Las redes de transporte se mueven hacia un modelo de redes formadas por routers IP/MPLS (Internet Protocol/Multiprotocol Laebel Switching) de altas prestaciones interconectadas a través redes troncales inteligentes. Actualmente la tecnología ATM está ampliamente desarrollada en dichas redes troncales que utilizan los protocolos PNNI (Private Network- Network Interface) como plano de control. En cambio la interoperabilidad entre redes IP/MPLS a través de redes PNNI-ATM es todavía un aspecto en proceso de estudio. Por otro lado, la tendencia futura de Internet es ir hacia redes troncales completamente ópticas con capacidad automática de conmutación para permitir un mejor tratamiento del tráfico solicitado. Debido al esfuerzo realizado por los organismos de estandarización sobre redes ópticas, se ha definido un primer modelo de red llamado ASON (Automatic Switched Optical Network). Mientras las redes actuales basadas en SDH (Synchronous Digital Hierarchy) ofrecen sólo capacidad de transporte, la futura ASON permitirá el establecimiento y la liberación de canales ópticos de forma automática. Un aspecto clave para conseguir esta funcionalidad es la definición de un plano de control óptico que será el responsable de realizar las funciones de señalización y encaminamiento.Diferentes estudios han sido realizados para conseguir interoperabilidad entre redes con tecnología IP/MPLS y ATM basados esencialmente en la distribución de información de señalización MPLS a través de una red troncal ATM. Una de las soluciones planteadas se basa en la utilización sobre cada uno de los conmutadores ATM, un dispositivo capaz de procesar información MPLS, llamado LSR (Label Switched Router). Otra, en cambio, propone el establecimiento de un camino MPLS, llamado LSP (Label Switched Path), encapsulado dentro de un camino ATM o VPC (Virtual Path Connection). Ambas soluciones presentan el inconveniente de utilizar un tiempo de establecimiento demasiado elevado.Respecto al plano de control para ASON, decir que una de las opciones propuestas es la de utilizar el GMPLS (Generalizad MPLS) que es una extensión del modelo MPLS con ingeniería de tráfico. Sin embargo, recientemente se ha iniciado un debate en lo foros de estandarización sobre la posibilidad de utilizar el PNNI como plano de control en ASON. Los argumentos que justifican esta opción son que el PNNI, después de unas apropiadas modificaciones, puede ser adecuado para ASON y lleva años funcionando en muchas de las actuales redes de transporte.Esta tesis está basada en el estudio de los dos casos mencionados anteriormente. El primero caso es el de dos redes IP/MPLS conectadas a través de una red troncal ATM la cual utiliza el PNNI como plano de control. En este contexto, el objetivo principal será el de definir un mecanismo rápido de establecimiento de la conexión que proporcione los parámetros requeridos de calidad deservicio entre dos nodos pertenecientes a cada una de las redes IP/MPLS. Para conseguirlo se realizarán las modificaciones pertinentes en el PNNI y se añadirán nuevos elementos de señalización.El segundo caso consiste en interconectar dos redes IP/MPLS a través de una red tronca l´óptica. En primer lugar se adaptará el PNNI para conseguir un protocolo de encaminamiento para ASON con el fin de proporcionar un establecimiento rápido de la conexión en un entorno IP/MPLS-ASON. Finalmente, se definirá un plano de control, llamado O-PNNI (Optical PNNI) basado en la adaptación total del ATM PNNI a redes ASON. Esta tesis finaliza con un análisis de las ventajas y desventajas de los modelos GMPLS y O-PNNI como planos de control en ASON.

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<p>The eukaryotic genome integrity is safeguarded by the DNA damage response, which is composed of a network of signal transduction pathways that upon genotoxic stresses, arrest cell cycle progression, motivate repair processes, or induce apoptosis or senescence when cells incur irreparable DNA damage. During this process, DNA damage-induced post-translational modifications, most notably protein phosphorylation, of a variety of DNA damage-responsive proteins has been shown to mediate the initiation, transduction and reception of the DNA damage signals, resulting in alterations of their stability, activities or subcellular localizations, ultimately leading to activation of various downstream effector pathways. </p><p>While a lot has been elucidated on the downstream events of the DNA damage response, little is known about how DNA damage is detected. Two still ongoing studies of this dissertation attempt to address this question. Our preliminary work on ATM indicates that serine 2546 is critical for its kinase activity. Substitution of this residue with phosphomimetic aspartate, but not nonphosphorylable alanine, abrogates the kinase activity of ATM and fails to rescue the checkpoint-deficient phenotype exhibited by the ATM-deficient cells, suggesting that removal of an inhibitory phospho group at S2546 might be required for the activation of ATM. In another study, we identified a novel DNA-damage responsive threonine residue (T622) in Rad17, which undergoes ATM/ATR-dependent phosphorylation in vitro and in vivo. Ectopic expression of a phosphodeficient mutant (T622A) of Rad17, but not its wild-type control, shows a pronounced defect in sustaining Chk1 phosphorylation and the corresponding G2/M checkpoint upon DNA damage, suggesting that phosphorylation at T622 might complement that on the two previously reported phosphorylation sites, S635 and S645, to mediate G2/M checkpoint activation while the latter is primarily responsible for intra-S phase checkpoint. </p><p>Although a large amount of knowledge has been accumulated about the initiation and activation process of the DNA damage response, how cells recover, the equally important flip side of the response, has remained poorly understood. We have found that in cells recovering from replication stress, RPA32 phosphorylation at ATM/ATR-responsive sites T21 and S33, which reportedly suppresses DNA replication and recruiting other checkpoint and repair proteins to the DNA lesions, is reversed by the serine/threonine protein phosphatase 2A (PP2A). Cells with a RPA32 persistent-phosphorylation mimic (T21D/S33D) exhibit normal checkpoint activation and re-enter the cell cycle normally after recovery, but display a pronounced defect in the repair of DNA breaks. These data indicate that PP2A-mediated RPA32 dephosphorylation may be a required event during the repair process in the DNA damage response. </p><p>In summary, these studies in this dissertation highlight the importance of reversible phosphorylation and dephosphorylation in the modulation of the DNA damage response. What's more, they also extend our knowledge and deepen our understanding of this process by revealing that dephosphorylation may positively regulate the activation of cell cycle checkpoints, which is seemingly dominated by protein phosphorylation upon DNA damage, that phosphorylation of certain checkpoint proteins at different sites may result in distinct consequences, and that dephosphorylation of some activated checkpoint/repair proteins may function as an important mechanism for cells to recover from the DNA damage response.</p> / Dissertation

<p>Cancer cells often have elevated frequencies of chromosomal aberrations, and it is likely that loss of genome stability is one driving force behind tumorigenesis. Deficiencies in DNA replication, DNA repair, or cell cycle checkpoints can all contribute to increased rates of chromosomal duplications, deletions and translocations. The human ATM and ATR proteins are known to participate in the DNA damage response and DNA replication checkpoint pathways and are critical to maintaining genome stability. The <italic>Saccharomyces cerevisiae</italic> homologues of ATM and ATR are Tel1p and Mec1p, respectively. Because Tel1p and Mec1p are partially functionally redundant, loss of both Tel1p and Mec1p in haploid yeast cells (<italic>tel1 mec1</italic> strains) results in synergistically elevated rates of chromosomal aberrations, including terminal duplications, chromosomal duplications, and telomere-telomere fusions. To determine the effect of Tel1p and Mec1p on chromosome aberrations that cannot be recovered in haploid strains, such as chromosome loss, I investigated the phenotypes associated with the <italic>tel1 mec1</italic> mutations in diploid cells. In the absence of induced DNA damage, <italic>tel1 mec1</italic> diploid yeast strains exhibit extremely high rates of aneuploidy and chromosome rearrangements. There is a significant bias towards trisomy of chromosomes II, VIII, X, and XII, whereas the smallest chromosomes I and VI are commonly monosomic. </p> <p> The telomere defects associated with <italic>tel1 mec1</italic> strains do not cause the high rates of aneuploidy, as restoring wild-type telomere length in these strains by expression of the Cdc13p-Est2p fusion protein does not prevent cells from becoming aneuploid. The <italic>tel1 mec1</italic> diploids are not sensitive to the microtubule-destabilizing drug benomyl, nor do they arrest the cell cycle in response to the drug, indicating that the spindle assembly checkpoint is functional. The chromosome missegregation phenotypes of <italic>tel1 mec1</italic> diploids mimic those observed in mutant strains that do not achieve biorientation of sister chromatids during mitosis. </p> <p> The chromosome rearrangements in <italic>tel1 mec1</italic> cells reflect both homologous recombination between non-allelic Ty elements, as well as non-homologous end joining (NHEJ) events. Restoring wild-type telomere length with the Cdc13p-Est2p fusion protein substantially reduces the levels of chromosome rearrangements (terminal additions and deletions of chromosome arms, interstitial duplications, and translocations). This result suggests that most of the rearrangements in <italic>tel1 mec1</italic> diploids are initiated by telomere-telomere fusions. One common chromosome rearrangement in <italic>tel1 mec1</italic> strains is an amplification of sequences on chromosome XII between the left telomere and rDNA sequences on the right arm. I have termed this aberration a "schromosome." Preliminary evidence indicates that the schromosome exists in the <italic>tel1 mec1</italic> cells as an uncapped chromosome fragment that gets resected over time.</p> / Dissertation

Asynchronous Transfer Mode (ATM) network is being deployed in carrier backbone. ATM can transmit a wide variety of traffic, such as video, voice, and data. Available Bit Rate (ABR) service is one of six ATM services, which is now under intensive research for its closed loop feedback control feature. ABR service supports two types of connections: unicast and multicast. There are also three types of multicast connections: point-to-multipoint, multipoint-to-point, and multipoint-to-multipoint. Multipoint communication is the exchange of information among multiple senders and multiple receivers, forming a multicast group. Examples of multicast applications include audio and video conferencing, video on demand, tele-metering, distributed games, and data distribution applications. In this dissertation, we focus on queuing and packet scheduling management for multipoint-to-point ABR connections. Although there are so many proposed fairness definitions for all ABR sources in a multipoint-to-point connection, there are still problems about queue lengths, queuing delays, and throughputs, when ABR sources are with variable-length packets. From the nature of VC-merge scheme on merged points in a multipoint-to-point connection, merged switches cannot transmit cell-stream of a packet out until the packet is completely and totally queued. If there is no complete packets queued, the switch can then choose an incomplete packet for cut-through forwarding for efficiency. Therefore, if the switch chooses a long packet from a branch that has smaller cell input rate, for cut-through forwarding, the throughput of output ports will experience severe oscillations. At the same time, ABR queue lengths will be also occupied with severe growth, and ABR cells will be experienced long queuing delays. We proposed a scheme, named MWTF (Minimum Waiting Time First), which is architecture-independent of any rate allocation schemes and fairness definitions, to resolve the problems by providing length of each packet to merged switches. Thereby the scheduler can choose an appropriate incomplete packet for cut-through forwarding, by selecting the packet that has the smallest packet waiting time. Simulation results show that merged switch has good performances. Throughput will be no severe oscillations and will be getting smoother. Also cells have smaller and smoother queuing delays in average, and the switches have much smaller queue lengths and smoother variations.

In this dissertation, we present performance prediction models for rate-based and window¡Vbased flow control mechanisms. For rate-based flow control, such as in ATM network, we derive two analytical models to predict the ACR rates for congestion-free and congestion networks, respectively. To coordinate the cooperative problems of TCP over ATM networks, we propose a new algorithm to monitor the states of ATM switches and adjust TCP congestion window size based on RM cells. For window-based flow control mechanisms, such as in TCP-Reno and TCP-SACK, we respectively present analytical models to systematically capture the characteristics of multiple consecutive packet losses in TCP windows. Through fast retransmission, the lost packets may or may not be recovered. Thus, we present upper bound analyses for slow start and congestion avoidance phases to study the effects of multiple packet losses on TCP performance. Above the proposed upper bounds, the lost packets may not be successfully recovered through fast retransmission. Finally, we develop a model to study the TCP performance in terms of throughput degradation resulted from multiple consecutive packet losses. The analytical results from the throughput degradation model are validated through OPNET simulation.

Most proposed regulation methods do not take advantage of the state information of the underlying scheduler, resulting in a waste of resources. We propose a dynamic regulation approach in which the regulation function is modulated by both the tagged stream's characteristics and the state information fed-back from the scheduler. The transmission speed of a regulator is accelerated when too much traffic has been sent to the scheduler by the other regulators or when the scheduler's queue is empty. As a result, the mean delay of the traffic can be reduced and the scheduler's throughput can be increased. Since no complicated computation is involved, our approach is suitable for the use in high-speed networks.

<p>Today the utilization of all kind of multimedia services in networks increases and due to this demand for real-time communication gets higher for every day. One of the most common protocols used today is Ethernet. It is of interest to find real-time protocols that are useful together with already existing protocols since it is expensive to rebuild the network infrastructure. Several new protocols have been proposed to solve the upcoming problems.</p><p>The objective of this project is to make an inventory and a comparison between Ethernet and these new protocols. During this project four different protocols capability to fulfill the demands for real-time communication have been studied and compared with Ethernet. Three of the protocols are built on the same basic technique as Ethernet and these are PCSMA, CSMA-DCR and DOD-CSMA-CD. The fourth protocol is ATM and it transmits in a different way over communication networks.</p><p>The analysis of this project is pointing out advantages, similarities and differences between the protocols from a real-time perspective. All four protocols are more suitable for real-time requirements than Ethernet.</p>

Στόχος της εργασίας είναι να εμβαθύνει πάνω στο σημαντικό θέμα της ποιότητας υπηρεσίας, εξειδικεύοντας το θέμα για τα ATM switches. Μελετά τους αλγορίθμους που εφαρμόζονται ή λειτουργούν σε θεωρητικό επίπεδο για τα ATM switches και τον τρόπο που επηρεάζουν τις διάφορες παραμέτρους του QoS. Για το λόγο αυτό ορισμένοι αλγόριθμοι εφαρμόζονται σε εξομοιωτή δικτύων και με βάση τη συμπεριφορά τους εκτιμάται η επίδραση των διαφόρων αλγορίθμων στην απόδοση και τη συμπεριφορά των δικτύων. / This research examines closely the important issue of quality of service, specializing the issue on ATM switches. It examines the algorithms that are applied or used on theoretical level on ATM switches and the way they affect the QoS parameters. For this reason some algorithms are applied on a network simulator and according the network’s behavior we estimate the effect of different algorithms on networks’ performance and behavior.

Στη μεταπτυχιακή αυτή εργασίας γίνεται μελέτη και υλοποίηση ενός αλγορίθμου χρονοπρογραμματισμού για μεταγωγέα ΑΤΜ της κατηγορίας αλγορίθμων ranking, ο οποίος χρησιμοποιεί μνήμη οργανωμένη σε πολλαπλές ουρές εισόδου για την αποθήκευση των πακέτων πριν την δρομολόγησή τους. O αλγόριθμος ROLM (Randomized On – Line Matching) επιτυγχάνει μέγιστο ταίριασμα εισόδων – εξόδων λόγω του permutation των εισόδων που γίνεται πριν την είσοδο των αιτήσεων. Επίσης, στοχεύει στη μείωση του latency που αφορά τη hardware υλοποίηση (χάρις στον υπολογισμό του τυχαίου permutation) και σε υψηλά ποσοστά δικαιοσύνης και throughput. Η υλοποίησηση του αλγορίθμου ROLM εκτελείται με δύο τρόπους: α) σε υλικό (FPGA) και β) σε λογισμικό (κώδικας C για AVR). Η πλατφόρμα FPSLIC μας επιτρέπει να αξιολογήσουμε και να συγκρίνουμε τις hardware και software υλοποιήσεις του αλγορίθμου κατά έναν ρεαλιστικό τρόπο, καθώς τόσο ο μικροελεγκτής ΑVR, όσο και η προγραμματιζόμενη λογική FPGA είναι κατασκευασμένα με την ίδια ακριβώς τεχνολογία, ενσωματωμένα σε μια μονολιθική συσκευή. Εξάγονται τα αποτελέσματα μετρήσεων της ταχύτητας και επιφάνειας του χρονοπρογραμματιστή και γίνεται σύγκριση για διαφορετικά μεγέθη μεταγωγέα στην απόδοση μεταξύ των δύο υλοποιήσεων του αλγορίθμου μεταξύ τους. Γίνεται επίσης σύγκριση μεταξύ αποτελεσμάτων του αλγόριθμου ROLM και του αλγορίθμου FIRM, που έχουν ληφθεί από παρεμφερή εργασία. / In this study the design and implementation of a scheduler ranking algorithm for ATM switches is presented. The algorithm employs a multiple-queue input memory for storing packets prior to sending them out. It is the ROLM (Randomized On-Line Matching) algorithm, which performs a high level of input-output matching due to pre-request input permutation. It also reduces hardware-related latency (due to the calculation of random permutation), and achieves fairness and high throughput. The ROLM algorithm was implemented in two ways: one implementation for hardware (FPGA) and one for software (using code C for AVR). The FPSLIC platform allowed for a reliable assessment of the algorithm's hardware and software implementation since the AVR microcontroller and the FGPA programming logic are technologically compatible and integrated on a single device. Measurement results are presented on the controller's surface and speed for different switch sizes as well as a performance comparison is conducted on published results between ROLM and FIRM algorithms.