High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP

This paper explores the pros and cons of reconfigurable computing in the form of FPGAs for high performance efficient computing. In particular, the paper presents the results of a comparative study between three different acceleration technologies, namely, Field Programmable Gate Arrays (FPGAs), Graphics Processor Units (GPUs), and IBM’s Cell Broadband Engine (Cell BE), in the design and implementation of the widely-used Smith-Waterman pairwise sequence alignment algorithm, with general purpose processors as a base reference implementation. Comparison criteria include speed, energy consumption, and purchase and development costs. The study shows that FPGAs largely outperform all other implementation platforms on performance per watt criterion and perform better than all other platforms on performance per dollar criterion, although by a much smaller margin. Cell BE and GPU come second and third, respectively, on both performance per watt and performance per dollar criteria. In general, in order to outperform other technologies on performance per dollar criterion (using currently available hardware and development tools), FPGAs need to achieve at least two orders of magnitude speed-up compared to general-purpose processors and one order of magnitude speed-up compared to domain-specific technologies such as GPUs

Smartphone-Based pH Sensor for Home Monitoring of Pulmonary Exacerbations in Cystic Fibrosis.

Currently, Cystic Fibrosis (CF) patients lack the ability to track their lung health at home, relying instead on doctor checkups leading to delayed treatment and lung damage. By leveraging the ubiquity of the smartphone to lower costs and increase portability, a smartphone-based peripheral pH measurement device was designed to attach directly to the headphone port to harvest power and communicate with a smartphone application. This platform was tested using prepared pH buffers and sputum samples from CF patients. The system matches within ~0.03 pH of a benchtop pH meter while fully powering itself and communicating with a Samsung Galaxy S3 smartphone paired with either a glass or Iridium Oxide (IrOx) electrode. The IrOx electrodes were found to have 25% higher sensitivity than the glass probes at the expense of larger drift and matrix sensitivity that can be addressed with proper calibration. The smartphone-based platform has been demonstrated as a portable replacement for laboratory pH meters, and supports both highly robust glass probes and the sensitive and miniature IrOx electrodes with calibration. This tool can enable more frequent pH sputum tracking for CF patients to help detect the onset of pulmonary exacerbation to provide timely and appropriate treatment before serious damage occurs

Spirituality and business: An interdisciplinary overview

The paper gives an interdisciplinary overview of the emerging field of spirituality and business. It uses insights from business ethics, theology, neuroscience, psychology, gender studies, and philosophy to economics, management, organizational science, and banking and refers to different religious convictions including Christianity, Judaism, Islam, Hinduism, Buddhism, Confucianism, the Baha'i faith, and the North-American aboriginal worldview. The authors argue that the materialistic management paradigm has failed. They explore new values for post-materialistic management: frugality, deep ecology, trust, reciprocity, responsibility for future generations, and authenticity. Within this framework profit and growth are no longer ultimate aims but elements in a wider set of values. Similarly, cost-benefit calculations are no longer the essence of management but are part of a broader concept of wisdom in leadership. Spirit-driven businesses require intrinsic motivation for serving the common good and using holistic evaluation schemes for measuring success. The Palgrave Handbook of Business and Spirituality, edited by the authors, is a response to developments that simultaneously challenge the “business as usual” mindset

Scalable Solutions for Automated Single Pulse Identification and Classification in Radio Astronomy

Data collection for scientific applications is increasing exponentially and is forecasted to soon reach peta- and exabyte scales. Applications which process and analyze scientific data must be scalable and focus on execution performance to keep pace. In the field of radio astronomy, in addition to increasingly large datasets, tasks such as the identification of transient radio signals from extrasolar sources are computationally expensive. We present a scalable approach to radio pulsar detection written in Scala that parallelizes candidate identification to take advantage of in-memory task processing using Apache Spark on a YARN distributed system. Furthermore, we introduce a novel automated multiclass supervised machine learning technique that we combine with feature selection to reduce the time required for candidate classification. Experimental testing on a Beowulf cluster with 15 data nodes shows that the parallel implementation of the identification algorithm offers a speedup of up to 5X that of a similar multithreaded implementation. Further, we show that the combination of automated multiclass classification and feature selection speeds up the execution performance of the RandomForest machine learning algorithm by an average of 54% with less than a 2% average reduction in the algorithm's ability to correctly classify pulsars. The generalizability of these results is demonstrated by using two real-world radio astronomy data sets.Comment: In Proceedings of the 47th International Conference on Parallel Processing (ICPP 2018). ACM, New York, NY, USA, Article 11, 11 page

Microsimulation - A Survey of Methods and Applications for Analyzing Economic and Social Policy

This essential dimensions of microsimulation as an instrument to analyze and forecast the individual impacts of alternative economic and social policy measures are surveyed in this study. The basic principles of microsimulation, which is a tool for practical policy advising as well as for research and teaching, are pointed out and the static and dynamic (cross-section and life-cycle) approaches are compared to one another. Present and past developments of microsimulation models and their areas of application are reviewed, focusing on the US, Europe and Australia. Based on general requirements and components of microsimulation models a microsimulation model's actual working mechanism are discussed by a concrete example: the concept and realization of MICSIM, a PC microsimulation model based on a relational database system, an offspring of the Sfb 3 Statitic Microsimulation Model. Common issues of microsimulation modeling are regarded: micro/macro link, behavioural response and the important question of evaluating microsimulation results. The concluding remarks accentuate the increasing use of microcomputers for microsimulation models also for teaching purposes.Microsimulation, Microanalytic Simulation Models, Microanalysis, Economic and Social Policy Analysis

Impact identification strategies for evaluating business incentive programs.

Although business incentive programs of different forms have been the bulk of local economic development policies in many industrialized countries for more than the last three decades, evaluating their impact on employment or local economic growth outcomes remains a challenging task due to the persisting lack of randomized experiments and the presence of many confounding factors which affect firms and economic growth outcomes. Moreover, much of the recent advancements in the statistical program evaluation methodology applicable to non-experimental settings do not make any direct reference to the specificities posed by business incentive policies. This paper aims at offering some clear guidance on how to choose the appropriate focus of the evaluation, the policy relevant evaluation parameters and empirical impact identification strategies when applying statistical methods attempting to estimate how much of the different outcomes between treatment and control groups are attributable to the program/s being evaluated. Each methodological option discussed in the paper is linked to the different features of commonly implemented US and EU policies and to whether or not the analysis focuses on outcomes recorded at a firm-level or at the level of the geographic areas in which the assisted firms are located.Impact evaluation, Business Incentives Policies; Comparison-group designs, Identification strategies

A QHD-capable parallel H.264 decoder

Video coding follows the trend of demanding higher performance every new generation, and therefore could utilize many-cores. A complete parallelization of H.264, which is the most advanced video coding standard, was found to be difficult due to the complexity of the standard. In this paper a parallel implementation of a complete H.264 decoder is presented. Our parallelization strategy exploits function-level as well as data-level parallelism. Function-level parallelism is used to pipeline the H.264 decoding stages. Data-level parallelism is exploited within the two most time consuming stages, the entropy decoding stage and the macroblock decoding stage. The parallelization strategy has been implemented and optimized on three platforms with very different memory architectures, namely an 8-core SMP, a 64-core cc-NUMA, and an 18-core Cell platform. Evaluations have been performed using 4kx2k QHD sequences. On the SMP platform a maximum speedup of 4.5x is achieved. The SMP-implementation is reasonably performance portable as it achieves a speedup of 26.6x on the cc-NUMA system. However, to obtain the highest performance (speedup of 33.4x and throughput of 200 QHD frames per second), several cc-NUMA specific optimizations are necessary such as optimizing the page placement and statically assigning threads to cores. Finally, on the Cell platform a near ideal speedup of 16.5x is achieved by completely hiding the communication latency.EC/FP7/248647/EU/ENabling technologies for a programmable many-CORE/ENCOR

Enron: An In-Depth Analysis Of The Hedging Schemes

N/