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PubMed1993

Temperature regulation in subtropical tree bats.

1. Rate of metabolism and temperature regulation were studied in five species of subtropical tree bats (Lasiurus seminolus, L. borealis, L. intermedius, L. cinereus and Nycticeius humeralis). 2. All species showed two states while resting below thermal neutrality: normothermia and torpor. Below 0-5 degrees C, bats in torpor maintained an intermediate body temperature. 3. Basal rate of metabolism was lower than expected on the basis of body mass (44-78%) and average body temperature in the normothermic state ranged between 32.5 and 35.7 degrees C. 4. Lasiurines have a high thermogenic capacity. 5. The metabolic and thermoregulatory traits studied in tree bats are generally similar to those of non-tropical bats roosting in caves and buildings.

Animals↗

PubMed1999

Xpose--an S-PLUS based population pharmacokinetic/pharmacodynamic model building aid for NONMEM.

The building of population pharmacokinetic/pharmacodynamic (PK/PD) models is a time consuming and complicated task. This is partly due the lack of specialized tools for the visualization and exploration requirements of this type of analysis. In this paper we present Xpose, a model building aid for population PK/PD analysis using NONMEM, which simplifies the task of producing documentation, data set checkout plots, goodness of fit plots and graphical model comparison. It also facilitates covariate model building by the use of stepwise generalized additive modeling (GAM), bootstrap of the GAM analyses and tree based modeling. The plots and analyses are presented in the form of a text based menu system and the only thing the user has to do is to make NONMEM produce one or more table files named in a specific way.

Computer Simulation↗

PubMed2000

Dynamic high-spatial-resolution MR imaging of suspicious breast lesions: diagnostic criteria and interobserver variability.

OBJECTIVE: Our study was undertaken to develop diagnostic rules and to assess the reproducibility of dynamic and morphologic parameters for the characterization of suspicious breast lesions using dynamic high-spatial-resolution MR imaging. MATERIALS AND METHODS: Fifty-seven patients with suspicious mammographic or palpable findings underwent preoperative contrast-enhanced MR imaging of the breast using a three-time-point method of acquisition. Each lesion was prospectively analyzed by two independent radiologists for morphologic and visual dynamic enhancement characteristics. A classification and regression tree was used to examine the optimal order, cutoff points, and combination of imaging parameters to build a diagnostic rule separating benign from malignant lesions using histopathology findings as the standard of reference. Kappa statistics were used to determine observer variability. RESULTS: Among 23 benign and 34 malignant lesions (12 invasive, three ductal carcinoma in situ, and 19 mixed cancer), margin morphology (p = 0.001) and enhancement pattern (p = 0.001) were the most significant MR imaging findings for lesion characterization. Focal mass lesions were classified as malignant when spiculated margins or both the washout enhancement pattern and "nonsmooth" margins were present. Interobserver agreement was almost perfect for washout pattern and substantial for margin assessment. In the limited population tested retrospectively, the diagnostic rule yielded a sensitivity and positive predictive value of 97% each and a specificity and negative predictive value of 96% each. CONCLUSION: The washout enhancement pattern combined with lesion margin assessment on dynamic contrast-enhanced high-resolution MR imaging of the breast allows reproducible lesion characterization and may be a highly specific diagnostic tool.

Adult↗

PubMed2002

[Allergic seasonal rhinoconjunctivitis without indigenous pollen sensitization: the example of the Arizona cypress].

A 37-year old man from Lithuania presented with the typical symptoms of allergic rhinoconjunctivitis that appeared in spring this and the year preceding presentation. Skin prick tests for aeroallergens indigenous in Switzerland were all negative. A detailed history revealed that the patient was working in a building of a United Nation's agency surrounded by a park with numerous cypresses of Arizona trees. A skin prick test for pollens from Cupressus arizona was strongly positive, supporting the diagnosis of allergic rhinoconjunctivitis to pollens from this tree. Allergy to pollens from C. arizona is a widely prevalent as winter pollinosis in subtropical and Mediterranean areas but is exceptional in the continental and alpine climates of Switzerland. Five cases of C. arizona pollinosis have been diagnosed in the last 3 years in Geneva. It is notoriously difficult to diagnose cypressus pollen allergy, mainly because of the poor quality of in vivo and in vitro available tests. Horticulture with non-indigenous plants is responsible for pollinosis from C. arizona in Switzerland. The specialists in countries in which pollinosis from C. arizona is not endemic, need to be aware of arboriculture with non-indigenous plants, as well as the possibility of allergy to C. arizona.

Adult↗

PubMed2003

The link between symptoms of office building occupants and in-office air pollution: the Indoor Air Pollution Index.

The lack of an effective indoor air quality (IAQ) metric causes communication concerns among building tenants (the public), building managers (decision-makers), and IAQ investigators (engineers). The Indoor Air Pollution Index (IAPI) is developed for office buildings to bridge this communication discord. The index, simple and easily understood, employs the range of pollutant concentrations and concentrations in the subject building to estimate a unitless single number, the IAPI, between 0 (lowest pollution level and best IAQ) and ten (highest pollution level and worst IAQ). The index provides a relative measure of indoor air pollution for office buildings and ranks office indoor air pollution relative to the index distribution of the US office building population. Furthermore, the index associates well with occupant symptoms, percentage of occupants with persistent symptoms. A tree-structured method is utilized in conjunction with the arithmetic mean as the aggregation function. The hierarchical structure of the method renders not only one index value, but also several sub-index values that are critical in the study of an office air environment. The use of the IAPI for IAQ management is illustrated with an example. The decomposition of the index leads to the ranking of sampled pollutants by their relative contribution to the index and the identification of dominant pollutant(s). This information can be applied to design an effective strategy for reducing in-office air pollution.

Air Pollution, Indoor↗

PubMed2000

The neurology of syntax: language use without Broca's area.

A new view of the functional role of the left anterior cortex in language use is proposed. The experimental record indicates that most human linguistic abilities are not localized in this region. In particular, most of syntax (long thought to be there) is not located in Broca's area and its vicinity (operculum, insula, and subjacent white matter). This cerebral region, implicated in Broca's aphasia, does have a role in syntactic processing, but a highly specific one: It is the neural home to receptive mechanisms involved in the computation of the relation between transformationally moved phrasal constituents and their extraction sites (in line with the Trace-Deletion Hypothesis). It is also involved in the construction of higher parts of the syntactic tree in speech production. By contrast, basic combinatorial capacities necessary for language processing--for example, structure-building operations, lexical insertion--are not supported by the neural tissue of this cerebral region, nor is lexical or combinatorial semantics. The dense body of empirical evidence supporting this restrictive view comes mainly from several angles on lesion studies of syntax in agrammatic Broca's aphasia. Five empirical arguments are presented: experiments in sentence comprehension, cross-linguistic considerations (where aphasia findings from several language types are pooled and scrutinized comparatively), grammaticality and plausibility judgments, real-time processing of complex sentences, and rehabilitation. Also discussed are recent results from functional neuroimaging and from structured observations on speech production of Broca's aphasics. Syntactic abilities are nonetheless distinct from other cognitive skills and are represented entirely and exclusively in the left cerebral hemisphere. Although more widespread in the left hemisphere than previously thought, they are clearly distinct from other human combinatorial and intellectual abilities. The neurological record (based on functional imaging, split-brain and right-hemisphere-damaged patients, as well as patients suffering from a breakdown of mathematical skills) indicates that language is a distinct, modularly organized neurological entity. Combinatorial aspects of the language faculty reside in the human left cerebral hemisphere, but only the transformational component (or algorithms that implement it in use) is located in and around Broca's area.

Aphasia, Broca↗

PubMedDate not supplied

A family of ring system-based structural fragments for use in structure-activity studies: database mining and recursive partitioning.

In earlier work from our laboratory, we have described the use of the ring system and ring scaffold as descriptors. We showed that these descriptors could be used for fast compound clustering, novelty determination, compound acquisition, and combinatorial library design. Here we extend the concept to a whole family of structural descriptors with the ring system as the centerpiece. We show how this simple idea can be used to build powerful search tools for mining chemical databases in useful ways. We have also built recursive partition trees using these fragments as descriptors. We will discuss how these trees can help in analyzing complex structure-activity data.

Drug Design↗

PubMed1995

Independence divergence-generated binary trees of amino acids.

The discovery of the relationship between amino acids is important in terms of the replacement ability, as used in protein engineering homology studies, and gaining a better understanding of the roles which various properties of the residues play in the creation of a unique, stable, 3-D protein structure. Amino acid sequences of proteins edited by evolution are anything but random. The measure of nonrandomness, i.e. the level of editing, can be characterized by an independence divergence value. This parameter is used to generate binary tree relationships between amino acids. The relationships of residues presented in this paper are based on protein building features and not on the physico-chemical characteristics of amino acids. This approach is not biased by the tautology present in all sequence similarity-based relationship studies. The roles which various physico-chemical characteristics play in the determination of the relationships between amino acids are also discussed.

Amino Acid Sequence↗

PubMed1989

[The Optec hsp procedure. Concepts and laboratory fabrication].

Feldspatic porcelains are usually material in cosmetic dentistry, but they cannot be used without a reinforcement system. Aluminous or metallic frames produce a strong internal specular reflexion, which destroys the deep natural appearance of teeth. Inspired from glass ceramic industry, the concept of strengthening in Optec hsp is induced by a high level of micro-crystalline dispersion, spread in the material. Micro-crystals increase strength by division of stresses and improve the scattering of light as we observe in the natural tooth. The laboratory method is based on routine technics of porcelain building. No special equipment, or high temperature are necessary for producing, laminate veneers, inlays, onlays, crowns, and tree units anterior bridges.

Crowns↗

PubMed2001

Evaluating training data suitability for decision tree induction.

Decision tree induction, as well as other inductive learning methods, requires training data of high quality to be able to generate accurate and reliable classification models. Example cases should form a representative sample from the application area, and the attributes used to describe example cases should be relevant and adequate for the classification task to be solved. In this paper, measures of the strength of association and an entropy-based approach have been used to assess the quality of the training data. Studied classification tasks related to three otological data sets: a conscript data set, a vertigo data set, and a postoperative nausea and vomiting data set. The paper suggests that the studied approaches give some guidelines about the quality of the training data, but other approaches are also needed to guide training data building.

Adolescent↗

PubMed2003

Protein family classification using sparse markov transducers.

We present a method for classifying proteins into families based on short subsequences of amino acids using a new probabilistic model called sparse Markov transducers (SMT). We classify a protein by estimating probability distributions over subsequences of amino acids from the protein. Sparse Markov transducers, similar to probabilistic suffix trees, estimate a probability distribution conditioned on an input sequence. SMTs generalize probabilistic suffix trees by allowing for wild-cards in the conditioning sequences. Since substitutions of amino acids are common in protein families, incorporating wild-cards into the model significantly improves classification performance. We present two models for building protein family classifiers using SMTs. As protein databases become larger, data driven learning algorithms for probabilistic models such as SMTs will require vast amounts of memory. We therefore describe and use efficient data structures to improve the memory usage of SMTs. We evaluate SMTs by building protein family classifiers using the Pfam and SCOP databases and compare our results to previously published results and state-of-the-art protein homology detection methods. SMTs outperform previous probabilistic suffix tree methods and under certain conditions perform comparably to state-of-the-art protein homology methods.

Algorithms↗

PubMed2003

Capacity planning seeing the forest for the trees.

Strategies for responding to today's rise in demand for inpatient services are many. The following are a few "tried-and-true" strategies: Build new and replacement hospitals Spin off specialty services Convert space occupied by less-profitable specialty services Improve patient management Reclaim mothballed space Implement urgent care tracks for appropriate ED patients.

Bed Occupancy↗

PubMed2003

Characterization of the horse (Equus caballus) IGHA gene.

Nucleotide sequences of the immunoglobulin constant heavy chain genes of the horse have been described for IGHM, IGHG and IGHE genes, but not for IGHA. Here, we provide the nucleotide sequence of the genomic IGHA gene of the horse ( Equus caballus), including its secretion region and the transmembrane exon. The equine IGHA gene shows the typical structure of a mammalian IGHA gene, with only three exons, separated by two introns of similar size. The hinge exon is located at the 5' end of the CH2 exon and encodes a hinge region of 11 amino acids, which contains five proline residues. The coding nucleotide sequence of the secreted form of the equine IGHA gene shares around 72% identity with the human IGHA1 and IGHA2 genes, as well as the bovine, ovine, porcine and canine IGHA genes, without distinct preference for any of these species. The same species also cluster together in a phylogenetic tree of the IGHA coding regions of various mammals, whereas rodent, rabbit, marsupial and monotreme IGHA genes each build a separate cluster.

Amino Acid Sequence↗

PubMed2005

Implementation of new legislative measures on industrial risks prevention and control in urban areas.

Incompatible at first sight, but vital to each other, the industry and the city have been developing a complex relationship for decades. From 1810 on in France, risk prevention and control in and around major industrial sites evolves step-by-step, learning from accidents. Land-use planning in the vicinity of SEVESO establishments becomes one of the key policies in the prevention of major industrial accident hazard on European level in 1996, focussing on historical situation of concern [M.D. Christou, S. Porter, Guidance on Land-use Planning as required by the council Directive 96/82/EC. Joint Research Centre, European Commission, 1999]. The Toulouse (F) accidents, on 21 September 2001 evidenced the need for new tools to reinforce protective action and ease the situation of clusters of factories engulfed in the urban setting. In France, new legislative measures adopted on 30 July 2003 deeply modified the approach to land-use planning around the main dangerous facilities (622 establishments). The implementation of technological risk prevention plans [Fr. "PPRT"] will limit the exposition of the population to the consequences of accidents. These plans, derived from the risk assessment (safety reports) produced by the operators of the hazardous facilities, will delineate areas within which requirements can be imposed on existing and future buildings and within which future building rights may be restricted. On the grounds of extremely serious danger that threatens human life, pre-existing constructions may be progressively expropriated. The financing of the corresponding measures, estimated a rough 2-4 billions euro, will be defined by agreements among the Central Government, the industrial company and the local and regional bodies.

Accidents, Occupational↗

PubMed2003

Models of the primary and secondary structure for the 12S rRNA of birds: a guideline for sequence alignment.

Models of the primary and secondary structure for the 12S ribosomal RNA (rRNA) gene of birds is presented based on a comparison of 100 species. Preliminary higher-order structures were delimited following the model for vertebrates. Paired regions were refined following a complementary base-pairing criterion and compensatory mutations were considered as a further confirmation of their existence. The model shows 40 stems, 20 internal loops and 17 external loops, arranged in the typical four domains suggested for the small subunit rRNA. The higher-order structures recovered in the model were used to build a multiple sequence alignment appropriate for phylogenetic analysis. The phylogeny recovered from this alignment was compared with trees inferred from alignments assembled using different alignment parameters in the program ClustalW. The alignment based on the secondary structure is sensitive to positional covariation of stems. Nonetheless, the phylogeny recovered with this method resulted in relationships that are more congruent with non-molecular data than those inferred from alternative alignments.

Amino Acid Sequence↗

PubMed1998

Putative multiadhesive protein from the marine sponge Geodia cydonium: cloning of the cDNA encoding a fibronectin-, an SRCR-, and a complement control protein module.

Sponges (Porifera) representing the simplest metazoan phylum so far have been thought to possess no basal lamina tissue structures. One major extracellular matrix protein that is also a constitutive glycoprotein of the basal lamina is fibronectin. It was the aim of the present study to identify the native protein from the marine sponge Geodia cydonium and to isolate the corresponding cDNA. In crude extracts from this sponge protein(s) of M(r) of approximately 230 and approximately 210 kDa could be visualized by Western-blotting using an anti-fibronectin [human] antibody. By PCR cloning from a cDNA library of G. cydonium we isolated a cDNA comprising one element of fibronectin, the type-III (FN3) module. The cDNA (2.3 kb long), encoding a 701 amino acid [aa] long putative "multiadhesive protein" termed MAP_GEOCY, was found to contain (i) a fibronectin-, (ii) a scavenger receptor cysteine-rich [SRCR]-, and (iii) a short consensus repeat [SCR] module. The 89 aa long fibronectin module comprises the characteristic topology and conserved aa found in fibronectin type-III (FN3) elements. The SRCR module (101 aa) features the characteristics of group B SRCR molecules. The predominant proteins belonging to this group are the mammalian WC1-, M130-, CD6- and CD5 antigens that probably are involved in immunological reactions. The SCR module (54 aa) shows the characteristics of type III SCR modules found in complement receptors. Phylogenetic analyses performed with all three building blocks of the "multiadhesive protein" showed that the respective sponge modules form independent, possibly basal, lineages in trees that include the corresponding modules from higher metazoan animals. In summary, these data demonstrate for the first time that the phylogenetically oldest Metazoa, the sponges, contain protein modules seen in higher animals in proteins of the extracellular matrix and in molecules involved in cell-mediated immune reactions in vertebrates.

Amino Acid Sequence↗

PubMed2002

Automatic generation of a metamodel from an existing knowledge base to assist the development of a new analogous knowledge base.

Knowledge acquisition is a key step in the development of knowledge-based systems and methods have been proposed to help elicitating a domain-specific task model from a generic task model. We explored how an existing validated knowledge base (KB) represented by a decision tree could be automatically processed to infer a higher level domain-specific task model. On-codoc is a guideline-based decision support system applied to breast cancer therapy. Assuming task identity and ontological proximity between breast and lung cancer domains, the generalization of the breast can-cer KB should allow to build a metamodel to serve as a guide for the elaboration of a new specific KB on lung cancer. Two types of parametrized generalization methods based on tree structure simplification and ontological abstraction were used. We defined a similarity distance and a generalization coefficient to select the best metamodel identified as the closest to the original decision tree of the most generalized metamodels.

Artificial Intelligence↗

PubMed1998

Hypertextual navigation operationalizing generic clinical practice guidelines for patient-specific therapeutic decisions.

Despite the proliferation of implemented clinical practice guidelines, there is still little evidence of physicians compliance to formal standards. The ONCODOC project proposes a framework for elaborating generic decision support guidelines in a document-based paradigm with a knowledge-based approach. It has been first applied to assist clinicians in the treatment of breast cancer patients. Therapeutic expertise has been encoded as a decision tree. The decision process is driven by the clinician who interactively browses a hypertext version of the decision tree. During the navigation, he incrementally assigns values to decision parameters on the basis of his free interpretation of his patient's condition and thus builds a clinical context leading to patient-specific therapeutic recommendations. These guidelines are distributed on a hospital intranet and are evaluated at the point of care in an oncology department.

Breast Neoplasms↗