Cooperative memory and database transactions

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do Grau de Mestre em Engenharia Informática

Static detection of anomalies in transactional memory programs

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do Grau de Mestre em Engenharia Informática

Vibration control with shape-memory alloys in civil engineering structures

Dissertação apresentada à Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Doutor em Engenharia Civil

Rely-guarantee protocols for safe interference over shared memory

Mutable state can be useful in certain algorithms, to structure programs, or for efficiency purposes. However, when shared mutable state is used in non-local or nonobvious ways, the interactions that can occur via aliases to that shared memory can be a source of program errors. Undisciplined uses of shared state may unsafely interfere with local reasoning as other aliases may interleave their changes to the shared state in unexpected ways. We propose a novel technique, rely-guarantee protocols, that structures the interactions between aliases and ensures that only safe interference is possible. We present a linear type system outfitted with our novel sharing mechanism that enables controlled interference over shared mutable resources. Each alias is assigned separate, local roles encoded in a protocol abstraction that constrains how an alias can legally use that shared state. By following the spirit of rely-guarantee reasoning, our rely-guarantee protocols ensure that only safe interference can occur but still allow many interesting uses of shared state, such as going beyond invariant and monotonic usages. This thesis describes the three core mechanisms that enable our type-based technique to work: 1) we show how a protocol models an alias’s perspective on how the shared state evolves and constrains that alias’s interactions with the shared state; 2) we show how protocols can be used while enforcing the agreed interference contract; and finally, 3) we show how to check that all local protocols to some shared state can be safely composed to ensure globally safe interference over that shared memory. The interference caused by shared state is rooted at how the uses of di↵erent aliases to that state may be interleaved (perhaps even in non-deterministic ways) at run-time. Therefore, our technique is mostly agnostic as to whether this interference was the result of alias interleaving caused by sequential or concurrent semantics. We show implementations of our technique in both settings, and highlight their di↵erences. Because sharing is “first-class” (and not tied to a module), we show a polymorphic procedure that enables abstract compositions of protocols. Thus, protocols can be specialized or extended without requiring specific knowledge of the interference produce by other protocols to that state. We show that protocol composition can ensure safety even when considering abstracted protocols. We show that this core composition mechanism is sound, decidable (without the need for manual intervention), and provide an algorithm implementation.

The use of canonical correlation analysis to assess the relationship between executive functioning and verbal memory in older adults

Executive functioning (EF), which is considered to govern complex cognition, and verbal memory (VM) are constructs assumed to be related. However, it is not known the magnitude of the association between EF and VM, and how sociodemographic and psychological factors may affect this relationship, including in normal aging. In this study, we assessed different EF and VM parameters, via a battery of neurocognitive/psychological tests, and performed a Canonical Correlation Analysis (CCA) to explore the connection between these constructs, in a sample of middle- aged and older healthy individuals without cognitive impairment (N = 563, 50+ years of age). The analysis revealed a positive and moderate association between EF and VM independently of gender, age, education, global cognitive performance level, and mood. These results confirm that EF presents a significant association with VM performance.

A Novel Memory-centric Architecture and Organization of Processors and Computers

The modern computer systems that are in use nowadays are mostly processor-dominant, which means that their memory is treated as a slave element that has one major task – to serve execution units data requirements. This organization is based on the classical Von Neumann's computer model, proposed seven decades ago in the 1950ties. This model suffers from a substantial processor-memory bottleneck, because of the huge disparity between the processor and memory working speeds. In order to solve this problem, in this paper we propose a novel architecture and organization of processors and computers that attempts to provide stronger match between the processing and memory elements in the system. The proposed model utilizes a memory-centric architecture, wherein the execution hardware is added to the memory code blocks, allowing them to perform instructions scheduling and execution, management of data requests and responses, and direct communication with the data memory blocks without using registers. This organization allows concurrent execution of all threads, processes or program segments that fit in the memory at a given time. Therefore, in this paper we describe several possibilities for organizing the proposed memory-centric system with multiple data and logicmemory merged blocks, by utilizing a high-speed interconnection switching network.

Programme de remédiation cognitive pour patients présentant une schizophrénie ou un trouble associé (Recos) : résultats préliminaires [Cognitive remediation program for individuals living with schizophrenia (Recos): preliminary results].

BACKGROUND: Nowadays, cognitive remediation is widely accepted as an effective treatment for patients with schizophrenia. In French-speaking countries, techniques used in cognitive remediation for patients with schizophrenia have been applied from those used for patients with cerebral injury. As cognitive impairment is a core feature of schizophrenia, the Département de psychiatrie du CHUV in Lausanne (DP-CHUV) intended to develop a cognitive remediation program for patients with a schizophrenia spectrum disease (Recos-Vianin, 2007). Numerous studies show that the specific cognitive deficits greatly differ from one patient to another. Consequently, Recos aims at providing individualized cognitive remediation therapy. In this feasibility trial, we measured the benefits of this individualized therapy for patients with schizophrenia. Before treatment, the patients were evaluated with a large battery of cognitive tests in order to determine which of the five specific training modules - Verbal memory, visuospatial memory and attention, working memory, selective attention, reasoning - could provide the best benefit depending on their deficit. OBJECTIVES: The study was designed to evaluate the benefits of the Recos program by comparing cognitive functioning before and after treatment. METHOD: Twenty-eight patients with schizophrenia spectrum disorders (schizophrenia [n=18], schizoaffective disorder [n=5], schizotypal disorder [n=4], schizophreniform disorder [n=1], DSM-IV-TR) participated in between one and three of the cognitive modules. The choice of the training module was based on the results of the cognitive tests obtained during the first evaluation. The patients participated in 20 training sessions per module (one session per week). At the end of the training period, the cognitive functioning of each patient was reevaluated by using the same neuropsychological battery. RESULTS: The results showed a greater improvement in the cognitive functions, which were specifically trained, compared to the cognitive functions, which were not trained. However, an improvement was also observed in both types of cognitive functions, suggesting an indirect cognitive gain. CONCLUSION: In our view, the great heterogeneity of the observed cognitive deficits in schizophrenia necessitates a detailed neuropsychological investigation as well as an individualized cognitive remediation therapy. These preliminary results need to be confirmed with a more extended sample of patients.

On the significance of CD8 alpha alpha expression for T cell memory.

Longitudinal studies on the kinetics of viral antigen specific CD8 T cell responses have led to a model whereby a relatively small subset of the primary effector CD8 T cells expanding after the first week of acute viral infection initiate a program of cell survival and differentiation into long lived memory T cells. These T cells are then critical for maintaining protective immunity to subsequent viral infection. Recent observations, using fluorescent tetramers of the MHC class Ib molecule TL, link transient expression of CD8alphaalpha homodimers on expanding primary effector CD8 T cells to the generation of memory cells. At present it is controversial what the role of CD8alphaalpha is in the generation of memory CD8 T cells. The involvement of the high affinity CD8alphaalpha ligand, the TL molecule, is not understood either. However, evidence from two viral infection models in mice, including one paper in this issue of the European Journal of Immunology, suggest a role for CD8alphaalpha in this process and call for additional research focus into these issues.

Astrocytes: powering memory.

Creating long-term memory requires a cellular program in neurons involving gene expression, protein synthesis, and formation of new synaptic connections. Suzuki et al. (2011) show that astrocytes, glial cells of the brain, play a necessary role in this program by converting glycogen to lactate and transporting it to neurons.

Immune Memory and Exhaustion: Clinically Relevant Lessons from the LCMV Model.

The development of dysfunctional or exhausted T cells is characteristic of immune responses to chronic viral infections and cancer. Exhausted T cells are defined by reduced effector function, sustained upregulation of multiple inhibitory receptors, an altered transcriptional program and perturbations of normal memory development and homeostasis. This review focuses on (a) illustrating milestone discoveries that led to our present understanding of T cell exhaustion, (b) summarizing recent developments in the field, and (c) identifying new challenges for translational research. Exhausted T cells are now recognized as key therapeutic targets in human infections and cancer. Much of our knowledge of the clinically relevant process of exhaustion derives from studies in the mouse model of Lymphocytic choriomeningitis virus (LCMV) infection. Studies using this model have formed the foundation for our understanding of human T cell memory and exhaustion. We will use this example to discuss recent advances in our understanding of T cell exhaustion and illustrate the value of integrated mouse and human studies and will emphasize the benefits of bi-directional mouse-to-human and human-to-mouse research approaches.

Neuropsychological rehabilitation of memory deficits and activities of daily living in patients with Alzheimer's disease: a pilot study

Patients with Alzheimer's disease (AD) gradually lose their cognitive competence, particularly memory, and the ability to perform daily life tasks. Neuropsychological rehabilitation is used to improve cognitive functions by facilitating memory performance through the use of external aids and internal strategies. The effect of neuropsychological rehabilitation through memory training - motor movements, verbal association, and categorization - and activities of daily living (ADL) training was tested in a sample of 5 elderly out-patients (mean age: 77.4 ± 2.88 years), with mild AD (Mini-Mental State Examination score: 22.20 ± 2.17) and their caregivers. All patients had been taking rivastigmine (6-12 mg/day) for at least 3 months before being assigned to the rehabilitation sessions, and they continued to take the medication during the whole program. Just before and after the 14-week neuropsychological rehabilitation program all patients were assessed by interviewers that did not participate in the cognitive training, using the Mini-Mental State Examination, Montgomery-Alsberg Depression Rating Scale, Hamilton Anxiety Scale, Interview to Determine Deterioration in Functioning in Dementia, Functional Test, Memory Questionnaire of Daily Living for patient and caregiver, Quality of Life Questionnaire for patient and caregiver, and a neuropsychological battery. The results showed a statistically significant improvement in ADL measured by Functional Test (P = 0.04), and only a small improvement in memory and psychiatric symptoms. Our results support the view that weekly stimulation of memory and training of ADL is believed to be of great value in AD treatment, not only delaying the progress of the disease, but also improving some cognitive functions and ADL, even though AD is a progressively degenerative disease.

Graffiti, memory and contested space : mnemonic initiatives following trauma and/or repression in Buenos Aires, Argentina

Graffiti, Memory and Contested Space: Mnemonic Initiatives Following Periods of Trauma and/or Repression in Buenos Aires, Argentina This thesis concerns the popular articulation ofmemory following periods or incidents of trauma in Argentina. I am interested in how groups lay claim to various public spaces in the city and how they convert these spaces into mnemonic battlegrounds. In considering these spaces of trauma and places of memory, I am primarily interested in how graffiti writing (stencils, spray-paint, signatures, etchings, wall-paintings, murals and installations) is used to make these spaces transmit particular memories that impugn official versions of the past. This thesis draws on literatures focused on popular/public memory. Scholars argue that memory is socially constructed and thus actively contested. Marginal initiatives such as graffiti writing challenge the memory projects of the state as well as state projects that are perceived by citizens to be 'inadequate,' 'inappropriate,' and/or as promoting the erasure of memory. Many of these initiatives are a reaction to the proreconciliation and pro-oblivion strategies of previous governments. I outline that the history of silences and impunity, and a longstanding emphasis on reconciliation at the expense of truth and justice has created an environment of vulnerable memory in Argentina. Popular memory entrepreneurs react by aggressively articulating their memories in time and in space. As a result of this intense memory work, the built landscape in Buenos Aires is dotted with mnemonic initiatives that aim to contradict or subvert officially sanctioned memories. I also suggest that memory workers in Argentina persistently and carefially use the sites of trauma as well as key public spaces to ensure official as well as popular audiences . The data for this project was collected in five spaces in Buenos Aires, the Plaza de Mayo, Plaza Congreso, La Republica Cromanon nightclub, Avellaneda Train Station and El Olimpo, a former detention centre from the military dictatorship.

Memory Usage Inference for Object-Oriented Programs

We present a type-based approach to statically derive symbolic closed-form formulae that characterize the bounds of heap memory usages of programs written in object-oriented languages. Given a program with size and alias annotations, our inference system will compute the amount of memory required by the methods to execute successfully as well as the amount of memory released when methods return. The obtained analysis results are useful for networked devices with limited computational resources as well as embedded software.

Failure-Oblivious Computing and Boundless Memory Blocks

Memory errors are a common cause of incorrect software execution and security vulnerabilities. We have developed two new techniques that help software continue to execute successfully through memory errors: failure-oblivious computing and boundless memory blocks. The foundation of both techniques is a compiler that generates code that checks accesses via pointers to detect out of bounds accesses. Instead of terminating or throwing an exception, the generated code takes another action that keeps the program executing without memory corruption. Failure-oblivious code simply discards invalid writes and manufactures values to return for invalid reads, enabling the program to continue its normal execution path. Code that implements boundless memory blocks stores invalid writes away in a hash table to return as the values for corresponding out of bounds reads. he net effect is to (conceptually) give each allocated memory block unbounded size and to eliminate out of bounds accesses as a programming error. We have implemented both techniques and acquired several widely used open source servers (Apache, Sendmail, Pine, Mutt, and Midnight Commander).With standard compilers, all of these servers are vulnerable to buffer overflow attacks as documented at security tracking web sites. Both failure-oblivious computing and boundless memory blocks eliminate these security vulnerabilities (as well as other memory errors). Our results show that our compiler enables the servers to execute successfully through buffer overflow attacks to continue to correctly service user requests without security vulnerabilities.