TINNiK: inference of the tree of blobs of a species network under the coalescent model.

The tree of blobs of a species network shows only the tree-like aspects of relationships of taxa on a network, omitting information on network substructures where hybridization or other types of lateral transfer of genetic information occur. By isolating such regions of a network, inference of the tree of blobs can serve as a starting point for a more detailed investigation, or indicate the limit of what may be inferrable without additional assumptions. Building on our theoretical work on the identifiability of the tree of blobs from gene quartet distributions under the Network Multispecies Coalescent model, we develop an algorithm, TINNiK, for statistically consistent tree of blobs inference.

Low Ventricular Stiffness Is Associated With Suboptimal Outcomes in Patients With a Single Right Ventricle After the Fontan Operation: A Novel Phenotype.

Background: Despite a rigorous screening process, including cardiac catheterization, a subset of patients with a single right ventricle (SRV) demonstrates suboptimal short-term outcomes after the Fontan operation. The goal of this study was to perform a comprehensive assessment of diastolic function in pre-Fontan patients with an SRV using invasive reference-standard measures and determine their associations with post-Fontan outcomes.

Methods And Results: Children aged 2 to 6 years with SRV physiology undergoing pre-Fontan heart catheterization were recruited prospectively.

Identifiability of Level-1 Species Networks from Gene Tree Quartets.

When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several recently proposed methods are based on quartet concordance factors-the probabilities that a tree relating a gene sampled from the species displays the possible 4-taxon relationships. Building on earlier results, we investigate what level-1 network features are identifiable from concordance factors under the network multispecies coalescent model.

Differences in outcomes between surgical pericardial window and pericardiocentesis in children with postpericardiotomy syndrome.

Children with postpericardiotomy syndrome may develop hemodynamically significant pericardial effusions warranting drainage by surgical pericardial window or pericardiocentesis. The optimal approach is unknown. We performed a retrospective observational study at two pediatric cardiac centers.

TINNiK: Inference of the Tree of Blobs of a Species Network Under the Coalescent.

The tree of blobs of a species network shows only the tree-like aspects of relationships of taxa on a network, omitting information on network substructures where hybridization or other types of lateral transfer of genetic information occur. By isolating such regions of a network, inference of the tree of blobs can serve as a starting point for a more detailed investigation, or indicate the limit of what may be inferrable without additional assumptions. Building on our theoretical work on the identifiability of the tree of blobs from gene quartet distributions under the Network Multispecies Coalescent model, we develop an algorithm, TINNiK, for statistically consistent tree of blobs inference.

Prognostic Factors Affecting the Outcome of Surgical Root Canal Treatment-A Retrospective Cone-Beam Computed Tomography Cohort Study.

To assess the association between demographic and clinical variables and the outcome of root-end surgery using digital periapical radiographs (PA) and cone-beam computed tomography (CBCT). One hundred and fifty teeth that received endodontic microsurgery were clinically and radiographically examined (PA and CBCT scans) after 1 and 2 years. Two calibrated endodontists evaluated the radiographic healing based on a six-point outcome classification.

"Fontan Conduit Stent-Angioplasty and Progression of Fontan-Associated Liver Disease".

Patients with Fontan circulation insidiously develop congestive hepatopathy related to chronically reduced cardiac output and central venous hypertension, also known as Fontan-associated liver disease (FALD). Fontan pathway obstruction is increasingly detected and may accelerate FALD. The impact of conduit stent angioplasty on FALD is unknown.

Anomalous networks under the multispecies coalescent: theory and prevalence.

Reticulations in a phylogenetic network represent processes such as gene flow, admixture, recombination and hybrid speciation. Extending definitions from the tree setting, an anomalous network is one in which some unrooted tree topology displayed in the network appears in gene trees with a lower frequency than a tree not displayed in the network. We investigate anomalous networks under the Network Multispecies Coalescent Model with possible correlated inheritance at reticulations.

IDENTIFIABILITY OF LEVEL-1 SPECIES NETWORKS FROM GENE TREE QUARTETS.

When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several recently proposed methods are based on quartet concordance factors - the probabilities that a tree relating a gene sampled from the species displays the possible 4-taxon relationships. Building on earlier results, we investigate what level-1 network features are identifiable from concordance factors under the network multispecies coalescent model.

Design and Harmonization Approach for the Multi-Institutional Neurocognitive Discovery Study (MINDS) of Adult Congenital Heart Disease (ACHD) Neuroimaging Ancillary Study: A Technical Note.

Dramatic advances in the management of congenital heart disease (CHD) have improved survival to adulthood from less than 10% in the 1960s to over 90% in the current era, such that adult CHD (ACHD) patients now outnumber their pediatric counterparts. ACHD patients demonstrate domain-specific neurocognitive deficits associated with reduced quality of life that include deficits in educational attainment and social interaction. Our hypothesis is that ACHD patients exhibit vascular brain injury and structural/physiological brain alterations that are predictive of specific neurocognitive deficits modified by behavioral and environmental enrichment proxies of cognitive reserve (e.

ANOMALOUS NETWORKS UNDER THE MULTISPECIES COALESCENT: THEORY AND PREVALENCE.

Reticulations in a phylogenetic network represent processes such as gene flow, admixture, recombination and hybrid speciation. Extending definitions from the tree setting, an network is one in which some unrooted tree topology displayed in the network appears in gene trees with a lower frequency than a tree not displayed in the network. We investigate anomalous networks under the Network Multispecies Coalescent Model with possible correlated inheritance at reticulations.

Phylogenomic Models from Tree Symmetries.

A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting. Chifman and Kubatko initiated the study of such models, leading to the development of the SVDquartets methods of species tree inference. A key observation was that symmetries in an ultrametric species tree led to symmetries in the joint distribution of bases at the taxa.

Parameter Identifiability of a Multitype Pure-Birth Model of Speciation.

Diversification models describe the random growth of evolutionary trees, modeling the historical relationships of species through speciation and extinction events. One class of such models allows for independently changing traits, or types, of the species within the tree, upon which speciation and extinction rates depend. Although identifiability of parameters is necessary to justify parameter estimation with a model, it has not been formally established for these models, despite their adoption for inference.

Recovering from first episode psychotic mania: The experience of people diagnosed with bipolar disorder.

Aim: Early intervention for people diagnosed with bipolar disorder is a priority, but little is known about how recovery from first episode psychotic mania is experienced by this group. This study aimed to explore the experience of recovery from first episode psychotic mania for people diagnosed with bipolar disorder.

Methods: Semi-structured interviews were conducted with 11 young adults during recovery from first episode psychotic mania and were analysed using Interpretative Phenomenological Analysis.

The tree of blobs of a species network: identifiability under the coalescent.

Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands. It also remains unclear how complicated networks can be for consistent inference to be possible. As a step toward inferring a general species network, this work considers its tree of blobs, in which non-cut edges are contracted to nodes, so only tree-like relationships between the taxa are shown.

Testing Multispecies Coalescent Simulators Using Summary Statistics.

As genomic-scale datasets motivate research on species tree inference, simulators of the multispecies coalescent (MSC) process have become essential for the testing and evaluation of new inference methods. However, the simulators themselves must be tested to ensure that they give valid samples. This work develops methods for checking whether a collection of gene trees is in accord with the MSC model on a given species tree.

Identifiability of species network topologies from genomic sequences using the logDet distance.

Inference of network-like evolutionary relationships between species from genomic data must address the interwoven signals from both gene flow and incomplete lineage sorting. The heavy computational demands of standard approaches to this problem severely limit the size of datasets that may be analyzed, in both the number of species and the number of genetic loci. Here we provide a theoretical pointer to more efficient methods, by showing that logDet distances computed from genomic-scale sequences retain sufficient information to recover network relationships in the level-1 ultrametric case.

Long-Term Outcomes After Melody Transcatheter Pulmonary Valve Replacement in the US Investigational Device Exemption Trial.

Background: The Melody valve was developed to extend the useful life of previously implanted right ventricular outflow tract (RVOT) conduits or bioprosthetic pulmonary valves, while preserving RV function and reducing the lifetime burden of surgery for patients with complex congenital heart disease.

Methods: Enrollment for the US Investigational Device Exemption study of the Melody valve began in 2007. Extended follow-up was completed in 2020.

Atrial fibrillation after closure of patent foramen ovale in the REDUCE clinical study.

Objectives: To describe the occurrence of postprocedural atrial fibrillation (AF) among patients with cryptogenic stroke undergoing patent foramen ovale (PFO) closure in the REDUCE clinical study and analyze for potential risk factors for the development of postprocedural AF.

Background: AF is an adverse event that might potentially counterbalance the stroke prevention benefit from PFO closure. Data on AF after transcatheter PFO closure are sparse.

Patent Foramen Ovale Closure Decreases the Incidence but Not the Size of New Brain Infarction on Magnetic Resonance Imaging: An Analysis of the REDUCE Trial.

Background And Purpose: Randomized patent foramen ovale closure trials have used open-label end point ascertainment which increases the risk of bias and undermines confidence in the conclusions. The Gore REDUCE trial prospectively performed baseline and follow-up magnetic resonance imaging (MRIs) for all subjects providing an objective measure of the effectiveness of closure.

Methods: We performed blinded evaluations of the presence, location, and volume of new infarct on diffusion-weighted imaging of recurrent clinical stroke or new infarct (>3 mm) on T2/fluid attenuated inversion recovery from baseline to follow-up MRI at 2 years, comparing closure to medical therapy alone.

Parameter Identifiability for a Profile Mixture Model of Protein Evolution.

A profile mixture (PM) model is a model of protein evolution, describing sequence data in which sites are assumed to follow many related substitution processes on a single evolutionary tree. The processes depend, in part, on different amino acid distributions, or profiles, varying over sites in aligned sequences. A fundamental question for any stochastic model, which must be answered positively to justify model-based inference, is whether the parameters are identifiable from the probability distribution they determine.

Ventricular septal defect complicating delayed presentation of acute myocardial infarction during COVID-19 lockdown: a case report.

Background: Post-myocardial infarction ventricular septal defects (VSDs) have become rare in the reperfusion era but remain associated with very high morbidity and mortality. As patients defer prompt evaluation and management of acute coronary syndromes during the COVID-19 global pandemic, the incidence of these and other post-infarction mechanical complications is expected to increase.

Case Summary: A 37-year-old gentleman with multiple coronary artery disease risk factors presented with intermittent chest discomfort and 1 week of heart failure symptoms.

Radiographic periapical healing associated with root-treated teeth accessed through existing crowns: a historical controlled cohort study.

Objectives: The aim of this study was to determine the periapical healing rate and complications arising from non-surgical root canal treatment (NSRCT) conducted through the existing and retained restoration, compared to that conducted after removal of restoration (direct or indirect) with subsequent placement of a new crown.

Materials And Methods: Two-hundred-and-forty-five teeth met the inclusion criteria and were followed up for 2 years. One-hundred-and-six teeth had NSRCT completed through existing cast restorations, and 57 and 82 had the existing crowns and direct restorations removed (respectively) and received a new crown after NSRCT.