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PubMed2003

Characteristics of trees drawn by patients with paranoid schizophrenia.

The objective of the present study was to investigate the relationship between schizophrenia subtype and morphological characteristics of trees drawn in the Baum test. Subjects comprised the following three groups: 20 patients diagnosed with paranoid schizophrenia according to International Classification of Diseases (10th revision; ICD-10) criteria; 26 patients with non-paranoid schizophrenia according to ICD-10 criteria; and 53 healthy individuals. Differences in psychiatric symptoms as assessed using the Brief Psychiatric Rating Scale (BPRS) score were compared between patients with paranoid and non-paranoid schizophrenia. In addition, differences in two morphological characteristics of trees, namely trunk-to-crown ratio and trunk end opening, were compared between the three groups. No differences in psychiatric symptoms were identified between patients with paranoid and non-paranoid schizophrenia. Conversely, mean +/- SD trunk-to-crown ratio was 13.1 +/- 8.0 for patients with non-paranoid schizophrenia, 8.8 +/- 4.6 for patients with paranoid schizophrenia, and 5.4 +/- 3.4 for healthy individuals. Significant differences were identified between all three groups. Furthermore, mean trunk end opening was 0.80 +/- 0.7 for patients with paranoid schizophrenia, 0.38 +/- 0.6 for patients with non-paranoid schizophrenia, and 0.06 +/- 0.3 for healthy individuals. Again, significant differences were apparent between all three groups. These findings suggest that morphological differences in trees drawn in the Baum test can be observed between the two schizophrenia subtypes in terms of not only psychopathological interpretation, but also gestalt formation, as assessed on the basis of trees with collapsed gestalt or with some degree of gestalt. This suggests the possibility of multiple disorders at a physiological level. The present study confirmed that the Baum test can quantitatively assess facets of schizophrenia that existing scales such as BPRS are unable to analyze, and is useful for investigating brain function in patients with schizophrenia.

Adult↗
PubMed2003

Marked diffuse dilations of the biliary tree associated with intrahepatic calculi, biliary sludges and a mucinous cyst of the pancreatic head in a 99-year-old woman.

A 99-year-old woman was admitted to Shizuoka Shimizu Municipal Hospital because of fever and anasarca. Imaging and laboratory tests showed pneumonia, urinary tract infection, and cardiac failure. The patient died 20 days after admission. An autopsy revealed marked diffuse dilations of the biliary tree ranging from the lower common bile duct to intrahepatic bile ducts. Intrahepatic calcium bilirubinate stones and biliary sludges were recognized within the dilated bile ducts. A unilocular cyst (2 cm in diameter) was present in the pancreatic head adjacent to the lower common bile duct, and it appeared to compress the common bile duct. Histologically, the walls of the dilated biliary tree showed proliferation of peribiliary glands, fibrosis, and infiltration of lymphocytes and neutrophils (cholangitis). The lumens of the dilated biliary ducts contained neutral and acidic mucins, fibrinous materials, bacteria, neutrophils, and Aspergillus fungi, in addition to the calculi and sludges. The background liver showed atrophy (400 g). The pancreatic unilocular cyst was composed of mucous columnar cells with a few infoldings, and the pancreas also showed foci of mucinous duct hyperplasia and ectasia; the pathological diagnosis of the cyst was cystic dilations of a pancreatic duct branch (mucinous ductal ectasia or mucinous cyst). Other lesions included aspiration pneumonia, emaciation, atrophy of systemic organs, gastric leiomyoma, serous cystadenoma of the right ovary, and arteriosclerotic nephrosclerosis. The present case suggests that a mucinous cyst of the pancreas may compress the biliary tree and lead to marked diffuse dilations of the biliary tree. Alternatively, the dilations of the bile ducts may be associated with aging or may be of congenital origin. The dilated bile ducts may, in turn, give rise to bacterial and fungal cholangitis and formation of biliary sludges and intrahepatic calcium bilirubinate stones.

Aged↗
PubMed2004

Retrospectively ECG-gated multi-detector row CT of the chest: does ECG-gating improve three-dimensional visualization of the bronchial tree?

PURPOSE: To determine the impact of retrospectively ECG-gated multi-detector row CT (MDCT) on three-dimensional (3D) visualization of the bronchial tree and virtual bronchoscopy (VB) as compared to non-ECG-gated data acquisition. MATERIALS AND METHODS: Contrast-enhanced retrospectively ECG-gated and non-ECG-gated MDCT of the chest was performed in 25 consecutive patients referred for assessment of coronary artery bypass grafts and pathology of the ascending aorta. ECG-gated MDCT data were reconstructed in diastole using an absolute reverse delay of - 400 msec in all patients. In 10 patients additional reconstructions at - 200 msec, - 300 msec, and - 500 msec prior to the R-wave were performed. Shaded surface display (SSD) and virtual bronchoscopy (VB) for visualization of the bronchial segments was performed with ECG-gated and non-ECG-gated MDCT data. The visualization of the bronchial tree underwent blinded scoring. Effective radiation dose and signal-to-noise ratio (SNR) for both techniques were compared. RESULTS: There was no significant difference in visualizing single bronchial segments using ECG-gated compared to non-ECG-gated MDCT data. However, the total sum of scores for all bronchial segments visualized with non-ECG-gated MDCT was significantly higher compared to ECG-gated MDCT (P < 0.05). The summary scores for visualization of bronchial segments for different diastolic reconstructions did not differ significantly. The effective radiation dose and the SNR were significantly higher with the ECG-gated acquisition technique (P < 0.05). CONCLUSION: The bronchial tree is significantly better visualized when using non-ECG-gated MDCT compared to ECG-gated MDCT. Additionally, non-ECG-gated techniques require less radiation exposure. Thus, the current retrospective ECG-gating technique does not provide any additional benefit for 3D visualization of the bronchial tree and VB.

Adult↗
PubMed2002

The atopic dog as a model of peanut and tree nut food allergy.

BACKGROUND: Animal models are needed that mimic human IgE-mediated peanut and tree nut allergy. Atopic dogs have been previously used in a model of food allergy to cow's milk, beef, wheat, and soy, with the demonstration of specific IgE production and positive oral challenges similar to those seen in human subjects. OBJECTIVE: We sought to sensitize dogs to peanut, walnut, and Brazil nut and to assess whether sensitization is accompanied by clinical reactions and whether there is cross-reactivity among the different preparations. METHODS: Eleven dogs were sensitized subcutaneously by using an established protocol with 1 microg each of peanut, English walnut, or Brazil nut protein extracts in alum first at birth and then after modified live virus vaccinations at 3, 7, and 11 weeks of age. The dogs were sensitized to other allergens, including soy and either wheat or barley. Intradermal skin tests, IgE immunoblotting to nut proteins, and oral challenges were performed with ground nut preparations. RESULTS: At 6 months of age, the dogs' intradermal skin test responses were positive to the nut extracts. IgE immunoblotting to peanut, walnut, and Brazil nut showed strong recognition of proteins in the aqueous preparations. Each of the 4 peanut- and the 3 Brazil nut-sensitized dogs and 3 of the 4 walnut-sensitized dogs reacted on oral challenge with the corresponding primary immunogen at age 2 years. None of the peanut-sensitized dogs reacted clinically with walnut or Brazil nut challenges. One of the walnut-sensitized dogs had delayed (overnight) vomiting to Brazil nut. CONCLUSIONS: On the basis of measurements of the mean amount of allergen eliciting a skin test response in dogs, the hierarchy of reactivity by skin testing is similar to the clinical experience in human subjects (peanut > tree nuts > wheat > soy > barley). Cross-reactivity, which was not apparent between soy and peanut or tree nuts or between peanut and tree nuts, was slight between walnut and Brazil nut. The results give further support to the dog as a model of human food allergy.

Animals↗
PubMed2002

A long-term analysis of 1018 patients with melanoma by classic Cox regression and tree-structured survival analysis at a major referral center: Implications on the future of cancer staging.

BACKGROUND: Traditional statistical analysis of 2 surgeons' experiences with resectable malignant melanoma during a 30-year period (November 1970-July 2000) was compared with new tree-structured recursive partitioning regression analysis. METHODS: A total of 1018 consecutive patients were registered and 983 patients were evaluable. Disease-free survival (DFS) and melanoma survival (MS) were calculated by Kaplan-Meier method for stage, thickness, ulceration, site, lymph node involvement, age, sex, and type; and compared with log-rank tests. Cox proportional hazards model was used for multivariate analysis. Multivariate predictors were used to analyze DFS and MS with a classification and regression tree model that partitioned patients into progressively more homogenous prognostic groups with significantly different Kaplan-Meier curves. RESULTS: Multivariate correlations were with thickness (millimeters), ulceration, age (per year), type, and sex in predicting DFS (relative risk = 1.18, 2.10, 1.05, 1.71, and 1.71, respectively). Thickness, ulceration, age, and type remained significant predictors of MS (relative risk = 1.14, 3.02, 1.02, and 2.30, respectively). Classification and regression tree analysis showed thickness, age, ulceration, and sex affected DFS. Only thickness and ulceration were significant in predicting MS. CONCLUSION: The Cox model is an important tool for analysis of clinical data but has flaws. New statistical technology to predict outcome should be considered. Classification and regression tree analysis of larger published series may reveal new predictors useful for staging, prognosis, and guiding clinical decisions.

Adult↗
PubMed1979

Calculation of evolutionary trees from sequence data.

Evolutionary trees are usually calculated from comparisons of protein or nucleic acid sequences from present-day organisms by use of algorithms that use only the difference matrix, where the difference matrix is constructed from the sequence differences between pairs of sequences from the organisms. The difference matrix alone cannot define uniquely the correct position of the ancestor of the present-day organisms (root of the tree). Furthermore, methods using the difference matrix alone often fail to give the correct pattern of tree branching (topology) when the different sequences evolve at different rates. Only for equal rates of evolution can the difference matrix (when used with the so-called matrix method) yield exactly the correct topology and root. In this paper we present a method for calculating evolutionary trees from sequence data that uses, along with the difference matrix, the rate of evolution of the various sequences from their common ancestor. It is proven analytically that this method uniquely determines both the correct topology and root in theory for unequal rates of sequence evolution. How one would estimate an ancestral sequence to be used in the method is discussed in particular for the 5S RNA sequences from prokaryotes and eukaryotes and for ferredoxin sequences.

Amino Acid Sequence↗
PubMed1981

Simple method for constructing phylogenetic trees from distance matrices.

A simple method is proposed for constructing phylogenetic trees from distance matrices. The procedure for constructing tree topologies is similar to that of the unweighted pair-group method (UPG method) but makes corrections for unequal rates of evolution among lineages. The procedure for estimating branch lengths is the same as that of the Fitch and Margoliash method (F-M method) except that it allows no negative branch lengths. The performance of the present procedure for the construction of tree topologies is compared with that of the UPG method, the F-M method, Farris' method, and the modified Farris method by using Tateno's simulation outputs for nucleotide sequence divergence and his results for the performances of the latter four methods [Tateno, Y. (1978) Dissertation (Univ. Texas, Houston, TX). In this limited comparison, the present method performs considerably better than the UPG method and the F-M method and about equally well as the last two methods. The present method appears to be preferable to the UPG method for analysis of data from populations that have not differentiated much. Indeed, an application of the present method to gene frequency data from some Amerindian populations gives a tree topology far more reasonable than that obtained by the UPG method.

Biological Evolution↗
PubMed1986

Evidence against use of bacterial amino acid sequence data for construction of all-inclusive phylogenetic trees.

It has been proposed that phylogenetic trees, intended to show divergence of eukaryotic protein and nucleic acid sequences, be extended to include those from bacteria. However, we have compared the amino acid sequences of 18 of the most divergent mitochondrial cytochromes c with those of 18 bacterial cytochromes c2 and have found that the average percentage difference between these mitochondrial cytochromes c and cytochromes c2 was not significantly greater than that among the cytochromes c2 alone. The large discontinuities in physical-chemical properties recognized between the prokaryote and eukaryote cytochromes render it highly improbable that members of the two classes should be no more different from one another than members of either class alone, assuming that sequence differences can accurately reveal evolutionary divergence. Instead, we propose that divergent amino acid sequences approach a limit of change considerably less than for comparison of random sequences. This limit of change presumably is determined by the structure/function relationship. When two homologous protein sequences have reached such a limit, convergence or back-mutations and parallel mutations become as frequent as divergent mutations. As two diverging proteins approach this steady-state condition, sequence differences no longer reflect the numbers of mutations resulting in amino acid substitution and therefore species cannot be positioned on a phylogenetic tree. Insertions and deletions are less reversible than are amino acid substitutions and, provided they are well-documented, might be more reliable indicators of bacterial relationships. Nevertheless, we suggest that data available on bacterial protein sequences do not permit construction of all-inclusive phylogenetic trees. Comparisons of protein and rRNA trees suggest that similar restrictions apply to use of rRNA sequence data.

Amino Acid Sequence↗
PubMed1996

Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis.

Phylogenetic analyses are increasingly used in attempts to clarify transmission patterns of human immunodeficiency virus type 1 (HIV-1), but there is a continuing discussion about their validity because convergent evolution and transmission of minor HIV variants may obscure epidemiological patterns. Here we have studied a unique HIV-1 transmission cluster consisting of nine infected individuals, for whom the time and direction of each virus transmission was exactly known. Most of the transmissions occurred between 1981 and 1983, and a total of 13 blood samples were obtained approximately 2-12 years later. The p17 gag and env V3 regions of the HIV-1 genome were directly sequenced from uncultured lymphocytes. A true phylogenetic tree was constructed based on the knowledge about when the transmissions had occurred and when the samples were obtained. This complex, known HIV-1 transmission history was compared with reconstructed molecular trees, which were calculated from the DNA sequences by several commonly used phylogenetic inference methods [Fitch-Margoliash, neighbor-joining, minimum-evolution, maximum-likelihood, maximum-parsimony, unweighted pair group method using arithmetic averages (UPGMA), and a Fitch-Margoliash method assuming a molecular clock (KITSCH)]. A majority of the reconstructed trees were good estimates of the true phylogeny; 12 of 13 taxa were correctly positioned in the most accurate trees. The choice of gene fragment was found to be more important than the choice of phylogenetic method and substitution model. However, methods that are sensitive to unequal rates of change performed more poorly (such as UPGMA and KITSCH, which assume a constant molecular clock). The rapidly evolving V3 fragment gave better reconstructions than p17, but a combined data set of both p17 and V3 performed best. The accuracy of the phylogenetic methods justifies their use in HIV-1 research and argues against convergent evolution and selective transmission of certain virus variants.

Amino Acid Sequence↗
PubMed1998

Health of tree swallows (Tachycineta bicolor) nesting in pesticide-sprayed apple orchards in Ontario, Canada. II. Sex and thyroid hormone concentrations and testes development.

To investigate the effects of pesticides on wild birds, sex (17beta-estradiol; testosterone) and thyroid (triiodothyronine (T3) hormone concentrations, body mass, and testes mass were measured and the development of testes was evaluated in wild tree swallows (Tachycineta bicolor) nesting in four sprayed apple orchards and three nonsprayed sites in southern Ontario, Canada, in 1995-1996. In orchards, birds were exposed to asmany as 11 individual spray events and five sprays of mixtures of chemicals. Residues of organochlorine pesticides, PCBs, lead, and arsenic concentrations were low and not variable among sites except p,p'-DDE concentrations, which ranged from 0.36 to 2.23 microg/g wet weight in eggs. These persistent compounds were not correlated with any endocrine response measured in tree swallows. In 16-d-old male tree swallow chicks, body mass and concentrations of 17beta-estradiol (estradiol), testosterone, and T3 in plasma showed no significant differences between sprayed and nonsprayed groups and among sites within those groups. However, T3 concentrations were slightly elevated in the sprayed group compared to the nonsprayed group, and there was a significant and positive correlation between T3 and the number of mixtures of sprays applied during egg incubation through chick rearing. In 16-d-old female chicks, there were no significant differences among spray treatments or sites and no correlations with spray exposure for testosterone, estradiol, or T3 in plasma. Body mass was correlated positively with T3 and negatively with estradiol but showed no differences among spray exposure groups or sites. Histology of testes of 16-d-old male chicks indicated there were no significant differences among sprayed and nonsprayed birds in testes mass, area, or diameter, or the presence of Leydig cells in the interstitium, the distribution of the Sertoli cells, or the occurrence of heterophils in the testicular interstitium. For the percentage of spermatogonia present on the basement membrane, there were significant differences among sites, but these differences were not specifically associated with spray exposure. However, there was a marginally significant trend between increasing occurrence of a disrupted Sertoli cell population on the seminiferous tubular basement membranes as the number of mixtures of pesticides sprayed during chick rearing increased. In adult male and female parent tree swallows, there were no differences in hormone concentrations between birds from sprayed and nonsprayed sites. Nor were there any significant correlations between the concentration of any hormone and collection date, body mass, or any type of spray exposure for adults. The correlations between increasing pesticide exposure and abnormal thyroid hormone and testes development in male chicks indicate that further reductions of pesticide use in orchards may benefit the health of birds that nest there. However, it is unclear which of these pesticides or spray mixtures are responsible for these effects, and this needs to be examined in future studies.

Animals↗
PubMedDate not supplied

An evaluation of the decision tree approach for assessing priorities for safety testing of food additives.

In this publication we report an evaluation of the decision tree scheme of Cramer, Ford and Hall (1978) for assigning priorities for toxicity testing of chemicals. The original scheme has been modified to allow more chemical structures to be considered and to take into account recent advances in toxicology. The majority of the food additives permitted in either the UK, USA or Canada have been processed through the modified decision tree questionnaire and their classification compared with currently available chronic toxicity data. A large proportion of the additives (53/73) assigned to the lowest toxicity (I) class have a low order of chronic oral toxicity as do many of the compounds assigned to the moderate toxicity (II) class. Although the majority of the additives assigned to the highest toxicity (III) class are substantially more toxic than those in the lower toxicity classes, some relatively innocuous compounds reached this classification. In addition, a few toxic compounds were assigned to the lowest toxicity class. The reasons for these incorrect assignments are discussed. It was concluded that the decision tree approach, although less discriminating than originally suggested, remains a useful method for classifying compounds in terms of their probable toxicity and that further modifications to the tree could be made.

Accident Prevention↗
PubMed2002

The chronic psychosocial stress paradigm in male tree shrews: evaluation of a novel animal model for depressive disorders.

To improve our knowledge of the causal mechanisms of stress-related disorders such as depression, we need animal models that mirror the situation in patients. One promising model is the chronic psychosocial stress paradigm in male tree shrews, which is based on the territorial behaviour of these animals that can be used to establish naturally occurring challenging situations under experimental control in the laboratory. Co-existence of two males in visual and olfactory contact leads to a stable dominant-subordinate relationship, with subordinates showing distinct stress-induced behavioural and neuroendocrine alterations that are comparable to the symptoms observed during episodes of depression in patients such as constantly elevated circulating glucocorticoid hormones due to a chronic hyperactivity of the hypothalamic-pituitary-adrenal axis. To elucidate whether the chronic psychosocial stress model in tree shrews besides its "face validity" for depression also has "predictive validity", we treated subordinate tree shrews with the tricyclic antidepressant clomipramine and found a time-dependent restoration of both endocrine and behavioural parameters. In contrast, the anxiolytic diazepam was ineffective. Although the chronic psychosocial stress model in tree shrews requires further validation, it has sufficient face, predictive, and construct validity to become an interesting non-rodent model for research on the etiology and pathophysiology of depression.

Animals↗
PubMed2006

Effects of clear-cutting and soil preparation on natural 15N abundance in the soil and needles of two boreal conifer tree species.

This study presents the impacts of clear-cutting and site preparation on soil and needle 15N-fractionation of Scots pine (Pinus sylvestris, L.) and Norway spruce (Picea abies (L.), Karst). Three microsites on different methods of site preparation were used: (i) mound (broken O/E/B horizons piled upside down over undisturbed humus), (ii) deep (exposed C-horizon) and (iii) shallow (exposed E/B horizon). We found significant differences between species, between closed forest and clear-cuts as well as between different site preparations. For instance, in the context of interspecific variations, the mean needle nitrogen concentrations of both seedlings (1.15,+/-0.10 %) and mature (1.09,+/-0.07 %) pine trees were significantly higher compared to corresponding needle concentrations of seedlings (0.88,+/-0.06 %) and mature trees (0.79,+/-0.02 %) of spruce. Similarly, we observed significantly more 15N-enriched needles of mature spruces (-4.0,+/-0.20 per thousand) as well as of seedlings (-5.0,+/-0.11 per thousand) relative to that of mature pine needles (-5.6,+/-0.10 per thousand) and seedlings (-6.0,+/-0.31 per thousand). These variations were assumed to be caused by the variation in mycorrhizal associations between the species. We assume that the proportion of mycorrhizal N-uptake of pines might have been larger than that of spruce. Regarding the clear-cut effects on N and 15N of both tree species, we observed that, in the mature natural stand, needle N concentrations of both pine (1.09,+/-0.07 %) and spruce (0.79,+/-0.02 %) tree species did not change significantly after clear-cutting (pine: 1.01,+/-0.06 %; spruce: 0.74,+/-0.04 % ). However, clear-cutting resulted in the significant increase in needle 15N natural abundance of both pine (-2.70,+/-0.06 per thousand) and spruce (-2.09,+/-0.05 per thousand) in comparison to that of natural stand (pine:-5.60,+/-0.10 per thousand; spruce:-4.00,+/-0.20 per thousand), which is assumed to be due to the increased level of nitrification and leaching of nitrate after clear-cutting. In the context of site preparation methods, soil and needle N were observed to be more 15N-enriched in deep and shallow treatment sites compared to that of closed forest site and untreated clear-cut site, which indicated that the main source of N uptake seems to be mainly directly from the soil of the corresponding horizons of mineral soil with higher delta15N.

Forestry↗
PubMed2002

The effects of topological inaccuracy in evolutionary trees on the phylogenetic comparative method of independent contrasts.

Computer simulations were used to test the effect of increasing phylogenetic topological inaccuracy on the results obtained from correlation tests of independent contrasts. Predictably, increasing the number of disruptions in the tree increases the likelihood of significant error in the r values produced and in the statistical conclusions drawn from the analysis. However, the position of the disruption in the tree is important: Disruptions closer to the tips of the tree have a greater effect than do disruptions that are close to the root of the tree. Independent contrasts derived from inaccurate topologies are more likely to lead to erroneous conclusions when there is a true significant relationship between the variables being tested (i.e., they tend to be conservative). The results also suggest that random phylogenies perform no better than nonphylogenetic analyses and, under certain conditions, may perform even worse than analyses using raw species data. Therefore, the use of random phylogenies is not beneficial in the absence of knowledge of the true phylogeny.

Computer Simulation↗
PubMed2002

Whole-tree methods for detecting differential diversification rates.

Prolific cladogenesis, adaptive radiation, species selection, key innovations, and mass extinctions are a few examples of biological phenomena that lead to differential diversification among lineages. Central to the study of differential diversification rates is the ability to distinguish chance variation from that which requires deterministic explanation. To detect diversification rate variation among lineages, we propose a number of methods that incorporate information on the topological distribution of species diversity from all internal nodes of a phylogenetic tree. These whole-tree methods (M(Pi), M(Sigma), and M(R)) are explicitly connected to a null model of random diversification--the equal-rates Markov (ERM) random branching model--and an alternative model of differential diversification: M(Pi) is based on the product of individual nodal ERM probabilities; M(Sigma) is based on the sum of individual nodal ERM probabilities, and M(R) is based on a transformation of ERM probabilities that corresponds to a formalized system that orders trees by their relative symmetry. These methods have been implemented in a freely available computer program, SYMMETREE, to detect clades with variable diversification rates, thereby allowing the study of biological processes correlated with and possibly causal to shifts in diversification rate. Application of these methods to several published phylogenies demonstrates their ability to contend with relatively large, incompletely resolved trees. These topology-based methods do not require estimates of relative branch lengths, which should facilitate the analysis of phylogenies, such as supertrees, for which such data are unreliable or unavailable.

Animals↗
PubMed2006

Reciprocal illumination in the gene content tree of life.

Phylogenies based on gene content rely on statements of primary homology to characterize gene presence or absence. These statements (hypotheses) are usually determined by techniques based on threshold similarity or distance measurements between genes. This fundamental but problematic step can be examined by evaluating each homology hypothesis by the extent to which it is corroborated by the rest of the data. Here we test the effects of varying the stringency for making primary homology statements using a range of similarity (e-value) cutoffs in 166 fully sequenced and annotated genomes spanning the tree of life. By evaluating each resulting data set with tree-based measurements of character consistency and information content, we find a set of homology statements that optimizes overall corroboration. The resulting data set produces well-resolved and well-supported trees of life and greatly ameliorates previously noted inconsistencies such as the misclassification of small genomes. The method presented here, which can be used to test any technique for recognizing primary homology, provides an objective framework for evaluating phylogenetic hypotheses and data sets for the tree of life. It also can serve as a technique for identifying well-corroborated sets of homologous genes for functional genomic applications.

Algorithms↗
PubMed2003

Fractal properties of perfusion heterogeneity in optimized arterial trees: a model study.

Regional blood flows in the heart muscle are remarkably heterogeneous. It is very likely that the most important factor for this heterogeneity is the metabolic need of the tissue rather than flow dispersion by the branching network of the coronary vasculature. To model the contribution of tissue needs to the observed flow heterogeneities we use arterial trees generated on the computer by constrained constructive optimization. This method allows to prescribe terminal flows as independent boundary conditions, rather than obtaining these flows by the dispersive effects of the tree structure. We study two specific cases: equal terminal flows (model 1) and terminal flows set proportional to the volumes of Voronoi polyhedra used as a model for blood supply regions of terminal segments (model 2). Model 1 predicts, depending on the number Nterm of end-points, fractal dimensions D of perfusion heterogeneities in the range 1.20 to 1.40 and positively correlated nearest-neighbor regional flows, in good agreement with experimental data of the normal heart. Although model 2 yields reasonable terminal flows well approximated by a lognormal distribution, it fails to predict D and nearest-neighbor correlation coefficients r1 of regional flows under normal physiologic conditions: model 2 gives D = 1.69 +/- 0.02 and r1 = -0.18 +/- 0.03 (n = 5), independent of Nterm and consistent with experimental data observed under coronary stenosis and under the reduction of coronary perfusion pressure. In conclusion, flow heterogeneity can be modeled by terminal positions compatible with an existing tree structure without resorting to the flow-dispersive effects of a specific branching tree model to assign terminal flows.

Animals↗
PubMedDate not supplied

Natural use of heterothermy by a small, tree-roosting bat during summer.

Little is known about the use of heterothermy by wild bats during summer, especially for tree-roosting species. Because thermal conditions within tree roosts can fluctuate widely with ambient temperature, which affects thermoregulatory energy expenditure during diurnal roosting, we measured skin temperatures of free-ranging male Nyctophilus geoffroyi (8 g) to quantify the relation between summer torpor use and roost thermal conditions. Bats roosted under bark on the northern (sunny) side of trees and entered torpor every day, usually near sunrise. Bats exhibited two bouts of torpor on most days: the first occurred in the morning, was terminated by partially passive rewarming, and was followed by a period of normothermy during the warmest part of the day; a second torpor bout occurred in the late afternoon, with arousal near sunset. On the warmest days, bats had only a single, short morning bout. On the coolest days, bats remained torpid throughout the day, and one 2-d bout was observed. Thus, presumably owing to their poorly insulated roosts and the high energetic cost of normothermy at temperatures below 30 degrees C, the extent and timing of heterothermy was closely related to the cycle of diurnal temperatures. Our study indicates that torpor use is important for energy maintenance during summer diurnal roosting of N. geoffroyi and likely of other small, tree-roosting bats.

Animals↗