A test for the statistical significance of DNA sequence similarities for application in databank searches

A method is developed, based on word-searching, which provides a rapid test for the statistical significance of DNA sequence similarities for use in databank searching. The method makes allowance for the lengths and dinucleotide compositions of the sequences being compared. A way is also described to calculate the power of the test, i.e. the probability of detecting a given similarity as being statistically significant. The effects on the power of the test of the scoring method, word length, sequence length, and sequence composition are examined. A novel scoring method is shown to be superior to the method currently used in most word-searching algorithms.     

Purification of Ellagic Acid by UF Membranes

Ellagic acid (2, 3, 7, 8‐tetrahydroxy(1)benzopyrano(5, 4, 3‐cde)(1)benzopyran‐5, 10‐dione) was selected as a model pollutant which is present in the tannic fraction of cork processing wastewater. The ultrafiltration of aqueous ellagic acid solutions through three membranes was studied in tangential UF laboratory equipment. Two of the membranes were polyethersulfone (Biomax10K and Biomax5K, with MWCO of 10000 and 5000 Da, respectively), and the third made of regenerated cellulose (Ultracel5K, with MWCO of 5000 Da). The water hydraulic permeability was evaluated for each membrane. The evolution of the permeate flow rate with processing time was followed, and the influence of the main operating variables (feed flow rate, trans‐membrane pressure and nature of the membranes) on the permeate flux was also established. According to the hypothesis of the film theory, the intrinsic and apparent rejection coefficients, as well as the mass transfer coefficients, were also determined, and the values obtained were discussed as a function of the operating conditions used.     

An experiment for showing some kind of artificial understanding

In this paper we design an experiment which can be depicted as a simple scenario, a very limited 'world'. In this world, there are an actor that can pursue a project and an observer that is keeping its eyes on the actor. We try to show in the experiment that the observer can to some degree understand the actor based on its knowledge and some metaphors, i.e. understand what the actor is doing and why. As the conclusion of this experiment, we try to show some features of 'understanding'. These are (1) that 'understanding' has to be based on some preliminary knowledge; (2) that 'understanding' is a process of incremental learning; (3) that, as for symbolic systems, some metaphors are necessary for mapping real entities into concepts in mind.     

Standing on Solid Ground

The new Editor in Chief of IEEE Micro introduces himself and the first issue of 2007. He thanks outgoing Editor in Chief Pradip Bose for his outstanding work on Micro during his tenure. He assesses the current state of the microarchitecture field, speculates on the future, and asks readers for their suggestions on topics the magazine should cover in coming issues.     

Experimental Study of Ice Jam Thickening under Dynamic Flow Conditions

River ice jams are a common occurrence on northern rivers, and their formation can present a severe flood risk to nearby communities. As more and more river regulation projects are developed to provide an alternative to fossil fuels for electrical power-generating capacity, our need to understand the mechanisms associated with ice jam formation under variable flow conditions becomes more vital. This is because, at present, hydropeaking operations are often severely curtailed during the ice-affected seasons due to concerns that sudden flow fluctuations might instigate ice jams and associated flooding. Here, an experimental investigation explores the effects of rapid increases in discharge on ice jam formation and evolution. It is found that the thickness of ice jams formed under highly dynamic flow conditions tend to be slightly thinner than those formed during steady carrier flows for comparable discharges. Also, despite the highly dynamic nature of these consolidation events, the resulting ice thicknesses appear reasonably well approximated by steady flow theory.     

Bioavailability and Toxicity of Metal Nutrients during Anaerobic Digestion

This paper investigates the effect of chelating agents on the bioavailability of Fe and Cu during anaerobic digestion. The results on metal speciation and methane production in anaerobic serum bottles showed that biomass was able to grow in the presence of citrate 1?mM and nitrilotriacetic acid (NTA) 1?mM, suggesting that the binding sites at the cell surface competed efficiently for the metals with the chelating agents added. The presence of free ethylenediaminetetraacetic acid 1?mM inhibited methanogenesis, and this seemed to be related to a loss in metal uptake capacity. Although the addition of soluble microbial products (SMP) did not change metal distribution in anaerobic systems, it caused an increase in the rate of methane production, and it is believed that direct uptake of Cu-SMP complexes was responsible for this increase. The best protection against Cu toxicity occurred when stoichiometric amounts of NTA, which should complex and solubilize most of the Cu, was added, and it is likely that NTA prevented lethal concentrations of Cu from being adsorbed onto the cell and hence internalized.     

Impact of dimension uncertainty and model calibration on sewer system assessment.

Assessments of sewer performance are usually based on a single computation of CSO (combined sewer overflow) volumes using a time series of rainfall as system loads. A shortcoming of this method is that uncertainties in knowledge of sewer system dimensions are not taken into account. Moreover, sewer models are rarely calibrated. This paper presents the impacts of database errors and model calibration on return periods of calculated CSO volumes. The impact of uncertainties is illustrated with two examples. Variability of calculated CSO volumes is estimated using Monte Carlo simulations. The results show that calculated CSO volumes vary considerably due to database errors, especially uncertain dimensions of the catchment area. Furthermore, event-based calibration of a sewer model does not result in more reliable predictions because the calibrated parameters have low portability. However, it enables removal of database errors harmonising model predictions and 'reality'.     

The press as a vehicle for the introduction of a fashionable disease]

Two journalists wrote a book on HPU (haemopyrrol-lactamuria), a hitherto unknown metabolic disease that was alleged to cause a whole range of complaints. The book is based on the ideas of a biochemist who is also the director of a commercial organisation that offers a diagnostic test as well as a therapy (nutrition supplement) for HPU. The release of the book was accompanied by a press release that provoked various publications in both biomedical journals and the lay press. In response to these reports, the director sometimes registered a complaint with the Dutch Council for Journalism, but on other occasions he did not. The content of this book is in no way based on scientific research. In retrospect, it is obvious that the authors, the biochemist and the publishing company have joint commercial ties. All professional standards of scientific research and journalistic decency are thus being violated. In this way, they are doing harm to the independence and integrity of researchers and journalists in the public image. All the activities of the press seem to have been an essential part of a deliberate marketing strategy for the introduction of a non-disease.