A graphical tool for parasite genome annotation

A graphical tool to facilitate rapid primary annotation of genomic sequence has been developed. Within a single interface the user can import sequences or database entries, run feature prediction programs and similarity searches, filter results, add additional manually found features and notes, and finally export annotations for database submission. Integrated rule-based feature corroboration and a novel decision support heuristic using ORF orientation, length and base-composition further enhances the efficiency of the annotation process without compromising flexibility. The program has been explicitly tailored to use in protozoan parasite genome projects, but can constitute a useful tool for prokaryote annotation as well. It is successfully being used by our lab in the Trypanosoma cruzi genome project, and can be obtained from the authors upon request.     

Improved emission uniformity from a liquid-jet laser-plasma extreme-ultraviolet source

Many modern compact soft-x-ray and extreme-ultraviolet (EUV) imaging systems operate with small fields of view and therefore benefit from the use of small high-brightness sources. Such systems include water-window microscopes and EUV lithography tools. We show that the photon losses in such systems can be minimized while uniformity of object-plane illumination is maintained by controlled scanning of the source. The improved collection efficiency is demonstrated both theoretically and experimentally for a scanned laser-plasma source compared with static sources. A prospective aerial image microscope and a liquid-xenon-jet laser-plasma source are offered as examples of modern imaging tools that may benefit from such scanning of the source.     

Intermittent melphalan and prednisolone therapy in plasma cell myeloma

Thirty-two consecutive, previously untreated patients with plasma cell myeloma were treated with 4-day courses of melphalan (0.25 mg/kg/day) and prednisolone (2 mg/kg/day) every sixth week. The observation period ranged from 26 to 75 months and the total median survival time was 29 months. 75% of the patients responded to therapy and their median survival time was 42 months. Sex did not influence either the response rate or the survival time. Most patients were treated in an out-patient clinic and required a minimum of check-ups.     

Space-use strategy is an important determinant of PCB concentrations in female polar bears in the Barents Sea

Space-use was examined in 54 female polar bears (Ursus maritimus) from Svalbard and the Barents Sea that were collared with satellite transmitters to provide information on their spatial positions and annual home range sizes. Plasma samples from the same animals were analyzed for concentrations of six relevant PCB congeners (PCB-99, -153, -156, -180, -194, and -118). Factors related to space-use strategy (such as home range size; annual, spring, and winter longitudinal position; and spring and summer latitudinal position) were important determinants of PCB concentrations in plasma. In addition, reproductive status of the polar bears and plasma lipid content affected PCB concentrations. Among the tested variables, annual home range size was the variable that affected sigmaPCB5 (sum of PCB-99, -153, -156, -180, and -194) to the largest degree (r2 = 0.22). We propose that the positive effect of home range size on sigmaPCB5 in female polar bears is related to the higher energetic costs required to occupy large home range sizes as compared to small home range sizes. Polar bears with large home range sizes would need to consume more prey than bears with small home range sizes, and increased feeding without a change in elimination of persistent compounds can explain their higher sigmaPCB5 concentrations. Polar bears with large home range sizes were also more pelagic, inhabiting areas further east, closer to the ice-edge zone than animals with small home range sizes. Thus, prey choice associated with a pelagic space-use strategy may also explain the higher sigmaPCB5 in polar bears with large home range sizes.     

Dynamic intuition in military command and control: why it is important,and how it should be developed

This paper considers combat dynamic intuition (CDI). We define CDI as the cognitive capability possessed by a military commander when conducting operations. The paper serves two purposes: firstly, we briefly review the previous research on decision making and learning in dynamic systems, in order to discuss the role of microworlds as training environments to improve CDI. In particular, we focus on the advantages of applying system dynamics techniques when designing microworlds to represent "real world" operational challenges. Secondly, we draw implications from a microworld-based experiment, where task complexity is the manipulated variable. The results indicate that environment simplification in itself is not enough to enhance learning in a microworld setting—a conscious pedagogical program, aimed at increasing the training intensity, should also be developed in support of such training. The latter suggestion should be considered an opportunity for further research on CDI improvement.

Molecular tweezers and clips as synthetic receptors. Molecular recognition and dynamics in receptor-substrate complexes

The molecular tweezers (1, 2) and clips (3-7) containing naphthalene and benzene spacer units can be synthesized via repetitive Diels-Alder reactions by the use of a molecular "Lego" set consisting of bisdienophiles (8, 9, 14) and dienes (10, 13). The new receptors selectively bind electron-deficient neutral and cationic substrates in solution. Only the benzene-spaced tweezers form complexes with aliphatic substrates, whereas the other receptors bind aromatic substrates preferentially. HPLC studies with 1 and 2 chemically bonded to stationary phases give similar results for the heterogeneous systems. The formation of stable complexes between the water-soluble clip 5g and N-alkylpyridinium cations, such as N-methylnicotinamide and NAD(+), in aqueous solution illustrates the importance of the hydrophobic effect for arene-arene interactions. The dynamics of the complex formation and substrate mobility were investigated by the use of temperature-dependent liquid- and solid-state NMR spectroscopy. The electrostatic potential surface (EPS) of 1-7 is calculated to be surprisingly negative on the concave side of each molecule and, hence, complementary to the EPS of the electron-deficient substrates, suggesting that the attractive receptor-substrate interaction is here of predominantly electrostatic nature.     

Epidemiological investigation on chronic copper toxicity to children exposed via the public drinking water supply

Copper in drinking water has been associated with Non-Indian Childhood Cirrhosis (NICC), a form of early childhood liver cirrhosis. This epidemiological study examines the exposition of infants to increased copper concentrations through drinking water from public water supplies in Berlin, Germany, and if this dietary copper intake can cause liver damage in early childhood. In total, water samples from 2944 households with infants were tested for copper. Mean copper concentrations in the two different types of collected composite samples were 0.44 and 0.56 mg/l, respectively. Families having a copper concentration at or above 0.8 mg/l in one or both of the composite samples (29.9% of all sampled households) and a defined minimum ingestion of tap water of their infant were recommended to undergo a paediatric examination. Nearly every of the 541 recommended infants were examined by a local paediatrician and of these 183 received a blood serum analysis, too. None of the infants had clear signs of a liver disease although a few serum parameters lay outside the accompanying reference range and abdominal ultrasound imaging gave slightly unusual results in five cases. Additionally, no signs of a negative health effect could be found in the statistical analysis of the serum parameters GOT, GPT, GGT, total bilirubin, serum copper, or ceruloplasmin in relation to estimated daily and total copper intakes of the infants from tap water. No dose relation of serum parameters and estimated copper intakes could be established. From the results of the study, no confirmed indication of a liver malfunction in infants whose food had been prepared using tap water with an elevated copper concentration could be found and, therefore, no indication of a hazard due to copper pipes connected to public water supplies could be detected.     

Mechanical properties of young concrete: Part II: Determination of model parameters and test program proposals

The paper concerns testing and modelling of the mechanical properties required as input to calculation programs made for crack risk estimation of hardening concrete structures. The results from several test series on mechanical properties of young concrete as described in Part I of this paper, are further evaluated. Model parameters for the modified CEB 1990 Model Code-equations, are determined for six concrete mixes, all having a w/b-ratio on 0.40, for compressive strength, tensile strength and E-modulus. To make the models applicable for young concrete, at ₀-parameter is introduced to fix the time at which significant mechanical properties are present. A test program to determine the model parameters is proposed, based on the experience that compressive strength tests have the smallest statistical scatter and that they are simplest to carry out.     

Evaluations of the stability of sheathless electrospray ionization mass spectrometry emitters using electrochemical techniques

The processes that cause the failure of sheathless electrospray ionization (ESI) emitters, based on different kinds of gold coatings on fused-silica capillaries, are described and explained. The methods chosen for this study include electrochemical methods, ICPMS analysis of the electrolytes used, SEM studies, and electrospray experiments. Generally, the failure occurs by loss of the conductive coating. It is shown that emitters with sputter-coated gold lose their coatings because of mechanical stress caused by the gas evolution accompanying water oxidation or reduction. Emitters with gold coatings on top of adhesion layers of chromium and nickel alloy withstand this mechanical stress and have excellent durability when operating as cathodes. When operating as anodes, the adhesion layer is electrochemically dissolved through the gold film, and the gold film then flakes off. It is shown that the conductive coating behaves as a cathode even in the positive electrospray mode when the magnitude of a superimposed reductive electrophoretic current exceeds that of the oxidative electrospray current. Fairy-dust coatings developed in our laboratory (see Barnidge, D. R.; etal.Anal. Chem. 1999, 71, 4115-4118,) bygluing gold dust onto the emitter, are unaffected by the mechanical stress due to gas evolution. When oxidized, the fairy-dust coatings show an increased surface roughness and decreased conductivities due to the formation of gold oxide. The resistance of this oxide layer is however negligible in comparison with that of the gas phase in ESI. Furthermore, since no flaking and only negligible electrochemical etching of gold was found, practically unlimited emitter lifetimes may be achieved with fairy-dust coatings.     

A New Design Concept for High-Performance Fading Channel Simulators Using Set Partitioning

In this paper, we introduce a new technique for the design of high-performance Rayleigh fading channel simulators. The proposed design method uses set partitioning – a technique, which plays a key role in the design of trellis-coded modulation schemes. We show how set partitioning can be used to design multiple uncorrelated fading waveforms enabling the simulation of Rayleigh fading channels. For the important case of isotropic scattering, we show that the sample average of the generated waveforms results in a deterministic process, the autocorrelation function (ACF) of which tends to the zeroth-order Bessel function of the first kind as the number of sample functions increases. The proposed procedure is completely deterministic. The comparison with a stochastic procedure using Monte Carlo techniques will be made. A study of the performance shows clearly that the new technique using set partitioning outperforms by far existing Monte Carlo methods.