Cooperative and reconfigurable telecommunication systems based on FPGA

This work has been realized by the author in his PhD course in Electronics, Computer Science and Telecommunication at the University of Bologna, Faculty of Engineering, Italy. The subject of this thesis regards important channel estimation aspects in wideband wireless communication systems, such as echo cancellation in digital video broadcasting systems and pilot aided channel estimation through an innovative pilot design in Multi-Cell Multi-User MIMO-OFDM network. All the documentation here reported is a summary of years of work, under the supervision of Prof. Oreste Andrisano, coordinator of Wireless Communication Laboratory - WiLab, in Bologna. All the instrumentation that has been used for the characterization of the telecommunication systems belongs to CNR (National Research Council), CNIT (Italian Inter-University Center), and DEIS (Dept. of Electronics, Computer Science, and Systems). From November 2009 to May 2010, the author spent his time abroad, working in collaboration with DOCOMO - Communications Laboratories Europe GmbH (DOCOMO Euro-Labs) in Munich, Germany, in the Wireless Technologies Research Group. Some important scientific papers, submitted and/or published on IEEE journals and conferences have been produced by the author.

New Synthetic Polyamines as Multi-Target-Directed Ligands for the Treatment of Alzheimer's Disease and Cancer: Design, Synthesis and Biological Evaluation

Alzheimer's disease (AD) and cancer represent two of the main causes of death worldwide. They are complex multifactorial diseases and several biochemical targets have been recognized to play a fundamental role in their development. Basing on their complex nature, a promising therapeutical approach could be represented by the so-called "Multi-Target-Directed Ligand" approach. This new strategy is based on the assumption that a single molecule could hit several targets responsible for the onset and/or progression of the pathology. In particular in AD, most currently prescribed drugs aim to increase the level of acetylcholine in the brain by inhibiting the enzyme acetylcholinesterase (AChE). However, clinical experience shows that AChE inhibition is a palliative treatment, and the simple modulation of a single target does not address AD aetiology. Research into newer and more potent anti-AD agents is thus focused on compounds whose properties go beyond AChE inhibition (such as inhibition of the enzyme β-secretase and inhibition of the aggregation of beta-amyloid). Therefore, the MTDL strategy seems a more appropriate approach for addressing the complexity of AD and may provide new drugs for tackling its multifactorial nature. In this thesis, it is described the design of new MTDLs able to tackle the multifactorial nature of AD. Such new MTDLs designed are less flexible analogues of Caproctamine, one of the first MTDL owing biological properties useful for the AD treatment. These new compounds are able to inhibit the enzymes AChE, beta-secretase and to inhibit both AChE-induced and self-induced beta-amyloid aggregation. In particular, the most potent compound of the series is able to inhibit AChE in subnanomolar range, to inhibit β-secretase in micromolar concentration and to inhibit both AChE-induced and self-induced beta-amyloid aggregation in micromolar concentration. Cancer, as AD, is a very complex pathology and many different therapeutical approaches are currently use for the treatment of such pathology. However, due to its multifactorial nature the MTDL approach could be, in principle, apply also to this pathology. Aim of this thesis has been the development of new molecules owing different structural motifs able to simultaneously interact with some of the multitude of targets responsible for the pathology. The designed compounds displayed cytotoxic activity in different cancer cell lines. In particular, the most potent compounds of the series have been further evaluated and they were able to bind DNA resulting 100-fold more potent than the reference compound Mitonafide. Furthermore, these compounds were able to trigger apoptosis through caspases activation and to inhibit PIN1 (preliminary result). This last protein is a very promising target because it is overexpressed in many human cancers, it functions as critical catalyst for multiple oncogenic pathways and in several cancer cell lines depletion of PIN1 determines arrest of mitosis followed by apoptosis induction. In conclusion, this study may represent a promising starting pint for the development of new MTDLs hopefully useful for cancer and AD treatment.

The role of interleuchin 6 (IL-6) in the promotion of an aggressive and stem cell-like phenotype in human breast cancer cells and in stem/progenitor cells expanded in vitro as mammospheres

High serum levels of Interleukin-6 (IL-6) correlate with poor outcome in breast cancer patients. However no data are available on the relationship between IL-6 and stem/progenitor cells which may fuel the genesis of breast cancer in vivo. Herein, we address this issue in mammospheres (MS), multi-cellular structures enriched in stem/progenitor cells of the mammary gland, and also in MCF-7 breast cancer cells. We show that MS from node invasive breast carcinoma tissues express IL-6 mRNA at higher levels than MS from matched non-neoplastic mammary glands. We find that IL-6 mRNA is detectable only in basal-like breast carcinoma tissues, an aggressive variant showing stem cell features. Our results reveal that IL-6 triggers a Notch-3-dependent up-regulation of the Notch ligand Jagged-1, whose interaction with Notch-3 promotes the growth of MS and MCF-7 derived spheroids. Moreover, IL-6 induces a Notch-3-dependent up-regulation of the carbonic anhydrase IX gene, which promotes a hypoxia-resistant/invasive phenotype in MCF-7 cells and MS. Finally, an autocrine IL-6 loop relies upon Notch-3 activity to sustain the aggressive features of MCF-7-derived hypoxia-selected cells. In conclusion, our data support the hypothesis that IL-6 induces malignant features in Notch-3 expressing, stem/progenitor cells from human ductal breast carcinoma and normal mammary gland.

Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.

Cell-free cryopreserved arterial allografts from multiorgan donors: a new strategy to fabricate artificial blood vessels suited for peripheral vascular surgery

Critical lower limb ischemia is a severe disease. A common approach is infrainguinal bypass. Synthetic vascular prosthesis, are good conduits in high-flow low-resistance conditions but have difficulty in their performance as small diameter vessel grafts. A new approach is the use of native decellularized vascular tissues. Cell-free vessels are expected to have improved biocompatibility when compared to synthetic and are optimal natural 3D matrix templates for driving stem cell growth and tissue assembly in vivo. Decellularization of tissues represent a promising field for regenerative medicine, with the aim to develop a methodology to obtain small-diameter allografts to be used as a natural scaffold suited for in vivo cell growth and pseudo-tissue assembly, eliminating failure caused from immune response activation. Material and methods. Umbilical cord-derived mesenchymal cells isolated from human umbilical cord tissue were expanded in advanced DMEM. Immunofluorescence and molecular characterization revealed a stem cell profile. A non-enzymatic protocol, that associate hypotonic shock and low-concentration ionic detergent, was used to decellularize vessel segments. Cells were seeded cell-free scaffolds using a compound of fibrin and thrombin and incubated in DMEM, after 4 days of static culture they were placed for 2 weeks in a flow-bioreactor, mimicking the cardiovascular pulsatile flow. After dynamic culture, samples were processed for histological, biochemical and ultrastructural analysis. Discussion. Histology showed that the dynamic culture cells initiate to penetrate the extracellular matrix scaffold and to produce components of the ECM, as collagen fibres. Sirius Red staining showed layers of immature collagen type III and ultrastructural analysis revealed 30 nm thick collagen fibres, presumably corresponding to the immature collagen. These data confirm the ability of cord-derived cells to adhere and penetrate a natural decellularized tissue and to start to assembly into new tissue. This achievement makes natural 3D matrix templates prospectively valuable candidates for clinical bypass procedures

Computational modelling of human stem cell-derived cardiomyocytes - Texture descriptors for biological image processing

This thesis investigates two distinct research topics. The main topic (Part I) is the computational modelling of cardiomyocytes derived from human stem cells, both embryonic (hESC-CM) and induced-pluripotent (hiPSC-CM). The aim of this research line lies in developing models of the electrophysiology of hESC-CM and hiPSC-CM in order to integrate the available experimental data and getting in-silico models to be used for studying/making new hypotheses/planning experiments on aspects not fully understood yet, such as the maturation process, the functionality of the Ca2+ hangling or why the hESC-CM/hiPSC-CM action potentials (APs) show some differences with respect to APs from adult cardiomyocytes. Chapter I.1 introduces the main concepts about hESC-CMs/hiPSC-CMs, the cardiac AP, and computational modelling. Chapter I.2 presents the hESC-CM AP model, able to simulate the maturation process through two developmental stages, Early and Late, based on experimental and literature data. Chapter I.3 describes the hiPSC-CM AP model, able to simulate the ventricular-like and atrial-like phenotypes. This model was used to assess which currents are responsible for the differences between the ventricular-like AP and the adult ventricular AP. The secondary topic (Part II) consists in the study of texture descriptors for biological image processing. Chapter II.1 provides an overview on important texture descriptors such as Local Binary Pattern or Local Phase Quantization. Moreover the non-binary coding and the multi-threshold approach are here introduced. Chapter II.2 shows that the non-binary coding and the multi-threshold approach improve the classification performance of cellular/sub-cellular part images, taken from six datasets. Chapter II.3 describes the case study of the classification of indirect immunofluorescence images of HEp2 cells, used for the antinuclear antibody clinical test. Finally the general conclusions are reported.

Methodologies for Synthesizable Programmable Devices based on Multi-Stage Switching Networks

Nowadays the rise of non-recurring engineering (NRE) costs associated with complexity is becoming a major factor in SoC design, limiting both scaling opportunities and the flexibility advantages offered by the integration of complex computational units. The introduction of embedded programmable elements can represent an appealing solution, able both to guarantee the desired flexibility and upgradabilty and to widen the SoC market. In particular embedded FPGA (eFPGA) cores can provide bit-level optimization for those applications which benefits from synthesis, paying on the other side in terms of performance penalties and area overhead with respect to standard cell ASIC implementations. In this scenario this thesis proposes a design methodology for a synthesizable programmable device designed to be embedded in a SoC. A soft-core embedded FPGA (eFPGA) is hence presented and analyzed in terms of the opportunities given by a fully synthesizable approach, following an implementation flow based on Standard-Cell methodology. A key point of the proposed eFPGA template is that it adopts a Multi-Stage Switching Network (MSSN) as the foundation of the programmable interconnects, since it can be efficiently synthesized and optimized through a standard cell based implementation flow, ensuring at the same time an intrinsic congestion-free network topology. The evaluation of the flexibility potentialities of the eFPGA has been performed using different technology libraries (STMicroelectronics CMOS 65nm and BCD9s 0.11μm) through a design space exploration in terms of area-speed-leakage tradeoffs, enabled by the full synthesizability of the template. Since the most relevant disadvantage of the adopted soft approach, compared to a hardcore, is represented by a performance overhead increase, the eFPGA analysis has been made targeting small area budgets. The generation of the configuration bitstream has been obtained thanks to the implementation of a custom CAD flow environment, and has allowed functional verification and performance evaluation through an application-aware analysis.

Aragonite-based scaffold for the treatment of knee osteochondral defects: results of a prospective multi-center trial at 2 years' follow-up

PURPOSE: To evaluate the clinical and MRI outcomes after the implantation of a nanostructured cell free aragonite-based scaffold in patients affected by knee chondral and osteochondral lesions. METHODS: 126 patients (94 men, 32 women; age 32.7±8.8 years) were included according to the following criteria: grade III or IV chondra/osteochondral lesions in the femoral condyles or throclea; 2) no limb axial deviation (i.e. varus or valgus knee > 5°); 3) no signs of knee instability; 4) no concurrent tibial or patellar chondral/osteochondral defects. All patients were treated by arthrotomic implantation of an aragonite based-scaffold by a press-fit technique. Patients were prospectively evaluated by IKDC, Tegner, Lysholm and KOOS scores preoperatively and then at 6, 12, 18 and 24-months follow-up. MRI was also performed to evaluate the amount of defect filling by regenerated cartilage. Failures were defined as the need for re-intervention in the index knee within the follow-up period. RESULTS: Average defect size was 2±1.3 cm2 and in most cases a single scaffold was used. A significant improvement in each clinical score was recorded from basal level to 24 months’ follow-up. In particular, the IKDC subjective score increased from 42.14±16 to 70.94±24.69 and the Tegner score improved from 2.95±1.90 to 4.82±1.85 (p<0.0005). Lysholm score and all the subscales of KOOS showed a similar trend over time. Age of the patient at implantation, size of the defect and BMI were correlated with lower clinical outcome. The presence of OA didn’t influence the clinical results. MRI evaluation showed a significant increase in defect filling over time, with the highest value reached at 24 months. Failures occurred in eleven patients (8.7%). CONCLUSION: The aragonite-based biomimetic osteochondral scaffold proved to be safe, and encouraging clinical and radiographic outcomes were documented up to 2 years’ follow-up.

Development of novel multi-substituted apatite nanophases with advanced functionalities for bone regeneration

In the field of bone substitutes is highly researched an innovative material able to fill gaps with high mechanical performances and able to stimulate cell response, permitting the complete restoration of the bone portion. In this respect, the synthesis of new bioactive materials able to mimic the compositional, morphological and mechanical features of bone is considered as the elective approach for effective tissue regeneration. Hydroxyapatite (HA) is the main component of the inorganic part of bone. Additionally ionic substitution can be performed in the apatite lattice producing different effects, depending from the selected ions. Magnesium, in substitution of calcium, and carbonate, in substitution of phosphate, extensively present in the biological bones, are able to improve properties naturally present in the apatitic phase, (i.e. biomimicry, solubility e osteoinductive properties). Other ions can be used to give new useful properties, like antiresorptive or antimicrobial properties, to the apatitic phase. This thesis focused on the development of hydroxyapatite nanophases with multiple ionic substitutions including gallium, or zinc ions, in association with magnesium and carbonate, with the purpose to provide double synergistic functionality as osteogenic and antibacterial biomaterial. Were developed bioactive materials based on Sr-substituted hydroxyapatite in the form of sintered targets. The obtained targets were treated with Pulsed Plasma Deposition (PED) resulting in the deposition of thin film coatings able to improve the roughness and wettability of PEEK, enhancing its osteointegrability. Were investigated heterogeneous gas-solid reactions, addressed to the biomorphic transformations of natural 3D porous structures into bone scaffolds with biomimetic composition and hierarchical organization, for application in load-bearing sites. The kinetics of the different reactions of the process were optimized to achieve complete and controlled phase transformation, maintaining the original 3-D morphology. Massive porous scaffolds made of ion-substituted hydroxyapatite and bone-mimicking structure were developed and tested in 3-D cell culture models.

Advanced cell culture platforms: methods for drug testing with microfluidics and microstructured devices

Advanced cell cultures are developing rapidly in biomedical research. Nowadays, various approaches and technologies are being used, however, these culturing systems present limitations from increasing complexity, requiring high costs, and not easily customization. We present two versatile and cost-effective methods for developing culturing systems that integrate 3D cell culture and microfluidic platforms. Firstly, for drug screening applications, many high-quality cell spheres of homogeneous size and shape are required. Conventional approaches usually have a dearth of control over the size and geometry of cell spheres and require sample collection and manipulation. To overcome this difficulty, in this study, hundreds of spheroids of several cell lines were generated using multi-well plates that housed our microdevices. Tumor spheroids grow at a uniform rate (in scaffolded or scaffold-free environments) and can be harvested at will. Microscopy imaging are done in real time during or after the culture. After in situ immunostaining, fluorescence imaging can be conducted while keeping the spatial distribution of spheroids in the microwells. Drug effects were successfully observed through viability, growth, and morphologic investigations. Also, we fabricated a microfluidic device suitable for directed and selective cell culture treatments. The microfluidic device was used to reproduce and confirm in vitro investigations carried out using normal culture methods, using a microglia cell line. The device layout and the syringe pump system, entirely designed in our lab, successfully allowed culture growth and medium flow regulation. Solution flows can be finely controlled, allowing treatments and immunofluorescence in one single chamber selectively. To conclude, we propose the development of two culturing platforms (microstructured well devices and in-flow microfluidic chip), which are the result of separate scientific investigations but have the primary goal of performing treatments in a reproducible manner. Our devices shall improve future studies on drug exposure testing, representing adjustable and versatile cell culture systems.