Hardware Accelerated Fast FDTD of Time Dependent Maxwell’s Equations on Xilinx RF SoC

Electromagnetics, which govern the fields of wireless communications, radar, and remote sensing, are fully described using four first-order PDEs known as Maxwell’s Equations. The finite-difference time-domain (FDTD) algorithm invented by Yee in 1966 operates on a discrete space-time staggered grid-pair for the electric and magnetic fields, and solutions are obtained via leapfrog update equations. The field of computational electromagnetics makes extensive use of the FDTD algorithm for modeling involving various types of antennas, microwave filters, circuits, aerospace vehicles, and wireless systems. For accurate and dispersion-less solution, the discretization of the spatial and temporal variables require a high degree of over-sampling that is much higher than what is demanded by the Nyquist Sampling Theorem, in order for the discrete domain update equations to represent the behavior of a continuous linear PDE system. The highly-oversampled nature of FDTD results in high computational complexity and therefore long execution times on high-performance computing systems. Hardware acceleration is a technique to accelerate the computation of FDTD using application-specific integrated digital processor arrays that are custom designed for implementing FDTD without using any software at all. The hard-wired parallel computation allows very good acceleration compared to state-of-art computing solutions based on high-performance compute servers, GPU realizations, and cloud computing techniques. The talk reports on a hardware accelerator that supports real-time operation on a Xilinx RF SoC device. Comparison with GPUs are provided (interim results show better than x100)

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi

Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.B.R. and C.L.S. acknowledge support from the Intramural Research Program of the National Institutes of Health, National Library of MedicinePeer Reviewe

Semi-automated recommendation platform for data visualization: roopana

Information visualization is the final process of any data analytics project, which gives an overall insight about the identified trends, patterns and anomalies. Efforts in data analysis become useless when we fail to convey the results effectively. Among visualization methods graphs play a vital role and are used frequently. This paper introduces “Roopana”, a semi-automated platform for data visualization. It is capable of identifying the context of user data automatically, consider the purpose of data visualization (comparison, distribution, relationship, composition) and recommend the most accurate chart type to use. Considering chart types, “Roopana” is capable of proving recommendations from large number of charts. It then enables the use of less frequently used chart types, which are matching with data context and purpose of visualization. Further the system can alter the order of recommendations depending on user feedback enabling the most popular chart types to appear on top. Thus data scientists and developers can use “Roopana” to select most appropriate chart for their data without having an expert knowledge in the field of data visualization projects they are working on

Foliar pathogenic fungi: growing threats to global food security and ecosystem health

Globally, foliar pathogenic fungi cause serious losses of annual and perennial crops, ornamentals, landscape plants and forest trees. Plant pathogens that infect foliage are a diverse assemblage of fungi representing both phyla: Ascomycota and Basidiomycota. Although most of the species found on living leaves have been well studied by mycologists and plant pathologists, recent studies have remarkably enhanced the current understanding of species numbers and their evolutionary relationships. The impact of global climate change, the increasing international exchange of plant material and the lack of proper phytosanitary practices have resulted in the potential re-emergences of formerly known destructive fungi, infecting new hosts in new geographic locations. Routinely inspecting diseased plants and accurately identifying and naming causative agents are vital for mitigating the impact of invasive and other non-indigenous pathogens on crops and native flora. It is also necessary to characterise foliar pathogenic fungi based on molecular phylogeny, morphology, pathogenicity and the comparative analysis of fungal genomic data. This review provides an overview of prevalent groups of foliar pathogenic fungi, their diversity and economic impact, while emphasising emerging and destructive species that threaten global food security and ecosystem health

Addressing the information deficit in global health: lessons from a digital acute care platform in Sri Lanka

Lack of investment in low-income and middle-income countries (LMICs) in systems capturing continuous information regarding care of the acutely unwell patient is hindering global efforts to address inequalities, both at facility and national level. Furthermore, this of lack of data is disempowering frontline staff and those seeking to support them, from progressing setting-relevant research and quality improvement. In contrast to high-income country (HIC) settings, where electronic surveillance has boosted the capability of governments, clinicians and researchers to engage in service-wide healthcare evaluation, healthcare information in resource-limited settings remains almost exclusively paper based. In this practice paper, we describe the efforts of a collaboration of clinicians, administrators, researchers and healthcare informaticians working in South Asia, in addressing the inequality in access to patient information in acute care. Harnessing a clinician-led collaborative approach to design and evaluation, we have implemented a national acute care information platform in Sri Lanka that is tailored to priorities of frontline staff. Iterative adaptation has ensured the platform has the flexibility to integrate with legacy paper systems, support junior team members in advocating for acutely unwell patients and has made information captured accessible to diverse stakeholders to improve service delivery. The same platform is now empowering clinicians to participate in international research and drive forwards improvements in care. During this journey, we have also gained insights on how to overcome well-described barriers to implementation of digital information tools in LMIC. We anticipate that this north–south collaborative approach to addressing the challenges of health system implementation in acute care may provide learning and inspiration to other partnerships seeking to engage in similar work

Energy Tariff Policies for Renewable Energy Development: Comparison between Selected European Countries and Sri Lanka

This article is written within the European Project “THREE-Lanka” which has the aim of modernizing the higher education related to Renewable Energy (RE) in Sri Lanka. The paper presents the outcomes of analysing various incentive schemes to stimulate RE development. In Europe, there was substantial growth in RE installation through generous incentives in the first years. Then, to regulate this growth, in recent years, the auction system has been introduced to improve the competition among companies that install RE plants. In Sri Lanka, on the other hand, the main energy tariff policies focus on the spread of PhotoVoltaics (PV) through contributions based on the electricity fed into the grid. This paper provides an updated view of the evolution of the energy tariff policies in the relevant European countries with respect to Sri Lanka, covering some recent policy developments. Within the Sri Lankan framework, four case studies involving residential, commercial, and industrial users are outlined to suggest better mechanisms (in the case of not adequate current incentive tariff) for supporting the deployment of grid-connected PV systems in a wide power range. Such knowledge transfer in the THREE-Lanka project will demonstrate the enormous potential RE capacity in a developing country, still depending on fossil fuels but willing to follow the path towards sustainability