Prediction of the Containment of HIV Infection by Antiretroviral Therapy - a Variable Structure Control Approach

It is demonstrated that the reachability paradigm from variable structure control theory is a suitable framework to monitor and predict the progression of the human immunodeficiency virus (HIV) infection following initiation of antiretroviral therapy (ART). A manifold is selected which characterises the infection-free steady-state. A model of HIV infection together with an associated reachability analysis is used to formulate a dynamical condition for the containment of HIV infection on the manifold. This condition is tested using data from two different HIV clinical trials which contain measurements of the CD4+ T cell count and HIV load in the peripheral blood collected from HIV infected individuals for the six month period following initiation of ART. The biological rates of the model are estimated using the multi-point identification method and data points collected in the initial period of the trial. Using the parameter estimates and the numerical solutions of the model, the predictions of the reachability analysis are shown to be consistent with the clinical diagnosis at the conclusion of the trial. The methodology captures the dynamical characteristics of eventual successful, failed and marginal outcomes. The findings evidence that the reachability analysis is an appropriate tool to monitor and develop personalised antiretroviral treatment

Occurrence of HIV eradication for preexposure prophylaxis treatment with a deterministic HIV model

The authors examine the human immunodeficiency virus (HIV) eradication in this study using a mathematical model and analyse the occurrence of virus eradication during the early stage of infection. To this end they use a deterministic HIV-infection model, modify it to describe the pharmacological dynamics of antiretroviral HIV drugs, and consider the clinical experimental results of preexposure prophylaxis HIV treatment. They also use numerical simulation to model the experimental scenario, thereby supporting the clinical results with a model-based explanation. The study results indicate that the protocol employed in the experiment can eradicate HIV in infected patients at the early stage of the infection

Management of bone defects with Bio-oss

Introduction: The defects in the alveolar bone might appear as a result of congenital malformations, traumatic injuries, periodontal disease, surgical traumas, chronic periapical changes and tumors from benign or malignant origin. The aim of this study was to provide solid and healthy area with application of Bio-Oss in the defect. Materials and methods: Based on the clinical diagnosisestablished by previously taken history, clinical examination and radiographic images oral-surgery interventions was made. To realize the aim of this work, augmentative material was implicated in the bone defects made in the patients after removal of follicular cyst, chronic periapical lesion, and parodontopathia. During the first and seventh day of the interventions, the patients have been followed through from aspect of possible development of local and general complications after the oral-surgery intervention. After period of one, three and six mount control x-ray was made. Results: Obtained results confirmed that: volume of the socket and defect of the bone was kept, fast revascularization was achieved, bone formation and slow resorption of the augmentative material was achieved, and period of normal healing without infection was also achieved. Conclusions: The augmentative materials used for treatment of bone defects besides their basic chemical and physical characteristics referring to their solubility in the body fluids, the transformation, modulation and resorption must be completely safe or secure, i.e. not to bring any risk of infection, immunological risk, physiological intolerance or inhibition of the process of restitutio ad integrum. In our study Bio-Oss was confirmed as augmentative material who had this characteristics. Keywords: bone defect, resorption of the bone, augmentative material, Bio-Os

A Knowledge-based Integrative Modeling Approach for <em>In-Silico</em> Identification of Mechanistic Targets in Neurodegeneration with Focus on Alzheimer’s Disease

Dementia is the progressive decline in cognitive function due to damage or disease in the body beyond what might be expected from normal aging. Based on neuropathological and clinical criteria, dementia includes a spectrum of diseases, namely Alzheimer's dementia, Parkinson's dementia, Lewy Body disease, Alzheimer's dementia with Parkinson's, Pick's disease, Semantic dementia, and large and small vessel disease. It is thought that these disorders result from a combination of genetic and environmental risk factors. Despite accumulating knowledge that has been gained about pathophysiological and clinical characteristics of the disease, no coherent and integrative picture of molecular mechanisms underlying neurodegeneration in Alzheimer’s disease is available. Existing drugs only offer symptomatic relief to the patients and lack any efficient disease-modifying effects. The present research proposes a knowledge-based rationale towards integrative modeling of disease mechanism for identifying potential candidate targets and biomarkers in Alzheimer’s disease. Integrative disease modeling is an emerging knowledge-based paradigm in translational research that exploits the power of computational methods to collect, store, integrate, model and interpret accumulated disease information across different biological scales from molecules to phenotypes. It prepares the ground for transitioning from ‘descriptive’ to “mechanistic” representation of disease processes. The proposed approach was used to introduce an integrative framework, which integrates, on one hand, extracted knowledge from the literature using semantically supported text-mining technologies and, on the other hand, primary experimental data such as gene/protein expression or imaging readouts. The aim of such a hybrid integrative modeling approach was not only to provide a consolidated systems view on the disease mechanism as a whole but also to increase specificity and sensitivity of the mechanistic model by providing disease-specific context. This approach was successfully used for correlating clinical manifestations of the disease to their corresponding molecular events and led to the identification and modeling of three important mechanistic components underlying Alzheimer’s dementia, namely the CNS, the immune system and the endocrine components. These models were validated using a novel in-silico validation method, namely biomarker-guided pathway analysis and a pathway-based target identification approach was introduced, which resulted in the identification of the MAPK signaling pathway as a potential candidate target at the crossroad of the triad components underlying disease mechanism in Alzheimer’s dementia

Meta-heuristic Strategies in Scientific Judgment

In the first half of this dissertation, I develop a heuristic methodology for analyzing scientific solutions to the problem of underdetermination. Heuristics are rough-and-ready procedures used by scientists to construct models, design experiments, interpret evidence, etc. But as powerful as they are, heuristics are also error-prone. Therefore, I argue that they key to prudently using a heuristic is the articulation of meta-heuristics---guidelines to the kinds of problems for which a heuristic is well- or ill-suited. Given that heuristics will introduce certain errors into our scientific investigations, I emphasize the importance of a particular category of meta-heuristics involving the search for robust evidence. Robustness is understood to be the epistemic virtue bestowed by agreement amongst multiple modes of determination. The more modes we have at our disposal, and the more these confirm the same result, the more confident can we be that a result is not a mere artifact of some heuristic simplification. Through an analysis of case-studies in the philosophy of biology and clinical trials, I develop a principled method for modeling and evaluating heuristics and robustness claims in a qualitative problem space. The second half of the dissertation deploys the heuristic methodology to address ethical and epistemological issues in the science of clinical trials. To that end, I develop a network model for the problem space of clinical research, capable of representing the various kinds of experiments, epistemic relationships, and ethical justifications intrinsic to the domain. I then apply this model to ongoing research with the antibacterial agent, moxifloxacin, for the treatment of tuberculosis, tracking its development from initially successful and promising in vitro and animal studies to its disappointing and discordant performance across five human efficacy trials. Given this failure to find a robust result with moxifloxacin across animal and human studies, what should researchers now do? While my final analysis of this case does not definitively answer that question, I demonstrate how my methodology, unlike a statistical meta-analysis, helps to clarify the directions for further research

New Insight into Cerebrovascular Diseases

“Brain circulation is a true road map that consists of large extended navigation territories and a number of unimagined and undiscovered routes.” Dr. Patricia Bozzetto Ambrosi This book combines an update on the review of cerebrovascular diseases in the form of textbook chapters, which has been carefully reviewed by Dr. Patricia Bozzetto Ambrosi, Drs. Rufai Ahmad and Auwal Abdullahi and Dr. Amit Agrawal, high-performance academic editors with extensive experience in neurodisciplines, including neurology, neurosurgery, neuroscience, and neuroradiology, covering the best standards of neurological practice involving basic and clinical aspects of cerebrovascular diseases. Each topic was carefully revised and prepared using smooth, structured vocabulary, plus superb graphics and scientific illustrations. In emphasizing the most common aspects of cerebrovascular diseases: stroke burden, pathophysiology, hemodynamics, diagnosis, management, repair, and healing, the book is comprehensive but concise and should become the standard reference guide for this neurological approach

QSAR model development for early stage screening of monoclonal antibody therapeutics to facilitate rapid developability

PhD ThesisMonoclonal antibodies (mAbs) and related therapeutics are highly desirable from a biopharmaceutical perspective as they are highly target specific and well tolerated within the human system. Nevertheless, several mAbs have been discontinued or withdrawn based either on their inability to demonstrate efficacy and/or due to adverse effects. With nearly 80% of drugs failing in clinical development mainly due to lack of efficacy and safety there arises an urgent need for better understanding of biological activity, affinity, pharmacology, toxicity, immunogenicity etc. thus leading to early prediction of success/failure. In this study a hybrid modelling framework was developed that enabled early stage screening of mAbs. The applicability of the experimental methods was first tested on chemical compounds to assess the assay quality following which they were used to assess potential off target adverse effects of mAbs. Furthermore, hypersensitivity reactions were assessed using Skimune™, a non-artificial human skin explants based assay for safety and efficacy assessment of novel compounds and drugs, developed by Alcyomics Ltd. The suitability of Skimune™ for assessing the immune related adverse effects of aggregated mAbs was studied where aggregation was induced using a heat stress protocol. The aggregates were characterised by protein analysis techniques such as analytical ultra-centrifugation following which the immunogenicity tested using Skimune™ assay. Numerical features (descriptors) of mAbs were identified and generated using ProtDCal, EMBOSS Pepstat software as well as amino acid scales for different. Five independent and novel X block datasets consisting of these descriptors were generated based on the physicochemical, electronic, thermodynamic, electronic and topological properties of amino acids: Domain, Window, Substructure, Single Amino Acid, and Running Sum. This study describes the development of a hybrid QSAR based model with a structured workflow and clear evaluation metrics, with several optimisation steps, that could be beneficial for broader and more generic PLS modelling. Based on the results and observation from this study, it was demonstrated incremental improvement via selection of datasets and variables help in further optimisation of these hybrid models. Furthermore, using hypersensitivity and cross reactivity as responses and physicochemical characteristics of mAbs as descriptors, the QSAR models generated for different applicability domains allow for rapid early stage screening and developability. These models were validated with external test set comprising of proprietary compounds from industrial partners, thus paving way for enhanced developability that tackles manufacturing failures as well as attrition rates.European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie actions grant agreemen

A Study of the Synergies Between Control Mechanisms in the Immune System and the Variable Structure Control Paradigm

This thesis argues that variable structure control theory finds application in immunology. The immune system maintains a healthy state by using feedback to switch on and off immune responses. Experimental and mathematical work has analysed the dynamics of the immune response of T cells, relatively little attention has been paid to examine the underlying control paradigm. Besides, in modelling and simulation studies, it is necessary to evaluate the impact of uncertainty and perturbations on immunological dynamics. This is important to deliver robust predictions and insights. These facts motivate considering variable structure control techniques to investigate the control strategy and robustness of the immune system in the context of immunity to infection and tolerance. The results indicate that the dynamic response of T cells following foreign or self-antigen stimulation behaves as a naturally occurring switched control law. Further, the reachability analysis from sliding mode control highlights dynamical conditions to assess the performance and robustness of the T cell response dynamics. Additionally, this approach delivers dynamical conditions for the containment of Human Immunodeficiency Virus (HIV) infection by the HIV-specific CD8+ T cell response and antiretroviral therapy by enforcing a sliding mode on a manifold associated with the infection-free steady-state. This condition for immunity reveals particular patterns for early diagnosis of eventual success, marginal and failure cases of antiretroviral therapy. Together, the findings in this thesis evidence that variable structure control theory presents a useful framework to study health and disease dynamics as well as to monitor the performance of treatment regimes

In vitro expanded human CD4+CD25+ regulatory T cells suppress effector T cell proliferation.

Regulatory T cells (Tregs) have been shown to be critical in the balance between autoimmunity and tolerance and have been implicated in several human autoimmune diseases. However, the small number of Tregs in peripheral blood limits their therapeutic potential. Therefore, we developed a protocol that would allow for the expansion of Tregs while retaining their suppressive activity. We isolated CD4+CD25 hi cells from human peripheral blood and expanded them in vitro in the presence of anti-CD3 and anti-CD28 magnetic Xcyte Dynabeads and high concentrations of exogenous Interleukin (IL)-2. Tregs were effectively expanded up to 200-fold while maintaining surface expression of CD25 and other markers of Tregs: CD62L, HLA-DR, CCR6, and FOXP3. The expanded Tregs suppressed proliferation and cytokine secretion of responder PBMCs in co-cultures stimulated with anti-CD3 or alloantigen. Treg expansion is a critical first step before consideration of Tregs as a therapeutic intervention in patients with autoimmune or graft-versus-host disease