The comparative analysis of the energies of conjugated triple base triplets and their applications

We built 64 sets of 3D models of DNA triplex base triplets (TBT) and minimized their energies. The TBTs were divided into 32 pairs of conjugated ones on the basis of their sequence characteristic, and the energies of each pair of them were compared and analyzed, the results showed: (i) The duplex DNA of which any strand contains at least a couple of A or T, has a preference for selecting the oligodeoxyribonucleic acid (ODN) strand containing abundant T to form TBT. (ii) The duplex DNA of which any strand contains at least a couple of G or C has a preference for selecting ODN containing abundant G to form symmetric antiparallel TBT, but selecting ODN containing abundant C to form asymmetric parallel TBT. (iii) The duplex DNA of which any strand contains only one of A, T, G or C has a preference for selecting ODN containing abundant pyrimidines (T or C) to form antiparallel TBT. Additionally, two examples of TBTs applications, in designing ODN to form triplex with duplex were presented. The energy calculation result revealed that 15-TCG is the best ligand of the HIV PPT duplex. The comparative analysis of energies of the conjugated TBTs provides directive significance for designing ODN strand that is easy to form triplex in theory. (C) 2002 Elsevier Science B.V. All rights reserved.

The relation between translation speed and protein secondary structure

Based on the statistical analysis of 119 human and 92 E. coli proteins it was found that for both human and E. coli, the mRNA sequences consisting of tri-codon and tetra-codon with high translation speed preferably code for alpha helices more than for coils. For beta strand, the preference/ avoidance oscillates with the translation speed. Moreover, the non-homogeneous usages of tri-codon and tetra-codon with different translation speeds in a given secondary structure have also been found. These results cannot be simply explained by the effect of stochastic fluctuation.

Stable RNA hairpins in 88 coding regions of human mRNA

RNA hairpins containing UNCG, GNRA, CUUG (N = A, U, C or G, R = G or A) loops are unusually thermodynamic stable and conserved structures. The structural features of these hairpin loops are very special, and they play very important roles in vivo. They are prevalent in rRNA, catalytic RNA and non-coding mRNA. However, the 5' C(UUCG)G 3' hairpin is not found in the folding structure of 88 human mRNA coding regions. It is also different from rRNA in that there is no preference for certain sequences among tetraloops in these 88 mRNA folding structures.

Prices need no preferences: social trends determine decisions in experimental markets for pain relief.

OBJECTIVE: A standard view in health economics is that, although there is no market that determines the "prices" for health states, people can nonetheless associate health states with monetary values (or other scales, such as quality adjusted life year [QALYs] and disability adjusted life year [DALYs]). Such valuations can be used to shape health policy, and a major research challenge is to elicit such values from people; creating experimental "markets" for health states is a theoretically attractive way to address this. We explore the possibility that this framework may be fundamentally flawed-because there may not be any stable values to be revealed. Instead, perhaps people construct ad hoc values, influenced by contextual factors, such as the observed decisions of others. METHOD: The participants bid to buy relief from equally painful electrical shocks to the leg and arm in an experimental health market based on an interactive second-price auction. Thirty subjects were randomly assigned to two experimental conditions where the bids by "others" were manipulated to follow increasing or decreasing price trends for one, but not the other, pain. After the auction, a preference test asked the participants to choose which pain they prefer to experience for a longer duration. RESULTS: Players remained indifferent between the two pain-types throughout the auction. However, their bids were differentially attracted toward what others bid for each pain, with overbidding during decreasing prices and underbidding during increasing prices. CONCLUSION: Health preferences are dissociated from market prices, which are strongly referenced to others' choices. This suggests that the price of health care in a free-market has the capacity to become critically detached from people's underlying preferences.

The price of pain and the value of suffering.

Estimating the financial value of pain informs issues as diverse as the market price of analgesics, the cost-effectiveness of clinical treatments, compensation for injury, and the response to public hazards. Such valuations are assumed to reflect a stable trade-off between relief of discomfort and money. Here, using an auction-based health-market experiment, we show that the price people pay for relief of pain is strongly determined by the local context of the market, that is, by recent intensities of pain or immediately disposable income (but not overall wealth). The absence of a stable valuation metric suggests that the dynamic behavior of health markets is not predictable from the static behavior of individuals. We conclude that the results follow the dynamics of habit-formation models of economic theory, and thus, this study provides the first scientific basis for this type of preference modeling.

Crystallographically driven Au catalyst movement during growth of InAs/GaAs axial nanowire heterostructures

The movement of Au catalysts during growth of InAs on GaAs nanowires has been carefully investigated by transmission electron microscopy. It has been found that Au catalysts preferentially stay on { 112 } B GaAs sidewalls. Since a {112} surface is composed of a {111} facet and a {002} facet and since {111} facets are polar facets for the zinc-blende structure, this crystallographic preference is attributed to the different interface energies caused by the different polar facets. We anticipate that these observations will be useful for the design of nanowire heterostructure based devices. © 2009 American Institute of Physics.

Interactive multi-objective particle swarm optimisation using decision space interaction

The most common approach to decision making in multi-objective optimisation with metaheuristics is a posteriori preference articulation. Increased model complexity and a gradual increase of optimisation problems with three or more objectives have revived an interest in progressively interactive decision making, where a human decision maker interacts with the algorithm at regular intervals. This paper presents an interactive approach to multi-objective particle swarm optimisation (MOPSO) using a novel technique to preference articulation based on decision space interaction and visual preference articulation. The approach is tested on a 2D aerofoil design case study and comparisons are drawn to non-interactive MOPSO. © 2013 IEEE.

Dread and the disvalue of future pain.

Standard theories of decision-making involving delayed outcomes predict that people should defer a punishment, whilst advancing a reward. In some cases, such as pain, people seem to prefer to expedite punishment, implying that its anticipation carries a cost, often conceptualized as 'dread'. Despite empirical support for the existence of dread, whether and how it depends on prospective delay is unknown. Furthermore, it is unclear whether dread represents a stable component of value, or is modulated by biases such as framing effects. Here, we examine choices made between different numbers of painful shocks to be delivered faithfully at different time points up to 15 minutes in the future, as well as choices between hypothetical painful dental appointments at time points of up to approximately eight months in the future, to test alternative models for how future pain is disvalued. We show that future pain initially becomes increasingly aversive with increasing delay, but does so at a decreasing rate. This is consistent with a value model in which moment-by-moment dread increases up to the time of expected pain, such that dread becomes equivalent to the discounted expectation of pain. For a minority of individuals pain has maximum negative value at intermediate delay, suggesting that the dread function may itself be prospectively discounted in time. Framing an outcome as relief reduces the overall preference to expedite pain, which can be parameterized by reducing the rate of the dread-discounting function. Our data support an account of disvaluation for primary punishments such as pain, which differs fundamentally from existing models applied to financial punishments, in which dread exerts a powerful but time-dependent influence over choice.

Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila

Background: Cytochrome P450 monooxygenases play key roles in the metabolism of a wide variety of substrates and they are closely associated with endocellular physiological processes or detoxification metabolism under environmental exposure. To date, however, none has been systematically characterized in the phylum Ciliophora. T. thermophila possess many advantages as a eukaryotic model organism and it exhibits rapid and sensitive responses to xenobiotics, making it an ideal model system to study the evolutionary and functional diversity of the P450 monooxygenase gene family. Results: A total of 44 putative functional cytochrome P450 genes were identified and could be classified into 13 families and 21 sub-families according to standard nomenclature. The characteristics of both the conserved intron-exon organization and scaffold localization of tandem repeats within each P450 family clade suggested that the enlargement of T. thermophila P450 families probably resulted from recent separate small duplication events. Gene expression patterns of all T. thermophila P450s during three important cell physiological stages (vegetative growth, starvation and conjugation) were analyzed based on EST and microarray data, and three main categories of expression patterns were postulated. Evolutionary analysis including codon usage preference, sit-especific selection and gene-expression evolution patterns were investigated and the results indicated remarkable divergences among the T. thermophila P450 genes. Conclusion: The characterization, expression and evolutionary analysis of T. thermophila P450 monooxygenase genes in the current study provides useful information for understanding the characteristics and diversities of the P450 genes in the Ciliophora, and provides the baseline for functional analyses of individual P450 isoforms in this model ciliate species.

Crustacean zooplankton distribution patterns and their biomass as related to trophic indicators of 29 shallow subtropical lakes

A comparative limnological study was carried out to present a snapshot of crustacean zooplankton communities and their relations to environmental factors to test whether there is a consistent relationship between crustacean biomass and trophic indicators among lake groups with similar trophic conditions. The study lakes showed a wide range of trophic status, with total phosphorus (TP) ranging from 0.008 to 1.448mgL(-1), and chlorophyll a from 0.7 to 146.1 mu g L-1, respectively. About 38 species of Crustacea were found, of which Cladocera were represented by 25 taxa (20 genera), and Copepoda by 13 taxa (I I genera). The most common and dominant species were Bosmina coregoni, Moina micrura, Diaphanosoma brachyurum, Cyclops vicinus, Thermocyclops taihokuensis, Mesocyclops notius and Sinocalanus dorrii. Daphnia was rare in abundance. Canonical correspondence analysis showed that except for four species (D. hyalina, S. dorrii, C. vicinus and M. micrura), almost all the dominant species had the same preference for environmental factors. Temperature, predatory cyclopoids and planktivorous fishes seem to be the key factors determining species distribution. TP was a relatively better trophic indicator than chlorophyll a to predict crustacean biomass. Within the three groups of lakes, however, there was no consistent relationship between crustacean biomass and trophic indicators. The possible reason might be that top-down and bottom-up control on crustaceans vary with lake trophic state. The lack of significant negative correlation between crustacean biomass and chlorophyll a suggests that there was little control of phytoplankton biomass by macrozooplankton in these shallow subtropical lakes. (c) 2007 Elsevier GmbH. All rights reserved.

Is there a preferred classifier for operational thematic mapping?

The importance of properly exploiting a classifier's inherent geometric characteristics when developing a classification methodology is emphasized as a prerequisite to achieving near optimal performance when carrying out thematic mapping. When used properly, it is argued that the long-standing maximum likelihood approach and the more recent support vector machine can perform comparably. Both contain the flexibility to segment the spectral domain in such a manner as to match inherent class separations in the data, as do most reasonable classifiers. The choice of which classifier to use in practice is determined largely by preference and related considerations, such as ease of training, multiclass capabilities, and classification cost. © 1980-2012 IEEE.

Occurrence of Camallanus cotti in greatly diverse fish species from Danjiangkou Reservoir in central China

Two thousand four hundred fifty-eight fish comprised of 53 species were captured in the Danjiangkou Reservoir, in the northwestern part of Hubei Province, central China during 2004, to examine Camallanus cotti infections. We found that 19 cypriniform, 3 siluriforme, and 4 perciforme fishes were infected by the nematode. Our study revealed the species, Hemiculter bleekeri bleekeri, Culter oxycephaloide, Pseudolaubuca sinensis, Acanthobrama simony, Mylopharyngodon piceus, Ctenopharyngodon idella, Gnathopogon imberbis, G. argentatus, Saurogobio dabryi, S. dumerili, Gobiobotia ichangensis, Liobagrus marginatoides, and Ctenogobius shennongensis as new hosts of the worm. The number and range of fish host species found in this survey were much greater than any of the previous investigations. The mean prevalence, prevalence, mean abundance, and intensity of infection varied in different fish species, indicating a possible host preference. Moreover, we suggest that this nematode is a native parasite of cypriniform fishes in China, perhaps initially in the reaches of the Yangtze River.

The co-evolutionary relationship between bitterling fishes and freshwater mussels: insights from interspecific comparisons

Hypothesis: In parasites that use hosts for offspring development, adults may base oviposition decisions on a range of host traits related either to host quality or the co-evolutionary relationship between parasite and host. We examined whether host quality or co-evolutionary dynamics drive the use of hosts in the bitterling-mussel relationship. Organisms: Six species of bitterling fish (Acheilognathinae) and eight species of freshwater mussels (Unionidae, Corbiculidae) that are used by bitterling for oviposition. Site of experiments: Experimental tanks in Wuhan, China, at the site of the natural distribution of the studied species. Methods: Three experiments that controlled for host accessibility and interspecific interactions were conducted to identify host preferences among bitterling fishes and their mussel hosts. We started with a broad interspecific comparison. We then tested bitterling behavioural choices, their temporal stability, and mussel host ejection behaviour of the eggs of generalist and specialist bitterling species. Finally, we measured host mussel quality based on respiration rate and used published studies on mussel gill structure to infer mussel suitability as hosts for bitterling eggs. Results: We found significant interspecific differences among bitterling species in their use of mussel hosts. Bitterling species varied in their level of host specificity and identity of preferred hosts. Host preferences were flexible even among apparently specialized species and fishes switched their preferences adaptively when the quality of individuals of preferred host species declined. Mussels varied considerably in their response to oviposition through egg ejections. Host preference by a generalist bitterling species correlated positively with host quality measured as the efficiency of the mussel gills to extract oxygen from inhaled water. Host ability to eject bitterling eggs correlated positively with their relative respiration rate, probably due to a higher velocity of water circulating in the mussel gill chamber.

Gastropods on submersed macrophytes in Yangtze lakes: Community characteristics and empirical modelling

Epiphytic gastropods in Yangtze lakes have suffered from large-scale declines of submersed macrophytes during past decades. To better understand what controls gastropod community, monthly investigations were carried out in four Yangtze lakes during December, 2001-March, 2003. Composed of 23 species belonging to Pulmonata and Prosobranchia, the community is characterized by the constitution of small individuals. The average density and biomass were 417 +/- 160 ind/m(2) and 18.05 +/- 7.43 g/m(2), with maxima a-round August. Submersed macrophyte biomass is shown to be the key factor affecting species number, density, and biomass of gastropods. Accordingly, a series of annual and seasonal models yielding high predictive powers were generated. Preference analyses demonstrated that pulmonates and prosobranchs with different respiratory organs prefer different macrophyte functional groups.

Population dynamics of the water mite Unionicola arcuata (Unionicolidae) in the freshwater bivalve Cristaria plicata (Unionidae) in Poyang Lake, eastern China

Population dynamics of the water mite Unionicola arcuata were investigated in the freshwater bivalve Cristaria plicata during the period from January to December 2002 in Poyang Lake, East China. A pattern of seasonal variation was observed, with prevalence and abundance peaking in early spring and autumn. The number of mites in individual hosts was significantly correlated with the size, but not with the sex, of bivalves. The change in infection level of mites on different infection sites in C. plicata was significant, with > 58% of the mites found on the outer and inner gills, indicating that U. arcuata shows site preference.