Human single-stranded DNA binding protein 1 (hSSB1/NABP2) is required for the stability and repair of stalled replication forks

Aberrant DNA replication is a primary cause of mutations that are associated with pathological disorders including cancer. During DNA metabolism, the primary causes of replication fork stalling include secondary DNA structures, highly transcribed regions and damaged DNA. The restart of stalled replication forks is critical for the timely progression of the cell cycle and ultimately for the maintenance of genomic stability. Our previous work has implicated the single-stranded DNA binding protein, hSSB1/NABP2, in the repair of DNA double-strand breaks via homologous recombination. Here, we demonstrate that hSSB1 relocates to hydroxyurea (HU)-damaged replication forks where it is required for ATR and Chk1 activation and recruitment of Mre11 and Rad51. Consequently, hSSB1-depleted cells fail to repair and restart stalled replication forks. hSSB1 deficiency causes accumulation of DNA strand breaks and results in chromosome aberrations observed in mitosis, ultimately resulting in hSSB1 being required for survival to HU and camptothecin. Overall, our findings demonstrate the importance of hSSB1 in maintaining and repairing DNA replication forks and for overall genomic stability.

Middleware for Long-running Applications on Batch Grids. Student Research Symposium poster

Computational grids with multiple batch systems (batch grids) can be powerful infrastructures for executing long-running multicomponent parallel applications. In this paper, we have constructed a middleware framework for executing such long-running applications spanning multiple submissions to the queues on multiple batch systems. We have used our framework for execution of a foremost long-running multi-component application for climate modeling, the Community Climate System Model (CCSM). Our framework coordinates the distribution, execution, migration and restart of the components of CCSM on the multiple queues where the component jobs of the different queues can have different queue waiting and startup times.

ATM- and ATR-mediated phosphorylation of XRCC3 regulates DNA double-strand break-induced checkpoint activation and repair

The RAD51 paralogs XRCC3 and RAD51C have been implicated in homologous recombination (HR) and DNA damage responses. However, the molecular mechanism(s) by which these paralogs regulate HR and DNA damage signaling remains obscure. Here, we show that an SQ motif serine 225 in XRCC3 is phosphorylated by ATR kinase in an ATM signaling pathway. We find that RAD51C but not XRCC2 is essential for XRCC3 phosphorylation, and this modification follows end resection and is specific to S and G(2) phases. XRCC3 phosphorylation is required for chromatin loading of RAD51 and HR-mediated repair of double-strand breaks (DSBs). Notably, in response to DSBs, XRCC3 participates in the intra-S-phase checkpoint following its phosphorylation and in the G(2)/M checkpoint independently of its phosphorylation. Strikingly, we find that XRCC3 distinctly regulates recovery of stalled and collapsed replication forks such that phosphorylation is required for the HR-mediated recovery of collapsed replication forks but is dispensable for the restart of stalled replication forks. Together, these findings suggest that XRCC3 is a new player in the ATM/ATR-induced DNA damage responses to control checkpoint and HR-mediated repair.

A Novel Monte-Carlo-Sampling-Based Receiver for Large-Scale Uplink Multiuser MIMO Systems

In this paper, we propose low-complexity algorithms based on Monte Carlo sampling for signal detection and channel estimation on the uplink in large-scale multiuser multiple-input-multiple-output (MIMO) systems with tens to hundreds of antennas at the base station (BS) and a similar number of uplink users. A BS receiver that employs a novel mixed sampling technique (which makes a probabilistic choice between Gibbs sampling and random uniform sampling in each coordinate update) for detection and a Gibbs-sampling-based method for channel estimation is proposed. The algorithm proposed for detection alleviates the stalling problem encountered at high signal-to-noise ratios (SNRs) in conventional Gibbs-sampling-based detection and achieves near-optimal performance in large systems with M-ary quadrature amplitude modulation (M-QAM). A novel ingredient in the detection algorithm that is responsible for achieving near-optimal performance at low complexity is the joint use of a mixed Gibbs sampling (MGS) strategy coupled with a multiple restart (MR) strategy with an efficient restart criterion. Near-optimal detection performance is demonstrated for a large number of BS antennas and users (e. g., 64 and 128 BS antennas and users). The proposed Gibbs-sampling-based channel estimation algorithm refines an initial estimate of the channel obtained during the pilot phase through iterations with the proposed MGS-based detection during the data phase. In time-division duplex systems where channel reciprocity holds, these channel estimates can be used for multiuser MIMO precoding on the downlink. The proposed receiver is shown to achieve good performance and scale well for large dimensions.

A novel MCMC algorithm for near-optimal detection in large-scale uplink mulituser MIMO systems

In this paper, we propose a low-complexity algorithm based on Markov chain Monte Carlo (MCMC) technique for signal detection on the uplink in large scale multiuser multiple input multiple output (MIMO) systems with tens to hundreds of antennas at the base station (BS) and similar number of uplink users. The algorithm employs a randomized sampling method (which makes a probabilistic choice between Gibbs sampling and random sampling in each iteration) for detection. The proposed algorithm alleviates the stalling problem encountered at high SNRs in conventional MCMC algorithm and achieves near-optimal performance in large systems with M-QAM. A novel ingredient in the algorithm that is responsible for achieving near-optimal performance at low complexities is the joint use of a randomized MCMC (R-MCMC) strategy coupled with a multiple restart strategy with an efficient restart criterion. Near-optimal detection performance is demonstrated for large number of BS antennas and users (e.g., 64, 128, 256 BS antennas/users).

Rad51-Rad52 Mediated Maintenance of Centromeric Chromatin in Candida albicans

Specification of the centromere location in most eukaryotes is not solely dependent on the DNA sequence. However, the non-genetic determinants of centromere identity are not clearly defined. While multiple mechanisms, individually or in concert, may specify centromeres epigenetically, most studies in this area are focused on a universal factor, a centromere-specific histone H3 variant CENP-A, often considered as the epigenetic determinant of centromere identity. In spite of variable timing of its loading at centromeres across species, a replication coupled early S phase deposition of CENP-A is found in most yeast centromeres. Centromeres are the earliest replicating chromosomal regions in a pathogenic budding yeast Candida albicans. Using a 2-dimensional agarose gel electrophoresis assay, we identify replication origins (ORI7-LI and ORI7-RI) proximal to an early replicating centromere (CEN7) in C. albicans. We show that the replication forks stall at CEN7 in a kinetochore dependent manner and fork stalling is reduced in the absence of the homologous recombination (HR) proteins Rad51 and Rad52. Deletion of ORI7-RI causes a significant reduction in the stalled fork signal and an increased loss rate of the altered chromosome 7. The HR proteins, Rad51 and Rad52, have been shown to play a role in fork restart. Confocal microscopy shows declustered kinetochores in rad51 and rad52 mutants, which are evidence of kinetochore disintegrity. CENP-A(CaCse4) levels at centromeres, as determined by chromatin immunoprecipitation (ChIP) experiments, are reduced in absence of Rad51/Rad52 resulting in disruption of the kinetochore structure. Moreover, western blot analysis reveals that delocalized CENP-A molecules in HR mutants degrade in a similar fashion as in other kinetochore mutants described before. Finally, co-immunoprecipitation assays indicate that Rad51 and Rad52 physically interact with CENP-A(CaCse4) in vivo. Thus, the HR proteins Rad51 and Rad52 epigenetically maintain centromere functioning by regulating CENP-A(CaCse4) levels at the programmed stall sites of early replicating centromeres.

Router Attack toward NoC-enabled MPSoC and Monitoring Countermeasures against such Threat

The growing number of applications and processing units in modern Multiprocessor Systems-on-Chips (MPSoCs) come along with reduced time to market. Different IP cores can come from different vendors, and their trust levels are also different, but typically they use Network-on-Chip (NoC) as their communication infrastructure. An MPSoC can have multiple Trusted Execution Environments (TEEs). Apart from performance, power, and area research in the field of MPSoC, robust and secure system design is also gaining importance in the research community. To build a secure system, the designer must know beforehand all kinds of attack possibilities for the respective system (MPSoC). In this paper we survey the possible attack scenarios on present-day MPSoCs and investigate a new attack scenario, i.e., router attack targeted toward NoC architecture. We show the validity of this attack by analyzing different present-day NoC architectures and show that they are all vulnerable to this type of attack. By launching a router attack, an attacker can control the whole chip very easily, which makes it a very serious issue. Both routing tables and routing logic-based routers are vulnerable to such attacks. In this paper, we address attacks on routing tables. We propose different monitoring-based countermeasures against routing table-based router attack in an MPSoC having multiple TEEs. Synthesis results show that proposed countermeasures, viz. Runtime-monitor, Restart-monitor, Intermediate manager, and Auditor, occupy areas that are 26.6, 22, 0.2, and 12.2 % of a routing table-based router area. Apart from these, we propose Ejection address checker and Local monitoring module inside a router that cause 3.4 and 10.6 % increase of a router area, respectively. Simulation results are also given, which shows effectiveness of proposed monitoring-based countermeasures.

Essays on cooperation and reciprocity

This dissertation comprises three essays that use theory-based experiments to gain understanding of how cooperation and efficiency is affected by certain variables and institutions in different types of strategic interactions prevalent in our society.

Chapter 2 analyzes indefinite horizon two-person dynamic favor exchange games with private information in the laboratory. Using a novel experimental design to implement a dynamic game with a stochastic jump signal process, this study provides insights into a relation where cooperation is without immediate reciprocity. The primary finding is that favor provision under these conditions is considerably less than under the most efficient equilibrium. Also, individuals do not engage in exact score-keeping of net favors, rather, the time since the last favor was provided affects decisions to stop or restart providing favors.

Evidence from experiments in Cournot duopolies is presented in Chapter 3 where players indulge in a form of pre-play communication, termed as revision phase, before playing the one-shot game. During this revision phase individuals announce their tentative quantities, which are publicly observed, and revisions are costless. The payoffs are determined only by the quantities selected at the end under real time revision, whereas in a Poisson revision game, opportunities to revise arrive according to a synchronous Poisson process and the tentative quantity corresponding to the last revision opportunity is implemented. Contrasting results emerge. While real time revision of quantities results in choices that are more competitive than the static Cournot-Nash, significantly lower quantities are implemented in the Poisson revision games. This shows that partial cooperation can be sustained even when individuals interact only once.

Chapter 4 investigates the effect of varying the message space in a public good game with pre-play communication where player endowments are private information. We find that neither binary communication nor a larger finite numerical message space results in any efficiency gain relative to the situation without any form of communication. Payoffs and public good provision are higher only when participants are provided with a discussion period through unrestricted text chat.

A voz e a invocação para musicar a vida: ressonâncias entre música e psicanálise

A articulação entre a psicanálise e a música, mais especificamente a produzida a partir do paradigma de Arnold Schönberg, renovado por John Cage, se mostra emblemática para pensar a constituição do sujeito em Sigmund Freud e Jacques Lacan, bem como para refletir sobre a escuta clínica, o ato analítico enquanto poético, e a escrita pulsional do sujeito como resposta à invocação da voz. O momento de estruturação do sujeito implica a dimensão de musicalidade da linguagem que permite o ato da fala. O sujeito nasce em um ponto em que o significante (simbólico) escreve no real do corpo um possível, um começo, uma marca que invoca uma nota e uma letra, sendo estes os dois aspectos da linguagem: a musicalidade (continuidade) e a fala (descontinuidade em movimento). Este ponto escreve e cria um vazio no sujeito que está e estará sempre em pulsação. Se o real grita caoticamente, é possível que se cante e se musique a vida com a criação de notas singulares, efeito do movimento desejante e de uma escrita pelo circuito da pulsão invocante na partitura já dada pelo Outro e face aos encontros com pedaços de real. A música tem a capacidade de retirar o sujeito de uma surdez de seu próprio desejo, o convocando a recriar a linguagem por seus atos. O paradigma de Schönberg, bem como a música criada a partir deste momento, nos dá a ouvir um saber-fazer com a voz no qual a dimensão equivocante (de equivoco e de invocação) da linguagem pode ressurgir por uma via nova. A transmissão de um saber-fazer com o objeto voz por ele efetuado se apresenta como uma radicalização do efeito de verdade do real, ressoando borromeanamente sobre o simbólico e o imaginário, invocando o momento originário do sujeito, de um começo sempre a recomeçar, que se faz ouvir como uma invocação de musicar a vida de uma maneira ética, estética e poética. É através dos eixos acima expostos que nos é possível sustentar, com Lacan, uma prática clínica orientada para além da repetição em direção a um significante novo. Trata-se de uma orientação que parte dos encontros com o real aos quais o sujeito é confrontado ao acaso visando o movimento renascente pelo qual ele pode re-escutar o inaudito do real contínuo perdido, o que faz com que seu ritmo singular possa ser, uma vez mais e de modo inédito, reinventado. A psicanálise pode ser, portanto, entendida como uma prática invocante, como uma abertura para que o sujeito possa, com entusiasmo, musicar a vida.

Low-rank optimization with trace norm penalty

The paper addresses the problem of low-rank trace norm minimization. We propose an algorithm that alternates between fixed-rank optimization and rank-one updates. The fixed-rank optimization is characterized by an efficient factorization that makes the trace norm differentiable in the search space and the computation of duality gap numerically tractable. The search space is nonlinear but is equipped with a Riemannian structure that leads to efficient computations. We present a second-order trust-region algorithm with a guaranteed quadratic rate of convergence. Overall, the proposed optimization scheme converges superlinearly to the global solution while maintaining complexity that is linear in the number of rows and columns of the matrix. To compute a set of solutions efficiently for a grid of regularization parameters we propose a predictor-corrector approach that outperforms the naive warm-restart approach on the fixed-rank quotient manifold. The performance of the proposed algorithm is illustrated on problems of low-rank matrix completion and multivariate linear regression. © 2013 Society for Industrial and Applied Mathematics.

Multi-version Speculative Concurrency Control with Delayed Commit

This paper presents an algorithm which extends the relatively new notion of speculative concurrency control by delaying the commitment of transactions, thus allowing other conflicting transactions to continue execution and commit rather than restart. This algorithm propagates uncommitted data to other outstanding transactions thus allowing more speculative schedules to be considered. The algorithm is shown always to find a serializable schedule, and to avoid cascading aborts. Like speculative concurrency control, it considers strictly more schedules than traditional concurrency control algorithms. Further work is needed to determine which of these speculative methods performs better on actual transaction loads.

Reliability, Availability, Dependability and Performability: A User-centered View

Reliability and availability have long been considered twin system properties that could be enhanced by distribution. Paradoxically, the traditional definitions of these properties do not recognize the positive impact of recovery as distinct from simple repair and restart on reliability, nor the negative effect of recovery, and of internetworking of clients and servers, on availability. As a result of employing the standard definitions, reliability would tend to be underestimated, and availability overestimated. We offer revised definitions of these two critical metrics, which we call service reliability and service availability, that improve the match between their formal expression, and intuitive meaning. A fortuitous advantage of our approach is that the product of our two metrics yields a highly meaningful figure of merit for the overall dependability of a system. But techniques that enhance system dependability exact a performance cost, so we conclude with a cohesive definition of performability that rewards the system for performance that is delivered to its client applications, after discounting the following consequences of failure: service denial and interruption, lost work, and recovery cost.

A Self-initializing Eyebrow Tracker for Binary Switch Emulation

We designed the Eyebrow-Clicker, a camera-based human computer interface system that implements a new form of binary switch. When the user raises his or her eyebrows, the binary switch is activated and a selection command is issued. The Eyebrow-Clicker thus replaces the "click" functionality of a mouse. The system initializes itself by detecting the user's eyes and eyebrows, tracks these features at frame rate, and recovers in the event of errors. The initialization uses the natural blinking of the human eye to select suitable templates for tracking. Once execution has begun, a user therefore never has to restart the program or even touch the computer. In our experiments with human-computer interaction software, the system successfully determined 93% of the time when a user raised his eyebrows.

How different are the correlates of onset and continuation of civil wars?

It is very common to analyse the factors associated with the onset and continuation of civil wars entirely separately, as if there were likely to be no similarity between them. This is an overstatement of the theoretical position, which has established only that they may be different (i.e. less than perfectly correlated). The hypothesis that the explanatory variables are the same is not theoretically excludable and is empirically testable, both for individual variables and for combinations of them. Starting from this approach yields a rather different picture of the factors associated with the continuation of civil wars, because the relatively small sample size means that confidence intervals on individual coefficients are wide in this case. It is shown here that country size, mountainous terrain and (in most datasets) ethnic diversity seem significant for the continuation of civil wars, starting from the null hypothesis that variables affect onset and continuation probabilities identically, rather than entirely independently. One variable that affects onset and continuation significantly differently is anocracy, which we find to matter only for onset. Civil war is more likely if it occurred two years previously, as well as one year previously, which indicates that wars are more likely to restart after only one year of peace, and also more likely to stop in their first year. The combined model strengthens the result that ethnic diversity matters (it is consistently significant across datasets, whereas it is not when onset is analysed separately), although in the UCD/PRIO dataset it is significant only for onset. By contrast, if continuation is analysed independently, virtually nothing is significant except a pre-1991 dummy and a dummy for civil war two years previously.

Acompanhamento da III fase do aterro sanitário da Meia Serra

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Civil na Área de Especialização de Hidráulica