Simultaneous Reconstruction of Duplication Episodes and Gene-Species Mappings

We present a novel problem, called MetaEC, which aims to infer gene-species assignments in a collection of gene trees with missing labels by minimizing the size of duplication episode clustering (EC). This problem is particularly relevant in metagenomics, where incomplete data often poses a challenge in the accurate reconstruction of gene histories. To solve MetaEC, we propose a polynomial time dynamic programming (DP) formulation that verifies the existence of a set of duplication episodes from a predefined set of episode candidates. We then demonstrate how to use DP to design an algorithm that solves MetaEC. Although the algorithm is exponential in the worst case, we introduce a heuristic modification of the algorithm that provides a solution with the knowledge that it is exact. To evaluate our method, we perform two computational experiments on simulated and empirical data containing whole genome duplication events, showing that our algorithm is able to accurately infer the corresponding events

Conflict Resolution Algorithms for Deep Coalescence Phylogenetic Networks

We address the problem of inferring an optimal tree displayed by a network, given a gene tree G and a tree-child network N, under the deep coalescence cost. We propose an O(|G||N|)-time dynamic programming algorithm (DP) to compute a lower bound of the optimal displayed tree cost, where |G| and |N| are the sizes of G and N, respectively. This algorithm has the ability to state whether the cost is exact or is a lower bound. In addition, our algorithm provides a set of reticulation edges that correspond to the obtained cost. If the cost is exact, the set induces an optimal displayed tree that yields the cost. If the cost is a lower bound, the set contains pairs of conflicting edges, that is, edges sharing a reticulation node. Next, we show a conflict resolution algorithm that requires 2^{r+1}-1 invocations of DP in the worst case, where r is a number of reticulations. We propose a similar O(2^k|G||N|)-time algorithm for level-k networks and a branch and bound solution to compute lower and upper bounds of optimal costs. We also show how our algorithms can be extended to a broader class of phylogenetic networks. Despite their exponential complexity in the worst case, our solutions perform significantly well on empirical and simulated datasets, thanks to the strategy of resolving internal dissimilarities between gene trees and networks. In particular, experiments on simulated data indicate that the runtime of our solution is ?(2^{0.543 k}|G||N|) on average. Therefore, our solution is an efficient alternative to enumeration strategies commonly proposed in the literature and enables analyses of complex networks with dozens of reticulations

Autoimmunologiczne choroby pęcherzowe skóry — analiza retrospektywna

Introduction: Autoimmune bullous disorders is a group of chronic diseases. Bullous pemphigoid is the most common autoimmune bullous disease of all, affecting mainly elderly people in the 8th decade of life, without gender predilection. Pemphigus manifests usually between 45 and 65 years of age, with a female predilection reported in most epidemiological studies. Aim of the study was assessing the prevalence of bullous diseases with respect to their types in different age groups, coexistence with neoplasms and other diseases.Material and methods: Retrospective analysis of medical histories of patients hospitalized in the Department of Dermatology, Sexually Transmitted Diseases, and Clinical Immunology at the University of Warmia and Mazury in Olsztyn with a diagnosis of bullous diseases between 2015 and 2021.Results: Seventy-two patients diagnosed with autoimmune bullous diseases were treated in the Department of Dermatology from 2015 to 2021. The mean age of patients was 76 years for pemphigoid diseases and 58 years for pemphigus. A causative agent such as drugs or consumption of bulbous plants was suspected in 10 patients (13.9%). Coexisting neoplasms were present in 12 patients (16.7%). The subjects also had comorbidities, the most common of which was hypertension (23 patients).Conclusions: The study confirmed most of the epidemiological data: bullous pemphigoid mainly affects the elderly, in the 8th decade of life, while pemphigus usually manifests itself before the age of 65. Symptoms can be provoked by external factors such as drugs, pathogens, UV light, diet, and stress. They can also coexist with other autoimmune and cardiovascular diseases.Wstęp: Autoimmunologiczne choroby pęcherzowe skóry to szeroka grupa chorób przewlekłych. Pemfigoid pęcherzowy jest najczęstszym autoimmunologicznym schorzeniem pęcherzowym, dotyczy głównie osób starszych w 8. dekadzie życia, bez predylekcji do płci. Pęcherzyca ujawnia się zwykle pomiędzy 45. a 65. rokiem życia, w większości badań epidemiologicznych odnotowano przewagę kobiet. Celem pracy była ocena częstości występowania chorób pęcherzowych z uwzględnieniem ich rodzajów w różnych grupach wiekowych, współistnienia z chorobami nowotworowymi i innymi schorzeniami dodatkowymi. Materiał i metody: Retrospektywna analiza historii chorób pacjentów, którzy w latach 2015–2021 byli hospitalizowani w Klinice Dermatologii, Chorób Przenoszonych Drogą Płciową i Immunologii Klinicznej Uniwersytetu Warmińsko-Mazurskiego w Olsztynie z rozpoznaniem chorób pęcherzowych. Wyniki: W Klinice Dermatologii w latach 2015–2021 leczono 72 pacjentów z rozpoznaniem autoimmunologicznych chorób pęcherzowych. W przypadku chorób z grupy pemfigoidu średnia wieku wynosiła 76 lat, a w przypadku pęcherzycy 58. U 10 pacjentów (13,9%) podejrzewano istnienie czynnika wywołującego, takiego jak leki czy spożywanie roślin cebulowatych. Nowotwory występowały u 12 pacjentów (16,7%). U badanych obserwowano również współistnienie innych chorób, z których najczęstsze było nadciśnienie tętnicze — 23 pacjentów (31,9%). Wnioski: Badanie potwierdziło większość danych epidemiologicznych: pemfigoid pęcherzowy dotyczy głównie osób starszych, w 8. dekadzie życia, natomiast pęcherzyca ujawnia się zwykle przed 65. rokiem życia. Pojawienie się objawów może być sprowokowane przez czynniki zewnętrzne, jak leki, patogeny, światło UV, dieta i stres. Mogą także współistnieć z innymi chorobami autoimmunologicznymi, a także sercowo-naczyniowymi