SEProf: A high-level software energy profiling tool for an embedded processor enabling power management functions

Energy efficiency has become one of the most important design issues for embedded systems. To examine the power consumption of an embedded system, an energy profiling tool is highly demanded. Although a number of energy profiling tools have been proposed, they are not directly applicable to the embedded processors with power management functions that are widely utilized in battery-operated embedded systems to reduce power consumption. Hence, this study presents a high-level energy profiling tool, called SEProf, that estimates the energy consumption of an embedded system running multithread software and a multitasking operating system (OS) that supports power management functions. This study implements the proposed SEProf in Linux 2.6.19 and evaluates its performance on an ARM11 MPCore processor. Experimental results demonstrate that the proposed tool can provide accurate energy profiling results with a low profiling overhead.     

Fabrication of three-dimensional magnetic microdevices with embedded microcoils for magnetic potential concentration

Novel magnetic microdevices were developed for magnetic field generation and concentration and successfully characterized and tested for magnetic potential focusing which is very important for various MEMS applications such as magnetic particles manipulation. These microdevices have been fabricated using an innovative processing sequence which eliminates many problems associated with other fabrication techniques and provides a platform for adding other subsequent fabrication steps required to integrate the microcoils with other microcomponents. They consist of high aspect ratio planar coils made of electroplated copper embedded in the silicon substrate, with ferromagnetic pillars and backside plates made of a CoNiP ternary alloy. A large magnetic field gradient is generated and enhanced by two structural parameters: the small width and high aspect ratio of each single conductor and the ferromagnetic pillars positioned at high flux density locations. This arrangement creates very steep magnetic potential wells, in particular at the vicinity of the pillars. The manipulation of micromagnetic particles in a static and continuous flow conditions has been demonstrated.     

Identification and validation of novel CSF biomarkers for early stages of Alzheimer's disease

The pathology of Alzheimer's disease (AD) begins years prior to clinical diagnosis. The development of antecedent biomarkers that indicate the presence of AD pathology and predict risk for decline in both cognitively normal and mildly impaired individuals will be useful as effective therapies are developed. While cerebrospinal fluid (CSF) markers such as amyloid-β (Aβ) 42 and tau are useful, additional biomarkers are needed. To identify new markers, we utilized 2-D difference gel electrophoresis (2-D DIGE) of individual CSF samples from subjects with very mild AD versus controls after depletion of high-abundant proteins. Protein spots displaying differential abundance between the two groups were identified with MS. A number of candidate biomarkers were identified in 18 gel features. Selected candidates were quantified in a larger clinical set using ELISA. The mean levels of α1-antichymotrypsin (ACT), antithrombin III (ATIII), and zinc-α2-glycoprotein (ZAG) were significantly higher in the mild AD group, and the mean level of carnosinase 1 (CNDP1) was decreased. When these biomarkers are optimally combined, there is a strong trend toward greater specificity and sensitivity based on clinical diagnosis than when used individually. Our findings provide novel biomarker candidates for very mild and mild AD that can be further assessed as antecedent markers and predictors of clinical progression.     

Auditory brainstem response classification for threshold detection using estimated evoked potential data: comparison with ensemble averaged data

Auditory brainstem response (ABR) has become a routine clinical tool in neurological and audiological assessment. ABR measurement process with ensemble averaging is very time-consuming and uncomfortable for subjects due to the more repetition of single trials. This condition also restricts the wide usability of ABR in clinical applications. Therefore, the reduction in repetitions has a great importance in ABR measurements. In this study, 488 ABR responses are used for creating two different data sets. The first set is created conventionally by ensemble averaging of 1,024 single trials for each ABR pattern. The second set is obtained from the first estimated 64 single trials of the same records for each ABRs. Estimation is realized by using a nonlinear adaptive filtering algorithm. In classification stage, a powerful classifier integrated with a feature selection algorithm is performed for each data set. In result, the classification performance for estimated ABR data with 64 repetitions is better than the classification performance of the ensemble averaged data with 1,024 repetitions. The proposed system is resulted in an accuracy of 96% for estimated ABRs. So, the proposed system can effectively be used for threshold detection in auditory assessment providing a high accuracy. While the obtained results contribute to the practical ABR usage in clinics, the great significance of it arises from the reduction in repetitions via estimation of ABRs.     

Adipokines: a treasure trove for the discovery of biomarkers for metabolic disorders

Adipose tissue is a major endocrine organ, releasing signaling and mediator proteins, termed adipokines, via which adipose tissue communicates with other organs. Expansion of adipose tissue in obesity alters adipokine secretion which may contribute to the development of metabolic diseases. Consequently, this correlation has emphasized the importance to further characterize the adipocyte secretion profile, and several attempts have been made to characterize the complex nature of the adipose tissue secretome by utilizing diverse proteomic profiling approaches. Although the entirety of human adipokines is still incompletely characterized, to date more than 600 potentially secretory proteins were identified providing a rich source to identify putative novel biomarkers associated with metabolic diseases.     

Visualizing the runtime behavior of embedded network systems: A toolkit for TinyOS

TinyOS is an effective platform for developing lightweight embedded network applications. But the platform’s lean programming model and power-efficient operation come at a price: TinyOS applications are notoriously difficult to construct, debug, and maintain. The development difficulties stem largely from a programming model founded on events and deferred execution. In short, the model introduces non-determinism in the execution ordering of primitive actions — an issue exacerbated by the fact that embedded network systems are inherently distributed and reactive. The resulting set of possible execution sequences for a given system is typically large and can swamp developers’ unaided ability to reason about program behavior.In this paper, we present a visualization toolkit for TinyOS 2.0 to aid in program comprehension. The goal is to assist developers in reasoning about the computation forest underlying a system under test and the particular branches chosen during each run. The toolkit supports comprehension activities involving both local and distributed runtime behavior. The constituent components include (i) a full-featured static analysis and instrumentation library, (ii) a selection-based probe insertion system, (iii) a lightweight event recording service, (iv) a trace extraction and reconstruction tool, and (v) three visualization front-ends. We demonstrate the utility of the toolkit using both standard and custom system examples and present an analysis of the toolkit’s resource usage and performance characteristics.     

Cypress: compression and encryption of data and code for embedded multimedia systems

Copyright protection of sensitive data plays a significant part in the design of multimedia systems. This article introduces a hardware platform that enables both compression and encryption for data and code in a unified architecture. Besides being parameterizable, the platform features software tools for evaluating and optimizing specific multimedia applications.     

InRob: An approach for testing interoperability and robustness of real-time embedded software

Advances in digital technologies have contributed for significant reduction in accidents caused by hardware failures. However, the growing complexity of functions performed by embedded software has increased the number of accidents caused by software faults in critical systems. Moreover, due to the highly competitive market, software intensive subsystems are usually developed by different suppliers. Often these subsystems are required to interact with each other in order to provide a collaborative service. Testing approaches for subsystems integration support verification of the quality of service, focusing on the subsystems interfaces. The increasing complexity and tight coupling of real-time subsystems make integration testing unmanageable. The ad-hoc approach for testing is becoming less effective and more expensive. This article presents an integration testing approach denominated InRob, designed to verify the interoperability and robustness related to timing constraints of real-time embedded software. InRob guides the construction of services, based on formal models, aiming at the specifications of interoperability and robustness of test cases related to delays and time-outs of the messages exchanged in the interfaces of interconnected subsystems. The proposed formalism supports automatic test cases generation by verifying the relevant properties in the service behavioral model. As timing constraints are critical properties of aerospace systems, the feasibility of InRob is showed in the integration testing process of a telescope onboard in a satellite. The process is instantiated with existing testing tools and the case study is the software embedded in the telescope.     

VERTAF: an application framework for the design and verification of embedded real-time software

The growing complexity of embedded real-time software requirements calls for the design of reusable software components, the synthesis and generation of software code, and the automatic guarantee of nonfunctional properties such as performance, time constraints, reliability, and security. Available application frameworks targeted at the automatic design of embedded real-time software are poor in integrating functional and nonfunctional requirements. To bridge this gap, we reveal the design flow and the internal architecture of a newly proposed framework called verifiable embedded real-time application framework (VERTAF), which integrates software component-based reuse, formal synthesis, and formal verification. A formal UML-based embedded real-time object model is proposed for component reuse. Formal synthesis employs quasistatic and quasidynamic scheduling with automatic generation of multilayer portable efficient code. Formal verification integrates a model checker kernel from SGM, by adapting it for embedded software. The proposed architecture for VERTAF is component-based and allows plug-and-play for the scheduler and the verifier. Using VERTAF to develop application examples significantly reduced design effort and illustrated how high-level reuse of software components combined with automatic synthesis and verification can increase design productivity.     

Customizing host IDE for non-programming users of pure embedded DSLs: A case study

Pure embedding as an implementation strategy of domain-specific languages (DSLs) benefits from low implementation costs. On the other hand, it introduces undesired syntactic noise that impedes involvement of non-programming domain experts. Due to this, pure embedded DSLs are generally not intended for, nor used by, non-programmers. In this work, we try to challenge this state by experimenting with inexpensive customizations of the host IDE (Integrated Development Environment) to reduce the negative impact of syntactic noise. We present several techniques and recommendations based on standard IDE features (e.g., file templates, code folding, etc.) that aim to reduce syntactic noise and generally improve the user experience with pure embedded DSLs. The techniques are presented using a NetBeans IDE case study. The goal of the proposed techniques is to improve the user experience with pure embedded DSLs with a focus on the involvement of non-programming domain experts (or non-programmers in general). The proposed techniques were evaluated using a controlled experiment. The experiment compared a group using Ruby and non-modified RubyMine IDE versus a group using Java and NetBeans IDE customized to use the proposed techniques. Experiment results indicate that even inexpensive host IDE customizations can significantly alleviate issues caused by the syntactic noise: Java with its inflexible syntax performed better than Ruby with its concise syntax.     

Using aspects for testing of embedded software: experiences from two industrial case studies

Aspect-oriented software testing is emerging as an important alternative to conventional procedural and object-oriented testing techniques. This paper reports experiences from two case studies where aspects were used for the testing of embedded software in the context of an industrial application. In the first study, we used code-level aspects for testing non-functional properties. The methodology we used for deriving test aspect code was based on translating high-level requirements into test objectives, which were then implemented using test aspects in AspectC++. In the second study, we used high-level visual scenario-based models for the test specification, test generation, and aspect-based test execution. To specify scenario-based tests, we used a UML2-compliant variant of live sequence charts. To automatically generate test code from the models, a modified version of the S2A Compiler, outputting AspectC++ code, was used. Finally, to examine the results of the tests, we used the Tracer, a prototype tool for model-based trace visualization and exploration. The results of the two case studies show that aspects offer benefits over conventional techniques in the context of testing embedded software; these benefits are discussed in detail. Finally, towards the end of the paper, we also discuss the lessons learned, including the technological and other barriers to the future successful use of aspects in the testing of embedded software in industry.     

Identification of potential bivalent inhibitors from natural compounds for acetylcholinesterase through in silico screening using multiple pharmacophores

The symptomatic cure observed in the treatment of Alzheimer's disease (AD) by FDA approved drugs could possibly be due to their specificity against the active site of acetylcholinesterase (AChE) and not by targeting its pathogenicity. The AD pathogenicity involved in AChE protein is mainly due to amyloid beta peptide aggregation, which is triggered specifically by peripheral anionic site (PAS) of AChE. In the present study, a workflow has been developed for the identification and prioritization of potential compounds that could interact not only with the catalytic site but also with the PAS of AChE. To elucidate the essential structural elements of such inhibitors, pharmacophore models were constructed using PHASE, based on a set of fifteen best known AChE inhibitors. All these models on validation were further restricted to the best seven. These were transferred to PHASE database screening platform for screening 89,425 molecules deposited at the “ZINC natural product database”. Novel lead molecules retrieved were subsequently subjected to molecular docking and ADME profiling. A set of 12 compounds were identified with high pharmacophore fit values and good predicted biological activity scores. These compounds not only showed higher affinity for catalytic residues, but also for Trp86 and Trp286, which are important, at PAS of AChE. The knowledge gained from this study, could lead to the discovery of potential AChE inhibitors that are highly specific for AD treatment as they are bivalent lead molecules endowed with dual binding ability for both catalytic site and PAS of AChE.     

Harnessing global expertise: A comparative study of expertise profiling methods for online communities

Building expertise profiles in global online communities is a critical step in leveraging the range of expertise available in the global knowledge economy. In this paper we introduce a three-stage framework that automatically generates expertise profiles of online community members. In the first two stages, document-topic relevance and user-document association are estimated for calculating users’ expertise levels on individual topics. We empirically compare two state-of-the-art information retrieval techniques, the vector space model and the language model, with a Latent Dirichlet Allocation (LDA) based model for computing document-topic relevance as well as the direct and indirect association models for computing user-document association. In the third stage we test whether a filtering strategy can improve the performance of expert profiling. Our experimental results using two real datasets provide useful insights on how to select the best models for profiling users’ expertise in online communities that can work across a range of global communities.     

Protein folding: a prototype for control of complex systems

One of the basic problems of the theory of control in complex systems involves determining the circumstances under which a set of control parameters can effectively manipulate a much larger number of degrees of freedom in the controlled system. Such a control capability obviously requires the presence of additional constraints relating the quantities to be controlled. We explore this general question in the context of a specific situation; namely, in terms of an algorithm recently proposed to compute the three-dimensional structures of folded polypeptides from their amino acid sequences. In this algorithm, a small number of average geometric properties (the control parameters) are utilized to determine a much larger set of inter-residue distances in the folded structure. We derive the specific condition which assures that the algorithm converges pointwise to the correct structure, which in this case turns out to involve relating rates of change of coordinates to increments in the distances consistent with a particular set of values for the control parameters. Some further implications of this kind of result are briefly discussed.     

An experimental investigation of menu selection for immersive virtual environments: fixed versus handheld menus

Virtual Reality - With the development of consumer-grade virtual reality (VR) systems, the interface and interaction design for immersive virtual environments have become a critical issue for VR...     

Comparative performance evaluation of Java threads for embedded applications: Linux Thread vs. Green Thread

Despite the portability and platform independence of Java programs, their performance depends on the threading mechanisms of the host operating system. In this paper, we measure the performance of Java threads for two different multi-threading implementations, Linux Thread and Green Thread, using PersonalJava (TM) on a Linux-based platform. The experimental results show the relative strengths and weaknesses of the two threading mechanisms with respect to synchronization overhead, I/O efficiency, and thread control.