Inferring phylogenetic networks from multifurcating trees via cherry picking and machine learning.

The Hybridization problem asks to reconcile a set of conflicting phylogenetic trees into a single phylogenetic network with the smallest possible number of reticulation nodes. This problem is computationally hard and previous solutions are limited to small and/or severely restricted data sets, for example, a set of binary trees with the same taxon set or only two non-binary trees with non-equal taxon sets. Building on our previous work on binary trees, we present FHyNCH, the first algorithmic framework to heuristically solve the Hybridization problem for large sets of multifurcating trees whose sets of taxa may differ.

Determinants of Physical Activity among Patients with Colorectal Cancer: From Diagnosis to 5 Years after Diagnosis.

Introduction: Physical activity (PA) is associated with higher quality of life and probably better prognosis among colorectal cancer (CRC) patients. This study focuses on determinants of PA among CRC patients from diagnosis until 5 yr postdiagnosis.

Methods: Sociodemographic and disease-related factors of participants of two large CRC cohort studies were combined.

Constructing phylogenetic networks via cherry picking and machine learning.

Background: Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers of phylogenetic trees or are limited to severely restricted classes of networks.

Results: In this paper, we apply the recently-introduced theoretical framework of cherry picking to design a class of efficient heuristics that are guaranteed to produce a network containing each of the input trees, for practical-size datasets consisting of binary trees.

Differential effects of ankle constraints on foot placement control between normal and split belt treadmills.

Mediolateral ankle moment control contributes to gait stability. Ankle moments can be constrained by walking with a shoe with a ridge underneath the sole, narrowing the mediolateral support surface. In our previous study, such ankle moment constraints resulted in an increased step width and a decrease in the degree of foot placement control, as defined by the percentage of variance in foot placement that can be explained by CoM state.

Effects of Cigarette Smoke on Adipose and Skeletal Muscle Tissue: In Vivo and In Vitro Studies.

Chronic obstructive pulmonary disease (COPD), often caused by smoking, is a chronic lung disease with systemic manifestations including metabolic comorbidities. This study investigates adaptive and pathological alterations in adipose and skeletal muscle tissue following cigarette smoke exposure using in vivo and in vitro models. Mice were exposed to cigarette smoke or air for 72 days and the pre-adipose cell line 3T3-L1 was utilized as an in vitro model.

Orchard Networks are Trees with Additional Horizontal Arcs.

Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that orchard networks can be interpreted as trees with additional horizontal arcs.

Body mass index at diagnosis of a childhood brain tumor; a reflection of hypothalamic-pituitary dysfunction or lifestyle?

Purpose: Childhood brain tumor survivors (CBTS) are at risk of becoming overweight, which has been shown to be associated with hypothalamic-pituitary (HP) dysfunction during follow-up. Body mass index (BMI) at diagnosis is related to BMI at follow-up. It is uncertain, however, whether aberrant BMI at brain tumor diagnosis reflects early hypothalamic dysfunction or rather reflects genetic and sociodemographic characteristics.

Effect of targeted nutrient supplementation on physical activity and health-related quality of life in COPD: study protocol for the randomised controlled NUTRECOVER trial.

Introduction: Physical and mental health are often affected in chronic obstructive pulmonary disease (COPD) adversely affecting disease course and quality of life. Abnormalities in whole body and cellular energy metabolism, dietary and plasma nutrient status and intestinal permeability have been well established in these patients as systemic determinants of functional decline and underexplored treatable traits. The aim of this study is to investigate the efficacy of 1 year targeted nutrient supplementation on physical activity level and health-related quality of life in patients with COPD.

Applicability of several rooted phylogenetic network algorithms for representing the evolutionary history of SARS-CoV-2.

Background: Rooted phylogenetic networks are used to display complex evolutionary history involving so-called reticulation events, such as genetic recombination. Various methods have been developed to construct such networks, using for example a multiple sequence alignment or multiple phylogenetic trees as input data. Coronaviruses are known to recombine frequently, but rooted phylogenetic networks have not yet been used extensively to describe their evolutionary history.

Nutrition as a modifiable factor in the onset and progression of pulmonary function impairment in COPD: a systematic review.

Context: Chronic obstructive lung disease (COPD) is a progressive lung disease characterized by persistent airflow limitation. An increasing amount of evidence suggests an effect of dietary quality on the risk of COPD in the general population and pulmonary function decline in patients with COPD.

Objective: The association of dietary intake and nutrient status with COPD risk and onset, as well as pulmonary function decline (change in forced expiratory volume in 1 second, forced vital capacity, or the ratio of the former to the latter) in patients with COPD was investigated in this systematic review.

Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes.

Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such as hybridization, introgression, and lateral gene transfer. Recently, network-based Markov models of DNA sequence evolution have been introduced along with model-based methods for reconstructing phylogenetic networks.

Prevalence and risk factors of hypothalamic-pituitary dysfunction in infant and toddler childhood brain tumor survivors.

Objective: Childhood brain tumor survivors (CBTS) are at risk to develop hypothalamic-pituitary (HP) dysfunction (HPD). The risk for HPD may vary between different age groups due to maturation of the brain and differences in oncologic treatment protocols. Specific studies on HPD in infant brain tumor survivors (infant-BTS, 0-1 years at diagnosis) or toddler brain tumor survivors (toddler-BTS, ≥1-3 years) have not been performed.

High Prevalence of Weight Gain in Childhood Brain Tumor Survivors and Its Association With Hypothalamic-Pituitary Dysfunction.

Purpose: Childhood brain tumor survivors (CBTS) are at risk for developing obesity, which negatively influences cardiometabolic health. The prevalence of obesity in CBTS may have been overestimated in previous cohorts because of inclusion of children with craniopharyngioma. On the contrary, the degree of weight gain may have been underestimated because of exclusion of CBTS who experienced weight gain, but were neither overweight nor obese.

Hypothalamic-Pituitary Dysfunctions Other Than Growth Hormone Deficiency in Cancer Survivors.

Hypothalamic-pituitary (HP) dysfunctions are commonly reported complications in survivors of childhood cancer. These include growth hormone deficiency, luteinizing hormone/follicle-stimulating hormone deficiency, thyroid-stimulating hormone deficiency, adrenocorticotropic hormone deficiency, central precocious puberty, hyperprolactinemia, and central diabetes insipidus. Local tumor invasion and surgical or radiation-induced injury represent the highest risk factors.

The effect of citrus flavonoid extract supplementation on anaerobic capacity in moderately trained athletes: a randomized controlled trial.

Background: Nutritional supplementation is commonly used by athletes to improve their exercise performance. Previous studies demonstrated that citrus flavonoid extract (CFE) supplementation may be an effective strategy to improve exercise performance in male athletes. Yet, no conclusive research has been performed to investigate the effect of chronic CFE supplementation on high-intensity exercise performance under anaerobic conditions.

Clinical impact of hypothalamic-pituitary disorders after conformal radiation therapy for pediatric low-grade glioma or ependymoma.

Background: To determine the impact of hypothalamic-pituitary (HP) disorders on health outcomes in children and adolescents who received conformal radiation therapy (RT) for central nervous system tumors.

Procedure: Cohort study including 355 patients (age ≤25 years at diagnosis) treated with high-dose (50.4-59.

Experiences with Glucagon-Like Peptide-1 Receptor Agonist in Children with Acquired Hypothalamic Obesity.

Objective: Hypothalamic obesity (HO) in children after treatment for a tumor in the suprasellar region has severe implications. Previous studies have shown various effects of glucagon-like peptide-1 (GLP-1) receptor agonist in acquired HO, but in adults only. We present our experience of GLP-1 receptor agonist (exenatide) treatment during a 1-year period on body mass index (BMI) in children with acquired HO.

Leydig Cell Function in Male Survivors of Childhood Cancer: A Report From the St Jude Lifetime Cohort Study.

Purpose: Direct assessment of Leydig cell function in childhood cancer survivors has been limited. The objectives of this study were to describe the prevalence of and risk factors for Leydig cell failure (LCF), Leydig cell dysfunction (LCD), and associated adverse health outcomes.

Patients And Methods: In this retrospective study with cross-sectional health outcomes analysis, we evaluated 1,516 participants (median age, 30.

Polynomial-Time Algorithms for Phylogenetic Inference Problems involving duplication and reticulation.

A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree based on a model with speciation and duplication where duplications are clustered in duplication episodes.

Hypothalamic-Pituitary Disorders in Childhood Cancer Survivors: Prevalence, Risk Factors and Long-Term Health Outcomes.

Context: Data on hypothalamic-pituitary (HP) disorders in systematically evaluated childhood cancer survivors are limited.

Objective: To describe prevalence, risk factors, and associated adverse health outcomes of deficiencies in GH deficiency (GHD), TSH deficiency (TSHD), LH/FSH deficiency (LH/FSHD), and ACTH deficiency (ACTHD), and central precocious puberty (CPP).

Design: Retrospective with cross-sectional health outcomes analysis.

Not all phylogenetic networks are leaf-reconstructible.

Unrooted phylogenetic networks are graphs used to represent reticulate evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all unrooted phylogenetic networks for at least five taxa can be uniquely reconstructed from their subnetworks obtained by deleting a single taxon.

Reconstructing Tree-Child Networks from Reticulate-Edge-Deleted Subnetworks.

Network reconstruction lies at the heart of phylogenetic research. Two well-studied classes of phylogenetic networks include tree-child networks and level-k networks. In a tree-child network, every non-leaf node has a child that is a tree node or a leaf.

Clinical Importance of Free Thyroxine Concentration Decline After Radiotherapy for Pediatric and Adolescent Brain Tumors.

Context: Clinical significance of a decline in free T4 (FT4) concentrations across the reference range in children with brain tumors treated with radiation therapy (RT) is uncertain.

Objectives: To study trends in FT4 in children after RT and risk factors and health outcomes associated with plasma FT4 concentrations.

Design And Setting: Longitudinal, single-center retrospective cohort study.