Stochastic Simulation Model Research Articles

Preventing evolutionary rescue in cancer.

First-line cancer treatment frequently fails due to initially rare therapeutic resistance. An important clinical question is then how to schedule subsequent treatments to maximize the probability of tumour eradication. Here, we provide a theoretical solution to this problem by using mathematical analysis and extensive stochastic simulations within the framework of evolutionary rescue theory to determine how best to exploit the vulnerability of small tumours to stochastic extinction. Whereas standard clinical practice is to wait for evidence of relapse, we confirm a recent hypothesis that the optimal time to switch to a second treatment is when the tumour is close to its minimum size before relapse, when it is likely undetectable. This optimum can lie slightly before or slightly after the nadir, depending on tumour parameters. Given that this exact time point may be difficult to determine in practice, we study windows of high extinction probability that lie around the optimal switching point, showing that switching after the relapse has begun is typically better than switching too early. We further reveal how treatment dose and tumour demographic and evolutionary parameters influence the predicted clinical outcome, and we determine how best to schedule drugs of unequal efficacy. Our work establishes a foundation for further experimental and clinical investigation of this evolutionarily-informed "extinction therapy" strategy.

Versatile stochastic model for predictive KMC simulation of fcc metal nanostructure evolution with realistic kinetics.

Stochastic lattice-gas models provide the natural framework for analysis of the surface diffusion-mediated evolution of crystalline metal nanostructures on the appropriate time scale (often 101-104s) and length scale. Model behavior can be precisely assessed by kinetic Monte Carlo simulation, typically incorporating a rejection-free algorithm to efficiently handle the broad range of Arrhenius rates for hopping of surface atoms. The model should realistically prescribe these rates, or the associated barriers, for a diversity of local surface environments. However, commonly used generic choices for barriers fail, even qualitatively, to simultaneously describe diffusion for different low-index facets, for terrace vs step edge diffusion, etc. We introduce an alternative Unconventional Interaction-Conventional Interaction formalism to prescribe these barriers, which, even with few parameters, can realistically capture most aspects of behavior. The model is illustrated for single-component fcc metal systems, mainly for the case of Ag. It is quite versatile and can be applied to describe both the post-deposition evolution of 2D nanostructures in homoepitaxial thin films (e.g., reshaping and coalescence of 2D islands) and the post-synthesis evolution of 3D nanocrystals (e.g., reshaping of nanocrystals synthesized with various faceted non-equilibrium shapes back to 3D equilibrium Wulff shapes).

The economic effect of cow-based reproductive management programs with a systematic use of reproductive hormones

Hormone-based reproductive management programs can be beneficial to improve dairy cow's reproductive performance. This study aimed to compare the economic impact of reproductive management programs using systematic hormonal treatments to individual cows with a specific DIM range with a reproductive management program using cow-specific hormonal treatment based on a veterinary diagnosis of ovarian dysfunction during a fertility check. An existing individual cow-based, dynamic, and stochastic bio-economic simulation model, mimicking the production dynamics of a 200 cow-herd in daily time steps, was extended with ovarian dysfunction and fertility inputs. Four hormone-based reproductive management programs were modeled. In the default reproductive management program, reflecting the current reproductive management of Dutch herds, lactating dairy cows are inseminated based on detection of estrus and non-cyclic dairy cows are treated with hormones based on a veterinary diagnosis of ovarian dysfunction during a fertility check. Hormone treatments prescribed by the veterinarian for anestrus, cystic, and sub-estrus cows were an 8-d progesterone-releasing intravaginal device (PRID)-Synch protocol (PRIDsynch), an Ovsynch protocol, and a PGF2⍺ treatment, respectively. The 3 other reproductive management programs reflected systematic hormonal treatments to cows at specific DIM and included a 1) Double-Ovsynch protocol for TAI with nonpregnant cows submitted to a resynchronization protocol (FTAI), 2) Double-Ovsynch protocol for TAI with nonpregnant cows detected in estrus or submitted to a resynchronization protocol (FTAI+ED), and 3) detection of estrus with cows not detected submitted to a PRIDsynch protocol (ED+TAI). All nonpregnant cows were submitted to a resynchronization protocol based on the absence (PRIDsynch) or presence (Ovsynch protocol) of a corpus luteum (CL). The annual mean net economic return (NER) was calculated for all reproductive management programs. Compared with the default reproductive management program, the highest NER was observed for the FTAI+ED reproductive management program with €23,764 higher net revenues, followed by the FTAI and the ED+TAI reproductive management programs with €19,550 and €14,314 higher net revenues, respectively. Overall, systematic hormone-based reproductive management programs gave higher costs due to more hormones administered and higher calving and feed costs due to more pregnant cows. Nevertheless, the additional revenues of milk and calves in the systematic hormone-based reproductive management programs outweighed the total cost. For instance, the FTAI+ED reproductive management program gave €8,953 higher total cost per year compared with the default but with €32,654 higher revenues. In summary, reproductive management programs where hormones were systematically used gave economic advantages over the current default reproductive management program in which hormones are administered to individual cows based on a veterinary diagnosis of ovarian dysfunction during a fertility check.

An ensemble learning paradigm for subsurface stratigraphy from sparse measurements and augmented training images

The performance of computer vision-based techniques for stratigraphic modeling relies heavily on qualified training images to capture the complex stratigraphic connectivity. In geotechnical engineering, only limited training images are available for a specific site. Stochastic simulation modelling based on limited training data may be biased as the collected images that reflect prior geological knowledge may not encompass all potential stratigraphic patterns. Therefore, it is crucial to establish a high-quality, domain-specific training image database for effective stratigraphic modelling. In this study, an ensemble learning paradigm is proposed to tackle this issue and develop subsurface geological cross-sections from sparse data by reconstruction and redistribution of stratigraphic statistics revealed from limited training images. A domain-specific training image database is first established using generative adversarial networks (GAN) that enable the generation of arbitrary sized image samples from a single training image. Subsequently, multiple qualified image samples that are compatible with site-specific data are adaptively selected and utilized for the ensemble learning of geological cross-sections. The performance of the proposed framework is demonstrated using real geological cross-sections collected from a reclamation site and a tunnelling project in Hong Kong. The results indicate that the proposed method can effectively generate diverse image samples that encompass stratigraphic features beyond those reflected in a single training image. More importantly, the ensemble learning framework can capture the complex spatial stratigraphic connectivity of soil layers with enhanced prediction accuracy.

Utilization of stochastic ground motion simulations for scenario-based performance assessment of geo-structures

Probabilistic seismic performance assessments of engineered structures can be highly sensitive to the seismic input excitation and its variability. In the present study, the scenario-based performance assessment recommended by Federal Emergency Management Agency (FEMA) P-58 guidelines is adopted to estimate seismic fragility of concrete dams for various seismic hazard scenarios. Due to the scarcity of recorded ground motions and thereby their poor representation of uncertainties, stochastic ground motion simulation methods are utilized to obtain the required input excitations. Moreover, to understand the uncertainty in ground motion simulation models, two broadband stochastic simulation models are used to generate input excitations representing six seismic hazard scenarios defined by earthquake magnitude, source-to-site distance, and soil conditions.Optimal intensity measure parameters for each scenario are identified using a systematic procedure that considers criteria such as efficiency, practicality, proficiency, sufficiency, and hazard compatibility. Fragility curves and surfaces are derived using the cloud analysis technique, taking into account various damage measures and limit state functions. The study finds that the derived fragility curves are particularly sensitive to the selection of earthquake scenarios, the choice of records, and the methods used to calculate fragility curves, with less sensitivity observed to different engineering demand parameters. Given this sensitivity, particularly to ground motion selection, the study highlights the necessity of incorporating both model-to-model variability (epistemic uncertainty) and record-to-record variability (aleatory uncertainty), alongside the established material and modeling uncertainties, in the probabilistic seismic assessment.

Shelter location–allocation problem for disaster evacuation planning: A simulation optimization approach

Immediately after a major earthquake strikes, a segment of the people in the disaster region must evacuate to relief shelters. If the evacuation proceeds in an efficient and safe manner, many lives can potentially be saved as the effects of secondary factors, e.g., secondary collapses, stampedes, and aftershocks, can largely be mitigated, while at the same time the people taking refuge can quickly gain access to vital relief goods. Formulating the best possible protocols for post-earthquake evacuation is a crucial, yet highly challenging problem considering the profound uncertainty which is present in the post-disaster environment, including the location and degree of infrastructural damage, the number and location of people who need to evacuate, the behavior and psychology of evacuees, etc. In this research, we formulate a two-stage stochastic evacuation simulation model capable of credibly accounting for these uncertainties. We develop a solution methodology to solve the shelter location–allocation problem represented by the two-stage model, finding the optimal location of shelters to be open as the first stage solution and the optimal assignment of evacuees to shelters as the second stage solution to minimize the total expected cost. The cost-based objective function consists of the cost of opening shelters, a deprivation cost component, the cost of trapped evacuees, and the cost of shelters exceeding capacity. In developing this framework, we collaborate with the National Science and Technology Center for Disaster Reduction (NCDR) in utilizing GIS-based probabilistic models of road damage. We apply the proposed framework to run an extensive numerical study and present various valuable observations and insights which can be gained.

Dairy farmer income, working time, and antimicrobial use under different dry cow therapy protocols

Mastitis is one of the most common diseases of dairy cattle. It has a high impact on farm economy, farmers' working time, and antimicrobial usage (AMU). Selective dry cow therapy (SDCT) is an effective means of reducing AMU without negatively affecting udder health. The objective of our study was to evaluate the impact of SDCT implementation on farmer's income, working time, and AMU, using a bioeconomic model. A stochastic dairy simulation model (DairyHealthSim) based on a weekly model was used to simulate herd dynamics, reproduction, milk production, culling decisions, health outcomes, and the management of health events. A specific module was developed for the simulation of quarter-level intramammary infection (IMI) acquisition and elimination during the lactation and dry-off periods, and 25 different farm settings were defined to represent herds with various udder health situations. We then defined 20 scenarios of SDCT by combining both the use of different thresholds of somatic cell count and milk bacteriology for treatment allocation and the use of internal teat sealant (ITS). All SDCT protocols had a low impact on farmer's income, and we identified some protocols with a positive farm gross margin (up to 15.83 CA$/dried- cow). We also found that adding an ITS to all cows led to greater economic gain. The application of SDCT had a low impact on farmers' working time, except when milk bacteriology was used for decision-making. Antimicrobial treatment to all cows above 200,000 cells/mL at last control, with the use of ITS on all cows, seems a good choice in most dairy farms. These findings could be used to convince farmers to adopt this strategy at dry-off.

Stochastic Optimization of the Management Schedule of Korean Pine Plantations

Korean pine is one of the most important tree species in northeastern China, where Korean pine plantations produce timber and edible seeds. Often, seeds create more income than timber. Predicting the timber and cone yields of alternative management schedules of the plantations involves uncertainty because the future climatic conditions for tree growth and cone production are unknown. This study developed a simulation model that generates stochastic variation around the predictions of tree growth and cone yield models, allowing the forest manager to seek cutting schedules that maximize the expected amounts of timber or cones, or the expected economic profit, under uncertain future states of nature. Stochastic analysis also facilitates management optimizations for different risk attitudes. The differential evolution algorithm and the developed stochastic simulation model were used to optimize the management of planted Korean pine. Timber and cone yields of a management schedule were calculated under 100 different scenarios for tree growth and cone production. When the growth and cone yield scenarios were stationary (no temporal trends), the optimal management schedules were similar to those of deterministic optimization. The benefits of stochastic optimization increased when it was assumed that the tree growth scenarios may contain climate-change-induced trends. Non-stationary growth variation led to shorter optimal rotation lengths than stationary growth variation. Increasing risk tolerance shortened optimal rotations.

Energy flexibility in aerospace manufacturing: The case of low carbon intensity production

In this paper, the prospects of energy flexibility in mitigating the environmental impact of aerospace manufacturing are explored. In collaboration with a UK-based aerospace manufacturing enterprise, demand response, in particular production time, is explored under different stochastic scenarios. This is done through a decision-support framework that consists of a stochastic discrete-event simulation model that tests different scenarios under a full factorial design of experiments framework. The simulation model tests various improvement strategies pertaining to prioritisation rules, production start-up rules, and operating hours. The model aids in scheduling energy-intensive processes, so the time of performing such processes can coincide with times of the day when the energy’s carbon intensity is at its lowest. The use case constitutes a family of aluminium structural aerospace components that are characterised by high production rate. Results demonstrate promising potential of the proposed approach, with the best-case scenario resulting in a 7% reduction in CO2e emissions. Analysis of the results demonstrate that operational decisions that do not require infrastructural changes or capital expenditures can contribute favourably to achieving net-zero targets. This research offers useful insights on leveraging operational short-term decisions to meet the aerospace manufacturing’s sector decarbonisation targets.

Effects of extending dairy cow longevity by adjusted reproduction management decisions on partial net return and greenhouse gas emissions: A dynamic stochastic herd simulation study

Prolonging dairy cattle longevity is regarded as one of the options to contribute to more sustainable milk production. Because failure to conceive is one of the main reasons for culling, this study investigates how adjustments in reproduction management affect partial net return at herd level and greenhouse gas emissions per unit of milk, using a dynamic stochastic simulation model. The effects of reproduction decisions that extend cattle longevity on milk yield, calving interval and pregnancy rate were derived from actual performance of Dutch commercial dairy cows over multiple lactations. The model simulated lactations, calving, and health status events of individual cows for herds of 100 cows. Scenarios evaluated differed in the maximum number of consecutive AI attempts (4, 5, or 6 services), or the production threshold (20, 15, or 10 kg of milk/d) at which cows that failed to conceive are culled (reproductive culling). Annual partial net return was computed from revenues of sold milk, calves, and slaughtered cows, and the costs from feed consumption, rearing replacement heifers, AI services, and treatment for clinical mastitis and lameness. Greenhouse gas emissions were computed for feed production, enteric fermentation, and manure management, and were expressed as total CO2 equivalents (CO2-eq). Average age at culling increased with an increased maximum number of AI services. This increase was larger when going from a maximum of 4 to 5 AI attempts (108 d) than from a maximum of 5 to 6 attempts (47 d). Similarly, the average age at culling increased from 1,968 to 2,040 and 2,132 d when the threshold for reproductive culling decreased from 20, to 15 and 10 kg of milk/d, respectively. Average annual partial net return increased by 1.1% from €165,850 per 100 cows at a maximum of 4 AI to €167,670 per 100 cows at a maximum of 6 AI, and increased by 4.3% from €161,210 per 100 cows at a reproductive culling threshold of 10 kg/d to €168,190 per 100 cows at a threshold of 20 kg/d. Greenhouse gas emissions decreased by 1.2% from 0.926 to 0.915 kg CO2-eq per kg of fat- and protein-corrected milk (FPCM) with an increase in a maximum number of AI from 4 to 6 AI. Conversely, greenhouse gas emissions increased by 0.2% from 0.926 kg at a threshold of reproductive culling of 20 kg/d to 0.928 kg CO2-eq/kg FPCM at a threshold of 10 kg/d. Although lowering the threshold for reproductive culling has the potential to extend cattle longevity more than increasing the maximum number of AI services, only the increase in AI services benefits a farm's partial net return, while reducing greenhouse gas emissions.

Reliability-driven time-of-use tariffs for efficient plug-in electric vehicle integration

Demand response (DR) plays a crucial role in balancing electricity supply and demand, but existing studies on price-based DR for plug-in electric vehicle (PEV) load management lack comprehensive considerations. Therefore, this study designs reliability-driven time-of-use (TOU) tariffs for the integration of PEVs, considering various factors such as random component failures, the stochastic characteristics of non-dispatchable components, and fluctuations in load patterns and uncertainties. The proposed framework employs advanced stochastic simulation models to assess generation facility reliability amidst extensive PEV deployment in three steps. First, individual components, including conventional generation capacity, renewable energy sources, and demand, as well as PEV load models, are developed. Then, a system reserve margin assessment is carried out via the generation of seasonal synthetic time series data. During this step, innovative techniques, including box-plot methods and expert rules, are used to simplify the representation of the system reserve margin at each hour. Finally, optimized TOU pricing schedules for PEVs are generated. These pricing hours are initially categorized as off-peak, mid-peak, or on-peak, streamlining scenario analysis and aligning PEV charging profiles with predefined pricing schedules for grid reliability evaluation. Case studies have shown that the proposed method can improve the reliability indices by effectively mitigating the impacts.

Mathematical Modelling of Parasite Dynamics: A Stochastic Simulation-Based Approach and Parameter Estimation via Modified Sequential-Type Approximate Bayesian Computation

The development of mathematical models for studying newly emerging and re-emerging infectious diseases has gained momentum due to global events. The gyrodactylid-fish system, like many host-parasite systems, serves as a valuable resource for ecological, evolutionary, and epidemiological investigations owing to its ease of experimental manipulation and long-term monitoring. Although this system has an existing individual-based model, it falls short in capturing information about species-specific microhabitat preferences and other biological details for different Gyrodactylus strains across diverse fish populations. This current study introduces a new individual-based stochastic simulation model that uses a hybrid τ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ au $$\\end{document}-leaping algorithm to incorporate this essential data, enhancing our understanding of the complexity of the gyrodactylid-fish system. We compare the infection dynamics of three gyrodactylid strains across three host populations. A modified sequential-type approximate Bayesian computation (ABC) method, based on sequential Monte Carlo and sequential importance sampling, is developed. Additionally, we establish two penalised local-linear regression methods (based on L1 and L2 regularisations) for ABC post-processing analysis to fit our model using existing empirical data. With the support of experimental data and the fitted mathematical model, we address open biological questions for the first time and propose directions for future studies on the gyrodactylid-fish system. The adaptability of the mathematical model extends beyond the gyrodactylid-fish system to other host-parasite systems. Furthermore, the modified ABC methodologies provide efficient calibration for other multi-parameter models characterised by a large set of correlated or independent summary statistics.

Simulation of Full HIV Cluster Networks in a Nationally Representative Model Indicates Intervention Opportunities.

Clusters of rapid HIV transmission in the United States are increasingly recognized through analysis of HIV molecular sequence data reported to the National HIV Surveillance System. Understanding the full extent of cluster networks is important to assess intervention opportunities. However, full cluster networks include undiagnosed and other infections that cannot be systematically observed in real life. We replicated HIV molecular cluster networks during 2015-2017 in the United States using a stochastic dynamic network simulation model of sexual transmission of HIV. Clusters were defined at the 0.5% genetic distance threshold. Ongoing priority clusters had growth of ≥3 diagnoses/year in multiple years; new priority clusters first had ≥3 diagnoses/year in 2017. We assessed the full extent, composition, and transmission rates of new and ongoing priority clusters. Full clusters were 3-9 times larger than detected clusters, with median detected cluster sizes in new and ongoing priority clusters of 4 (range 3-9) and 11 (range 3-33), respectively, corresponding to full cluster sizes with a median of 14 (3-74) and 94 (7-318), respectively. A median of 36.3% (range 11.1%-72.6%) of infections in the full new priority clusters were undiagnosed. HIV transmission rates in these clusters were >4 times the overall rate observed in the entire simulation. Priority clusters reflect networks with rapid HIV transmission. The substantially larger full extent of these clusters, high proportion of undiagnosed infections, and high transmission rates indicate opportunities for public health intervention and impact.

Release potential, neglected leakage and reduction countermeasures of COD and Ammonia in MSWLs

In order to eliminate the impact of the industrial revolution on the environment and improve the water ecological environment, pollutant discharge reduction is imperative. With the acceleration of global discharge reduction process, the huge pollutant release potential and potential environmental effects of municipal solid waste landfills gradually appear, but its release amount and intensity have not been quantitatively revealed. We propose a coupling method of parameter stochastic simulation and physical process model simulation to estimate the hidden leakage of large-scale regional municipal solid waste landfills, and provide a methodology for estimating the hidden leakage of landfills in other countries and even in the whole world by taking China, which has the largest amount of waste generation among developing countries, as an example. Prior to the implementation of stringent construction quality control and assurance management requirements, the average annual leachate generation potential over the entire life cycle of 2600 landfills in China was estimated to be 4.66 × 108 m3, in which the concentrations of COD and NH3-N are 5.38 × 102–6.48 × 104 mg/L and 6.10–3.50 × 103 mg/L, respectively, and the total amounts are 5.21 × 103–7.81 × 108 t and 8.09 × 102–6.65 × 107 t, respectively. About 14 % of these pollutants may leak into the environmental media through the landfill liner with the average number of holes of 21.5/ha. For different regions, the overall release, discharge and leakage of COD and NH3-N in East China account for 35.70 %, 36.68 % and 29.60 % respectively, making it the region with the highest potential for discharge and risk of leakage. Meanwhile, the implementation of mandatory regulations related to leachate generation and control has led to a significant reduction in the leakage of pollutants. For instance, comprehensively detecting and repair of holes in the impermeable liner has reduced the number of holes to 2/ha, resulting in a reduction of >90 % in the leakage of pollutants.

COVSIM: A stochastic agent-based COVID-19 SIMulation model for North Carolina

We document the evolution and use of the stochastic agent-based COVID-19 simulation model (COVSIM) to study the impact of population behaviors and public health policy on disease spread within age, race/ethnicity, and urbanicity subpopulations in North Carolina. We detail the methodologies used to model the complexities of COVID-19, including multiple agent attributes (i.e., age, race/ethnicity, high-risk medical status), census tract-level interaction network, disease state network, agent behavior (i.e., masking, pharmaceutical intervention (PI) uptake, quarantine, mobility), and variants. We describe its uses outside of the COVID-19 Scenario Modeling Hub (CSMH), which has focused on the interplay of nonpharmaceutical and pharmaceutical interventions, equitability of vaccine distribution, and supporting local county decision-makers in North Carolina. This work has led to multiple publications and meetings with a variety of local stakeholders. When COVSIM joined the CSMH in January 2022, we found it was a sustainable way to support new COVID-19 challenges and allowed the group to focus on broader scientific questions. The CSMH has informed adaptions to our modeling approach, including redesigning our high-performance computing implementation.

Mbit/s-range alkali vapour spin noise quantum random number generators

Spin noise based quantum random number generators first appeared in 2008 and have since then garnered little further interest, in part because their bit rate is limited by the transverse relaxation time T2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$T_{2}$\\end{document} which for coated alkali vapour cells is typically in the kbit/s range. Here we present two advances. The first is an improved bit generation protocol that allows generating bits at rates exceeding 1/T2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$1/T_{2}$\\end{document} with only a minor increase of serial correlations. The second is a significant reduction of the time T2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$T_{2}$\\end{document} itself by removing the coating, increasing the vapour temperature and introducing a magnetic-field gradient. In this way we managed to increase the bit generation rate to 1.04 Mbit/s. We analyse the quality of the generated random bits using entropy estimation and we discuss the extraction methods to obtain high-entropy bitstreams. We accurately predict the entropy output of the device backed with a stochastic model and numerical simulations.

Are all avian influenza outbreaks in poultry the same? The predicted impact of poultry species and virus subtype.

Outbreaks of avian influenza in poultry farms are currently increasing in frequency, with devastating consequences for animal welfare, farmers and supply chains. Some studies have documented the direct spread of the avian influenza virus between farms. Prevention of spread between farms relies on biosecurity surveillance and control measures. However, the evolution of an outbreak on a farm might vary depending on the virus strain and poultry species involved; this would have important implications for surveillance systems, epidemiological investigations and control measures. In this study, we utilized existing parameter estimates from the literature to evaluate the predicted course of an epidemic in a standard poultry flock with 10,000 birds. We used a stochastic SEIR simulation model to simulate outbreaks in different species and with different virus subtypes. The simulations predicted large differences in the duration and severity of outbreaks, depending on the virus subtypes. For both turkeys and chickens, outbreaks with HPAI were of shorter duration than outbreaks with LPAI. In outbreaks involving the infection of chickens with different virus subtypes, the shortest epidemic involved H7N7 and HPAIV H5N1 (median duration of 9 and 17 days, respectively) and the longest involved H5N2 (median duration of 68 days). The most severe outbreaks (number of chickens infected) were predicted for H5N1, H7N1 and H7N3 virus subtypes, and the least severe for H5N2 and H7N7, in which outbreaks for the latter subtype were predicted to develop most slowly. These simulation results suggest that surveillance of certain subtypes of avian influenza virus, in chicken flocks in particular, needs to be sensitive and timely if infection is to be detected with sufficient time to implement control measures. The variability in the predictions highlights that avian influenza outbreaks are different in severity, speed and duration, so surveillance and disease response need to be nuanced and fit the specific context of poultry species and virus subtypes.

Identification of groundwater pollution sources and health risk assessment in the Songnen Plain based on PCA-APCS-MLR and trapezoidal fuzzy number-Monte Carlo stochastic simulation model

The source of inorganic pollutants in the groundwater of the Songnen Plain are complex; therefore, it is urgent to analyze the pollution sources and their contribution rates, and to determine the effects of pollutants on human health. In this study, the solution for the insufficient extraction of characteristic information and subjective weight in principal component analysis (PCA) was found using log-centralization and the entropy weight method. Based on 896 groundwater samples, the types and distribution characteristics of pollution sources were identified, and the APCS-MLR receptor model was used to quantitatively characterize the contribution of pollution sources to water quality. Considering the uncertainty of the health risk assessment process, a trapezoidal fuzzy number-Monte Carlo stochastic simulation model (TFN-MCS) was constructed. Overcoming the inapplicability of triangular fuzzy numbers in dealing with highly discrete water quality data. The results showed that: (1) The five potential pollution sources in the Songnen Plain were salinity factor (34.086 %), agricultural pollution factor (15.854 %), geological background factor (13.11 %), industrial pollution factor (10.382 %) and organic pollution factor (7.382 %). The degree of groundwater pollution in the study area is controlled by the terrain, hydrogeological conditions, land use type, and industrial layout. (2) The APCS-MLR receptor model was suitable for the allocation of potential sources of groundwater pollution. The average contributions rate of the five common factors to groundwater pollution were 38.86, 14.12, 15.73, 14.6, and 6.77 %. Salinity factor plays a major role in groundwater quality. (3) The THI of children and adults were 2.15–15.03 and 0.86–7.261, respectively, much higher than the safety threshold of one. In general, the THI of children from ingesting contaminated groundwater is twice that to adults. NO3– and F- are the primary risk control indicators for groundwater in the study area. These results support the formulation of effective groundwater pollution control strategies.

A brief overview of mathematical modeling of the within-host dynamics of Mycobacterium tuberculosis

Tuberculosis (TB), a disease caused by bacteria Mycobacterium tuberculosis (Mtb), remains one of the major infectious diseases of humans with 10 million TB cases and 1.5 million deaths due to TB worldwide yearly. Upon exposure of a new host to Mtb, bacteria typically infect one local site in the lung, but over time, Mtb disseminates in the lung and in some cases to extrapulmonary sites. The contribution of various host components such as immune cells to Mtb dynamics in the lung, its dissemination in the lung and outside of the lung, remains incompletely understood. Here we overview different types of mathematical models used to gain insights in within-host dynamics of Mtb; these include models based on ordinary or partial differential equations (ODEs and PDEs), stochastic simulation models based on ODEs, agent-based models (ABMs), and hybrid models (ODE-based models linked to ABMs). We illustrate results from several of such models and identify areas for future resesarch.

Deep-Learning-Based Seismic-Signal P-Wave First-Arrival Picking Detection Using Spectrogram Images

The accurate detection of P-wave FAP (First-Arrival Picking) in seismic signals is crucial across various industrial domains, including coal and oil exploration, tunnel construction, hydraulic fracturing, and earthquake early warning systems. At present, P-wave FAP detection relies on manual identification by experts and automated methods using Short-Term Average to Long-Term Average algorithms. However, these approaches encounter significant performance challenges, especially in the presence of real-time background noise. To overcome this limitation, this study proposes a novel P-wave FAP detection method that employs the U-Net model and incorporates spectrogram transformation techniques for seismic signals. Seismic signals, similar to those encountered in South Korea, were generated using the stochastic model simulation program. Synthesized WGN (White Gaussian Noise) was added to replicate background noise. The resulting signals were transformed into 2D spectrogram images and used as input data for the U-Net model, ensuring precise P-wave FAP detection. In the experimental result, it demonstrated strong performance metrics, achieving an MSE of 0.0031 and an MAE of 0.0177, and an RMSE of 0.0195. Additionally, it exhibited precise FAP detection capabilities in image prediction. The developed U-Net-based model exhibited exceptional performance in accurately detecting P-wave FAP in seismic signals with varying amplitudes. Through the developed model, we aim to contribute to the advancement of microseismic monitoring technology used in various industrial fields.