Improving glioma drug delivery: A multifaceted approach for glioma drug development.

Glioma is one of the most common central nervous system (CNS) cancers that can be found within the brain and the spinal cord. One of the pressing issues plaguing the development of therapeutics for glioma originates from the selective and semipermeable CNS membranes: the blood-brain barrier (BBB) and blood-spinal cord barrier (BSCB). It is difficult to bypass these membranes and target the desired cancerous tissue because the purpose of the BBB and BSCB is to filter toxins and foreign material from invading CNS spaces. There are currently four varieties of Food and Drug Administration (FDA)-approved drug treatment for glioma; yet these therapies have limitations including, but not limited to, relatively low transmission through the BBB/BSCB, despite pharmacokinetic characteristics that allow them to cross the barriers. Steps must be taken to improve the development of novel and repurposed glioma treatments through the consideration of pharmacological profiles and innovative drug delivery techniques. This review addresses current FDA-approved glioma treatments' gaps, shortcomings, and challenges. We then outline how incorporating computational BBB/BSCB models and innovative drug delivery mechanisms will help motivate clinical advancements in glioma drug delivery. Ultimately, considering these attributes will improve the process of novel and repurposed drug development in glioma and the efficacy of glioma treatment.

Simulating combined monoaminergic depletions in a PD animal model through a bio-constrained differential equations system.

Introduction: Historically, Parkinson's Disease (PD) research has focused on the dysfunction of dopamine-producing cells in the substantia nigra pars compacta, which is linked to motor regulation in the basal ganglia. Therapies have mainly aimed at restoring dopamine (DA) levels, showing effectiveness but variable outcomes and side effects. Recent evidence indicates that PD complexity implicates disruptions in DA, noradrenaline (NA), and serotonin (5-HT) systems, which may underlie the variations in therapy effects. Methods: We present a system-level bio-constrained computational model that comprehensively investigates the dynamic interactions between these neurotransmitter systems. The model was designed to replicate experimental data demonstrating the impact of NA and 5-HT depletion in a PD animal model, providing insights into the causal relationships between basal ganglia regions and neuromodulator release areas. Results: The model successfully replicates experimental data and generates predictions regarding changes in unexplored brain regions, suggesting avenues for further investigation. It highlights the potential efficacy of alternative treatments targeting the locus coeruleus and dorsal raphe nucleus, though these preliminary findings require further validation. Sensitivity analysis identifies critical model parameters, offering insights into key factors influencing brain area activity. A stability analysis underscores the robustness of our mathematical formulation, bolstering the model validity. Discussion: Our holistic approach emphasizes that PD is a multifactorial disorder and opens promising avenues for early diagnostic tools that harness the intricate interactions among monoaminergic systems. Investigating NA and 5-HT systems alongside the DA system may yield more effective, subtype-specific therapies. The exploration of multisystem dysregulation in PD is poised to revolutionize our understanding and management of this complex neurodegenerative disorder.

Numerical and computational analysis on a dissipative dynamical system: Slow invariant manifold for complex chemical mechanism.

This article presents the notion about Slow Invariant Manifold (SIM) and their fundamental role in model reduction techniques (MRTs) for challenges encountered in mechanical engineering within dissipative systems of chemical kinetics. Focusing on the reaction routes of complex mechanisms, we construct and compare primary approximations of the SIM through MRTs, including the Spectral Quasi Equilibrium Manifold (SQEM) and Intrinsic Low Dimensional Manifold (ILDM). These methods effectively transform high-dimensional complex problems into lower dimensions, solving them without compromising crucial information about the complex systems modified for homogeneous reactive systems. Employing the sensitivity analysis by using the MATLAB's toolbox, we present the numerical findings in a tabular format obtained through MRTs. This study provides the understanding about the accessible exploration of numerical solutions, improving insights of the complex variation within the system.

Understanding the effects of mineralization and structure on the mechanical properties of tendon-bone insertion using mesoscale computational modeling.

Tendon-bone fibrocartilaginous insertion, or enthesis, is a specialized interfacial region that connects tendon and bone, effectively transferring forces while minimizing stress concentrations. Previous studies have shown that insertion features gradient mineralization and branching fiber structure, which are believed to play critical roles in its excellent function. However, the specific structure-function relationship, particularly the effects of mineralization and structure at the mesoscale fiber level on the properties and function of insertion, remains poorly understood. In this study, we develop mesoscale computational models of the distinct fiber organization at tendon-bone insertions, capturing the branching network from tendon to interface fibers and the different mineralization scales. We specifically analyze three key descriptors: the mineralization scale of interface fibers, the mean, and relative standard deviation of the local branching angles of interface fibers. Tensile test simulations on insertion models with varying mineralization scales of interface fibers and structures are performed to mimic the primary loading condition applied to the insertion. We measure and analyze five representative mechanical properties: Young's modulus, strength, toughness, resilience, and failure strain. Our results reveal that mechanical properties are significantly influenced by the three key descriptors, with tradeoffs observed between mutually exclusive properties. For instance, strength and resilience plateau beyond a certain mineralization scale, while failure strain and Young's modulus exhibit monotonic decreasing and increasing trends, respectively. Consequently, there exists an optimal mineralization scale for toughness due to these tradeoffs. By analyzing the mesoscale deformation and failure mechanisms from simulation trajectories, we identify three fracture regimes closely related to the trends in mechanical properties, supporting the observed tradeoffs. Additionally, we examine in detail the effects of the mean and relative standard deviation of local branching angles on mechanical properties and deformation mechanisms. Overall, our study enhances the fundamental understanding of the composition-structure-function relationships at the tendon-bone insertion, complementing recent experimental studies. The mechanical insights from our work have the potential to guide the future biomimetic design of fibrillar adhesives and interfaces for joining soft and hard materials.

Systematic transcriptomic analysis and temporal modelling of human fibroblast senescence.

Cellular senescence is a diverse phenotype characterised by permanent cell cycle arrest and an associated secretory phenotype (SASP) which includes inflammatory cytokines. Typically, senescent cells are removed by the immune system, but this process becomes dysregulated with age causing senescent cells to accumulate and induce chronic inflammatory signalling. Identifying senescent cells is challenging due to senescence phenotype heterogeneity, and senotherapy often requires a combinatorial approach. Here we systematically collected 119 transcriptomic datasets related to human fibroblasts, forming an online database describing the relevant variables for each study allowing users to filter for variables and genes of interest. Our own analysis of the database identified 28 genes significantly up- or downregulated across four senescence types (DNA damage induced senescence (DDIS), oncogene induced senescence (OIS), replicative senescence, and bystander induced senescence) compared to proliferating controls. We also found gene expression patterns of conventional senescence markers were highly specific and reliable for different senescence inducers, cell lines, and timepoints. Our comprehensive data supported several observations made in existing studies using single datasets, including stronger p53 signalling in DDIS compared to OIS. However, contrary to some early observations, both p16 and p21 mRNA levels rise quickly, depending on senescence type, and persist for at least 8-11 days. Additionally, little evidence was found to support an initial TGFß-centric SASP. To support our transcriptomic analysis, we computationally modelled temporal protein changes of select core senescence proteins during DDIS and OIS, as well as perform knockdown interventions. We conclude that while universal biomarkers of senescence are difficult to identify, conventional senescence markers follow predictable profiles and construction of a framework for studying senescence could lead to more reproducible data and understanding of senescence heterogeneity.

A microscopic oxygen transport model for ultra-high dose rate radiotherapy in vivo: The impact of physiological conditions on FLASH effect.

BACKGROUND: Ultra-high dose rate irradiation (≥40 Gy/s, FLASH) has been shown to reduce normal tissue toxicity, while maintaining tumor control compared to conventional dose-rate radiotherapy. The radiolytic oxygen (O2) depletion (ROD) resulting from FLASH has been proposed to explain the normal tissue protection effect; however, in vivo experiments have not confirmed that FLASH induced global tissue hypoxia. Nonetheless, the experiments reported are based on volume-averaged measurement, which have inherent limitations in detecting microscopic phenomena, including the potential preservation of stem cells niches due to local FLASH-induced O2 depletion. Computational modeling offers a complementary approach to understand the ROD caused by FLASH at the microscopic level. PURPOSE: We developed a comprehensive model to describe the spatial and temporal dynamics of O2 consumption and transport in response to irradiation in vivo. The change of oxygen enhancement ratio (OER) was used to quantify and investigate the FLASH effect as a function of physiological and radiation parameters at microscopic scale. METHODS: We considered time-dependent O2 supply and consumption in a 3D cylindrical geometry, incorporating blood flow linking the O2 concentration ([O2]) in the capillary to that within the tissue through the Hill equation, radial and axial diffusion of O2, metabolic and zero-order radiolytic O2 consumption, and a pulsed radiation structure. Time-evolved distributions of [O2] were obtained by numerically solving perfusion-diffusion equations. The model enables the computation of dynamic O2 distribution and the relative change of OER (δROD) under various physiological and radiation conditions in vivo. RESULTS: Initial [O2] level and the subsequent changes during irradiation determined δROD distribution, which strongly depends on physiological parameters, i.e., intercapillary spacing, ultimately determining the tissue area with enhanced radioresistance. We observed that the δROD/FLASH effect is affected by and sensitive to the interplay effect among physiological and radiation parameters. It renders that the FLASH effect can be tissue environment dependent. The saturation of FLASH normal tissue protection upon dose and dose rate was shown. Beyond ∼60 Gy/s, no significant decrease in radiosensitivity within tissue region was observed. In turn, for a given dose rate, the change of radiosensitivity became saturated after a certain dose level. Pulse structures with the same dose and instantaneous dose rate but with different delivery times were shown to have distinguishable δROD thus tissue sparing, suggesting the average dose rate could be a metric assessing the FLASH effect and demonstrating the capability of our model to support experimental findings. CONCLUSION: On a macroscopic scale, the modeling results align with the experimental findings in terms of dose and dose rate thresholds, and it also indicates that pulse structure can vary the FLASH effect. At the microscopic level, this model enables us to examine the spatially resolved FLASH effect based on physiological and irradiation parameters. Our model thus provides a complementary approach to experimental methods for understanding the underlying mechanism of FLASH radiotherapy. Our results show that physiological conditions can potentially determine the FLASH efficacy in tissue protection. The FLASH effect may be observed under optimal combination of physiological parameters, not limited to radiation conditions alone.

(Mal)adaptive Mentalizing in the Cognitive Hierarchy, and Its Link to Paranoia.

Humans need to be on their toes when interacting with competitive others to avoid being taken advantage of. Too much caution out of context can, however, be detrimental and produce false beliefs of intended harm. Here, we offer a formal account of this phenomenon through the lens of Theory of Mind. We simulate agents of different depths of mentalizing within a simple game theoretic paradigm and show how, if aligned well, deep recursive mentalization gives rise to both successful deception as well as reasonable skepticism. However, we also show that if a self is mentalizing too deeply - hyper-mentalizing - false beliefs arise that a partner is trying to trick them maliciously, resulting in a material loss to the self. Importantly, we show that this is only true when hypermentalizing agents believe observed actions are generated intentionally. This theory offers a potential cognitive mechanism for suspiciousness, paranoia, and conspiratorial ideation. Rather than a deficit in Theory of Mind, paranoia may arise from the application of overly strategic thinking to ingenuous behaviour. Author Summary: Interacting competitively requires vigilance to avoid deception. However, excessive caution can have adverse effects, stemming from false beliefs of intentional harm. So far there is no formal cognitive account of what may cause this suspiciousness. Here we present an examination of this phenomenon through the lens of Theory of Mind - the cognitive ability to consider the beliefs, intentions, and desires of others. By simulating interacting computer agents we illustrate how well-aligned agents can give rise to successful deception and justified skepticism. Crucially, we also reveal that overly cautious agents develop false beliefs that an ingenuous partner is attempting malicious trickery, leading to tangible losses. As well as formally defining a plausible mechanism for suspiciousness, paranoia, and conspiratorial thinking, our theory indicates that rather than a deficit in Theory of Mind, paranoia may involve an over-application of strategy to genuine behaviour.

Computational account for the naturalness perception of others' jumping motion based on a vertical projectile motion model.

The visual naturalness of a rendered character's motion is an important factor in computer graphics work, and the rendering of jumping motions is no exception to this. However, the computational mechanism that underlies the observer's judgement of the naturalness of a jumping motion has not yet been fully elucidated. We hypothesized that observers would perceive a jumping motion as more natural when the jump trajectory was consistent with the trajectory of a vertical projectile motion based on Earth's gravity. We asked human participants to evaluate the naturalness of point-light jumping motions whose height and duration were modulated. The results showed that the observers' naturalness rating varied with the modulation ratios of the jump height and duration. Interestingly, the ratings were high even when the height and duration differed from the actual jump. To explain this tendency, we constructed computational models that predicted the theoretical trajectory of a jump based on the projectile motion formula and calculated the errors between the theoretical and observed trajectories. The pattern of the errors correlated closely with the participants' ratings. Our results suggest that observers judge the naturalness of observed jumping motion based on the error between observed and predicted jump trajectories.

A Subcortical Model for Auditory Forward Masking with Efferent Control of Cochlear Gain.

Previous physiological and psychophysical studies have explored whether feedback to the cochlea from the efferent system influences forward masking. The present work proposes that the limited growth-of-masking (GOM) observed in auditory nerve (AN) fibers may have been misunderstood; namely, that this limitation may be due to the influence of anesthesia on the efferent system. Building on the premise that the unanesthetized AN may exhibit GOM similar to more central nuclei, the present computational modeling study demonstrates that feedback from the medial olivocochlear (MOC) efferents may contribute to GOM observed physiologically in onset-type neurons in both the cochlear nucleus and inferior colliculus (IC). Additionally, the computational model of MOC efferents used here generates a decrease in masking with longer masker-signal delays similar to that observed in IC physiology and in psychophysical studies. An advantage of this explanation over alternative physiological explanations (e.g., that forward masking requires inhibition from the superior paraolivary nucleus) is that this theory can explain forward masking observed in the brainstem, early in the ascending pathway. For explaining psychoacoustic results, one strength of this model is that it can account for the lack of elevation in thresholds observed when masker level is randomly varied from interval-to-interval, a result that is difficult to explain using the conventional temporal window model of psychophysical forward masking. Future directions for evaluating the efferent mechanism as a contributing mechanism for psychoacoustic results are discussed.

A multi-network model of Parkinson's disease tremor: exploring the finger-dimmer-switch theory and role of dopamine in thalamic self-inhibition.

BACKGROUND: Tremor is a cardinal symptom of Parkinson's disease (PD) that manifests itself through complex oscillatory activity across multiple neuronal populations. According to the finger-dimmer-switch (FDS) theory, tremor is triggered by transient pathological activity in the basal ganglia-thalamo-cortical (BTC) network (the finger) and transitions into an oscillatory form within the inner circuitry of the thalamus (the switch). The cerebello-thalamo-cortical (CTC) network (the dimmer) is then involved in sustaining and amplifying tremor amplitude. In this study, we aimed to investigate the generation and progression dynamics of PD tremor oscillations by developing a comprehensive and interacting FDS model that transitions sequentially from healthy to PD to tremor and then to tremor-off state. Methods: We constructed a computational model consisting of 700 neurons in 11 regions of BTC, CTC, and thalamic networks. Transition from healthy to PD state was simulated through modulating dopaminergic synaptic connections; and further from PD to tremor and tremor-off by modulating projections between the thalamic reticular nucleus (TRN), anterior ventrolateral nucleus (VLa), and posterior ventrolateral nucleus (VLp). Results: Sustained oscillations in the frequency range of PD tremor emerged in thalamic VLp (5 Hz) and cerebellar dentate nucleus (3 Hz). Increasing self-inhibition in the thalamus through dopaminergic modulation significantly decreased tremor amplitude. Conclusion/Significance: Our results confirm the mechanistic power of the FDS theory in describing the PD tremor phenomenon and emphasize the role of dopaminergic modulation on thalamic self-inhibition. These insights pave the way for novel therapeutic strategies aimed at reducing the tremor by strengthening thalamic self-inhibition, particularly in dopamine-resistant patients.

m5c-iDeep: 5-Methylcytosine sites identification through deep learning.

5-Methylcytosine (m5c) is a modified cytosine base which is formed as the result of addition of methyl group added at position 5 of carbon. This modification is one of the most common PTM that used to occur in almost all types of RNA. The conventional laboratory methods do not provide quick reliable identification of m5c sites. However, the sequence data readiness has made it feasible to develop computationally intelligent models that optimize the identification process for accuracy and robustness. The present research focused on the development of in-silico methods built using deep learning models. The encoded data was then fed into deep learning models, which included gated recurrent unit (GRU), long short-term memory (LSTM), and bi-directional LSTM (Bi-LSTM). After that, the models were subjected to a rigorous evaluation process that included both independent set testing and 10-fold cross validation. The results revealed that LSTM-based model, m5c-iDeep, outperformed revealing 99.9 % accuracy while comparing with existing m5c predictors. In order to facilitate researchers, m5c-iDeep was also deployed on a web-based server which is accessible at https://taseersuleman-m5c-ideep-m5c-ideep.streamlit.app/.

Neural pathways associated with reduced rigidity during pallidal deep brain stimulation for Parkinson's disease.

Deep brain stimulation (DBS) of the internal segment of the globus pallidus (GPi) can markedly reduce muscle rigidity in people with Parkinson's disease (PD); however, the mechanisms mediating this effect are poorly understood. Computational modeling of DBS provides a method to estimate the relative contributions of neural pathway activations to changes in outcomes. In this study, we generated subject-specific biophysical models of GPi DBS (derived from individual 7-T MRI), including pallidal efferent, putamenal efferent, and internal capsule pathways, to investigate how activation of neural pathways contributed to changes in forearm rigidity in PD. Ten individuals (17 arms) were tested off medication under four conditions: off stimulation, on clinically optimized stimulation, and on stimulation specifically targeting the dorsal GPi or ventral GPi. Quantitative measures of forearm rigidity, with and without a contralateral activation maneuver, were obtained with a robotic manipulandum. Clinically optimized GPi DBS settings significantly reduced forearm rigidity (P < 0.001), which aligned with GPi efferent fiber activation. The model demonstrated that GPi efferent axons could be activated at any location along the GPi dorsal-ventral axis. These results provide evidence that rigidity reduction produced by GPi DBS is mediated by preferential activation of GPi efferents to the thalamus, likely leading to a reduction in excitability of the muscle stretch reflex via overdriving pallidofugal output.NEW & NOTEWORTHY Subject-specific computational models of pallidal deep brain stimulation, in conjunction with quantitative measures of forearm rigidity, were used to examine the neural pathways mediating stimulation-induced changes in rigidity in people with Parkinson's disease. The model uniquely included internal, efferent and adjacent pathways of the basal ganglia. The results demonstrate that reductions in rigidity evoked by deep brain stimulation were principally mediated by the activation of globus pallidus internus efferent pathways.

A biophysical model for dopamine modulating working memory through reward system in obsessive-compulsive disorder.

Dopamine modulates working memory in the prefrontal cortex (PFC) and is crucial for obsessive-compulsive disorder (OCD). However, the mechanism is unclear. Here we establish a biophysical model of the effect of dopamine (DA) in PFC to explain the mechanism of how high dopamine concentrations induce persistent neuronal activities with the network plunging into a deep, stable attractor state. The state develops a defect in working memory and tends to obsession and compulsion. Weakening the reuptake of dopamine acts on synaptic plasticity according to Hebbian learning rules and reward learning, which in turn affects the strength of neuronal synaptic connections, resulting in the tendency of compulsion and learned obsession. In addition, we elucidate the potential mechanisms of dopamine antagonists in OCD, indicating that dopaminergic drugs might be available for treatment, even if the abnormality is a consequence of glutamate hypermetabolism rather than dopamine. The theory highlights the significance of early intervention and behavioural therapies for obsessive-compulsive disorder. It potentially offers new approaches to dopaminergic pharmacotherapy and psychotherapy for OCD patients.

Computational study of associations between the synaptic conductance of STN and GPe and the development of Parkinson's disease.

There is evidence that the subthalamic nucleus (STN) and globus pallidus pars externa (GPe) involve in the development of Parkinson's disease, a neurodegenerative disorder characterized by motor and non-motor symptoms and loss of dopaminergic neurons in which the error index (EI) in firing patterns is widely used to address the related issues. Whether and how this interaction mechanism of STN and GPe affects EI in Parkinson's disease is uncertain. To account for this, we propose a kind of basal ganglia-thalamic network model associated with Parkinson's disease coupled with neurons, and investigate the effect of synaptic conductance of STN and GPe on EI in this network, as well as their internal relationship under EI as an index. The results show a relationship like a piecewise function between the error index and the slope of the state transition function of synaptic conductance from STN to GPe ( g snge ) and from GPe to STN ( g gesn ). And there is an approximate negative correlation between EI and g gesn . Increasing g snge and decreasing g gesn can improve the fidelity of thalamus information transmission and alleviate Parkinson's disease effectively. These obtained results can give some theoretical evidence that the abnormal synaptic releases of STN and GPe may be the symptoms of the development of Parkinson's disease, and further enrich the understanding of the pathogenesis and treatment mechanism of Parkinson's disease.

Evaluating the role of sex-related structure-function differences on airway aerosol transport and deposition.

Several experimental studies have found that females have higher deposition of particles in the airways compared with males. This has implications for the delivery of aerosolized therapeutics and for understanding sex differences in respiratory system response to environmental exposures. This study evaluates several factors that potentially contribute to sex differences in particle deposition, using scale-specific structure-function models of 1D ventilation distribution, particle transport, and deposition. The impact of gravity, inhalation flow rate, and dead space are evaluated in 12 structure-based models (seven female; five male). Females were found to have significantly higher total, bronchial, and alveolar deposition than males across a particle size range from 0.01 to 10 . Results suggest that higher deposition fraction in females is due to higher alveolar deposition for smaller particle sizes, and higher bronchial deposition for larger particles. Females had higher alveolar deposition in the lower lobes, and slightly lower particle concentration in the left upper lobe. Males were found to be more sensitive to changes due to gravity, showing greater reduction in bronchial deposition fraction. Males were also more sensitive to change in inhalation flow rate, and to scaling of dead space due to the larger male baseline airway size. Predictions of sex differences in particle deposition - that are consistent with the literature - suggest that sex-based characteristics of lung and airway size interacting with particle size gives rise to differences in regional deposition.

Viewpoint adaptation revealed potential representational differences between 2D images and 3D objects.

For convenience and experimental control, cognitive science has relied largely on images as stimuli rather than the real, tangible objects encountered in the real world. Recent evidence suggests that the cognitive processing of images may differ from real objects, especially in the processing of spatial locations and actions, thought to be mediated by the dorsal visual stream. Perceptual and semantic processing in the ventral visual stream, however, has been assumed to be largely unaffected by the realism of objects. Several studies have found that one key difference accounting for differences between real objects and images is actability; however, less research has investigated another potential difference - the three-dimensional nature of real objects as conveyed by cues like binocular disparity. To investigate the extent to which perception is affected by the realism of a stimulus, we compared viewpoint adaptation when stimuli (a face or a kettle) were 2D (flat images without binocular disparity) vs. 3D (i.e., real, tangible objects or stereoscopic images with binocular disparity). For both faces and kettles, adaptation to 3D stimuli induced stronger viewpoint aftereffects than adaptation to 2D images when the adapting orientation was rightward. A computational model suggested that the difference in aftereffects could be explained by broader viewpoint tuning for 3D compared to 2D stimuli. Overall, our finding narrowed the gap between understanding the neural processing of visual images and real-world objects by suggesting that compared to 2D images, real and simulated 3D objects evoke more broadly tuned neural representations, which may result in stronger viewpoint invariance.

Resolving artefacts in voltage-clamp experiments with computational modelling: an application to fast sodium current recordings.

Cellular electrophysiology is the foundation of many fields, from basic science in neurology, cardiology, oncology to safety critical applications for drug safety testing, clinical phenotyping, etc. Patch-clamp voltage clamp is the gold standard technique for studying cellular electrophysiology. Yet, the quality of these experiments is not always transparent, which may lead to erroneous conclusions for studies and applications. Here, we have developed a new computational approach that allows us to explain and predict the experimental artefacts in voltage-clamp experiments. The computational model captures the experimental procedure and its inadequacies, including: voltage offset, series resistance, membrane capacitance and (imperfect) amplifier compensations, such as series resistance compensation and supercharging. The computational model was validated through a series of electrical model cell experiments. Using this computational approach, the artefacts in voltage-clamp experiments of cardiac fast sodium current, one of the most challenging currents to voltage clamp, were able to be resolved and explained through coupling the observed current and the simulated membrane voltage, including some typically observed shifts and delays in the recorded currents. We further demonstrated that the typical way of averaging data for current-voltage relationships would lead to biases in the peak current and shifts in the peak voltage, and such biases can be in the same order of magnitude as those differences reported for disease-causing mutations. Therefore, the presented new computational pipeline will provide a new standard of assessing the voltage-clamp experiments and interpreting the experimental data, which may be able to rectify and provide a better understanding of ion channel mutations and other related applications.

A computational model for potential microbe-disease association detection based on improved graph convolutional networks and multi-channel autoencoders.

Introduction: Accumulating evidence shows that human health and disease are closely related to the microbes in the human body. Methods: In this manuscript, a new computational model based on graph attention networks and sparse autoencoders, called GCANCAE, was proposed for inferring possible microbe-disease associations. In GCANCAE, we first constructed a heterogeneous network by combining known microbe-disease relationships, disease similarity, and microbial similarity. Then, we adopted the improved GCN and the CSAE to extract neighbor relations in the adjacency matrix and novel feature representations in heterogeneous networks. After that, in order to estimate the likelihood of a potential microbe associated with a disease, we integrated these two types of representations to create unique eigenmatrices for diseases and microbes, respectively, and obtained predicted scores for potential microbe-disease associations by calculating the inner product of these two types of eigenmatrices. Results and discussion: Based on the baseline databases such as the HMDAD and the Disbiome, intensive experiments were conducted to evaluate the prediction ability of GCANCAE, and the experimental results demonstrated that GCANCAE achieved better performance than state-of-the-art competitive methods under the frameworks of both 2-fold and 5-fold CV. Furthermore, case studies of three categories of common diseases, such as asthma, irritable bowel syndrome (IBS), and type 2 diabetes (T2D), confirmed the efficiency of GCANCAE.

Design and comparison of computationally efficient uniaxial stress-strain models of the lung parenchyma for real-time applications.

Real-time clinical applications such as robotic lung surgery, tumor localization, atelectasis diagnosis, tumor motion prediction for radiation therapy of lung cancer, or surgery training are in need of biomechanical models of lungs, not necessarily highly accurate, but with good computational properties. These properties can include one or several of the following: low computation time, low memory resource requirement, a low number of parameters, and ease of parameter identification in real-time. Among the numerous existing models of lung parenchyma, some may be well suited for real-time applications; however, they should be extensively assessed against both accuracy and computational efficiency criteria to make an informed choice depending on the requirements of the application. After demonstrating how to derive a real-time compliant force-indentation model from a unixial stress-strain model with rational expression, the core purpose of this paper is to propose such an evaluation of selected models in fitting human lung parenchyma experimental and synthetic data of uniaxial tension. Furthermore, new uniaxial stress-strain models are developed based on an empirical observation of the volumetric behavior of the lungs along with an emphasis on computational performance. These new proposed models are competitive with existing one in terms of computational efficiency and compliance with experimental and synthetic data. One of them reduces the prediction error by 2 compared to other investigated models while maintaining an excellent adjusted coefficient of determination between 0.999 and 1 across various datasets. It exhibits excellent real-time capabilities with an explicit rational expression, only 3 parameters and linear numerator and denominator in the parameters. It is computed with only 20 floating point operations (flops) while another proposed model even requires as few as 2 flops.

An Insight into Perfusion Anisotropy within Solid Murine Lung Cancer Tumors.

Blood vessels are essential for maintaining tumor growth, progression, and metastasis, yet the tumor vasculature is under a constant state of remodeling. Since the tumor vasculature is an attractive therapeutic target, there is a need to predict the dynamic changes in intratumoral fluid pressure and velocity that occur across the tumor microenvironment (TME). The goal of this study was to obtain insight into perfusion anisotropy within lung tumors. To achieve this goal, we used the perfusion marker Hoechst 33342 and vascular endothelial marker CD31 to stain tumor sections from C57BL/6 mice harboring Lewis lung carcinoma tumors on their flank. Vasculature, capillary diameter, and permeability distribution were extracted at different time points along the tumor growth curve. A computational model was generated by applying a unique modeling approach based on the smeared physical fields (Kojic Transport Model, KTM). KTM predicts spatial and temporal changes in intratumoral pressure and fluid velocity within the growing tumor. Anisotropic perfusion occurs within two domains: capillary and extracellular space. Anisotropy in tumor structure causes the nonuniform distribution of pressure and fluid velocity. These results provide insights regarding local vascular distribution for optimal drug dosing and delivery to better predict distribution and duration of retention within the TME.