The N-terminal tails of histone proteins protrude from the nucleosome core and are extensively post-translationally modified. These modifications are proposed to affect many DNA-based processes such as transcription, DNA replication and repair. Post-translational modifications on histone tails do not act independently but are subject to crosstalk. One example of crosstalk is on histone H3 between lysine 14 (H3K14) and trimethylated lysine 4 (H3K4me3), a modification found at the 5’ end of most active or poised genes. In this work, Western blots and chromatin immunoprecipitation (ChIP) experiments show that different amino acid substitutions at histone H3 position 14 cause varying degrees of H3K4me3 loss, indicating that H3K14 is not essential for H3K4me3 but acts as a modulator of H3K4me3 levels. A neighbouring residue, H3P16 is also important for H3K4me3 and may operate in concert with H3K14 to control H3K4me3. These crosstalk pathways have gene-specific effects and the levels of H3K4me3 are influenced to different extents on genes that fall into functionally distinct classes. A model is proposed to explain how H3K14/H3P16 may exert these varying effects on H3K4me3 at individual genes. In addition to its ability to regulate H3K4me3, H3K14 also influences the levels of two modifications on H3K18, acetylation and monomethylation. A ChIP-sequencing experiment has shown that H3K18me1, a previously uncharacterised modification in S. cerevisiae, is widely distributed throughout the genome and correlates strongly with histone H3 levels. The potential for a functional acetyl/methyl switch at H3K18 is explored. Together, these data indicate that, with gene-specific effects, crosstalk between histone modifications may be even more complex than originally thought.

Submitted by Edisangela Bastos (edisangela@ufpa.br) on 2013-01-31T19:20:25Z No. of bitstreams: 2 license_rdf: 23898 bytes, checksum: e363e809996cf46ada20da1accfcd9c7 (MD5) Dissertacao_MedidasCaracterizcaoCrosstalk.pdf: 2130898 bytes, checksum: fefbf7aec981ced586091231873c1a8e (MD5) / Approved for entry into archive by Ana Rosa Silva(arosa@ufpa.br) on 2013-02-05T14:41:01Z (GMT) No. of bitstreams: 2 license_rdf: 23898 bytes, checksum: e363e809996cf46ada20da1accfcd9c7 (MD5) Dissertacao_MedidasCaracterizcaoCrosstalk.pdf: 2130898 bytes, checksum: fefbf7aec981ced586091231873c1a8e (MD5) / Made available in DSpace on 2013-02-05T14:41:02Z (GMT). No. of bitstreams: 2 license_rdf: 23898 bytes, checksum: e363e809996cf46ada20da1accfcd9c7 (MD5) Dissertacao_MedidasCaracterizcaoCrosstalk.pdf: 2130898 bytes, checksum: fefbf7aec981ced586091231873c1a8e (MD5) Previous issue date: 2009-09 / O presente trabalho apresenta testes e experimentos laboratoriais para medição de crosstalk e ruído impulsivo em sistemas DSL, os quais são de grande importância para o aperfeiçoamento e evolução deste tipo de tecnologia. O estudo do crosstalk voltou-se a uma campanha de medições em cabos telefônicos reais de curto comprimento e operando em altas frequências. Os resultados destas medidas foram utilizados no cálculo da capacidade de transmissão de sistemas DSL operando neste cenário ainda pouco explorado. O estudo do ruído impulsivo foi focado no desenvolvimento de um sistema digitalizador de sinais de linha telefônica possibilitando a medição real deste tipo de fenômeno. / The current work presents tests and laboratory experiments to measure crosstalk and impulsive noise in DSL systems, which are of great importance for the improvement and development of this technology. The crosstalk study was focused in a measurements campaign of short-length cables operating at extremely high frequencies. The results were used in the transmission rates calculation of DSL systems operating in this type of unexplored scenario. The impulsive noise study focused on the development of a telephone line digitizing system allowing real measurements of the noise.

Capacitive crosstalk noise can affect the delay of a switching signal or induce a glitch on a static signal causing timing violations or chip failure. Crosstalk noise depends on coupling parasitics, driver strength, signal timing characteristics, and signal transition patterns. Layout level crosstalk analysis techniques are generally pessimistic and computationally expensive for large designs due to lack of design flexibility at lower-levels of design hierarchy. The architectural decisions such as type of interconnect architecture, number of storage and execution units, network of communicating units, data bus width, etc., have a major impact on the quality of design attributes such as area, speed, power, and noise. To address all these concerns, we propose a high-level synthesis framework to optimize for worst-case crosstalk patterns on coupled nets, a floorplan driven high-level synthesis framework to minimize coupling capacitance, and an on-chip technique to dynamically detect and eliminate worst-case crosstalk pattern on bus-based macro-cell designs. Due to Miller coupling effect, the switching activity pattern on adjacent nets may increase the effective capacitance seen by a victim net and thereby it may cause a worst-case signal delay on the victim net. However, signal activity pattern on coupled nets are dependent on data correlations which in turn depend on resource sharing. The resource sharing in turn depends on scheduling, allocation, and binding during high-level synthesis flow. Therefore, we propose a Simulated Annealing (SA) based design space exploration of HLS design subspace, bus line re-ordering, and encoding subspaces to optimize for worst-case crosstalk pattern in bus-based macro-cell designs. We demonstrate that the proposed framework will aid layout level techniques in eliminating false positive violations. We also propose an SA based algorithm to explore floorplan and HLS subspaces to optimize coupling capacitances in bus-based macro-cell designs. We have integrated an RTL floorplanner in HLS flow to estimate coupling capacitances between bus lines. Crosstalk analysis using Cadence Celtic shows that the designs generated by the proposed framework results in less number of crosstalk violations compared to designs generated through traditional ASIC design flow. We also propose an on-chip crosstalk detection and elimination technique that dynamically detects and eliminates worst-case crosstalk pattern with minimum area penalty compared to other layout level techniques reported in the literature.

The continuous scaling of interconnect wires in deep submicron (DSM)circuits result in increased interconnect delay, power and crosstalk noise. In this dissertation, we address the problem of multi-metric optimization at post layout level in the design of deep submicron designs and develop a game theoretic framework for its solution. Traditional approaches in the literature can only perform single metric optimization and cannot handle multiple metrics. However, in interconnect optimization, the simultaneous optimization of multiple parameters such as delay, crosstalk noise and power is necessary and critical. Thus, the work described in this dissertation research addressing multi-metric optimization is an important contribution.Specifically, we address the problems of simultaneous optimization of interconnect delay and crosstalk noise during (i) wire sizing (ii) gate sizing (iii) integrated gate and wire sizing, and (iv) gate sizing considering process variations. Game the ory provides a natural framework for handling conflicting situations and allows optimization of multiple parameters. This property is exploited in modeling the simultaneous optimization of various design parameters such as interconnect delay, crosstalk noise and power, which are conflicting in nature. The problem of multi-metric optimization is formulated as a normal form game model and solved using Nash equilibrium theory. In wire sizing formulations, the net segments within a channel are modeled as the players and the range of possible wire sizes forms the set of strategies. The payoff function is modeled as (i) the geometric mean of interconnect delay andcrosstalk noise and (ii) the weighted-sum of interconnect delay, power and crosstalk noise, in order to study the impact of different costfunctions with two and three metrics respectively. In gate sizing formulations, the range of possible gate sizes is modeled as the set of strategies and the payoff function is modeled as the geome tric mean of interconnect delay and crosstalk noise. The gates are modeled as the players while performing gate sizing, whereas, the interconnect delay and crosstalk noise are modeled as players for integrated wire and gate sizing framework as well as for statistical gate sizing under the impact of process variations.The various algorithms proposed in this dissertation (i) perform multi-metric optimization (ii) achieve significantly better optimization and run times than other methods such as simulated annealing, genetic search, and Lagrangian relaxation (iii) have linear time and space complexities, and hence can be applied to very large SOC designs, and (iv) do not require rerouting or incur any area overhead. Thecomputational complexity analysis of the proposed algorithms as well as their software implementations are described, and experimental results are provided that establish the efficacy of the proposed algorithms.

Die Zellteilung/Zytokinese ist ein grundlegender zellulärer Prozess und essentiell für das Wachstum von einzelligen und mehrzelligen Organismen. Reguliert wird dieser Prozess durch komplexe molekulare Mechanismen sowie einer Vielzahl von interaktiven Netzwerken. In Pilzen koordiniert eine Kinase-Kaskade, das Septierungs-Initiierungs Netzwerk (SIN) das Fortschreiten des Zellzyklus mit dem Beginn der Zellteilung und kontrolliert die Septenbildung. Fehlregulation des homologen Hippo Netzwerks in Tieren führt zu Gewebewucherungen und Tumorbildung, was die konservierte Bedeutung dieser Regulationsnetzwerke in verschiedenen Organismen unterstreicht. Obwohl die Septenbildung essentiell für das Wachstum und die Differenzierung von Schimmelpilzen ist, bleibt die Frage wie die Septierung reguliert wird und aus welchen Komponenten sich das SIN Netzwerk in filamentösen Pilzen zusammensetzt bisher noch unbeantwortet. Mit Hilfe von in silico Analysen konnten homologe Proteine für fast alle SIN Netzwerk Komponenten im Modellorganismus Neurospora crassa identifiziert werden. Die Analyse dieser vorhergesagten SIN Komponenten ermöglichte die Charakterisierung der SIN-Kinase-Kaskade, bestehend aus CDC-7, SID-1 und DBF-2 sowie den entsprechenden, regulatorischen Untereinheiten CDC-14 und MOB-1. Es konnte gezeigt werden, dass DBF-2 durch SID-1 am hydrophoben Motiv phosphoryliert und aktiviert wird und dass eine SID-1 abhängige Stimulation von DBF-2 durch Zugabe von CDC-7 weiter gesteigert wird. Diese Daten liefern den ersten biochemischen Nachweis für die schrittweise Aktivierung einer dreistufigen SIN-Kinase-Kaskade in Pilzen. Es wurde weiterhin gezeigt, dass die gesamte SIN Kaskade konstitutiv und Zellzyklus unabhängig an den Spindelpolkörpern akkumuliert und dass alle SIN Proteine an kontrahierenden Septen lokalisieren. Demzufolge ist im Gegensatz zu den einzelligen Pilzen die Lokalisation und Aktivität der SIN Komponenten in Synzytium-bildenden Ascomyzeten Zellzyklus unabhängig. Darüber hinaus deutet die Charakterisierung von DBF-2 Mutanten, in denen die beiden regulatorischen Aminosäuren (Ser499 and Thr671) mutiert sind, darauf hin, dass ein dynamischer Phosphorylierungs-/Dephosphorylierungszyklus des Ser499 entscheidend für die Aktivität und Funktion von DBF-2 in N. crassa ist. Diese Daten haben Einfluss auf das allgemeine Verständnis der Aktivierung von NDR Kinasen, denn bisher wurde für NDR Kinasen höherer Eukaryonten eine folgegebundene Phosphorylierung beider regulatorischer Reste angenommen. Der Ste20-verwandten Kinase MST-1 konnte eine Funktion als SIN-assoziierte Kinase, die parallel zu SID-1 agiert, zugeordnet werden. SID-1 und MST-1 werden auf entgegengesetzte Weise von der oberhalb agierenden SIN Kinase CDC-7 reguliert, was nahelegt, dass MST-1 für die Feinabstimmung des SIN erforderlich ist. Lifeact- und Formin-GFP Reporter Konstrukte zeigten, dass in der Δmst-1 Mutante abnormale, kortikale Actomyosin-Ringe gebildet werden, was eine Fehlpositionierung der Septen und die Bildung von unregelmäßigen Spiralen zur Folge hat. Diese Defekte entsprechen partiell jenen der MOR Mutanten. Diese Mutanten weisen ein defektes NDR Kinase Netzwerk auf, welches für das polare Wachstum verantwortlich ist (MOR). Es stellte sich heraus, dass MST-1 mit den zentralen MOR Kinasen POD-6 und COT-1 interagiert und sowohl die SIN Effektor Kinase DBF-2 als auch die MOR Effektor Kinase COT-1 aktiviert. Somit fungiert MST-1 als dual-spezifisches Enzym. Eine weitere Vernetzung beider Signalwege ist durch die Bildung von Heterodimeren gegeben. Die in dieser Studie identifizierten verschiedenen Ebenen der Vernetzung des SIN und MOR, sowie entsprechende Daten aus anderen Modellorganismen wie S. pombe und D. melanogaster, lassen vermuten, dass antagonistische Interaktionen zwischen homologen NDR Kinase Netzwerken ein genereller Mechanismus zur Koordination beider Signalwege darstellt und auch in höheren Organismen konserviert ist. Durch die Annotierung mehrerer Pilzgenome wurden zahlreiche Gene mit einer Homologie zu den S. cerevisiae BUD Genen auch in filamentösen Pilzen identifiziert. Epistatische und biochemische Analysen ergaben, dass das MOR Netzwerk als negativer Regulator der Septenbildung oberhalb des BUD komplex fungiert und dass COT-1 im Gegensatz zu DBF-2, die beiden Septierungsmarkerproteine BUD-3/BUD-4 phosphoryliert. Folglich könnte die Regulation von BUD-3 (und eventuell auch BUD-4) durch COT-1 ein Mechanismus des MOR Netzwerks sein, um die Septenbildung in N. crassa zu inhibieren.

Darbo tikslas nustatyti skirstymo baltymo GAB1 ryšį su anti-apoptoziniu PI3K/Akt bei mitogeniniu Ras/MAPK signalo perdavimo keliais ir įvertinti GAB1 įtaką šių kelių sąveikai EGFR signalo perdavimo tinkle. Darbo uždaviniai: įvertinti epitelinių ląstelių endogeninio GAB1 veiksmingumą EGF signalo perdavimo metu; nustatyti sąveikos pobūdį tarp PI3K/Akt ir Ras/MAPK kelių EGF signalo metu; kiekybiškai įvertinti GAB1 svarbą EGF signalo perdavimui per PI3K/Akt ir Ras/MAPK kelių in vivo, rezultatus lyginant su matematinio modelio prognozėmis in silico; nustatyti GAB1 veiksmingumo ir jo reguliacijos grįžtamaisiais ryšiais įtaką PI3K-MAPK sąveikos stiprumui priklausomai nuo EGF dozės ir laiko; ištirti GAB1 svarbą EGFR ir insulino receptoriaus signalo perdavimo tinklų sąveikai; modifikuoti Westerno pernašos metodą palyginamajai kiekybinei ir kokybinei baltymų analizei. Darbo išvados: stimuliavus EGFR, skirstymo baltymas GAB1 tampa veiksmingu; EGF lemia reciprokinę PI3K/Akt ir Ras/MAPK signalo perdavimo kelių sąveiką per GAB1; GAB1 yra pagrindinis teigiamo atgalinio ryšio elementas PI3K kelyje, padedąs pagreitinti, stiprinti ir išlaikyti MEK/ERK kinazių atsaką; PI3K-MAPK sąveikos stiprumas kinta laike ir yra atvirkščiai proporcingas EGF signalo stiprumui; GAB1 reikalingas sinergistiškai stiprinti insulinu ir mažomis EGF dozėmis stimuliuojamų ląstelių Ras/MAPK atsaką; sukurtas „Multi-juostelių“ imunopernašos metodas yra tinkamas palyginamajai kiekybinei ir kokybinei baltymų analizei... [toliau žr. visą tekstą] / The aim of the thesis was to determine a connection of endogenous docking protein GAB1 with anti-apoptotic PI3/Akt and Ras/MAPK signaling pathways and to estimate GAB1 contribution to their crosstalk in EGFR signaling network. The tasks: to evaluate GAB1 efficacy upon EGFR stimulation; to examine the nature of crosstalk between PI3K/Akt and Ras/MAPK pathways; to evaluate the contribution of GAB1 to EGF signaling via PI3K/Akt and Ras/MAPK pathways in vivo comparing the results with prognosis in silico; to estimate the EGF dose- and time-dependent impact of GAB1 efficacy and its feedback regulation on the strength of PI3K-MAPK interaction; to investigate the role of GAB1 for crosstalk of EGFR and insulin receptor signaling networks; to modify Western blotting procedure for comparative quantitative and qualitative protein analysis. The conclusions: the docking protein GAB1 is functional upon EGFR stimulation; PI3K/Akt and Ras/MAPK signaling pathways crosstalk reciprocally via GAB1 in response to EGF; GAB1 is major positive feedback element in PI3K pathway amplifying and sustaining MEK/ERK response to EGF; the strength of PI3K-MAPK interaction depends on time and is inversely proportional to EGF signal strength; GAB1 is required to synergistically potentate the Ras/MAPK response to tandem cell treatment with insulin and low EGF doses; the developed Multistrip immunoblotting method is suitable for comparative quantitative and qualitative protein analysis. In comparison with a... [to full text]

In this thesis the main objectives were to improve the liquid crystal shutters and to develop a stereoscopic vision application called 3D Dual View. The vision quality of a 3D system based on active glasses is direct related to the performance of the liquid crystal shutters. There are a lot of parameters that plays an important role in the quality of 3D glasses. Thus, efforts were concentrated in the organization of the liquid crystal molecules between the substrates and in the liquid crystal itself. We studied different configurations of shutters using nematic liquid crystal and ferroelectric liquid crystal (smectic), with and without polymer. Furthermore, the ferroelectric samples were analyzed using a full optical snapshot matrix Mueller polarimenter made by UBO (Université de Bretagne Occidentale) in partnership with Télécom-Bretagne. The second part was the development of 3D Dual View System. It is a stereoscopic vision system based on a mixture of active and passive 3D solution which displays a 3D image that can be viewed simultaneously by two spectators, but from different perspectives. To allow two different points-of-view of a scene or object in three dimensions, the system has to multiplex four images, one pair to form the 3D image for one viewer in one perspective and the other pair for the second viewer in other perspective. We describe different techniques to multiplex and demultiplex the video streams taking into account the physiological aspects, market, image quality and the crosstalk. The crosstalk between the images leads to an effect called ghosting, which the viewer sees a low intensity image that belongs to the other viewer. Then, we also characterized the ghosting effect (crosstalk) and proposed an algorithm of ghostbusting to compensate it.

Cost reduction has been and will continue to be a primary driving force in the evolution of hardware design and associated technologies. The objective of this research is to design low-cost signal acquisition systems for characterizing wideband and high-speed signals. As the bandwidth and the speed of such signals increase, the cost of testing also increases significantly; therefore, innovative hardware and algorithm co-design are needed to relieve this problem. In Chapter 2, a low-cost multi-rate system is proposed for characterizing the spectra of wideband signals. The design is low-cost in the sense of the actual component cost, the system complexity, and the effort required for calibration. The associated algorithms are designed such that the hardware can be implemented with low-complexity yet be robust enough to deal with various hardware variations. A hardware prototype is built not only to verify the proposed hardware scheme and algorithms but to serve as a concrete example that shows that characterizing signals with sub-Nyqusit sampling rate is feasible. Chapter 3 introduces a low-cost time-domain waveform reconstruction technique, which requires no mutual synchronization mechanisms. This brings down cost significantly and enables the implementation of systems capable of capturing tens of Gigahertz (GHz) signals for significantly lower cost than high-end oscilloscopes found in the market today. For the first time, band-interleaving and incoherent undersampling techniques are combined to form a low-cost solution for waveform reconstruction. This is enabled by co-designing the hardware and the back-end signal processing algorithms to compensate for the lack of coherent Nyquist rate sampling hardware. A hardware prototype was built to support this work. Chapter 4 describes a novel test methodology that significantly reduces the required time for crosstalk jitter characterization in parallel channels. This is done by using bit patterns with coprime periods as channel stimuli and using signal processing algorithms to separate multiple crosstalk coupling effects. This proposed test methodology can be applied seamlessly in conjunction with the current test methodology without re-designing the test setup. More importantly, the conclusion derived from the mathematical analysis shows that only such test stimuli give unbiased characterization results, which are critical in all high-precision test setups. Hardware measurement results and analysis are provided to support this methodology. This thesis starts with an overview of the background and a literature review. Three major previously mentioned works are addressed in three separate chapters. Each chapter documents the hardware designs, signal processing algorithms, and associated mathematical analyses. For the purpose of verification, the hardware measurement setups and results are discussed at the end of these three chapters. The last chapter presents conclusions and future directions for work from this thesis.

The main focus of this thesis is placed on high frequency PCB signal Integrity Is-sues and RF/Microwave filters using EBG structures. From the signal Integrity aspect, two topics were mainly discussed. On one hand, the effect of increasing frequency on classical design rules for crosstalk reduction in PCBs was investigated experimentally and by full-wave simulations. An emphasis was placed on the 3×W spacing rule and the use of guard traces. Single-ended and differential transmission lines were considered. S-parameter measurements and simu-lations were carried out at high-frequency (up to 20 GHz). The results emphasize the necessity to reevaluate traditional design rules for their suitability in high frequency applications. Also, the impacts of using guard traces for high frequency crosstalk re-duction were clearly pointed out. On the other hand, the effect of high loss PCB ma-terials on the signal transmission characteristics of microstrip lines at high frequency (up to 20 GHz) was treated. Comparative studies were carried out on different micro-strip configurations using standard FR4 substrate and a high frequency dielectric ma-terial from Rogers, Corporation. The experimental results highlight the dramatic im-pact of high dielectric loss materials (FR4 and solder mask) and magnetic plating metal (nickel) on the high frequency signal attenuation and loss of microstrip trans-mission lines. Besides, the epoxy-based SU8 photoresist was characterized at high frequency (up to 50 GHz) using on-wafer conductor-backed coplanar waveguide transmission lines. A relative dielectric constant of 3.2 was obtained at 30 GHz. Some issues related to the processing of this material, such as cracks, hard-skin, etc, were also discussed. Regarding RF/Microwave filters, the concept of Electromagnetic Band Gap (EBG) was used to design and fabricate novel microstrip bandstop filters using periodically modified substrate. The proposed EBG structures, which don’t suffer conductor backing issues, exhibit interesting frequency response characteristics. The limitations of modeling and simulation tools in terms of speed and accuracy are also examined in this thesis. Experiments and simulations were carried out show-ing the inadequacies of the Spice diode model for the simulations in power electronics. Also, an Artificial Neural Network (ANN) model was proposed as an alternative and a complement to full-wave solvers, for a quick and sufficiently accurate simulation of interconnects. A software implementation of this model using Matlab’s ANN toolbox was shown to considerably reduce (by over 800 times) the simulation time of microstrip lines using full-wave solvers such as Ansoft’s HFSS and CST’s MWS. Finally, a novel cooling structure using a double heatsink for high performance electronics was presented. Methods for optimizing this structure were also discussed. / QC 20100809

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