Reducing variability of crossvalidation for smoothing-parameter choice

One of the attractions of crossvalidation, as a tool for smoothing-parameterchoice, is its applicability to a wide variety of estimatortypes and contexts. However, its detractors comment adverselyon the relatively high variance of crossvalidatory smoothingparameters, noting that this compromises the performance ofthe estimators in which those parameters are used. We show thatthe variability can be reduced simply, significantly and reliablyby employing bootstrap aggregation or bagging. We establishthat in theory, when bagging is implemented using an adaptivelychosen resample size, the variability of crossvalidation canbe reduced by an order of magnitude. However, it is arguablymore attractive to use a simpler approach, based for exampleon half-sample bagging, which can reduce variability by approximately50%.     

The in vitro anti-platelet,antioxidant and cellular immunity activity of <Emphasis Type="Italic">Phellinus gilvus</Emphasis> fractional extracts

The in vitro anti-platelet and antioxidant activities of various solvent extracts from Phellinus gilvus (PG), and the effects of hot water extract from PG (PGW) on murine cellular immunity were investigated. Chloroform extract (CE), methanol extract (ME) and butanol extract (BE) from PG could significantly inhibit platelet aggregation induced by thrombin. Ethyl acetate extract (EAE), BE, ME from PG had significant 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activity compared with the control, and the EAE showed the highest effect with IC₅₀ values of 13.34 μg/ml, which is higher than that of ascorbic acid (40 μg/ml). In addition, EAE displayed the inhibition of xanthine oxidase (XO) activity with IC₅₀ value of 2.45 μg/ml. As to the cellular immunity activity, PGW could enhance both the lipopolysaccharide (LPS)-induced B lymphocyte proliferation and concanavalin A (Con A)-induced T lymphocyte proliferation in vitro. The phagocytosis of both peritoneal macrophages and RAW264.7 macrophage cells were also increased by the addition of PGW. Moreover, PGW was found to inhibit the nitric oxide (NO) production of RAW264.7 macrophages induced by LPS in a concentration-dependant manner.     

Frequency-dependent conspecific attraction to food patches

In many ecological situations, resources are difficult to find but become more apparent to nearby searchers after one of their numbers discovers and begins to exploit them. If the discoverer cannot monopolize the resources, then others may benefit from joining the discoverer and sharing their discovery. Existing theories for this type of conspecific attraction have often used very simple rules for how the decision to join a discovered resource patch should be influenced by the number of individuals already exploiting that patch. We use a mechanistic, spatially explicit model to demonstrate that individuals should not necessarily simply join patches more often as the number of individuals exploiting the patch increases, because those patches are likely to be exhausted soon or joining them will intensify future local competition. Furthermore, we show that this decision should be sensitive to the nature of the resource patches, with individuals being more responsive to discoveries in general and more tolerant of larger numbers of existing exploiters on a patch when patches are resource-rich and challenging to locate alone. As such, we argue that this greater focus on underlying joining mechanisms suggests that conspecific attraction is a more sophisticated and flexible tactic than currently appreciated.     

Influence of denatured and intermediate states of folding on protein aggregation

We simulate the aggregation thermodynamics and kinetics of proteins L and G, each of which self-assembles to the same alpha/beta [corrected] topology through distinct folding mechanisms. We find that the aggregation kinetics of both proteins at an experimentally relevant concentration exhibit both fast and slow aggregation pathways, although a greater proportion of protein G aggregation events are slow relative to those of found for protein L. These kinetic differences are correlated with the amount and distribution of intrachain contacts formed in the denatured state ensemble (DSE), or an intermediate state ensemble (ISE) if it exists, as well as the folding timescales of the two proteins. Protein G aggregates more slowly than protein L due to its rapidly formed folding intermediate, which exhibits native intrachain contacts spread across the protein, suggesting that certain early folding intermediates may be selected for by evolution due to their protective role against unwanted aggregation. Protein L shows only localized native structure in the DSE with timescales of folding that are commensurate with the aggregation timescale, leaving it vulnerable to domain swapping or nonnative interactions with other chains that increase the aggregation rate. Folding experiments that characterize the structural signatures of the DSE, ISE, or the transition state ensemble (TSE) under nonaggregating conditions should be able to predict regions where interchain contacts will be made in the aggregate, and to predict slower aggregation rates for proteins with contacts that are dispersed across the fold. Since proteins L and G can both form amyloid fibrils, this work also provides mechanistic and structural insight into the formation of prefibrillar species.     

Delimiting species: comparing methods for Mendelian characters using lizards of the Sceloporus grammicus (Squamata: Phrynosomatidae) complex

Species form the fundamental units of analysis in many areas of biology and, therefore, rigorous delimitation of this unit is important to a broad array of researchers. Recently, many new empirical methods have been proposed to delimit species in nature, and a large literature exists on the theoretical merit and superiority of each method. However, few empirical studies actually compare the results of these methods applied in the same study system. We used a large allozyme and chromosome dataset to apply a number of genetic-distance, character-based, and tree-based methods to a well-studied, data-rich system: the Sceloporus grammicus lizard complex of central Mexico. We hypothesized species boundaries under a general lineage or evolutionary species conceptual framework in an a priori fashion using mapped restriction-site data (mitochondrial DNA and nuclear rDNA), allozymes, and morphology. We then compared the ability of different methods to recover the "hypothesized evolutionary species" (HES). Highton's genetic-distance method and a tree-based method consistently recovered all four HES, although sometimes with weak support. With two exceptions, other methods recovered the same HES, but additional groups were weakly delimited and nested within the HES. Given the apparent recent divergence of some of the chromosome races and distinct populations in this complex, these are encouraging results. We emphasize the value of specifying testable criteria as clearly as possible and testing these with methods that make use of different properties of a single dataset.     

Interaction of pheromones during food exploitation by the termite Schedorhinotermes lamanianus

Abstract. Chemical signals from secretions of different exocrine glands modulate a variety of behavioural patterns in termite societies. These signals have multiple functions and may be interactive. During food exploitation workers of the African termite Schedorhinotermes lamanianus (Isoptera: Rhinotermitidae) employ, on foraging trails, the secretion from the sternal gland both for orientation and recruitment to a food source. The secretion from the labial gland, released onto the food by gnawing termites, stimulates additional workers to gnaw at the same site, thereby forming aggregations of gnawing termites. An interaction between these two pheromones during food exploitation is demonstrated for the first time. The volatile signal from the sternal gland inhibits in a dose-dependent manner the non-volatile, highly persistent, signal from the labial gland. The development of gnawing aggregations is inhibited and established ones are dissolved. Behavioural evidence for the perception of both the volatile signal from the sternal gland by olfactory neurones and of the non-volatile signal from the labial gland by gustatory neurones on the antennae is given. The interaction of the two pheromones as a basis for the development of distinct commuting and gnawing zones on the food source, and as a means for a dynamic regulation of food exploitation, is discussed.     

Field monitoring of onion maggot (Delia antiqua) fly through improved trapping

Onion maggot (Delia antiqua) is an economically important pest of Allium crops in temperate regions throughout the world. Management of this pest is necessary to achieve economic returns and depends on insecticide regimes and cultural management. Current cultural management especially altering planting date, field location and crop rotation depend on monitoring. We evaluated the effect of shape, size, colour and chemical attractants on trap catch of field populations of adult D. antiqua flies in upstate New York. White, large diameter, spherical traps in conjunction with Delia Lure attractant performed the best in attracting and catching D. antiqua adults. These results suggest an improved means of attracting and capturing D. antiqua populations which could be useful in monitoring efforts and development of attract and kill strategies for pest control.     

Parasitism and decreased response to sex pheromones in malePeriplaneta americana (Dictyoptera: Blattidae)

Parasites are known to alter the behavior of their hosts, but little is known about their effects on responses to sexual stimuli. Periplaneta americanainfected with the acanthocephalan Moniliformis moniliformiswere compared to uninfected animals in their behavioral and electroantennogram responses to a synthetic P. americanapheromone component, periplanone-B, and a pheromone mimic, bornyl acetate. In a t-maze there was no significant difference between infected animals' responses to periplanone-B and a random binomial distribution; the responses of uninfected animals were significantly nonrandom. The electroan-tennogram responses of infected and uninfected animals to bornyl acetate or periplanone-B did not differ significantly, however, indicating that the alteration probably does not occur at the peripheral level but at a central nervous system level.     

Sexual deception in a cannibalistic mating system? Testing the Femme Fatale hypothesis

Animal communication theory holds that in order to be evolutionarily stable, signals must be honest on average, but significant dishonesty (i.e. deception) by a subset of the population may also evolve. A typical praying mantid mating system involves active mate searching by males, which is guided by airborne sex pheromones in most species for which mate-searching cues have been studied. The Femme Fatale hypothesis suggests that female mantids may be selected to exploit conspecific males as prey if they benefit nutritionally from cannibalism. Such a benefit exists in the false garden mantid Pseudomantis albofimbriata—females use the resources gained from male consumption to significantly increase their body condition and reproductive output. This study aimed to examine the potential for chemical deception among the subset of females most likely to benefit from cannibalism (poorly fed females). Females were placed into one of four feeding treatments (‘Very Poor’, ‘Poor’, ‘Medium’ and ‘Good’), and males were given the opportunity to choose between visually obscured females in each of the treatments. Female body condition and fecundity varied linearly with food quantity; however, female attractiveness did not. That is, Very Poor females attracted significantly more males than any of the other female treatments, even though these females were in significantly poorer condition, less fecund (in this study) and more likely to cannibalise (in a previous study). In addition, there was a positive correlation between fecundity and attractiveness if Very Poor females were removed from the analysis, suggesting an inherently honest signalling system with a subset of dishonest individuals. This is the first empirical study to provide evidence of sexual deception via chemical cues, and the first to provide support for the Femme Fatale hypothesis.     

Lysozyme inactivation and aggregation in stirred-reactor

Mechanisms of enzyme inactivation and aggregation are still poorly understood. In this work, we are considering the characterisation of both inactivation and aggregation in stirred tank reactor, with lysozyme as the model enzyme.

The inactivation kinetics are first order. For stirring speeds in the range of 0–700 rpm, the kinetic constant is found to be proportional to the power brought by the impeller. It suggests that inactivation depends on collisions between enzyme molecules. Efficient collisions between native and inactive molecules induce native molecules to turn into inactive molecules and lead to lysozyme aggregation.

During inactivation, enzymes are found to aggregate as shown by light scattering measurements. The structure of aggregates was studied on samples treated for chemical denaturation and reduction. The aggregates are supramolecular edifices, mainly made up of inactivated enzymes linked by weak forces. But aggregates are also made up of dimers and trimers of lysozyme, linked by disulfide bridges. Dimers and trimers are 18% and 5%, respectively, of the total amount of lysozyme aggregates.

Whatever the stage of aggregate formation and the initial enzyme concentration are, these aggregates are irreversibly inactivated. Enzyme activity is definitely lost even if stirring is stopped and/or temperature decreased.

This study points out the importance of hydrodynamics in bioreactors and highlights the nature of the aggregates resulting from the interactions between native and inactive enzymes.