Polyhedral+Dataflow Graphs

This research presents an intermediate compiler representation that is designed for optimization, and emphasizes the temporary storage requirements and execution schedule of a given computation to guide optimization decisions. The representation is expressed as a dataflow graph that describes computational statements and data mappings within the polyhedral compilation model. The targeted applications include both the regular and irregular scientific domains. The intermediate representation can be integrated into existing compiler infrastructures. A specification language implemented as a domain specific language in C++ describes the graph components and the transformations that can be applied. The visual representation allows users to reason about optimizations. Graph variants can be translated into source code or other representation. The language, intermediate representation, and associated transformations have been applied to improve the performance of differential equation solvers, or sparse matrix operations, tensor decomposition, and structured multigrid methods

A threatened ecological community: Research advances and priorities for Banksia woodlands

The rapid expansion of urban areas worldwide is leading to native habitat loss and ecosystem fragmentation and degradation. Although the study of urbanisation\u27s impact on biodiversity is gaining increasing interest globally, there is still a disconnect between research recommendations and urbanisation strategies. Expansion of the Perth metropolitan area on the Swan Coastal Plain in south-western Australia, one of the world\u27s thirty-six biodiversity hotspots, continues to affect the Banksia Woodlands (BWs) ecosystem, a federally listed Threatened Ecological Community (TEC). Here, we utilise the framework of a 1989 review of the state of knowledge of BWs ecology and conservation to examine scientific advances made in understanding the composition, processes and functions of BWs and BWs\u27 species over the last 30 years. We highlight key advances in our understanding of the ecological function and role of mechanisms in BWs that are critical to the management of this ecosystem. The most encouraging change since 1989 is the integration of research between historically disparate ecological disciplines. We outline remaining ecological knowledge gaps and identify key research priorities to improve conservation efforts for this TEC. We promote a holistic consideration of BWs with our review providing a comprehensive document that researchers, planners and managers may reference. To effectively conserve ecosystems threatened by urban expansion, a range of stakeholders must be involved in the development and implementation of best practices to conserve and maintain both biodiversity and human wellbeing

Buffalo, Bush Meat, and the Zoonotic Threat of Brucellosis in Botswana

Brucellosis is a zoonotic disease of global importance infecting humans, domestic animals, and wildlife. Little is known about the epidemiology and persistence of brucellosis in wildlife in Southern Africa, particularly in Botswana.Archived wildlife samples from Botswana (1995-2000) were screened with the Rose Bengal Test (RBT) and fluorescence polarization assay (FPA) and included the African buffalo (247), bushbuck (1), eland (5), elephant (25), gemsbok (1), giraffe (9), hartebeest (12), impala (171), kudu (27), red lechwe (10), reedbuck (1), rhino (2), springbok (5), steenbok (2), warthog (24), waterbuck (1), wildebeest (33), honey badger (1), lion (43), and zebra (21). Human case data were extracted from government annual health reports (1974-2006).Only buffalo (6%, 95% CI 3.04%-8.96%) and giraffe (11%, 95% CI 0-38.43%) were confirmed seropositive on both tests. Seropositive buffalo were widely distributed across the buffalo range where cattle density was low. Human infections were reported in low numbers with most infections (46%) occurring in children (<14 years old) and no cases were reported among people working in the agricultural sector.Low seroprevalence of brucellosis in Botswana buffalo in a previous study in 1974 and again in this survey suggests an endemic status of the disease in this species. Buffalo, a preferred source of bush meat, is utilized both legally and illegally in Botswana. Household meat processing practices can provide widespread pathogen exposure risk to family members and the community, identifying an important source of zoonotic pathogen transmission potential. Although brucellosis may be controlled in livestock populations, public health officials need to be alert to the possibility of human infections arising from the use of bush meat. This study illustrates the need for a unified approach in infectious disease research that includes consideration of both domestic and wildlife sources of infection in determining public health risks from zoonotic disease invasions

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

A prenylated dsRNA sensor protects against severe COVID-19

Inherited genetic factors can influence the severity of COVID-19, but the molecular explanation underpinning a genetic association is often unclear. Intracellular antiviral defenses can inhibit the replication of viruses and reduce disease severity. To better understand the antiviral defenses relevant to COVID-19, we used interferon-stimulated gene (ISG) expression screening to reveal that OAS1, through RNase L, potently inhibits SARS-CoV-2. We show that a common splice-acceptor SNP (Rs10774671) governs whether people express prenylated OAS1 isoforms that are membrane-associated and sense specific regions of SARS-CoV-2 RNAs, or only express cytosolic, nonprenylated OAS1 that does not efficiently detect SARS-CoV-2. Importantly, in hospitalized patients, expression of prenylated OAS1 was associated with protection from severe COVID-19, suggesting this antiviral defense is a major component of a protective antiviral response

Sparse Computation Data Dependence Simplification for Efficient Compiler-Generated Inspectors

This paper presents a combined compile-time and runtime loop-carried dependence analysis of sparse matrix codes and evaluates its performance in the context of wavefront parallellism. Sparse computations incorporate indirect memory accesses such as x[col[j]] whose memory locations cannot be determined until runtime. The key contributions of this paper are two compile-time techniques for significantly reducing the overhead of runtime dependence testing: (1) identifying new equality constraints that result in more efficient runtime inspectors, and (2) identifying subset relations between dependence constraints such that one dependence test subsumes another one that is therefore eliminated. New equality constraints discovery is enabled by taking advantage of domain-specific knowledge about index arrays, such as col[j]. These simplifications lead to automatically-generated inspectors that make it practical to parallelize such computations. We analyze our simplification methods for a collection of seven sparse computations. The evaluation shows our methods reduce the complexity of the runtime inspectors significantly. Experimental results for a collection of five large matrices show parallel speedups ranging from 2x to more than 8x running on a 8-core CPU

Transforming Loop Chains via Macro Dataflow Graphs

This paper describes an approach to performance optimization using modified macro dataflow graphs, which contain nodes representing the loops and data involved in the stencil computation. The targeted applications include existing scientific applications that contain a series of stencil computations that share data, i.e. loop chains. The performance of stencil applications can be improved by modifying the execution schedules. However, modern architectures are increasingly constrained by the memory subsystem bandwidth. To fully realize the benefits of the schedule changes for improved locality, temporary storage allocation must also be minimized. We present a macro dataflow graph variant that includes dataset nodes, a cost model that quantifies the memory interactions required by a given graph, a set of transformations that can be performed on the graphs such as fusion and tiling, and an approach for generating code to implement the transformed graph. We include a performance comparison with Halide and PolyMage implementations of the benchmark. Our fastest variant outperforms the auto-tuned variants produced by both frameworks

A Structured Grid Solver with Polyhedral+Dataflow Representation

Proto is a C++ embedded Domain Specific Library for stencil-based computations. Proto is augmented in this work with a polyhedral dataflow intermediate representation (IR). The IR exposes several promising transformations. Each IR instances produces a performance model, and source code in C++. Generated code is annotated with OpenMP or OpenACC pragmas for shared-memory or accelerator parallelism. Performance is measured on modern multicore CPU and GPU platforms

Data Storage in Cellular DNA: Contextualizing Diverse Encoding Schemes

Nature has been using DNA to store biological data for millions of years, and fnally humans are learning to use the same medium for our own data. In this paper, we survey the feld of cellular DNA encoding, where encoding schemes are used to insert data into pcDNA and ncDNA areas while bypassing the biological restrictions associated with those areas. We frst characterize the unique bio-restrictions associated with existing cellular DNA encoding schemes, then we contrast the schemes with respect to the restrictions they meet, supported features, and implementation details. We discuss the pros and cons of the implementation of each encoding scheme, and make recommendations accordingly. Finally, we highlight existing gaps, and provide our insight into future research directions