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PubMed2004

Identification of the structural requirements for mutagenicity by incorporating molecular flexibility and metabolic activation of chemicals I: TA100 model.

Traditional attempts to model genotoxicity data have been limited to congeneric data sets, primarily because the mechanism of action was ignored, and frequently, the chemicals required metabolism to the active species. In this exercise, the COmmon REactivity PAtterns (COREPA) approach was used to delineate the structural requirements for eliciting mutagenicity in terms of ranges of descriptors associated with three-dimensional molecular structures. The database used to build the mutagenicity model includes 1196 structurally diverse chemicals tested in the Ames assay by the National Toxicology Program. This manuscript describes the development of the TA100 model that predicts the results of mutagenicity testing using only the Ames TA100 strain. The TA100 model was developed using 148 chemicals that tested positive in TA100 strain without rat liver enzymes (S-9) and 188 chemicals that tested positive in TA100 strain with rat liver enzymes. A decision tree was developed by first comparing the reactivity profile of chemicals that were positive in TA100 without rat liver enzymes to the reactivity profile of the remaining 1048 chemicals. This approach correctly identified 82% of the primary acting mutagens and 94% of the nonmutagens in the training set. The 188 chemicals in the training set that are positive only in the presence of metabolic activation would pass through the decision tree as negative. The next step was to identify the chemicals that are positive only in the presence of metabolic activation. To accomplish this, a series of hierarchically ordered metabolic transformations were used to develop an S-9 metabolism simulator that was applied to each of the 1048 chemicals. The potential metabolites were then screened through the decision tree to identify reactive mutagens. This model correctly identified 77% of the metabolically activated chemicals in a training set. A computer system that applies the COREPA models and predicts mutagenicity of chemicals, including their metabolic activation, was developed. Each prediction is accompanied by a probabilistic estimate of the chemical being in the structural domain covered by the training set.

Biotransformation↗

PubMed2004

Performance of an iterated T-HMM for homology detection.

MOTIVATION: Much information about new protein sequences is derived from identifying homologous proteins. Such tasks are difficult when the evolutionary relationships are distant. Some modern methods achieve better results by building a model of a set of related sequences, and then identifying new proteins that fit the model. A further advance was the development of iterative methods that refine the model as more homologs are discovered. These methods are generally limited by ad hoc methods of sequence weighting, neglect of underlying evolutionary relationships and the representation of the set with a single one-size-fits-all model. These limitations are avoided through the use of a Tree hidden Markov model (T-HMM) approach. Our previous work described how a non-iterative version of the T-HMM method could identify distant homologs with superior performance compared with other non-iterated approaches, and described how this method was particularly appropriate for being implemented as an iterative algorithm. RESULTS: We describe an iterative version of the T-HMM algorithm, and evaluate its performance for the detection of distant homologs. Significant improvement over other commonly used methods is found. AVAILABILITY: The software (C++, Perl) is available from the corresponding author.

Algorithms↗

PubMed2005

Prediction of protein-protein interactions using random decision forest framework.

MOTIVATION: Protein interactions are of biological interest because they orchestrate a number of cellular processes such as metabolic pathways and immunological recognition. Domains are the building blocks of proteins; therefore, proteins are assumed to interact as a result of their interacting domains. Many domain-based models for protein interaction prediction have been developed, and preliminary results have demonstrated their feasibility. Most of the existing domain-based methods, however, consider only single-domain pairs (one domain from one protein) and assume independence between domain-domain interactions. RESULTS: In this paper, we introduce a domain-based random forest of decision trees to infer protein interactions. Our proposed method is capable of exploring all possible domain interactions and making predictions based on all the protein domains. Experimental results on Saccharomyces cerevisiae dataset demonstrate that our approach can predict protein-protein interactions with higher sensitivity (79.78%) and specificity (64.38%) compared with that of the maximum likelihood approach. Furthermore, our model can be used to infer interactions not only for single-domain pairs but also for multiple domain pairs.

Computational Biology↗

PubMed2006

The use of non-wood forest products by migrants in a new settlement: experiences of a Visayan community in Palawan, Philippines.

Migrants are often constrained by a lack of knowledge regarding their new environment and require new skills for their livelihood. In Palawan, some of these necessary skills and knowledge are related to the collection and use of non-wood forest products (NWFPs), many of which the migrants were previously not familiar with. The predominantly Visayan migrants have been successful in familiarizing themselves with the NWFPs in the surrounding forests, with assistance from some of the local indigenous people, in this case the Tagbanua, and from previous migrant settlers. The NWFPs they know about and the extent of use are presented. Currently, except for almaciga (Agathis philippinensis Warb.) resin and house-building materials, NWFPs are considered as supplements to agricultural products, not as main source of either subsistence or income.

Adult↗

PubMedDate not supplied

Structure-based methods for the prediction of the dominant P450 enzyme in human drug biotransformation: consideration of CYP3A4, CYP2C9, CYP2D6.

Metabolic drug-drug interactions are receiving more and more attention from the in silico community. Early prediction of such interactions would not only improve drug safety but also contribute to make drug design more predictable and rational. The aim of this study was to build a simple and interpretable model for the determination of the P450 enzyme predominantly responsible for a drug's metabolism. The P450 enzymes taken into consideration were CYP3A4, CYP2D6 and CYP2C9. Physico-chemical descriptors and structural descriptors for 96 currently marketed drugs were submitted to statistical analysis using the formal inference-based recursive modelling (FIRM) method, a form of recursive partitioning. Generally accepted knowledge on metabolism by these enzymes was also used to construct a hierarchical decision tree. Robust methods of variable selection using recursive partitioning were utilised. The descriptive ability of the resulting hierarchical model is very satisfactory, with 94% of the compounds correctly classified.

Aryl Hydrocarbon Hydroxylases↗

PubMedDate not supplied

[Modular evolution of Bsp-repeats: formation of subrepeats and monomers preceded the divergence of four species of Canidae].

Determination of two nucleotide sequences of satellite-like DNA (Bsp-repeats) segments from the raccoon-like dog genome and analysis of these and three other homologous sequences from distantly related genomes of Canidae (silver fox, domestic dog, and gray fox) show that all these DNA fragments consist of five types of subrepeats (A, B, C, D, and E) and two types of monomers-ACB and ACED. Raccoon-like dog repeated segment of 1620 bp is composed of both type of monomers: ACBACED. Different monomers of the same type could be distinguished by subtypes of subrepeats. Building of a cladogram of 18 subrepeats and analysis of the structures of monomers and higher-order repeated units allowed us to reveal probable evolution events which have determined the hierarchical order in Bsp-repeat organization. Approximate periods of time for these evolution events were calculated from the number of substitutions per branch. Five main types of subrepeats and two types of monomers have been generated and propagated through several steps before divergence of the main phylogenetic trees of Canidae. Combinatorial variability appears to play a fundamental role in forming the hierarchical layers in Bsp-repeats structure.

Animals↗

PubMed2005

Forest and farmland conservation effects of Oregon's (USA) land-use planning program.

Oregon's land-use planning program is often cited as an exemplary approach to forest and farmland conservation, but analyses of its effectiveness are limited. This article examines Oregon's land-use planning program using detailed spatial data describing building densities in western Oregon. An empirical model describes changes in building densities on forest and agricultural lands from 1974 to 1994, as a function of a gravity index of land's commuting distance to cities of various sizes, topographic characteristics, and zoning adopted under Oregon's land-use planning program. The effectiveness of Oregon's land-use planning program is evaluated based on the statistical significance of zoning variables and by computing estimated areas of forest and agricultural lands falling into undeveloped, low-density developed, and developed building density categories, with and without land-use zoning in effect. Results suggest that Oregon's land-use planning program has provided a measurable degree of protection to forest and agricultural lands since its implementation.

Agriculture↗

PubMedDate not supplied

Communicating news of patients' deaths to unrelated stem cell donors.

AIM: To identify the most appropriate method of breaking news of a patient's death to unrelated stem cell donors, and to establish best practice guidelines based on the findings. METHOD: In this retrospective study, 100 unrelated stem cell donors from the Welsh Bone Marrow Donor Registry were interviewed regarding their experiences of receiving news of a patient's death. results were analysed by counting responses to the interview schedule, and identifying common themes from the open comments. RESULTS: Of the 100 participants, 78 had been informed of the patient's death by letter and 22 by telephone with the option of a follow-up letter. Overall, 61 per cent (n=61) of donors interviewed preferred to be contacted by telephone, 25 per cent (n=25) by letter and 13 per cent (n=13) by face-to-face contact at a visit. CONCLUSION: There is no easy way to break bad news, and each individual responds to grief in a unique way. By building up a trusting relationship with the donor, the healthcare professional can assess the individual to ascertain which method of receiving news of a patient's death would be most appropriate.

Adaptation, Psychological↗

PubMed2006

Landscape history, fragmentation, and patch occupancy: models for a forest bird with limited dispersal.

We developed and tested patch occupancy models for an endemic understory bird with limited dispersal ability, the Chucao Tapaculo (Scelorchilus rubecula), in two South American temperate rain forest landscapes that differed in levels and duration of forest loss. We assessed cover changes since 1961 in each landscape and surveyed patches for Chucao Tapaculo occupancy. We then developed incidence-based predictive models independently for each landscape and tested each model reciprocally in the alternative study area. We thereby assessed the domain of model applicability and identified those predictor variables with general effects and those that varied between the two landscapes. The two models were consistent regarding variable selection, and predictive accuracy of each model was high in the landscape where training data were collected. However, the models differed substantially in the magnitudes of effects related to patch size, with larger unoccupied patches observed in the landscape with the more advanced stage of fragmentation. Due to this discrepancy, each model performed poorly when applied to the alternative landscape, potentially reflecting the contrasting stages of habitat loss. Although it was impossible to dissociate effects of level and duration of forest loss, we viewed the landscapes as representing two extremes along a continuum of fragmentation, providing insights into potential trajectories for portions of the biome where deforestation is occurring. Further, our data suggest that static equilibrium models developed from distribution patterns in recently fragmented landscapes may overestimate persistence when used as a forecasting tool, or when extrapolated to alternative landscapes where fragmentation is more advanced. Thus, we suggest that landscapes used as standards for model building should be selected with caution. We recommend that distribution patterns be obtained from landscapes where fragmentation is advanced, preferably with histories of fragmentation long enough that time-delayed extinctions already would have occurred.

Animals↗

PubMed2005

Effect of urban vegetation on psychological restorativeness.

The present study analyzes the contribution which natural elements in the city make to restorativeness, that is, the potential of certain environments to help recover the capacity to focus attention, reduce mental fatigue, and reduce stress. We presented photographs of 12 urban scenes (streets, industrial areas, and buildings) with and without vegetation to 214 university students, divided into 12 groups who then completed the Perceived Restorativeness Scale. The results support the hypothesis, i.e., urban environments with natural elements yield higher restorativeness than urban environments lacking these.

Adolescent↗

PubMed2006

Expanding our conceptualization of program implementation: lessons from the genealogy of a school-based nutrition program.

This work presents a theoretical framework in which health promotion and health education program implementation can be conceived as an open dynamic system. By tracing the evolution of an elementary school-based nutrition program from its conception to its recent form, we construct a program genealogy. Data were derived from two interviews and three historical documents from which historical events were identified and reconstructed in the form of a tree analogy. Data analysis ensued using concepts from the actor-network theory about social innovation. These concepts identified social and technical program attributes and situated them within a process which evolved over time, thus permitting the program's genealogy to appear. The genealogy was found to be influenced by the ways in which the involved actors interpreted the issue of food security, namely, as a professional issue, with a nutrition education response and as a social issue, with a community-building response. The interaction between the interests of the actors and the technical components of the program resulted in three temporal program iterations. The results highlight the important role played by the involved actors during program implementation and suggest the need to take these interests into consideration during all phases of program planning.

Community Networks↗

PubMedDate not supplied

The feasibility of axiomatically-based expert systems.

We distinguish axiomatically-based expert systems, whose design and implementation are guided by one or more axiomatically-based theories of decision-making (e.g., decision theory, Bayesian probability theory, maximum entropy theory), from traditional expert systems. An analysis of the knowledge acquisition and computational needs of axiomatically-based expert systems is presented. An explicit quantitative comparison is made between the actual knowledge acquisition effort required to build an existing expert system, and the effort that would be required to build an analogous axiomatically-based advice system. The costs and benefits of the axiomatic approach are discussed. The analysis suggests that the small additional cost of knowledge acquisition for the axiomatic approach are outweighed by the long-term benefits this approach provides.

Computer Simulation↗

PubMed2001

Efficiency of parallel direct optimization.

Tremendous progress has been made at the level of sequential computation in phylogenetics. However, little attention has been paid to parallel computation. Parallel computing is particularly suited to phylogenetics because of the many ways large computational problems can be broken into parts that can be analyzed concurrently. In this paper, we investigate the scaling factors and efficiency of random addition and tree refinement strategies using the direct optimization software, POY, on a small (10 slave processors) and a large (256 slave processors) cluster of networked PCs running LINUX. These algorithms were tested on several data sets composed of DNA and morphology ranging from 40 to 500 taxa. Various algorithms in POY show fundamentally different properties within and between clusters. All algorithms are efficient on the small cluster for the 40-taxon data set. On the large cluster, multibuilding exhibits excellent parallel efficiency, whereas parallel building is inefficient. These results are independent of data set size. Branch swapping in parallel shows excellent speed-up for 16 slave processors on the large cluster. However, there is no appreciable speed-up for branch swapping with the further addition of slave processors (>16). This result is independent of data set size. Ratcheting in parallel is efficient with the addition of up to 32 processors in the large cluster. This result is independent of data set size.

Algorithms↗

PubMed2005

PAP IB, a new member of the Reg gene family: cloning, expression, structural properties, and evolution by gene duplication.

Reg proteins are expressed in various organs and are involved in cancers and neurodegenerative diseases. They display a typical C-type lectin-like domain but possess additional highly conserved amino acids. By studying human databases and Expressed Sequence Tags library, we identified a new member called PAP IB. Using probabilistic approaches, we established a phylogenetic tree of eighteen Reg proteins. The dendogram showed that they constitute a superfamily composed of three distinct families (FI to FIII) of paralogues that resulted from duplication. We therefore focused on two proteins, REG Ialpha and PAP IB, belonging to the more closely related FI and FII families, respectively. REG Ialpha and PAP IB share 50% sequence identity. After cloning PAP IB, however, we found that it was expressed almost only in pancreas, unlike REG Ialpha, whose expression is ubiquitous. In addition, by building a model of the structure of PAP IB based on the X-ray structure of REG Ialpha, we observed that the two proteins displayed distinctive surface charge distribution, which may lead to different ligands binding. In spite of their common fold that should result in closely related functions, REG Ialpha and PAP IB are a good example of duplication and divergence, probably with the acquisition of new functions, thus participating in the evolution of the protein repertoire.

Amino Acid Sequence↗

PubMed2006

FlexNovo: structure-based searching in large fragment spaces.

We present a new molecular design program, FlexNovo, for structure-based searching within large fragment spaces following a sequential growth strategy. The fragment spaces consist of several thousands of chemical fragments and a corresponding set of rules that specify how the fragments can be connected. FlexNovo is based on the FlexX molecular docking software and makes use of its incremental construction algorithm and the underlying chemical models. Interaction energies are calculated by using standard scoring functions. Several placement geometry, physicochemical property (drug-likeness), and diversity filter criteria are directly integrated into the "build-up" process. FlexNovo has been used to design potential inhibitors for four targets of pharmaceutical interest (dihydrofolate reductase, cyclin-dependant kinase 2, cyclooxygenase-2, and the estrogen receptor). We have carried out calculations using different diversity parameters for each of these targets and generated solution sets containing up to 50 molecules. The compounds obtained show that FlexNovo is able to generate a diverse set of reasonable molecules with drug-like properties. The results, including an automated similarity analysis with the Feature Tree program, indicate that FlexNovo often reproduces structural motifs as well as the corresponding binding modes seen in known active structures.

Cyclin-Dependent Kinase 2↗

PubMed2000

Predicting the outcome of neonatal bacterial meningitis.

OBJECTIVE: To build predictive models of severe adverse outcome at various times in the course of neonatal bacterial meningitis. STUDY DESIGN: Retrospective cohort study with follow-up to a minimum age of 1 year of term and near-term infants, admitted between 1979 and 1998 to a regional tertiary care center. Predictors of adverse outcome detectable at 1 year of age (death or moderate or severe neurosensory impairment) were identified by univariate analysis. Independent predictors of adverse outcome were identified by multivariate analysis. Predictive tree models were constructed at 12, 24, 48, and 96 hours after admission and at discharge. RESULTS: Of 101 infants admitted with definitive bacterial meningitis, 13 died and 17 had moderate or severe disability at 1 year of age. Outcomes are known for all patients, to 1 year of age. Twelve hours after admission the important predictors of adverse outcome were presence of seizures, presence of coma, use of inotropes, and leukopenia (sensitivity: 68%; specificity: 100%). At 96 hours the predictors were seizure duration of >72 hours, presence of coma, use of inotropes, and leukopenia (sensitivity: 88%; specificity: 99%). CONCLUSIONS: Most infants at risk for adverse outcome can be identified within 12 hours of admission. Duration of seizures for >72 hours, presence of coma, use of inotropes, and leukopenia were the most important predictors of adverse outcome. Although these models have good predictive accuracy, they need to be validated in a contemporary cohort in large multicenter studies.

Humans↗

PubMed1989

Inexpensive outdoor enclosure for Japanese macaques used in biobehavioral research.

For studies of alcohol self-administration in a monkey social group, we effectively and humanely enclosed nine Japanese macaques (Macaca fuscata) in an ellipse 32 x 40m, with a 1 m high chain-link fence surmounted by a 3 m curtain of electrically conductive nylon net. High-voltage brief-pulse charges prevent climbing on the net. Materials for this fence cost less than $14.50 per running meter. Weeds and grass grew freely within the ellipse, and seven dead trees interconnected with ropes permitted climbing and swinging. An open, roofed gazebo provided sun and rain shelter, and its single wall blocked the prevailing wind. Mouth activated drinkometer spouts in the corral supplied solutions for voluntary alcohol self-administration. Automatic counters informed an observer of exact doses consumed by each subject. Another observer recorded the frequency of occurrence of various social behaviors. A small kennel run, roofed over with chain-link fencing, connected the corral with a paddock-like, partially heated building, to and from which the monkeys usually had free access. It contained three interconnected chain-link pens. A raceway opening from the pens incorporated a squeeze cage used for weighing animals, drawing blood samples, or administering medications. This unique facility promotes the psychological well-being of research primates, which is being mandated by federal law.

Alcohol Drinking↗

PubMed2000

A quantitative analysis of the local connectivity between pyramidal neurons in layers 2/3 of the rat visual cortex.

This study provides a detailed quantitative estimate for local synaptic connectivity between neocortical pyramidal neurons. A new way of obtaining such an estimate is presented. In acute slices of the rat visual cortex, four layer 2 and four layer 3 pyramidal neurons were intracellularly injected with biocytin. Axonal and dendritic arborizations were three-dimensionally reconstructed with the aid of a computer-based camera lucida system. In a computer experiment, pairs of pre- and postsynaptic neurons were formed and potential synaptic contacts were calculated. For each pair, the calculations were carried out for a whole range of distances (0 to 500 microm) between the presynaptic and the postsynaptic neuron, in order to estimate cortical connectivity as a function of the spatial separation of neurons. It was also differentiated whether neurons were situated in the same or in different cortical layers. The data thus obtained was used to compute connection probabilities, the average number of contacts between neurons, the frequency of specific numbers of contacts and the total number of contacts a dendritic tree receives from the surrounding cortical volume. Connection probabilities ranged from 50% to 80% for directly adjacent neurons and from 0% to 15% for neurons 500 microm apart. In many cases, connections were mediated by one contact only. However, close neighbors made on average up to 3 contacts with each other. The question as to whether the method employed in this study yields a realistic estimate of synaptic connectivity is discussed. It is argued that the results can be used as a detailed blueprint for building artificial neural networks with a cortex-like architecture.

Animals↗