Minimalist Hardware Architectures for Agent Tracking and Guidance

The philosophy of minimalism in robotics promotes gaining an understanding of sensing and computational requirements for solving a task. This minimalist approach lies in contrast to the common practice of first taking an existing sensory motor system, and only afterwards determining how to apply the robotic system to the task. While it may seem convenient to simply apply existing hardware systems to the task at hand, this design philosophy often proves to be wasteful in terms of energy consumption and cost, along with unnecessary complexity and decreased reliability. While impressive in terms of their versatility, complex robots such as the PR2 (which cost hundreds of thousands of dollars) are impractical for many common applications. Instead, if a specific task is required, sensing and computational requirements can be determined specific to that task, and a clever hardware implementation can be built to accomplish the task. Since this minimalist hardware would be designed around accomplishing the specified task, significant reductions in hardware complexity can be obtained. This can lead to huge advantages in battery life, cost, and reliability. Even if cost is of no concern, battery life is often a limiting factor in many applications. Thus, a minimalist hardware system is critical in achieving the system requirements. In this thesis, we will discuss an implementation of a counting, tracking, and actuation system as it relates to ergodic bodies to illustrate a minimalist design methodology.

Garbage collection optimization for non uniform memory access architectures

Cache-coherent non uniform memory access (ccNUMA) architecture is a standard design pattern for contemporary multicore processors, and future generations of architectures are likely to be NUMA. NUMA architectures create new challenges for managed runtime systems. Memory-intensive applications use the system’s distributed memory banks to allocate data, and the automatic memory manager collects garbage left in these memory banks. The garbage collector may need to access remote memory banks, which entails access latency overhead and potential bandwidth saturation for the interconnection between memory banks. This dissertation makes five significant contributions to garbage collection on NUMA systems, with a case study implementation using the Hotspot Java Virtual Machine. It empirically studies data locality for a Stop-The-World garbage collector when tracing connected objects in NUMA heaps. First, it identifies a locality richness which exists naturally in connected objects that contain a root object and its reachable set— ‘rooted sub-graphs’. Second, this dissertation leverages the locality characteristic of rooted sub-graphs to develop a new NUMA-aware garbage collection mechanism. A garbage collector thread processes a local root and its reachable set, which is likely to have a large number of objects in the same NUMA node. Third, a garbage collector thread steals references from sibling threads that run on the same NUMA node to improve data locality. This research evaluates the new NUMA-aware garbage collector using seven benchmarks of an established real-world DaCapo benchmark suite. In addition, evaluation involves a widely used SPECjbb benchmark and Neo4J graph database Java benchmark, as well as an artificial benchmark. The results of the NUMA-aware garbage collector on a multi-hop NUMA architecture show an average of 15% performance improvement. Furthermore, this performance gain is shown to be as a result of an improved NUMA memory access in a ccNUMA system. Fourth, the existing Hotspot JVM adaptive policy for configuring the number of garbage collection threads is shown to be suboptimal for current NUMA machines. The policy uses outdated assumptions and it generates a constant thread count. In fact, the Hotspot JVM still uses this policy in the production version. This research shows that the optimal number of garbage collection threads is application-specific and configuring the optimal number of garbage collection threads yields better collection throughput than the default policy. Fifth, this dissertation designs and implements a runtime technique, which involves heuristics from dynamic collection behavior to calculate an optimal number of garbage collector threads for each collection cycle. The results show an average of 21% improvements to the garbage collection performance for DaCapo benchmarks.

Self-Organizing Map Neural Architectures Based on Limit Cycle Attractors

Recent efforts to develop large-scale neural architectures have paid relatively little attention to the use of self-organizing maps (SOMs). Part of the reason is that most conventional SOMs use a static encoding representation: Each input is typically represented by the fixed activation of a single node in the map layer. This not only carries information in an inefficient and unreliable way that impedes building robust multi-SOM neural architectures, but it is also inconsistent with rhythmic oscillations in biological neural networks. Here I develop and study an alternative encoding scheme that instead uses limit cycle attractors of multi-focal activity patterns to represent input patterns/sequences. Such a fundamental change in representation raises several questions: Can this be done effectively and reliably? If so, will map formation still occur? What properties would limit cycle SOMs exhibit? Could multiple such SOMs interact effectively? Could robust architectures based on such SOMs be built for practical applications? The principal results of examining these questions are as follows. First, conditions are established for limit cycle attractors to emerge in a SOM through self-organization when encoding both static and temporal sequence inputs. It is found that under appropriate conditions a set of learned limit cycles are stable, unique, and preserve input relationships. In spite of the continually changing activity in a limit cycle SOM, map formation continues to occur reliably. Next, associations between limit cycles in different SOMs are learned. It is shown that limit cycles in one SOM can be successfully retrieved by another SOM’s limit cycle activity. Control timings can be set quite arbitrarily during both training and activation. Importantly, the learned associations generalize to new inputs that have never been seen during training. Finally, a complete neural architecture based on multiple limit cycle SOMs is presented for robotic arm control. This architecture combines open-loop and closed-loop methods to achieve high accuracy and fast movements through smooth trajectories. The architecture is robust in that disrupting or damaging the system in a variety of ways does not completely destroy the system. I conclude that limit cycle SOMs have great potentials for use in constructing robust neural architectures.

Hierarchical active inference for cognitive architectures

This thesis explores the methods based on the free energy principle and active inference for modelling cognition. Active inference is an emerging framework for designing intelligent agents where psychological processes are cast in terms of Bayesian inference. Here, I appeal to it to test the design of a set of cognitive architectures, via simulation. These architectures are defined in terms of generative models where an agent executes a task under the assumption that all cognitive processes aspire to the same objective: the minimization of variational free energy. Chapter 1 introduces the free energy principle and its assumptions about self-organizing systems. Chapter 2 describes how from the mechanics of self-organization can emerge a minimal form of cognition able to achieve autopoiesis. In chapter 3 I present the method of how I formalize generative models for action and perception. The architectures proposed allow providing a more biologically plausible account of more complex cognitive processing that entails deep temporal features. I then present three simulation studies that aim to show different aspects of cognition, their associated behavior and the underlying neural dynamics. In chapter 4, the first study proposes an architecture that represents the visuomotor system for the encoding of actions during action observation, understanding and imitation. In chapter 5, the generative model is extended and is lesioned to simulate brain damage and neuropsychological patterns observed in apraxic patients. In chapter 6, the third study proposes an architecture for cognitive control and the modulation of attention for action selection. At last, I argue how active inference can provide a formal account of information processing in the brain and how the adaptive capabilities of the simulated agents are a mere consequence of the architecture of the generative models. Cognitive processing, then, becomes an emergent property of the minimization of variational free energy.

Obesity And Inflammation And The Effect On The Hematopoietic System.

Bone marrow is organized in specialized microenvironments known as 'marrow niches'. These are important for the maintenance of stem cells and their hematopoietic progenitors whose homeostasis also depends on other cell types present in the tissue. Extrinsic factors, such as infection and inflammatory states, may affect this system by causing cytokine dysregulation (imbalance in cytokine production) and changes in cell proliferation and self-renewal rates, and may also induce changes in the metabolism and cell cycle. Known to relate to chronic inflammation, obesity is responsible for systemic changes that are best studied in the cardiovascular system. Little is known regarding the changes in the hematopoietic system induced by the inflammatory state carried by obesity or the cell and molecular mechanisms involved. The understanding of the biological behavior of hematopoietic stem cells under obesity-induced chronic inflammation could help elucidate the pathophysiological mechanisms involved in other inflammatory processes, such as neoplastic diseases and bone marrow failure syndromes.

The Value Of The 2005 International Society Of Urological Pathology (isup) Modified Gleason Grading System As A Predictor Of Biochemical Recurrence After Radical Prostatectomy.

To compare time and risk to biochemical recurrence (BR) after radical prostatectomy of two chronologically different groups of patients using the standard and the modified Gleason system (MGS). Cohort 1 comprised biopsies of 197 patients graded according to the standard Gleason system (SGS) in the period 1997/2004, and cohort 2, 176 biopsies graded according to the modified system in the period 2005/2011. Time to BR was analyzed with the Kaplan-Meier product-limit analysis and prediction of shorter time to recurrence using univariate and multivariate Cox proportional hazards model. Patients in cohort 2 reflected time-related changes: striking increase in clinical stage T1c, systematic use of extended biopsies, and lower percentage of total length of cancer in millimeter in all cores. The MGS used in cohort 2 showed fewer biopsies with Gleason score ≤ 6 and more biopsies of the intermediate Gleason score 7. Time to BR using the Kaplan-Meier curves showed statistical significance using the MGS in cohort 2, but not the SGS in cohort 1. Only the MGS predicted shorter time to BR on univariate analysis and on multivariate analysis was an independent predictor. The results favor that the 2005 International Society of Urological Pathology modified system is a refinement of the Gleason grading and valuable for contemporary clinical practice.

The Applicability Of Ordered Mesoporous Sba-15 And Its Hydrophobic Glutaraldehyde-bridge Derivative To Improve Ibuprofen-loading In Releasing System.

The mesoporous SBA-15 silica with uniform hexagonal pore, narrow pore size distribution and tuneable pore diameter was organofunctionalized with glutaraldehyde-bridged silylating agent. The precursor and its derivative silicas were ibuprofen-loaded for controlled delivery in simulated biological fluids. The synthesized silicas were characterized by elemental analysis, infrared spectroscopy, (13)C and (29)Si solid state NMR spectroscopy, nitrogen adsorption, X-ray diffractometry, thermogravimetry and scanning electron microscopy. Surface functionalization with amine containing bridged hydrophobic structure resulted in significantly decreased surface area from 802.4 to 63.0 m(2) g(-1) and pore diameter 8.0-6.0 nm, which ultimately increased the drug-loading capacity from 18.0% up to 28.3% and a very slow release rate of ibuprofen over the period of 72.5h. The in vitro drug release demonstrated that SBA-15 presented the fastest release from 25% to 27% and SBA-15GA gave near 10% of drug release in all fluids during 72.5 h. The Korsmeyer-Peppas model better fits the release data with the Fickian diffusion mechanism and zero order kinetics for synthesized mesoporous silicas. Both pore sizes and hydrophobicity influenced the rate of the release process, indicating that the chemically modified silica can be suggested to design formulation of slow and constant release over a defined period, to avoid repeated administration.

Electronic And Structural Study Of Pt-modified Au Vicinal Surfaces: A Model System For Pt-au Catalysts.

Two single crystalline surfaces of Au vicinal to the (111) plane were modified with Pt and studied using scanning tunneling microscopy (STM) and X-ray photoemission spectroscopy (XPS) in ultra-high vacuum environment. The vicinal surfaces studied are Au(332) and Au(887) and different Pt coverage (θPt) were deposited on each surface. From STM images we determine that Pt deposits on both surfaces as nanoislands with heights ranging from 1 ML to 3 ML depending on θPt. On both surfaces the early growth of Pt ad-islands occurs at the lower part of the step edge, with Pt ad-atoms being incorporated into the steps in some cases. XPS results indicate that partial alloying of Pt occurs at the interface at room temperature and at all coverage, as suggested by the negative chemical shift of Pt 4f core line, indicating an upward shift of the d-band center of the alloyed Pt. Also, the existence of a segregated Pt phase especially at higher coverage is detected by XPS. Sample annealing indicates that the temperature rise promotes a further incorporation of Pt atoms into the Au substrate as supported by STM and XPS results. Additionally, the catalytic activity of different PtAu systems reported in the literature for some electrochemical reactions is discussed considering our findings.

Inhibitory Effects Of A Cured Antibacterial Bonding System On Viability And Metabolic Activity Of Oral Bacteria.

To evaluate the antimicrobial efficacy of Clearfil SE Protect (CP) and Clearfil SE Bond (CB) after curing and rinsed against five individual oral microorganisms as well as a mixture of bacterial culture prepared from the selected test organisms. Bacterial suspensions were prepared from single species of Streptococcus mutans, Streptococcus sobrinus, Streptococcus gordonii, Actinomyces viscosus and Lactobacillus lactis, as well as mixed bacterial suspensions from these organisms. Dentin bonding system discs (6 mm×2 mm) were prepared, cured, washed and placed on the bacterial suspension of single species or multispecies bacteria for 15, 30 and 60 min. MTT, Live/Dead bacterial viability (antibacterial effect), and XTT (metabolic activity) assays were used to test the two dentin system's antibacterial effect. All assays were done in triplicates and each experiment repeated at least three times. Data were submitted to ANOVA and Scheffe's f-test (5%). Greater than 40% bacteria killing was seen within 15 min, and the killing progressed with increasing time of incubation with CP discs. However, a longer (60 min) period of incubation was required by CP to achieve similar antimicrobial effect against mixed bacterial suspension. CB had no significant effect on the viability or metabolic activity of the test microorganisms when compared to the control bacterial culture. CP was significantly effective in reducing the viability and metabolic activity of the test organisms. The results demonstrated the antimicrobial efficacy of CP both on single and multispecies bacterial culture. CP may be beneficial in reducing bacterial infections in cavity preparations in clinical dentistry.

Blockade Of Renin-angiotensin System Prevents Micturition Dysfunction In Renovascular Hypertensive Rats.

Association between hypertension and bladder symptoms has been described. We hypothesized that micturition dysfunction may be associated with renin-angiotensin system (RAS) acting in urethra. The effects of the anti-hypertensive drugs losartan (AT1 antagonist) and captopril (angiotensin-converting enzyme inhibitor) in comparison with atenolol (β1-adrenoceptor antagonist independently of RAS blockade) have been investigated in bladder and urethral dysfunctions during renovascular hypertension in rats. Two kidney-1 clip (2K-1C) rats were treated with losartan (30 mg/kg/day), captopril (50mg/kg/day) or atenolol (90 mg/kg/day) for eight weeks. Cystometric study, bladder and urethra smooth muscle reactivities, measurement of cAMP levels and p38 MAPK phosphorylation in urinary tract were determined. Losartan and captopril markedly reduced blood pressure in 2K-1C rats. The increases in non-voiding contractions, voiding frequency and bladder capacity in 2K-1C rats were prevented by treatments with both drugs. Likewise, losartan and captopril prevented the enhanced bladder contractions to electrical-field stimulation (EFS) and carbachol, along with the impaired relaxations to β-adrenergic-cAMP stimulation. Enhanced neurogenic contractions and impaired nitrergic relaxations were observed in urethra from 2K-1C rats. Angiotensin II also produced greater urethral contractions that were accompanied by higher phosphorylation of p38 MAPK in urethral tissues of 2K-1C rats. Losartan and captopril normalized the urethral dysfunctions in 2K-1C rats. In contrast, atenolol treatment largely reduced the blood pressure in 2K-1C rats but failed to affect the urinary tract smooth muscle dysfunction. The urinary tract smooth muscle dysfunction in 2K-1C rats takes place by local RAS activation irrespective of levels of arterial blood pressure.

On The Distinct Molecular Architectures Of Dipping- And Spray-lbl Films Containing Lipid Vesicles.

The introduction of spraying procedures to fabricate layer-by-layer (LbL) films has brought new possibilities for the control of molecular architectures and for making the LbL technique compliant with industrial processes. In this study we show that significantly distinct architectures are produced for dipping and spray-LbL films of the same components, which included DODAB/DPPG vesicles. The films differed notably in their thickness and stratified nature. The electrical response of the two types of films to aqueous solutions containing erythrosin was also different. With multidimensional projections we showed that the impedance for the DODAB/DPPG spray-LbL film is more sensitive to changes in concentration, being therefore more promising as sensing units. Furthermore, with surface-enhanced Raman scattering (SERS) we could ascribe the high sensitivity of the LbL films to adsorption of erythrosin.

Transmission Of Intra-cellular Genetic Information: A System Proposal.

One of the great challenges of the scientific community on theories of genetic information, genetic communication and genetic coding is to determine a mathematical structure related to DNA sequences. In this paper we propose a model of an intra-cellular transmission system of genetic information similar to a model of a power and bandwidth efficient digital communication system in order to identify a mathematical structure in DNA sequences where such sequences are biologically relevant. The model of a transmission system of genetic information is concerned with the identification, reproduction and mathematical classification of the nucleotide sequence of single stranded DNA by the genetic encoder. Hence, a genetic encoder is devised where labelings and cyclic codes are established. The establishment of the algebraic structure of the corresponding codes alphabets, mappings, labelings, primitive polynomials (p(x)) and code generator polynomials (g(x)) are quite important in characterizing error-correcting codes subclasses of G-linear codes. These latter codes are useful for the identification, reproduction and mathematical classification of DNA sequences. The characterization of this model may contribute to the development of a methodology that can be applied in mutational analysis and polymorphisms, production of new drugs and genetic improvement, among other things, resulting in the reduction of time and laboratory costs.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

Hypothalamic Inflammation And The Central Nervous System Control Of Energy Homeostasis.

The control of energy homeostasis relies on robust neuronal circuits that regulate food intake and energy expenditure. Although the physiology of these circuits is well understood, the molecular and cellular response of this program to chronic diseases is still largely unclear. Hypothalamic inflammation has emerged as a major driver of energy homeostasis dysfunction in both obesity and anorexia. Importantly, this inflammation disrupts the action of metabolic signals promoting anabolism or supporting catabolism. In this review, we address the evidence that favors hypothalamic inflammation as a factor that resets energy homeostasis in pathological states.

Culturable Bacterial Diversity From A Feed Water Of A Reverse Osmosis System, Evaluation Of Biofilm Formation And Biocontrol Using Phages.

Biofilm formation on reverse osmosis (RO) systems represents a drawback in the application of this technology by different industries, including oil refineries. In RO systems the feed water maybe a source of microbial contamination and thus contributes for the formation of biofilm and consequent biofouling. In this study the planktonic culturable bacterial community was characterized from a feed water of a RO system and their capacities were evaluated to form biofilm in vitro. Bacterial motility and biofilm control were also analysed using phages. As results, diverse Protobacteria, Actinobacteria and Bacteroidetes were identified. Alphaproteobacteria was the predominant group and Brevundimonas, Pseudomonas and Mycobacterium the most abundant genera. Among the 30 isolates, 11 showed at least one type of motility and 11 were classified as good biofilm formers. Additionally, the influence of non-specific bacteriophage in the bacterial biofilms formed in vitro was investigated by action of phages enzymes or phage infection. The vB_AspP-UFV1 (Podoviridae) interfered in biofilm formation of most tested bacteria and may represent a good alternative in biofilm control. These findings provide important information about the bacterial community from the feed water of a RO system that may be used for the development of strategies for biofilm prevention and control in such systems.