Taxis-driven complex patterns of a plankton model.

This paper reports an important conclusion that self-diffusion is not a necessary condition for inducing Turing patterns, while taxis could establish complex pattern phenomena. We investigate pattern formation in a zooplankton-phytoplankton model incorporating phytoplankton-taxis, where phytoplankton-taxis describes the zooplankton that tends to move toward the high-densities region of the phytoplankton population. By using the phytoplankton-taxis sensitivity coefficient as the Turing instability threshold, one shows that the model exhibits Turing instability only when repulsive phytoplankton-taxis is added into the system, while the attractive-type phytoplankton-taxis cannot induce Turing instability of the system. In addition, the system does not exhibit Turing instability when the phytoplankton-taxis disappears. Numerically, we display the complex patterns in 1D, 2D domains and on spherical and zebra surfaces, respectively. In summary, our results indicate that the phytoplankton-taxis plays a pivotal role in giving rise to the Turing pattern formation of the model. Additionally, these theoretical and numerical results contribute to our understanding of the complex interaction dynamics between zooplankton and phytoplankton populations.

Updated fiducial distribution of parameters in the associated delta-lognormal population.

In this paper we consider a special kind of semicontinous distribution. We try to concern with the situation where the probability of zero observation is associated with the location and scale parameters in lognormal distribution. We first propose a goodness-of-fit test to ensure that the data can be fit by the associated delta-lognormal distribution. Then we define the updated fiducial distributions of the parameters and establish the results that the confidence interval has asymtotically correct level while the significance level of the hypothesis testing is also asymtotically correct. We propose an exact sampling method to sample from the updated fiducial distribution. It can be seen in our simulation study that the inference on the parameters is largely improved. A real data example is also used to illustrate our method.

Nonlinear compartmental modeling to monitor ovarian follicle population dynamics on the whole lifespan.

In this work, we introduce a compartmental model of ovarian follicle development all along lifespan, based on ordinary differential equations. The model predicts the changes in the follicle numbers in different maturation stages with aging. Ovarian follicles may either move forward to the next compartment (unidirectional migration) or degenerate and disappear (death). The migration from the first follicle compartment corresponds to the activation of quiescent follicles, which is responsible for the progressive exhaustion of the follicle reserve (ovarian aging) until cessation of reproductive activity. The model consists of a data-driven layer embedded into a more comprehensive, knowledge-driven layer encompassing the earliest events in follicle development. The data-driven layer is designed according to the most densely sampled experimental dataset available on follicle numbers in the mouse. Its salient feature is the nonlinear formulation of the activation rate, whose formulation includes a feedback term from growing follicles. The knowledge-based, coating layer accounts for cutting-edge studies on the initiation of follicle development around birth. Its salient feature is the co-existence of two follicle subpopulations of different embryonic origins. We then setup a complete estimation strategy, including the study of structural identifiability, the elaboration of a relevant optimization criterion combining different sources of data (the initial dataset on follicle numbers, together with data in conditions of perturbed activation, and data discriminating the subpopulations) with appropriate error models, and a model selection step. We finally illustrate the model potential for experimental design (suggestion of targeted new data acquisition) and in silico experiments.

Simulating Healthy Participant Pharmacokinetics for Renal and Hepatic Impairment Studies: Retrospective Assessment of the Approach.

The recruitment of a parallel, healthy participants (HPs) arm in renal and hepatic impairment (RI and HI) studies is a common strategy to assess differences in pharmacokinetics. Limitations in this approach include the underpowered estimate of exposure differences and the use of the drug in a population for which there is no benefit. Recently, a method was published by Purohit et. al. (2023) that leveraged prior population pharmacokinetic (PopPK) modeling-based simulation to infer the distribution of exposure ratios between the RI/HI arms and HPs. The approach was successful, but it was a single example with a robust model having several iterations of development and fitting to extensive HP data. To test in more studies and models at different stages of development, our catalogue of RI/HI studies was searched, and those with suitable properties and from programs with available models were analyzed with the simulation approach. There were 9 studies included in the analysis. Most studies were associated with models that would have been available at the time (ATT) of the study, and all had a current, final model. For 3 studies, the HP PK was not predicted well by the ATT (2) or final (1) models. In comparison to conventional analysis of variance (ANOVA), the simulation approach provided similar point estimates and confidence intervals of exposure ratios. This PopPK based approach can be considered as a method of choice in situations where the simulation of HP data would not be an extrapolation, and when no other complicating factors are present.

Force/position tracking control of fracture reduction robot based on nonlinear disturbance observer and neural network.

BACKGROUND: For the fracture reduction robot, the position tracking accuracy and compliance are affected by dynamic loads from muscle stretching, uncertainties in robot dynamics models, and various internal and external disturbances. METHODS: A control method that integrates a Radial Basis Function Neural Network (RBFNN) with Nonlinear Disturbance Observer is proposed to enhance position tracking accuracy. Additionally, an admittance control is employed for force tracking to enhance the robot's compliance, thereby improving the safety. RESULTS: Experiments are conducted on a long bone fracture model with simulated muscle forces and the results demonstrate that the position tracking error is less than ±0.2 mm, the angular displacement error is less than ±0.3°, and the maximum force tracking error is 26.28 N. This result can meet surgery requirements. CONCLUSIONS: The control method shows promising outcomes in enhancing the safety and accuracy of long bone fracture reduction with robotic assistance.

Rethinking Exoskeleton Simulation-Based Design: The Effect of Using Different Cost Functions.

Designing an exoskeleton that can improve user capabilities is a challenging task, and most designs rely on experiments to achieve this goal. A different approach is to use simulation-based designs to determine optimal device parameters. Most of these simulations use full trajectory tracking limb kinematics during a natural gait as a reference. However, exoskeletons typically change the natural gait kinematics of the user. Other types of simulations assume that human gait is optimized for a cost function that combines several objectives, such as the cost of transport, injury prevention, and stabilization. In this study, we use a 2D OpenSim model consisting of 10 degrees of freedom and considering 18 muscles, together with the Moco optimization tool, to investigate the differences between these two approaches with respect to running with a passive knee exoskeleton. Utilizing this model, we test the effect of a full trajectory tracking objective with different weights (representing the importance of the objective in the optimization cost function) and show that when using weights that are typically used in the literature, there is no deviation from the experimental data. Next, we develop a multi-objective cost function with foot clearance term based on peak knee angle during swing, that achieves trajectories similar (RMSE=7.4 deg) to experimental running data. Finally, we investigate the effect of different parameters in the design of a clutch-based passive knee exoskeleton (1.5 kg at each leg) and find that a design that utilizes a 2.5 Nm/deg spring achieves an improvement of up to 8% in net metabolic energy. Our results show that tracking objectives in the cost function, even with a low weight, hinders the simulation's ability to change the gait trajectory. Thus, there is a need for other predictive simulation methods for exoskeletons.

Survival analysis for AdVerse events with VarYing follow-up times (SAVVY): summary of findings and assessment of existing guidelines.

BACKGROUND: The SAVVY project aims to improve the analyses of adverse events (AEs) in clinical trials through the use of survival techniques appropriately dealing with varying follow-up times and competing events (CEs). This paper summarizes key features and conclusions from the various SAVVY papers. METHODS: Summarizing several papers reporting theoretical investigations using simulations and an empirical study including randomized clinical trials from several sponsor organizations, biases from ignoring varying follow-up times or CEs are investigated. The bias of commonly used estimators of the absolute (incidence proportion and one minus Kaplan-Meier) and relative (risk and hazard ratio) AE risk is quantified. Furthermore, we provide a cursory assessment of how pertinent guidelines for the analysis of safety data deal with the features of varying follow-up time and CEs. RESULTS: SAVVY finds that for both, avoiding bias and categorization of evidence with respect to treatment effect on AE risk into categories, the choice of the estimator is key and more important than features of the underlying data such as percentage of censoring, CEs, amount of follow-up, or value of the gold-standard. CONCLUSIONS: The choice of the estimator of the cumulative AE probability and the definition of CEs are crucial. Whenever varying follow-up times and/or CEs are present in the assessment of AEs, SAVVY recommends using the Aalen-Johansen estimator (AJE) with an appropriate definition of CEs to quantify AE risk. There is an urgent need to improve pertinent clinical trial reporting guidelines for reporting AEs so that incidence proportions or one minus Kaplan-Meier estimators are finally replaced by the AJE with appropriate definition of CEs.

Optimal control strategies for toxoplasmosis disease transmission dynamics via harmonic mean-type incident rate.

Toxoplasma infection in humans is considered due to direct contact with infected cats. Toxoplasma infection (an endemic disease) has the potential to affect various organs and systems (brain, eyes, heart, lungs, liver, and lymph nodes). Bilinear incidence rate and constant population (birth rate is equal to death rate) are used in the literature to explain the dynamics of Toxoplasmosis disease transmission in humans and cats. The goal of this study is to consider the mathematical model of Toxoplasma disease with harmonic mean type incident rate and also consider that the population of humans and cats is not equal (birth rate and the death rate are not equal). In examining Toxoplasma transmission dynamics in humans and cats, harmonic mean incidence rates are better than bilinear incidence rates. The disease dynamics are first schematically illustrated, and then the law of mass action is applied to obtain nonlinear ordinary differential equations (ODEs). Analysis of the boundedness, positivity, and equilibrium points of the system has been analyzed. The reproduction number is calculated using the next-generation matrix technique. The stability of disease-free and endemic equilibrium are analyzed. Sensitivity analysis is also done for reproduction number. Numerical simulation shows that the infection is spread in the population when the contact rate ß h and ß c increases while the infection is reduced when the recovery rate δ h increases. This study investigates the impact of various optimal control strategies, such as vaccinations for the control of disease and the awareness of disease awareness, on the management of disease.

In-silico and in-vitro studies revealed alpha-amyrin as a potent pnhibitor of TLR2 for the therapeutics of bacterial infection and sepsis.

This study employed a multifaceted approach to investigate the inhibitory potential of alpha-amyrin against TLR2, a key player in bacterial infection and sepsis. A high-resolution TLR2 model was constructed using Swiss-MODEL, exhibiting excellent quality with 100% sequence identity and coverage. Cavity detection revealed five significant cavities on TLR2. Molecular docking identifies alpha-amyrin as a potent inhibitor, displaying a strong binding affinity of -8.6 kcal/mol. Comprehensive analyses, including ADMET predictions, PASS analysis, and SwissTargetPrediction, affirm alpha-amyrin's drug-like properties and diverse biological activities. Cytotoxicity assays on HEK-293 cells confirm its safety, and fluorescence-based inhibition assays provide empirical evidence of its inhibitory potency on TLR2 enzymatic activity. Further validations in HUVECs show a significant decrease in TLR2 mRNA expression (p<0.01) and activity (p<0.05) upon alpha-amyrin treatment. In conclusion, this integrative study positions alpha-amyrin as a promising therapeutic candidate for TLR2 inhibition, emphasizing its potential in combating bacterial infections with safety and efficacy.

Oscillations in Neuronal Activity: A Neuron-Centered Spatiotemporal Model of the Unfolded Protein Response in Prion Diseases.

Many neurodegenerative diseases (NDs) are characterized by the slow spatial spread of toxic protein species in the brain. The toxic proteins can induce neuronal stress, triggering the Unfolded Protein Response (UPR), which slows or stops protein translation and can indirectly reduce the toxic load. However, the UPR may also trigger processes leading to apoptotic cell death and the UPR is implicated in the progression of several NDs. In this paper, we develop a novel mathematical model to describe the spatiotemporal dynamics of the UPR mechanism for prion diseases. Our model is centered around a single neuron, with representative proteins P (healthy) and S (toxic) interacting with heterodimer dynamics (S interacts with P to form two S's). The model takes the form of a coupled system of nonlinear reaction-diffusion equations with a delayed, nonlinear flux for P (delay from the UPR). Through the delay, we find parameter regimes that exhibit oscillations in the P- and S-protein levels. We find that oscillations are more pronounced when the S-clearance rate and S-diffusivity are small in comparison to the P-clearance rate and P-diffusivity, respectively. The oscillations become more pronounced as delays in initiating the UPR increase. We also consider quasi-realistic clinical parameters to understand how possible drug therapies can alter the course of a prion disease. We find that decreasing the production of P, decreasing the recruitment rate, increasing the diffusivity of S, increasing the UPR S-threshold, and increasing the S clearance rate appear to be the most powerful modifications to reduce the mean UPR intensity and potentially moderate the disease progression.

Phytochemical investigation and characterisation of methanolic extract of Glycine max seeds using LCMS/MS and in silico studies for wound healing activity.

Soybean is scientifically known as Glycine max. It belongs to the Fabaceae family. It consists of a lot of bioactive phytochemicals like saponin, phenolic acid, flavonoid, sphingolipids and phytosterols. It also owns excellent immune-active effects in the physiological system. Soy and its phytochemicals have been found to have pharmacological properties that include anticancer, antioxidant, anti-hypercholesterolaemic, anti-diabetic, oestrogenic, anti-hyperlipidaemic, anti-inflammatory, anti-obesity, anti-hypertensive, anti-mutagenic, immunomodulatory, anti-osteoporotic, antiviral, hepatoprotective, antimicrobial, goitrogenic anti-skin ageing, wound healing, neuroprotective and anti-photoageing activities. Present study has been designed to set standard pharmacognostical extraction method, complexation of compounds, qualitative evaluation through phytochemical screening, identification by TLC, physicochemical properties, solubility profile, total phenolic, flavonoid content as well as analytical evaluation or characterisation like UV and FT-IR of methanolic extract of G. max. The final observations like physicochemical properties such as total ash value, LOD and pH were recorded. Phytochemical screenings show the presence of flavonoid, alkaloid, saponin, carbohydrate, tannins, protein, gums and mucilage, fixed oils and fats. The results were found significant. Further in silico studies proved creatinine and euparin to be potent wound healing agents.

On exact randomization-based covariate-adjusted confidence intervals.

Randomization-based inference using the Fisher randomization test allows for the computation of Fisher-exact P-values, making it an attractive option for the analysis of small, randomized experiments with non-normal outcomes. Two common test statistics used to perform Fisher randomization tests are the difference-in-means between the treatment and control groups and the covariate-adjusted version of the difference-in-means using analysis of covariance. Modern computing allows for fast computation of the Fisher-exact P-value, but confidence intervals have typically been obtained by inverting the Fisher randomization test over a range of possible effect sizes. The test inversion procedure is computationally expensive, limiting the usage of randomization-based inference in applied work. A recent paper by Zhu and Liu developed a closed form expression for the randomization-based confidence interval using the difference-in-means statistic. We develop an important extension of Zhu and Liu to obtain a closed form expression for the randomization-based covariate-adjusted confidence interval and give practitioners a sufficiency condition that can be checked using observed data and that guarantees that these confidence intervals have correct coverage. Simulations show that our procedure generates randomization-based covariate-adjusted confidence intervals that are robust to non-normality and that can be calculated in nearly the same time as it takes to calculate the Fisher-exact P-value, thus removing the computational barrier to performing randomization-based inference when adjusting for covariates. We also demonstrate our method on a re-analysis of phase I clinical trial data.

Incorporating nonparametric methods for estimating causal excursion effects in mobile health with zero-inflated count outcomes.

In mobile health, tailoring interventions for real-time delivery is of paramount importance. Micro-randomized trials have emerged as the "gold-standard" methodology for developing such interventions. Analyzing data from these trials provides insights into the efficacy of interventions and the potential moderation by specific covariates. The "causal excursion effect," a novel class of causal estimand, addresses these inquiries. Yet, existing research mainly focuses on continuous or binary data, leaving count data largely unexplored. The current work is motivated by the Drink Less micro-randomized trial from the UK, which focuses on a zero-inflated proximal outcome, i.e., the number of screen views in the subsequent hour following the intervention decision point. To be specific, we revisit the concept of causal excursion effect, specifically for zero-inflated count outcomes, and introduce novel estimation approaches that incorporate nonparametric techniques. Bidirectional asymptotics are established for the proposed estimators. Simulation studies are conducted to evaluate the performance of the proposed methods. As an illustration, we also implement these methods to the Drink Less trial data.

Detecting local perturbations of networks in a latent hyperbolic embedding space.

This paper introduces two novel scores for detecting local perturbations in networks. For this, we consider a non-Euclidean representation of networks, namely, their embedding onto the Poincaré disk model of hyperbolic geometry. We numerically evaluate the performances of these scores for the detection and localization of perturbations on homogeneous and heterogeneous network models. To illustrate our approach, we study latent geometric representations of real brain networks to identify and quantify the impact of epilepsy surgery on brain regions. Results suggest that our approach can provide a powerful tool for representing and analyzing changes in brain networks following surgical intervention, marking the first application of geometric network embedding in epilepsy research.

Chaos and bifurcations of a two-dimensional hepatitis C virus model with hepatocyte homeostasis.

In this paper, we delve into the intricate local dynamics at equilibria within a two-dimensional model of hepatitis C virus (HCV) alongside hepatocyte homeostasis. The study investigates the existence of bifurcation sets and conducts a comprehensive bifurcation analysis to elucidate the system's behavior under varying conditions. A significant focus lies on understanding how changes in parameters can lead to bifurcations, which are pivotal points where the qualitative behavior of the system undergoes fundamental transformations. Moreover, the paper introduces and employs hybrid control feedback and Ott-Grebogi-Yorke strategies as tools to manage and mitigate chaos inherent within the HCV model. This chaos arises due to the presence of flip and Neimark-Sacker bifurcations, which can induce erratic behavior in the system. Through the implementation of these control strategies, the study aims to stabilize the system and restore it to a more manageable and predictable state. Furthermore, to validate the theoretical findings and the efficacy of the proposed control strategies, extensive numerical simulations are conducted. These simulations serve as a means of confirming the theoretical predictions and provide insight into the practical implications of the proposed control methodologies. By combining theoretical analysis with computational simulations, the paper offers a comprehensive understanding of the dynamics of the HCV model and provides valuable insights into potential strategies for controlling and managing chaos in such complex biological systems.

Dental Versus Zygomatic Implants in the Treatment of Maxillectomy: A Finite Element Analysis.

This study analyzed the stress distributions on zygomatic and dental implants placed in the zygomatic bone, supporting bones, and superstructures under occlusal loads after maxillary reconstruction with obturator prostheses. A total of 12 scenarios of 3-dimensional finite element models were constructed based on computerized tomography scans of a hemimaxillectomy patient. Two obturator prostheses were analyzed for each model. A total force of 600 N was applied from the palatal to buccal bones at an angle of 45°. The maximum and minimum principal stress values for bone and von Mises stress values for dental implants and prostheses were calculated. When zygomatic implants were applied to the defect area, the maximum principal stresses were similar in intensity to the other models; however, the minimum principal stress values were higher than in scenarios without zygomatic implants. In models that used zygomatic implants in the defect area, von Mises stress levels were significantly higher in zygomatic implants than in dental implants. In scenarios where the prosthesis was supported by tissue in the nondefect area, the maximum and minimum principal stress values on cortical bone were higher than in scenarios where implants were applied to defect and nondefect areas. In patients who lack an alveolar crest after maxillectomy, a custom bar-retained prosthesis placed on the dental implant should reduce stress on the zygomatic bone. The stress was higher on zygomatic implants without alveolar crest support than on dental implants.

Aerodynamic Simulation of Small Airway Resistance: A New Imaging Biomarker for Chronic Obstructive Pulmonary Disease.

Purpose: To develop a novel method for calculating small airway resistance using computational fluid dynamics (CFD) based on CT data and evaluate its value to identify COPD. Patients and Methods: 24 subjects who underwent chest CT scans and pulmonary function tests between August 2020 and December 2020 were enrolled retrospectively. Subjects were divided into three groups: normal (10), high-risk (6), and COPD (8). The airway from the trachea down to the sixth generation of bronchioles was reconstructed by a 3D slicer. The small airway resistance (RSA) and RSA as a percentage of total airway resistance (RSA%) were calculated by CFD combined with airway resistance and FEV1 measured by pulmonary function test. A correlation analysis was conducted between RSA and pulmonary function parameters, including FEV1/FVC, FEV1% predicted, MEF50% predicted, MEF75% predicted and MMEF75/25% predicted. Results: The RSA and RSA% were significantly different among the three groups (p<0.05) and related to FEV1/FVC (r = -0.70, p < 0.001; r = -0.67, p < 0.001), FEV1% predicted (r = -0.60, p = 0.002; r = -0.57, p = 0.004), MEF50% predicted (r = -0.64, p = 0.001; r = -0.64, p = 0.001), MEF75% predicted (r = -0.71, p < 0.001; r = -0.60, p = 0.002) and MMEF 75/25% predicted (r = -0.64, p = 0.001; r = -0.64, p = 0.001). Conclusion: Airway CFD is a valuable method for estimating the small airway resistance, where the derived RSA will aid in the early diagnosis of COPD.

The effectiveness of intervention measures on MERS-CoV transmission by using the contact networks reconstructed from link prediction data.

Introduction: Mitigating the spread of infectious diseases is of paramount concern for societal safety, necessitating the development of effective intervention measures. Epidemic simulation is widely used to evaluate the efficacy of such measures, but realistic simulation environments are crucial for meaningful insights. Despite the common use of contact-tracing data to construct realistic networks, they have inherent limitations. This study explores reconstructing simulation networks using link prediction methods as an alternative approach. Methods: The primary objective of this study is to assess the effectiveness of intervention measures on the reconstructed network, focusing on the 2015 MERS-CoV outbreak in South Korea. Contact-tracing data were acquired, and simulation networks were reconstructed using the graph autoencoder (GAE)-based link prediction method. A scale-free (SF) network was employed for comparison purposes. Epidemic simulations were conducted to evaluate three intervention strategies: Mass Quarantine (MQ), Isolation, and Isolation combined with Acquaintance Quarantine (AQ + Isolation). Results: Simulation results showed that AQ + Isolation was the most effective intervention on the GAE network, resulting in consistent epidemic curves due to high clustering coefficients. Conversely, MQ and AQ + Isolation were highly effective on the SF network, attributed to its low clustering coefficient and intervention sensitivity. Isolation alone exhibited reduced effectiveness. These findings emphasize the significant impact of network structure on intervention outcomes and suggest a potential overestimation of effectiveness in SF networks. Additionally, they highlight the complementary use of link prediction methods. Discussion: This innovative methodology provides inspiration for enhancing simulation environments in future endeavors. It also offers valuable insights for informing public health decision-making processes, emphasizing the importance of realistic simulation environments and the potential of link prediction methods.

High-dimensional mediation analysis for continuous outcome with confounders using overlap weighting method in observational epigenetic study.

BACKGROUND: Mediation analysis is a powerful tool to identify factors mediating the causal pathway of exposure to health outcomes. Mediation analysis has been extended to study a large number of potential mediators in high-dimensional data settings. The presence of confounding in observational studies is inevitable. Hence, it's an essential part of high-dimensional mediation analysis (HDMA) to adjust for the potential confounders. Although the propensity score (PS) related method such as propensity score regression adjustment (PSR) and inverse probability weighting (IPW) has been proposed to tackle this problem, the characteristics with extreme propensity score distribution of the PS-based method would result in the biased estimation. METHODS: In this article, we integrated the overlapping weighting (OW) technique into HDMA workflow and proposed a concise and powerful high-dimensional mediation analysis procedure consisting of OW confounding adjustment, sure independence screening (SIS), de-biased Lasso penalization, and joint-significance testing underlying the mixture null distribution. We compared the proposed method with the existing method consisting of PS-based confounding adjustment, SIS, minimax concave penalty (MCP) variable selection, and classical joint-significance testing. RESULTS: Simulation studies demonstrate the proposed procedure has the best performance in mediator selection and estimation. The proposed procedure yielded the highest true positive rate, acceptable false discovery proportion level, and lower mean square error. In the empirical study based on the GSE117859 dataset in the Gene Expression Omnibus database using the proposed method, we found that smoking history may lead to the estimated natural killer (NK) cell level reduction through the mediation effect of some methylation markers, mainly including methylation sites cg13917614 in CNP gene and cg16893868 in LILRA2 gene. CONCLUSIONS: The proposed method has higher power, sufficient false discovery rate control, and precise mediation effect estimation. Meanwhile, it is feasible to be implemented with the presence of confounders. Hence, our method is worth considering in HDMA studies.

In silico prediction of polyketide biosynthetic gene clusters in the genomes of Hypericum-borne endophytic fungi.

BACKGROUND: The search for new bioactive natural compounds with anticancer activity is still of great importance. Even though their potential for diagnostics and treatment of cancer has already been proved, the availability is still limited. Hypericin, a naphthodianthrone isolated essentially from plant source Hypericum perforatum L. along with other related anthraquinones and bisanthraquinones belongs to this group of compounds. Although it has been proven that hypericin is synthesized by the polyketide pathway in plants, none of the candidate genes coding for key enzymes has been experimentally validated yet. Despite the rare occurrence of anthraquinones in plants, their presence in microorganisms, including endophytic fungi, is quite common. Unlike plants, several biosynthetic genes grouped into clusters (BGCs) in fungal endophytes have already been characterized. RESULTS: The aim of this work was to predict, identify and characterize the anthraquinone BGCs in de novo assembled and functionally annotated genomes of selected endophytic fungal isolates (Fusarium oxysporum, Plectosphaerella cucumerina, Scedosporium apiospermum, Diaporthe eres, Canariomyces subthermophilus) obtained from different tissues of Hypericum spp. The number of predicted type I polyketide synthase (PKS) BGCs in the studied genomes varied. The non-reducing type I PKS lacking thioesterase domain and adjacent discrete gene encoding protein with product release function were identified only in the genomes of C. subthermophilus and D. eres. A candidate bisanthraquinone BGC was predicted in C. subthermophilus genome and comprised genes coding the enzymes that catalyze formation of the basic anthraquinone skeleton (PKS, metallo-beta-lactamase, decarboxylase, anthrone oxygenase), putative dimerization enzyme (cytochrome P450 monooxygenase), other tailoring enzymes (oxidoreductase, dehydrogenase/reductase), and non-catalytic proteins (fungal transcription factor, transporter protein). CONCLUSIONS: The results provide an insight into genetic background of anthraquinone biosynthesis in Hypericum-borne endophytes. The predicted bisanthraquinone gene cluster represents a basis for functional validation of the candidate biosynthetic genes in a simple eukaryotic system as a prospective biotechnological alternative for production of hypericin and related bioactive anthraquinones.