GraphStep: A System Architecture for Sparse-Graph Algorithms

Many important applications are organized around long-lived, irregular sparse graphs (e.g., data and knowledge bases, CAD optimization, numerical problems, simulations). The graph structures are large, and the applications need regular access to a large, data-dependent portion of the graph for each operation (e.g., the algorithm may need to walk the graph, visiting all nodes, or propagate changes through many nodes in the graph). On conventional microprocessors, the graph structures exceed on-chip cache capacities, making main-memory bandwidth and latency the key performance limiters. To avoid this “memory wall,” we introduce a concurrent system architecture for sparse graph algorithms that places graph nodes in small distributed memories paired with specialized graph processing nodes interconnected by a lightweight network. This gives us a scalable way to map these applications so that they can exploit the high-bandwidth and low-latency capabilities of embedded memories (e.g., FPGA Block RAMs). On typical spreading activation queries on the ConceptNet Knowledge Base, a sample application, this translates into an order of magnitude speedup per FPGA compared to a state-of-the-art Pentium processor

Jejunal Occlusion Caused by Heterotopic Gastric and Duodenal Mucosa: A Late Complication of a Complex Intestinal Malformation

We report a rare case of late complication of a complex intestinal malformation. At day 1 of life, a baby girl underwent resection of an atretic jejunal segment, associated with an enteric duplication harboring foci of gastric and duodenal heterotopia. After an asymptomatic period of 19 years, the patient presented with acute bowel obstruction. Recurrence of the jejunal occlusion at the previous anastomotic site was caused by mucosa hyperplasia in association with heterotopic gastric and duodenal tissue. A Wnt/β-catenin pathway deregulation was hypothesized but not confirmed by CTNNB1 exon 3 mutation analysis. This case illustrates a rare association of 3 pathologies-namely, intestinal atresia, enteric duplication, and heterotopia, with a late-occurring acute complication

Immune Response, Ciprofloxacin Activity, and Gender Differences after Human Experimental Challenge by Two Strains of Enterotoxigenic Escherichia coli

In order to test vaccines against enterotoxigenic Escherichia coli (ETEC)-induced diarrhea, challenge models are needed. In this study we compared clinical and immunological responses after North American volunteers were orally challenged by two ETEC strains. Groups of approximately eight volunteers received 10(9) or 10(10) CFU of E. coli B7A (LT(+) ST(+) CS6(+)) or 10(8) or 10(9) CFU of E. coli H10407 (LT(+) ST(+) CFA/I(+)). About 75% of the volunteers developed diarrhea after challenge with 10(10) CFU B7A or either dose of H10407. B7A had a shorter incubation period than H10407 (P = 0.001) and caused milder illness; the mean diarrheal output after H10407 challenge was nearly twice that after B7A challenge (P = 0.01). Females had more abdominal complaints, and males had a higher incidence of fever. Ciprofloxacin generally diminished or stopped symptoms and shedding by the second day of antibiotic treatment, but four subjects shed for one to four additional days. The immune responses to colonization factors CS6 and colonization factor antigen I (CFA/I) and to heat-labile toxin (LT) were measured. The responses to CFA/I were the most robust responses; all volunteers who received H10407 had serum immunoglobulin A (IgA) and IgG responses, and all but one volunteer had antibody-secreting cell (ASC) responses. One-half the volunteers who received B7A had an ASC response to CS6, and about one-third had serum IgA or IgG responses. Despite the differences in clinical illness and immune responses to colonization factors, the immune responses to LT were similar in all groups and were intermediate between the CFA/I and CS6 responses. These results provide standards for immune responses after ETEC vaccination

Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair

Pseudouridine (Ψ) is the most common chemical modification present in RNA. In general, Ψ increases the thermodynamic stability of RNA. However, the degree of stabilization depends on the sequence and structural context. To explain experimentally observed sequence dependence of the effect of Ψ on the thermodynamic stability of RNA duplexes, we investigated the structure, dynamics and hydration of RNA duplexes with an internal Ψ-A base pair in different nearest-neighbor sequence contexts. The structures of two RNA duplexes containing 5′-GΨC/3′-CAG and 5′-CΨG/3′-GAC motifs were determined using NMR spectroscopy. To gain insight into the effect of Ψ on duplex dynamics and hydration, we performed molecular dynamics (MD) simulations of RNA duplexes with 5′-GΨC/3′-CAG, 5′-CΨG/3′-GAC, 5′-AΨU/3′-UAA and 5′-UΨA/3′-AAU motifs and their unmodified counterparts. Our results showed a subtle impact from Ψ modification on the structure and dynamics of the RNA duplexes studied. The MD simulations confirmed the change in hydration pattern when U is replaced with Ψ. Quantum chemical calculations showed that the replacement of U with Ψ affected the intrinsic stacking energies at the base pair steps depending on the sequence context. The calculated intrinsic stacking energies help to explain the experimentally observed sequence dependent changes in the duplex stability from Ψ modification.</p