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PubMed1976

Atmospheric pollen counts in Tehran, Iran, 1974.

Daily pollen counts were made in Tehran by placing a Durham sampler on the roof of the College of Pharmacy building at the University of Tehran. Three pollen seasons were identified in Tehran. Tree season extended from the first week of February through the middle of October. Important pollens of tree season were Willow, Cedar, Sycamore, Pine, Alder, Walnuts, Elm, Cottonwood, Oak and/or Maple, Birch, and Beech. The grass season started from the first week of May and extended into the second week of November. The weed season began at the middle of May and lasted until the last week of December. Important weed pollens belonged to various members of the Order Chenopodials, particularly Burning Bush, and Russian Thistle. Sagebrush and English Plantain were also abundant during the weed season.

Air Pollution↗

PubMed2001

[Study on molecular phylogeny of Schistosoma sinensium based on nuclear ribosomal DNA].

OBJECTIVE: To determine the phylogenetic relationships between Schistosoma sinensium and other Schistosomatid species using DNA sequence data. Two segments of the nuclear rDNA repeat, the second internal spacer (ITS2) and large subunit (LSU/12S) were selected for sequencing. METHODS: Adult worms stored in 100% methanol were washed 3 times with 0.1 x TE (pH8.0) and the genomic DNA was extracted by the GNT-K method. The target regions were amplified by PCR using specific primers. The PCR products were purified before ligation into the plasmid pT-adv (Clontech). Recombinant plasmids were amplified in E. coli (strain TOP10), extracted and purified using routine methods and then sequenced using M13 primers (F/R) on a Licor long-read auto-sequencer. Sequences of related schistosomes were retrieved from GenBank and aligned with our data in the sequence editor ESEE. Gene trees were constructed in PHYLIP (Version 3.6 alpha July, 2,000) and MEGA (version 2.0 beta build 3) using both Maximum Parsimony and Neighbor-Joining methods. For parsimony analysis, all characters were treated as unordered and with equal weights. At least 3,000 cycles of bootstrapping were carried out. For analysis in MEGA, all gap columns were deleted. Schistosomatium douthitti and Trichobilharzia were used as outgroups. RESULTS: The ITS2 and LSU sequences of Schistosoma sinensium were obtained. The ITS2 sequence of Trichobilharzia sp. was reported here for the first time. CONCLUSION: The phylogenetic trees from these data of nuclear rDNA suggested that S. sinensium belongs to the Asian schistosome group. And this species might be an ancient member in the Asian clade.

Animals↗

PubMed2004

A beam tracing method for interactive architectural acoustics.

A difficult challenge in geometrical acoustic modeling is computing propagation paths from sound sources to receivers fast enough for interactive applications. This paper describes a beam tracing method that enables interactive updates of propagation paths from a stationary source to a moving receiver in large building interiors. During a precomputation phase, convex polyhedral beams traced from the location of each sound source are stored in a "beam tree" representing the regions of space reachable by potential sequences of transmissions, diffractions, and specular reflections at surfaces of a 3D polygonal model. Then, during an interactive phase, the precomputed beam tree(s) are used to generate propagation paths from the source(s) to any receiver location at interactive rates. The key features of this beam tracing method are (1) it scales to support large building environments, (2) it models propagation due to edge diffraction, (3) it finds all propagation paths up to a given termination criterion without exhaustive search or risk of under-sampling, and (4) it updates propagation paths at interactive rates. The method has been demonstrated to work effectively in interactive acoustic design and virtual walkthrough applications.

Journal Article↗

PubMedDate not supplied

Genotyping of mature trees of Entandrophragma cylindricum with microsatellites.

We have characterized 10 microsatellite loci for the tropical tree Entandrophragma cylindricum (Sprague) Sprague (sapelli) in order to genotype individuals in forest stands for estimation of the genetic diversity of the species. We used the technique of building a (GA)n microsatellite-enriched library by capture with streptavidin-coated magnetic beads. We assessed the polymorphism of seven microsatellites in 186 mature trees in a selectively logged stand (Dimako) and an unlogged stand (Ndama), both in Cameroon. All the loci were polymorphic, and the number of alleles was high, ranging from eight to 36, with a mean of 22.1. Both stands showed the same high level of genetic diversity (mean H(E) = 0.85) and a low genetic differentiation (FST = 0.007), indicating that genetic diversity was within rather than among populations. Five and three out seven loci in Dimako and Ndama, respectively, showed a deficit of heterozygotes. The seven loci enabled more than 97% of the mature trees in each stand to be identified. It was concluded that these markers can be efficiently used for gene flow studies.

Cameroon↗

PubMed2003

Effect of aromatic cedar mulch on Argentine ant (Hymenoptera: Formicidae) foraging activity and nest establishment.

In the laboratory, Argentine ant, Linepithema humile (Mayr), mortality was positively correlated to the length of an aromatic cedar mulch section that had to be crossed before food could be reached. When ants could access food without crossing the mulch, mortality was not correlated to mulch section length. In the field, Argentine ants showed a tendency to avoid aromatic cedar mulch as a nesting substrate. In plant beds alongside buildings the number of ant nests (pockets containing brood) found was not significantly different between aromatic cedar and cypress mulch. However, when pine straw mulch around oak trees was replaced with aromatic cedar or cypress mulch, a similar number of ant nests was found in the cypress mulch as in the original pine straw, whereas numbers in aromatic cedar mulch were significantly lower. Also, fewer ants were trailing on the trees surrounded by aromatic cedar mulch compared with cypress mulch or the original pine straw. The number of ants attracted to apple jelly baits placed alongside the buildings did not differ between mulch types; neither did the number of ant trails crossing the mulch beds around the buildings. We suggest that aromatic cedar mulch may help control Argentine ants and reduce insecticide input when applied in combination with conventional control methods.

Animals↗

PubMed2006

The excellence of Aomori Hiba (Hinokiasunaro) in its use as building materials of Buddhist temples and Shinto shrines.

Five hinokitiol-related compounds (hinokitiol (beta-thujaplicin), beta-dolabrin, gamma-thujaplicin, 4-acetyltropolone and alpha -thujaplicin) isolated from the acid oil of Aomori Hiba (Thujopsis dolabrata Sieb. et Zucc. var hondai MAKINO) showed clear antifungal activity against wood-rotting fungi. These compounds have obvious insecticidal effects on termites. They also exhibited potent acaricidal activity against mites. The above-mentioned features suggest that Konjiki-do, a well known national treasure, one of the buildings in Chuson-ji Temple of Iwate Prefecture, Japan, which was built of wood from the tree containing these five compounds, was kept from harm against noxious insects and wood-rotting fungi for a long time of about 840 years, until it was extensively repaired in 1962. In addition to Konjiki-do, there are some old famous Buddhist temples and Shinto shrines using Aomori Hiba. From the results, it was found that Aomori Hiba (Hinokiasunaro) is excellent for use as building materials.

Buddhism↗

PubMed2002

Evolution in medical decision making.

The classical approach to medical decision making can be limited by the underlying theories. The evolutionary computation is a different concept, which can find many different solutions of the problem. In medicine, this is useful because of different expectations the decision system must face. We implemented a tool for genetic induction of vector decision trees, which are a good choice for a medical decision model because of their simplicity and transparency. The vector decision tree gives multiple classifications in one single pass. Evolutionary development of such trees achieved good results when the results were statistically compared to those of other classical methods. For medical interpretation however a cooperation with doctors is needed to verify the model build.

Algorithms↗

PubMed2001

Exact morphometric modeling of rat lungs for predicting mechanical impedance.

We have developed a computational approach that allows for one-to-one mapping of the airway anatomy when predicting the overall lung mechanical properties and their response to explicit constriction patterns imposed on the airway tree. Specifically, we have exploited the database from Raabe et al. (LF-53 Albuquerque, NM: Lovelace foundation for radical Education and Research), to build the first anatomically based computational model of the rat. The model was then used to predict the response to homogeneous and heterogeneous peripheral airway constriction. Unlike in humans, the inherent asymmetry in the airway tree of rats is predicted to be a dominant contributor to the frequency dependence of lung resistance and elastance even if the constriction is imposed homogeneously. A similar approach would, in principal, be applicable for humans, but the Raabe data is not sufficiently complete to permit this.

Algorithms↗

PubMedDate not supplied

2D QSAR consensus prediction for high-throughput virtual screening. An application to COX-2 inhibition modeling and screening of the NCI database.

Using classification (SOM, LVQ, Binary, Decision Tree) and regression algorithms (PLS, BRANN, k-NN, Linear), this paper details the building of eight 2D-QSAR models from a 266 COX-2 inhibitor training set. The predictive performances of these eight models were subsequently compared using an 88 COX-2 inhibitor test set. Each ligand is described by 52 2D descriptors expressed as van der Waals Surface Areas (P_VSA) and its COX-2 binding IC50. One of our best predictive models is the neural network model (BRANN), which is able to select a subset, from the 88 ligand test set, that contains 94% COX-2 active inhibitors (pIC50>7.5) and detects 71% of all the actives. We then introduce a QSAR consensus prediction protocol that is shown to be more predictive than any single QSAR model: our C3 consensus approach is able to select a subset from the 88 ligand test set that contains 94% active inhibitors and 83% of all the actives. The 2D QSAR consensus protocol was finally applied to the high-throughput virtual screening of the NCI database, containing 193,477 organic compounds.

Cyclooxygenase 2↗

PubMedDate not supplied

CliniWeb: managing clinical information on the World Wide Web.

The World Wide Web is a powerful new way to deliver on-line clinical information, but several problems limit its value to health care professionals: content is highly distributed and difficult to find, clinical information is not separated from non-clinical information, and the current Web technology is unable to support some advanced retrieval capabilities. A system called CliniWeb has been developed to address these problems. CliniWeb is an index to clinical information on the World Wide Web, providing a browsing and searching interface to clinical content at the level of the health care student or provider. Its database contains a list of clinical information resources on the Web that are indexed by terms from the Medical Subject Headings disease tree and retrieved with the assistance of SAPHIRE. Limitations of the processes used to build the database are discussed, together with directions for future research.

Abstracting and Indexing↗

PubMed2002

Accelerating approximate subsequence search on large protein sequence databases.

Bioinformatics has become an active research area in recent years. The amount of mapped sequences doubles every fourteen months. BLAST has been widely employed for retrieving sequences which has similar portion(s) to a given sequence. However, BLAST has to scan the entire database every time when a query is issued. This can be very time consuming especially when the database is large. In this paper, we study the problem on how to build a persistent index structure for protein sequences to support approximate match. The suffix tree has been proposed as a solution to index sequence database and has been deployed on organizing DNA sequences (Hunt et al. 2001). Unfortunately, it suffers from the problem of "memory bottleneck" that prevents it from being applied efficiently to a large database. The performance even degrades further for protein database due to a larger fanout at each node. Here, we employ an indexing structure, called BASS-tree, to support approximate match in sublinear time on a large protein database. We call this indexing method as sequence approximate match (SAM) index method. The search of approximate matches can be properly directed to the portion in the database with a high potential of matching quickly. It has been demonstrated in our experiments that the potential performance improvement is in an order of magnitude over alternative methods such as the BLAST algorithm and the suffix tree.

Algorithms↗

PubMed1999

Distribution of domestic Psocoptera in Madrid apartments.

Domestic Psocoptera were sampled in Madrid throughout a complete year (1991-92) by means of sticky traps in bathrooms, kitchens and inside windows. A total of 409 individuals comprising ten species of psocids was caught from 4056 traps inspected fortnightly. The predominant species were Liposcelis decolor, Li. brunnea, Psyllipsocus ramburi, Li. bostrychophila, Li. pearmani, Dorypteryx domestica and Lachesilla pedicularia, in descending order of abundance. Apartments were classified according to eight quantitative variables: age and area of building, level of apartment (i.e. storey), numbers of windows, inhabitants, their pets (birds and mammals), ornamental plants indoors; and two qualitative factors: floor material and presence or absence of trees adjacent to the house. Psocid communities in human habitations were assessed by the island biogeography theory: diversity increased with apartment size and the number of species decreased with building date. Psocid populations were most abundant in bathrooms, which presumably act as sources for dispersal to other parts of the premises. No other significant correlations were found with the other housing factors investigated. Whereas psocids were active indoors during all months of the year, the peak prevalence was in summer, July and August, one or two months ahead of the local seasonal pattern for non-domestic psocids. Although psocids are usually not seriously unhygienic, causing only minor problems of contamination and allergies, this information should help towards their environmental control.

Animals↗

PubMed2003

Genetic characterization of environmental isolates of the Cryptococcus neoformans species complex from Brazil.

The genetic affiliation of a large number of isolates of the Cryptococcus neoformans species complex from environmental sources in Brazil has been investigated using amplified fragment length polymorphism (AFLP). The strains of C. neoformans isolated from a single tree, as well as from neighbouring trees, showed high similarity values (> 95%) of their AFLP patterns, thus suggesting considerable genetic homogeneity. The majority of isolates of C. neoformans belonged to AFLP genotype 1, and had serotype A and mating type alpha (= C. neoformans var. grubii). Three isolates belonged to AFLP genotype 2, with serotype D and mating type alpha (= C. neoformans var. neoformans). One isolate, obtained from a building in Rio de Janeiro inhabited by pigeons, belonged to the AD hybrid AFLP genotype 3. All isolates from trees of C. neoformans var. gattii (= C. gattii) belonged to AFLP genotype 6, and their banding patterns showed relatively low genetic homogeneity with a similarity value of about 76%. Isolates of this genotype occupy an environmental niche in the Americas, and they may cause disease in non-AIDS and AIDS patients as well.

Air Microbiology↗

PubMed2004

Aerosol particle deposition and distribution in bifurcating ventilation ducts.

The quantitative information gained from detailed studies of particle deposition in ducts is important, for example, to evaluate human exposure to particles within buildings, implement cleaning strategies for ventilation ducts and also understand particulate deposition in the respiratory tree. For this purpose, an experimental study for aerosol particles of diameters ranging from 8.1 to 23.2 microm was conducted in a curved bifurcating ventilation duct. At the bend segment of the duct, the particle size, bend angle, curvature ratio and Reynolds number affect aerosol deposition significantly. On the other hand, tests conducted on the bifurcating segments show that deposition increases with particle size and Reynolds number. Accumulation of particles occurs mainly around the bend segment and the ridge of carina of the bifurcation. In all segments of the duct models, particle deposition is found to be enhanced with increasing humidity which increases from 66 to 95% (i.e., close the saturation). A physical interpretation of the results obtained is also presented.

Aerosols↗

PubMedDate not supplied

[Economic evaluation of voriconazole versus amphotericin B in the treatment of invasive aspergilosis].

OBJECTIVE: Invasive aspergillosis is an infection with high incidence and mortality. Voriconazole is a new antifungal agent that presents a high efficacy against Aspergillus. The aim of this evaluation was to carry out a pharmacoeconomic analysis of the use of voriconazole versus amphotericin B deoxycholate in the treatment of invasive aspergillosis in Spain. MATERIAL AND METHODS: A cost-effectiveness analysis has been performed by building a decision analytical model. Effectiveness data, probabilities of the different branches of the decision tree and consumption of healthcare resources were obtained from a clinical trial that compared voriconazole versus amphotericin B in the treatment of invasive aspergillosis and from a local expert panel in order to incorporate the model in the daily medical practice in our country. Only direct medical costs were included in the model (drug acquisition, length of hospital stay, analytical tests and treatment of therapeutic failures). The perspective chosen for this analysis was hospital assistance and the time horizon selected was 12 weeks, the maximum time that patients were followed up in the referenced clinical trial. RESULTS: Therapeutic success was reached in 52.8% of patients treated with voriconazole and in 31.6% of the group treated with amphotericin B. The cost of treating a patient with voriconazole or amphotericin B was of 56,296 and 56,382 Euros respectively, while the cost/effectiveness ratio was of 106,621 and 178,424 Euros. The incremental analysis performed shows how the use of voriconazole versus amphotericin B produces a healthcare resources saving of 406 Euros per patient. CONCLUSIONS: Voriconazole is more efficient than amphotericin B deoxycholate in the treatment of invasive aspergillosis, (thus) resulting in healthcare resources saving due to better clinical results with lower associated costs.

Pyrimidines↗

PubMed2006

Importance of species interactions to community heritability: a genetic basis to trophic-level interactions.

Recent community genetics studies have shown that specific genotypes of a host plant support distinct arthropod communities. Building upon these findings, we examined the hypothesis that a trophic community consisting of cottonwood trees, a galling herbivore and avian predators could also be related to the genetics of the host tree. We found genetic correlations among phytochemistry of individual tree genotypes, the density of a galling herbivore, and the intensity of avian predation on these herbivores. We detected significant broad-sense heritability of these interactions that range from H(B)2 = 0.70 to 0.83. The genetic basis of these interactions tended to increase across trophic levels suggesting that small genetic changes in the cottonwood phenotype could have major consequences at higher trophic levels affecting species interactions and energy flow. These findings show a heritable basis to trophic-level interactions indicating that there is a significant genetic basis to community composition and energy flow that is predictable by plant genotype. Our data clearly link plant genetics to patterns of avian foraging and show that species interactions are important components of community heritability and ecosystem processes. Overall, these data support the hypothesis that evolution of plant traits can alter trophic-level interactions and community composition.

Animals↗

PubMed2002

Building an asynchronous web-based tool for machine learning classification.

Various unsupervised and supervised learning methods including support vector machines, classification trees, linear discriminant analysis and nearest neighbor classifiers have been used to classify high-throughput gene expression data. Simpler and more widely accepted statistical tools have not yet been used for this purpose, hence proper comparisons between classification methods have not been conducted. We developed free software that implements logistic regression with stepwise variable selection as a quick and simple method for initial exploration of important genetic markers in disease classification. To implement the algorithm and allow our collaborators in remote locations to evaluate and compare its results against those of other methods, we developed a user-friendly asynchronous web-based application with a minimal amount of programming using free, downloadable software tools. With this program, we show that classification using logistic regression can perform as well as other more sophisticated algorithms, and it has the advantages of being easy to interpret and reproduce. By making the tool freely and easily available, we hope to promote the comparison of classification methods. In addition, we believe our web application can be used as a model for other bioinformatics laboratories that need to develop web-based analysis tools in a short amount of time and on a limited budget.

Algorithms↗

PubMed2006

Imputation methods to improve inference in SNP association studies.

Missing single nucleotide polymorphisms (SNPs) are quite common in genetic association studies. Subjects with missing SNPs are often discarded in analyses, which may seriously undermine the inference of SNP-disease association. In this article, we develop two haplotype-based imputation approaches and one tree-based imputation approach for association studies. The emphasis is to evaluate the impact of imputation on parameter estimation, compared to the standard practice of ignoring missing data. Haplotype-based approaches build on haplotype reconstruction by the expectation-maximization (EM) algorithm or a weighted EM (WEM) algorithm, depending on whether case-control status is taken into account. The tree-based approach uses a Gibbs sampler to iteratively sample from a full conditional distribution, which is obtained from the classification and regression tree (CART) algorithm. We employ a standard multiple imputation procedure to account for the uncertainty of imputation. We apply the methods to simulated data as well as a case-control study on developmental dyslexia. Our results suggest that imputation generally improves efficiency over the standard practice of ignoring missing data. The tree-based approach performs comparably well as haplotype-based approaches, but the former has a computational advantage. The WEM approach yields the smallest bias at a price of increased variance.

Algorithms↗