Gene selection by cooperative competition clustering

Clustering analysis of data from DNA microarray hybridization studies is an essential task for identifying biologically relevant groups of genes. Attribute cluster algorithm (ACA) has provided an attractive way to group and select meaningful genes. However, ACA needs much prior knowledge about the genes to set the number of clusters. In practical applications, if the number of clusters is misspecified, the performance of the ACA will deteriorate rapidly. In fact, it is a very demanding to do that because of our little knowledge. We propose the Cooperative Competition Cluster Algorithm (CCCA) in this paper. In the algorithm, we assume that both cooperation and competition exist simultaneously between clusters in the process of clustering. By using this principle of Cooperative Competition, the number of clusters can be found in the process of clustering. Experimental results on a synthetic and gene expression data are demonstrated. The results show that CCCA can choose the number of clusters automatically and get excellent performance with respect to other competing methods.

The masses of the cataclysmic variables AC Cancri and V363 Aurigae

We present time-resolved spectroscopy and photometry of the double-lined eclipsing cataclysmic variables AC Cnc and V363 Aur (=Lanning 10). There is evidence of irradiation on the inner hemisphere of the secondary star in both systems, which we correct for using a model that reproduces the observations remarkably well. We find the radial velocity of the secondary star in AC Cnc to be K-R=176+/-3 km s(-1) and its rotational velocity to be v sin i=135+/-3 km s(-1). From these parameters we obtain masses of M-1=0.76+/-0.03 M-circle dot for the white-dwarf primary and M-2=0.77+/-0.05 M-circle dot for the K2+/-1 V secondary star, giving a mass ratio of q=1.02+/-0.04. We measure the radial and rotational velocities of the G7+/-2V secondary star in V363 Aur to be K-R=168+/-5 km s(-1) and v sin i=143+/-5 km s(-1), respectively. The component masses of V363 Aur are M-1=0.90+/-0.06M(circle dot) and M-2=1.06+/-0.11 M-circle dot giving a mass ratio of q=1.17+/-0.07. The mass ratios for AC Cnc and V363 Aur fall within the theoretical limits for dynamically and thermally stable mass transfer. Both systems are similar to the SW Sex stars, exhibiting single-peaked emission lines with transient absorption features, high-velocity S-wave components and phase-offsets in their radial-velocity curves. The Balmer lines in V363 Aur show a rapid increase in flux around phase 0 followed by a rapid decrease, which we attribute to the eclipse of an optically thick region at the centre of the disc. This model could also account for the behaviour of other SW Sex stars where the Balmer lines show only a shallow eclipse compared to the continuum.

The relationship between counterfactual thinking and emotional reactions to event outcomes: Does one account fit all?

By enabling a comparison between what is and what might have been, counterfactual thoughts amplify our emotional responses to bad outcomes. Well-known demonstrations such as the action effect (the tendency to attribute most regret to a character whose actions brought about a bad outcome) and the temporal order effect (the tendency to undo the last in a series of events leading up to a bad outcome) are often explained in this way. An important difference between these effects is that outcomes are due to decisions in the action effect, whereas in the temporal order effect outcomes are achieved by chance. In Experiment 1, we showed that imposing time pressure leads to a significant reduction in the action but not in the temporal order effect. In Experiment 2, we found that asking participants to evaluate the protagonists (

Do development and learning really decrease memory? On similarity and category-based induction in adults and children

In a recently published study, Sloutsky and Fisher [Sloutsky, V. M., & Fisher, A.V. (2004a). When development and learning decrease memory: Evidence against category-based induction in children. Psychological Science, 15, 553-558; Sloutsky, V. M., & Fisher, A. V. (2004b). Induction and categorization in young children: A similarity-based model. Journal of Experimental Psychology: General, 133, 166-188.] demonstrated that children have better memory for the items that they generalise to than do adults. On the basis of this finding, they claim that children and adults use different mechanisms for inductive generalisations;whereas adults focus on shared category membership, children project properties on the basis of perceptual similarity. Sloutsky & Fisher attribute children's enhanced recognition memory to the more detailed processing required by this similarity-based mechanism. In Experiment I we show that children look at the stimulus items for longer than adults. In Experiment 2 we demonstrate that although when given just 250 ms to inspect the items children remain capable of making accurate inferences, their subsequent memory for those items decreases significantly. These findings suggest that there are no necessary conclusions to be drawn from Sloutsky & Fisher's results about developmental differences in generalisation strategy. (C) 2007 Elsevier B.V. All rights reserved.

Comparisons, mental models, and the action effect in judgments of regret

People tend to attribute more regret to a character who has decided to take action and experienced a negative outcome than to one who has decided not to act and experienced a negative outcome. For some decisions, however, this finding is not observed in a between-participants design and thus appears to rely on comparisons between people's representations of action and their representations of inaction. In this article, we outline a mental models account that explains findings from studies that have used within- and between-participants designs, and we suggest that, for decisions with uncertain counterfactual outcomes, information about the consequences of a decision to act causes people to flesh out their representation of the counterfactual states of affairs for inaction. In three experiments, we confirm our predictions about participants' fleshing out of representations, demonstrating that an action effect occurs only when information about the consequences of action is available to participants as they rate the nonactor and when this information about action is informative with respect to judgments about inaction. It is important to note that the action effect always occurs when the decision scenario specifies certain counterfactual outcomes. These results suggest that people sometimes base their attributions of regret on comparisons among different sets of mental models.

Spatial genetic structuring in a vagile species, the European wood mouse

We examined the genetic structure of natural populations of the European wood mouse Apodemus sylvaticus at the microgeographic ( 30 km) scales. Ecological and behavioural studies indicate that this species exhibits considerable dispersal relative to its home-range size. Thus, there is potential for high gene flow over larger geographic areas. As levels of population genetic structure are related to gene flow, we hypothesized that population genetic structuring at the microgeographic level should be negligible, increasing only with geographic distance. To test this, four sites were sampled within a microgeographic scale with two additional samples at the macrogeographic level. Individuals (n=415) were screened and analysed for seven polymorphic microsatellite loci. Contrary to our hypothesis, significant levels of population structuring were detected at both scales. Comparing genetic differentiation with geographic distance suggests increasing genetic isolation with distance. However, this distance effect was non-significant being confounded by surprisingly high levels of differentiation among microgeographic samples. We attribute this pattern of genetic differentiation to the effect of habitat fragmentation, splitting large populations into components with small effective population sizes resulting in enhanced genetic drift. Our results indicate that it is incorrect to assume genetic homogeneity among populations even where there is no evidence of physical barriers and dispersal can occur freely. In the case of A. sylvaticus, it is not clear whether dispersal does not occur across habitat barriers or behavioural dispersal occurs without consequent gene flow.

Fully fluorinated imidodiphosphinate shells for visible- and NIR-Emitting lanthanides: Hitherto unexpected effects of sensitizer fluorination on lanthanide emission properties

In this paper we demonstrate that the effect of aromatic C-F substitution in ligands does not always abide by conventional wisdom for ligand design to enhance sensitisation for visible lanthanide emission, in contrast with NIR emission for which the same effect coupled with shell formation leads to unprecedented long luminescence lifetimes. We have chosen an imidodiphosphinate ligand, N-{P,P-di-(pentafluorophinoyl)}-P,P-dipentafluoro-phenylphosphinimidic acid (HF(20)tpip), to form ideal fluorinated shells about all visible- and NIR-emitting lanthanides. The shell, formed by three ligands, comprises twelve fully fluorinated aryl sensitiser groups, yet no-high energy X-H vibrations that quench lanthanide emission. The synthesis, full characterisation including X-ray and NMR analysis as well as the photophysical properties of the emissive complexes [Ln(F(20)tpip)(3)], in which Ln=Nd, Sm, Eu, Gd, Tb, Dy, Er, Yb, Y, Gd, are reported. The photophysical results contrast previous studies, in which fluorination of alkyl chains tends to lead to more emissive lanthanide complexes for both visible and NIR emission. Analysis of the fluorescence properties of the HF(20)tpip and [Gd(F(20)tpip)(3)] reveals that there is a low-lying state at around 715 nm that is responsible for partially quenching of the signal of the visible emitting lanthanides and we attribute it to a pi-sigma* state. However, all visible emitting lanthanides have long lifetimes and unexpectedly the [Dy(F(20)tpip)(3)] complex shows a lifetime of 0.3 ms, indicating that the elimination of high-energy vibrations from the ligand framework is particularly favourable for Dy. The NIR emitting lanthanides show strong emission signals in powder and solution with unprecedented lifetimes. The luminescence lifetimes of [Nd(F(20)tpip)(3)], [Er(F(20)tpip)(3)] and [Yb(F(20)tpip)(3)] in deuteurated acetonitrile are 44, 741 and 1111 mu s. The highest value observed for the [Yb(F(20)tpip)(3)] complex is more than half the value of the Yb ion radiative lifetime.

Hylambatin and (Thr)11-hylambatin from the skin secretion of the African hyperoliid frog, Kassina maculata: Structural characterisation, precursor cDNA cloning and preliminary pharmacological testing

The tachykinins hylambatin and (Thr)11-hylambatin have been isolated from the defensive skin secretion of the African hyperoliid frog, Kassina maculata,. Hylambatin (DPPDPNRFYGMMamide) is revised in structure from the original sequence by a single site substitution (Asn/Asp at position 6), and (Thr)11-hylambatin, a novel tachykinin, differs in structure from hylambatin by a single Thr/Met substitution. (Thr)11-hylambatin is five- to ten-fold more abundant than hylambatin in secretions. Synthetic replicates of both peptides were active in smooth muscle preparations including the rat tail artery, rat ileum and bovine trachea. While hylambatin displayed activity consistent with an NK1-receptor ligand, (Thr)11-hylambatin was more active than either substance P or neurokinin A in both NK1- and NK-2 receptor rich preparations. Incorporation of a threoninyl residue rather than the canonical leucyl residue at the penultimate position in both substance P and neurokinin A, generated active ligands in both arterial and intestinal smooth muscle preparations. Hylambatin precursor cDNAs, designated HYBN-1 and HYBN-2, respectively, were cloned from a skin library by 3'- and 5'-RACE reactions. Both were highly-homologous containing open-reading frames of 66 amino acids encoding single copies of either hylambatin or (Thr)11-hylambatin. These data reveal a hitherto unrecognized structure/activity attribute of mammalian tachykinin receptors revealed though discovery of a novel amphibian skin-derived, site-substituted peptide ligand.

Millimeter-wave stealth radio for special operations forces

For Special Operations Forces, an important attribute of any future radio will be the ability to conceal transmissions from the enemy while transmitting large amounts of data for situational awareness and communications. These requirements will mean that military wireless systems designers will need to consider operating frequencies in the mm-wave bands: The high data rates that are achievable at these frequencies and the propagation characteristics at this wavelength will provide many benefits for the implementation of 'stealth radio'. This article discusses some of the recent advances in RF front-end technology, alongside physical layer transmission schemes that could be employed for millimeter-wave soldier-mounted radio. The operation of a hypothetical millimeter-wave soldier-to-soldier communications system that makes use of smart antenna technology is also described.

SuperWASP observations of long timescale photometric variations in cataclysmic variables

Aims: We investigated whether the predictions and results of Stanishev et al. (2002, A&A, 394, 625) concerning a possible relationship between eclipse depths in PX And and its retrograde disc precession phase, could be confirmed in long term observations made by SuperWASP. In addition, two further CVs (DQ Her and V795 Her) in the same SuperWASP data set were investigated to see whether evidence of superhump periods and disc precession periods were present and what other, if any, long term periods could be detected. Methods: Long term photometry of PX And, V795 Her and DQ Her was carried out and Lomb-Scargle periodogram analysis undertaken on the resulting light curves. For the two eclipsing CVs, PX And and DQ Her, we analysed the potential variations in the depth of the eclipse with cycle number. Results: The results of our period and eclipse analysis on PX And confirm that the negative superhump period is 0.1417 ± 0.0001d. We find no evidence of positive superhumps in our data suggesting that PX And may have been in a low state during our observations. We improve on existing estimates of the disc precession period and find it to be 4.43 ± 0.05d. Our results confirm the predictions of Stanishev et al. (2002). We find that DQ Her does not appear to show a similar variation for we find no evidence of negative superhumps or of a retrograde disc precession. We also find no evidence of positive superhumps or of a prograde disc precession and we attribute the lack of positive superhumps in DQ Her to be due to the high mass ratio of this CV. We do however find evidence for a modulation of the eclipse depth over a period of 100 days which may be linked with solar-type magnetic cycles which give rise to long term photometric variations. The periodogram analysis for V795 Her detected the likely positive superhump period 0.1165d, however, neither the 0.10826d orbital period nor the prograde 1.53d disc precession period were seen. Here though we have found a variation in the periodogram power function at the positive superhump period, over a period of at least 120 days.

Extensive optical and near-infrared observations of the nearby, narrow-lined type Ic SN 2007gr: days 5 to 415

We present photometric and spectroscopic observations at optical and near-infrared wavelengths of the nearby type Ic supernova 2007gr. These represent the most extensive data-set to date of any supernova of this sub-type, with frequent coverage from shortly after discovery to more than one year post-explosion. We deduce a rise time to B-band maximum of 11.5 +/- 2.7 d. We find a peak B-band magnitude of M-B = -16.8, and light curves which are remarkably similar to the so-called "hypernova" SN 2002ap. In contrast, the spectra of SNe 2007gr and 2002ap show marked differences, not least in their respective expansion velocities. We attribute these differences primarily to the density profiles of their progenitor stars at the time of explosion i.e. a more compact star for SN 2007gr compared to SN 2002ap. From the quasi-bolometric light curve of SN 2007gr, we estimate that 0.076 +/- 0.010 M-circle dot of Ni-56 was produced in the explosion. Our near-infrared (IR) spectra clearly show the onset and disappearance of the first overtone of carbon monoxide (CO) between similar to 70 to 175 d relative to B-band maximum. The detection of the CO molecule implies that ionised He was not microscopically mixed within the carbon/oxygen layers. From the optical spectra, near-IR light curves, and colour evolution, we find no evidence for dust condensation in the ejecta out to about +400 d. Given the combination of unprecedented temporal coverage, and high signal-to-noise data, we suggest that SN 2007gr could be used as a template object for supernovae of this sub-class.

A Scalable and Programmable Modular Traffic Manager Architecture

A key issue in the design of next generation Internet routers and switches will be provision of traffic manager (TM) functionality in the datapaths of their high speed switching fabrics. A new architecture that allows dynamic deployment of different TM functions is presented. By considering the processing requirements of operations such as policing and congestion, queuing, shaping and scheduling, a solution has been derived that is scalable with a consistent programmable interface. Programmability is achieved using a function computation unit which determines the action (e.g. drop, queue, remark, forward) based on the packet attribute information and a memory storage part. Results of a Xilinx Virtex-5 FPGA reference design are presented.

The development of national in-group bias: English children's attributions of characteristics to English, American and German people

This study investigated the development of national in-group bias in 5-11-year-old children. Three hundred and seven English children were asked to attribute characteristics to their own national group either on its own or in conjunction with attributing characteristics to one of two national out-groups, either Americans or Germans. The importance which the children ascribed to their own national identity in relationship to their other social identities was also assessed. It was found that, with increasing age, there was an increase in the number of negative characteristics attributed to the national in-group, and an increase in the number of positive characteristics attributed to the two out-groups, the net result being an overall reduction in in-group bias across this age range. However, in-group favouritism was still exhibited at all ages. Greater importance was attributed to national identity with increasing age. However, the characteristics attributed to the English in-group did not vary as a function of the comparative out-group which was present while the attributions were being made. The presence of a comparative out-group also did not affect the importance that was ascribed to the national identity. These findings suggest that children are relatively insensitive to the prevailing comparative context when making judgments about national groups.

Testing the stability of the benefit transfer function for discrete choice contingent valuation data

This paper examines the stability of the benefit transfer function across 42 recreational forests in the British Isles. A working definition of reliable function transfer is Put forward, and a suitable statistical test is provided. A novel split sample method is used to test the sensitivity of the models' log-likelihood values to the removal of contingent valuation (CV) responses collected at individual forest sites, We find that a stable function improves Our measure of transfer reliability, but not by much. We conclude that, in empirical Studies on transferability, considerations of function stability are secondary to the availability and quality of site attribute data. Modellers' can study the advantages of transfer function stability vis-a-vis the value of additional information on recreation site attributes. (c) 2008 Elsevier GmbH. All rights reserved.

Children’s attributions of belief to humans and God: cross-cultural evidence

The capacity to attribute beliefs to others in order to understand action is one of the mainstays of human cognition. Yet it is debatable whether children attribute beliefs in the same way to all agents. In this paper, we present the results of a false-belief task concerning humans and God run with a sample of Maya children aged 4–7, and place them in the context of several psychological theories of cognitive development. Children were found to attribute beliefs in different ways to humans and God. The evidence also speaks to the debate concerning the universality and uniformity of the development of folk-psychological reasoning.