IN SITU MEASUREMENTS OF THE ACOUSTIC TARGET STRENGTH OF CAPE HORSE MACKEREL TRACHURUS TRACHURUS CAPENSIS OFF NAMIBIA

The acoustic target strength (TS) of Cape horse mackerel Trachurus trachurus capensis was measured in situ at 38 kHz during two surveys over the Namibian continental shelf in 1998 and 1999 using a SIMRAD EK500 echosounder/ES38D submersible split-beam transducer. Scattered aggregations of horse mackerel 100–200 m deep were ensonified. The transducer was lowered to a depth of 85–140 m in order to resolve single targets at short ranges (5–50 m). Individual fish were tracked using specially developed software. Samples of ensonified fish were obtained using pelagic and demersal trawls; the former was fitted with a codend Multisampler for depth-specific sampling. Recorded TS estimates were low, producing b20-values ranging from -77.5 to -74.9 dB (-76.0 dB &#177 1.3), considerably lower than published estimates for horse mackerel (-73.4 dB &#60 b20 &#60 -65.2 dB). An explanation for the weak acoustic backscattering may be swimbladder compression. Surface-projected b20 values, which were computed using the depth of each target and the scattering area reduction rate previously found for herring (γ &#61 -0.29), corresponded to -72.6 dB. This value is close to the TS constant of -72 dB currently applied for horse mackerel in Namibian and Angolan waters.Afr. J. mar. Sci. 25: 239–25

Energy-Efficient Algorithms

We initiate the systematic study of the energy complexity of algorithms (in addition to time and space complexity) based on Landauer's Principle in physics, which gives a lower bound on the amount of energy a system must dissipate if it destroys information. We propose energy-aware variations of three standard models of computation: circuit RAM, word RAM, and transdichotomous RAM. On top of these models, we build familiar high-level primitives such as control logic, memory allocation, and garbage collection with zero energy complexity and only constant-factor overheads in space and time complexity, enabling simple expression of energy-efficient algorithms. We analyze several classic algorithms in our models and develop low-energy variations: comparison sort, insertion sort, counting sort, breadth-first search, Bellman-Ford, Floyd-Warshall, matrix all-pairs shortest paths, AVL trees, binary heaps, and dynamic arrays. We explore the time/space/energy trade-off and develop several general techniques for analyzing algorithms and reducing their energy complexity. These results lay a theoretical foundation for a new field of semi-reversible computing and provide a new framework for the investigation of algorithms.Comment: 40 pages, 8 pdf figures, full version of work published in ITCS 201

Antigens in human glioblastomas and meningiomas: Search for tumour and onco-foetal antigens. Estimation of S-100 and GFA protein.

Extracts of glioblastomas and meningiomas were analysed by quantitative immunoelectrophoresis for the presence of foetal brain antigens and tumour-associated antigens, and levels of 2 normal brain-specific proteins were also determined. The following antibodies were used: monospecific anti-S-100 (glia specific); monospecific anti-GFA (glial fibrillary acidic protein), (astroglia specific); polyspecific anti-foetal brain (12-16th week of gestation); a polyspecific anti-glioblastoma antiserum, absorbed with insolubilized serum, haemolysate and normal brain extract; polyspecific anti-alpha-foetoprotein; and monospecific anti-ferritin. Using the antibodies raised against the tumours, several antigens not present in foetal or adult normal brain were found in the glioblastomas and the meningiomas. These antigens cross-reacted with antigens present in normal liver and were therefore not tumour-associated. S-100 was found in glioblastomas in approximately one tenth the amount in whole brain homogenate, whereas GFA was found 2-4 times enriched. The 2 proteins were absent in meningiomas. The possible use of the GFA protein as a marker for astroglial neoplasia is discussed. Five foetal antigens were found in foetal brain, but none in the tumours. alpha-Foetoprotein could only be demonstrated in foetal tissue extracts, including foetal brain, but not in tumours. Ferritin was detected in all tumour extracts, although the amounts determined were unrelated to histological tumour type

Unequally egalitarian? Defending the credentials of social egalitarianism

In his new book, Luck Egalitarianism, Kasper Lippert-Rasmussen responds to challenges raised by social egalitarians against luck egalitarianism. Social egalitarianism is the view according to which a just society is one where people relate to each other as equals, while the basic premise of luck egalitarianism is that it is unfair if people are worse-off than others through no fault or choice of their own. Lippert-Rasmussen argues that the most important objections to luck egalitarianism made by social egalitarians can either be largely accommodated by luck egalitarians or lack the argumentative force that its proponents believe them to have. While Lippert-Rasmussen does offer a version of luck egalitarianism that seems to avoid some of the main lines of criticism, he mischaracterizes parts of both the form and the content of the disagreement, and thus ultimately misses the mark. In this paper, we provide a substantive, a methodological and a political defense of social egalitarianism by elaborating on this mischaracterization. More work must be done, we argue, if social egalitarianism is to be dismissed and its concerns genuinely incorporated in the luck egalitarian framework. Until this is done, the supposed theoretical superiority of luck egalitarianism remains contested

Updates in Rhea-a manually curated resource of biochemical reactions.

Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Rhea has been designed for the functional annotation of enzymes and the description of genome-scale metabolic networks, providing stoichiometrically balanced enzyme-catalyzed reactions (covering the IUBMB Enzyme Nomenclature list and additional reactions), transport reactions and spontaneously occurring reactions. Rhea reactions are extensively curated with links to source literature and are mapped to other publicly available enzyme and pathway databases such as Reactome, BioCyc, KEGG and UniPathway, through manual curation and computational methods. Here we describe developments in Rhea since our last report in the 2012 database issue of Nucleic Acids Research. These include significant growth in the number of Rhea reactions and the inclusion of reactions involving complex macromolecules such as proteins, nucleic acids and other polymers that lie outside the scope of ChEBI. Together these developments will significantly increase the utility of Rhea as a tool for the description, analysis and reconciliation of genome-scale metabolic models

Crowdsourcing Content Creation for SQL Practice

Crowdsourcing refers to the act of using the crowd to create content or to collect feedback on some particular tasks or ideas. Within computer science education, crowdsourcing has been used -- for example -- to create rehearsal questions and programming assignments. As a part of their computer science education, students often learn relational databases as well as working with the databases using SQL statements. In this article, we describe a system for practicing SQL statements. The system uses teacher-provided topics and assignments, augmented with crowdsourced assignments and reviews. We study how students use the system, what sort of feedback students provide to the teacher-generated and crowdsourced assignments, and how practice affects the feedback. Our results suggest that students rate assignments highly, and there are only minor differences between assignments generated by students and assignments generated by the instructor.Peer reviewe

Updates in Rhea - an expert curated resource of biochemical reactions.

Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation of enzymes and the description of metabolic networks. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions, using entities from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Here we describe developments in Rhea since our last report in the database issue of Nucleic Acids Research. These include the first implementation of a simple hierarchical classification of reactions, improved coverage of the IUBMB Enzyme Nomenclature list and additional reactions through continuing expert curation, and the development of a new website to serve this improved dataset

The yeast P5 type ATPase, Spf1, regulates manganese transport into the endoplasmic reticulum

The endoplasmic reticulum (ER) is a large, multifunctional and essential organelle. Despite intense research, the function of more than a third of ER proteins remains unknown even in the well-studied model organism Saccharomyces cerevisiae. One such protein is Spf1, which is a highly conserved, ER localized, putative P-type ATPase. Deletion of SPF1 causes a wide variety of phenotypes including severe ER stress suggesting that this protein is essential for the normal function of the ER. The closest homologue of Spf1 is the vacuolar P-type ATPase Ypk9 that influences Mn2+ homeostasis. However in vitro reconstitution assays with Spf1 have not yielded insight into its transport specificity. Here we took an in vivo approach to detect the direct and indirect effects of deleting SPF1. We found a specific reduction in the luminal concentration of Mn2+ in ∆spf1 cells and an increase following it’s overexpression. In agreement with the observed loss of luminal Mn2+ we could observe concurrent reduction in many Mn2+-related process in the ER lumen. Conversely, cytosolic Mn2+-dependent processes were increased. Together, these data support a role for Spf1p in Mn2+ transport in the cell. We also demonstrate that the human sequence homologue, ATP13A1, is a functionally conserved orthologue. Since ATP13A1 is highly expressed in developing neuronal tissues and in the brain, this should help in the study of Mn2+-dependent neurological disorders

A Putative Plant Aminophospholipid Flippase, the Arabidopsis P4 ATPase ALA1, Localizes to the Plasma Membrane following Association with a β-Subunit

Plasma membranes in eukaryotic cells display asymmetric lipid distributions with aminophospholipids concentrated in the inner leaflet and sphingolipids in the outer leaflet. This unequal distribution of lipids between leaflets is, amongst several proposed functions, hypothesized to be a prerequisite for endocytosis. P4 ATPases, belonging to the P-type ATPase superfamily of pumps, are involved in establishing lipid asymmetry across plasma membranes, but P4 ATPases have not been identified in plant plasma membranes. Here we report that the plant P4 ATPase ALA1, which previously has been connected with cold tolerance of Arabidopsis thaliana, is targeted to the plasma membrane and does so following association in the endoplasmic reticulum with an ALIS protein β-subunit