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PubMed1992

Immunohistochemical organization of the ventral lateral geniculate nucleus in the tree shrew.

The ventral lateral geniculate nucleus (vLGN) of the tree shrew (Tupaia belangeri) was differentiated into multiple subdivisions (dorsal cap, intergeniculate leaflet, parvicellular segment, and internal and external magnocellular laminae, the latter being further divisible into a lateral and medial division) on the basis of retinal projections, immunochemistry, and histochemistry. Retinal projections traced with intravitreal injections of wheat germ agglutinin conjugated horseradish peroxidase revealed direct bilateral input to all subregions of the vLGN, except for the internal magnocellular lamina (which received only contralateral input) and the parvicellular segment (which was not retinorecipient). Furthermore, retinal inputs clearly distinguished the relatively heavily retinorecipient intergeniculate leaflet from the less prominently labeled dorsal cap. Immunohistochemical localization of Neuropeptide Y (NPY) perikarya revealed their prominence in the intergeniculate leaflet and the external magnocellular laminae with a concentration along the optic tract. NPY immunoreactive fibers were seen in all but the parvicellular subregion. Gamma amino butyric acid immunoreactivity was seen throughout the vLGN, but was most concentrated in the dorsal cap and the magnocellular laminae, followed by the intergeniculate leaflet. Histochemical studies of cytochrome oxidase and nicotinamide adenosine dinucleotide phosphate (NADPH)-diaphorase localization revealed similar patterns of dense reactivity within the external magnocellular lamina, intergeniculate leaflet and dorsal cap, and somewhat less dense, but substantial reactivity in the internal magnocellular lamina. Within the external magnocellular lamina, cells reactive for cytochrome oxidase were noted in the lateral portion bordering the optic tract, whereas those specific for NADPH-diaphorase were dispersed throughout the lamina. Poor reactivity for both histochemical markers was evident in the parvicellular segment. Overall, the markedly different patterns of retinal input and neurochemical organization between the subdivisions of the tree shrew vLGN suggest their involvement in diverse functions. Furthermore, the basic similarity of the organization of the tree shrew vLGN to that of the taxonomically unrelated ground squirrel may indicate a common mammalian scheme.

Animals↗

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↗

PubMed1992

Sex differences in cortical thickness and the dendritic tree in the monocular and binocular subfields of the rat visual cortex at weaning age.

The visual cortex of adult rats is sexually dimorphic at both the gross size and dendritic levels [Brain Res., 295 (1984) 27-34; J. Comp. Neurol., in press]. In addition, sex differences in the dendritic tree are dynamic and can be altered by environmental conditions imposed at weaning [Brain Res., 295 (1984) 27-34]. The present study examines sex differences in cortical thickness and in the dendritic tree of the monocular (Oc1M) and binocular (Oc1B) subfields in littermate male and female pairs of Long-Evans rats at weaning age (25 days). From Nissl-stained tissue, it was found that the whole cortex and layer II-IV of Oc1B was thicker in males than females. No sex differences were found in the thickness of Oc1M. Golgi-Cox-stained pyramidal neurons in layer III from the Oc1M and Oc1B regions were quantified in 7 littermate pairs of weaning-age rats. There were no sex differences in the basilar tree, while the apical oblique branches were sexually dimorphic, especially in the monocular region. Females had greater total dendritic length and longer terminal branches in Oc1M compared to males. Females also had longer bifurcating branches in both Oc1M and Oc1B than males. The present study found that sex differences at weaning age do not completely mirror the dimorphisms found in the visual cortex of the adult rat. This study also indicates that related subfields can differ in their morphology and should be examined separately.

Analysis of Variance↗

PubMed1992

The nature of the last universal ancestor and the root of the tree of life, still open questions.

The nature of the last universal ancestor to all extent cellular organisms and the rooting of the universal tree of life are fundamental questions which can now be addressed by molecular evolutionists. Several scenarios have been proposed during the last years, based on the phylogenies of ribosomal RNA and of duplicated proteins, which suggest that the last universal ancestor was either an RNA progenote or an hyperthermophilic prokaryote. We discuss these hypotheses in the light of new data on the evolution of DNA metabolizing enzymes and of contradictions between different protein phylogenies. We conclude that the last universal ancestor was a member of the DNA world already containing several DNA polymerases and DNA topoisomerases. Furthermore, we criticize current data which suggest that the rooting of the universal tree of life is located in the eubacterial branch and we conclude that both rooting the universal tree and the nature of the last universal ancestor are still open questions.

Archaea↗

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↗

PubMed1992

An exploratory analysis of survival with AIDS using a nonparametric tree-structured approach.

We illustrate an analysis with classification and regression trees applied to survival data. Through this application, we provide a description of the opportunistic diseases and sociodemographic factors that contribute to survival among people with human immunodeficiency virus disease. The analyses are based on 43,795 cases reported to the Centers for Disease Control between January 1, 1984, and December 31, 1987. We used vital status as of December 31, 1989, to estimate mortality rates. We identified Kaposi's sarcoma and opportunistic diseases causing central nervous system damage (cryptococcosis, primary lymphoma of the brain, cytomegalovirus disease, and progressive multifocal leukoencephalopathy) as important predictors of death. In addition, advanced age at diagnosis (50+), race (white/other), and history of illicit drug use were found to be important determinants. Estimates of the cumulative probability of survival for subgroups of individuals defined by the tree structure illustrate the effect of these determinants on mortality. For the purpose of comparison, two proportional hazards models were also fit to the data using factors identified in the tree structure as the determinants of interest. This application illustrates the utility and limitations of both this new technique and proportional hazards models for epidemiologic research.

Acquired Immunodeficiency Syndrome↗

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↗

PubMed1992

Branching patterns in the porcine coronary arterial tree. Estimation of flow heterogeneity.

The aim of this study is to quantify the porcine coronary arterial branching pattern and to use this quantification for the interpretation of flow heterogeneity. Two casts of the coronary arterial tree were made at diastolic arrest and maximal dilation. The relation between length and diameter of arterial segments was quantified, as well as the area expansion ratio and diameter symmetry of vascular nodes. These relations were used to construct computer models of the coronary arterial tree, covering diameters between 10 and 500 microns. Topology of these simulated trees was analyzed using Strahler ordering: Bifurcation ratio, diameter ratio, and length ratio were constant along orders 2-8 and equal to 3.30, 1.51, and 1.63, respectively. In each order, the number of segments per Strahler vessel was almost geometrically distributed. For the lowest orders, these predictions were confirmed by direct observations. From the network model, local pressure and flow were also predicted: Pressure fell from 90 to 32 mm Hg at the 10-microns level. The coefficient of variation (CV) of flow in individual segments was dependent on the number of perfused terminal segments (Nt) according to the fractal relation CV(Nt) approximately Nt(1-D), where D is the fractal dimension (1.20). CV of flow in 1-g tissue units was predicted to be 18%. This study shows that the structure of the coronary arterial bed is an important determinant of the fractal nature of local flow heterogeneity.

Animals↗

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↗

PubMed1976

An account of the longitudinal mucosal corrugations of the human tracheo-bronchial tree, with observations on those of some animals.

A description is given of the distribution of the longitudinal mucosal corrugations in the human tracheo-bronchial tree. It has been shown that they are made up of elastic tissue in a collagen matrix, and that the elastic fibres continue into the smallest bronchioles beyond where the corrugations are no longer visible. An examination has also been made of the tracheo-bronchial trees of the hen, rat, raccoon, pig, sheep, llama and tiger. Corrugations are present in all these animals, except the hen and the raccoon, and they have been compared and contrasted with the condition in Man. The functional significance of these corrugations remains unknown, but, they could be important in equalizing tension in the tracheo-bronchial tree during inspiration, as well as in providing elastic recoil during expiration.

Adult↗

PubMedDate not supplied

[Aerodynamic characteristics of the human right lung bronchial tree].

A new method of studying the aerodynamical characteristics of normal right bronchial tree in 17 natural preparations is described. The authors have found that 24 to 44 per cent of the total airflow entering the right main bronchus pass through the upper lobe bronchus, 9-26 per cent through the middle lobe bronchus and 38-56 per cent through the lower lobe bronchus. The data obtained show good agreement with the volume of the corresponding lobe expressed as percentage to the total right lung volume. Bronchial tree preparations differ greatly in their carrying capacities due to their corresponding aerodynamical resistances (+50% +25%). The relationship between resistance coefficient of the bronchial tree preparations and their geometrical parameters has been found.

Airway Resistance↗

PubMedDate not supplied

Use of a decision tree to improve accuracy of diagnosis.

Thirty triads of nurses matched for educational background, length of experience, and previous performance were studied to determine if use of a decision tree would improve diagnostic accuracy. One experimental and two control groups were given a written case study and asked to list all possible diagnoses that could cause the change in behavior exhibited by the patient. Experimental group nurses were given a set of decision trees to enable them to use the information systematically to determine if characteristics of each condition were present. Significant improvement in diagnostic accuracy was shown by nurses who used the decision trees.

Decision Making↗

PubMed1977

Random censoring and dendritic trees.

The motivating problem is the estimation of the branching parameters of dendritic trees when some of the branches are cut. A primary element of this problem is the estimation of a bivariate discrete distribution when, because of partial censoring, some of the observations are incomplete. (This is similar to the problem of a multinomial cross-classification with supplemental partially cross-classified data.) Tests for randomness of censoring and estimators of parameters under random censoring are derived. The results on random censoring are applied in the dendritic tree context to obtain estimators for certain branching and cutting parameters. The testing and estimation procedures are applied to a set of dendritic tree data.

Dendrites↗