Packet Level Coding for Mobile Broadcasting

The thesis deals with channel coding theory applied to upper layers in the protocol stack of a communication link and it is the outcome of four year research activity. A specific aspect of this activity has been the continuous interaction between the natural curiosity related to the academic blue-sky research and the system oriented design deriving from the collaboration with European industry in the framework of European funded research projects. In this dissertation, the classical channel coding techniques, that are traditionally applied at physical layer, find their application at upper layers where the encoding units (symbols) are packets of bits and not just single bits, thus explaining why such upper layer coding techniques are usually referred to as packet layer coding. The rationale behind the adoption of packet layer techniques is in that physical layer channel coding is a suitable countermeasure to cope with small-scale fading, while it is less efficient against large-scale fading. This is mainly due to the limitation of the time diversity inherent in the necessity of adopting a physical layer interleaver of a reasonable size so as to avoid increasing the modem complexity and the latency of all services. Packet layer techniques, thanks to the longer codeword duration (each codeword is composed of several packets of bits), have an intrinsic longer protection against long fading events. Furthermore, being they are implemented at upper layer, Packet layer techniques have the indisputable advantages of simpler implementations (very close to software implementation) and of a selective applicability to different services, thus enabling a better matching with the service requirements (e.g. latency constraints). Packet coding technique improvement has been largely recognized in the recent communication standards as a viable and efficient coding solution: Digital Video Broadcasting standards, like DVB-H, DVB-SH, and DVB-RCS mobile, and 3GPP standards (MBMS) employ packet coding techniques working at layers higher than the physical one. In this framework, the aim of the research work has been the study of the state-of-the-art coding techniques working at upper layer, the performance evaluation of these techniques in realistic propagation scenario, and the design of new coding schemes for upper layer applications. After a review of the most important packet layer codes, i.e. Reed Solomon, LDPC and Fountain codes, in the thesis focus our attention on the performance evaluation of ideal codes (i.e. Maximum Distance Separable codes) working at UL. In particular, we analyze the performance of UL-FEC techniques in Land Mobile Satellite channels. We derive an analytical framework which is a useful tool for system design allowing to foresee the performance of the upper layer decoder. We also analyze a system in which upper layer and physical layer codes work together, and we derive the optimal splitting of redundancy when a frequency non-selective slowly varying fading channel is taken into account. The whole analysis is supported and validated through computer simulation. In the last part of the dissertation, we propose LDPC Convolutional Codes (LDPCCC) as possible coding scheme for future UL-FEC application. Since one of the main drawbacks related to the adoption of packet layer codes is the large decoding latency, we introduce a latency-constrained decoder for LDPCCC (called windowed erasure decoder). We analyze the performance of the state-of-the-art LDPCCC when our decoder is adopted. Finally, we propose a design rule which allows to trade-off performance and latency.

Near-Optimum Coding for q-ary Symmetric Channel with Application to Space Communications

Questa Tesi aspira a mostrare un codice a livello di pacchetto, che abbia performance molto vicine a quello ottimo, per progetti di comunicazioni Satellitari. L’altro scopo di questa Tesi è quello di capire se rimane ancora molto più difficile maneggiare direttamente gli errori piuttosto che le erasures. Le applicazioni per comunicazioni satellitari ora come ora usano tutte packet erasure coding per codificare e decodificare l’informazione. La struttura dell’erasure decoding è molto semplice, perché abbiamo solamente bisogno di un Cyclic Redundancy Check (CRC) per realizzarla. Il problema nasce quando abbiamo pacchetti di dimensioni medie o piccole (per esempio più piccole di 100 bits) perché in queste situazioni il costo del CRC risulta essere troppo dispendioso. La soluzione la possiamo trovare utilizzando il Vector Symbol Decoding (VSD) per raggiungere le stesse performance degli erasure codes, ma senza la necessità di usare il CRC. Per prima cosa viene fatta una breve introduzione su come è nata e su come si è evoluta la codifica a livello di pacchetto. In seguito è stato introdotto il canale q-ary Symmetric Channel (qSC), con sia la derivazione della sua capacità che quella del suo Random Coding Bound (RCB). VSD è stato poi proposto con la speranza di superare in prestazioni il Verification Based Decoding (VBD) su il canale qSC. Infine, le effettive performance del VSD sono state stimate via simulazioni numeriche. I possibili miglioramenti delle performance, per quanto riguarda il VBD sono state discusse, come anche le possibili applicazioni future. Inoltre abbiamo anche risposto alla domande se è ancora così tanto più difficile maneggiare gli errori piuttosto che le erasure.

Coding of reaching in 3-D space

Many psychophysical studies suggest that target depth and direction during reaches are processed independently, but the neurophysiological support to this view is so far limited. Here, we investigated the representation of reach depth and direction by single neurons in an area of the medial posterior parietal cortex (V6A). Single-unit activity was recorded from V6A in two Macaca fascicularis monkeys performing a fixation-to-reach task to targets at different depths and directions. We found that in a substantial percentage of V6A neurons depth and direction signals jointly influenced fixation, planning and arm movement-related activity in 3D space. While target depth and direction were equally encoded during fixation, depth tuning became stronger during arm movement planning, execution and target holding. The spatial tuning of fixation activity was often maintained across epochs, and this occurred more frequently in depth. These findings support for the first time the existence of a common neural substrate for the encoding of target depth and direction during reaching movements in the posterior parietal cortex. Present results also highlight the presence in V6A of several types of cells that process independently or jointly eye position and arm movement planning and execution signals in order to control reaches in 3D space. It is possible that depth and direction influence also the metrics of the reach action and that this effect on the reach kinematic variables can account for the spatial tuning we found in V6A neural activity. For this reason, we recorded and analyzed behavioral data when one monkey performed reaching movements in 3-D space. We evaluated how the target spatial position, in particular target depth and target direction, affected the kinematic parameters and trajectories describing the motor action properties.

Coarse-graining methods and polymer dynamics

This thesis studies molecular dynamics simulations on two levels of resolution: the detailed level of atomistic simulations, where the motion of explicit atoms in a many-particle system is considered, and the coarse-grained level, where the motion of superatoms composed of up to 10 atoms is modeled. While atomistic models are capable of describing material specific effects on small scales, the time and length scales they can cover are limited due to their computational costs. Polymer systems are typically characterized by effects on a broad range of length and time scales. Therefore it is often impossible to atomistically simulate processes, which determine macroscopic properties in polymer systems. Coarse-grained (CG) simulations extend the range of accessible time and length scales by three to four orders of magnitude. However, no standardized coarse-graining procedure has been established yet. Following the ideas of structure-based coarse-graining, a coarse-grained model for polystyrene is presented. Structure-based methods parameterize CG models to reproduce static properties of atomistic melts such as radial distribution functions between superatoms or other probability distributions for coarse-grained degrees of freedom. Two enhancements of the coarse-graining methodology are suggested. Correlations between local degrees of freedom are implicitly taken into account by additional potentials acting between neighboring superatoms in the polymer chain. This improves the reproduction of local chain conformations and allows the study of different tacticities of polystyrene. It also gives better control of the chain stiffness, which agrees perfectly with the atomistic model, and leads to a reproduction of experimental results for overall chain dimensions, such as the characteristic ratio, for all different tacticities. The second new aspect is the computationally cheap development of nonbonded CG potentials based on the sampling of pairs of oligomers in vacuum. Static properties of polymer melts are obtained as predictions of the CG model in contrast to other structure-based CG models, which are iteratively refined to reproduce reference melt structures. The dynamics of simulations at the two levels of resolution are compared. The time scales of dynamical processes in atomistic and coarse-grained simulations can be connected by a time scaling factor, which depends on several specific system properties as molecular weight, density, temperature, and other components in mixtures. In this thesis the influence of molecular weight in systems of oligomers and the situation in two-component mixtures is studied. For a system of small additives in a melt of long polymer chains the temperature dependence of the additive diffusion is predicted and compared to experiments.

Architettura di supporto al peer-to-peer gaming basata su network coding

La popolarita` dei giochi online e` in crescita, ma allo stesso tempo le architetture proposte dagli sviluppatori e le connessioni di cui sono dotati gli utenti sembrano restare non adeguate a questo. Nella tesi si descrive un'architettura peer-to-peer che riesce ad effettuare una riduzione nella perdita dei pacchetti grazie al meccanismo del Network Coding senza effetti collaterali per la latenza.

Coarse-graining and quantum-classical adaptive coupling in soft matter

Die vorliegende Arbeit untersucht den Zusammenhang zwischen Skalen in Systemen weicher Materie, der für Multiskalen-Simulationen eine wichtige Rolle spielt. Zu diesem Zweck wurde eine Methode entwickelt, die die Approximation der Separierbarkeit von Variablen für die Molekulardynamik und ähnliche Anwendungen bewertet. Der zweite und größere Teil dieser Arbeit beschäftigt sich mit der konzeptionellen und technischen Erweiterung des Adaptive Resolution Scheme'' (AdResS), einer Methode zur gleichzeitigen Simulation von Systemen mit mehreren Auflösungsebenen. Diese Methode wurde auf Systeme erweitert, in denen klassische und quantenmechanische Effekte eine Rolle spielen.rnrnDie oben genannte erste Methode benötigt nur die analytische Form der Potentiale, wie sie die meisten Molekulardynamik-Programme zur Verfügung stellen. Die Anwendung der Methode auf ein spezielles Problem gibt bei erfolgreichem Ausgang einen numerischen Hinweis auf die Gültigkeit der Variablenseparation. Bei nicht erfolgreichem Ausgang garantiert sie, dass keine Separation der Variablen möglich ist. Die Methode wird exemplarisch auf ein zweiatomiges Molekül auf einer Oberfläche und für die zweidimensionale Version des Rotational Isomer State (RIS) Modells einer Polymerkette angewandt.rnrnDer zweite Teil der Arbeit behandelt die Entwicklung eines Algorithmus zur adaptiven Simulation von Systemen, in denen Quanteneffekte berücksichtigt werden. Die Quantennatur von Atomen wird dabei in der Pfadintegral-Methode durch einen klassischen Polymerring repräsentiert. Die adaptive Pfadintegral-Methode wird zunächst für einatomige Flüssigkeiten und tetraedrische Moleküle unter normalen thermodynamischen Bedingungen getestet. Schließlich wird die Stabilität der Methode durch ihre Anwendung auf flüssigen para-Wasserstoff bei niedrigen Temperaturen geprüft.

Coarse-grained peptide models: conformational sampling, peptide association and dynamical properties for peptides

In dieser Arbeit wird ein vergröbertes (engl. coarse-grained, CG) Simulationsmodell für Peptide in wässriger Lösung entwickelt. In einem CG Verfahren reduziert man die Anzahl der Freiheitsgrade des Systems, so dass manrngrössere Systeme auf längeren Zeitskalen untersuchen kann. Die Wechselwirkungspotentiale des CG Modells sind so aufgebaut, dass die Peptid Konformationen eines höher aufgelösten (atomistischen) Modells reproduziert werden.rnIn dieser Arbeit wird der Einfluss unterschiedlicher bindender Wechsel-rnwirkungspotentiale in der CG Simulation untersucht, insbesondere daraufhin,rnin wie weit das Konformationsgleichgewicht der atomistischen Simulation reproduziert werden kann. Im CG Verfahren verliert man per Konstruktionrnmikroskopische strukturelle Details des Peptids, zum Beispiel, Korrelationen zwischen Freiheitsgraden entlang der Peptidkette. In der Dissertationrnwird gezeigt, dass diese “verlorenen” Eigenschaften in einem Rückabbildungsverfahren wiederhergestellt werden können, in dem die atomistischen Freiheitsgrade wieder in die CG-Strukturen eingefügt werden. Dies gelingt, solange die Konformationen des CG Modells grundsätzlich gut mit der atomistischen Ebene übereinstimmen. Die erwähnten Korrelationen spielen einerngrosse Rolle bei der Bildung von Sekundärstrukturen und sind somit vonrnentscheidender Bedeutung für ein realistisches Ensemble von Peptidkonformationen. Es wird gezeigt, dass für eine gute Übereinstimmung zwischen CG und atomistischen Kettenkonformationen spezielle bindende Wechselwirkungen wie zum Beispiel 1-5 Bindungs- und 1,3,5-Winkelpotentiale erforderlich sind. Die intramolekularen Parameter (d.h. Bindungen, Winkel, Torsionen), die für kurze Oligopeptide parametrisiert wurden, sind übertragbarrnauf längere Peptidsequenzen. Allerdings können diese gebundenen Wechselwirkungen nur in Kombination mit solchen nichtbindenden Wechselwirkungspotentialen kombiniert werden, die bei der Parametrisierung verwendet werden, sind also zum Beispiel nicht ohne weiteres mit einem andere Wasser-Modell kombinierbar. Da die Energielandschaft in CG-Simulationen glatter ist als im atomistischen Modell, gibt es eine Beschleunigung in der Dynamik. Diese Beschleunigung ist unterschiedlich für verschiedene dynamische Prozesse, zum Beispiel für verschiedene Arten von Bewegungen (Rotation und Translation). Dies ist ein wichtiger Aspekt bei der Untersuchung der Kinetik von Strukturbildungsprozessen, zum Beispiel Peptid Aggregation.rn

Role of Non-coding RNAs in chemotherapeutic treatments

The transcribed ultraconserved regions (T-UCRs) are a group of long non-coding RNAs involved in human carcinogenesis. The factors regulating the expression of T-UCRs and their mechanism of action in human cancers are unknown. In this work it was shown that high expression of uc.339 associates with lower survival in 204 non-small cell lung cancer (NSCLC) patients. Moreover, it was shown that uc.339 found up-regulated in archival NSCLC samples, acts as a decoy RNA for miR-339-3p, -663-3p and -95-5p. So, Cyclin E2, a direct target of three microRNAs is up-regulated, inducing cancer growth and migration. Evidence of this mechanism was provided from cell lines and primary samples confirming that TP53 directly regulates uc.339. These results support a key role for uc.339 in lung cancer.

Scale bridging concepts in molecular simulation : coarse-graining and thermodynamic coupling

In dieser Arbeit wurden Simulation von Flüssigkeiten auf molekularer Ebene durchgeführt, wobei unterschiedliche Multi-Skalen Techniken verwendet wurden. Diese erlauben eine effektive Beschreibung der Flüssigkeit, die weniger Rechenzeit im Computer benötigt und somit Phänomene auf längeren Zeit- und Längenskalen beschreiben kann.rnrnEin wesentlicher Aspekt ist dabei ein vereinfachtes (“coarse-grained”) Modell, welches in einem systematischen Verfahren aus Simulationen des detaillierten Modells gewonnen wird. Dabei werden ausgewählte Eigenschaften des detaillierten Modells (z.B. Paar-Korrelationsfunktion, Druck, etc) reproduziert.rnrnEs wurden Algorithmen untersucht, die eine gleichzeitige Kopplung von detaillierten und vereinfachten Modell erlauben (“Adaptive Resolution Scheme”, AdResS). Dabei wird das detaillierte Modell in einem vordefinierten Teilvolumen der Flüssigkeit (z.B. nahe einer Oberfläche) verwendet, während der Rest mithilfe des vereinfachten Modells beschrieben wird.rnrnHierzu wurde eine Methode (“Thermodynamische Kraft”) entwickelt um die Kopplung auch dann zu ermöglichen, wenn die Modelle in verschiedenen thermodynamischen Zuständen befinden. Zudem wurde ein neuartiger Algorithmus der Kopplung beschrieben (H-AdResS) der die Kopplung mittels einer Hamilton-Funktion beschreibt. In diesem Algorithmus ist eine zur Thermodynamischen Kraft analoge Korrektur mit weniger Rechenaufwand möglich.rnrnAls Anwendung dieser grundlegenden Techniken wurden Pfadintegral Molekulardynamik (MD) Simulationen von Wasser untersucht. Mithilfe dieser Methode ist es möglich, quantenmechanische Effekte der Kerne (Delokalisation, Nullpunktsenergie) in die Simulation einzubeziehen. Hierbei wurde zuerst eine Multi-Skalen Technik (“Force-matching”) verwendet um eine effektive Wechselwirkung aus einer detaillierten Simulation auf Basis der Dichtefunktionaltheorie zu extrahieren. Die Pfadintegral MD Simulation verbessert die Beschreibung der intra-molekularen Struktur im Vergleich mit experimentellen Daten. Das Modell eignet sich auch zur gleichzeitigen Kopplung in einer Simulation, wobei ein Wassermolekül (beschrieben durch 48 Punktteilchen im Pfadintegral-MD Modell) mit einem vereinfachten Modell (ein Punktteilchen) gekoppelt wird. Auf diese Weise konnte eine Wasser-Vakuum Grenzfläche simuliert werden, wobei nur die Oberfläche im Pfadintegral Modell und der Rest im vereinfachten Modell beschrieben wird.

Variation of vector quantisation and speech waveform coding

A new idea for waveform coding using vector quantisation (VQ) is introduced. This idea makes it possible to deal with codevectors much larger than before for a fixed bit per sample rate. Also a solution to the matching problem (inherent in the present context) in the &-norm describing a measure of neamess is presented. The overall computational complexity of this solution is O(n3 log, n). Sample results are presented to demonstrate the advantage of using this technique in the context of coding of speech waveforms.

Differential block coding of bilevel images

Abstract- In this correspondence, a simple one-dimensional (1-D) differencing operation is applied to bilevel images prior to block coding to produce a sparse binary image that can be encoded efficiently using any of a number of well-known techniques. The difference image can be encoded more efficiently than the original bilevel image whenever the average run length of black pixels in the original image is greater than two. Compression is achieved because the correlation between adjacent pixels is reduced compared with the original image. The encoding/decoding operations are described and compression performance is presented for a set of standard bilevel images.

Non-coding keratin variants associate with liver fibrosis progression in patients with hemochromatosis

Background Keratins 8 and 18 (K8/K18) are intermediate filament proteins that protect the liver from various forms of injury. Exonic K8/K18 variants associate with adverse outcome in acute liver failure and with liver fibrosis progression in patients with chronic hepatitis C infection or primary biliary cirrhosis. Given the association of K8/K18 variants with end-stage liver disease and progression in several chronic liver disorders, we studied the importance of keratin variants in patients with hemochromatosis. Methods The entire K8/K18 exonic regions were analyzed in 162 hemochromatosis patients carrying homozygous C282Y HFE (hemochromatosis gene) mutations. 234 liver-healthy subjects were used as controls. Exonic regions were PCR-amplified and analyzed using denaturing high-performance liquid chromatography and DNA sequencing. Previously-generated transgenic mice overexpressing K8 G62C were studied for their susceptibility to iron overload. Susceptibility to iron toxicity of primary hepatocytes that express K8 wild-type and G62C was also assessed. Results We identified amino-acid-altering keratin heterozygous variants in 10 of 162 hemochromatosis patients (6.2%) and non-coding heterozygous variants in 6 additional patients (3.7%). Two novel K8 variants (Q169E/R275W) were found. K8 R341H was the most common amino-acid altering variant (4 patients), and exclusively associated with an intronic KRT8 IVS7+10delC deletion. Intronic, but not amino-acid-altering variants associated with the development of liver fibrosis. In mice, or ex vivo, the K8 G62C variant did not affect iron-accumulation in response to iron-rich diet or the extent of iron-induced hepatocellular injury. Conclusion In patients with hemochromatosis, intronic but not exonic K8/K18 variants associate with liver fibrosis development.