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PubMed2001

Indirect carbon reduction by residential vegetation and planting strategies in Chicago, USA.

Concern about climate change has evoked interest in the potential for urban vegetation to help reduce the levels of atmospheric carbon. This study applied computer simulations to try to quantify the modifying effects of existing vegetation on the indirect reduction of atmospheric carbon for two residential neighborhoods in north-west Chicago. The effects of shading, evapotranspiration, and windspeed reduction were considered and were found to have decreased carbon emissions by 3.2 to 3.9% per year for building types in study block 1 where tree cover was 33%, and -0.2 to 3.8% in block 2 where tree cover was 11%. This resulted in a total annual reduction of carbon emission averaging 158.7 (+/- 12.8) kg per residence in block 1 and 18.1 (+/- 5.4) kg per residence in block 2. Windspeed reduction greatly contributed to the decrease of carbon emission. However, shading increased annual carbon emission from the combined change in heating and cooling energy use due to many trees in the wrong locations, which increase heating energy use during the winter. The increase of carbon emission from shading is somewhat specific to Chicago, due in part to the large amount of clean, nuclear-generated cooling energy and the long heating season. In Chicago, heating energy is required for about eight months from October to May and cooling energy is used for the remaining 4 months from June to September. If fossil fuels had been the primary source for cooling energy and the heating season had been shorter, the shading effects on the reduction of carbon emission would be greater. Planting of large trees close to the west wall of buildings, dense planting on the north, and avoidance of planting on the south are recommended to maximize indirect carbon reduction by residential vegetation, in Chicago and other mid and high-latitude cities with long heating seasons.

Air Pollutants↗
PubMed1989

Pattern conserving data structure and algorithms for computations on dendritic trees.

The linked list is offered as a pattern conserving data structure, useful for storing neuronal dendritic trees. A BASIC language algorithm is described. Modifications of this algorithm for building linked lists, graphing dendritic trees, and tarry ordering trees are presented. Brief mention is made of the last in first out stack as a alternative data structure for computations on dendritic trees.

Algorithms↗
PubMed2006

A fully resolved consensus between fully resolved phylogenetic trees.

Nowadays, there are many phylogeny reconstruction methods, each with advantages and disadvantages. We explored the advantages of each method, putting together the common parts of trees constructed by several methods, by means of a consensus computation. A number of phylogenetic consensus methods are already known. Unfortunately, there is also a taboo concerning consensus methods, because most biologists see them mainly as comparators and not as phylogenetic tree constructors. We challenged this taboo by defining a consensus method that builds a fully resolved phylogenetic tree based on the most common parts of fully resolved trees in a given collection. We also generated results showing that this consensus is in a way a kind of "median" of the input trees; as such it can be closer to the correct tree in many situations.

Algorithms↗
PubMed2006

A hierarchical clustering method for estimating copy number variation.

Microarray technologies allow for simultaneous measurement of DNA copy number at thousands of positions in a genome. Gains and losses of DNA sequences reveal themselves through characteristic patterns of hybridization intensity. To identify change points along the chromosomes, we develop a marker clustering method which consists of 2 parts. First, a "circular clustering tree test statistic" attaches a statistic to each marker that measures the likelihood that it is a change point. Then construction of the marker statistics is followed by outlier detection approaches. The method provides a new way to build up a binary tree that can accurately capture change-point signals and is easy to perform. A simulation study shows good performance in change-point detection, and cancer cell line data are used to illustrate performance when regions of true copy number changes are known.

Algorithms↗
PubMed2006

Management of non-complicated BPH: proposition of a renewed decision tree.

Nowadays the management of benign prostatic hypertrophia (BPH) is undergoing striking changes. The standard medical treatments are represented by three families which are the phytotherapy, the alpha-blockers and the 5-alpha-reductase inhibitors. These treatments were deemed as symptomatic and used only as monotherapy. Recent numerous studies bring new assessments on BPH: the medical treatment is able to modify the natural history of BPH especially by reducing the risk of acute urinary retention. Furthermore the association of two different therapeutic classes seems to be more efficient than the use of a monotherapy in some cases. Similarly the place of two instrumental techniques, the thermotherapy by microwaves or by radiofrequencies, previously proposed as alternatives to the surgical treatment seems to find their way rather as alternatives to the medical treatment. These different elements allow building a renewed decision tree which decisions are shared with the patient at each stage. This decision tree of the management of patients having non-complicated BPH symptoms must include initial clinical characteristics of the patient and its disease and the evolution under treatment which has not been yet considered in the international recommendations. It also considers the possibilities of associations with other therapeutic classes.

Decision Trees↗
PubMed2001

Potential for ammonia recapture by farm woodlands: design and application of a new experimental facility.

There has been increasing pressure on farmers in Europe to reduce the emissions of ammonia from their land. Due to the current financial climate in which farmers have to operate, it is important to identify ammonia control measures that can be adopted with minimum cost. The planting of trees around farmland and buildings has been identified as a potentially effective and low-cost measure to enhance ammonia recapture at a farm level and reduce long-range atmospheric transport. This work assesses experimentally what fraction of ammonia farm woodlands could potentially remove from the atmosphere. We constructed an experimental facility in southern Scotland to simulate a woodland shelterbelt planted in proximity to a small poultry unit. By measuring horizontal and vertical ammonia concentration profiles within the woodland, and comparing this to the concentration of an inert tracer (SF6) we estimate the depletion of ammonia due to dry deposition to the woodland canopy. Together with measurements of mean ammonia concentrations and throughfall fluxes of nitrogen, this information is used to provide a first estimate of the fraction of emitted ammonia that is recaptured by the woodland canopy. Analysis of these data give a lower limit of recapture of emitted ammonia, at the experimental facility, of 3%. By careful design of shelterbelt woodlands this figure could be significantly higher.

Agriculture↗
PubMed1986

[Principles of decisional analysis applied to the screening for occupational diseases: the example of occupational fluorosis].

In this paper, two oral presentations are combined. The first described the broad aspects of decision analysis and the second mentioned those medical data which need to be gathered in order to apply the model to industrial fluorosis. For this purpose, biological and medical observations were collected, both from workers of the aluminium industry and from controls. The five successive steps for building up a decision tree are then demonstrated, the aim of which being to evaluate the fitness of a screening strategy. A computer programme has been developed which may be applied both to occupational or non occupational diseases. Referring to industrial fluorosis, the computerized decision tree showed that screening with preshift urinary fluor, clinical and radiological signs, plus bone fluor rate is required, as soon as the risk corresponds to a 7% prevalence of the disease.

Aluminum↗
PubMed2005

Development of SCAR markers linked to three disease resistances based on AFLP within Nicotiana tabacum L.

Amplified fragment length polymorphism (AFLP) was conducted on a set of 92 Nicotiana tabacum L. accessions from diverse types (flue-cured, dark air-cured, burley, oriental, and cigar wrapper) and breeding origins to identify markers associated with disease resistances. Eleven primer combinations were required to identify 33 polymorphic fragments. This allowed the identification of 92% of these accessions, and yielded sufficient information for building a neighbor joining tree. Clusters of accessions with common traits or breeding origins were observed. An important part of this polymorphism could be related to interspecific introgressions from other Nicotiana species, performed during the breeding history of N. tabacum to confer resistance to pathogens. Seven fragments were associated with three different resistances: two for the blue-mold (Peronospora tabacina Adam) resistance derived from Nicotiana debneyi Domin, two for the Va gene (Potato Virus Y susceptibility), and three for the black root rot (Chalara elegans) resistance of N. debneyi origin. Some of these markers were converted into sequence characterized amplified region markers, and validated on recombinant inbred lines or doubled-haploid lines.

Chromosome Segregation↗
PubMed1995

Reconstructing strings from substrings.

We consider an interactive approach to DNA sequencing by hybridization, where we are permitted to ask questions of the form "is s a substring of the unknown sequence S?", where s is a specific query string. We are not told where s occurs in S, nor how many times it occurs, just whether or not s a substring of S. Our goal is to determine the exact contents of S using as few queries as possible. Through interaction, far fewer queries are necessary than using conventional fixed sequencing by hybridization (SBH) sequencing chips. We provide tight bounds on the complexity of reconstructing unknown strings from substring queries. Our lower bound, which holds even for a stronger model that returns the number of occurrence of s as a substring of S, relies on interesting arguments based on de Bruijn sequences. We also demonstrate that subsequence queries are significantly more powerful than substring queries, matching the information theoretic lower bound. Finally, in certain applications, something may already be known about the unknown string, and hence it can be determined faster than an arbitrary string. We show that building an optimal decision tree is NP-complete, then give an approximation algorithm that gives trees within a constant multiplicative factor of optimal.

Algorithms↗
PubMed2026

PhyloNaP: a user-friendly database of phylogeny for natural product-producing enzymes.

SUMMARY: Phylogenetic analysis is widely used to predict enzyme function, yet building annotated and reusable trees is labor-intensive and requires extensive knowledge about the specific enzymes. Existing resources rarely cover biosynthetic enzymes and lack the context needed for meaningful analysis. We present PhyloNaP, the first large-scale resource dedicated to phylogenies of biosynthetic enzymes. PhyloNaP provides ∼51 000 annotated and interactive trees enriched with chemical, functional, and taxonomic information. Users can classify their own sequences via phylogenetic placement, enabling functional inference in an evolutionary context. A contribution portal allows the community to submit curated trees. By combining scale, breadth of annotation, and interactive functionality, PhyloNaP fills a major gap in bioinformatics resources for enzyme discovery and annotation, with immediate applications to secondary metabolism and beyond. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at https://phylonap.cs.uni-tuebingen.de.

Phylogeny↗
PubMed1992

Histamine and antihistamines in anaesthesia and surgery: from experimental pharmacology to clinical decision making.

The problem of whether antihistamines (histamine H1 + H2-antagonists) should be administered prophylactically before surgical interventions rose after animal experiments with hypnotics, opioids, muscle relaxants and plasma substitutes. It could, however, not be solved by classical biomedical research, but needed a heuristic problem-solving strategy. This strategy was formalized and in this way changed into a scientific structure by the thinking-aloud technique and the building of a decision tree with 9 nodes and various study designs to answer questions at particular decision nodes. The first question, whether the incidence of the reactions was high, was answered by several controlled clinical trials. The second question of life-threatening degrees of severity in single cases, was answered by a drug surveillance study. The third question, of whether severe incidents could always be avoided was answered by medical audit. The same was the case if death had to be considered as the final therapeutic failure. The fifth question was, "are the risks of histamine release comparable to other risks in the perioperative period?" They were--if thromboembolism, infection and stress ulcers were considered. The sixth and seventh questions referred to an experimentally and clinically effective prophylaxis. They were answered by animal and clinical studies with histamine antagonists, mainly with dimetindene and cimetidine. Undesired, adverse reactions to prophylaxis are rare since the drugs are given only once. Prophylaxis was calculated to be fairly cost-effective. Problem-solving strategies are very helpful in transferring facts and conclusions from experimental basic research to clinical decision making. This was convincingly demonstrated in antihistamine prophylaxis in anaesthesia and surgery.

Anesthesia↗
PubMed1988

DNA and protein polymorphism: application to anthropology and human genetics.

In this paper, the author analyses the different approaches of the DNA polymorphism. Mitochondrial DNA, RFLP haplotypes associated with serum protein polymorphism, variability of some small regions of the genome detected by minisatellite probes are now well developed and often adapted to population analysis. The data gathered are used to build phylogenic or genealogic trees. Despite the limited number sampled in these investigations, it is obvious that they were obtained to establish a beginning of geographical map distribution of the DNA polymorphisms and to answer basic questions in Anthropology. In this sense, DNA polymorphism is a new way to obtain a large amount of information not available through the different polymorphisms previously performed. Today, the interpretation of the data on DNA polymorphism is based on archeological and prehistorical hypotheses. It is highly probable that for a long time, no phylogenic analysis will be able to determine the step of speciation, the period of emergence of primitive man and of his geographical origins. In some fields of anthropological investigations, studies on the DNA structure and organisation may bring new information on the genetic of skin pigmentation, eye and hair colours, body size, etc. But the essential aim of studies on humans cannot exist out of multidisciplinary follow up including sociology, biology, linguistics, behaviour and economy. Molecular biology of DNA is an additional method from which we can learn a lot about human genetic heterogeneity but man is a group, a society, a population, a tribe and not a certain amount of allele frequencies.

Anthropology, Physical↗
PubMed1996

Circular clustering of protein dihedral angles by Minimum Message Length.

Early work on proteins identified the existence of helices and extended sheets in protein secondary structures, a high-level classification which remains popular today. Using the Snob program for information-theoretic Minimum Message Length (MML) classification, we are able to take the protein dihedral angles as determined by X-ray crystallography, and cluster sets of dihedral angles into groups. Previous work by Hunter and States has applied a similar Bayesian classification method, AutoClass, to protein data with site position represented by 3 Cartesian co-ordinates for each of the alpha-Carbon, beta-Carbon and Nitrogen, totalling 9 co-ordinates. By using the von Mises circular distribution in the Snob program, we are instead able to represent local site properties by the two dihedral angles, phi and psi. Since each site can be modelled as having 2 degrees of freedom, this orientation-invariant dihedral angle representation of the data is more compact than that of nine highly-correlated Cartesian co-ordinates. Using the information-theoretic message length concepts discussed in the paper, such a more concise model is more likely to represent the underlying generating process from which the data came. We report on the results of our classification, plotting the classes in (phi, psi) space; and introducing a symmetric information-theoretic distance measure to build a minimum spanning tree between the classes. We also give a transition matrix between the classes and note the existence of three classes in the region phi approximately -1.09 rad and psi approximately -0.75 rad which are close on the spanning tree and have high inter-transition probabilities. This gives rise to a tight, abundant and self-perpetuating structure.

Computational Biology↗
PubMed1993

Synaptic integration in an excitable dendritic tree.

1. Compartmental modeling experiments were carried out in an anatomically characterized neocortical pyramidal cell to study the integrative behavior of a complex dendritic tree containing active membrane mechanisms. Building on a previously presented hypothesis, this work provides further support for a novel principle of dendritic information processing that could underlie a capacity for nonlinear pattern discrimination and/or sensory processing within the dendritic trees of individual nerve cells. 2. It was previously demonstrated that when excitatory synaptic input to a pyramidal cell is dominated by voltage-dependent N-methyl-D-aspartate (NMDA)-type channels, the cell responds more strongly when synaptic drive is concentrated within several dendritic regions than when it is delivered diffusely across the dendritic arbor. This effect, called dendritic "cluster sensitivity," persisted under wide-ranging parameter variations and directly implicated the spatial ordering of afferent synaptic connections onto the dendritic tree as an important determinant of neuronal response selectivity. 3. In this work, the sensitivity of neocortical dendrites to spatially clustered synaptic drive has been further studied with fast sodium and slow calcium spiking mechanisms present in the dendritic membrane. Several spatial distributions of the dendritic spiking mechanisms were tested with and without NMDA synapses. Results of numerous simulations reveal that dendritic cluster sensitivity is a highly robust phenomenon in dendrites containing a sufficiency of excitatory membrane mechanisms and is only weakly dependent on their detailed spatial distribution, peak conductances, or kinetics. Factors that either work against or make irrelevant the dendritic cluster sensitivity effect include 1) very high-resistance spine necks, 2) very large synaptic conductances, 3) very high baseline levels of synaptic activity, and 4) large fluctuations in level of synaptic activity on short time scales. 4. The functional significance of dendritic cluster sensitivity has been previously discussed in the context of associative learning and memory. Here it is demonstrated that the dendritic tree of a cluster-sensitive neuron implements an approximative spatial correlation, or sum of products operation, such as that which could underlie nonlinear disparity tuning in binocular visual neurons.

Animals↗
PubMedDate not supplied

Automated critiquing of medical decision trees.

The authors developed a decision tree-critiquing program (called BUNYAN) that identifies potential modeling errors in medical decision trees. The program's critiques are based on the structure of a decision problem, obtained from an abstract description specifying only the basic semantic categories of the model's components. A taxonomy of node and branch types supplies the primitive building blocks for representing decision trees. Bunyan detects potential problems in a model by matching general pattern expressions that refer to these primitives. A small set of general principles justifies critiquing rules that detect four categories of potential structural problems: impossible strategies, dominated strategies, unaccountable violations of symmetry, and omission of apparently reasonable strategies. Although critiquing based on structure alone has clear limitations, principled structural analysis constitutes the core of a methodology for reasoning about decision models.

Decision Trees↗
PubMed2004

Automated soil resources mapping based on decision tree and Bayesian predictive modeling.

This article presents two approaches for automated building of knowledge bases of soil resources mapping. These methods used decision tree and Bayesian predictive modeling, respectively to generate knowledge from training data. With these methods, building a knowledge base for automated soil mapping is easier than using the conventional knowledge acquisition approach. The knowledge bases built by these two methods were used by the knowledge classifier for soil type classification of the Longyou area, Zhejiang Province, China using TM bi-temporal imageries and GIS data. To evaluate the performance of the resultant knowledge bases, the classification results were compared to existing soil map based on field survey. The accuracy assessment and analysis of the resultant soil maps suggested that the knowledge bases built by these two methods were of good quality for mapping distribution model of soil classes over the study area.

Algorithms↗
PubMed2005

Shortest triplet clustering: reconstructing large phylogenies using representative sets.

BACKGROUND: Understanding the evolutionary relationships among species based on their genetic information is one of the primary objectives in phylogenetic analysis. Reconstructing phylogenies for large data sets is still a challenging task in Bioinformatics. RESULTS: We propose a new distance-based clustering method, the shortest triplet clustering algorithm (STC), to reconstruct phylogenies. The main idea is the introduction of a natural definition of so-called k-representative sets. Based on k-representative sets, shortest triplets are reconstructed and serve as building blocks for the STC algorithm to agglomerate sequences for tree reconstruction in O(n2) time for n sequences. Simulations show that STC gives better topological accuracy than other tested methods that also build a first starting tree. STC appears as a very good method to start the tree reconstruction. However, all tested methods give similar results if balanced nearest neighbor interchange (BNNI) is applied as a post-processing step. BNNI leads to an improvement in all instances. The program is available at http://www.bi.uni-duesseldorf.de/software/stc/. CONCLUSION: The results demonstrate that the new approach efficiently reconstructs phylogenies for large data sets. We found that BNNI boosts the topological accuracy of all methods including STC, therefore, one should use BNNI as a post-processing step to get better topological accuracy.

Algorithms↗