Risk mitigation and resource savings for biological drug product with computational fluid dynamics simulation

Computational Fluid Dynamics (CFD) Simulation is used to predict uniformity of biological formulations and impact from mixing equipment changes. Such changes occur during process transfer from one site to the other or upon batch size alterations. Experimental runs are traditionally required during such switch, which could be expensive and resource-intensive, especially if it occurs in a commercial manufacture environment. The current study is aimed to reduce the number of experimental runs at scale by using CFD. Steady state CFD mixing models are developed at smaller scales using physical properties of surrogate fluids. Experimental runs are designed and conducted to verify the validity of assumption made in the CFD models, such as the negligibility of starting period. The results show that assumptions made in the CFD models are valid and the CFD models yield outcomes similar to that of experiment, i.e., a tracer is uniformly distributed at similar time frame between the CFD simulations and the corresponding experiments. Large scale mixing models are further developed and used to support an equipment change as well as a batch size increase in the same mixer while mixing parameters are requested to be maintained. The CFD simulation suggest there is negligible impact in both cases and mixing process parameters can be maintained. Validation of the CFD models at the large scale with experiment is planned

Study of Interactions of DNA with RECA and Other Proteins.

This thesis describes different methods of stretching DNA using flow fields and investigates the aggregation behavior of RecA-DNA filaments in addition to the preliminary work on the kinetics of RecA-mediated strand exchanges. Using fluorescence microscopy, we compared DNA stretching by droplet evaporation, suctioning of a droplet with pipette tips, and blowing of a droplet with nitrogen or air and found that the best stretching was achieved in fast flows using suctioning and blowing. A statistical analysis of the average length and the surface deposition density of stretched lambda phage DNA molecules showed that both the hydrophobicity of the surface and the pH of the solution affect the stretching of DNA molecules greatly, but the hydrophobic interaction itself is not enough to explain the broad distribution of the stretch observed. The stretched DNA molecules can be used in the study of DNA/protein interactions, as exemplified by our observation of the motion of DNAse I during its interaction with stretched DNA molecules using a dual-color imaging system. We characterized the interwound or so-called “supercoiled” aggregates of RecA-DNA filaments using atomic force microscopy. Both RecA-dsDNA and RecA-ssDNA filaments showed mostly left-handedness and we found that single stranded DNA binding protein is necessary for the formation of ordered bundles of RecA-ssDNA filaments. We have suggested that the additional torsional stress generated when filaments approach each other is responsible for this observed coiling of RecA-DNA filaments. We reported the dual roles of ATP hydrolysis and RecA dissociation during strand exchange interactions based on the preliminary experimental observations of the two optimum conditions for fast strand exchanges. While the reaction with a length of 3.7kbp of incoming dsDNA yields maximum products with other conditions maintained, the reaction at 10mM phosphocreatine also produces most products compared with other concentrations. The observed optimums were correlated to the ATP hydrolysis and RecA dissociation during strand exchange interactions. The possible dual roles of these two steps could explain the observation of the two optimums.Ph.D.Chemical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/58526/1/wshi_1.pd

Spatiotemporal Attention Enhances Lidar-Based Robot Navigation in Dynamic Environments

Foresighted robot navigation in dynamic indoor environments with cost-efficient hardware necessitates the use of a lightweight yet dependable controller. So inferring the scene dynamics from sensor readings without explicit object tracking is a pivotal aspect of foresighted navigation among pedestrians. In this paper, we introduce a spatiotemporal attention pipeline for enhanced navigation based on 2D lidar sensor readings. This pipeline is complemented by a novel lidar-state representation that emphasizes dynamic obstacles over static ones. Subsequently, the attention mechanism enables selective scene perception across both space and time, resulting in improved overall navigation performance within dynamic scenarios. We thoroughly evaluated the approach in different scenarios and simulators, finding good generalization to unseen environments. The results demonstrate outstanding performance compared to state-of-the-art methods, thereby enabling the seamless deployment of the learned controller on a real robot

Review of an Influenza Surveillance System, Beijing, People’s Republic of China

This system enabled detection of the onset and peak of an epidemic

Effects of nitrate on the treatment of lead contaminated groundwater by nanoscale zerovalent iron

Nanoscale zerovalent iron (nZVI) is efficient for removing Pb(2+) and nitrate from water. However, the influence of nitrate, a common groundwater anion, on Pb(2+) removal by nZVI is not well understood. In this study, we showed that under excess Fe(0) conditions (molar ratio of Fe(0)/nitrate>4), Pb(2+) ions were immobilized more quickly (<5 min) than in nitrate-free systems (∼ 15 min) due to increasing pH. With nitrate in excess (molar ratio of Fe(0)/nitrate<4), nitrate stimulated the formation of crystal PbxFe3-xO4 (ferrite), which provided additional Pb(2+) removal. However, ∼ 7% of immobilized Pb(2+) ions were released into aqueous phase within 2h due to ferrite deformation. Oxidation-reduction potential (ORP) values below -600 mV correlated with excess Fe(0) conditions (complete Pb(2+) immobilization), while ORP values ≥-475 mV characterized excess nitrate conditions (ferrite process and Pb(2+) release occurrence). This study indicates that ORP monitoring is important for proper management of nZVI-based remediation in the subsurface to avoid lead remobilization in the presence of nitrate

Antimicrobial susceptibility and genotyping of Mycoplasma pneumoniae isolates in Beijing, China, from 2014 to 2016

Abstract Background The presence of macrolide-resistant Myocplasma pneumoniae has been frequently reported in recent years, especially in China. In this study, we investigated the antimicrobial susceptibility and genotype against M. pneumoniae isolates from 2014 to 2016, Beijing. Methods We investigated the activities of four antibiotics against 81 M. pneumoniae isolates in vitro. All isolates were amplification of domains II and V of the 23S rRNA gene and the L4 and L22 ribosomal protein fragments. All isolates were genotyped with duplex real-time PCR, MLVA and VNTR detection in p1 gene. Results The macrolide resistance rate was 65.4% (53/81). Each of the macrolide-resistant M. pneumoniae isolates was resistant to erythromycin (Minimum Inhibitory Concentration, MIC, ≥256 μg/ml) and azithromycin (MIC, 2–64 μg/ml), but susceptible to tetracycline and levofloxacin in vitro. Fifty two macrolide-resistant isolates harbored the A2063G mutation, and only 1 macrolide-resistant isolates harbored the A2064G mutation in domain V of the 23S ribosomal RNA gene. The C162A, A430G, and T279C mutations in the L4 and L22 ribosomal protein genes were not responsible for macrolide resistance, but they were related to the particular genotype of M. pneumoniae. 95.7% of type 1 isolates (45/47) were macrolide-resistance, and 23.5% of the type 2 isolates (8/34) were macrolide-resistance. Type 2 M. pneumoniae macrolide-resistance rate was 50.6% higher than that of the previous reports in China. The eight macrolide-resistant type 2 M. pneumoniae isolates were belong to 3/5/6/2 and 3/5/7/2 MLVA genotypes. Conclusion To our knowledge, this phenomenon likely resulted from a combination of genotype shifting from type1 to type 2 and antibiotic selection pressure in M. pneumoniae in China in recent years. The increase of resistance in type 2 is not due to the spread of same clone. However, the relationship between genotype shifts and macrolide resistance in M. pneumoniae needs to be further verified with more extensive surveillance data

Screening and Analysis of Serum Protein Biomarkers Infected by Coronavirus Disease 2019 (COVID-19)

Coronavirus disease 2019 (COVID-19) has spread widely around the world, and in-depth research on COVID-19 is necessary for biomarkers and target drug discovery. This analysis collected serum from six COVID-19-infected patients and six healthy people. The protein changes in the infected and healthy control serum samples were evaluated by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and high-performance liquid chromatography (HPLC). The differential protein signature in both groups was retrieved and analyzed by the Kyoto Encyclopedia of Gene and Genomes (KEGG), Gene ontology, COG/KOG, protein–protein interaction, and protein domain interactions tools. We shortlisted 24 differentially expressed proteins between both groups. Ten genes were significantly up-regulated in the infection group, and fourteen genes were significantly down-regulated. The GO and KEGG pathway enrichment analysis suggested that the chromosomal part and chromosome were the most enriched items. The oxytocin signaling pathway was the most enriched item of KEGG analysis. The netrin module (non-TIMP type) was the most enriched protein domain in this study. Functional analysis of S100A9, PIGR, C4B, IL-6R, IGLV3-19, IGLV3-1, and IGLV5-45 revealed that SARS-CoV-2 was closely related to immune response