucosidase alfa (n=51) with alglucosidase alfa (n=49) in treatment-naïve LOPD. Methods: Primary objective: determine avalglucosidase alfa effect on respiratory muscle function. Secondary/other objectives include: avalglucosidase alfa effect on functional endurance, inspiratory/expiratory muscle strength, lower/upper extremity muscle strength, motor function, health-related quality of life, safety. Results: At Week 49, change (LSmean±SE) from baseline in upright forced vital capacity %predicted was greater with avalglucosidase alfa (2.89%±0.88%) versus alglucosidase alfa (0.46%±0.93%)(absolute difference+2.43%). The primary objective, achieving statistical non-inferiority (p=0.0074), was met. Superiority testing was borderline significant (p=0.0626). Week 49 change from baseline in 6-minute walk test was 30.01-meters greater for avalglucosidase alfa (32.21±9.93m) versus alglucosidase alfa (2.19±10.40m). Positive results for avalglucosidase alfa were seen for all secondary/other efficacy endpoints. Treatment-emergent adverse events (AEs) occurred in 86.3% of avalglucosidase alfa-treated and 91.8% of alglucosidase alfa-treated participants. Five participants withdrew, 4 for AEs, all on alglucosidase alfa. Serious AEs occurred in 8 avalglucosidase alfa-treated and 12 alglucosidase alfa-treated participants. IgG antidrug antibody responses were similar in both. High titers and neutralizing antibodies were more common for alglucosidase alfa. Conclusions: Results demonstrate improvements in clinically meaningful outcome measures and a more favorable safety profile with avalglucosidase alfa versus alglucosidase alfa. Funding: Sanofi Genzyme

Masturbation is a common sexual practice in men, and saliva is often used as a lubricant during masturbation by men who have sex with men. However, the role of saliva use during masturbation in the transmission of chlamydia is still unclear. We developed population-level, susceptible-infected-susceptible compartmental models to explore the role of saliva use during masturbation on the transmission of chlamydia at multiple anatomical sites. In this study, we simulated both solo masturbation and mutual masturbation. Our baseline model did not include masturbation but included transmission routes (anal sex, oral-penile sex, rimming, kissing and sequential sexual practices) we have previously validated (model 1). We added masturbation to model 1 to develop the second model (model 2). We calibrated the model to five clinical datasets separately to assess the effects of masturbation on the prevalence of site-specific infection. The inclusion of masturbation (model 2) significantly worsened the ability of the models to replicate the prevalence of C. trachomatis. Using model 2 and the five data sets, we estimated that saliva use during masturbation was responsible for between 3.9% [95% confidence interval (CI) 2.0–6.8] and 6.2% (95% CI 3.8–10.5) of incident chlamydia cases at all sites. Our models suggest that saliva use during masturbation is unlikely to play a major role in chlamydia transmission between men, and even if it does have a role, about one in seven cases of urethral chlamydia might arise from masturbation.

This paper describes a computational investigation of multimode instability growth and multimaterial mixing induced by multiple shock waves in a high-energy-density (HED) environment, where pressures exceed 1 Mbar. The simulations are based on a series of experiments performed at the National Ignition Facility (NIF) and designed as an HED analogue of non-HED shock-tube studies of the Richtmyer–Meshkov instability and turbulent mixing. A three-dimensional computational modelling framework is presented. It treats many complications absent from canonical non-HED shock-tube flows, including distinct ion and free-electron internal energies, non-ideal equations of state, radiation transport and plasma-state mass diffusivities, viscosities and thermal conductivities. The simulations are tuned to the available NIF data, and traditional statistical quantities of turbulence are analysed. Integrated measures of turbulent kinetic energy and enstrophy both increase by over an order of magnitude due to reshock. Large contributions to enstrophy production during reshock are seen from both the baroclinic source and enstrophy–dilatation terms, highlighting the significance of fluid compressibility in the HED regime. Dimensional analysis reveals that Reynolds numbers and diffusive Péclet numbers in the HED flow are similar to those in a canonical non-HED analogue, but conductive Péclet numbers are much smaller in the HED flow due to efficient thermal conduction by free electrons. It is shown that the mechanism of electron thermal conduction significantly softens local spanwise gradients of both temperature and density, which causes a minor but non-negligible decrease in enstrophy production and small-scale mixing relative to a flow without this mechanism.

The current study investigated associations between variation in the bovine perilipin-2 gene (PLIN2) and milk traits (milk fat content, milk protein content, milk yield and milk fatty acid (FA) component levels) in 409 New Zealand pasture-grazed Holstein-Friesian × Jersey-cross (HF × J-cross or Kiwicross™) cows. Five nucleotide sequence variants were found in three regions of the gene, including c.17C>T in exon 2, c.53A>G in exon 3, c.595+23G>A and c.595+104_595+108del in intron 5, and c.*302T>C in the 3′-untranslated region. The c.*302T>C substitution produces two nucleotide sequence variants (A5 and B5), and this variation was associated with variation in milk protein content and milkfat composition for C10:0, C11:0, C12:0, C13:0 and C16:0 FA and medium-chain fatty acid (MCFA) and long-chain fatty acid (LCFA) groups. After correcting for the effect of variation in the diacylglycerol acyl-CoA acyltransferase 1 gene (DGAT1) that results in the amino acid substitution p.K232A, variation in the FA binding protein 4 gene (FABP4) and variation in the stearoyl-CoA desaturase (Δ-9-desaturase) gene (SCD) that results in the amino acids substitution p.A293V, significant differences between A5A5 and B5B5 cows were found for C10:0, C11:0, C12:0, C13:0, C16:0, and the MCFA, LCFA, total saturated FA and C10:1 index groups. This suggests that nucleotide sequence variation in PLIN2 may be affecting milk FA component levels.

This work investigated the photophysical pathways for light absorption, charge generation, and charge separation in donor–acceptor nanoparticle blends of poly(3-hexylthiophene) and indene-C60-bisadduct. Optical modeling combined with steady-state and time-resolved optoelectronic characterization revealed that the nanoparticle blends experience a photocurrent limited to 60% of a bulk solution mixture. This discrepancy resulted from imperfect free charge generation inside the nanoparticles. High-resolution transmission electron microscopy and chemically resolved X-ray mapping showed that enhanced miscibility of materials did improve the donor–acceptor blending at the center of the nanoparticles; however, a residual shell of almost pure donor still restricted energy generation from these nanoparticles.

Considering the decision-making requirements of airport, airlines and passengers, a bilevel programming model which contains two parts was proposed in this paper. One part is to improve the utilization of gates of the airport (upper level), so the objective function of the upper level to the minimum overall variance of slack time between two consecutive air crafts at the same gate. The other part looks at maximize the airline revenue and passengers more conveniently and comfortably (lower level). The lower level has two objective functions — the minimum passenger transfer failure and the minimum passenger average transfer time, respectively. According to the latest data of an airport in Eastern China, the adaptive genetic algorithm is used to solve the above-mentioned bilevel optimisation problems. The numerical experiment shows that the model not only reduces the variance of the relaxation time, but also optimises the flight gate allocation and achieves the initial goal.

Introduction: Inhaled toxins from tobacco smoking, cannabis leaf smoking as well as vaping/e-cigarette products use are known causes of cardio-respiratory injury. While tobacco smoking has decreased among Canadian adults, there are now several other forms of legal inhalant products. While legal, the evidence of benefit and safety of vaping is limited. Of concern, cases of e-cigarette or vaping products use associated lung injury (EVALI) have been accumulating in the U.S. and now in Canada. Despite this, very little is known about the inhalation exposure of emergency department (ED) patients; this study was designed to explore lung health in the ED. Methods: We investigated the prevalence of exposure to vaping, tobacco and cannabis among patients presenting to a Canadian ED from July to November 2019. Ambulatory (CTAS 2 to 5), stable, adult (≥ 17 years) patients were prospectively identified and invited to complete a survey addressing factors related to lung health (previous diagnosis of respiratory conditions and respiratory symptoms at the ED presentation) and information on current exposure to vaping, tobacco and cannabis smoking. Categorical variables are reported as frequencies and percentages; continuous variables are reported as medians with interquartile range (IQR). The study was approved by the Health Research Ethics Board. Results: Overall, 1024 (71%) of 1433 eligible patients completed the survey. The median age was 43.5 (IQR: 29, 60), and 51% were female. A total of 351 (31%) participants reported having been previously diagnosed with ≥1 respiratory conditions, and 177 (17%) were visiting the ED as a result of ≥1 respiratory symptoms (e.g., cough, shortness of breath, wheezing). Daily tobacco smoking was reported by 190 (19%), and 83 (8%) reported using vaping/e-cigarette products. Cannabis use within 30 days was described by 80 (15%) respondents. Exposure to tobacco and vaping products was reported by 39 (4%) participants, 63 (6%) reported using tobacco in combination with cannabis smoking, and 3% reported combining vaping and cannabis use. Conclusion: Patients seeking care in the ED are exposed to a large quantity of inhaled toxins. Vaping products, considered the cause of the most recent epidemic of severe lung injury, are used in isolation and in combination with other smoking products in Canada. These exposures should be documented and may increase the risk of lung health injuries and exacerbations of chronic respiratory conditions.