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. We provide examples of its application to both simulated and empirical datasets, utilizing an implementation in the MSCquartets 2.0 R package.

Early intervention in psychosis for first episode psychotic mania: the experience of people diagnosed with bipolar disorder.

BACKGROUND: Early intervention for people diagnosed with bipolar disorder has been identified as a priority, but little is known about how existing early intervention services are experienced by this group or could be tailored to their needs. AIMS: This study examined the experience of early intervention in psychosis (EIP) services for people diagnosed with bipolar disorder, following first episode psychotic mania. METHOD: Semi-structured interviews were conducted with 11 adults in EIP services and analysed using Interpretative Phenomenological Analysis. RESULTS: One superordinate theme was formed, Rebuilding within EIP service, consisting of five subthemes: (i) Piecing together episode through talking to staff; (ii) Exploring other perspectives during CBT; (iii) Empowered through shared decision-making; (iv) Reconsidering future and purpose; (v) Service as safety-net. EIP provision was pivotal in helping participants understand their episode, adjust their perspective, build confidence and progress. CONCLUSIONS: Aspects of the service that were valued, including person-centred relationships with staff, shared decision-making and the development of motivation and opportunities, reflect key principles of mental health care for young people following first episode psychosis. Furthermore, findings point to elements that may be particularly relevant to early intervention following first episode psychotic mania including managing mood escalation and individualised approaches to goals.

"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. Retrospective, single-center review of patients with Fontan circulation who underwent conduit stent angioplasty at cardiac catheterization over 5-year period. Demographics and cardiac histories were reviewed. Labs, liver ultrasound elastography, echocardiogram, hemodynamic and angiographic data at catheterization were recorded pre- and post-stent angioplasty. Primary outcome was change in hepatic function via MELD-XI scores and liver stiffness (kPa), with secondary outcomes of ventricular function, BNP, and repeat catheterization hemodynamics. 33 patients underwent Fontan conduit stent angioplasty, 19.3 ± 7.0 years from Fontan operation. Original conduit diameter was 19.1 ± 1.9 mm. Prior to angioplasty, conduit size was reduced to a cross-sectional area 132 (91, 173) mm2 and increased to 314 (255, 363) mm2 post-stent. Subjects' baseline median MELD-XI of 11 (9, 12) increased to 12 (9, 13) at 19 ± 15.5 months post-angioplasty (n = 22, p = 0.053). There was no significant change in liver stiffness at 12.1 ± 8.9 months post-angioplasty (n = 15, p = 0.13). Median total bilirubin significantly increased (1.4 [0.9, 1.8]), from baseline 1.1 [0.7, 1.5], p = 0.04), as did median BNP (41 [0, 148] from baseline 34 [15, 79]; p = 0.02). There were no significant changes in ventricular function or repeat invasive hemodynamics (n = 8 subjects). Mid-term follow-up of Fontan subjects post-conduit stent angioplasty did not show improvements in non-invasive markers of FALD.

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

Aim: 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). Methodology: 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. The outcome was classified using both strict (healed) and loose (healing) criteria. The success rates were calculated, and several outcome prognostic factors were assessed. Results: One hundred and fifty teeth were assessed with both radiographic systems. When "loose" success criteria were applied using PA, 90% (n = 135) of teeth were assessed as having had a favourable outcome (90%; 95% CI: 85.2-94.8%), whereas 90.7% (n = 136) of teeth showed a successful outcome when assessed with CBCT (90.7%; 95% CI: 86.0-95.3%). When "strict" success criteria were applied, there was a statistically significant difference (p = 0.018) between the success rates of mineral trioxide aggregate (MTA) (63.7%) and Biodentine (95.5%). Conclusions: Within the limitations of this study, endodontic microsurgery showed a high success rate. Among all the demographic and clinical variables assessed, in the multiregression analysis, only the use of Biodentine was associated with a higher proportion of "complete" healings compared to MTA or Intermediate Restorative Material (IRM) when assessed using CBCT. MTA and Biodentine performed similarly when "incomplete" healings were regarded as successful outcomes.

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. Focusing on subsets of 4 taxa, we describe a new algorithm to calculate quartet concordance factors on networks of any level, faster than previous algorithms because of its focus on 4 taxa. We then study topological properties required for a 4-taxon network to be anomalous, uncovering the key role of [Formula: see text]-cycles: cycles of 3 edges parent to a sister group of 2 taxa. Under the model of common inheritance, that is, when each gene tree coalesces within a species tree displayed in the network, we prove that 4-taxon networks are never anomalous. Under independent and various levels of correlated inheritance, we use simulations under realistic parameters to quantify the prevalence of anomalous 4-taxon networks, finding that truly anomalous networks are rare. At the same time, however, we find a significant fraction of networks close enough to the anomaly zone to appear anomalous, when considering the quartet concordance factors observed from a few hundred genes. These apparent anomalies may challenge network inference methods.

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. We obtain results on both topological features of the network, and numerical parameters, uncovering a number of failures of identifiability related to 3-cycles in the network.

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. Focusing on subsets of 4 taxa, we describe a new algorithm to calculate quartet concordance factors on networks of any level, faster than previous algorithms because of its focus on 4 taxa. We then study topological properties required for a 4-taxon network to be anomalous, uncovering the key role of 32-cycles: cycles of 3 edges parent to a sister group of 2 taxa. Under the model of common inheritance, that is, when each gene tree coalesces within a species tree displayed in the network, we prove that 4-taxon networks are never anomalous. Under independent and various levels of correlated inheritance, we use simulations under realistic parameters to quantify the prevalence of anomalous 4-taxon networks, finding that truly anomalous networks are rare. At the same time, however, we find a significant fraction of networks close enough to the anomaly zone to appear anomalous, when considering the quartet concordance factors observed from a few hundred genes. These apparent anomalies may challenge network inference methods.

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.g., level of education and lifestyle/social habits). This technical note describes an ancillary study to the National Heart, Lung, and Blood Institute (NHLBI)-funded Pediatric Heart Network (PHN) "Multi-Institutional Neurocognitive Discovery Study (MINDS) in Adult Congenital Heart Disease (ACHD)". Leveraging clinical, neuropsychological, and biospecimen data from the parent study, our study will provide structural-physiological correlates of neurocognitive outcomes, representing the first multi-center neuroimaging initiative to be performed in ACHD patients. Limitations of the study include recruitment challenges inherent to an ancillary study, implantable cardiac devices, and harmonization of neuroimaging biomarkers. Results from this research will help shape the care of ACHD patients and further our understanding of the interplay between brain injury and cognitive reserve.

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. In this work, we explore the implications of such symmetry more fully, defining new models incorporating only the symmetries of this distribution, regardless of the mechanism that might have produced them. The models are thus supermodels of many standard ones with mechanistic parameterizations. We study phylogenetic invariants for the models, and establish identifiability of species tree topologies using them.

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. This work establishes generic identifiability up to label swapping for the parameters of one of the simpler forms of such a model, a multitype pure birth model of speciation, from an asymptotic distribution derived from a single tree observation as its depth goes to infinity. Crucially for applications to available data, no observation of types is needed at any internal points in the tree, nor even at the leaves.

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. RESULTS: Three themes were identified: (i) 'Possession of purpose and staying well', (ii) 'Coping with compromise' and (iii) 'Manic relapse: pressure and proving self'. On becoming well, the participants experienced a sense of purpose through engaging with activities and goals that also drove their efforts to engage in strategies to stay well. However, these strategies created feelings of compromise that not all were prepared to accept. Though having purpose and goals created a positive sense of direction, for a minority of the participants they also created additional pressure, contributing to manic relapse. CONCLUSIONS: The purpose created by engaging with aspirations and career-related activities during early intervention was found to be important for a meaningful recovery from first episode bipolar disorder. This instilled positivity and purpose, motivating efforts to maintain wellness. The feelings of compromise that some participants experienced point to the need for individually tailored interventions. Findings suggest a delicate relationship between the positivity of engaging in goals and the risk of manic relapse during recovery from first episode psychotic mania.

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. When applied to well-known simulators, we find that several give flawed samples. The tests presented are capable of validating both topological and metric properties of gene tree samples, and are implemented in a freely available R package MSCsimtester so that developers and users may easily apply them.

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. We included 42 children aged <18 years who developed postpericardiotomy syndrome following cardiac surgery between 2014 and 2021. Thirty-two patients underwent pericardial window and 10 underwent pericardiocentesis. Patients in the pericardial window group presented with postpericardiotomy syndrome sooner than those who underwent pericardiocentesis (median 7.5 days vs. 14.5 days, P = 0.03) and tended to undergo earlier intervention (median 8 days vs. 16 days, P = 0.16). No patient required subsequent drainage. There were no differences between groups in days of pericardial tube duration (median 4 days), complications, and subsequent days of intensive care or hospitalization. For children with postpericardiotomy syndrome with a pericardial effusion warranting drainage, these data suggest that pericardial window and pericardiocentesis have similar efficacy, safety, and resource utilization.

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. An identifiability theorem, that most features of the unrooted tree of blobs can be determined from the distribution of gene quartet topologies, is established. This depends upon an analysis of gene quartet concordance factors under the model, together with a new combinatorial inference rule. The arguments for this theoretical result suggest a practical algorithm for tree of blobs inference, to be fully developed in a subsequent work.

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. This result is obtained under the Network Multispecies Coalescent model combined with a mixture of General Time-Reversible sequence evolution models across individual gene trees. It applies to both unlinked site data, such as for SNPs, and to sequence data in which many contiguous sites may have evolved on a common tree, such as concatenated gene sequences. Thus under standard stochastic models statistically justifiable inference of network relationships from sequences can be accomplished without consideration of individual genes or gene trees.

Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent.

A simple graphical device, the simplex plot of quartet concordance factors, is introduced to aid in the exploration of a collection of gene trees on a common set of taxa. A single plot summarizes all gene tree discord and allows for visual comparison to the expected discord from the multispecies coalescent model (MSC) of incomplete lineage sorting on a species tree. A formal statistical procedure is described that can quantify the deviation from expectation for each subset of four taxa, suggesting when the data are not in accord with the MSC, and thus that either gene tree inference error is substantial or a more complex model such as that on a network may be required. If the collection of gene trees is in accord with the MSC, the plots reveal when substantial incomplete lineage sorting is present. Applications to both simulated and empirical multilocus data sets illustrate the insights provided. [Gene tree discordance; hypothesis test; multispecies coalescent model; quartet concordance factor; simplex plot; species tree].

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. METHODS: We evaluated data from patients having PFO closure (Gore HELEX or Gore Cardioform Septal Occluder) in the REDUCE clinical trial (n = 408) in at post hoc explorative analysis. Median follow-up was 5.0 years. RESULTS: AF occurred in 30 patients (7.4%) after PFO closure with a total of 34 AF events. Most were reported as non-serious (68%), detected within 45 days post-procedure (79%), and resolved within 2 weeks of onset (63%). One subject with AF had recurrent stroke. Postprocedural AF occurred more frequently among subjects with higher age and large device sizes. Male sex was the only independent predictor of postprocedural AF. We found no association between the type of occluder (HELEX or Gore Cardioform Septal Occluder) or PFO anatomical characteristics and post-procedural AF. CONCLUSION: In the REDUCE clinical study, postprocedural atrial fibrillation was mostly early onset, transient and with no later recurrence. Postprocedural AF occurred more frequently among patients with higher age and larger devices. Male sex was the only independent predictor of postprocedural AF.

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. The primary outcome was freedom from transcatheter pulmonary valve (TPV) dysfunction (freedom from reoperation, reintervention, moderate or severe pulmonary regurgitation, and/or mean RVOT gradient >40 mm Hg). Secondary end points included stent fracture, catheter reintervention, surgical conduit replacement, and death. RESULTS: One hundred seventy-one subjects with RVOT conduit or bioprosthetic pulmonary valve dysfunction were enrolled. One hundred fifty underwent Melody TPV replacement. Median age was 19 years (Q1-Q3: 15-26). Median discharge mean RVOT Doppler gradient was 17 mm Hg (Q1-Q3: 12-22). The 149 patients implanted >24 hours were followed for a median of 8.4 years (Q1-Q3: 5.4-10.1). At 10 years, estimated freedom from mortality was 90%, from reoperation 79%, and from any reintervention 60%. Ten-year freedom from TPV dysfunction was 53% and was significantly shorter in children than in adults. Estimated freedom from TPV-related endocarditis was 81% at 10 years (95% CI, 69%-89%), with an annualized rate of 2.0% per patient-year. CONCLUSIONS: Ten-year outcomes from the Melody Investigational Device Exemption trial affirm the benefits of Melody TPV replacement in the lifetime management of patients with RVOT conduits and bioprosthetic pulmonary valves by providing sustained symptomatic and hemodynamic improvement in the majority of patients. Registration: URL: https://www.clinicaltrials.gov; Unique identifier: NCT00740870.

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. We also examined the effect of shunt size and the development of atrial fibrillation on infarct burden at follow-up. Results: At follow-up, new clinical stroke or silent MRI infarct occurred in 18/383 (4.7%) patients who underwent closure and 19/177 (10.7%) medication-only patients (relative risk, 0.44 [95% CI, 0.24­0.81], P=0.02). Clinical strokes were less common in closure patients compared with medically treated patients, 5 (1.3%) versus 12 (6.8%), P=0.001, while silent MRI infarcts were similar, 13 (3.4%) versus 7 (4.0%), P=0.81. There were no differences in number, volumes, and distribution of new infarct comparing closure patients to those treated with medication alone. There were also no differences of number, volumes, and distribution comparing silent infarcts to clinical strokes. Infarct burden was also similar for patients who developed atrial fibrillation and for those with large shunts. Conclusions: The REDUCE trial demonstrates that patent foramen ovale closure prevents recurrent brain infarction based on the objective outcome of new infarcts on MRI. Only clinical strokes were reduced by closure while silent infarctions were similar between study arms, and there were no differences in infarct volume or location comparing silent infarcts to clinical strokes. Registration: URL: https://www.clinicaltrials.gov; Unique identifier: NCT00738894.

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. Here, using algebraic methods, we show that a PM model has identifiable parameters under circumstances in which it is likely to be used for empirical analyses. In particular, for a tree relating 9 or more taxa, both the tree topology and all numerical parameters are generically identifiable when the number of profiles is less than 74.