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PubMed2006

Modular learning models in forecasting natural phenomena.

Modular model is a particular type of committee machine and is comprised of a set of specialized (local) models each of which is responsible for a particular region of the input space, and may be trained on a subset of training set. Many algorithms for allocating such regions to local models typically do this in automatic fashion. In forecasting natural processes, however, domain experts want to bring in more knowledge into such allocation, and to have certain control over the choice of models. This paper presents a number of approaches to building modular models based on various types of splits of training set and combining the models' outputs (hard splits, statistically and deterministically driven soft combinations of models, 'fuzzy committees', etc.). An issue of including a domain expert into the modeling process is also discussed, and new algorithms in the class of model trees (piece-wise linear modular regression models) are presented. Comparison of the algorithms based on modular local modeling to the more traditional 'global' learning models on a number of benchmark tests and river flow forecasting problems shows their higher accuracy and transparency of the resulting models.

Artificial Intelligence↗

PubMed2006

Who will be the shade of our tree when you leave? Collaborating as women to advance community emancipation.

In 1994, out of a population of 45 million people an estimated 7.7 million people lived in informal settlements in South Africa (South African Institute of Race Relations, 1994). This article focuses on one community whose residents' desperation to own housing contributed to community disintegration, typified by infighting among women, and threats to human life. Issues of diversity became more prominent and destabilized community-building efforts. One effort to collaboratively break down barriers that deterred women from working together is presented to illustrate how these women created bonds based on "discovered similarities." The participatory and personal-experience approach described here contributed to their becoming active protagonists of their learning and encouraged tolerance and understanding among community women from differing ethnic, linguistic, and political backgrounds. The article concludes with a discussion of the critical importance of recognizing and working with and through differences within the current South African reality.

Adult↗

PubMed2004

Three-dimensional path planning for virtual bronchoscopy.

Multidetector computed-tomography (MDCT) scanners provide large high-resolution three-dimensional (3-D) images of the chest. MDCT scanning, when used in tandem with bronchoscopy, provides a state-of-the-art approach for lung-cancer assessment. We have been building and validating a lung-cancer assessment system, which enables virtual-bronchoscopic 3-D MDCT image analysis and follow-on image-guided bronchoscopy. A suitable path planning method is needed, however, for using this system. We describe a rapid, robust method for computing a set of 3-D airway-tree paths from MDCT images. The method first defines the skeleton of a given segmented 3-D chest image and then performs a multistage refinement of the skeleton to arrive at a final tree structure. The tree consists of a series of paths and branch structural data, suitable for quantitative airway analysis and smooth virtual navigation. A comparison of the method to a previously devised path-planning approach, using a set of human MDCT images, illustrates the efficacy of the method. Results are also presented for human lung-cancer assessment and the guidance of bronchoscopy.

Algorithms↗

PubMed1996

[Environmental factors influencing sensitization and onset of Japanese cedar pollinosis among junior high school students].

Japanese cedar pollinosis has shown large increases especially in city areas, rather than in the rural, with increases being remarkable especially among people of young age. In order to elucidate factors for sensitization and onset of Japanese cedar pollinosis, a questionnaire survey was conducted and serum IgE antibody levels examined in junior high school students living in three different areas, i.e., city, seaside and mountainous areas in Aichi prefecture. Prevalence rate of Japanese cedar pollinosis, estimated from the number of students having both nasal or ocular allergic symptoms and positive RAST, was the 30.1% in the mountainous area with high Japanese cedar pollen count, being greater than the 15.3% in the city area and the 5.8% in the seaside area, both with low pollen counts. Among the students showing high serum mite (Dermatophagoides farinae) antibody levels, greater positive rates for sensitization to Japanese cedar or orchard grass pollens was observed, compared to mite-unsensitized students. This result suggests that sensitization to seasonal antigens may be corresponding to the capability for sensitization to the mites. Besides this finding, the analysis of replies to the questionnaires showed that students living in concrete or steel-frame buildings had greater serum levels of antibody to Japanese cedar pollen than those living in wood buildings, indicating a possible relationship between the pollen sensitization and indoor environments.

Adolescent↗

PubMed2002

A phylogeny of the megapodes (Aves: Megapodiidae) based on nuclear and mitochondrial DNA sequences.

DNA sequences from the first intron of the nuclear gene rhodopsin (RDP1) and from the mitochondrial gene ND2 were used to construct a phylogeny of the avian family Megapodiidae. RDP1 sequences evolved about six times more slowly than ND2 and showed less homoplasy, substitution bias, and rate heterogeneity across sites. Analysis of RDP1 produced a phylogeny that was well resolved at the genus level, but RDP1 did not evolve rapidly enough for intrageneric comparisons. The ND2 phylogeny resolved intrageneric relationships and was congruent with the RDP1 phylogeny except for a single node: this node was the only aspect of tree topology sensitive to weighting in parsimony analyses. Despite differences in sequence evolution, RDP1 and ND2 contained congruent phylogenetic signal and were combined to produce a phylogeny that reflects the resolving power of both genes. This phylogeny shows an early split within the megapodes, leading to two major clades: (1) Macrocephalon and the mound-building genera Talegalla, Leipoa, Aepypodius, and Alectura, and (2) Eulipoa and Megapodius. It differs significantly from previous hypotheses based on morphology but is consistent with affiliations suggested by a recent study of parasitic chewing lice.

Animals↗

PubMed2005

Universal sharing patterns in proteomes and evolution of protein fold architecture and life.

Protein evolution is imprinted in both the sequence and the structure of evolutionary building blocks known as protein domains. These domains share a common ancestry and can be unified into a comparatively small set of folding architectures, the protein folds. We have traced the distribution of protein folds between and within proteomes belonging to Eukarya, Archaea, and Bacteria along the branches of a universal phylogeny of protein architecture. This tree was reconstructed from global fold-usage statistics derived from a structural census of proteomes. We found that folds shared by the three organismal domains were placed almost exclusively at the base of the rooted tree and that there were marked heterogeneities in fold distribution and clear evolutionary patterns related to protein architecture and organismal diversification. These include a relative timing for the emergence of prokaryotes, congruent episodes of architectural loss and diversification in Archaea and Bacteria, and a late and quite massive rise of architectural novelties in Eukarya perhaps linked to multicellularity.

Evolution, Molecular↗

PubMed2000

Alternative sources of natural rubber.

Rubber (cis-1,4-polyisoprene) is one of the most important polymers naturally produced by plants because it is a strategic raw material used in more than 40,000 products, including more than 400 medical devices. The sole commercial source, at present, is natural rubber harvested from the Brazilian rubber tree, Hevea brasiliensis. Primarily due to its molecular structure and high molecular weight (> 1 million daltons) this rubber has high performance properties that cannot easily be mimicked by artificially produced polymers, such as those derived from, e.g., bacterial poly-hydroxyalkanoates (PHAs). These high performance properties include resilience, elasticity, abrasion resistance, efficient heat dispersion (minimizing heat build-up under friction), and impact resistance. Medical rubber gloves need to fit well, be break-resistant, allow the wearer to retain fine tactile sensation, and provide an effective barrier against pathogens. The sum of all these characteristics cannot yet be achieved using synthetic gloves. The lack of biodiversity in natural rubber production renders continuity of supply insecure, because of the risk of crop failure, diminishing acreage, and other disadvantages outlined below. A search for alternative sources of natural rubber production has already resulted in a large number of interesting plants and prospects for immediate industrial exploitation of guayule (Parthenium argentatum) as a source of high quality latex. Metabolic engineering will permit the production of new crops designed to accumulate new types of valued isoprenoid metabolites, such as rubber and carotenoids, and new combinations extractable from the same crop. Currently, experiments are underway to genetically improve guayule rubber production strains in both quantitative and qualitative respects. Since the choice for gene activities to be introduced or changed is under debate, we have set up a complementary approach to guayule with yeast species, which may more quickly show the applicability and relevance of genes selected. Although economic considerations may prevent commercial exploitation of new rubber-producing microorganisms, transgenic yeasts and bacteria may yield intermediate or alternative (poly-)isoprenes suitable for specific applications.

Amino Acid Sequence↗

PubMed1984

View through a window may influence recovery from surgery.

Records on recovery after cholecystectomy of patients in a suburban Pennsylvania hospital between 1972 and 1981 were examined to determine whether assignment to a room with a window view of a natural setting might have restorative influences. Twenty-three surgical patients assigned to rooms with windows looking out on a natural scene had shorter postoperative hospital stays, received fewer negative evaluative comments in nurses' notes, and took fewer potent analgesics than 23 matched patients in similar rooms with windows facing a brick building wall.

Adult↗

PubMed2005

Linear scaling computation of the Fock matrix. VII. Periodic density functional theory at the Gamma point.

Linear scaling quantum chemical methods for density functional theory are extended to the condensed phase at the Gamma point. For the two-electron Coulomb matrix, this is achieved with a tree-code algorithm for fast Coulomb summation [M. Challacombe and E. Schwegler, J. Chem. Phys. 106, 5526 (1997)], together with multipole representation of the crystal field [M. Challacombe, C. White, and M. Head-Gordon, J. Chem. Phys. 107, 10131 (1997)]. A periodic version of the hierarchical cubature algorithm [M. Challacombe, J. Chem. Phys. 113, 10037 (2000)], which builds a telescoping adaptive grid for numerical integration of the exchange-correlation matrix, is shown to be efficient when the problem is posed as integration over the unit cell. Commonalities between the Coulomb and exchange-correlation algorithms are discussed, with an emphasis on achieving linear scaling through the use of modern data structures. With these developments, convergence of the Gamma-point supercell approximation to the k-space integration limit is demonstrated for MgO and NaCl. Linear scaling construction of the Fockian and control of error is demonstrated for RBLYP6-21G* diamond up to 512 atoms.

Journal Article↗

PubMed2006

Prognostic groups in colorectal carcinoma patients based on tumor cell proliferation and classification and regression tree (CART) survival analysis.

BACKGROUND: In this study, an alternative analytical method was used to model colorectal cancer (CRC) patients' long-term survival by assessing the prognostic value of the Ki-67 protein as a marker of tumor cell proliferation, and to illustrate the interaction between standard clinicopathologic variables and the proliferation marker in relation to their impact on survival. METHODS: A cohort of 106 surgically treated CRC patients was used for analysis. The expression of the cell-cycle-related Ki-67 protein in tumor samples was evaluated by immunohistochemistry. A score was assigned as the percentage of positive tumor cell staining, denoted as proliferation index (PI), and was used in a multivariate analysis using a recursive partitioning algorithm referred to as classification and regression tree (CART) to characterize the long-term survival after surgery. RESULTS: Of the covariates selected for their prognostic value, PI contributed most to the classification of survival status of patients. However, CART analysis selected the presence of distant metastasis as the best first split-up factor for predicting 5-year survival. CART then selected the following covariates for building up subgroups at risk for death: (1) PI; (2) pathological lymph node metastasis; (3) tumor size. Seven terminal subgroups were formed, with an overall misclassification rate of 16%. CONCLUSIONS: These analyses demonstrated that a Ki-67-protein-based tumor proliferation index appeared as an independent prognostic variable that was consistently applied by the CART algorithm to classify patients into groups with similar clinical features and survival.

Adult↗

PubMed2005

Distribution of Batrachochytrium dendrobatidis and pathology in the skin of green tree frogs Litoria caerulea with severe chytridiomycosis.

Although histopathology is used routinely for diagnosis of chytridiomycosis in live and dead amphibians, there are no quantitative data on the distribution of the causative fungus, Batrachochytrium dendrobatidis, in the skin. We performed quantitative histological examinations on 6 sites on the body and 4 toes of 10 free-ranging adult green tree frogs Litoria caerulea found recently dead or dying from chytridiomycosis. Large numbers of sporangia occurred in all areas of ventral skin and toes; on average there were 94.3 sporangia mm(-1) of superficial epidermis. The number of sporangia was highly variable and this appeared to be related to the stage in the cycle of sloughing. The stratum corneum tends to build up with high intensities of infection and then sheds entirely rather than being shed continuously. Very few or no sporangia occurred on dorsal skin. This distribution could be explained by the dryness of the dorsal skin or possibly by the greater number of serous glands, which produce antifungal peptides, on the dorsum. In some frogs, ulceration and erosions occurred on skin on the back in the absence of sporangia. Other pathological changes such as hyperkeratosis and congestion occurred much more frequently on ventral surfaces.

Animals↗

PubMed2004

Sclerophylly and leaf anatomical traits of five field-grown olive cultivars growing under drought conditions.

Leaf-level morphological and structural adaptations to reduce water loss were examined in five olive (Olea europaea L.) tree cultivars (Arbequina, Blanqueta, Cobrançosa, Manzanilla and Negrinha) growing under field conditions with low water availability. Leaf measurements included leaf tissue thickness, stomatal density, leaf area, leaf mass per unit area, density of leaf tissue, relative water content, succulence, water saturation deficit, water content at saturation and cuticular transpiration rate. We found considerable genotypic differences among the cultivars. Negrinha, Manzanilla and Cobrançosa had more morphological and structural leaf adaptations to protect against water loss than the other cultivars. Manzanilla and Negrinha enhanced their sclerophylly by building parenchyma tissues and increasing protective structures like the upper cuticle and both the upper and lower epidermis. Cobrançosa exhibited good protection against water loss through high density of foliar tissue and by thick cuticle and trichome layers. Compared with the Negrinha, Manzanilla and Cobrançosa cultivars, Arbequina leaves had a thinner trichome layer, implying that the leaves were less protected against water loss; however, the development of smaller leaves may reduce water loss at the whole-plant level. Among cultivars, Blanqueta had the largest leaves and some anatomical traits that may lead to high water loss, especially from the adaxial surface. The mechanisms employed by the cultivars to cope with summer stress are discussed at the morpho-structural level.

Dehydration↗

PubMed2001

Transient, highly populated, building blocks folding model.

Protein folding is a hierarchical event, in which transiently formed local structural elements assemble to yield the native conformation. In principle, multiple paths glide down the energy landscape, but, in practice, only a few of the paths are highly traveled. Here, the literature is reviewed in this light, and, particularly, a hierarchical, building block protein-folding model is presented, putting it in the context of a broad range of experimental and theoretical results published over the past few years. The model is based on two premises: First, although the local building block elements may be unstable, they nevertheless have higher population times than all alternate conformations; and, second, protein folding progresses through a combinatorial assembly of these elements. Through the binding of the most favorable building block conformers, there is a redistribution of the conformers in solution, propagating the protein-folding reaction. We describe the algorithm, and illustrate its usefulness, then we focus on its utility in assigning simple vs complex folding pathways, on chaperonin-assisted folding, on its relevance to domain-swapping processes, and on its relevance and relationship to disconnectivity graphs and tree diagrams. Considering protein folding as initiating from local transient structural elements is consistent with available experimental and theoretical results. Here, we have shown that, early in the folding process, sequential interactions are likely to take place, even if the final native fold is a complex, nonsequential one. Such a route is favorable kinetically and entropically. Through the construction of anatomy trees, the model enables derivation of the major folding pathways and their bumps, and qualitatively explains the kinetics of protein folding.

Biophysics↗

PubMed2026

Plant species identification by genome skimming across the vascular plant tree of life.

Accurate species identification is essential for biodiversity conservation and sustainable use, yet standard plant DNA barcoding often fails to achieve species-level resolution. We present a large-scale empirical evaluation of genome skimming as a tool to improve plant species discrimination. Using standardised data from 1969 individuals representing 475 species from 32 genera across major lineages of the vascular plant tree of life, we compare conventional plastid + internal transcribed spacer (ITS) barcodes with genome skimming approaches. Standard barcoding using rbcL, matK, trnH-psbA and ITS resolved about half of species (49.3%), with six genera showing < 25% species discrimination. By contrast, genome skimming enabled the recovery of complete plastid genomes, yielding 57.6% species discrimination. It also generated sufficient nuclear genomic data for additional resolution from k-mer analysis, achieving 66.8% species discrimination - an average gain of 17.5% over standard barcodes - while eliminating cases of extreme failure (< 25% resolution). The recovery of complete plastomes and ribosomal DNAs from genome skims also ensures backward compatibility with existing barcode datasets. Our results demonstrate that genome skimming provides data that substantially improves species-level resolution across diverse plant lineages and offers a scalable, high-throughput approach for building comprehensive reference resources to support global biodiversity initiatives.

DNA Barcoding, Taxonomic↗

PubMedDate not supplied

Ensemble of linear models for predicting drug properties.

We propose a new classification method for the prediction of drug properties, called random feature subset boosting for linear discriminant analysis (LDA). The main novelty of this method is the ability to overcome the problems with constructing ensembles of linear discriminant models based on generalized eigenvectors of covariance matrices. Such linear models are popular in building classification-based structure-activity relationships. The introduction of ensembles of LDA models allows for an analysis of more complex problems than by using single LDA, for example, those involving multiple mechanisms of action. Using four data sets, we show experimentally that the method is competitive with other recently studied chemoinformatic methods, including support vector machines and models based on decision trees. We present an easy scheme for interpreting the model despite its apparent sophistication. We also outline theoretical evidence as to why, contrary to the conventional AdaBoost ensemble algorithm, this method is able to increase the accuracy of LDA models.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2026

The mechanistic and evolutionary diversity of programmed DNA elimination.

Beyond somatic mutations, the genetic makeup of an organism is often assumed to remain constant across all cells or nuclei within individuals. However, some organisms exhibit programmed DNA elimination (PDE), whereby specific cell lineages lose DNA segments or whole chromosomes. Building evidence indicates that PDE occurs in a wide range of eukaryotes and is linked to diverse cellular processes including gene silencing, germline differentiation, genome defence and sex determination. Here we compare PDE across broad phylogenetic groups, highlighting the mechanistic diversity, overlooked plasticity in genome integrity and the considerable gaps in our understanding of why PDE emerged recurrently and is maintained across the Tree of Life.

Journal Article↗

PubMedDate not supplied

Support surfaces and their use in the prevention and treatment of pressure ulcers.

Pressure ulcers are an important health concern. A wide range of options are available for their prevention and treatment. Support surfaces are building blocks in the endeavor to reduce or relieve interface pressures. This article examines and classifies support surfaces, provides critical assessment criteria for patient selection, and discusses areas to be evaluated in the selection of support surfaces.

Beds↗

PubMed2002

DiffTool: building, visualizing and querying protein clusters.

UNLABELLED: DiffTool is a resource to build and visualize protein clusters computed from a sequence database. The package provides a clustering tool to construct protein families according to sequence similarities and a web interface to query the corresponding clusters. A subtractive genome analysis tool selects protein families specific for a genome or a group of genomes. For each protein cluster, DiffTool includes access to sequences, coloured multiple alignments and phylogenetic trees. AVAILABILITY: A cluster database built from yeast and complete prokaryotic genomes is queryable at http://bioweb.pasteur.fr/seqanal/difftool. All the Perl sources are freely available to non-profit organizations upon request.

Cluster Analysis↗