Accelerating Binary String Comparisons with a Scalable, Streaming-Based System Architecture Based on FPGAs

Pilz S, Porrmann F, Kaiser M, Hagemeyer J, Hogan JM, Rückert U. Accelerating Binary String Comparisons with a Scalable, Streaming-Based System Architecture Based on FPGAs. Algorithms. 2020;13(2): 47.This paper is concerned with Field Programmable Gate Arrays (FPGA)-based systems for energy-efficient high-throughput string comparison. Modern applications which involve comparisons across large data sets—such as large sequence sets in molecular biology—are by their nature computationally intensive. In this work, we present a scalable FPGA-based system architecture to accelerate the comparison of binary strings. The current architecture supports arbitrary lengths in the range 16 to 2048-bit, covering a wide range of possible applications. In our example application, we consider DNA sequences embedded in a binary vector space through Locality Sensitive Hashing (LSH) one of several possible encodings that enable us to avoid more costly character-based operations. Here the resulting encoding is a 512-bit binary signature with comparisons based on the Hamming distance. In this approach, most of the load arises from the calculation of the O ( m ∗ n ) Hamming distances between the signatures, where m is the number of queries and n is the number of signatures contained in the database. Signature generation only needs to be performed once, and we do not consider it further, focusing instead on accelerating the signature comparisons. The proposed FPGA-based architecture is optimized for high-throughput using hundreds of computing elements, arranged in a systolic array. These core computing elements can be adapted to support other string comparison algorithms with little effort, while the other infrastructure stays the same. On a Xilinx Virtex UltraScale+ FPGA (XCVU9P-2), a peak throughput of 75.4 billion comparisons per second—of 512-bit signatures—was achieved, using a design with 384 parallel processing elements and a clock frequency of 200 MHz. This makes our FPGA design 86 times faster than a highly optimized CPU implementation. Compared to a GPU design, executed on an NVIDIA GTX1060, it performs nearly five times faster

Development of Energy Models for Design Space Exploration of Embedded Many-Core Systems

This paper introduces a methodology to develop energy models for the design space exploration of embedded many-core systems. The design process of such systems can benefit from sophisticated models. Software and hardware can be specifically optimized based on comprehensive knowledge about application scenario and hardware behavior. The contribution of our work is an automated framework to estimate the energy consumption at an arbitrary abstraction level without the need to provide further information about the system. We validated our framework with the configurable many-core system CoreVA-MPSoC. Compared to a simulation of the CoreVA-MPSoC on gate level in a 28nm FD-SOI standard cell technology, our framework shows an average estimation error of about 4%.Comment: Presented at HIP3ES, 201

Allele-Dependent Similarity between Viral and Self-Peptide Presentation by Hla-B27 Subtypes

Molecular mimicry is discussed as a possible mechanism that may contribute to the development of autoimmune diseases. It could also be involved in the differential association of the human major histocompatibility subtypes HLA-B(*)2705 and HLA-B(*)2709 with ankylosing spondylitis. These two subtypes differ only in residue 116 of the heavy chain (Asp in B(*)2705 and His in B(*)2709), but the reason for the differential disease association is not understood. Using x-ray crystallography, we show here that the viral peptide pLMP2 (RRRWRRLTV, derived from latent membrane protein 2 (residues 236-244) of Epstein-Barr virus) is presented by the B(*)2705 and B(*)2709 molecules in two drastically deviating conformations. Extensive structural similarity between pLMP2 and the self-peptide pVIPR (RRKWRRWHL, derived from vasoactive intestinal peptide type 1 receptor (residues 400-408)) is observed only when the peptides are presented by B(*)2705 because of a salt bridge between Arg(5) of both peptides and the subtype-specific heavy chain residue Asp(116). Combined with functional studies using pLMP2/pVIPR-cross-reactive cytotoxic T cell lines and clones, together with target cells presenting these peptides or a modified peptide analogue, our results reveal that a pathogen-derived peptide can exhibit major histocompatibility complex class I subtype-dependent, drastically distinct binding modes. Furthermore, the results demonstrate that molecular mimicry between pLMP2 and pVIPR in the HLA-B27 context is an allele-dependent property

Traveling Wave Magnetic Particle Imaging for determining the iron-distribution in rock: Traveling Wave Magnetic Particle Imaging for determining the iron-distribution in rock

Determining the composition of solid materials is of high interest in areas such as material research or quality assurance. There are several modalities at disposal with which various parameters of the material can be observed, but of those only magnetic resonance imaging (MRI) or computer tomography (CT) offer anon-destructive determination of material distribution in 3D. A novel non-destructive imaging method is Magnetic Particle Imaging (MPI), which uses dynamic magnetic fields for a direct determination of the distribution of magnetic materials in 3D. With this approach, it is possible to determine and differentiate magnetic and non-magnetic behaviour. In this paper, the first proof-of-principle measurements of magnetic properties in solid environments are presented using a home-built traveling wave magnetic particle imaging scanner

Microparticles globally reprogram Streptomyces albus toward accelerated morphogenesis, streamlined carbon core metabolism, and enhanced production of the antituberculosis polyketide pamamycin

Streptomyces spp. are a rich source for natural products with recognized industrial value, explaining the high interest to improve and streamline the performance of in these microbes. Here, we studied the production of pamamycins, macrodiolide homologs with a high activity against multiresistant pathogenic microbes, using recombinant Streptomyces albus J1074/R2. Talc particles (hydrous magnesium silicate, 3MgO·4SiO2·H2O) of micrometer size, added to submerged cultures of the recombinant strain, tripled pamamycin production up to 50 mg/L. Furthermore, they strongly affected morphology, reduced the size of cell pellets formed by the filamentous microbe during the process up to sixfold, and shifted the pamamycin spectrum to larger derivatives. Integrated analysis of transcriptome and precursor (CoA thioester) supply of particle‐enhanced and control cultures provided detailed insights into the underlying molecular changes. The microparticles affected the expression of 3,341 genes (56% of all genes), revealing a global and fundamental impact on metabolism. Morphology‐associated genes, encoding major regulators such as SsgA, RelA, EshA, Factor C, as well as chaplins and rodlins, were found massively upregulated, indicating that the particles caused a substantially accelerated morphogenesis. In line, the pamamycin cluster was strongly upregulated (up to 1,024‐fold). Furthermore, the microparticles perturbed genes encoding for CoA‐ester metabolism, which were mainly activated. The altered expression resulted in changes in the availability of intracellular CoA‐esters, the building blocks of pamamycin. Notably, the ratio between methylmalonyl CoA and malonyl‐CoA was increased fourfold. Both metabolites compete for incorporation into pamamycin so that the altered availability explained the pronounced preference for larger derivatives in the microparticle‐enhanced process. The novel insights into the behavior of S. albus in response to talc appears of general relevance to further explore and upgrade the concept of microparticle enhanced cultivation, widely used for filamentous microbes

Streptomyces spp. From the Marine Sponge Antho dichotoma: Analyses of Secondary Metabolite Biosynthesis Gene Clusters and Some of Their Products

Guerrero-Garzón JF, Zehl M, Schneider O, et al. Streptomyces spp. From the Marine Sponge Antho dichotoma: Analyses of Secondary Metabolite Biosynthesis Gene Clusters and Some of Their Products. Frontiers in Microbiology. 2020;11: 437.Actinomycete bacteria from marine environments represent a potential source for new antibiotics and anti-tumor drugs. Ten strains belonging to the genus Streptomyces isolated from the marine sponge Antho dichotoma collected at the bottom of the Trondheim fjord (Norway) were screened for antibiotic activity. Since only few isolates proved to be bioactive in the conditions tested, we decided to gain an insight into their biosynthetic potential using genome sequencing and analysis. Draft genomes were analyzed for the presence of secondary metabolite biosynthesis gene clusters (BGCs) using antiSMASH software. BGCs specifying both known and potentially novel secondary metabolites were identified, suggesting that these isolates might be sources for new bioactive compounds. The results of this analysis also implied horizontal transfer of several gene clusters between the studied isolates, which was especially evident for the lantibiotic- and thiopeptide-encoding BGCs. The latter implies the significance of particular secondary metabolites for the adaptation of Streptomyces to the spatially enclosed marine environments such as marine sponges. Two bioactive isolates, one showing activity against both yeast and Bacillus subtilis, and one only against yeast were analyzed in details, leading to the identification of cycloheximide, linearmycins, and echinomycins that are presumably responsible for the observed bioactivities

Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis

Follmann M, Ochrombel I, Kraemer R, et al. Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis. BMC Genomics. 2009;10(1):621.Background: The maintenance of internal pH in bacterial cells is challenged by natural stress conditions, during host infection or in biotechnological production processes. Comprehensive transcriptomic and proteomic analyses has been conducted in several bacterial model systems, yet questions remain as to the mechanisms of pH homeostasis. Results: Here we present the comprehensive analysis of pH homeostasis in C. glutamicum, a bacterium of industrial importance. At pH values between 6 and 9 effective maintenance of the internal pH at 7.5 +/- 0.5 pH units was found. By DNA microarray analyses differential mRNA patterns were identified. The expression profiles were validated and extended by 1D-LC-ESI-MS/MS based quantification of soluble and membrane proteins. Regulators involved were identified and thereby participation of numerous signaling modules in pH response was found. The functional analysis revealed for the first time the occurrence of oxidative stress in C. glutamicum cells at neutral and low pH conditions accompanied by activation of the iron starvation response. Intracellular metabolite pool analysis unraveled inhibition of the TCA and other pathways at low pH. Methionine and cysteine synthesis were found to be activated via the McbR regulator, cysteine accumulation was observed and addition of cysteine was shown to be toxic under acidic conditions. Conclusions: Novel limitations for C. glutamicum at non-optimal pH values were identified by a comprehensive analysis on the level of the transcriptome, proteome, and metabolome indicating a functional link between pH acclimatization, oxidative stress, iron homeostasis, and metabolic alterations. The results offer new insights into bacterial stress physiology and new starting points for bacterial strain design or pathogen defense

Isolation and genome sequencing of four Arctic marine Psychrobacter strains exhibiting multicopper oxidase activity

Moghadam MS, Albersmeier A, Winkler A, et al. Isolation and genome sequencing of four Arctic marine Psychrobacter strains exhibiting multicopper oxidase activity. BMC Genomics. 2016;17(1): 117

Do proton pump inhibitors increase the risk of dementia? A systematic review, meta‐analysis and bias analysis

AimPrevious studies on the association between proton pump inhibitor (PPI) intake and the increased risk of dementia has shown discrepancies in their conclusions. We aimed to provide updated evidence based on extensive bias assessments and quantitative sensitivity analyses. MethodsWe searched the databases PubMed, EMBASE, SCOPUS, CENTRAL and for prospective studies that examined an association between PPI use and dementia, up to February 2022. Each study was assessed using the Cochrane risk of bias assessment tools for non-randomized studies of interventions (ROBINS-I) or randomized trials (RoB2). Pooled risk ratios (RRs) and 95% prediction intervals were computed using random-effects models. Sensitivity analyses were adjusted for small-study bias. ResultsWe included nine observational studies with 204 108 dementia cases in the primary analysis on the association between PPI use vs. non-use and dementia, and the RR was 1.16 (95% CI = 1.00;1.35). After adjusting for small-study bias by Copas selection model and Rucker's shrinkage procedure, the RR was 1.16 (1.02;1.32) and 1.15 (1.13;1.17), respectively. A subgroup analysis of PPI use vs. non-use regarding Alzheimer's disease risk yielded an RR of 1.15 (0.89;1.50). The secondary analysis on the risk of dementia by use of PPI vs. histamine-2 receptor antagonist showed an RR of 1.03 (0.66;1.62). ConclusionThis meta-analysis provided no clear evidence for an association between PPI intake and the risk of dementia. Due to discrepancies in sensitivity analyses, however, some risk of dementia by PPI use cannot be ruled out. Since an unequivocal conclusion is still pending, further research is warranted

Emulating a target trial of proton pump inhibitors and dementia risk using claims data

Background and purpose Understanding the adverse effects of proton pump inhibitors (PPIs) is important due to their widespread use, but the available evidence for an increased dementia risk amongst patients taking PPIs is inconclusive. The present study aimed to estimate the causal effect of PPIs on the risk of dementia by target trial emulation and time-varying exposure modeling. Methods Using claims data of 2,698,176 insured people of a large German statutory health insurer, a target trial was conceptualized in which individuals aged 40 years and older were classified as PPI initiators or non-initiators between 2008 and 2018, and were followed until diagnosis of dementia, death, loss to follow-up or end of study. Incidence of dementia (International Classification of Diseases 10 codes F00, F01, F03, F05.1, G30, G31.0, G31.1, G31.9 and F02.8+G31.82) was defined applying a 1-year lag window. Weighted Cox models were used to estimate the effect of PPI initiation versus non-initiation on dementia risk and weighted pooled logistic regression was used to estimate the effect of time-varying use versus non-use. Results In all, 29,746 PPI initiators (4.4%) and 26,830 non-initiators (1.3%) were diagnosed with dementia. Comparing PPI initiation with no initiation, the hazard ratio for dementia was 1.54 (95% confidence interval 1.51-1.58). The hazard ratio for time-dependent PPI use versus non-use was 1.56 (95% confidence interval 1.50-1.63). Differentiated subtypes, including unspecified dementia, Alzheimer's disease and vascular dementia, showed increased risk by PPI initiation and time-varying PPI use. Conclusions This study suggests that PPI initiation and time-varying PPI use may increase overall dementia risk