Biology subjects

Yeh, C.-A.

Publications and source records attributed to Yeh, C.-A..

3 recordsLinked to original sources

bioRxiv2024

Modeling the transmission dynamics of African swine fever virus within commercial swine barns: Quantifying the contribution of multiple transmission pathways

Transmission of the African swine fever virus (ASFV) within commercial swine barns occurs through direct and indirect pathways. Identifying and quantifying the roles of ASFV dissemination within barns is crucial for the development of effective disease control strategies. We developed a stochastic transmission model to examine the ASFV dissemination dynamics through eight transmission routes within commercial swine barns. We consider seven transmission routes at three disease dynamics levels: within-pens, between-pens, and within-room transmission, along with the transfer of pigs between pens within the same room. We simulated ASFV spread within barns of various sizes and layouts from rooms with a median of 32 pens (IQR:28-40), where each pen housing a median of 34 pigs (IQR: 29-36). Our model enables the tracking of the viral load in each pen and the monitoring of the disease status at the pen level. Simulation results show that between-pen transmission pathways exhibited the highest contribution to ASFV spread, accounting for 71.4%, where within-pen and within-room pathways account for 20.1% and 8.5%, respectively. Among the direct transmission pathways, nose-to-nose contact between pens was the primary route of dissemination, comprising an average of 49%, while the fecal transmission between pens contributed 21%. On the other hand, aerosol transmission within pens had the lowest contribution, accounting for less than 1%. Furthermore, we show that the daily transfer of pigs between pens did not impact the spread of ASFV. The combination of passive surveillance of daily detection and active surveillance focused on mortality allowed the detection of ASFV within three Days, with peak detection occurring when mortality rates peaked. The model also allows us to pinpoint where the majority of infections and viral load are concentrated during the ASFV spread. This work significantly deepens our understanding of ASFV spread within commercial swine production farms in the U.S. and highlights the main transmission pathways that should be prioritized when implementing ASFV countermeasure actions at the room level.

ecology↗

bioRxiv2024

Modeling the impact of optimized airflow and sick pen management on the spread of infectious diseases in swine barns

The airborne spread of infectious livestock diseases plays a crucial role in the propagation of epidemics, particularly in populations confined to densely populated facilities, such as commercial swine barns. Therefore, quantitative assessments for the performance of barn ventilation systems may serve as an alternative biocontainment control strategy to reduce the spread of infectious pathogens. In this study, we present a framework to simulate airborne disease dissemination within swine barns and facilitate the strategic design of control actions, including optimization of ventilation and placement of sick animals (sick pen). This framework is based on a susceptible-infected-recovered (SIR) model that accounts for the between-pen disease spread within swine barns. A pen-to-pen contact network is used to construct a transmission matrix according to the transport of airborne respiratory pathogens across pens in the barns, via our Reynolds-averaged Navier-Stokes computational fluid dynamics (CFD) solver. By employing this CFD-augmented SIR model, we demonstrated that the location of the sick pen and the barn ventilation configuration played crucial roles in modifying disease dissemination dynamics at the barn level. In addition, we examined the effect of natural ventilation through different curtain adjustments. We observed that curtain adjustments either suppress the disease spread by an average of 56.5% or exacerbate the outbreak potential by an average of 5.7%, compared to the scenario where side curtains are not raised. Furthermore, we optimize the ventilation configuration via the selection and placement of ventilation fans through the integration of the CFD-augmented framework with the genetic algorithm to minimize the dissemination of swine disease within barns. Compared to regular barn ventilation settings, our optimized ventilation system significantly reduced disease spread by an average of 43.2%. Our study emphasizes the role of airborne transmission and a strategy for sick pen management in controlling the spread of within-barn disease.

bioengineering↗

bioRxiv2023

CytoPb: Segmentation-free and threshold-free analysis of highly multiplexed images of biological tissue

We present a novel method and code, CytoPb, for the analysis of multiplexed images that is segmentation-free and threshold-free and produces results that correlate well with existing methods but is faster to run, needs minimal training and removes subjectivity associated with the validation of single-cell segmentation and thresholding. In three data sets cell abundance measures correlate with previous methods (Pearsons coef. >0.75). Neighbourhood analysis and cell-cell proximity are possible.

immunology↗