SEARCH · PubMed Health

Results for “Trees”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources

PubMed1978

Allergy to pollen from different deciduous trees in Sweden. An investigation with skin tests, provocation tests and the radioallergosorbent test (RAST) in springtime hay fever patients.

92 adult patients with springtime allergy were investigated with skin tests, provocation tests and the RAST. Allergen extracts from 12 different deciduous trees were used. Positive reactions, often of high intensity, were most often found with birch, alder, bog-myrtle, beech and hazel allergens whereas oak, aspen, linden, elm, sallow, maple and poplar allergens more often gave negative or only weak positive test results. Cross sensitizations were found between botanically related as well as between less related species of the trees. Almost all patients with a clinically relevant tree pollen allergy had positive provocation tests with birch pollen. No patient had positive reactions to all the 12 allergens included in the study. 68% had positive provocation tests with the combination birch, alder and hazel. It is concluded that for diagnostic screening purposes it is sufficient to use birch pollen allergen. If the majority of relevant tree pollens are to be included in a diagnostic or therapeutic programme in Western Sweden it should contain birch, alder, hazel, beech and bog-myrtle allergens.

Adolescent↗

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↗

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↗

PubMed2025

Bayesian inference of fitness landscapes via tree-structured branching processes.

MOTIVATION: The complex dynamics of cancer evolution, driven by mutation and selection, underlies the molecular heterogeneity observed in tumors. The evolutionary histories of tumors of different patients can be encoded as mutation trees and reconstructed in high resolution from single-cell sequencing data, offering crucial insights for studying fitness effects of and epistasis among mutations. Existing models, however, either fail to separate mutation and selection or neglect the evolutionary histories encoded by the tumor phylogenetic trees. RESULTS: We introduce FiTree, a tree-structured multi-type branching process model with epistatic fitness parameterization and a Bayesian inference scheme to learn fitness landscapes from single-cell tumor mutation trees. Through simulations, we demonstrate that FiTree outperforms state-of-the-art methods in inferring the fitness landscape underlying tumor evolution. Applying FiTree to a single-cell acute myeloid leukemia dataset, we identify epistatic fitness effects consistent with known biological findings and quantify uncertainty in predicting future mutational events. The new model unifies probabilistic graphical models of cancer progression with population genetics, offering a principled framework for understanding tumor evolution and informing therapeutic strategies. AVAILABILITY AND IMPLEMENTATION: The Python package FiTree and the analysis workflows are available at https://github.com/cbg-ethz/FiTree.

Bayes Theorem↗

PubMed1976

Induction of liver tumors by aflatoxin B1 in the tree shrew (Tupaia glis), a nonhuman primate.

The epidemiological studies suggest that aflatoxins, the toxic metabolites of the ubiquitous mold Aspergillus flavus, may play a significant role in the evolution of hepatocellular carcinoma in man in certain geographic areas of the world. To ascertain their carcinogenicity in nonhuman primates, we have administered highly purified aflatoxin B1, intermittently in the diet at 2 ppm, to 10 female and 8 male tree shrews. The tree shrew (Tupaia glis) is a nonhuman primate occurring throughout Southeast Asia which can be reared easily in captivity. Of 12 animals that survived, 6 of 6 female (100%) and 3 of 6 male (50%) tree shrews developed hepatocellular carcinomas between 74 and 172 weeks after the beginning of the experiment. None of the 8 control animals developed liver cancers. The estimated total amount of aflatoxin B1 consumed by these animals ranged from 24 to 66 mg. The development of liver tumors did not follow a specific pattern; considerable variation in hepatocellular responses to aflatoxin B1 was noted in these animals. In 2 tree shrews, the liver tumors were associated with severe post necrotic scarring; in the other 7 tumor-bearing livers, only mild to moderate portal fibrosis was encountered. This individual variation in hepatocellular response and in the amount of aflatoxin B1 required to induce hepatocellular carcinomas is attributed to inherent differences in the susceptibility within a given species of outbred animals and suggests extreme caution in proposing the "permissible" or "safe" levels of contamination of carcinogens in the food-stuffs.

Aflatoxins↗

PubMed1976

The lead, copper and zinc content of tree rings and bark. A measurement of local metallic pollution.

Analysis of samples of wood taken from different tree rings for lead by atomic absorption spectrometry showed that there was little correlation between the sample site or ring age and air borne lead concentrations. However, the concentration of lead in tree bark at several sites was particularly sensitive to traffic flow at that site. The concentration of lead, zinc and copper in the tree bark decreased with increased distance from the road and with height above the ground. The method offers a simple technique for effectively tracing atmospheric metal concentrations.

Air Pollutants↗

PubMed2026

No evidence of fine-scale local adaptation of winter moths to variable tree phenology.

Spatial variation in plant phenology can impose strong selective pressures on herbivorous insects whose fitness relies on synchrony with host plants, promoting local adaptation to host timing. Winter moths (Operophtera brumata) have been shown to synchronize egg hatching with host budburst, but whether this reflects local adaptation remains unclear. We used three complementary approaches to assess small-scale local adaptation of winter moths to oak phenology in Wytham Woods, UK, a 385-hectare woodland with repeatable variation in individual oak budburst phenology. We experimentally investigated whether host tree phenology predicts hatch timing using common gardens across multiple temperatures, evaluated fitness benefits of synchrony using translocations, and assessed population structure and gene-environment associations using whole-genome sequencing. We found no support for local adaptation to individual trees. Common garden experiments revealed systematic differences in hatch timing which were unrelated to host budburst, while translocations indicated no fitness consequences of asynchrony. Genetic analyses showed no detectable population structure or association with budburst timing. Local adaptation to host phenology therefore appears not to arise on individual trees but may instead occur at broader spatial scales. Understanding the scale of local adaptation is essential for predicting how insect-plant synchrony will respond to environmental change across heterogeneous landscapes.

Animals↗

PubMed1977

Tree host range and world distribution of the extomycorrhizal fungus Pisolithus tinctorius.

The natural occurrence of Pisolithus tinctorius has been confirmed in 33 countries of the world and in 38 states in the United States. This ectomycorrhizal fungus is found associated with various tree species in nurseries, urban areas, orchards, forests, and strip-mined spoils. Experiments have proved that this fungal symbiont forms ectomycorrhizae with Abies procera, Betula pendula, Carya illnoensis, 11 species of Eucalyptus, 30 species of Pinus, Pseudotsuga menziesii var. meniziesii, 2 species of Quercus, and Tsuga heterophylla. Pisolithus has also been reported growing under natural conditions in association with three additional species of Betula, two species of Eucalyptus, nine species of Pinus, and eight species of Quercus, Populus tremuloides, Pseudotsuga grandidenta, and Salix humilis. This fungal symbiont has great potential in forestation efforts because of (1) the availability of practical techniques for artificially introducing in into nursery soils; (2) its ability to improve tree survival and growth in the nursery and the field; (3) its near worldwide distribution on a variety of sites; and (4) its broad host range encompassing many of the world's most important tree species.

Basidiomycota↗

PubMed1978

Falls from trees.

A prospective review of sixty consecutive patients who fell out of trees in a year was made. Fall from tree is an occupational hazard of traditional farmers, a rare cause of trauma, but a common cause of severe, crippling and often multiple injuries. It frequently resulted in spinal injury, and was the commonest cause of traumatic quadriplegia and paraplegia. The risk of fall and of sustaining spinal injury increased with age. Some school children also fell from fruit trees but they generally stood a better chance of getting away with relatively minor injuries. Methods of preventing or minimising the risk of this injury in farmers are highlighted.

Accident Prevention↗

PubMed1978

Bacterial contamination of the biliary tree after choledochostomy.

Secondary exogenous contamination of bile after choledochostomy could be an important cause of long-term morbidity if infection persists after removal of the T tube. Surprisingly, documentation of the frequency of conversion of sterile to infected bile after choledochostomy has rarely been recorded. Patients undergoing exploration and T-tube drainage of the common bile duct between July 1966 and January 1975, in whom intraoperative and postoperative cultures of bile were available, were studied. Postoperative cultures were obtained from five to forty days after operation. Of ninety-five patients available for study, contamination developed postoperatively in previously sterile bile in 44 per cent. The common duct bile contained bacteria at operation in 42 per cent and remained sterile throughout in 14 per cent. The most common secondary contaminants were klebsiella group and Escherichia coli. The fate of the contaminating organisms in a biliary tree without anatomic abnormalities is unknown. Two cases are presented which suggest that persistent infection may linger in the biliary tree for many years and give rise to pigment calculi. Since bacterial cannot be eradicated so long as a foreign body remains in the common duct and because such bacteria may cause symptoms even in an anatomically normal biliary tree, we suggest that a closed system of biliary drainage be employed and that appropriate antibiotic therapy be instituted for seven to ten days after removal of the T tubes.

Aged↗

PubMed1977

Postnatal growth of the dog's bronchial tree.

Polyester resin casts of the bronchial tree were made from the lungs of four Labrador dogs which weighed 0.5, 3.4, 7.5 and 30.0 kg, respectively. The branching trees were ordered by the method of Strahler and plots made of number, mean diameter and mean length of branches in each order. The four length plots were found to lie parallel to each other, as did three of the four diameter plots. When data are divided by the cube root of body weight the length plots almost coincide, as do the diameter plots. This indicates that the bronchial tree grows in constant proportion to the cube root of body weight.

Aging↗

PubMed2026

Comparison of paralog identification methods and their impact on species tree topologies in target capture phylogenomics within the Sindora clade (Detarioideae: Leguminosae).

Target capture is a common method of generating high throughput DNA sequencing data for phylogenetic reconstruction of species relationships, for which single copy genes are usually most informative. However, a pervasive problem with target capture is that putatively single copy genes may in fact be paralogs resulting from gene duplication, which are problematic for phylogenetic inference because their evolutionary history may differ from the divergence history of species. Here, we use as a case study a target enrichment dataset of 88 species of Detarioideae (Leguminosae) with a focus on the Sindora clade to examine approaches for handling paralogs, including the built-in paralog handling functions in HybPiper and CAPTUS, plus subsequent steps using Putative Paralog Detection and the tree-based Yang & Smith orthology inference approach. We compare the paralogs flagged using these methods and verify their performance with BLAST mapping against a reference genome sequence of Sindora glabra, and then subsequently compare the species tree topologies produced across these methods. Our comparisons of paralogs flagged across the Sindora clade show that the Putative Paralog Detection pipeline was the most accurate in identifying paralogs in terms of its similarity to the BLAST mapping, followed by the built-in paralog identification function of CAPTUS. However, the results we recovered for the Detarioideae subfamily suggest that the largest differences in species tree topology resulted from the use of paralog-filtered alignments (such as with the Putative Paralog Detection pipeline and the Yang & Smith orthology inference approaches) rather than just by removing the sequences of identified paralogous genes. This was the true for HybPiper-assembled datasets but was not seen in CAPTUS-assembled datasets. In all comparisons, the topological differences caused by different paralog handling methods tended to be confined to clades where processes such as hybridisation and introgression are prevalent. Our study provides a roadmap to establish the best approach to identify, eliminate or separate paralogs in the absence of a chromosomally contiguous reference genome for a study group, and highlights the importance of careful data inspection and processing in addition to understanding the extent of paralogy and paralog characteristics (e.g. sequence divergence between copies) for their study group.

Phylogeny↗

PubMed2023

Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree.

Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints in sequencing coverage, assembly and annotation quality, especially for large datasets. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes and bypasses traditional steps in phylogeny inference, such as genome assembly, annotation and all-versus-all sequence comparisons, while retaining accuracy. In a benchmark encompassing a broad variety of datasets, Read2Tree is 10-100 times faster than assembly-based approaches and in most cases more accurate-the exception being when sequencing coverage is high and reference species very distant. Here, to illustrate the broad applicability of the tool, we reconstruct a yeast tree of life of 435 species spanning 590 million years of evolution. We also apply Read2Tree to >10,000 Coronaviridae samples, accurately classifying highly diverse animal samples and near-identical severe acute respiratory syndrome coronavirus 2 sequences on a single tree. The speed, accuracy and versatility of Read2Tree enable comparative genomics at scale.

Animals↗

PubMed2026

Phylogenomics reveals persistent gene-tree discordance in the Chenopodium album aggregate.

BACKGROUND AND AIMS: Complex genomic histories shaped by hybridisation and polyploidy can influence traits related to plant defence, stress tolerance and toxicity, particularly in Amaranthaceae, which includes crops such as quinoa and spinach. Within this family, white goosefoot (Chenopodium album), a widespread agricultural weed and traditional food resource, belongs to a diploid-polyploid aggregate with extensive phylogenetic discordance. Clarifying its evolutionary history provides context for interpreting ecologically and agronomically relevant trait variation across the aggregate. Building on the established genome-lineage framework, we tested whether discordance persists when constituent genome-lineage components are represented separately and whether the remaining signal is compatible with reticulate evolution. METHODS: We analysed 2,298 conserved nuclear BUSCO families across 27 assembly-level terminals using tree- and network-based approaches. Genome-lineage-aware analyses used 2,156 families after separating polyploid Chenopodium into A-H components, with Dysphania ambrosioides as outgroup. HyDe tested site-pattern asymmetry under global false-discovery-rate correction. KEY RESULTS: Assembly-level analyses grouped the Danish C. album aggregate accession Ca6-1 with hexaploid C. album sensu stricto dcCheAlbu1.1, whereas relationships among surrounding Chenopodium taxa were less stable. Genome-lineage-aware analyses recovered the expected B-, C- and D-affinity relationships, but substantial gene-family heterogeneity persisted. Reticulate network models fitted the assembly-level data better than bifurcating models, although inferred patterns differed between methods. HyDe detected significant site-pattern asymmetry in a small subset of loci, with most retained signal shared between the focal assemblies. CONCLUSIONS: Gene-tree discordance persists in the C. album aggregate after genome-lineage separation. The established genome-lineage framework captures the dominant phylogenomic structure, while residual heterogeneity is compatible with both tree-like and reticulate processes without identifying direct progenitors or a unique hybridisation history. This framework supports future analyses of lineage-specific and trait-associated loci related to plant defence, food quality and toxicity in C. album and related Amaranthaceae.

Chenopodium album↗

PubMed2026

Bayesian inference of lineage trees by joint analysis of single-cell multimodal lineage-tracing data with BiLinT.

The advent of single-cell lineage-tracing technologies has enabled the simultaneous profiling of gene expression and lineage barcodes. However, accurate, high-resolution reconstruction of cell lineage trees remains challenging because most existing approaches treat these modalities separately and therefore fail to fully exploit their complementary information. Here we present BiLinT, a Bayesian framework that jointly models multimodal single-cell lineage-tracing data for lineage tree reconstruction. BiLinT integrates barcode evolution (a continuous-time Markov chain) with gene expression dynamics (an Ornstein-Uhlenbeck process) within a unified probabilistic model. Across synthetic and real data sets, BiLinT provides accurate lineage-tree reconstruction and reveals differentiation-associated clonal structure and developmental fate biases.

Journal Article↗

PubMed1979

Apparent volume of the biliary tree in the dog.

The apparent volume of the biliary tree (ABV) in the dog was determined by measuring the mean biliary transit time of injected [14C]taurocholate ([14C]TC). After bolus injection of [14C]TC, entry of bile salt into the lumen of the biliary tree is signaled by an increase in bile flow. The volume of bile collected at the common duct from onset of choleresis until maximal concentration of 14C radioactivity is reached in bile minus the calculated quantity of bile that contains radioactivity and the cannula volume yields a value for the volume of the biliary tree present just prior to injection of [14C]TC. The mean value for ABV in 19 dogs was 2.49 +/- 0.65 microL/g liver (mean +/- SD).

Animals↗

PubMed1978

Ultrasonic study of the normal and dilated biliary tree. The "shotgun" sign.

With the advent of real time scanners, segments of the normal biliary tree can now be seen regularly. Normally, the biliary junction is narrower than the portal vein or the portal division. With early dilatation of the bile ducts the diameters of the two systems tend to equalize. Thus, the presence of two parallel ducts with similar diameters is pathologic. As the dilatation of the biliary tree progresses, the portal system may become flattened, thus reversing the initial proportion between the diameter of the biliary junction and that of the biliary tree.

Bile Ducts↗

PubMed2025

ScITree: Scalable Bayesian inference of transmission tree from epidemiological and genomic data.

Phylodynamic models capture joint epidemiological-evolutionary dynamics during an outbreak, providing a powerful tool to enhance understanding and management of disease transmission. Existing phylodynamic approaches, however, mostly rely on various non-mechanistic or semi-mechanistic approximations of the underlying epidemiological-evolutionary process. Previous work by Lau and colleagues has shown that full Bayesian mechanistic models, without relying on these approximations, can enable highly accurate joint inference of the epidemiological-evolutionary dynamics including the unobserved transmission tree. However, the Lau method faces major computational bottlenecks. As the volume of genomic data collected during outbreaks continues to grow, it is crucial to develop scalable yet accurate phylodynamic methods. Here we propose a new Bayesian phylodynamic model, overcoming the major scalability issue in the previous method and enabling a readily deployable, yet accurate, phylodynamic modeling framework. Specifically, we develop a scalable spatio-temporal phylodynamic framework for inferring the transmission tree (ScITree) and other key epidemiological parameters considering the infinite sites assumption in modeling mutation on the sequence level, in contrast to the Lau method in which mutation was modeled explicitly on the nucleotide level. Our approach features full Bayesian implementation utilizing an exact likelihood to mechanistically integrate epidemiological and evolutionary processes. We develop a computationally-efficient data-augmentation Markov Chain Monte Carlo algorithm, inferring key model parameters and unobserved dynamics including the transmission tree. We assess performance of our method using multiple simulated outbreak datasets. Our results indicate that our method can achieve high inference accuracy, comparable to the performance of the Lau method. Additionally, our method scales significantly more efficiently for large outbreaks, with computing time increasing linearly with outbreak size, compared to the exponential scaling of the Lau method. We also demonstrate our method's utility by applying our validated modeling framework to a dataset describing a foot-and-mouth disease outbreak in the UK. Our results show that our method is able to generate estimates of the transmission dynamics consistent with those from the prior method, further demonstrating the robustness of our new approach. In summary, our method provides a computationally-efficient, highly scalable, accurate modeling framework for inferring the joint spatio-temporal dynamics of epidemiological and evolutionary processes, facilitating timely and effective outbreak responses in space and time. Our method is implemented in our R package ScITree.

Bayes Theorem↗