Applications and nanotoxicity of carbon nanotubes and graphene in biomedicine

Owing to their unique mechanical, electrical, optical, and thermal properties, carbon nanostructures including carbon nanotubes and graphenes show great promise for advancing the fields of biology and medicine. Many reports have demonstrated the promise of these carbon nanostructures and their hybrid structures (composites with polymers, ceramics, and metal nanoparticles, etc.) for a variety of biomedical areas ranging from biosensing, drug delivery, and diagnostics, to cancer treatment, tissue engineering, and bioterrorism prevention. However, the issue of the safety and toxicity of these carbon nanostructures, which is vital to their use as diagnostic and therapeutic tools in biomedical fields, has not been completely resolved. This paper aims to provide a summary of the features of carbon nanotube and graphene-based materials and current research progress in biomedical applications. We also highlight the current opinions within the scientific community on the toxicity and safety of these carbon structures.

ZnO layers for opto-electronic applications from solution-based and low-temperature processing of an organometallic precursor

As printed and flexible plastic electronic gadgets become increasingly viable today, there is a need to develop materials that suit the fabrication processes involved. Two desirable requirements are solution-processable active materials or precursors and low-temperature processability. In this article, we describe a straightforward method of depositing ZnO films by simple spin coating of an organometallic diethylzinc precursor solution and annealing the resulting film at low temperatures (≤200 °C) without involving any synthetic steps. By controlling the humidity in which annealing is conducted, we are able to adjust the intrinsic doping level and carrier concentration in diethylzinc-derived ZnO. Doped or conducting transport layers are greatly preferable to undoped layers as they enable low-resistance contacts and minimize the potential drops. This ability to controllably realize doped ZnO is a key feature of the fabrication process that we describe in this article. We employ field-effect measurements as a diagnostic tool to measure doping levels and mobilities in ZnO and demonstrate that doped ZnO with high charge carrier concentration is ideal for solar cell applications. Respectable power conversion efficiencies (up to 4.5%) are achieved in inverted solar cells that incorporate diethylzinc-derived ZnO films as the electron transport layer and organic blends as the active material. Extensions of this approach to grow ternary and quaternary films with organometallic precursor chemicals will enable solution based growth of a number of semiconductor films as well as a method to dope them.

Cardiovascular diseases and vulnerable plaques: data, modeling, predictions and clinical applications PREFACE

Introduction Two symposia on “cardiovascular diseases and vulnerable plaques” Cardiovascular disease (CVD) is the leading cause of death worldwide. Huge effort has been made in many disciplines including medical imaging, computational modeling, bio- mechanics, bioengineering, medical devices, animal and clinical studies, population studies as well as genomic, molecular, cellular and organ-level studies seeking improved methods for early detection, diagnosis, prevention and treatment of these diseases [1-14]. However, the mechanisms governing the initiation, progression and the occurrence of final acute clinical CVD events are still poorly understood. A large number of victims of these dis- eases who are apparently healthy die suddenly without prior symptoms. Available screening and diagnostic methods are insufficient to identify the victims before the event occurs [8,9]. Most cardiovascular diseases are associated with vulnerable plaques. A grand challenge here is to develop new imaging techniques, predictive methods and patient screening tools to identify vulnerable plaques and patients who are more vulnerable to plaque rupture and associated clinical events such as stroke and heart attack, and recommend proper treatment plans to prevent those clinical events from happening. Articles in this special issue came from two symposia held recently focusing on “Cardio-vascular Diseases and Vulnerable Plaques: Data, Modeling, Predictions and Clinical Applications.” One was held at Worcester Polytechnic Institute (WPI), Worcester, MA, USA, July 13-14, 2014, right after the 7th World Congress of Biomechanics. This symposium was endorsed by the World Council of Biomechanics, and partially supported by a grant from NIH-National Institute of Biomedical Image and Bioengineering. The other was held at Southeast University (SEU), Nanjing, China, April 18-20, 2014.

Myotonic dystrophy type 2 (DM2) : Diagnostic methods and molecular pathology

Myotonic dystrophies type 1 (DM1) and type 2 (DM2) are the most common forms of muscular dystrophy affecting adults. They are autosomal dominant diseases caused by microsatellite tri- or tetranucleotide repeat expansion mutations in transcribed but not translated gene regions. The mutant RNA accumulates in nuclei disturbing the expression of several genes. The more recently identified DM2 disease is less well known, yet more than 300 patients have been confirmed in Finland thus far, and the true number is believed to be much higher. DM1 and DM2 share some features in general clinical presentation and molecular pathology, yet they show distinctive differences, including disease severity and differential muscle and fiber type involvement. However, the molecular differences underlying DM1 and DM2 muscle pathology are not well understood. Although the primary tissue affected is muscle, both DMs show a multisystemic phenotype due to wide expression of the mutation-carrying genes. DM2 is particularly intriguing, as it shows an incredibly wide spectrum of clinical manifestations. For this reason, it constitutes a real diagnostic challenge. The core symptoms in DM2 include proximal muscle weakness, muscle pain, myotonia, cataracts, cardiac conduction defects and endocrinological disturbations; however, none of these is mandatory for the disease. Myalgic pains may be the most disabling symptom for decades, sometimes leading to incapacity for work. In addition, DM2 may cause major socio-economical consequences for the patient, if not diagnosed, due to misunderstanding and false stigmatization. In this thesis work, we have (I) improved DM2 differential diagnostics based on muscle biopsy, and (II) described abnormalities in mRNA and protein expression in DM1 and DM2 patient skeletal muscles, showing partial differences between the two diseases, which may contribute to muscle pathology in these diseases. This is the first description of histopathological differences between DM1 and DM2, which can be used in differential diagnostics. Two novel high-resolution applications of in situ -hybridization have been described, which can be used for direct visualization of the DM2 mutation in muscle biopsy sections, or mutation size determination on extended DNA-fibers. By measuring protein and mRNA expression in the samples, differential changes in expression patterns affecting contractile proteins, other structural proteins and calcium handling proteins in DM2 compared to DM1 were found. The dysregulation at mRNA level was caused by altered transciption and abnormal splicing. The findings reported here indicate that the extent of aberrant splicing is higher in DM2 compared to DM1. In addition, the described abnormalities to some extent correlate to the differences in fiber type involvement in the two disorders.

Theranostic applications of fluorescent liquid crystalline nanoparticles

Lipid liquid crystalline nanoparticles can find application as nanocarriers in several fields of the daily life but, very likely, the pharmaceutical arena is the most relevant. Indeed, several problems encountered in drugs administration (e.g. critical sideeffects from antitumor drugs) require alternative, less invasive, but simultaneously efficient therapeutic routes to be explored. Novel fields of personalized nanomedicine are developing in this direction. One of the most interesting is theranostic, which calls for the design of platforms capable of combining therapeutic and diagnostic functionalities. In this optic, we explored the potential of monoolein-based cubosomes and hexosomes as nanocarriers for theranostic purposes. Our work focussed on the design of lipid nanoparticles able to deliver antineoplastic drugs and imaging probes for fluorescent optical in vitro and in vivo imaging. We developed cubosome formulations loaded with antineoplastic drugs and useful for the fluorescence imaging of cells. Such formulations were also actively targeted to cancer cells and coupled with a NIR-emitting fluorophore, which was the promise for in vivo applications. We also investigated hexosomes with encouraging results encapsulating in their lipid matrix a BODIPY derivative with solvatochromic properties, helpful for the understanding of the dye localization. Importantly, we reported (manuscript submitted) the first proof-of-principle for in vivo fluorescence optical imaging application using monoolein-based cubosomes in a healthy mouse animal model. Finally, since relatively little is known about the interaction of cubosomes with biological systems, their effects on lipid droplets, mitochondria and lipid profile of HeLa cells were deeply studied. This thesis is divided in two main parts. The introduction section reports on the essential background of the research field, and it is followed by the publications (published or submitted) resulting from these three years of work.

Computer-Based Diagnostic Systems: Computer-Based Troubleshooting

ISBN: 3-540-76198-5 (out of print)

Artefact detection and removal algorithms for EEG diagnostic systems

The electroencephalogram (EEG) is a medical technology that is used in the monitoring of the brain and in the diagnosis of many neurological illnesses. Although coarse in its precision, the EEG is a non-invasive tool that requires minimal set-up times, and is suitably unobtrusive and mobile to allow continuous monitoring of the patient, either in clinical or domestic environments. Consequently, the EEG is the current tool-of-choice with which to continuously monitor the brain where temporal resolution, ease-of- use and mobility are important. Traditionally, EEG data are examined by a trained clinician who identifies neurological events of interest. However, recent advances in signal processing and machine learning techniques have allowed the automated detection of neurological events for many medical applications. In doing so, the burden of work on the clinician has been significantly reduced, improving the response time to illness, and allowing the relevant medical treatment to be administered within minutes rather than hours. However, as typical EEG signals are of the order of microvolts (μV ), contamination by signals arising from sources other than the brain is frequent. These extra-cerebral sources, known as artefacts, can significantly distort the EEG signal, making its interpretation difficult, and can dramatically disimprove automatic neurological event detection classification performance. This thesis therefore, contributes to the further improvement of auto- mated neurological event detection systems, by identifying some of the major obstacles in deploying these EEG systems in ambulatory and clinical environments so that the EEG technologies can emerge from the laboratory towards real-world settings, where they can have a real-impact on the lives of patients. In this context, the thesis tackles three major problems in EEG monitoring, namely: (i) the problem of head-movement artefacts in ambulatory EEG, (ii) the high numbers of false detections in state-of-the-art, automated, epileptiform activity detection systems and (iii) false detections in state-of-the-art, automated neonatal seizure detection systems. To accomplish this, the thesis employs a wide range of statistical, signal processing and machine learning techniques drawn from mathematics, engineering and computer science. The first body of work outlined in this thesis proposes a system to automatically detect head-movement artefacts in ambulatory EEG and utilises supervised machine learning classifiers to do so. The resulting head-movement artefact detection system is the first of its kind and offers accurate detection of head-movement artefacts in ambulatory EEG. Subsequently, addtional physiological signals, in the form of gyroscopes, are used to detect head-movements and in doing so, bring additional information to the head- movement artefact detection task. A framework for combining EEG and gyroscope signals is then developed, offering improved head-movement arte- fact detection. The artefact detection methods developed for ambulatory EEG are subsequently adapted for use in an automated epileptiform activity detection system. Information from support vector machines classifiers used to detect epileptiform activity is fused with information from artefact-specific detection classifiers in order to significantly reduce the number of false detections in the epileptiform activity detection system. By this means, epileptiform activity detection which compares favourably with other state-of-the-art systems is achieved. Finally, the problem of false detections in automated neonatal seizure detection is approached in an alternative manner; blind source separation techniques, complimented with information from additional physiological signals are used to remove respiration artefact from the EEG. In utilising these methods, some encouraging advances have been made in detecting and removing respiration artefacts from the neonatal EEG, and in doing so, the performance of the underlying diagnostic technology is improved, bringing its deployment in the real-world, clinical domain one step closer.

Validation of Next Generation Sequencing Technologies in Comparison to Current Diagnostic Gold Standards for BRAF, EGFR and KRAS Mutational Analysis

Next Generation Sequencing (NGS) has the potential of becoming an important tool in clinical diagnosis and therapeutic decision-making in oncology owing to its enhanced sensitivity in DNA mutation detection, fast-turnaround of samples in comparison to current gold standard methods and the potential to sequence a large number of cancer-driving genes at the one time. We aim to test the diagnostic accuracy of current NGS technology in the analysis of mutations that represent current standard-of-care, and its reliability to generate concomitant information on other key genes in human oncogenesis. Thirteen clinical samples (8 lung adenocarcinomas, 3 colon carcinomas and 2 malignant melanomas) already genotyped for EGFR, KRAS and BRAF mutations by current standard-of-care methods (Sanger Sequencing and q-PCR), were analysed for detection of mutations in the same three genes using two NGS platforms and an additional 43 genes with one of these platforms. The results were analysed using closed platform-specific proprietary bioinformatics software as well as open third party applications. Our results indicate that the existing format of the NGS technology performed well in detecting the clinically relevant mutations stated above but may not be reliable for a broader unsupervised analysis of the wider genome in its current design. Our study represents a diagnostically lead validation of the major strengths and weaknesses of this technology before consideration for diagnostic use.

Two potential clinical applications of the alkaline single-cell gel electrophoresis assay .1. Human bladder washings and transitional cell carcinoma of the bladder .2. Human sperm and male infertility

Part 1: The alkaline single-cell gel electrophoresis (comet) assay was used to analyse the integrity and DNA content of exfoliated cells extracted from bladder washing specimens from 9 transitional cell carcinoma patients and 15 control patients. DNA damage, as expressed by % tail DNA and tail moment values, was observed to occur in cells from both control and bladder cancer samples. The extent of the damage was, however, found to be significantly greater in the cancer group than in the control group. Comet optical density values were also recorded for each cell analysed in the comet assay and although differences observed between tumour grades were not found to be statistically significant, the mean comet optical density value was observed to be greater in the cancer group than in the control population studied, These preliminary results suggest that the comet assay may have potential as a diagnostic tool and as a prognostic indicator in transitional cell carcinoma, Part 2: Baseline DNA damage in sperm cells from 13 normozoospermic fertile males, 17 normozoospermic infertile males and 11 asthenozoospermic infertile males were compared using a modified alkaline comet assay technique. No significant difference in the level of baseline DNA damage was observed between the 3 categories of sperm studied; however the untreated sperm cells were observed to display approximately 20% tail DNA. This is notably higher than the background DNA damage observed in somatic cells where the % tail DNA is normally less than 5%. Sperm from the 3 groups of men studied were also compared for sensitivity to DNA breakage, using the modified alkaline comet assay, following X-ray irradiations (5, 10 and 30 Gy) and hydrogen peroxide treatments (40, 100 and 200 mu M). Significant levels of X-ray-induced damage were found relative to untreated control sperm in the two infertile groups following 30 Gy irradiation. Significant damage in hydrogen peroxide-treated sperm was observed in sperm from fertile samples, at 200 mu M and in infertile samples at 100- and 200-mu M doses relative to controls. These results therefore indicate that fertile sperm samples are more resistant to X-ray- and hydrogen peroxide-induced DNA breakage than infertile samples. Further studies involving greater numbers of individuals are currently in progress to confirm these findings.

Next-generation sequencing: a change of paradigm in molecular diagnostic validation

Next-generation sequencing (NGS) is beginning to show its full potential for diagnostic and therapeutic applications. In particular, it is enunciating its capacity to contribute to a molecular taxonomy of cancer, to be used as a standard approach for diagnostic mutation detection, and to open new treatment options that are not exclusively organ-specific. If this is the case, how much validation is necessary and what should be the validation strategy, when bringing NGS into the diagnostic/clinical practice? This validation strategy should address key issues such as: what is the overall extent of the validation? Should essential indicators of test performance such as sensitivity of specificity be calculated for every target or sample type? Should bioinformatic interpretation approaches be validated with the same rigour? What is a competitive clinical turnaround time for a NGS-based test, and when does it become a cost-effective testing proposition? While we address these and other related topics in this commentary, we also suggest that a single set of international guidelines for the validation and use of NGS technology in routine diagnostics may allow us all to make a much more effective use of resources.

Electrical characterization of metal-oxide-polymer devices for non-volatile memory applications

The objective of this thesis is to study the properties of resistive switching effect based on bistable resistive memory which is fabricated in the form of Al2O3/polymer diodes and to contribute to the elucidation of resistive switching mechanisms. Resistive memories were characterized using a variety of electrical techniques, including current-voltage measurements, small-signal impedance, and electrical noise based techniques. All the measurements were carried out over a large temperature range. Fast voltage ramps were used to elucidate the dynamic response of the memory to rapid varying electric fields. The temperature dependence of the current provided insight into the role of trapped charges in resistive switching. The analysis of fast current fluctuations using electric noise techniques contributed to the elucidation of the kinetics involved in filament formation/rupture, the filament size and correspondent current capabilities. The results reported in this thesis provide insight into a number of issues namely: (i) The fundamental limitations on the speed of operation of a bi-layer resistive memory are the time and voltage dependences of the switch-on mechanism. (ii) The results explain the wide spread in switching times reported in the literature and the apparently anomalous behaviour of the high conductance state namely the disappearance of the negative differential resistance region at high voltage scan rates which is commonly attributed to a “dead time” phenomenon which had remained elusive since it was first reported in the ‘60s. (iii) Assuming that the current is filamentary, Comsol simulations were performed and used to explain the observed dynamic properties of the current-voltage characteristics. Furthermore, the simulations suggest that filaments can interact with each other. (iv) The current-voltage characteristics have been studied as a function of temperature. The findings indicate that creation and annihilation of filaments is controlled by filling and neutralizing traps localized at the oxide/polymer interface. (v) Resistive switching was also studied in small-molecule OLEDs. It was shown that the degradation that leads to a loss of light output during operation is caused by the presence of a resistive switching layer. A diagnostic tool that predicts premature failure of OLEDs was devised and proposed. Resistive switching is a property of oxides. These layers can grow in a number of devices including, organic light emitting diodes (OLEDs), spin-valve transistors and photovoltaic devices fabricated in different types of material. Under strong electric fields the oxides can undergo dielectric breakdown and become resistive switching layers. Resistive switching strongly modifies the charge injection causing a number of deleterious effects and eventually device failure. In this respect the findings in this thesis are relevant to understand reliability issues in devices across a very broad field.

Coronary Optical Coherence Tomography: A Practical Overview of Current Clinical Applications

Coronary optical coherence tomography has emerged as the most powerful in-vivo imaging modality to evaluate vessel structure in detail. It is a useful research tool that provides insights into the pathogenesis of coronary artery disease. This technology has an important clinical role that is still being developed. We review the evidence on the wide spectrum of potential clinical applications for coronary optical coherence tomography, which encompass the successive stages in coronary artery disease management: accurate lesion characterization and quantification of stenosis, guidance for the decision to perform percutaneous coronary intervention and subsequent planning, and evaluation of immediate and long-term results following intervention.

Monocouches peptidiques auto-assemblées et applications dans le domaine des biocapteurs de résonance de plasmon de surfaces

Ces travaux visent à étendre les applications de la résonance de plasmons de surface (SPR) L’objectif est d’offrir des outils diagnostics plus rapides, efficaces et simple d’utilisation pour diagnostiquer ou effectuer le suivi de conditions cliniques. Pour se faire, un nouveau type d’instrumentation SPR basé sur l’utilisation d’un prisme d’inversion (dove) a permis d’atteindre une limite de détection (LOD) de 10-6 unité d’indice de réfraction (RIU), une valeur comparable aux instruments commerciaux complexes tout en demeurant peu dispendieux, robuste et simple d’utilisation. Les travaux présentés dans cet ouvrage visent, dans un second temps, à réduire les interactions nonspécifiques (NSB) entre la surface des biocapteurs SPR et les composants de la matrice biologique complexe telles que: l’urine, le lysat cellulaire, le sérum et le sang. Ces dernières induisent des réponses empêchant l’utilisation de biocapteurs SPR en milieux complexes. Les acides aminés (AA) offrent une grande variété de propriétés physico-chimiques permettant la mise au point de monocouches auto-assemblées (SAM) aux propriétés diverses. Initialement, 19 des 20 acides aminés naturels ont été attachés à l’acide 3-mercaptopropionique (3-MPA) formant des SAMs peptidomimétiques. La quantité d’interactions nonspécifiques engendrées par ces différentes surfaces a été mesurée en exposant ces surfaces au sérum sanguin bovin complet variant de 400 ng/cm² jusqu’à 800 ng/cm². La détection à l’aide de ces surfaces de la β-lactamase (une enzyme responsable de la résistance aux antibiotiques au niveau μM) a démontré la possibilité d’employer ces surfaces pour bâtir des biocapteurs SPR. Des peptides de longueur allant de 2 à 5 résidus attachés à 3-MPA ont été synthétisés sur support solide. Cette étude a démontré que l’augmentation de la longueur des peptides formés d’AA résistants aux NBS accroit leur résistance jusqu’à 5 résidus. Le composé le plus performant de ce type (3-MPA-(Ser)5-OH) a permis d’atteindre 180 ng/cm². Cette valeur est similaire à celle des meilleures surfaces disponibles commercialement, notamment les surfaces de polyethylène glycol (PEG) à 100 ng/cm². Des surfaces de 3-MPA-(Ser)5-OH ont permis l’étalonnage de la β-lactamase et sa quantification directe dans un lysat cellulaire. La LOD pour ces biocapteurs est de 10 nM. Une troisième génération de surfaces peptidiques binaires a permis la réduction de la NSB jusqu’à un niveau de 23±10 ng/cm² une valeur comparable aux meilleures surfaces disponibles. Ces surfaces ont permis l’étalonnage d’un indicateur potentiel du cancer la metalloprotéinase-3 de matrice (MMP-3). Les surfaces formées de peptides binaires (3-MPA-H3D2-OH) ont permis la quantification directe de la MMP-3 dans le sérum sanguin complet. Une quatrième génération de surfaces peptidiques a permis de réduire davantage le niveau de NSB jusqu’à une valeur de 12 ± 11 ng/cm². Ces surfaces ont été modifiées en y attachant une terminaison de type acide nitriloacétique (NTA) afin d’y attacher des biomolécules marquées par six résidus histidines terminaux. Ces surfaces ont permis le développement d’une méthode rapide de balayage des ligands ciblant le « cluster of differenciation-36 » (CD36). L’étude d’électroformation des monocouches de peptide a permis de déterminer les conditions de formation optimales d’une couche de 3-MPA-HHHDD-OH permettant ainsi la formation de monocouches résistantes au NSB en moins de 6 minutes en appliquant un potentiel de formation de 200mV vs Ag/AgCl.

Statistiques appliquées en chirurgie cardiaque adulte : analyses de survie et applications du “propensity score”

L'objectif principal de ce travail est d’étudier en profondeur certaines techniques biostatistiques avancées en recherche évaluative en chirurgie cardiaque adulte. Les études ont été conçues pour intégrer les concepts d'analyse de survie, analyse de régression avec “propensity score”, et analyse de coûts. Le premier manuscrit évalue la survie après la réparation chirurgicale de la dissection aigüe de l’aorte ascendante. Les analyses statistiques utilisées comprennent : analyses de survie avec régression paramétrique des phases de risque et d'autres méthodes paramétriques (exponentielle, Weibull), semi-paramétriques (Cox) ou non-paramétriques (Kaplan-Meier) ; survie comparée à une cohorte appariée pour l’âge, le sexe et la race utilisant des tables de statistiques de survie gouvernementales ; modèles de régression avec “bootstrapping” et “multinomial logit model”. L'étude a démontrée que la survie s'est améliorée sur 25 ans en lien avec des changements dans les techniques chirurgicales et d’imagerie diagnostique. Le second manuscrit est axé sur les résultats des pontages coronariens isolés chez des patients ayant des antécédents d'intervention coronarienne percutanée. Les analyses statistiques utilisées comprennent : modèles de régression avec “propensity score” ; algorithme complexe d'appariement (1:3) ; analyses statistiques appropriées pour les groupes appariés (différences standardisées, “generalized estimating equations”, modèle de Cox stratifié). L'étude a démontrée que l’intervention coronarienne percutanée subie 14 jours ou plus avant la chirurgie de pontages coronariens n'est pas associée à des résultats négatifs à court ou long terme. Le troisième manuscrit évalue les conséquences financières et les changements démographiques survenant pour un centre hospitalier universitaire suite à la mise en place d'un programme de chirurgie cardiaque satellite. Les analyses statistiques utilisées comprennent : modèles de régression multivariée “two-way” ANOVA (logistique, linéaire ou ordinale) ; “propensity score” ; analyses de coûts avec modèles paramétriques Log-Normal. Des modèles d’analyse de « survie » ont également été explorés, utilisant les «coûts» au lieu du « temps » comme variable dépendante, et ont menés à des conclusions similaires. L'étude a démontrée que, après la mise en place du programme satellite, moins de patients de faible complexité étaient référés de la région du programme satellite au centre hospitalier universitaire, avec une augmentation de la charge de travail infirmier et des coûts.