Phage therapy: A software system for phage quantification and kinetic model inference.

One of the most serious problems of the modern medicine is the growing emergence of antibiotic resistance among pathogenic bacteria. In this circumstance, different and innovative approaches for treating infections caused by multidrug-resistant bacteria are imperatively required. Bacteriophage Therapy is one among the fascinating approaches to be taken into account. This consists of the use of bacteriophages, viruses that infect bacteria, in order to defeat specific bacterial pathogens. Phage therapy is not an innovative idea, indeed, it was widely used around the world in the 1930s and 1940s, in order to treat various infection diseases, and it is still used in Eastern Europe and the former Soviet Union. Nevertheless, Western scientists mostly lost interest in further use and study of phage therapy and abandoned it after the discovery and the spread of antibiotics. The advancement of scientific knowledge of the last years, together with the encouraging results from recent animal studies using phages to treat bacterial infections, and above all the urgent need for novel and effective antimicrobials, have given a prompt for additional rigorous researches in this field. In particular, in the laboratory of synthetic biology of the department of Life Sciences at the University of Warwick, a novel approach was adopted, starting from the original concept of phage therapy, in order to study a concrete alternative to antibiotics. The innovative idea of the project consists in the development of experimental methodologies, which allow to engineer a programmable synthetic phage system using a combination of directed evolution, automation and microfluidics. The main aim is to make “the therapeutics of tomorrow individualized, specific, and self-regulated” (Jaramillo, 2015). In this context, one of the most important key points is the Bacteriophage Quantification. Therefore, in this research work, a mathematical model describing complex dynamics occurring in biological systems involving continuous growth of bacteriophages, modulated by the performance of the host organisms, was implemented as algorithms into a working software using MATLAB. The developed program is able to predict different unknown concentrations of phages much faster than the classical overnight Plaque Assay. What is more, it gives a meaning and an explanation to the obtained data, making inference about the parameter set of the model, that are representative of the bacteriophage-host interaction.

Keller-Segel system, chemotaxis and applications to a mathematical model for Alzheimer's disease

In questa tesi viene presentato il modello di Keller-Segel per la chemiotassi, un sistema di tipo parabolico-ellittico che appare nella descrizione di molti fenomeni in ambito biologico e medico. Viene mostrata l'esistenza globale della soluzione debole del modello, per dati iniziali sufficientemente piccoli in dimensione N>2. La scelta di dati iniziali abbastanza grandi invece può causare il blow-up della soluzione e viene mostrato sotto quali condizioni questo si verifica. Infine il modello della chemiotassi è stato applicato per descrivere una fase della malattia di Alzheimer ed è stata effettuata un'analisi di stabilità del sistema.

The effects of a flexible visual acuity-driven ranibizumab treatment regimen in age-related macular degeneration: outcomes of a drug and disease model

Differences in treatment responses to ranibizumab injections observed within trials involving monthly (MARINA and ANCHOR studies) and quarterly (PIER study) treatment suggest that an individualized treatment regimen may be effective in neovascular age-related macular degeneration. In the present study, a drug and disease model was used to evaluate the impact of an individualized, flexible treatment regimen on disease progression.

An insulin infusion advisory system based on autotuning nonlinear model-predictive control

This paper aims at the development and evaluation of a personalized insulin infusion advisory system (IIAS), able to provide real-time estimations of the appropriate insulin infusion rate for type 1 diabetes mellitus (T1DM) patients using continuous glucose monitors and insulin pumps. The system is based on a nonlinear model-predictive controller (NMPC) that uses a personalized glucose-insulin metabolism model, consisting of two compartmental models and a recurrent neural network. The model takes as input patient's information regarding meal intake, glucose measurements, and insulin infusion rates, and provides glucose predictions. The predictions are fed to the NMPC, in order for the latter to estimate the optimum insulin infusion rates. An algorithm based on fuzzy logic has been developed for the on-line adaptation of the NMPC control parameters. The IIAS has been in silico evaluated using an appropriate simulation environment (UVa T1DM simulator). The IIAS was able to handle various meal profiles, fasting conditions, interpatient variability, intraday variation in physiological parameters, and errors in meal amount estimations.

Visual histological grading system for the evaluation of in vitro-generated neocartilage

Here we present the development of a visual evaluation system for routine assessment of in vitro-engineered cartilaginous tissue. Neocartilage was produced by culturing human articular chondrocytes in pellet culture systems or in a scaffold-free bioreactor system. All engineered tissues were embedded in paraffin and were sectioned and stained with Safranin O-fast green. The evaluation of each sample was broken into 3 categories (uniformity and intensity of Safranin O stain, distance between cells/amount of matrix produced, and cell morphology), and each category had 4 components with a score ranging from 0 to 3. Three observers evaluated each sample, and the new system was independently tested against an objective computer-based histomorphometry system. Pellets were also assessed biochemically for glycosaminoglycan (GAG) content. Pellet histology scores correlated significantly with GAG contents and were in agreement with the computer-based histomorphometry system. This system allows a valid and rapid assessment of in vitro-generated cartilaginous tissue that has a relevant association with objective parameters indicative of cartilage quality.

Behavioral and anatomical abnormalities in a sodium iodate-induced model of retinal pigment epithelium degeneration

We characterized changes in the visual behavior of mice in which a loss of the retinal pigment epithelium (RPE) was experimentally induced with intravenous (i.v.) administration of sodium iodate (NaIO3). We compared and correlated these changes with alterations in neural retinal structure and function. RPE loss was induced in 4-6 week old male C57BL/6 mice with an i.v. injection of 1% NaIO3 at three concentrations: 35, 50, or 70 mg/kg. At 1, 3, 7, 14, 21, and 28 days (d) as well as 6 months post injection (PI) a behavioral test was performed in previously trained mice to evaluate visual function. Eye morphology was then assessed for changes in both the RPE and neural retina. NaIO3-induced RPE degeneration was both dose and PI time dependent. Our low dose showed no effects, while our high dose caused the most damage, as did longer PI times at our intermediate dose. Using the intermediate dose, no changes were detectable in either visual behavior or retinal morphology at 1 d PI. However, at 3 d PI visual behavior became abnormal and patchy RPE cell loss was observed. From 7 d PI onward, changes in retinal morphology and visual behavior became more severe. At 6 months PI, no recovery was seen in any of these measures in mice administered the intermediate dose. These results show that NaIO3 dosage and/or time PI can be varied to produce different, yet permanent deficits in retinal morphology and visual function. Thus, this approach should provide a unique system in which the onset and severity of RPE damage, and its consequences can be manipulated. As such, it should be useful in the assessment of rescue or mitigating effects of retinal or stem cell transplantation on visual function.

Establishment of a novel intervertebral disc/endplate culture model: analysis of an ex vivo in vitro whole-organ rabbit culture system

STUDY DESIGN: Ex vivo in vitro study evaluating a novel intervertebral disc/endplate culture system. OBJECTIVES: To establish a whole-organ intervertebral disc culture model for the study of disc degeneration in vitro, including the characterization of basic cell and organ function. SUMMARY OF BACKGROUND DATA: With current in vivo models for the study of disc and endplate degeneration, it remains difficult to investigate the complex disc metabolism and signaling cascades. In contrast, more controlled but simplified in vitro systems using isolated cells or disc fragments are difficult to culture due to the unconstrained conditions, with often-observed cell death or cell dedifferentiation. Therefore, there is a demand for a controlled culture model with preserved cell function that offers the possibility to investigate disc and endplate pathologies in a structurally intact organ. METHODS: Naturally constrained intervertebral disc/endplate units from rabbits were cultured in multi-well plates. Cell viability, metabolic activity, matrix composition, and matrix gene expression profile were monitored using the Live/Dead cell viability test (Invitrogen, Basel, Switzerland), tetrazolium salt reduction (WST-8), proteoglycan and deoxyribonucleic acid quantification assays, and quantitative polymerase chain reaction. RESULTS: Viability and organ integrity were preserved for at least 4 weeks, while proteoglycan and deoxyribonucleic acid content decreased slightly, and matrix genes exhibited a degenerative profile with up-regulation of type I collagen and suppression of collagen type II and aggrecan genes. Additionally, cell metabolic activity was reduced to one third of the initial value. CONCLUSIONS: Naturally constrained intervertebral rabbit discs could be cultured for several weeks without losing cell viability. Structural integrity and matrix composition were retained. However, the organ responded to the artificial environment with a degenerative gene expression pattern and decreased metabolic rate. Therefore, the described system serves as a promising in vitro model to study disc degeneration in a whole organ.

Spastin in the human and mouse central nervous system with special reference to its expression in the hippocampus of mouse pilocarpine model of status epilepticus and temporal lobe epilepsy

In the present in situ hybridization and immunocytochemical studies in the mouse central nervous system (CNS), a strong expression of spastin mRNA and protein was found in Purkinje cells and dentate nucleus in the cerebellum, in hippocampal principal cells and hilar neurons, in amygdala, substantia nigra, striatum, in the motor nuclei of the cranial nerves and in different layers of the cerebral cortex except piriform and entorhinal cortices where only neurons in layer II were strongly stained. Spastin protein and mRNA were weakly expressed in most of the thalamic nuclei. In selected human brain regions such as the cerebral cortex, cerebellum, hippocampus, amygdala, substania nigra and striatum, similar results were obtained. Electron microscopy showed spastin immunopositive staining in the cytoplasma, dendrites, axon terminals and nucleus. In the mouse pilocarpine model of status epilepticus and subsequent temporal lobe epilepsy, spastin expression disappeared in hilar neurons as early as at 2h during pilocarpine induced status epilepticus, and never recovered. At 7 days and 2 months after pilocarpine induced status epilepticus, spastin expression was down-regulated in granule cells in the dentate gyrus, but induced expression was found in reactive astrocytes. The demonstration of widespread distribution of spastin in functionally different brain regions in the present study may provide neuroanatomical basis to explain why different neurological, psychological disorders and cognitive impairment occur in patients with spastin mutation. Down-regulation or loss of spastin expression in hilar neurons may be related to their degeneration and may therefore initiate epileptogenetic events, leading to temporal lobe epilepsy.

Hydrologic analysis of a limestone quarry using EPA's HELP Version 3.08 Model

Aggregates were historically a low cost commodity but with communities and governmental agencies reducing the amount of mining the cost is increasing dramatically. An awareness needs to be brought to communities that aggregate production is necessary for ensuring the existing infrastructure in today’s world. This can be accomplished using proven technologies in other areas and applying them to show how viable reclamation is feasible. A proposed mine reclamation, Douglas Township quarry (DTQ), in Dakota Township, MN was evaluated using Visual Hydrologic Evaluation of Landfill Performance (HELP) model. The HELP is commonly employed for estimating the water budget of a landfill, however, it was applied to determine the water budget of the DTQ following mining. Using an environmental impact statement as the case study, modeling predictions indicated the DTQ will adequately drain the water being put into the system. The height of the groundwater table will rise slightly due to the mining excavations but no ponding will occur. The application of HELP model determined the water budget of the DTQ and can be used as a viable option for mining companies to demonstrate how land can be reclaimed following mining operations.

A FIREWALL MODEL OF FILE SYSTEM SECURITY

File system security is fundamental to the security of UNIX and Linux systems since in these systems almost everything is in the form of a file. To protect the system files and other sensitive user files from unauthorized accesses, certain security schemes are chosen and used by different organizations in their computer systems. A file system security model provides a formal description of a protection system. Each security model is associated with specified security policies which focus on one or more of the security principles: confidentiality, integrity and availability. The security policy is not only about “who” can access an object, but also about “how” a subject can access an object. To enforce the security policies, each access request is checked against the specified policies to decide whether it is allowed or rejected. The current protection schemes in UNIX/Linux systems focus on the access control. Besides the basic access control scheme of the system itself, which includes permission bits, setuid and seteuid mechanism and the root, there are other protection models, such as Capabilities, Domain Type Enforcement (DTE) and Role-Based Access Control (RBAC), supported and used in certain organizations. These models protect the confidentiality of the data directly. The integrity of the data is protected indirectly by only allowing trusted users to operate on the objects. The access control decisions of these models depend on either the identity of the user or the attributes of the process the user can execute, and the attributes of the objects. Adoption of these sophisticated models has been slow; this is likely due to the enormous complexity of specifying controls over a large file system and the need for system administrators to learn a new paradigm for file protection. We propose a new security model: file system firewall. It is an adoption of the familiar network firewall protection model, used to control the data that flows between networked computers, toward file system protection. This model can support decisions of access control based on any system generated attributes about the access requests, e.g., time of day. The access control decisions are not on one entity, such as the account in traditional discretionary access control or the domain name in DTE. In file system firewall, the access decisions are made upon situations on multiple entities. A situation is programmable with predicates on the attributes of subject, object and the system. File system firewall specifies the appropriate actions on these situations. We implemented the prototype of file system firewall on SUSE Linux. Preliminary results of performance tests on the prototype indicate that the runtime overhead is acceptable. We compared file system firewall with TE in SELinux to show that firewall model can accommodate many other access control models. Finally, we show the ease of use of firewall model. When firewall system is restricted to specified part of the system, all the other resources are not affected. This enables a relatively smooth adoption. This fact and that it is a familiar model to system administrators will facilitate adoption and correct use. The user study we conducted on traditional UNIX access control, SELinux and file system firewall confirmed that. The beginner users found it easier to use and faster to learn then traditional UNIX access control scheme and SELinux.