Benchmarking a many-core neuromorphic platform with an MPI-based DNA sequence matching algorithm

SpiNNaker is a neuromorphic globally asynchronous locally synchronous (GALS)multi-core architecture designed for simulating a spiking neural network (SNN) in real-time. Several studies have shown that neuromorphic platforms allow flexible and efficient simulations of SNN by exploiting the efficient communication infrastructure optimised for transmitting small packets across the many cores of the platform. However, the effectiveness of neuromorphic platforms in executing massively parallel general-purpose algorithms, while promising, is still to be explored. In this paper, we present an implementation of a parallel DNA sequence matching algorithm implemented by using the MPI programming paradigm ported to the SpiNNaker platform. In our implementation, all cores available in the board are configured for executing in parallel an optimised version of the Boyer-Moore (BM) algorithm. Exploiting this application, we benchmarked the SpiNNaker platform in terms of scalability and synchronisation latency. Experimental results indicate that the SpiNNaker parallel architecture allows a linear performance increase with the number of used cores and shows better scalability compared to a general-purpose multi-core computing platform

Source Code Classification for Energy Efficiency in Parallel Ultra Low-Power Microcontrollers

The analysis of source code through machine learning techniques is an increasingly explored research topic aiming at increasing smartness in the software toolchain to exploit modern architectures in the best possible way. In the case of low-power, parallel embedded architectures, this means finding the configuration, for instance in terms of the number of cores, leading to minimum energy consumption. Depending on the kernel to be executed, the energy optimal scaling configuration is not trivial. While recent work has focused on general-purpose systems to learn and predict the best execution target in terms of the execution time of a snippet of code or kernel (e.g. offload OpenCL kernel on multicore CPU or GPU), in this work we focus on static compile-time features to assess if they can be successfully used to predict the minimum energy configuration on PULP, an ultra-low-power architecture featuring an on-chip cluster of RISC-V processors. Experiments show that using machine learning models on the source code to select the best energy scaling configuration automatically is viable and has the potential to be used in the context of automatic system configuration for energy minimisation

Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2′-exo (north) and 3′-exo (south) ‘locked’ templates

The biophysical properties of oligodeoxyribonucleotides (ODNs) selectively modified with conformationally ‘locked’ bicyclo[3.1.0]hexane pseudosugars (Maier,M.A., Choi,Y., Gaus,H., Barchi,J.J. Jr, Marquez,V.E., Manoharan,M. (2004) Synthesis and characterization of oligonucleotides containing conformationally constrained bicyclo[3.1.0]hexane pseudosugar analogs Nucleic Acids Res., 32, 3642–3650) have been studied by various techniques. Six separate synthetic ODNs based on the Dickerson Drew dodecamer sequence (CGCGAAT*T*CGCG) were examined where each one (or both) of the thymidines (T*) were substituted with a bicyclic pseudosugar locked in either a North (2′-exo) or South (3′-exo) ring pucker. Circular dichroism spectroscopy, differential scanning calorimetry and 1H NMR spectroscopy were used to examine the duplex stability and conformational properties of the ODNs. Replacement of one or both thymidines with North-locked sugars (RNA-like) into the dodecamer did not greatly affect duplex formation or melt temperatures but distinct differences in thermodynamic parameters were observed. In contrast, incorporation of South-locked sugar derivatives that were predicted to stabilize this standard B-DNA, had the unexpected effect of causing a conformational equilibrium between different duplex forms at specific strand and salt concentrations. Our data and those of others suggest that although DNA can tolerate modifications with RNA-like (North) nucleotides, a more complicated spectrum of changes emerges with modifications restricted to South (DNA-like) puckers

SEISMIC ANISOTROPY AND MICRO-SEISMICITY IN THE UPPER CRUST AT NORTH OF GUBBIO BASIN (CENTRAL ITALY): RELATION WITH THE SUBSURFACE GEOLOGICAL STRUCTURES AND THE ACTIVE STRESS FIELD

During the months of April and May 2010, a seismic sequence (here named “Pietralunga seismic sequence”) took place in the northeastern part of the Gubbio basin (Northern Apennines); this area is well known to be interested by a continuous background micro-seismic activity. The sequence was recorded both by the INGV National Seismic Network, and by the stations installed by the Project “AIRPLANE” (financially supported by MIUR-Italian Ministry of Education and Research) with the aim of investigating the seismogenetic processes in the Alto Tiberina Fault (ATF) system region. In this work we present the anisotropic results at four stations: ATFO, ATPC, ATPI, ATVO located around the northern termination of the Gubbio basin that well delimit both the seismic se- quence and the whole 2010 seismicity (about 2500 events). The study of seismic anisotropy has provided useful information for the interpretation and evaluation of the stress field and active crustal deformation. Seismic anisotropy can yield valuable information on upper crustal structure, fracture field, and presence of fluid-saturated rocks. Moreover, the large number of seismic waveforms recorded especially during the Pietralunga sequence allows us also to study the spatio-temporal changes of anisotropic parameters to better understand its evolution and the possible correlation to the presence and migration of fluids

Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family

This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops

Grafting vigour is associated with DNA de-methylation in eggplant.

In horticulture, grafting is a popular technique used to combine positive traits from two different plants. This is achieved by joining the plant top part (scion) onto a rootstock which contains the stem and roots. Rootstocks can provide resistance to stress and increase plant production, but despite their wide use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype remain largely unknown. Given that epigenetics plays a relevant role during distance signalling in plants, we studied the genome-wide DNA methylation changes induced in eggplant (Solanum melongena) scion using two interspecific rootstocks to increase vigour. We found that vigour was associated with a change in scion gene expression and a genome-wide hypomethylation in the CHH context. Interestingly, this hypomethylation correlated with the downregulation of younger and potentially more active long terminal repeat retrotransposable elements (LTR-TEs), suggesting that graft-induced epigenetic modifications are associated with both physiological and molecular phenotypes in grafted plants. Our results indicate that the enhanced vigour induced by heterografting in eggplant is associated with epigenetic modifications, as also observed in some heterotic hybrids