Neuroarchitecture of the color and polarization vision system of the stomatopod haptosquilla

The apposition compound eyes of stomatopod crustaceans contain a morphologically distinct eye region specialized for color and polarization vision, called the mid-band. In two stomatopod superfamilies, the mid-band is constructed from six rows of enlarged ommatidia containing multiple photoreceptor classes for spectral and polarization vision. The aim of this study was to begin to analyze the underlying neuroarchitecture, the design of which might reveal clues how the visual system interprets and communicates to deeper levels of the brain the multiple channels of information supplied by the retina. Reduced silver methods were used to investigate the axon pathways from different retinal regions to the lamina ganglionaris and from there to the medulla externa, the medulla interna, and the medulla terminalis. A swollen band of neuropil-here termed the accessory lobe-projects across the equator of. the lamina ganglionaris, the medulla externa, and the medulla interna and represents, structurally, the retina's mid-band. Serial semithin and ultrathin resin sections were used to reconstruct the projection of photoreceptor axons from the retina to the lamina ganglionaris. The eight axons originating from one ommatidium project to the same lamina cartridge. Seven short visual fibers end at two distinct levels in each lamina cartridge, thus geometrically separating the two channels of polarization and spectral information. The eighth visual fiber runs axially through the cartridge and terminates in the medulla externa. We conclude that spatial, color, and polarization information is divided into three parallel data streams from the retina to the central nervous system. (C) 2003 Wiley-Liss, Inc.

Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system

Background: A major goal in the post-genomic era is to identify and characterise disease susceptibility genes and to apply this knowledge to disease prevention and treatment. Rodents and humans have remarkably similar genomes and share closely related biochemical, physiological and pathological pathways. In this work we utilised the latest information on the mouse transcriptome as revealed by the RIKEN FANTOM2 project to identify novel human disease-related candidate genes. We define a new term patholog to mean a homolog of a human disease-related gene encoding a product ( transcript, anti-sense or protein) potentially relevant to disease. Rather than just focus on Mendelian inheritance, we applied the analysis to all potential pathologs regardless of their inheritance pattern. Results: Bioinformatic analysis and human curation of 60,770 RIKEN full-length mouse cDNA clones produced 2,578 sequences that showed similarity ( 70 - 85% identity) to known human-disease genes. Using a newly developed biological information extraction and annotation tool ( FACTS) in parallel with human expert analysis of 17,051 MEDLINE scientific abstracts we identified 182 novel potential pathologs. Of these, 36 were identified by computational tools only, 49 by human expert analysis only and 97 by both methods. These pathologs were related to neoplastic ( 53%), hereditary ( 24%), immunological ( 5%), cardio-vascular (4%), or other (14%), disorders. Conclusions: Large scale genome projects continue to produce a vast amount of data with potential application to the study of human disease. For this potential to be realised we need intelligent strategies for data categorisation and the ability to link sequence data with relevant literature. This paper demonstrates the power of combining human expert annotation with FACTS, a newly developed bioinformatics tool, to identify novel pathologs from within large-scale mouse transcript datasets.

Use of confocal microscopy to follow the development of penetrative hyphae during growth of Rhizopus oligosporus in an artificial solid-state fermentation system

Two methods were compared for determining the concentration of penetrative biomass during growth of Rhizopus oligosporus on an artificial solid substrate consisting of an inert gel and starch as the sole source of carbon and energy. The first method was based on the use of a hand microtome to make sections of approximately 0.2- to 0.4-mm thickness parallel to the substrate surface and the determination of the glucosamine content in each slice. Use of glucosamine measurements to estimate biomass concentrations was shown to be problematic due to the large variations in glucosamine content with mycelial age. The second method was a novel method based on the use of confocal scanning laser microscopy to estimate the fractional volume occupied by the biomass. Although it is not simple to translate fractional volumes into dry weights of hyphae due to the lack of experimentally determined conversion factors, measurement of the fractional volumes in themselves is useful for characterizing fungal penetration into the substrate. Growth of penetrative biomass in the artificial model substrate showed two forms of growth with an indistinct mass in the region close to the substrate surface and a few hyphae penetrating perpendicularly to the surface in regions further away from the substrate surface. The biomass profiles against depth obtained from the confocal microscopy showed two linear regions on log-linear plots, which are possibly related to different oxygen availability at different depths within the substrate. Confocal microscopy has the potential to be a powerful tool in the investigation of fungal growth mechanisms in solid-state fermentation. (C) 2003 Wiley Periodicals, Inc.

Towards the wide implementation of standards IEC 61968/70 (CIM) and IEC 61850 in the distribution system (CIGRÉ C6-105_2010)

Currently, power systems (PS) already accommodate a substantial penetration of distributed generation (DG) and operate in competitive environments. In the future, as the result of the liberalisation and political regulations, PS will have to deal with large-scale integration of DG and other distributed energy resources (DER), such as storage and provide market agents to ensure a flexible and secure operation. This cannot be done with the traditional PS operational tools used today like the quite restricted information systems Supervisory Control and Data Acquisition (SCADA) [1]. The trend to use the local generation in the active operation of the power system requires new solutions for data management system. The relevant standards have been developed separately in the last few years so there is a need to unify them in order to receive a common and interoperable solution. For the distribution operation the CIM models described in the IEC 61968/70 are especially relevant. In Europe dispersed and renewable energy resources (D&RER) are mostly operated without remote control mechanisms and feed the maximal amount of available power into the grid. To improve the network operation performance the idea of virtual power plants (VPP) will become a reality. In the future power generation of D&RER will be scheduled with a high accuracy. In order to realize VPP decentralized energy management, communication facilities are needed that have standardized interfaces and protocols. IEC 61850 is suitable to serve as a general standard for all communication tasks in power systems [2]. The paper deals with international activities and experiences in the implementation of a new data management and communication concept in the distribution system. The difficulties in the coordination of the inconsistent developed in parallel communication and data management standards - are first addressed in the paper. The upcoming unification work taking into account the growing role of D&RER in the PS is shown. It is possible to overcome the lag in current practical experiences using new tools for creating and maintenance the CIM data and simulation of the IEC 61850 protocol – the prototype of which is presented in the paper –. The origin and the accuracy of the data requirements depend on the data use (e.g. operation or planning) so some remarks concerning the definition of the digital interface incorporated in the merging unit idea from the power utility point of view are presented in the paper too. To summarize some required future work has been identified.

Supporting real-time parallel task models with work-stealing

Dynamic parallel scheduling using work-stealing has gained popularity in academia and industry for its good performance, ease of implementation and theoretical bounds on space and time. Cores treat their own double-ended queues (deques) as a stack, pushing and popping threads from the bottom, but treat the deque of another randomly selected busy core as a queue, stealing threads only from the top, whenever they are idle. However, this standard approach cannot be directly applied to real-time systems, where the importance of parallelising tasks is increasing due to the limitations of multiprocessor scheduling theory regarding parallelism. Using one deque per core is obviously a source of priority inversion since high priority tasks may eventually be enqueued after lower priority tasks, possibly leading to deadline misses as in this case the lower priority tasks are the candidates when a stealing operation occurs. Our proposal is to replace the single non-priority deque of work-stealing with ordered per-processor priority deques of ready threads. The scheduling algorithm starts with a single deque per-core, but unlike traditional work-stealing, the total number of deques in the system may now exceed the number of processors. Instead of stealing randomly, cores steal from the highest priority deque.

A framework for the development of parallel and distributed real-time embedded systems

Embedded real-time applications increasingly present high computation requirements, which need to be completed within specific deadlines, but that present highly variable patterns, depending on the set of data available in a determined instant. The current trend to provide parallel processing in the embedded domain allows providing higher processing power; however, it does not address the variability in the processing pattern. Dimensioning each device for its worst-case scenario implies lower average utilization, and increased available, but unusable, processing in the overall system. A solution for this problem is to extend the parallel execution of the applications, allowing networked nodes to distribute the workload, on peak situations, to neighbour nodes. In this context, this report proposes a framework to develop parallel and distributed real-time embedded applications, transparently using OpenMP and Message Passing Interface (MPI), within a programming model based on OpenMP. The technical report also devises an integrated timing model, which enables the structured reasoning on the timing behaviour of these hybrid architectures.

Dynamic global scheduling of parallel real-time tasks

High-level parallel languages offer a simple way for application programmers to specify parallelism in a form that easily scales with problem size, leaving the scheduling of the tasks onto processors to be performed at runtime. Therefore, if the underlying system cannot efficiently execute those applications on the available cores, the benefits will be lost. In this paper, we consider how to schedule highly heterogenous parallel applications that require real-time performance guarantees on multicore processors. The paper proposes a novel scheduling approach that combines the global Earliest Deadline First (EDF) scheduler with a priority-aware work-stealing load balancing scheme, which enables parallel realtime tasks to be executed on more than one processor at a given time instant. Experimental results demonstrate the better scalability and lower scheduling overhead of the proposed approach comparatively to an existing real-time deadline-oriented scheduling class for the Linux kernel.

Control of a 6-DOF parallel manipulator through a mechatronic approach

This paper shows that a hierarchical architecture, distributing several control actions in growing levels of complexity and using resources of reconfigurable computing, enables one to take into account the ease of future modifications, updates and improvements in robotic applications. An experimental example of a Stewart—Gough platform control (a platform applied as the solution to countless practical problems) is presented using reconfigurable computing. The software and hardware developed are structured in independent blocks. This open architecture implementation allows easy expansion of the system and better adaptation of the platform to its related tasks.

A many-core co-processor for embedded parallel computing on FPGA

Single processor architectures are unable to provide the required performance of high performance embedded systems. Parallel processing based on general-purpose processors can achieve these performances with a considerable increase of required resources. However, in many cases, simplified optimized parallel cores can be used instead of general-purpose processors achieving better performance at lower resource utilization. In this paper, we propose a configurable many-core architecture to serve as a co-processor for high-performance embedded computing on Field-Programmable Gate Arrays. The architecture consists of an array of configurable simple cores with support for floating-point operations interconnected with a configurable interconnection network. For each core it is possible to configure the size of the internal memory, the supported operations and number of interfacing ports. The architecture was tested in a ZYNQ-7020 FPGA in the execution of several parallel algorithms. The results show that the proposed many-core architecture achieves better performance than that achieved with a parallel generalpurpose processor and that up to 32 floating-point cores can be implemented in a ZYNQ-7020 SoC FPGA.

Methodologies for the WCET Analysis of Parallel Applications on Many-core Architectures

Euromicro Conference on Digital System Design (DSD 2015), Funchal, Portugal.

Online Admission of Parallel Real-Time Tasks

6th Real-Time Scheduling Open Problems Seminar (RTSOPS 2015), Lund, Sweden.

Allocation of Parallel Real-Time Tasks in Distributed Multi-core Architectures supported by an FTT-SE Network

Distributed real-time systems such as automotive applications are becoming larger and more complex, thus, requiring the use of more powerful hardware and software architectures. Furthermore, those distributed applications commonly have stringent real-time constraints. This implies that such applications would gain in flexibility if they were parallelized and distributed over the system. In this paper, we consider the problem of allocating fixed-priority fork-join Parallel/Distributed real-time tasks onto distributed multi-core nodes connected through a Flexible Time Triggered Switched Ethernet network. We analyze the system requirements and present a set of formulations based on a constraint programming approach. Constraint programming allows us to express the relations between variables in the form of constraints. Our approach is guaranteed to find a feasible solution, if one exists, in contrast to other approaches based on heuristics. Furthermore, approaches based on constraint programming have shown to obtain solutions for these type of formulations in reasonable time.

A system model and stack for the parallelization of time-critical applications on many-core architectures

3rd Workshop on High-performance and Real-time Embedded Systems (HIRES 2015). 21, Jan, 2015. Amsterdam, Netherlands.

P-SOCRATES: A parallel software framework for time-critical many-core systems

Article in Press, Corrected Proof

In vitro and in situ activation of the complement system by the fungus Lacazia loboi

Since there are no studies evaluating the participation of the complement system (CS) in Jorge Lobo's disease and its activity on the fungus Lacazia loboi, we carried out the present investigation. Fungal cells with a viability index of 48% were obtained from the footpads of BALB/c mice and incubated with a pool of inactivated serum from patients with the mycosis or with sterile saline for 30 min at 37 ºC. Next, the tubes were incubated for 2 h with a pool of noninactivated AB+ serum, inactivated serum, serum diluted in EGTA-MgCl2, and serum diluted in EDTA. The viability of L. loboi was evaluated and the fungal suspension was cytocentrifuged. The slides were submitted to immunofluorescence staining using human anti-C3 antibody. The results revealed that 98% of the fungi activated the CS by the alternative pathway and no significant difference in L. loboi viability was observed after CS activation. In parallel, frozen histological sections from 11 patients were analyzed regarding the presence of C3 and IgG by immunofluorescence staining. C3 and IgG deposits were observed in the fungal wall of 100% and 91% of the lesions evaluated, respectively. The results suggest that the CS and immunoglobulins may contribute to the defense mechanisms of the host against L. loboi.