Detecting and sorting targeting peptides wtih neural networks and support vector machines

This paper presents a composite multi-layer classifier system for predicting the subcellular localization of proteins based on their amino acid sequence. The work is an extension of our previous predictor PProwler v1.1 which is itself built upon the series of predictors SignalP and TargetP. In this study we outline experiments conducted to improve the classifier design. The major improvement came from using Support Vector machines as a "smart gate" sorting the outputs of several different targeting peptide detection networks. Our final model (PProwler v1.2) gives MCC values of 0.873 for non-plant and 0.849 for plant proteins. The model improves upon the accuracy of our previous subcellular localization predictor (PProwler v1.1) by 2% for plant data (which represents 7.5% improvement upon TargetP).

Nocturnal activity in the green sea turtle alters daily profiles of melatonin and corticosterone

In nature, green turtles (Chelonia mydas) can exhibit nocturnal activity in addition to their typically diurnal activity cycle. We examined whether nocturnal activity in captive and free-living green turtles altered daily plasma profiles of melatonin (MEL) and corticosterone (CORT). In captivity, diurnally active green turtles expressed distinct diel cycles in MEL and CORT; a nocturnal rise was observed in MEL and a diurnal rise was observed in CORT. However, when induced to perform both low- and high-intensity nocturnal activity, captive green turtles exhibited a significant decrease in MEL, compared to inactive controls. In contrast, plasma CORT increased significantly with nocturnal activity, and further, the relative increase in CORT was correlated with the intensity of the nocturnal behavior. In free-living green turtles that performed nocturnal activity including: nesting, mate searching, and feeding/swimming behaviors, plasma profiles in MEL and CORT exhibited relatively little, or no, daily fluctuation. Our findings demonstrate that nocturnal activity in green turtles is often associated with MEL and CORT profiles that resemble those measured during the day. We speculate that these conspicuous changes in MEL and CORT during nocturnal activity could either support or promote behaviors that enable acquisition of transient resources important to the survival and reproductive success of green turtles. (C) 2002 Elsevier Science (USA).

Contrary effects of jasmonate treatment of two closely related plant species on attraction of and oviposition by a specialist herbivore

Elevated jasmonic acid (JA) concentrations in response to herbivory can induce wounded plants to produce defences against herbivores. In laboratory and field experiments we compared the effects of exogenous JA treatment to two closely related cabbage species on the host-searching and oviposition preference of the diamondback moth (DBM), Plutella xylostella. JA-treated Chinese cabbage (Brassica campestris) was less attractive than untreated Chinese cabbage to ovipositing DBM, while JA-treatment of common cabbage (B. oleracea) made plants more attractive than untreated controls for oviposition by this insect. Similar effects were observed when plants of the two species were damaged by DBM larvae. In the absence of insect-feeding, or JA application, Chinese cabbage is much more attractive to DBM than common cabbage. Inducible resistance therefore appears to occur in a more susceptible plant and induced susceptibility appears to occur in a more resistant plant, suggesting a possible balance mechanism between constitutive and inducible defences to a specialist herbivore.

Eradicating feral cats to protect Galapagos Land Iguanas: methods and strategies

A three-year programme to eradicate Feral Cats Felis catus from the island of Baltra in the Galapagos archipelago achieved good results by Initially poisoning with sodium monofluoroacetate (compound 1080) then trapping or shooting the remaining cats. The poisoning campaign removed 90% of the cats, its success being attributable to pre-baiting with unpolsoned baits to accustom cats to eating baits and placing enough baits to ensure that all cats encountered several baits within their home range. This, together with the use of metaclopromide (Pileran) as an anti-emetic, overcame a problem associated with poor retention of 1080 in thawed fish baits that limited the dose available to 1 mg 1080lbait, a quality Insufficient to kill large cats. Removal of the remaining cats was delayed by a weather-Induced irruption of Black Rats Rattus rattus and House Mice Mus musculus that enabled recruitment of kittens in 2002, but made cats more susceptible to trapping and shooting in 2003 when rodent populations collapsed. Since July 2003 no sign of a cat has been detected on Baltra despite extensive searching and monitoring throughout 2004. As cat abundance has decreased there have been more locally-bred Juvenile iguanas (Conolophus subcristatus) seen during annual censuses. However, such recruitment may reflect the increasing maturity and higher fecundity of iguanas repatriated from 1991 onwards rather than being a direct result of reduced cat predation alone. More time is necessary to determine the benefits of reduced cat predation on the Iguana population.

Male reproductive tactics and female choice in the solitary, promiscuous bridled nailtail wallaby (Onychogalea fraenata)

Several behavioral studies of large, gregarious, and sexually dimorphic macropods have shown that males form dominance hierarchies and large males have the highest reproductive success. The bridled nailtail wallaby (Onychogalea fraenata) is a smaller and strongly sexually dimorphic macropod, but is also highly solitary and males do not form dominance hierarchies that are maintained temporally or spatially. Genetic studies of paternity have shown that large males are the most reproductively successful and only one-quarter of males sire offspring at any one time. The aim of this study was to investigate the tactics that males adopt to secure access to females at the time of estrus and to investigate whether females can influence which males have access to them. This study was conducted using 2 wild, free-ranging populations of bridled nailtail wallabies. Females in estrus were located and observed. and the total number of males present, the relative weight rank of each mate, and interactions between individuals were recorded. Females showed a preference for large males and incited male-male competition when the group of males present was large. Unlike other dimorphic macropods, fights among males were rare and were restricted to males of similar size. Large males gained access to females by guarding and following them closely and threatening other males who attempted to gain access. Smaller males spent less time with females, suggesting that small males may leave multimale groups in an attempt to locate unguarded females. Given the solitary nature of this species and the lack of a stable dominance hierarchy to influence male reproductive success. mate searching and mate guarding may be important male reproductive tactics in this species.

A synchronous multimedia annotation system for secure collaboratories

In this paper, we describe the Vannotea system - an application designed to enable collaborating groups to discuss and annotate collections of high quality images, video, audio or 3D objects. The system has been designed specifically to capture and share scholarly discourse and annotations about multimedia research data by teams of trusted colleagues within a research or academic environment. As such, it provides: authenticated access to a web browser search interface for discovering and retrieving media objects; a media replay window that can incorporate a variety of embedded plug-ins to render different scientific media formats; an annotation authoring, editing, searching and browsing tool; and session logging and replay capabilities. Annotations are personal remarks, interpretations, questions or references that can be attached to whole files, segments or regions. Vannotea enables annotations to be attached either synchronously (using jabber message passing and audio/video conferencing) or asynchronously and stand-alone. The annotations are stored on an Annotea server, extended for multimedia content. Their access, retrieval and re-use is controlled via Shibboleth identity management and XACML access policies.

Experience-induced preference for oviposition repellents derived from a non-host plant by a specialist herbivore

Foraging adults of phytophagous insects are attracted by host-plant volatiles and supposedly repelled by volatiles from non-host plants. In behavioural control of pest insects, chemicals derived from non-host plants applied to crops are expected to repel searching adults and thereby reduce egg laying. How experience by searching adults of non-host volatiles affects their subsequent searching and oviposition behaviour has been rarely tested. In laboratory experiments, we examined the effect of experience of a non-host-plant extract on the oviposition behaviour of the diamondback moth (DBM), Plutella xylostella, a specialist herbivore of cruciferous plants. Naive ovipositing DBM females were repelled by an extract of dried leaves of Chrysanthemum morifolium, a non-host plant of DBM, but experienced females were not repelled. Instead they were attracted by host plants treated with the non-host-plant extract and laid a higher proportion of eggs on treated than on untreated host plants. Such behavioural changes induced by experience could lead to host-plant range expansion in phytophagous insects and play an important role in determining outcome for pest management of some behavioural manipulation methods.

Contextual binding of p120ctn to E-cadherin at the basolateral plasma membrane in polarized epithelia

E-cadherin-catenin complexes mediate cell-cell adhesion on the basolateral membrane of epithelial cells. The cytoplasmic tail of E-cadherin supports multiple protein interactions, including binding of beta-catenin at the C terminus and of p120(ctn) to the juxtamembrane domain. The temporal assembly and polarized trafficking of the complex or its individual components to the basolateral membrane are not fully understood. In Madin-Darby canine kidney cells at steady state and after treatment with cycloheximide or temperature blocks, E-cadherin and beta-catenin localized to the Golgi complex, but p120ctn was found only at the basolateral plasma membrane. We previously identified a dileucine sorting motif (Leu(586)-Leu(587), termed S1) in the juxtamembrane domain of E-cadherin and now show that it is required to target full-length E-cadherin to the basolateral membrane. Removal of S1 resulted in missorting of E-cadherin mutants (EcadDeltaS1) to the apical membrane; beta-catenin was simultaneously missorted and appeared at the apical membrane. p120(ctn) was not mistargeted with EcadDeltaS1, but could be recruited to the E-cadherin-catenin complex only at the basolateral membrane. These findings help define the temporal assembly and sorting of the E-cadherin-catenin complex and show that membrane recruitment of p120(ctn) in polarized cells is contextual and confined to the basolateral membrane.

Family centred care: a review of qualitative studies

Aim. To review systematically qualitative studies, which were found during a literature search for a Cochrane systematic review of the use of family centred care in children's hospitals. Background. Family centred care has become a cornerstone of paediatric practice, however, its effectiveness is not known. No single definition exists, rather a list of elements that constitute family centred care. However, it is recognized to involve the parents in care planning for a child in health services. A new definition is presented here. Methods. The papers were found in wide range of databases, by hand searching and by contacting the authors where necessary, using terms given in detail in the protocol in the Cochrane Library, in 2004. Qualitative studies could not be used for statistical analysis, but are still important to the review and so are described separately in this paper. Results. Negotiation between staff and families, perceptions held by both parents and staff roles influenced the delivery of family centred care. A sub-theme of cost of family centred care to families and staffs was discovered and this included both financial and emotional costs. Conclusion. Further research is needed to generate evidence about family centred care in situations arising from modern models of care in which family centred care is thought to be an inherent part, but which leave families with the care of sick children with little or no support. Relevance to clinical practice. Family centred care is said to be used widely in practice. More research is needed to ensure that is it being implemented correctly.

Reflective web interface agent

Web interface agent is used with web browsers to assist users in searching and interactions with the WWW. It is used for a variety of purposes, such as web-enabled remote control, web interactive visualization, and e-commerce activities. User may be aware or unaware of its existence. The intelligence of interface agent consists in its capability of learning and decision-making in performing interactive functions on behalf of a user. However, since web is an open system environment, the reasoning mechanism in an agent should be able to adapt changes and make decisions on exceptional situations, and therefore use meta knowledge. This paper proposes a framework of Reflective Web Interface Agent (RWIA) that is to provide causal connections between the application interfaces and the knowledge model of the interface agent. A prototype is also implemented for the purpose of demonstration.

Using the Amazon metric to construct an image database based on what people do, not what they say

Current image database metadata schemas require users to adopt a specific text-based vocabulary. Text-based metadata is good for searching but not for browsing. Existing image-based search facilities, on the other hand, are highly specialised and so suffer similar problems. Wexelblat's semantic dimensional spatial visualisation schemas go some way towards addressing this problem by making both searching and browsing more accessible to the user in a single interface. But the question of how and what initial metadata to enter a database remains. Different people see different things in an image and will organise a collection in equally diverse ways. However, we can find some similarity across groups of users regardless of their reasoning. For example, a search on Amazon.com returns other products also, based on an averaging of how users navigate the database. In this paper, we report on applying this concept to a set of images for which we have visualised them using traditional methods and the Amazon.com method. We report on the findings of this comparative investigation in a case study setting involving a group of randomly selected participants. We conclude with the recommendation that in combination, the traditional and averaging methods would provide an enhancement to current database visualisation, searching, and browsing facilities.

The Modified Card Sorting Test: Test-retest stability and relationships with demographic variables in a healthy older adult sample

Objectives. To investigate the test-retest stability of a standardized version of Nelson's (1976) Modified Card Sorting Test (MCST) and its relationships with demographic variables in a sample of healthy older adults. Design. A standard card order and administration were devised for the MCST and administered to participants at an initial assessment, and again at a second session conducted a minimum of six months later in order to examine its test-retest stability. Participants were also administered the WAIS-R at initial assessment in order to provide a measure of psychometric intelligence. Methods. Thirty-six (24 female, 12 male) healthy older adults aged 52 to 77 years with mean education 12.42 years (SD = 3.53) completed the MCST on two occasions approximately 7.5 months (SD = 1.61) apart. Stability coefficients and test-retest differences were calculated for the range of scores. The effect of gender on MCST performance was examined. Correlations between MCST scores and age, education and WAIS-R IQs were also determined. Results. Stability coefficients ranged from .26 for the percent perseverative errors measure to .49 for the failure to maintain set measure. Several measures were significantly correlated with age, education and WAIS-R IQs, although no effect of gender on MCST performance was found. Conclusions. None of the stability coefficients reached the level required for clinical decision making. The results indicate that participants' age, education, and intelligence need to be considered when interpreting MCST performance. Normative studies of MCST performance as well as further studies with patients with executive dysfunction are needed.

Searching behaviour and diet of Oystercatcher Haematopus ostralegus pairs feeding in their territories

Search path, searching behaviour and diet of pairs of Oystercatchers feeding in mudflat territories were studied during spring. females ate Nereis, Mya, small unidentified prey, probably Corophium, and a few Macoma, whereas males primarily ate Macoma. Even when female and male foraged in the same site, they often caught different prey. The combination of 'The Search-rate/Detection Model' (Gendron & Staddon 1983) and 'The Harvestable Prey Model' (Zwarts & Wanink 1993) provide the theoretical framework in which to explain these differences in diet. Macoma are thought to be more cryptic than Nereis, Mya and Corophium. Therefore females, while searching at a faster rate than their respective mates, caught far fewer cryptic prey, but a greater number of more conspicuous prey than their mates. On the basis of distances moved before and after capturing prey, males exhibited area-restricted searching for Macoma and Corophium. In contrast, females did not exhibit any area-restricted searching. it is suggested that the distribution of Macoma and Corophium available to males searching slowly was more clumped than that of these two prey species available to females searching more quickly.