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PubMed2004

Fractal analysis of the vascular tree in the human retina.

The retinal circulation of the normal human retinal vasculature is statistically self-similar and fractal. Studies from several groups present strong evidence that the fractal dimension of the blood vessels in the normal human retina is approximately 1.7. This is the same fractal dimension that is found for a diffusion-limited growth process, and it may have implications for the embryological development of the retinal vascular system. The methods of determining the fractal dimension for branching trees are reviewed together with proposed models for the optimal formation (Murray Principle) of the branching vascular tree in the human retina and the branching pattern of the human bronchial tree. The limitations of fractal analysis of branching biological structures are evaluated. Understanding the design principles of branching vascular systems and the human bronchial tree may find applications in tissue and organ engineering, i.e., bioartificial organs for both liver and kidney.

Animals↗
PubMed1993

Stochastic model of the pulmonary airway tree and its implications for bronchial responsiveness.

The resistance of the pulmonary conducting airway tree (Raw) is a consequence of the resistances of its component airways and how they are connected together. To date, theoretical calculations of Raw have been performed with the aid of mathematical models of the airway tree that are purely deterministic. That is, the mechanical properties of the component airways in these models are precisely defined functions of generation number. Such models take no account of the fact that the airways of a given generation are not all exactly the same but rather exhibit a spectrum of wall thicknesses, amounts of smooth muscle, and number of parenchymal attachments. In the present study, the properties of a 10-generation stochastic airway tree model are investigated. The lengths and radii of the airways in the tree are drawn randomly from probability distribution functions (PDFs), the means of which are deterministic functions of generation number and the standard deviations are assigned various values. Monte Carlo simulation is used to estimate the PDF of Raw itself in various conditions. We show that the relative width of the PDF of Raw may be comparable to that of the PDFs from which the individual airway radii were drawn. It is also shown that when bronchoconstriction is simulated by narrowing each airway by a random amount the resulting PDF for Raw may increase in width many times. We conclude that the variations in airway responsiveness seen in nature can only be properly understood when the distribution of airway properties within the lung are taken into account.

Airway Resistance↗
PubMed1998

Transit time dispersion in the pulmonary arterial tree.

Knowledge of the contributions of arterial and venous transit time dispersion to the pulmonary vascular transit time distribution is important for understanding lung function and for interpreting various kinds of data containing information about pulmonary function. Thus, to determine the dispersion of blood transit times occurring within the pulmonary arterial and venous trees, images of a bolus of contrast medium passing through the vasculature of pump-perfused dog lung lobes were acquired by using an X-ray microfocal angiography system. Time-absorbance curves from the lobar artery and vein and from selected locations within the intrapulmonary arterial tree were measured from the images. Overall dispersion within the lung lobe was determined from the difference in the first and second moments (mean transit time and variance, respectively) of the inlet arterial and outlet venous time-absorbance curves. Moments at selected locations within the arterial tree were also calculated and compared with those of the lobar artery curve. Transit times for the arterial pathways upstream from the smallest measured arteries (200-micron diameter) were less than approximately 20% of the total lung lobe mean transit time. Transit time variance among these arterial pathways (interpathway dispersion) was less than approximately 5% of the total variance imparted on the bolus as it passed through the lung lobe. On average, the dispersion that occurred along a given pathway (intrapathway dispersion) was negligible. Similar results were obtained for the venous tree. Taken together, the results suggest that most of the variation in transit time in the intrapulmonary vasculature occurs within the pulmonary capillary bed rather than in conducting arteries or veins.

Algorithms↗
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↗
PubMed2005

Biochemical and immunological characterization of pollen-derived beta-galactosidase reveals a new cross-reactive class of allergens among Mediterranean trees.

BACKGROUND: The most potent allergens in the Spermatophytae family exhibit significant homology with enzymes. Some of these are though to be involved in pectin metabolism, recognition of compatible stigma and delivery of sperm cells to the ovule. OBJECTIVE: To test if glycohydrolase activities from some Mediterranean tree pollens could act as allergens in sensitized hosts. METHODS: Freshly collected Cupressus and Olea pollens were investigated for their glycohydrolase activities by means of synthetic fluorogenic substrates and isoenzymes characterized by DEAE-cellulose ion-exchange chromatography. Binding of specific IgE was investigated by immunoblotting in 30 tree-sensitive subjects, as well as in 20 atopic non-tree-sensitive and 15 healthy controls. The enzymes were also adopted to stimulate proliferation of allergen-specific T cell clones. Finally, they were tested in vivo in a cutaneous immediate wheal and flare reaction. RESULTS: beta-Galactosidase (beta-GAL) is present with different isoenzymatic patterns on both pollen extracts, could be recognized by circulating IgE, as well as immunoprecipitated by sera from allergic subjects. The enzyme could stimulate the proliferation of T cells from allergic subjects, and favor the emergence of CD4+ T cell clones with specific in vitro reactivity to beta-GAL. Finally, the enzyme induced in vivo a cutaneous wheal and flare reaction in clinically sensitive subjects. CONCLUSIONS: Despite different isoenzymatic patterns, Olea-derived beta-GAL cross-reacted with that from cypress pollen, suggesting that these enzymatic glycoproteins may represent major native allergens among these Mediterranean trees.

Allergens↗
PubMed2006

Darkness causes myopia in visually experienced tree shrews.

PURPOSE: To examine the effect of a period of continuous darkness on the refractive state and vitreous chamber depth of normal light-reared juvenile tree shrew eyes, and to learn whether eyes that developed myopia in response to monocular minus-lens wear will recover in darkness. METHODS: Starting at 16 days of visual experience (VE), the refractive state of five dark-treatment tree shrews was measured daily to confirm that it was stable and nearly emmetropic. After corneal and ocular component dimension measures, the animals were placed into continuous darkness for 10 days. On removal of the animals from darkness, corneal and ocular component measures were repeated, and daily refractive measures were resumed. The refractive state of the dark-treatment group was compared with that of a normal-lighting group (n = 5) that received standard colony lighting throughout the measurement period. Five dark-recovery animals wore a monocular -5-D lens for 11 days to induce myopia before they were placed into continuous darkness for 10 days. RESULTS: The animals in the normal-lighting group completed the emmetropization process, stabilizing at approximately (mean +/- SEM) 0.7 +/- 0.3 D of hyperopia (noncycloplegic refraction, corrected for the small eye artifact) at 60 days of VE. Dark-treatment group eyes shifted toward myopia (mean +/- SEM, -4.3 +/- 0.5 D) in the dark. The vitreous chamber became elongated by 0.09 +/- 0.02 mm relative to normal eyes. Corneal power showed a small, near-normal decrease (1.4 +/- 0.3 D). Four of five myopic eyes in the dark-recovery group became more myopic (-2.2 +/- 0.9D) in darkness, and all the fellow control eyes shifted toward myopia (-2.8 +/- 0.5 D). CONCLUSIONS: Maintaining emmetropia is an active process. After eyes have achieved emmetropia or have compensated for a minus lens, continued visual guidance is necessary to maintain a match between the axial length and the focal plane or for recovery to occur. Absence of light is myopiagenic in tree shrews that have developed with normal diurnal lighting. This result contrasts with the apparent absence of a darkness effect in tree shrews reared in the dark from before normal eye opening.

Animals↗
PubMed1997

Foreign body in the tracheobronchial tree.

A 20-year experience with the treatment of 74 patients (83.8% children) for foreign body aspiration is reviewed. The object of this review is to show the clinical manifestations, the radiological findings, the nature and distribution in the bronchial tree, and complications due to longstanding (months or years) foreign bodies in the bronchial tree. The most common foreign bodies found were peanuts (13.5%), corn (13.5%), and beans (13.5%). The most frequent clinical manifestation was choking (67.5%), and the most frequent radiological finding was atelectasis (41.8%). The most serious complication was bronchiectasis needing resection in six patients who had the foreign body retained for years in the bronchial tree. In conclusion, in spite of an obvious foreign body in the tracheobronchial tree many cases are not diagnosed, and a longstanding foreign body in the airway may be responsible for irreversible complications.

Adolescent↗
PubMedDate not supplied

Determining indications for care common to competing guidelines by using classification tree analysis: application to the prevention of venous thromboembolism in medical inpatients.

BACKGROUND: Substantial variations have been reported in the advice given by competing guidelines addressing the same clinical problem. OBJECTIVE: This study aimed to assess the usefulness of classification tree analysis in comparing competing guidelines. METHOD: The authors implemented a classification tree-growing algorithm on cross-sectional data from 818 patients to determine indications for prophylactic heparin treatment common to 4 competing guidelines disseminated between 1998 and 2000 and addressing the prophylaxis of venous thromboembolism in medical inpatients. RESULTS: The resulting classification tree involved 10 terminal nodes. Its mean accuracy estimated by performing 10-fold cross-validation was 82% (s=3). The guidelines consistently supported prophylactic heparin treatment for 5 indications: a previous episode of deep vein thrombosis or pulmonary embolism, recent paralysis of lower limb(s), congestive heart failure with one or more risk factors, recent myocardial infarction, and malignancy with one or more risk factors. These indications involved 257 patients (31.4%) and were supported by robust scientific evidence. Deep vein thrombosis was detected in 27 of these patients (10.5%). Two consistent negative indications involved 347 patients (42.4%). Deep vein thrombosis was detected in 9 of these patients (2.6%). Three indications involving 214 patients (26.2%) were discordant over the 4 guidelines. CONCLUSION: Classification tree analysis of real patient data is a useful strategy to identify indications common to competing guidelines. These indications should be considered for inclusion when updating guidelines. The findings of recently completed randomized trials have partly resolved the disagreement among the 4 guidelines. This approach may be helpful when developing new guidelines or for identifying topics warranting further complementary clinical trials.

Algorithms↗
PubMed2006

A novel approach to phylogenetic tree construction using stochastic optimization and clustering.

BACKGROUND: The problem of inferring the evolutionary history and constructing the phylogenetic tree with high performance has become one of the major problems in computational biology. RESULTS: A new phylogenetic tree construction method from a given set of objects (proteins, species, etc.) is presented. As an extension of ant colony optimization, this method proposes an adaptive phylogenetic clustering algorithm based on a digraph to find a tree structure that defines the ancestral relationships among the given objects. CONCLUSION: Our phylogenetic tree construction method is tested to compare its results with that of the genetic algorithm (GA). Experimental results show that our algorithm converges much faster and also achieves higher quality than GA.

Algorithms↗
PubMed2006

Rooting the tree of life by transition analyses.

BACKGROUND: Despite great advances in clarifying the family tree of life, it is still not agreed where its root is or what properties the most ancient cells possessed--the most difficult problems in phylogeny. Protein paralogue trees can theoretically place the root, but are contradictory because of tree-reconstruction artefacts or poor resolution; ribosome-related and DNA-handling enzymes suggested one between neomura (eukaryotes plus archaebacteria) and eubacteria, whereas metabolic enzymes often place it within eubacteria but in contradictory places. Palaeontology shows that eubacteria are much more ancient than eukaryotes, and, together with phylogenetic evidence that archaebacteria are sisters not ancestral to eukaryotes, implies that the root is not within the neomura. Transition analysis, involving comparative/developmental and selective arguments, can polarize major transitions and thereby systematically exclude the root from major clades possessing derived characters and thus locate it; previously the 20 shared neomuran characters were thus argued to be derived, but whether the root was within eubacteria or between them and archaebacteria remained controversial. RESULTS: I analyze 13 major transitions within eubacteria, showing how they can all be congruently polarized. I infer the first fully resolved prokaryote tree, with a basal stem comprising the new infrakingdom Glidobacteria (Chlorobacteria, Hadobacteria, Cyanobacteria), which is entirely non-flagellate and probably ancestrally had gliding motility, and two derived branches (Gracilicutes and Unibacteria/Eurybacteria) that diverged immediately following the origin of flagella. Proteasome evolution shows that the universal root is outside a clade comprising neomura and Actinomycetales (proteates), and thus lies within other eubacteria, contrary to a widespread assumption that it is between eubacteria and neomura. Cell wall and flagellar evolution independently locate the root outside Posibacteria (Actinobacteria and Endobacteria), and thus among negibacteria with two membranes. Posibacteria are derived from Eurybacteria and ancestral to neomura. RNA polymerase and other insertions strongly favour the monophyly of Gracilicutes (Proteobacteria, Planctobacteria, Sphingobacteria, Spirochaetes). Evolution of the negibacterial outer membrane places the root within Eobacteria (Hadobacteria and Chlorobacteria, both primitively without lipopolysaccharide): as all phyla possessing the outer membrane beta-barrel protein Omp85 are highly probably derived, the root lies between them and Chlorobacteria, the only negibacteria without Omp85, or possibly within Chlorobacteria. CONCLUSION: Chlorobacteria are probably the oldest and Archaebacteria the youngest bacteria, with Posibacteria of intermediate age, requiring radical reassessment of dominant views of bacterial evolution. The last ancestor of all life was a eubacterium with acyl-ester membrane lipids, large genome, murein peptidoglycan walls, and fully developed eubacterial molecular biology and cell division. It was a non-flagellate negibacterium with two membranes, probably a photosynthetic green non-sulphur bacterium with relatively primitive secretory machinery, not a heterotrophic posibacterium with one membrane.

Journal Article↗
PubMed2006

Phylogenetic inference from homologous sequence data: minimum topological assumption, strict mutational compatibility consensus tree as the ultimate solution.

BACKGROUND: For the purposes of phylogenetic inference from molecular data sets many different methods are currently offered as alternatives for researchers in phylogenetic systematics. The vast majority of these methods are based on specific topological assumptions relating to the resultant genealogical tree. Each of these has been shown to perform effectively in special conditions and for specific data sets while yielding less reliable results in other instances. Moreover, the majority of the methods include information from homoplastic characters in spite of a universally accepted agreement in their ineffectiveness for phylogenetic inference, which may often lead to inaccuracy and inconsistency. As an alternative to such methods, a strict mutational compatibility consensus tree building method as a universally applicable and reliable method is reported. RESULTS: The analysis of a data set from a previously published experimental phylogeny demonstrates the accuracy of the strict mutational compatibility consensus tree building method and illustrates its potential for obtaining unambiguous and precise results with full resolution. CONCLUSION: The universal applicability of a simplified compatibility method in its algorithmic form for phylogenetic inference is described. Firstly, dismissal of topological assumptions creates a general potential for agreement of inferred with true phylogeny. Second, exclusion of irregular characters from analysis repeatably enables construction of consistent phylogeny. Third, a direct calculation of bootstrap proportion values for individual nodes of the resulting tree is possible rather than their empirical estimation. Finally, guidance is given for empirical assessment of the sample size necessary for full genealogical resolution and significant bootstrap proportions. REVIEWERS: This article was reviewed by Yuri I. Wolf (nominated by Eugene Koonin), Arcady Mushegian and Martijn Huynen.

Journal Article↗
PubMed2005

Body wiping behaviors associated with cutaneous lipids in hylid tree frogs of Florida.

Body wiping behavior, integumentary secretions and rates of evaporative water loss (EWL) were examined in six species of Florida tree frogs (Anura: Hylidae). Additionally, morphology of the integument and dermal glands were compared among these and one other Florida tree frog (Hyla andersonii), an arid-adapted tree frog (Phyllomedusa hypochondrialis), and a highly aquatic frog (Rana utricularia). An extra-epidermal layer of lipid and mucus, presumably secreted from dermal granular glands, was detected on the skin of all Florida hylid frogs examined. Distinct body wiping behaviors were observed in the hylid frogs, but these were less complex than those described previously in phyllomedusine frogs, which occupy arid habitats, secrete lipids onto their skin, and are regarded as relatively 'waterproof'. Florida hylids occupy seasonally arid habitats and appear to have reduced rates of EWL. The suite of traits we observed in these frogs have been previously documented in a rhacophorid tree frog from seasonally arid regions of India and likely represent an evolutionary convergent response to periodic dehydration stress. The presence of lipids that are spread by simple wiping behaviors to form an extra-epidermal water barrier may represent an early stage of the more advanced adaptations described in more waterproof arboreal frogs.

Animals↗
PubMed1983

Family trees representing the finitely proliferative nature of cultured rat liver cells.

Family trees of rat liver epithelial-like cells in primary culture were obtained by cinemicrographic analysis. With few exceptions the proliferative profiles reconstituted from these family trees showed limited proliferation. This limitation was not due to post-confluence inhibition of proliferation or to nutritional deprivation during time lapse cinemicrography, but to the finite potential of clonal proliferation. In these family trees a cell entered mitosis, incomplete division, death, or a long interphase with no detectable termination. These family trees successfully related the life phases of the individual cells that compose the population to the limited nature of proliferative potential as observed in clonal cell populations.

Animals↗
PubMed1989

Studies on the constituents of Japanese mistletoes from different host trees, and their antimicrobial and hypotensive properties.

The chemical constituents of Japanese mistletoes, Taxillus yadoriki Danser, Taxillus kaempferi Danser, and Korthalsella japonica Engler, epiphyting to different host trees were compared, and the antimicrobial and hypotensive properties of some isolated flavonoids were examined. Two known flavonoid glycosides, hyperin and quercitrin, were isolated from Taxillus yadoriki Danser, together with fatty acids, phytosterol, and phytosterol-glucoside. There was remarkable variation of contents of quercitrin among the plants on different host trees. From Taxillus kaempferi Danser, fatty acids, phytosterol, phytosterol-glucoside, quercetin, avicularin, and taxillusin were isolated, and quercitrin and hyperin were also identified. There was no remarkable variation of compositions of flavonoid glycosides among the plants on different host trees. A known flavone glycoside, chrysoeriol-4'-O-glucoside, was isolated from Korthalsella japonica Engler, together with fatty acids, phytosterol, oleanolic acid, and phytosterol-glucoside. Chrysoeriol-4'-O-glucoside is contained in this plant irrespective of the host trees.

Animals↗
PubMed2004

Bacterial taxonomics: finding the wood through the phylogenetic trees.

Bacterial taxonomy comprises systematics (theory of classification), nomenclature (formal process of naming), and identification. There are two basic approaches to classification. Similarities may be derived between microorganisms by numerical taxonomic methods based on a range of present-day observable characteristics (phenetics), drawing in particular on conventional morphological and physiological test characters as well as chemotaxonomic markers such as whole-cell protein profiles, mol% G+C content, and DNA-DNA homologies. By contrast, phylogenetics, the process of reconstructing possible evolutionary relationships, uses nucleotide sequences from conserved genes that act as molecular chronometers. A combination of both phenetics and phylogenetics is referred to as polyphasic taxonomy, and is the recommended strategy in description of new species and genera. Numerical analysis of small-subunit ribosomal RNA genes (rDNA) leading to the construction of branching trees representing the distance of divergence from a common ancestor has provided the mainstay of microbial phylogenetics. The approach has some limitations, particularly in the discrimination of closely related taxa, and there is a growing interest in the use of alternative loci as molecular chronometers, such as gyrA and RNAase P sequences. Comparison of the degree of congruence between phylogenetic trees derived from different genes provides a valuable test of the extent they represent gene trees or species trees. Rapid expansion in genome sequences will provide a rich source of data for future taxonomic analysis that should take into account population structure of taxa and novel methods for analysis of nonclonal bacterial populations.

Bacteria↗
PubMed2006

Ethanol production from pretreated olive tree wood and sunflower stalks by an SSF process.

Olive tree wood and sunflower stalks are agricultural residues largely available at low cost in Mediterranean countries. As renewable lignocellulosic materials, their bioconversion may allow both obtaining a value-added product, for fuel ethanol, and facilitating their elimination. In this work, the ethanol production from olive tree wood and sunflower stalks by a simultaneous saccharification and fermentation (SSF) process is studied. As a pretreatment, steam explosion at different temperatures was applied. The water insoluble fractions of steam-pretreated sunflower stalks and steamed, delignified olive tree wood were used as substrates at 10% w/v concentration for an SSF process by a cellulolytic commercial complex and Saccharomyces cerevisiae. After 72-h fermentation, ethanol concentrations up to 30 g/L were obtained in delignified steam-pretreated olive tree wood at 230 degrees C and 5 min. Sunflower stalks pretretated at 220 degrees C and 5 min gave maximum ethanol concentrations of 21 g/L in SSF experiments.

Cell Culture Techniques↗
PubMed1990

Activation of glycogenolysis by stimulation of the hepatic nerves in perfused livers of guinea pig and tree shrew as compared to rat: differences in the mode of action.

A study on the metabolic and hemodynamic actions of hepatic nerve stimulation in the perfused liver of guinea pig and tree shrew as compared to rat was performed, since the density of liver innervation was reported to be different. 1) Nerve stimulation resulted in an increase in glucose release and decrease in lactate uptake or in a shift to output as well as a decrease in portal flow in all three species. The change in glucose output was very similar, that in lactate balance and flow was smaller in tree shrew than in guinea pig and rat. Apparently, the metabolic and hemodynamic changes did not reflect the different densities of liver innervation. 2) The overflow of the neurotransmitter noradrenaline into the hepatic vein differed very clearly in the three animals. In the guinea pig and tree shrew the maximal increase in noradrenaline concentration measured in the effluent was about 6-7-fold higher than in the rat. 3) The content of noradrenaline in the liver in vivo was about five-fold higher in the guinea pig and again another four-fold higher in the tree shrew than in the rat. The contents of adrenaline and dopamine were very low in comparison to those of noradrenaline. The different hepatic noradrenaline contents of the three species investigated are in line with the anatomical findings on the different innervation density. 4) Inhibitors of eicosanoid synthesis reduced the nerve stimulation-dependent metabolic and hemodynamic alterations in guinea pig liver as in rat liver indicating a similar mechanism in these species. Apparently, prostaglandins might be involved as mediators or modulators of nerve actions also in the more densely innervated guinea pig liver and not only in the less densely innervated rat liver.(ABSTRACT TRUNCATED AT 250 WORDS)

Acetophenones↗
PubMed2006

Binomial sequential sampling plan for hemlock woolly adelgid (Hemiptera: Adelgidae) sistens infesting individual eastern hemlock trees.

The hemlock woolly adelgid, Adelges tsugae Annand (Hemiptera: Adelgidae), is an exotic insect pest that is killing eastern hemlock, Tsuga canadensis (L.) Carrière, and Carolina hemlock, Tsuga caroliniana Engelmann, in the eastern United States. We used the sequential interval procedure to develop a binomial sequential sampling plan for A. tsugae sistens on individual eastern hemlock trees that uses nondestructive sampling of new shoots. The actual a (type I) and beta (type II) error rates were essentially 5 and 10%, respectively. Tallies of new shoots infested by at least one A. tsugae sistens were compared with stop values for thresholds of 10 and 30% of new hemlock shoots infested. Twenty to 80 new shoots had to be examined per tree to render a low, high, or indeterminate classification, which took < 2 min per tree regardless of the threshold used. This plan should be an efficient and cost-effective tool in the management of A. tsugae infestations on individual, high-value eastern hemlock trees.

Animals↗