Activity and mechanisms of action of novel organosulfur derivatives of the HDAC inhibitor Valproic Acid in human experimental models of non-small-cell lung cancer

Non-small-cell lung cancer (NSCLC) represents the leading cause of cancer death worldwide, and 5-year survival is about 16% for patients diagnosed with advanced lung cancer and about 70-90% when the disease is diagnosed and treated at earlier stages. Treatment of NSCLC is changed in the last years with the introduction of targeted agents, such as gefitinib and erlotinib, that have dramatically changed the natural history of NSCLC patients carrying specific mutations in the EGFR gene, or crizotinib, for patients with the EML4-ALK translocation. However, such patients represent only about 15-20% of all NSCLC patients, and for the remaining individuals conventional chemotherapy represents the standard choice yet, but response rate to thise type of treatment is only about 20%. Development of new drugs and new therapeutic approaches are so needed to improve patients outcome. In this project we aimed to analyse the antitumoral activity of two compounds with the ability to inhibit histone deacethylases (ACS 2 and ACS 33), derived from Valproic Acid and conjugated with H2S, in human cancer cell lines derived from NSCLC tissues. We showed that ACS 2 represents the more promising agent. It showed strong antitumoral and pro-apoptotic activities, by inducing membrane depolarization, cytocrome-c release and caspase 3 and 9 activation. It was able to reduce the invasive capacity of cells, through inhibition of metalloproteinases expression, and to induce a reduced chromatin condensation. This last characteristic is probably responsible for the observed high synergistic activity in combination with cisplatin. In conclusion our results highlight the potential role of the ACS 2 compound as new therapeutic option for NSCLC patients, especially in combination with cisplatin. If validated in in vivo models, this compound should be worthy for phase I clinical trials.

Patterns in and kinetics of phase separation in binary mixtures

This work focused mainly on two aspects of kinetics of phase separation in binary mixtures. In the first part, we studied the interplay of hydrodynamics and the phase separation of binary mixtures. A considerably flat container (a laterally extended geometry), at an aspect ratio of 14:1 (diameter: height) was chosen, so that any hydrodynamic instabilities, if they arise, could be tracked. Two binary mixtures were studied. One was a mixture of methanol and hexane, doped with 5% ethanol, which phase separated under cooling. The second was a mixture of butoxyethanol and water, doped with 2% decane, which phase separated under heating. The dopants were added to bring down the phase transition temperature around room temperature.rnrnAlthough much work has been done already on classical hydrodynamic instabilities, not much has been done in the understanding of the coupling between phase separation and hydrodynamic instabilities. This work aimed at understanding the influence of phase separation in initiating any hydrodynamic instability, and also vice versa. Another aim was to understand the influence of the applied temperature protocol on the emergence of patterns characteristic to hydrodynamic instabilities. rnrnOn slowly cooling the system continuously, at specific cooling rates, patterns were observed in the first mixture, at the start of phase separation. They resembled the patterns observed in classical Rayleigh-Bénard instability, which arises when a liquid continuously is heated from below. To suppress this classical convection, the cooling setup was tuned such that the lower side of the sample always remained cooler by a few millikelvins, relative to the top. We found that the nature of patterns changed with different cooling rates, with stable patterns appearing for a specific cooling rate (1K/h). On the basis of the cooling protocol, we estimated a modified Rayleigh number for our system. We found that the estimated modified Rayleigh number is near the critical value for instability, for cooling rates between 0.5K/h and 1K/h. This is consistent with our experimental findings. rnrnThe origin of the patterns, in spite of the lower side being relatively colder with respect to the top, points to two possible reasons. 1) During phase separation droplets of either phases are formed, which releases a latent heat. Our microcalorimetry measurements show that the rise in temperature during the first phase separation is in the order of 10-20millikelvins, which in some cases is enough to reverse the applied temperature bias. Thus phase separation in itself initiates a hydrodynamic instability. 2) The second reason comes from the cooling protocol itself. The sample was cooled from above and below. At sufficiently high cooling rates, there are situations where the interior of the sample is relatively hotter than both top and bottom of the sample. This is sufficient to create an instability within the cell. Our experiments at higher cooling rates (5K/h and above) show complex patterns, which hints that there is enough convection even before phase separation occurs. Infact, theoretical work done by Dr.Hayase show that patterns could arise in a system without latent heat, with symmetrical cooling from top and bottom. The simulations also show that the patterns do not span the entire height of the sample cell. This is again consistent with the cell sizes measured in our experiment.rnrnThe second mixture also showed patterns at specific heating rates, when it was continuously heated inducing phase separation. In this case though, the sample was turbid for a long time until patterns appeared. A meniscus was most probably formed before the patterns emerged. We attribute the reason of patterns in this case to Marangoni convection, which is present in systems with an interface, where local differences in surface tension give rise to an instability. Our estimates for the Rayleigh number also show a significantly lower number than that's required for RB-type instability.rnrnIn the first part of the work, therefore, we identify two different kinds of hydrodynamic instabilities in two different mixtures. Both are observed during, or after the first phase separation. Our patterns compare with the classical convection patterns, but here the origins are from phase separation and the cooling protocol.rnrnIn the second part of the work, we focused on the kinetics of phase separation in a polymer solution (polystyrene and methylcyclohexane), which is cooled continuously far down into the two phase region. Oscillations in turbidity, denoting material exchange between the phases are seen. Three processes contribute to the phase separation: Nucleation of droplets, their growth and coalescence, and their subsequent sedimentation. Experiments in low molecular binary mixtures had led to models of oscillation [43] which considered sedimentation time scales much faster than the time scales of nucleation and growth. The size and shape of the sample therefore did not matter in such situations. The oscillations in turbidity were volume-dominated. The present work aimed at understanding the influence of sedimentation time scales for polymer mixtures. Three heights of the sample with same composition were studied side by side. We found that periods increased with the sample height, thus showing that sedimentation time determines the period of oscillations in the polymer solutions. We experimented with different cooling rates and different compositions of the mixture, and we found that periods are still determined by the sample height, and therefore by sedimentation time. rnrnWe also see that turbidity emerges in two ways; either from the interface, or throughout the sample. We suggest that oscillations starting from the interface are due to satellite droplets that are formed on droplet coalescence at the interface. These satellite droplets are then advected to the top of the sample, and they grow, coalesce and sediment. This type of an oscillation wouldn't require the system to pass the energy barrier required for homogenous nucleation throughout the sample. This mechanism would work best in sample where the droplets could be effectively advected throughout the sample. In our experiments, we see more interface dominated oscillations in the smaller cells and lower cooling rates, where droplet advection is favourable. In larger samples and higher cooling rates, we mostly see that the whole sample becomes turbid homogenously, which requires the system to pass the energy barrier for homogenous nucleation.rnrnOscillations, in principle, occur since the system needs to pass an energy barrier for nucleation. The height of the barrier decreases with increasing supersaturation, which in turn is from the temperature ramp applied. This gives rise to a period where the system is clear, in between the turbid periods. At certain specific cooling rates, the system can follow a path such that the start of a turbid period coincides with the vanishing of the last turbid period, thus eliminating the clear periods. This means suppressions of oscillations altogether. In fact we experimentally present a case where, at a certain cooling rate, oscillations indeed vanish. rnrnThus we find through this work that the kinetics of phase separation in polymer solution is different from that of a low molecular system; sedimentation time scales become relevant, and therefore so does the shape and size of the sample. The role of interface in initiating turbid periods also become much more prominent in this system compared to that in low molecular mixtures.rnrnIn summary, some fundamental properties in the kinetics of phase separation in binary mixtures were studied. While the first part of the work described the close interplay of the first phase separation with hydrodynamic instabilities, the second part investigated the nature and determining factors of oscillations, when the system was cooled deep into the two phase region. Both cases show how the geometry of the cell can affect the kinetics of phase separation. This study leads to further fundamental understandings of the factors contributing to the kinetics of phase separation, and to the understandings of what can be controlled and tuned in practical cases. rn

Periodicities in the Hodgkin-Huxley model and versions of this model with stochastic input

A field of computational neuroscience develops mathematical models to describe neuronal systems. The aim is to better understand the nervous system. Historically, the integrate-and-fire model, developed by Lapique in 1907, was the first model describing a neuron. In 1952 Hodgkin and Huxley [8] described the so called Hodgkin-Huxley model in the article “A Quantitative Description of Membrane Current and Its Application to Conduction and Excitation in Nerve”. The Hodgkin-Huxley model is one of the most successful and widely-used biological neuron models. Based on experimental data from the squid giant axon, Hodgkin and Huxley developed their mathematical model as a four-dimensional system of first-order ordinary differential equations. One of these equations characterizes the membrane potential as a process in time, whereas the other three equations depict the opening and closing state of sodium and potassium ion channels. The membrane potential is proportional to the sum of ionic current flowing across the membrane and an externally applied current. For various types of external input the membrane potential behaves differently. This thesis considers the following three types of input: (i) Rinzel and Miller [15] calculated an interval of amplitudes for a constant applied current, where the membrane potential is repetitively spiking; (ii) Aihara, Matsumoto and Ikegaya [1] said that dependent on the amplitude and the frequency of a periodic applied current the membrane potential responds periodically; (iii) Izhikevich [12] stated that brief pulses of positive and negative current with different amplitudes and frequencies can lead to a periodic response of the membrane potential. In chapter 1 the Hodgkin-Huxley model is introduced according to Izhikevich [12]. Besides the definition of the model, several biological and physiological notes are made, and further concepts are described by examples. Moreover, the numerical methods to solve the equations of the Hodgkin-Huxley model are presented which were used for the computer simulations in chapter 2 and chapter 3. In chapter 2 the statements for the three different inputs (i), (ii) and (iii) will be verified, and periodic behavior for the inputs (ii) and (iii) will be investigated. In chapter 3 the inputs are embedded in an Ornstein-Uhlenbeck process to see the influence of noise on the results of chapter 2.

Membrane properties and synaptic integration of identified neuronal populations in the developing rodent neocortex

In my PhD work I concentrated on three elementary questions that are essential to understand the interactions between the different neuronal cell populations in the developing neocortex. The questions regarded the identity of Cajal-Retzius (CR) cells, the ubiquitous expression of glycine receptors in all major cell populations of the immature neocortex, and the role of taurine in the modulation of immature neocortical network activity.rnTo unravel whether CR cells of different ontogenetic origin have divergent functions I investigated the electrophysiological properties of YFP+ (derived from the septum and borders of the pallium) and YFP− CR cells (derived from other neocortical origins). This study demonstrated that the passive and active electrophysiological properties as well as features of GABAergic PSCs and glutamatergic currents are similar between both CR cell populations. These findings suggest that CR cells of different origins most probably support similar functions within the neuronal networks of the early postnatal cerebral cortex.rnTo elucidate whether glycine receptors are expressed in all major cell populations of the developing neocortex I analyzed the functional expression of glycine receptors on subplate (SP) cells. Activation of glycine receptors by glycine, -alanine and taurine elicited membrane responses that could be blocked by the selective glycinergic antagonist strychnine. Pharmacological experiments suggest that SP cells express functional heteromeric glycine receptors that do not contain 1 subunits. The activation of glycine receptors by glycine and taurine induced a membrane depolarization, which mediated excitatory effects. Considering the key role of SP cells in immature cortical networks and the development of thalamocortical connections, this glycinergic excitation may influence the properties of early cortical networks and the formation of cortical circuits.rnIn the third part of my project I demonstrated that tonic taurine application induced a massive increase in the frequency of PSCs. Based on their reversal potential and their pharmacological properties these taurine-induced PSCs are exclusively transmitted via GABAA receptors to the pyramidal neurons, while both GABAA and glycine receptors were implicated in the generation of the presynaptic activity. Accordingly, whole-cell and cell-attached recordings from genetically labeled interneurons revealed the expression of glycine and GABAA receptors, which mediated an excitatory action on these cells. These findings suggest that low taurine concentrations can tonically activate exclusively GABAergic networks. The activity level maintained by this GABAergic activity in the immature nervous system may contribute to network properties and can facilitate the activity dependent formation of adequate synaptic projections.rnIn summary, the results of my studies complemented the knowledge about neuronal interactions in the immature neocortex and improve our understanding of cellular processes that guide neuronal development and thus shape the brain.rn

A two-body study of dynamical expansion in the XXZ spin chain and equivalent interacting fermion models

Lo scopo di questa tesi è studiare l'espansione dinamica di due fermioni interagenti in una catena unidimensionale cercando di definire il ruolo degli stati legati durante l'evoluzione temporale del sistema. Lo studio di questo modello viene effettuato a livello analitico tramite la tecnica del Bethe ansatz, che ci fornisce autovalori ed autovettori dell'hamiltoniana, e se ne valutano le proprietà statiche. Particolare attenzione è stata dedicata alle caratteristiche dello spettro al variare dell'interazione tra le due particelle e alle caratteristiche degli autostati. Dalla risoluzione dell'equazione di Bethe vengono ricercate le soluzioni che danno luogo a stati legati delle due particelle e se ne valuta lo spettro energetico in funzione del momento del centro di massa. Si è studiato inoltre l'andamento del numero delle soluzioni, in particolare delle soluzioni che danno luogo ad uno stato legato, al variare della lunghezza della catena e del parametro di interazione. La valutazione delle proprietà dinamiche del modello è stata effettuata tramite l'utilizzo dell'algoritmo t-DMRG (time dependent - Density Matrix Renormalization Group). Questo metodo numerico, che si basa sulla decimazione dello spazio di Hilbert, ci permette di avere accesso a quantità che caratterizzano la dinamica quali la densità e la velocità di espansione. Da queste sono stati estratti i proli dinamici della densità e della velocità di espansione al variare del valore del parametro di interazione.

Development of models and methods to simulate peptide-assisted nucleation and growth of calcium-minerals

In den vergangenen Jahren wurden einige bislang unbekannte Phänomene experimentell beobachtet, wie etwa die Existenz unterschiedlicher Prä-Nukleations-Strukturen. Diese haben zu einem neuen Verständnis von Prozessen, die auf molekularer Ebene während der Nukleation und dem Wachstum von Kristallen auftreten, beigetragen. Die Auswirkungen solcher Prä-Nukleations-Strukturen auf den Prozess der Biomineralisation sind noch nicht hinreichend verstanden. Die Mechanismen, mittels derer biomolekulare Modifikatoren, wie Peptide, mit Prä-Nukleations-Strukturen interagieren und somit den Nukleationsprozess von Mineralen beeinflussen könnten, sind vielfältig. Molekulare Simulationen sind zur Analyse der Formation von Prä-Nukleations-Strukturen in Anwesenheit von Modifikatoren gut geeignet. Die vorliegende Arbeit beschreibt einen Ansatz zur Analyse der Interaktion von Peptiden mit den in Lösung befindlichen Bestandteilen der entstehenden Kristalle mit Hilfe von Molekular-Dynamik Simulationen.rnUm informative Simulationen zu ermöglichen, wurde in einem ersten Schritt die Qualität bestehender Kraftfelder im Hinblick auf die Beschreibung von mit Calciumionen interagierenden Oligoglutamaten in wässrigen Lösungen untersucht. Es zeigte sich, dass große Unstimmigkeiten zwischen etablierten Kraftfeldern bestehen, und dass keines der untersuchten Kraftfelder eine realistische Beschreibung der Ionen-Paarung dieser komplexen Ionen widerspiegelte. Daher wurde eine Strategie zur Optimierung bestehender biomolekularer Kraftfelder in dieser Hinsicht entwickelt. Relativ geringe Veränderungen der auf die Ionen–Peptid van-der-Waals-Wechselwirkungen bezogenen Parameter reichten aus, um ein verlässliches Modell für das untersuchte System zu erzielen. rnDas umfassende Sampling des Phasenraumes der Systeme stellt aufgrund der zahlreichen Freiheitsgrade und der starken Interaktionen zwischen Calciumionen und Glutamat in Lösung eine besondere Herausforderung dar. Daher wurde die Methode der Biasing Potential Replica Exchange Molekular-Dynamik Simulationen im Hinblick auf das Sampling von Oligoglutamaten justiert und es erfolgte die Simulation von Peptiden verschiedener Kettenlängen in Anwesenheit von Calciumionen. Mit Hilfe der Sketch-Map Analyse konnten im Rahmen der Simulationen zahlreiche stabile Ionen-Peptid-Komplexe identifiziert werden, welche die Formation von Prä-Nukleations-Strukturen beeinflussen könnten. Abhängig von der Kettenlänge des Peptids weisen diese Komplexe charakteristische Abstände zwischen den Calciumionen auf. Diese ähneln einigen Abständen zwischen den Calciumionen in jenen Phasen von Calcium-Oxalat Kristallen, die in Anwesenheit von Oligoglutamaten gewachsen sind. Die Analogie der Abstände zwischen Calciumionen in gelösten Ionen-Peptid-Komplexen und in Calcium-Oxalat Kristallen könnte auf die Bedeutung von Ionen-Peptid-Komplexen im Prozess der Nukleation und des Wachstums von Biomineralen hindeuten und stellt einen möglichen Erklärungsansatz für die Fähigkeit von Oligoglutamaten zur Beeinflussung der Phase des sich formierenden Kristalls dar, die experimentell beobachtet wurde.

Visualization and validation of (Q)SAR models

Analyzing and modeling relationships between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects in chemical datasets is a challenging task for scientific researchers in the field of cheminformatics. Therefore, (Q)SAR model validation is essential to ensure future model predictivity on unseen compounds. Proper validation is also one of the requirements of regulatory authorities in order to approve its use in real-world scenarios as an alternative testing method. However, at the same time, the question of how to validate a (Q)SAR model is still under discussion. In this work, we empirically compare a k-fold cross-validation with external test set validation. The introduced workflow allows to apply the built and validated models to large amounts of unseen data, and to compare the performance of the different validation approaches. Our experimental results indicate that cross-validation produces (Q)SAR models with higher predictivity than external test set validation and reduces the variance of the results. Statistical validation is important to evaluate the performance of (Q)SAR models, but does not support the user in better understanding the properties of the model or the underlying correlations. We present the 3D molecular viewer CheS-Mapper (Chemical Space Mapper) that arranges compounds in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kinds of features, like structural fragments as well as quantitative chemical descriptors. Comprehensive functionalities including clustering, alignment of compounds according to their 3D structure, and feature highlighting aid the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. Even though visualization tools for analyzing (Q)SAR information in small molecule datasets exist, integrated visualization methods that allows for the investigation of model validation results are still lacking. We propose visual validation, as an approach for the graphical inspection of (Q)SAR model validation results. New functionalities in CheS-Mapper 2.0 facilitate the analysis of (Q)SAR information and allow the visual validation of (Q)SAR models. The tool enables the comparison of model predictions to the actual activity in feature space. Our approach reveals if the endpoint is modeled too specific or too generic and highlights common properties of misclassified compounds. Moreover, the researcher can use CheS-Mapper to inspect how the (Q)SAR model predicts activity cliffs. The CheS-Mapper software is freely available at http://ches-mapper.org.

Integration of Internet of Things and Cloud computing. A case study on vital signs monitoring.

Il progresso scientifico e le innovazioni tecnologiche nei campi dell'elettronica, informatica e telecomunicazioni, stanno aprendo la strada a nuove visioni e concetti. L'obiettivo della tesi è quello d'introdurre il modello del Cloud computing per rendere possibile l'attuale visione di Internet of Thing. Nel primo capitolo si introduce Ubiquitous computing come un nuovo modo di vedere i computer, cercando di fare chiarezza sulla sua definizione, la sua nascita e fornendo un breve quadro storico. Nel secondo capitolo viene presentata la visione di Internet of Thing (Internet delle “cose”) che si avvale di concetti e di problematiche in parte già considerate con Ubiquitous computing. Internet of Thing è una visione in cui la rete Internet viene estesa agli oggetti di tutti i giorni. Tracciare la posizione degli oggetti, monitorare pazienti da remoto, rilevare dati ambientali sono solo alcuni esempi. Per realizzare questo tipo di applicazioni le tecnologie wireless sono da considerare necessarie, sebbene questa visione non assuma nessuna specifica tecnologia di comunicazione. Inoltre, anche schede di sviluppo possono agevolare la prototipazione di tali applicazioni. Nel terzo capitolo si presenta Cloud computing come modello di business per utilizzare su richiesta risorse computazionali. Nel capitolo, vengono inizialmente descritte le caratteristiche principali e i vari tipi di modelli di servizio, poi viene argomentato il ruolo che i servizi di Cloud hanno per Internet of Thing. Questo modello permette di accelerare lo sviluppo e la distribuzione di applicazioni di Internet of Thing, mettendo a disposizione capacità di storage e di calcolo per l'elaborazione distribuita dell'enorme quantità di dati prodotta da sensori e dispositivi vari. Infine, nell'ultimo capitolo viene considerato, come esempio pratico, l'integrazione di tecnologie di Cloud computing in una applicazione IoT. Il caso di studio riguarda il monitoraggio remoto dei parametri vitali, considerando Raspberry Pi e la piattaforma e-Health sviluppata da Cooking Hacks per lo sviluppo di un sistema embedded, e utilizzando PubNub come servizio di Cloud per distribuire i dati ottenuti dai sensori. Il caso di studio metterà in evidenza sia i vantaggi sia le eventuali problematiche che possono scaturire utilizzando servizi di Cloud in applicazioni IoT.

Statistical mechanics of polymer models: rigorous results and applications

Monomer-dimer models are amongst the models in statistical mechanics which found application in many areas of science, ranging from biology to social sciences. This model describes a many-body system in which monoatomic and diatomic particles subject to hard-core interactions get deposited on a graph. In our work we provide an extension of this model to higher-order particles. The aim of our work is threefold: first we study the thermodynamic properties of the newly introduced model. We solve analytically some regular cases and find that, differently from the original, our extension admits phase transitions. Then we tackle the inverse problem, both from an analytical and numerical perspective. Finally we propose an application to aggregation phenomena in virtual messaging services.

Safety and Efficacy of Ranibizumab in Diabetic Macular Edema (RESOLVE Study): A 12-month, randomized, controlled, double-masked, multicenter phase II study

The expression of vascular endothelial growth factor (VEGF) is elevated in diabetic macular edema (DME). Ranibizumab binds to and inhibits multiple VEGF variants. We investigated the safety and efficacy of ranibizumab in DME involving the foveal center.

Efficacy of rituximab and cladribine in patients with chronic lymphocytic leukemia and feasibility of stem cell mobilization: a prospective multicenter phase II trial (protocol SAKK 34/02)

This phase II trial investigated rituximab and cladribine in chronic lymphocytic leukemia. Four induction cycles, comprising cladribine (0.1 mg/kg/day days 1-5, cycles 1-4) and rituximab (375 mg/m(2) day 1, cycles 2-4), were given every 28 days. Stem cell mobilization (rituximab 375 mg/m(2) days 1 and 8; cyclophosphamide 4 g/m(2) day 2; and granulocyte colony-stimulating factor 10 microg/kg/day, from day 4) was performed in responders. Of 42 patients, nine achieved complete remission (CR), 15 very good partial remission, and two nodular partial remission (overall response rate 62%). Stem cell mobilization and harvesting (> or = 2 x 10(6) stem cells/kg body weight) were successful in 12 of 20 patients. Rituximab infusion-related adverse events were moderate. The main grade 3/4 adverse events during induction were neutropenia and lymphocytopenia. Rituximab plus cladribine was effective; however, the CR rate was modest and stem cell harvest was impaired in a large number of responding patients.

A randomised comparison of novolimus-eluting and zotarolimus-eluting coronary stents: 9-month follow-up results of the EXCELLA II study

Novolimus, a macrocyclic lactone with anti-proliferative properties, has a similar efficacy to currently available agents; however it requires a lower dose, and less polymer, and is therefore conceivably safer.