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

A quantitative comparison of sRNA-based and protein-based gene regulation

Small, non-coding RNAs (sRNAs) play important roles as genetic regulators in prokaryotes. sRNAs act post-transcriptionally via complementary pairing with target mRNAs to regulate protein expression. We use a quantitative approach to compare and contrast sRNAs with conventional transcription factors (TFs) to better understand the advantages of each form of regulation. In particular, we calculate the steady-state behavior, noise properties, frequency-dependent gain (amplification), and dynamical response to large input signals of both forms of regulation. While the mean steady-state behavior of sRNA-regulated proteins exhibits a distinctive tunable threshold-linear behavior, our analysis shows that transcriptional bursting leads to significantly higher intrinsic noise in sRNA-based regulation than in TF-based regulation in a large range of expression levels and limits the ability of sRNAs to perform quantitative signaling. Nonetheless, we find that sRNAs are better than TFs at filtering noise in input signals. Additionally, we find that sRNAs allow cells to respond rapidly to large changes in input signals. These features suggest a niche for sRNAs in allowing cells to transition quickly yet reliably between distinct states. This functional niche is consistent with the widespread appearance of sRNAs in stress-response and quasi-developmental networks in prokaryotes.Comment: 26 pages, 8 figures; accepted for publication in Molecular Systems Biolog

Phytobezoar: an unusual cause of intestinal obstruction

Small bowel phytobezoars are rare and almost always obstructive. There have been previously reported cases of phytobezoars in the literature, however there are few reports on radiological findings for small bowel bezoars. Barium studies characteristically show an intraluminal filling defect of variable size that is not fixed to the bowel wall with barium filling the interstices giving a mottled appearance. On CT scan, the presence of a round or ovoid intraluminal mass with a ‘mottled gas’ pattern is believed to be pathognomonic. Since features on CT scans are characteristics and physical findings are of little assistance in the diagnosis of bezoar, the diagnostic value of CT needs to be emphasised

MicroRNA-143 is a potential tumor suppressor targeting DNA methyltransferases 3a in colorectal cancer

Gastroenterology, 2009, v. 136 n. 5, suppl.1, p. A165, abstract no. 10692009 DDW (Digestive Disease Week) Abstract Supplement , AGA (American Gastroenterological Association) Institute Topic Forum, Oral sessions: Scientific sessions: Microrna and digestive cancers, Oral presentation no. 1069postprin

WIJAM: a mobile collaborative improvisation platform under Master-players Paradigm

Music jamming is an extremely difficult task for musical novices. Trying to extend this meaningful and highly enjoyable activity to a larger recipient group, we present WIJAM, a mobile application for an ad-hoc group of musical novices to perform improvisation along with a music master. In this master-players' paradigm, the master offers a music backing, orchestrates the musical flow, and gives feedbacks to the players; the players improvise by tapping and sketching on their smartphones. We argue that this paradigm can be a significant contribution to the possibility of music playing by a group of novices with no instrumental training leading to decent musical results.published_or_final_versio

Rapid mixing of viscous liquids by electrical coiling

published_or_final_versio

Testing Ecological Theory with Lianas

Lianas constitute a diverse polyphyletic plant group that is advancing our understanding of ecological theory. Specifically, lianas are providing new insights into the mechanisms that control plant distribution and diversity maintenance. For example, there is now evidence that a single, scalable mechanism may explain local, regional, and pan‐tropical distribution of lianas, as well as the maintenance of liana species diversity. The ability to outcompete trees under dry, stressful conditions in seasonal forests provides lianas a growth advantage that, over time, results in relatively high abundance in seasonal forests and low abundance in aseasonal forests. Lianas may also gain a similar growth advantage following disturbance, thus explaining why liana density and diversity peak following disturbance at the local, forest scale. The study of ecology, however, is more than the effect of the environment on organisms; it also includes the effects of organisms on the environment. Considerable empirical evidence now indicates that lianas substantially alter their environment by consuming resources, suppressing tree performance, and influencing emergent properties of forests, such as ecosystem functioning, plant and animal diversity, and community composition. These recent studies using lianas are transcending classical tropical ecology research and are now providing novel insights into fundamental ecological theory

An H5N1-based matrix protein 2 ectodomain tetrameric peptide vaccine provides cross-protection against lethal infection with H7N9 influenza virus

published_or_final_versio