Program transformations using temporal logic side conditions

This paper describes an approach to program optimisation based on transformations, where temporal logic is used to specify side conditions, and strategies are created which expand the repertoire of transformations and provide a suitable level of abstraction. We demonstrate the power of this approach by developing a set of optimisations using our transformation language and showing how the transformations can be converted into a form which makes it easier to apply them, while maintaining trust in the resulting optimising steps. The approach is illustrated through a transformational case study where we apply several optimisations to a small program

What evidence exists for temporal variability in Arctic terrestrial and freshwater biodiversity throughout the Holocene? A systematic map protocol

Background: The Arctic tundra is subject to the greatest climate change-induced temperature rises of any biome. Both terrestrial and freshwater biota are responding to recent climate warming through variability in their distribution, abundance, and richness. However, uncertainty arises within models of future change when considering processes that operate over centennial timescales. A systematic evidence synthesis of centennial-scale variability in biodiversity does not currently exist for the Arctic biome. Here, we sought to address the primary research question: what evidence exists for temporal variability in Arctic terrestrial and freshwater biodiversity throughout the Holocene (11,650 years before present (yBP)-OyBP)? Methods: Consultation with stakeholders informed key definitions, scoping and the appropriateness of the research question. The research question was structured using a PECO framework-Arctic biota (P), a timestamped year in the Holocene (E), another year in the Holocene (C), and the dimensions of biodiversity that have been measured (O)-to inform the search strategy. Search strings were benchmarked against a test list of 100 known sources to ensure a specific and comprehensive return of literature. Searches will occur across 13 bibliographic databases. The eligibility criteria specify that sources must: (a) use 'proxy' methods to measure biodiversity; (b) fall within the spatial extent of the contemporary Arctic tundra biome; and (c) consist of a time-series that overlaps with 11,650yBP to OyBP (1950AD). Information coded from studies will include proxy-specific information to account for both temporal uncertainty (i.e., the characteristics of age-depth models and dating methods) and taxonomic uncertainty (i.e., the samples and processes used for taxonomic identification). We will assess temporal uncertainty within each source by determining the quality of dating methods and measures; this information will be used to harmonise dates onto the IntCa120 calibration curve and determine the available temporal resolution and extent of evidence through space. Key outputs of this systematic map will be: (1) a graph database containing the spatial-temporal properties of each study dataset with taxonomic harmonisation; and (2) a geographical map of the evidence base.Peer reviewe

ZooKeys, unlocking Earth's incredible biodiversity and building a sustainable bridge into the public domain: From "print-based" to "web-based" taxonomy, systematics, and natural history.

Publishing taxonomic and systematics studies in the digital era faces major challenges and requires new approaches, many of which are currently stimulating spirited discussions amongst taxonomists and systematists. New amendments to the International Code of Zoological Nomenclature are expected to regulate electronic publishing of new taxa and create a standard form for their registration (ZooBank). Responding to a perceived need, this editorial announces establishment of ZooKeys – a new online and print journal in zoological taxonomy and systematics, which aims to quickly respond and adapt to the newest developments in taxonomic publishing. Open Access is accepted as mandatory for ZooKeys. The rationale for and concept of ZooKeys is discussed in detail

ZooKeys, unlocking Earth’s incredible biodiversity and building a sustainable bridge into the public domain: From “print-based” to “web-based” taxonomy, systematics, and natural history. ZooKeys Editorial Opening Paper

This is the publisher's version, also available electronically from http://zookeys.pensoft.net/articles.php?id=1929.Publishing taxonomic and systematics studies in the digital era faces major challenges and requires new approaches, many of which are currently stimulating spirited discussions amongst taxonomists and systematists. New amendments to the International Code of Zoological Nomenclature are expected to regulate electronic publishing of new taxa and create a standard form for their registration (ZooBank). Responding to a perceived need, this editorial announces establishment of ZooKeys – a new online and print journal in zoological taxonomy and systematics, which aims to quickly respond and adapt to the newest developments in taxonomic publishing. Open Access is accepted as mandatory for ZooKeys. Th e rationale for and concept of ZooKeys is discussed in detail

Delivering sustained, coordinated and integrated observations of the Southern Ocean for global impact

The Southern Ocean is disproportionately important in its effect on the Earth system, impacting climatic, biogeochemical, and ecological systems, which makes recent observed changes to this system cause for global concern. The enhanced understanding and improvements in predictive skill needed for understanding and projecting future states of the Southern Ocean require sustained observations. Over the last decade, the Southern Ocean Observing System (SOOS) has established networks for enhancing regional coordination and research community groups to advance development of observing system capabilities. These networks support delivery of the SOOS 20-year vision, which is to develop a circumpolar system that ensures time series of key variables, and delivers the greatest impact from data to all key end-users. Although the Southern Ocean remains one of the least-observed ocean regions, enhanced international coordination and advances in autonomous platforms have resulted in progress toward sustained observations of this region. Since 2009, the Southern Ocean community has deployed over 5700 observational platforms south of 40°S. Large-scale, multi-year or sustained, multidisciplinary efforts have been supported and are now delivering observations of essential variables at space and time scales that enable assessment of changes being observed in Southern Ocean systems. The improved observational coverage, however, is predominantly for the open ocean, encompasses the summer, consists of primarily physical oceanographic variables, and covers surface to 2000 m. Significant gaps remain in observations of the ice-impacted ocean, the sea ice, depths >2000 m, the air-ocean-ice interface, biogeochemical and biological variables, and for seasons other than summer. Addressing these data gaps in a sustained way requires parallel advances in coordination networks, cyberinfrastructure and data management tools, observational platform and sensor technology, two-way platform interrogation and data-transmission technologies, modeling frameworks, intercalibration experiments, and development of internationally agreed sampling standards and requirements of key variables. This paper presents a community statement on the major scientific and observational progress of the last decade, and importantly, an assessment of key priorities for the coming decade, toward achieving the SOOS vision and delivering essential data to all end-users.Fil: Newman, Louise. University of Tasmania; AustraliaFil: Heil, Petra. Australian Antarctic Division; Australia. Antarctic Climate And Ecosystems Cooperative Research Centre; AustraliaFil: Trebilco, Rowan. Australian Antarctic Division; Australia. Antarctic Climate And Ecosystems Cooperative Research Centre; AustraliaFil: Katsumata, Katsuro. Japan Agency For Marine earth Science And Technology; JapónFil: Constable, Andrew J.. Antarctic Climate And Ecosystems Cooperative Research Centre; Australia. Australian Antarctic Division; AustraliaFil: Wijk, Esmee van. Commonwealth Scientific And Industrial Research Organization; Australia. Antarctic Climate And Ecosystems Cooperative Research Centre; AustraliaFil: Assmann, Karen. University Goteborg; SueciaFil: Beja, Joana. British Oceanographic Data Centre; AustraliaFil: Bricher, Phillippa. University of Tasmania; AustraliaFil: Coleman, Richard. University of Tasmania; AustraliaFil: Costa, Daniel. University of California; Estados UnidosFil: Diggs, Steve. University of California; Estados UnidosFil: Farneti, Riccardo. The Abdus Salam; Italia. The Abdus Salam. International Centre for Theoretical Physics; ItaliaFil: Fawcett, Sarah. University of Cape Town; SudáfricaFil: Gille, Sarah. University of California; Estados UnidosFil: Hendry, Katharine R.. University of Bristol; Reino UnidoFil: Henley, Sian F.. University of Edinburgh; Reino UnidoFil: Hofmann, Eileen. Old Dominion University; Estados UnidosFil: Maksym, Ted. University of California; Estados UnidosFil: Mazloff, Matthew. University of California; Estados UnidosFil: Meijers, Andrew J.. British Antartic Survey; Reino UnidoFil: Meredith, Michael. British Antartic Survey; Reino UnidoFil: Moreau, Sebastien. Norwegian Polar Institute; NoruegaFil: Ozsoy, Burcu. Istanbul Teknik Üniversitesi; TurquíaFil: Robertson, Robin. Xiamen University; ChinaFil: Schloss, Irene Ruth. Universidad Nacional de Tierra del Fuego; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Austral de Investigaciones Científicas; ArgentinaFil: Schofield, Oscar. State University of New Jersey; Estados UnidosFil: Shi, Jiuxin. Ocean University Of China; ChinaFil: Sikes, Elisabeth L.. State University of New Jersey; Estados UnidosFil: Smith, Inga J.. University of Otago; Nueva Zeland

The next generation of training for arabidopsis researchers: Bioinformatics and Quantitative Biology

It has been more than 50 years since Arabidopsis (Arabidopsis thaliana) was first introduced as a model organism to understand basic processes in plant biology. A well-organized scientific community has used this small reference plant species to make numerous fundamental plant biology discoveries (Provart et al., 2016). Due to an extremely well-annotated genome and advances in high-throughput sequencing, our understanding of this organism and other plant species has become even more intricate and complex. Computational resources, including CyVerse,3 Araport,4 The Arabidopsis Information Resource (TAIR),5 and BAR,6 have further facilitated novel findings with just the click of a mouse. As we move toward understanding biological systems, Arabidopsis researchers will need to use more quantitative and computational approaches to extract novel biological findings from these data. Here, we discuss guidelines, skill sets, and core competencies that should be considered when developing curricula or training undergraduate or graduate students, postdoctoral researchers, and faculty. A selected case study provides more specificity as to the concrete issues plant biologists face and how best to address such challenges