Direct Virtual Memory Access from FPGA for High-Productivity Heterogeneous Computing

Heterogeneous computing utilizing both CPU and FPGA requires access to data in the main memory from both devices. While a typical system relies on software executing on the CPU to orchestrate all data movements between the FPGA and the main memory, our demo presents a complementary FPGA-centric approach that allows gateware to directly access the virtual memory space as part of the executing process without involving the CPU. A caching address translation buffer was implemented alongside the user FPGA gateware to provide runtime mapping between virtual and physical memory addresses. The system was implemented on a commercial off-the-shelf FPGA add-on card to demonstrate the viability of such approach in low-cost systems. Experiment demonstrated reasonable performance improvement when compared to a typical software-centric implementation; while the number of context switches between FPGA and CPU in both kernel and user mode was significantly reduced, freeing the CPU for other concurrent user tasks. © 2013 IEEE.published_or_final_versio

A soft processor overlay with tightly-coupled FPGA accelerator

FPGA overlays are commonly implemented as coarse-grained reconfigurable architectures with a goal to improve designers’ productivity through balancing flexibility and ease of configuration of the underlying fabric. To truly facilitate full application acceleration, it is often necessary to also include a highly efficient processor that integrates and collaborates with the accelerators while maintaining the benefits of being implemented within the same overlay framework. This paper presents an open-source soft processor that is designed to tightly-couple with FPGA accelerators as part of an overlay framework. RISC-V is chosen as the instruction set for its openness and portability, and the soft processor is designed as a 4-stage pipeline to balance resource consumption and performance when implemented on FPGAs. The processor is generically implemented so as to promote design portability and compatibility across different FPGA platforms. Experimental results show that integrated software-hardware applications using the proposed tightly-coupled architecture achieve comparable performance as hardware-only accelerators while the proposed architecture provides additional run-time flexibility. The processor has been synthesized to both low-end and high-performance FPGA families from different vendors, achieving the highest frequency of 268:67MHz and resource consumption comparable to existing RISC-V designs.postprin

Automatic Nested Loop Acceleration on FPGAs Using Soft CGRA Overlay

Session 1: HLS Toolingpostprin

Opioid modulation of GABA release in the rat inferior colliculus

Background: The inferior colliculus, which receives almost all ascending and descending auditory signals, plays a crucial role in the processing of auditory information. While the majority of the recorded activities in the inferior colliculus are attributed to GABAergic and glutamatergic signalling, other neurotransmitter systems are expressed in this brain area including opiate peptides and their receptors which may play a modulatory role in neuronal communication.Results: Using a perfusion protocol we demonstrate that morphine can inhibit KCl-induced release of [H-3] GABA from rat inferior colliculus slices. DAMGO ([D-Ala(2), N-Me-Phe(4), Gly(5)ol]-enkephalin) but not DADLE ([D-Ala2, D-Leu5]-enkephalin or U69593 has the same effect as morphine indicating that mu rather than delta or kappa opioid receptors mediate this action. [H-3]GABA release was diminished by 16%, and this was not altered by the protein kinase C inhibitor bisindolylmaleimide I. Immunostaining of inferior colliculus cryosections shows extensive staining for glutamic acid decarboxylase, more limited staining for mu opiate receptors and relatively few neurons co-stained for both proteins.Conclusion: The results suggest that mu-opioid receptor ligands can modify neurotransmitter release in a sub population of GABAergic neurons of the inferior colliculus. This could have important physiological implications in the processing of hearing information and/or other functions attributed to the inferior colliculus such as audiogenic seizures and aversive behaviour

Improving polygenic risk prediction from summary statistics by an empirical Bayes approach

Polygenic risk scores (PRS) from genome-wide association studies (GWAS) are increasingly used to predict disease risks. However some included variants could be false positives and the raw estimates of effect sizes from them may be subject to selection bias. In addition, the standard PRS approach requires testing over a range of p-value thresholds, which are often chosen arbitrarily. The prediction error estimated from the optimized threshold may also be subject to an optimistic bias. To improve genomic risk prediction, we proposed new empirical Bayes approaches to recover the underlying effect sizes and used them as weights to construct PRS. We applied the new PRS to twelve cardio-metabolic traits in the Northern Finland Birth Cohort and demonstrated improvements in predictive power (in R2) when compared to standard PRS at the best p-value threshold. Importantly, for eleven out of the twelve traits studied, the predictive performance from the entire set of genome-wide markers outperformed the best R2 from standard PRS at optimal p-value thresholds. Our proposed methodology essentially enables an automatic PRS weighting scheme without the need of choosing tuning parameters. The new method also performed satisfactorily in simulations. It is computationally simple and does not require assumptions on the effect size distributions. Improving polygenic risk prediction from summary statistics by an empirical Bayes approach. Available from: https://www.researchgate.net/publication/313258278_Improving_polygenic_risk_prediction_from_summary_statistics_by_an_empirical_Bayes_approach [accessed Sep 29, 2017].published_or_final_versio

Increases in absenteeism among health care workers in Hong Kong during influenza epidemics, 2004–2009

published_or_final_versio

Constant Modulus Waveform Estimation and Interference Suppression via Two-stage Fractional Program-based Beamforming

In radar and communication systems, there exist a large class of signals with constant modulus property, including BPSK, QPSK, LFM, and phase-coded signals. In this paper, we focus on the problem of joint constant modulus waveform estimation and interference suppression from signals received at an antenna array. Instead of seeking a compromise between interference suppression and output noise power reduction by the Capon method or utilizing the interference direction (ID) prior to place perfect nulls at the IDs and subsequently minimize output noise power by the linearly constrained minimum variance (LCMV) beamformer, we devise a novel power ratio criterion, namely, interference-plus-noise-to-noise ratio (INNR) in the beamformer output to attain perfect interference nulling and minimal output noise power as in LCMV yet under the unknown ID case. A two-stage fractional program-based method is developed to jointly suppress the interferences and estimate the constant modulus waveform. In the first stage, we formulate an optimization model with a fractional objective function to minimize the INNR. Then, in the second stage, another fraction-constrained optimization problem is established to refine the weight vector from the solution space constrained by the INNR bound, to achieve approximately perfect nulls and minimum output noise power. Moreover, the solution is further extended to tackle the case with steering vector errors. Numerical results demonstrate the excellent performance of our methods

Transcriptional regulation of RET by Nkx2-1, Phox2b, Sox10, and Pax3

Background: The rearranged during transfection (RET) gene encodes a single-pass receptor whose proper expression and function are essential for the development of enteric nervous system. Mutations in RET regulatory regions are also associated with Hirschsprung disease (HSCR) (aganglionosis of the colon). We previously showed that 2 polymorphisms in RET promoter are associated with the increased risk of HSCR. These single nucleotide polymorphisms overlap with the NK2 homeobox 1 (Nkx2-1) binding motif interrupting the physical interaction of NKX2-1 with the RET promoter and result in reduced RET transcription. In this study, we further delineated Nkx2-1-mediated RET Transcription. Methods and results: First, we demonstrated that PHOX2B, like SOX10 and NKX2-1, is expressed in the mature enteric ganglions of human gut by immunohistochemistry. Second, subsequent dual-luciferase-reporter studies indicated that Nkx2-1 indeed works coordinately with Phox2b and Sox10, but not Pax3, to mediate RET transcription. In addition, identification of Phox2b responsive region in RET promoter further provides solid evidence of the potential functional interaction between Phox2b and RET. Conclusion: In sum, Phox2b and Sox10 act together with Nkx2.1 to modify RET signaling and this interaction may also contribute to HSCR susceptibility. © 2009 Elsevier Inc. All rights reserved.postprin

A Smart Card-Based Electronic School Absenteeism System for Influenza-Like Illness Surveillance in Hong Kong: Design, Implementation, and Feasibility Assessment

published_or_final_versio

Engineering current density over 5 kA mm-2 at 4.2 K, 14 T in thick film REBCO tapes

We report on remarkably high in-field performance at 4.2 K achieved in >4 μm thick rare earth barium copper oxide (REBCO) samples with Zr addition. Two different samples have been measured independently at Lawrence Berkeley National Laboratory and the National High Magnetic Field Laboratory, achieving critical current densities (J ) of 12.21 MA cm and 12.32 MA cm at 4.2 K, 14 T (), respectively, which corresponds to equivalent critical current (I ) values of 2247 and 2119 A/4 mm. These I values are about two times higher than the best reported performance of REBCO tapes to date and more than five times higher than the commercial HTS tapes reported in a recent study. The measured J values, with a pinning force of ∼1.7 T N m are almost identical to the highest value reported for thin (∼1 μm thick) REBCO at the field and temperature, but extended to very thick (>4 μm) films. This results in an engineering current density (J ) above 5 kA mm at 4.2 K, 14 T, which is more than five times higher than Nb Sn and nearly four times higher than the highest reported value of all superconductors other than REBCO at this field and temperature. The reported results have been achieved by utilizing an advanced metal organic chemical vapor deposition system. This study demonstrates the remarkable level of in-field performance achievable with REBCO conductors at 4.2 K and strong potential for high-field magnet applications. c c c c e 3 -2 -2 -3 -