Unleashing the Power of Induced Pluripotent stem Cells in in vitro Modelling of Lesch-Nyhan Disease.

Lesch-Nyhan disease (LND) is a monogenic rare neurodevelopmental disorder caused by a deficiency in hypoxanthine-guanine phosphoribosyltransferase (HPRT), the key enzyme of the purines salvage pathway. Beyond its well-documented metabolic consequences, HPRT deficiency leads to a distinctive neurobehavioral syndrome characterized by motor disabilities, cognitive deficits, and self-injurious behavior. Although various cell and animal models have been developed to investigate LND pathology, none have adequately elucidated the underlying mechanisms of its neurological alterations.

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.

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.

Inborn Errors of Purine Salvage and Catabolism.

Cellular purine nucleotides derive mainly from de novo synthesis or nucleic acid turnover and, only marginally, from dietary intake. They are subjected to catabolism, eventually forming uric acid in humans, while bases and nucleosides may be converted back to nucleotides through the salvage pathways. Inborn errors of the purine salvage pathway and catabolism have been described by several researchers and are usually referred to as rare diseases.

Effects of Nitisinone on Oxidative and Inflammatory Markers in Alkaptonuria: Results from SONIA1 and SONIA2 Studies.

Nitisinone (NTBC) was recently approved to treat alkaptonuria (AKU), but there is no information on its impact on oxidative stress and inflammation, which are observed in AKU. Therefore, serum samples collected during the clinical studies SONIA1 (40 AKU patients) and SONIA2 (138 AKU patients) were tested for Serum Amyloid A (SAA), CRP and IL-8 by ELISA; Advanced Oxidation Protein Products (AOPP) by spectrophotometry; and protein carbonyls by Western blot. Our results show that NTBC had no significant effects on the tested markers except for a slight but statistically significant effect for NTBC, but not for the combination of time and NTBC, on SAA levels in SONIA2 patients.

Alignment-Free Genotyping of Known Variations with MALVA.

The discovery and characterization of sequence variations in human populations are crucial in genetic studies. Standard methods for addressing this problem are computationally expensive and highly time consuming, thus impractical for clinical applications, where time is often an issue. When the task is to genotype variations that have been previously annotated, alignment-free methods come to the aid.

Survey on the Recent Advances in 4-Hydroxyphenylpyruvate Dioxygenase (HPPD) Inhibition by Diketone and Triketone Derivatives and Congeneric Compounds: Structural Analysis of HPPD/Inhibitor Complexes and Structure-Activity Relationship Considerations.

The serendipitous discovery of the HPPD inhibitors from allelopathic plants opened the way for searching new and effective herbicidal agents by application of classical hit-to-lead optimization approaches. A plethora of active and selective compounds were discovered that belong to three major classes of cyclohexane-based triketones, pyrazole-based diketones, and diketonitriles. In addition, to enhance inhibitory constant and herbicidal activity, many efforts were also made to gain broader weed control, crop safety, and eventual agricultural applicability.

Risk Factor Analysis for Crossing Failure in Primary Antegrade Wire-Catheter Approach for Femoropopliteal Chronic Total Occlusions.

Introduction: Antegrade wire-catheter crossing remains the primary approach for femoropopliteal interventions. Nonetheless, data reporting on crossing failure are limited. Aim of this study is to identify risk factors for antegrade crossing failure in patients with femoropopliteal chronic total occlusions (CTOs).

A meta-analysis of safety and efficacy of endovascular aneurysm repair in aneurysm patients with severe angulated infrarenal neck.

Objectives: A growing number of abdominal aortic aneurysms with severe angulated neck anatomy is treated by endovascular means. However, contradictory early and late outcomes have been reported. Our review and outcome analysis attempted to evaluate the available literature and provide clinicians with a base for clinical implementation and future research.

Long-term Results of Angulated Versus Hyperangulated Neck in Endovascular Aneurysm Repair With Endurant Endoprosthesis.

Purpose: Patients with a hyperangulated (>60°) proximal aortic neck and at high risk of open surgery have been treated with endovascular aortic repair (EVAR). However, long-term outcomes are not well reported. The aim of this study is to compare the technical and clinical success of EVAR in angulated (45°-60°) and hyperangulated (>60°) proximal neck angulation.

Homogentisic acid induces autophagy alterations leading to chondroptosis in human chondrocytes: Implications in Alkaptonuria.

Alkaptonuria (AKU) is an ultra-rare genetic disease caused by a deficient activity of the enzyme homogentisate 1,2-dioxygenase (HGD) leading to the accumulation of homogentisic acid (HGA) on connective tissues. Even though AKU is a multi-systemic disease, osteoarticular cartilage is the most affected system and the most damaged tissue by the disease. In chondrocytes, HGA causes oxidative stress dysfunctions, which induce a series of not fully characterized cellular responses.

A methodology for Response Gap Analysis in offshore oil spill emergency management.

In case of offshore oil spills, the success of emergency response largely depends on the meteorological and oceanographic conditions during and after the spill, which are expressed by a set of different environmental factors. A "gap" in the response may be caused by unfavourable environmental factors that could limit its effectiveness or even impede it. In this context, Response Gap Analysis (RGA) studies identify the environmental factors negatively influencing the emergency response in a given sea area and aim at assessing the percentage of time during which the response would be without success or impossible to deploy.

Use of Chimney Technique Does Not Improve the Outcome of Endovascular Aneurysm Repair in Patients With a Hyperangulated and Short Proximal Aortic Neck.

Purpose: We hypothesized that extending the proximal landing zone with the chimney technique could be beneficial in patients with a hyperangulated proximal aortic neck, defined as more > 60 degrees.

Material And Methods: We retrospectively analyzed the outcome of prospectively collected data of patients treated by endovascular aneurysm repair (EVAR) for infrarenal aortic aneurysm with a hyperangulated proximal aortic neck. In all, 104 out of 130 patients were treated without (Group A) and 24 with the chimney endovascular aortic repair (ChEVAR, Group B).

Leveraging proteomics in orphan disease research: pitfalls and potential.

: The term 'orphan diseases' includes conditions meeting prevalence-based or commercial viability criteria: they affect a small number of individuals and are considered an unviable market for drug development. Proteomics is an important technology to study them, providing information on mechanisms and evolution, biomarkers, and effects of therapeutic interventions.: Herein, we review how proteomics and bioinformatic tools could be applied to the study of rare diseases and discuss pitfalls and potential.

Triplet-based similarity score for fully multilabeled trees with poly-occurring labels.

Motivation: The latest advances in cancer sequencing, and the availability of a wide range of methods to infer the evolutionary history of tumors, have made it important to evaluate, reconcile and cluster different tumor phylogenies. Recently, several notions of distance or similarities have been proposed in the literature, but none of them has emerged as the golden standard. Moreover, none of the known similarity measures is able to manage mutations occurring multiple times in the tree, a circumstance often occurring in real cases.

Tumor-Associated Macrophages in Osteosarcoma: From Mechanisms to Therapy.

Osteosarcomas (OSs) are bone tumors most commonly found in pediatric and adolescent patients characterized by high risk of metastatic progression and recurrence after therapy. Effective therapeutic management of this disease still remains elusive as evidenced by poor patient survival rates. To achieve a more effective therapeutic management regimen, and hence patient survival, there is a need to identify more focused targeted therapies for OSs treatment in the clinical setting.

Antimicrobial Efficacy of Five Probiotic Strains Against Helicobacter pylori.

Unlabelled: Treatment of Helicobacter pylori (H. pylori) infection is a challenge for clinicians. The large increase in drug-resistant strains makes the formulation of new therapeutic strategies fundamental.

Machine learning application for development of a data-driven predictive model able to investigate quality of life scores in a rare disease.

Background: Alkaptonuria (AKU) is an ultra-rare autosomal recessive disease caused by a mutation in the homogentisate 1,2-dioxygenase (HGD) gene. One of the main obstacles in studying AKU, and other ultra-rare diseases, is the lack of a standardized methodology to assess disease severity or response to treatment. Quality of Life scores (QoL) are a reliable way to monitor patients' clinical condition and health status.

Homogentisic acid affects human osteoblastic functionality by oxidative stress and alteration of the Wnt/β-catenin signaling pathway.

Alkaptonuria (AKU) is a rare disease correlated with deficiency of the enzyme homogentisate 1,2 dioxygenase, which causes homogentisic acid (HGA) accumulation. HGA is subjected to oxidation/polymerization reactions, leading to the production of a peculiar melanin-like pigmentation (ochronosis) after chronic inflammation, which is considered as a triggering event for the generation of oxidative stress. Clinical manifestations of AKU are urine darkening, sclera pigmentation, early severe osteoarthropathy, and cardiovascular and renal complication.

Infection and Autoimmune Thyroid Diseases: The Role of Virulent Strains.

Aim: To verify a possible association between overall and CagA+ infection and autoimmune thyroid diseases (AITDs).

Methods: Consecutive patients with AITDs admitted to one single centre of Endocrinology during one solar year were examined. The diagnoses were Hashimoto thyroiditis (HT) in 76, Graves' Disease (GD) in 39, and aspecific thyroiditis (AT) in 44 patients.

Interactive alkaptonuria database: investigating clinical data to improve patient care in a rare disease.

Alkaptonuria (AKU) is an ultrarare autosomal recessive disorder (MIM 203500) that is caused byby a complex set of mutations in homogentisate 1,2-dioxygenasegene and consequent accumulation of homogentisic acid (HGA), causing a significant protein oxidation. A secondary form of amyloidosis was identified in AKU and related to high circulating serum amyloid A (SAA) levels, which are linked with inflammation and oxidative stress and might contribute to disease progression and patients' poor quality of life. Recently, we reported that inflammatory markers (SAA and chitotriosidase) and oxidative stress markers (protein thiolation index) might be disease activity markers in AKU.

Extract Promotes In Vitro Differentiation and Functionality of Human Primary Osteoblasts.

Marine algae have gained much importance in the development of nutraceutical products due to their high content of bioactive compounds. In this work, we investigated the activity of with the aim to demonstrate the pro-osteogenic ability of its extract on human primary osteoblast (HOb). Our data indicated that the acetonic extract of (EPP) is a safe product as it did not show any effect on osteoblast viability.

MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants.

The amount of genetic variation discovered in human populations is growing rapidly leading to challenging computational tasks, such as variant calling. Standard methods for addressing this problem include read mapping, a computationally expensive procedure; thus, mapping-free tools have been proposed in recent years. These tools focus on isolated, biallelic SNPs, providing limited support for multi-allelic SNPs and short insertions and deletions of nucleotides (indels).