Towards description and optimization of abstract machines in an extension of prolog

Competitive abstract machines for Prolog are usually large, intricate, and incorpórate sophisticated optimizations. This makes them difñcult to code, optimize, and, especially, maintain and extend. This is partly due to the fact that efñciency considerations make it necessary to use low-level languages in their implementation. Writing the abstract machine (and ancillary code) in a higher-level language can help harness this inherent complexity. In this paper we show how the semantics of basic components of an efficient virtual machine for Prolog can be described using (a variant of) Prolog which retains much of its semantics. These descriptions are then compiled to C and assembled to build a complete bytecode emulator. Thanks to the high level of the language used and its closeness to Prolog the abstract machine descriptions can be manipulated using standard Prolog compilation and optimization techniques with relative ease. We also show how, by applying program transformations selectively, we obtain abstract machine implementations whose performance can match and even exceed that of highly-tuned, hand-crafted emulators.

Ontology driven description and engineering of autonomous systems: application to process system engineering

Autonomous systems refer to systems capable of operating in a real world environment without any form of external control for extended periods of time. Autonomy is a desired goal for every system as it improves its performance, safety and profit. Ontologies are a way to conceptualize the knowledge of a specific domain. In this paper an ontology for the description of autonomous systems as well as for its development (engineering) is presented and applied to a process. This ontology is intended to be applied and used to generate final applications following a model driven methodology.

Simulating potential growth and yield of oil palm (Elaeis guineensis) with PALMSIM: Model description, evaluation and application.

Reducing the gap between water-limited potential yield and actual yield in oil palm production systems through intensification is seen as an important option for sustainably increasing palm oil production. Simulation models can play an important role in quantifying water-limited potential yield, and therefore the scope for intensification, but no oil palm model exists that is both simple enough and at the same time incorporates sufficient plant physiological knowledge to be generally applicable across sites with different growing conditions. The objectives of this study therefore were to develop a model (PALMSIM) that simulates, on a monthly time step, the potential growth of oil palm as determined by solar radiation and to evaluate model performance against measured oil palm yields under optimal water and nutrient management for a range of sites across Indonesia and Malaysia. The maximum observed yield in the field matches the corresponding simulated yield for dry bunch weight with a RMSE of 1.7 Mg ha?1 year?1 against an observed yield of 18.8 Mg ha?1. Sensitivity analysis showed that PALMSIM is robust: simulated changes in yield caused by modifying the parameters by 10% are comparable to other tree crop model evaluations. While we acknowledge that, depending on the soils and climatic environment, yields may be often water limited, we suggest a relatively simple physiological approach to simulate potential yield, which can be usefully applied to high rainfall environments and is considered as a first step in developing an oil palm model that also simulates water-limited potential yield. To illustrate the application possibil- ities of the model, PALMSIM was used to create a potential yield map for Indonesia and Malaysia by sim- ulating the growth and yield at a resolution of 0.1?. This map of potential yield is considered as a first step towards a decision support tool that can identify potentially productive, but at the moment degraded sites in Indonesia and Malaysia. ?

The living plant; a description and interpretation of its functions and structure, by William F. Ganong.

1913

Derivation and Validation of a Novel Prognostic Scale (Modified–Stroke Subtype, Oxfordshire Community Stroke Project Classification, Age, and Prestroke Modified Rankin) to Predict Early Mortality in Acute Stroke

© 2015 American Heart Association, Inc.

Description of microcolumnar ensembles in association cortex and their disruption in Alzheimer and Lewy body dementias

The cortex of the brain is organized into clear horizontal layers, laminae, which subserve much of the connectional anatomy of the brain. We hypothesize that there is also a vertical anatomical organization that might subserve local interactions of neuronal functional units, in accord with longstanding electrophysiological observations. We develop and apply a general quantitative method, inspired by analogous methods in condensed matter physics, to examine the anatomical organization of the cortex in human brain. We find, in addition to obvious laminae, anatomical evidence for tightly packed microcolumnar ensembles containing approximately 11 neurons, with a periodicity of about 80 μm. We examine the structural integrity of this new architectural feature in two common dementing illnesses, Alzheimer disease and dementia with Lewy bodies. In Alzheimer disease, there is a dramatic, nearly complete loss of microcolumnar ensemble organization. The relative degree of loss of microcolumnar ensembles is directly proportional to the number of neurofibrillary tangles, but not related to the amount of amyloid-β deposition. In dementia with Lewy bodies, a similar disruption of microcolumnar ensemble architecture occurs despite minimal neuronal loss. These observations show that quantitative analysis of complex cortical architecture can be applied to analyze the anatomical basis of brain disorders.

Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: Description of the folding pathway

Residual structure in the denatured state of a protein may contain clues about the early events in folding. We have simulated by molecular dynamics the denatured state of barnase, which has been studied by NMR spectroscopy. An ensemble of 104 structures was generated after 2 ns of unfolding and following for a further 2 ns. The ensemble was heterogeneous, but there was nonrandom, residual structure with persistent interactions. Helical structure in the C-terminal portion of helix α1 (residues 13–17) and in helix α2 as well as a turn and nonnative hydrophobic clustering between β3 and β4 were observed, consistent with NMR data. In addition, there were tertiary contacts between residues in α1 and the C-terminal portion of the β-sheet. The simulated structures allow the rudimentary NMR data to be fleshed out. The consistency between simulation and experiment inspires confidence in the methods. A description of the folding pathway of barnase from the denatured to the native state can be constructed by combining the simulation with experimental data from φ value analysis and NMR.

Phylogeny of genes for secretion NTPases: Identification of the widespread tadA subfamily and development of a diagnostic key for gene classification

Macromolecular transport systems in bacteria currently are classified by function and sequence comparisons into five basic types. In this classification system, type II and type IV secretion systems both possess members of a superfamily of genes for putative NTP hydrolase (NTPase) proteins that are strikingly similar in structure, function, and sequence. These include VirB11, TrbB, TraG, GspE, PilB, PilT, and ComG1. The predicted protein product of tadA, a recently discovered gene required for tenacious adherence of Actinobacillus actinomycetemcomitans, also has significant sequence similarity to members of this superfamily and to several unclassified and uncharacterized gene products of both Archaea and Bacteria. To understand the relationship of tadA and tadA-like genes to those encoding the putative NTPases of type II/IV secretion, we used a phylogenetic approach to obtain a genealogy of 148 NTPase genes and reconstruct a scenario of gene superfamily evolution. In this phylogeny, clear distinctions can be made between type II and type IV families and their constituent subfamilies. In addition, the subgroup containing tadA constitutes a novel and extremely widespread subfamily of the family encompassing all putative NTPases of type IV secretion systems. We report diagnostic amino acid residue positions for each major monophyletic family and subfamily in the phylogenetic tree, and we propose an easy method for precisely classifying and naming putative NTPase genes based on phylogeny. This molecular key-based method can be applied to other gene superfamilies and represents a valuable tool for genome analysis.

Redescription of Anomala eucoma Bates, 1888 and a description of three new species from Costa Rica (Coleoptera: Scarabaeidae: Rutelinae)

Anomala eucoma Bates, 1888 is redescribed and a lectotype from Guatemala is designated. Three new species from Costa Rica, A. flavacoma new species, A. megaparamera new species, and A. pseudoeucoma new species, are described, and a distribution map is given. The internal sac (endophallus) of the species covered is illustrated, and its use in separating closely related species in this region is discussed. An identification key for morphologically similar species from the Neotropical region is provided.

The entomologist's useful compendium; or, An introduction to the knowledge of British insects, comprising the best means of obtaining and preserving them, and a description of the apparatus generally used; together with the genera of Linné, and the modern method of arranging the classes...according to the views of Dr. Leach...with instructions for collecting and fitting up objects for the microscope.

1821

The brown-tail moth, Euproctis chrysorrhcea (L.). A report on the life history and habits of the imported brown-tail moth, together with a description of the remedies best suited for destroying it. By Charles H. Fernald ... and Archie H. Kirkland ... Pub. under the direction of the State board of agriculture by authority of the legislature.

1903

The brown-tail moth, Euproctis chrysorrhcea (L.). A report on the life history and habits of the imported brown-tail moth, together with a description of the remedies best suited for destroying it. By Charles H. Fernald ... and Archie H. Kirkland ... Pub. under the direction of the State board of agriculture by authority of the legislature.

1903

The natural history of Aleppo: containing a description of the city, and the principal natural productions in its neighbourhood : together with an account of the climate, inhabitants, and diseases, particularly of the plague

by Alex. Russell.