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At least 1,207 records · Page 67Linked to original sources
PubMed1988

Convection, diffusion and their interaction in the bronchial tree.

The bronchial tree is an asymmetric multi-generation conduit for air to pass through. Breathing is a time-varying, cyclic process. Therefore, gas transport in the bronchial tree during breathing is a problem with both spatial and temporal complexities. However, it is possible to gain a fair understanding of this complex process by examining the roles of bulk convection, molecular diffusion and the various modes of their interaction. Convection brings the inspired gas into the peripheral region of the lung and removes the mixed inspired-resident gas from the lung. During the post-inspiratory and post-expiratory pauses and in the very distal regions of the lung, molecular diffusion alone is responsible for the mixing process. Convection and diffusion together are responsible for establishing a quasi-steady front of the inspired gas in the peripheral lung region. The position of the front depends on lung volume, tidal volume, inspiratory flow-rate as well as diffusivity of the inspired gas. Taylor-type dispersion, while certainly existing in the lung, and despite its gas mixing potentials, is of questionable effectiveness in the overall gas transport process in the bronchial tree. The various modes of interaction between convection and diffusion are likely to improve gas mixing in the bronchial tree and have an effect on the phase II of the single-breath washout curve.

Animals↗
PubMed1995

Molecular phylogeny of Allomyces macrogynus: congruency between nuclear ribosomal RNA- and mitochondrial protein-based trees.

We have sequenced the nuclear and mitochondrial small subunit rRNA genes (rns) and the mitochondrial genes coding for subunits 1 and 3 of the cytochrome oxidase (cox1 and cox3, respectively) of the chytridiomycete Allomyces macrogynus. Phylogenetic trees inferred from the derived COX1 and COX3 proteins and the nuclear rns sequences show with good bootstrap support that A. macrogynus is an early diverging fungus. The trees inferred from mitochondrial rns sequences do not yield a topology that is supported by bootstrap analysis. The similarity and the relative robustness of the nuclear rns and the mitochondrial protein-derived phylogenetic trees suggest that protein sequences are of higher value than rRNA sequences for reconstructing mitochondrial evolution. In addition, our trees support a monophyletic origin of mitochondria for the range of analyzed eukaryotes.

Ascomycota↗
PubMed1994

Estimating errors and confidence intervals for branch lengths in phylogenetic trees by a bootstrap approach.

A method, based on the bootstrap procedure, is proposed for the estimation of branch-length errors and confidence intervals in a phylogenetic tree for which equal rates of substitution among lineages do not necessarily hold. The method can be used to test whether an estimated internodal distance is significantly greater than zero. In the application of the method, any estimator of genetic distances, as well as any tree reconstruction procedure (based on distance matrices), can be used. Also the method is not limited by the number of species involved in the phylogenetic tree. An example of the application of the method in the reconstruction of the phylogenetic tree for the four hominoid species--human, chimpanzee, gorilla, and orangutan--is shown.

Animals↗
PubMed1990

The development of the human placental villous tree.

The present investigation was undertaken in order to achieve a better understanding of the dynamics of placental villous differentiation. Villous trees from human placentas from different stages of pregnancy (first trimester to full term) were isolated and studied by light microscopy and scanning electron microscopy. For light microscopy the trees were serially sectioned and two-dimensionally reconstructed. For scanning electron microscopy complete villous trees or freeze-cracked villi were studied. The most important finding was that the mesenchymal villi are continuously newly formed out of the trophoblastic sprouts throughout pregnancy. Because of this they exist in all stages of pregnancy and have to be considered the basis for growth and differentiation of the villous trees. In the first two trimesters they are the forerunners of the immature intermediate villi, whereas in the last trimester the mesenchymal villi are transformed into mature intermediate villi. The immature intermediate villi formed during the first two trimesters are developmental steps towards the stem villi. On the other hand, the mature intermediate villi, which only are developed during the last trimester, produce numerous terminal villi. The latter are not active outgrowths caused by proliferation of the trophoblast, but rather passive protrusions induced by capillary coiling due to excessive longitudinal growth of the fetal capillaries within the mature intermediate villi.

Cell Differentiation↗
PubMed1991

Permanent alterations of the dendritic tree of cerebellar Purkinje neurons in the rat following postnatal exposure to cis-dichlorodiammineplatinum.

The aim of this study was to characterize further the effect of cis-dichlorodiammineplatinum (cisDDP) on cerebellar Purkinje neurons of the immature rat. Ten-day-old rats were treated with cisDDP subcutaneously and killed after 1, 7, 20 or 65 days. The cerebellar vermis was impregnated by the Golgi-Cox method to evaluate the extent of morphological maturation of the Purkinje cell dendritic tree. One day after treatment, the dendritic network of Purkinje cells of treated animals was poorly developed and the cell somata still showed numerous perisomatic processes. This indicates that cisDDP interferes with the organization of microtubules and microfilaments by the cell. Later, several abnormal shapes of the Purkinje cell dendritic tree were observed. These included: (1) elongated primary dendrites; (2) asymmetrical dendrites; (3) sprouting of secondary and spiny branches in two planes of the molecular layer; and (4) damming of spiny branchlets at the pial surface. Moreover, all the dendritic networks of Purkinje cells in treated animals were of a lower Strahler order than in controls. All these data suggest that the late anomalies of the dendritic trees are secondary to the general cisDDP-induced damage of the cerebellar cortex, rather than being a primary effect of the drug on the dendritic tree growth.

Animals↗
PubMed1989

Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea.

A maximum likelihood method for inferring evolutionary trees from DNA sequence data was developed by Felsenstein (1981). In evaluating the extent to which the maximum likelihood tree is a significantly better representation of the true tree, it is important to estimate the variance of the difference between log likelihood of different tree topologies. Bootstrap resampling can be used for this purpose (Hasegawa et al. 1988; Hasegawa and Kishino 1989), but it imposes a great computation burden. To overcome this difficulty, we developed a new method for estimating the variance by expressing it explicitly. The method was applied to DNA sequence data from primates in order to evaluate the maximum likelihood branching order among Hominoidea. It was shown that, although the orangutan is convincingly placed as an outgroup of a human and African apes clade, the branching order among human, chimpanzee, and gorilla cannot be determined confidently from the DNA sequence data presently available when the evolutionary rate constancy is not assumed.

Animals↗
PubMed1991

The branching order of mammals: phylogenetic trees inferred from nuclear and mitochondrial molecular data.

In order to clarify some controversial phylogenies such as those regarding the triplet of human, rodent, and cow and the evolutionary position of Lagomorpha with respect to other mammals, we have analyzed both nuclear and mitochondrial genes using the stationary Markov model developed in our laboratory. We found that the two sets of genes give different results. In particular the mitochondrial tree showed rabbit linked first to rodents and the rabbit-rodents branch linked to artiodactyls with human as the outgroup. The most favorite nuclear tree showed human linked first to artiodactyls and the human-artiodactyls branch linked to rabbit with rodents as the outgroup. The obvious questions, (1) which tree is the correct one, or (2) both trees can be incorrect, and (3) how can we explain such an evolutionary pattern, are discussed on the basis of our limited knowledge of factors that influence the clocklike behavior of biological macromolecules.

Animals↗
PubMed1991

Three-dimensional knowledge driven reconstruction of coronary trees.

A knowledge-driven approach to the three-dimensional reconstruction of coronary artery trees by means of two X-ray projections is proposed. The spatial reconstruction of the tree skeleton is discussed. A binary tree model of the arterial structure and its projections is employed. Consequently, the reconstruction of the three-dimensional tree skeleton is achieved by (a) matching the skeletons of corresponding pairs of vascular segments in the two views and (b) back-projecting the coupled skeleton projections. From a geometrical point of view, the matching problem is, in general, ill-conditioned. For this reason, additional information sources were used. Thus, the matching phase is accomplished by using both the imaging geometry information, as well as anatomical and topological knowledge, about the coronary arteries coded in a rule base. As far as the back-projection phase is concerned, an algorithm was developed based on: (1) the imaging geometry, (2) the bounding of the back-projection error and (3) a contiguity criterion.

Algorithms↗
PubMed2004

Toxicity of tributyltin to willow trees.

BACKGROUND: Tributyltin is an organotin compound, used as an antifouling agent in ship paint, with heavy impact on the marine environment. Contaminated dredged harbor sludge is now dumped on land. The toxicity of tributyltin (TBT) to trees has not yet been quantified. Eventually, a vegetation cover on the dumped sludge could be established for the purpose of non-food cash crop production and phytoremediation. METHODS: The phytotoxicity of tributyltin chloride (TBTCl) and tributyltin hydride (TBTH) was measured at pH 4 and at pH 7 using the willow tree transpiration test. Different pH levels of the nutrient solutions were achieved by adding ammonium salt (low pH) or nitrate (high pH) as nitrogen source. RESULTS AND DISCUSSION: At low pH (pH 4), all trees showed symptoms of poor health. Transpiration decreased at concentrations above or equal to 0.1 mg TBTCl/l and 1 mg TBTH/L. The TBT toxicity was more pronounced at pH 7. The trees survived even the highest dose of 10 mg/l TBTCl or TBTH, although their growth and transpiration was strongly reduced. CONCLUSION: In contrast to other organisms, TBTCl and TBTH were less toxic to higher plants. RECOMMENDATIONS AND OUTLOOK: The toxicity of TBT is no hindrance for establishing vegetation on TBT-contaminated sludge. Phytoremediation and cash crop production could be possible with suitable plants.

Environmental Pollutants↗
PubMed2005

Areal specialization of pyramidal cell structure in the visual cortex of the tree shrew: a new twist revealed in the evolution of cortical circuitry.

Cortical pyramidal cells, while having a characteristic morphology, show marked phenotypic variation in primates. Differences have been reported in their size, branching structure and spine density between cortical areas. In particular, there is a systematic increase in the complexity of the structure of pyramidal cells with anterior progression through occipito-temporal cortical visual areas. These differences reflect area-specific specializations in cortical circuitry, which are believed to be important for visual processing. However, it remains unknown as to whether these regional specializations in pyramidal cell structure are restricted to primates. Here we investigated pyramidal cell structure in the visual cortex of the tree shrew, including the primary (V1), second (V2) and temporal dorsal (TD) areas. As in primates, there was a trend for more complex branching structure with anterior progression through visual areas in the tree shrew. However, contrary to the trend reported in primates, cells in the tree shrew tended to become smaller with anterior progression through V1, V2 and TD. In addition, pyramidal cells in V1 of the tree shrew are more than twice as spinous as those in primates. These data suggest that variables that shape the structure of adult cortical pyramidal cells differ among species.

Animals↗
PubMed2006

Plant regeneration through somatic embryogenesis from tissues of mature oak trees: true-to-type conformity of plantlets by RAPD analysis.

Somatic embryogenesis was induced in expanding leaf explants excised from epicormic shoots forced from branch segments taken at four different times of year from a mature oak (Quercus robur L.). Branch segments 2-4 cm in diameter produced most shoots when collected in March. Somatic embryos were induced on explants derived from branches of all collection dates, although collection in November seemed to afford the best results. Germination and conversion ability of embryos of embryogenic lines derived from six oak trees depended heavily on genotype, conversion rates ranging from 0 to 70%. RAPD analyses found no evidence of genetic variation either within or between the embryogenic lines established from three of these trees, or between these lines and the trees of origin, or between somatic embryo derived plantlets and the trees of origin. The embryogenic system used in this study appears to be suitable for true-to-type clonal propagation of mature oak genotypes.

Culture Media↗
PubMed2005

A preliminary reconstruction (A.D. 1635-2000) of spring precipitation using oak tree rings in the western Black Sea region of Turkey.

Tree-ring data for Turkey are crucial to the understanding of the climatological effect of drought and rainfall from one era to the next. To this end, the present study reconstructed precipitation patterns in the western Black Sea region of Turkey. Tree-ring widths of oak trees were used to reconstruct March-June precipitation patterns for the years A.D. 1635-2000. According to the findings, during the past four centuries drought events in this region persisted for no more than 2 years, and extreme dry and wet events occurred generally in 1-year intervals. Historical records of droughts in Anatolia and neighboring countries corroborate the data furnished by tree-ring widths to indicate that major droughts and famine events occurred in 1725, 1757, 1887, 1890-1891, 1893-1894 and 1927-1928.

Climate↗
PubMed2006

Reproductive success and distance to conspecific adults in the sparsely distributed tree Kalopanax pictus.

To understand how a sparsely distributed species can maintain viable populations, and with a particular interest in distance-dependent reproductive success, we investigated the ovule survival and the factors that determine the survival for sparsely distributed Kalopanax pictus (Araliaceae) in a temperate forest landscape around the Ogawa Forest Reserve, central Japan. We found 154 potentially mature trees (>20 cm diameter at breast height) in a 600-ha site. The year 2000 was a mass flowering year for K. pictus; 96.8% of the trees examined flowered in that year; however, this was less than half of the trees that flowered in other years. The flowers of K. pictus include protandrous inflorescences, which bloom on individual tress in midsummer when few other tree species bloom. We conducted pollination experiments with out-crossed, self-pollinated, bagged, and control inflorescences. Results suggest that self-pollination is limited, partially by low self-compatibility and partially by protandry. Ovule survival from the flower to the seed stages was not dependent on the temporal flowering density of conspecific adults. The flowering habit and presence of effective pollinators may allow K. pictus to avoid the negative effects of sparse distribution on pollination efficiency. However, ovule survival during the ovary development stage depended on infection by a species-specific fungus, Mycosphaerella acanthopanacis. The fungus damages leaves, and the infection intensity depends on the distance between conspecific K. pictus adults. Thus, an advantage of sparse distribution in K. pictus is disease avoidance, whereas its disadvantages are overcome by pollination efficiency.

Ecosystem↗
PubMed2005

Analysis of telomere length and telomerase activity in tree species of various life-spans, and with age in the bristlecone pine Pinus longaeva.

Normal somatic cells have a finite replicative capacity. With each cell division, telomeres (the physical ends of linear chromosomes) progressively shorten until they reach a critical length, at which point the cells enter replicative senescence. Some cells maintain telomere length by the action of the telomerase enzyme. The bristlecone pine, Pinus longaeva, is the oldest known living eukaryotic organism, with the oldest on record turning 4770 years old in 2005. To determine what changes occur, if any, in telomere length and telomerase activity with age, and what roles, if any, telomere length and telomerase activity may play in contributing to the increased life-span and longevity of P. longaeva with age, as well as in other tree species of various life-spans, we undertook a detailed investigation of telomere length and telomerase activity in such trees. The results from this study support the hypothesis that both increased telomere length and telomerase activity may directly/indirectly contribute to the increased life-span and longevity evident in long-lived pine trees (2000-5000 year life-spans) compared to medium-lived (400-500 year life-span) and short-lived (100-200 year life-span) pine trees, as well as in P. longaeva with age.

Aging↗
PubMed2025

Beyond Level-1: Identifiability of a Class of Galled Tree-Child Networks.

Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in justifying methods. This work obtains strong identifiability results for large sub-classes of galled tree-child semidirected networks. Some of the conditions our proofs require, such as the identifiability of a network's tree of blobs or the circular order of 4 taxa around a cycle in a level-1 network, are already known to hold for many data types. We show that all these conditions hold for quartet concordance factor data under various gene tree models, yielding the strongest results from 2 or more samples per taxon. Although the network classes we consider have topological restrictions, they include non-planar networks of any level and are substantially more general than level-1 networks - the only class previously known to enjoy identifiability from many data types. Our work establishes a route for proving future identifiability results for tree-child galled networks from data types other than quartet concordance factors, by checking that explicit conditions are met.

Mathematical Concepts↗
PubMed2003

Tree nut allergy.

Tree nuts are clinically associated with severe immunoglobulin E-mediated systemic allergic reactions independent of pollen allergy and with reactions that are usually confined to the oral mucosa in patients with immunoglobulin E directed toward cross-reacting pollen allergens. The latter reactions can progress to severe and life-threatening episodes in some patients. Many patients with severe tree nut allergy are co-sensitized to peanut. Clinical studies on cross-reactivity between the tree nuts are few in number, but based on reports to date, avoidance of the other tree nuts once sensitivity is diagnosed appears prudent unless specific challenges are performed to ensure clinical tolerance. Even then, great care must be taken to avoid cross-contamination. As with other severe food allergies, a recurrent problem in clinical management is the failure of physicians to prescribe self-injectable epinephrine to patients who are at risk of anaphylaxis.

Clinical Trials as Topic↗
PubMed1976

The growth of the dendritic trees of Purkinje cells in the cerebellum of the rat.

The growth of Purkinje cell dendritic trees in the cerebellum of the rat was studied over the first 50 days of life, using the technique of network analysis and the Golgi-Cox impregnation method. Our findings showed that a growth spurt occurred from the 10th to 30th day post partum (pp) and involved the production of a massive number of branches of fairly constant length. Growth of the tree occurred firstly in the lateral domain, so that by 15 days pp most trees were of adult width. Thereafter, increases in height occurred until 30 days pp. Associated with this change in direction of growth, from the mainly transverse to the vertical plane, was a deviation from the normal random pattern of branching of the tree, but this was reestablished when reorientation was complete, and growth in the vertical plane underway. The lengths of proximal segments increased once they had become established, but distal branches probably maintained a constant length. The above results, together with changes in segment length, trichotomy, branching probability, and growth cone morphology during development have been discussed in relation to current concepts of dendritic growth.

Age Factors↗
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↗