A Projectile Concussive Impact Model Produces Neuroinflammation in Both Mild and Moderate-Severe Traumatic Brain Injury.

Traumatic brain injury (TBI) is a major cause of death and disability and is experienced by nearly 3 million people annually as a result of falls, vehicular accidents, or from being struck by or against an object. While TBIs can range in severity, the majority of injuries are considered to be mild. However, TBI of any severity has the potential to have long-lasting neurological effects, including headaches, cognitive/memory impairments, mood dysfunction, and fatigue as a result of neural damage and neuroinflammation. Here, we modified a projectile concussive impact (PCI) model of TBI to deliver a closed-head impact with variable severity dependent on the material of the ball-bearing projectile. Adult male Sprague Dawley rats were evaluated for neurobehavioral, neuroinflammatory, and neural damage endpoints both acutely and longer-term (up to 72 h) post-TBI following impact with either an aluminum or stainless-steel projectile. Animals that received TBI using the stainless-steel projectile exhibited outcomes strongly correlated to moderate-severe TBI, such as prolonged unconsciousness, impaired neurobehavior, increased risk for hematoma and death, as well as significant neuronal degeneration and neuroinflammation throughout the cortex, hippocampus, thalamus, and cerebellum. In contrast, rats that received TBI with the aluminum projectile exhibited characteristics more congruous with mild TBI, such as a trend for longer periods of unconsciousness in the absence of neurobehavioral deficits, a lack of neurodegeneration, and mild neuroinflammation. Moreover, alignment of cytokine mRNA expression from the cortex of these rats with a computational model of neuron-glia interaction found that the moderate-severe TBI produced by the stainless-steel projectile strongly associated with the neuroinflammatory state, while the mild TBI existed in a state between normal and inflammatory neuron-glia interactions. Thus, these modified PCI protocols are capable of producing TBIs that model the clinical and experimental manifestations associated with both moderate-severe and mild TBI producing relevant models for the evaluation of the potential underlying roles of neuroinflammation and other chronic pathophysiology in the long-term outcomes associated with TBI.

Fe3O4 supported UiO-66 (Zr) metal-organic framework for removal of drug contaminants from water: fuzzy logic modeling approach.

The increase in production and consumption of pharmaceuticals and personal care products causes environmental problems. In this study, naproxen and clofibric acid adsorption were studied using Fe3O4-supported UiO-66 (Zr) metal-organic framework (Mag-UiO-66). The adsorption processes were carried out in batch mode at pH value 3.0. The optimum adsorbent quantities, equilibrium periods, pseudo-first-order (PFO), pseudo-second-order (PSO), and intra-particles diffusion kinetic models were calculated. Non-linear Langmuir, Freundlich, Dubinin-Radushkevich (D-R), and Sips isotherm equations were applied to experimental data. Thermodynamic analyses of naproxen and clofibric acid adsorption were also carried out in this study. The Langmuir isotherm qm values were found as 14.15 mg/g for naproxen at 308 K and 41.87 mg/g for clofibric acid at 298 K. Both of the adsorption processes were exothermic. MISO (multi-input single-output) fuzzy logic models for removal of both naproxen and clofibric acid adsorptions were designed based on the experimental data to estimate the removal uptake values. It is noteworthy that the results obtained through designed fuzzy logic models matched well with the experimental data and the findings of this study emphasize the validity of designed fuzzy logic models.

Prediction of combination therapies based on topological modeling of the immune signaling network in multiple sclerosis.

BACKGROUND: Multiple sclerosis (MS) is a major health problem, leading to a significant disability and patient suffering. Although chronic activation of the immune system is a hallmark of the disease, its pathogenesis is poorly understood, while current treatments only ameliorate the disease and may produce severe side effects. METHODS: Here, we applied a network-based modeling approach based on phosphoproteomic data to uncover the differential activation in signaling wiring between healthy donors, untreated patients, and those under different treatments. Based in the patient-specific networks, we aimed to create a new approach to identify drug combinations that revert signaling to a healthy-like state. We performed ex vivo multiplexed phosphoproteomic assays upon perturbations with multiple drugs and ligands in primary immune cells from 169 subjects (MS patients, n=129 and matched healthy controls, n=40). Patients were either untreated or treated with fingolimod, natalizumab, interferon-ß, glatiramer acetate, or the experimental therapy epigallocatechin gallate (EGCG). We generated for each donor a dynamic logic model by fitting a bespoke literature-derived network of MS-related pathways to the perturbation data. Last, we developed an approach based on network topology to identify deregulated interactions whose activity could be reverted to a "healthy-like" status by combination therapy. The experimental autoimmune encephalomyelitis (EAE) mouse model of MS was used to validate the prediction of combination therapies. RESULTS: Analysis of the models uncovered features of healthy-, disease-, and drug-specific signaling networks. We predicted several combinations with approved MS drugs that could revert signaling to a healthy-like state. Specifically, TGF-ß activated kinase 1 (TAK1) kinase, involved in Transforming growth factor ß-1 proprotein (TGF-ß), Toll-like receptor, B cell receptor, and response to inflammation pathways, was found to be highly deregulated and co-druggable with all MS drugs studied. One of these predicted combinations, fingolimod with a TAK1 inhibitor, was validated in an animal model of MS. CONCLUSIONS: Our approach based on donor-specific signaling networks enables prediction of targets for combination therapy for MS and other complex diseases.

Assembling Disease Networks From Causal Interaction Resources.

The development of high-throughput high-content technologies and the increased ease in their application in clinical settings has raised the expectation of an important impact of these technologies on diagnosis and personalized therapy. Patient genomic and expression profiles yield lists of genes that are mutated or whose expression is modulated in specific disease conditions. The challenge remains of extracting from these lists functional information that may help to shed light on the mechanisms that are perturbed in the disease, thus setting a rational framework that may help clinical decisions. Network approaches are playing an increasing role in the organization and interpretation of patients' data. Biological networks are generated by connecting genes or gene products according to experimental evidence that demonstrates their interactions. Till recently most approaches have relied on networks based on physical interactions between proteins. Such networks miss an important piece of information as they lack details on the functional consequences of the interactions. Over the past few years, a number of resources have started collecting causal information of the type protein A activates/inactivates protein B, in a structured format. This information may be represented as signed directed graphs where physiological and pathological signaling can be conveniently inspected. In this review we will (i) present and compare these resources and discuss the different scope in comparison with pathway resources; (ii) compare resources that explicitly capture causality in terms of data content and proteome coverage (iii) review how causal-graphs can be used to extract disease-specific Boolean networks.

A Novel Hybrid Logic-ODE Modeling Approach to Overcome Knowledge Gaps.

Mathematical modeling allows using different formalisms to describe, investigate, and understand biological processes. However, despite the advent of high-throughput experimental techniques, quantitative information is still a challenge when looking for data to calibrate model parameters. Furthermore, quantitative formalisms must cope with stiffness and tractability problems, more so if used to describe multicellular systems. On the other hand, qualitative models may lack the proper granularity to describe the underlying kinetic processes. We propose a hybrid modeling approach that integrates ordinary differential equations and logical formalism to describe distinct biological layers and their communication. We focused on a multicellular system as a case study by applying the hybrid formalism to the well-known Delta-Notch signaling pathway. We used a differential equation model to describe the intracellular pathways while the cell-cell interactions were defined by logic rules. The hybrid approach herein employed allows us to combine the pros of different modeling techniques by overcoming the lack of quantitative information with a qualitative description that discretizes activation and inhibition processes, thus avoiding complexity.

Strategies to Enhance Logic Modeling-Based Cell Line-Specific Drug Synergy Prediction.

Discrete dynamical modeling shows promise in prioritizing drug combinations for screening efforts by reducing the experimental workload inherent to the vast numbers of possible drug combinations. We have investigated approaches to predict combination responses across different cancer cell lines using logic models generated from one generic prior-knowledge network representing 144 nodes covering major cancer signaling pathways. Cell-line specific models were configured to agree with baseline activity data from each unperturbed cell line. Testing against experimental data demonstrated a high number of true positive and true negative predictions, including also cell-specific responses. We demonstrate the possible enhancement of predictive capability of models by curation of literature knowledge further detailing subtle biologically founded signaling mechanisms in the model topology. In silico model analysis pinpointed a subset of network nodes highly influencing model predictions. Our results indicate that the performance of logic models can be improved by focusing on high-influence node protein activity data for model configuration and that these nodes accommodate high information flow in the regulatory network.

Optimizing Patient Experience in the Emergency Department.

Emergency department (ED) patient experience is a growing area of focus for leaders in the ED and throughout health care. While many factors intrinsic to the ED care environment add to the challenge of providing patients with an excellent experience, doing so holds many benefits, including improved patient compliance and health outcomes, improved workplace satisfaction and reduced provider and staff burnout, decreased malpractice risk, and increased revenue. Although wait time is a major driver of patient experience, provider and staff communication are critically important and excellent communication and perceived empathy may mitigate long waits, overcrowded environments, and other challenges.

Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies.

Mechanistic modeling of signaling pathways mediating patient-specific response to therapy can help to unveil resistance mechanisms and improve therapeutic strategies. Yet, creating such models for patients, in particular for solid malignancies, is challenging. A major hurdle to build these models is the limited material available that precludes the generation of large-scale perturbation data. Here, we present an approach that couples ex vivo high-throughput screenings of cancer biopsies using microfluidics with logic-based modeling to generate patient-specific dynamic models of extrinsic and intrinsic apoptosis signaling pathways. We used the resulting models to investigate heterogeneity in pancreatic cancer patients, showing dissimilarities especially in the PI3K-Akt pathway. Variation in model parameters reflected well the different tumor stages. Finally, we used our dynamic models to efficaciously predict new personalized combinatorial treatments. Our results suggest that our combination of microfluidic experiments and mathematical model can be a novel tool toward cancer precision medicine.

Data on fuzzy logic based-modelling and optimization of recovered lipid from microalgae.

This article presents the data of recovered lipid from microalgae using fuzzy logic based-modelling and particle swarm optimization (PSO) algorithm. The details of fuzzy model and optimization process were discussed in our work entitled "Application of Fuzzy Modelling and Particle Swarm Optimization to Enhance Lipid Extraction from Microalgae" (Nassef et al., 2019) [1]. The presented data are divided into two main parts. The first part represents the percentage of recovered lipid using fuzzy logic model and ANOVA. However, the second part shows the variation of the cost function (recovered lipid) for the 100 runs of PSO algorithm during optimization process. These data sets can be used as references to analyze the data obtained by any other optimization technique. The data sets are provided in the supplementary materials in Tables 1-2.

Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz.

The precision medicine paradigm is centered on therapies targeted to particular molecular entities that will elicit an anticipated and controlled therapeutic response. However, genetic alterations in the drug targets themselves or in genes whose products interact with the targets can affect how well a drug actually works for an individual patient. To better understand the effects of targeted therapies in patients, we need software tools capable of simultaneously visualizing patient-specific variations and drug targets in their biological context. This context can be provided using pathways, which are process-oriented representations of biological reactions, or biological networks, which represent pathway-spanning interactions among genes, proteins, and other biological entities. To address this need, we have recently enhanced the Reactome Cytoscape app, ReactomeFIViz, to assist researchers in visualizing and modeling drug and target interactions. ReactomeFIViz integrates drug-target interaction information with high quality manually curated pathways and a genome-wide human functional interaction network. Both the pathways and the functional interaction network are provided by Reactome, the most comprehensive open source biological pathway knowledgebase. We describe several examples demonstrating the application of these new features to the visualization of drugs in the contexts of pathways and networks. Complementing previous features in ReactomeFIViz, these new features enable researchers to ask focused questions about targeted therapies, such as drug sensitivity for patients with different mutation profiles, using a pathway or network perspective.

Robustness of Nutrient Signaling Is Maintained by Interconnectivity Between Signal Transduction Pathways.

Systems biology approaches provide means to study the interplay between biological processes leading to the mechanistic understanding of the properties of complex biological systems. Here, we developed a vector format rule-based Boolean logic model of the yeast S. cerevisiae cAMP-PKA, Snf1, and the Snf3-Rgt2 pathway to better understand the role of crosstalk on network robustness and function. We identified that phosphatases are the common unknown components of the network and that crosstalk from the cAMP-PKA pathway to other pathways plays a critical role in nutrient sensing events. The model was simulated with known crosstalk combinations and subsequent analysis led to the identification of characteristics and impact of pathway interconnections. Our results revealed that the interconnections between the Snf1 and Snf3-Rgt2 pathway led to increased robustness in these signaling pathways. Overall, our approach contributes to the understanding of the function and importance of crosstalk in nutrient signaling.

Fuzzy logic modeling of Pb (II) sorption onto mesoporous NiO/ZnCl2-Rosa Canina-L seeds activated carbon nanocomposite prepared by ultrasound-assisted co-precipitation technique.

In this study, NiO/Rosa Canina-L seeds activated carbon nanocomposite (NiO/ACNC) was prepared by adding dropwise NaOH solution (2mol/L) to raise the suspension pH to around 9 at room temperature under ultrasonic irradiation (200W) as an efficient method and characterized by FE-SEM, FTIR and N2 adsorption-desorption isotherm. The effect of different parameters such as contact time (0-120min), initial metal ion concentration (25-200mg/L), temperature (298, 318 and 333K), amount of adsorbent (0.002-0.007g) and the solution's initial pH (1-7) on the adsorption of Pb (II) was investigated in batch-scale experiments. The equilibrium data were well fitted by Langmuir model type 1 (R2>0.99). The maximum monolayer adsorption capacity (qm) of NiO/ACNC was 1428.57mg/L. Thermodynamic parameters (ΔG°, ΔH° and ΔS°) were also calculated. The results showed that the adsorption of Pb (II) onto NiO/ACNC was feasible, spontaneous and exothermic under studied conditions. In addition, a fuzzy-logic-based model including multiple inputs and one output was developed to predict the removal efficiency of Pb (II) from aqueous solution. Four input variables including pH, contact time (min), dosage (g) and initial concentration of Pb (II) were fuzzified using an artificial intelligence-based approach. The fuzzy subsets consisted of triangular membership functions with eight levels and a total of 26 rules in the IF-THEN approach which was implemented on a Mamdani-type of fuzzy inference system. Fuzzy data exhibited small deviation with satisfactory coefficient of determination (R2>0.98) that clearly proved very good performance of fuzzy-logic-based model in prediction of removal efficiency of Pb (II). It was confirmed that NiO/ACNC had a great potential as a novel adsorbent to remove Pb (II) from aqueous solution.

Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines.

In individuals, heterogeneous drug-response phenotypes result from a complex interplay of dose, drug specificity, genetic background, and environmental factors, thus challenging our understanding of the underlying processes and optimal use of drugs in the clinical setting. Here, we use mass-spectrometry-based quantification of molecular response phenotypes and logic modeling to explain drug-response differences in a panel of cell lines. We apply this approach to cellular cholesterol regulation, a biological process with high clinical relevance. From the quantified molecular phenotypes elicited by various targeted pharmacologic or genetic treatments, we generated cell-line-specific models that quantified the processes beneath the idiotypic intracellular drug responses. The models revealed that, in addition to drug uptake and metabolism, further cellular processes displayed significant pharmacodynamic response variability between the cell lines, resulting in cell-line-specific drug-response phenotypes. This study demonstrates the importance of integrating different types of quantitative systems-level molecular measurements with modeling to understand the effect of pharmacological perturbations on complex biological processes.

The Nursing Leadership Institute program evaluation: a critique.

A theory-driven program evaluation was conducted for a nursing leadership program, as a collaborative project between university faculty, the nurses' union, the provincial Ministry of Health, and its chief nursing officers. A collaborative logic model process was used to engage stakeholders, and mixed methods approaches were used to answer evaluation questions. Despite demonstrated, successful outcomes, the leadership program was not supported with continued funding. This paper examines what happened during the evaluation process: What factors failed to sustain this program?