A quantum wavelet uncertainty principle

The aim of this paper is to derive a new uncertainty principle for the generalized $q$-Bessel wavelet transform studied earlier in \cite{Rezguietal}. In this paper, an uncertainty principle associated with wavelet transforms in the $q$-calculus framework has been established. A two-parameters extension of the classical Bessel operator is applied to generate a wavelet function which is exploited next to explore a wavelet uncertainty principle already in the $q$-calculus framework.Comment: 16 page

A generalized Robinson-Foulds distance for labeled trees.

The Robinson-Foulds (RF) distance is a well-established measure between phylogenetic trees. Despite a lack of biological justification, it has the advantages of being a proper metric and being computable in linear time. For phylogenetic applications involving genes, however, a crucial aspect of the trees ignored by the RF metric is the type of the branching event (e.g. speciation, duplication, transfer, etc). We extend RF to trees with labeled internal nodes by including a node flip operation, alongside edge contractions and extensions. We explore properties of this extended RF distance in the case of a binary labeling. In particular, we show that contrary to the unlabeled case, an optimal edit path may require contracting "good" edges, i.e. edges shared between the two trees. We provide a 2-approximation algorithm which is shown to perform well empirically. Looking ahead, computing distances between labeled trees opens up a variety of new algorithmic directions.Implementation and simulations available at https://github.com/DessimozLab/pylabeledrf

A generalized Robinson-Foulds distance for labeled trees

Background: The Robinson-Foulds (RF) distance is a well-established measure between phylogenetic trees. Despite a lack of biological justification, it has the advantages of being a proper metric and being computable in linear time. For phylogenetic applications involving genes, however, a crucial aspect of the trees ignored by the RF metric is the type of the branching event (e.g. speciation, duplication, transfer, etc). Results: We extend RF to trees with labeled internal nodes by including a node flip operation, alongside edge contractions and extensions. We explore properties of this extended RF distance in the case of a binary labeling. In particular, we show that contrary to the unlabeled case, an optimal edit path may require contracting “good” edges, i.e. edges shared between the two trees. Conclusions: We provide a 2-approximation algorithm which is shown to perform well empirically. Looking ahead, computing distances between labeled trees opens up a variety of new algorithmic directions. Implementation and simulations available at https://github.com/DessimozLab/pylabeledrf

Identification of rheumatoid arthritis biomarkers based on single nucleotide polymorphisms and haplotype blocks: A systematic review and meta-analysis

AbstractGenetics of autoimmune diseases represent a growing domain with surpassing biomarker results with rapid progress. The exact cause of Rheumatoid Arthritis (RA) is unknown, but it is thought to have both a genetic and an environmental bases. Genetic biomarkers are capable of changing the supervision of RA by allowing not only the detection of susceptible individuals, but also early diagnosis, evaluation of disease severity, selection of therapy, and monitoring of response to therapy. This review is concerned with not only the genetic biomarkers of RA but also the methods of identifying them. Many of the identified genetic biomarkers of RA were identified in populations of European and Asian ancestries. The study of additional human populations may yield novel results. Most of the researchers in the field of identifying RA biomarkers use single nucleotide polymorphism (SNP) approaches to express the significance of their results. Although, haplotype block methods are expected to play a complementary role in the future of that field

Sorting by reversals, block interchanges, tandem duplications, and deletions

<p>Abstract</p> <p>Background</p> <p>Finding sequences of evolutionary operations that transform one genome into another is a classic problem in comparative genomics. While most of the genome rearrangement algorithms assume that there is exactly one copy of each gene in both genomes, this does not reflect the biological reality very well – most of the studied genomes contain duplicated gene content, which has to be removed before applying those algorithms. However, dealing with unequal gene content is a very challenging task, and only few algorithms allow operations like duplications and deletions. Almost all of these algorithms restrict these operations to have a fixed size.</p> <p>Results</p> <p>In this paper, we present a heuristic algorithm to sort an ancestral genome (with unique gene content) into a genome of a descendant (with arbitrary gene content) by reversals, block interchanges, tandem duplications, and deletions, where tandem duplications and deletions are of arbitrary size.</p> <p>Conclusion</p> <p>Experimental results show that our algorithm finds sorting sequences that are close to an optimal sorting sequence when the ancestor and the descendant are closely related. The quality of the results decreases when the genomes get more diverged or the genome size increases. Nevertheless, the calculated distances give a good approximation of the true evolutionary distances.</p

A Unifying Model of Genome Evolution Under Parsimony

We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double cut and join (DCJ) rearrangements in the presence of duplications. The problem of constructing parsimonious history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconstruction and genome rearrangement. We show that tractable functions can be used to define upper and lower bounds on the minimum number of substitutions and DCJ rearrangements needed to explain any history graph. These bounds become tight for a special type of unambiguous history graph called an ancestral variation graph (AVG), which constrains in its combinatorial structure the number of operations required. We finally demonstrate that for a given history graph $G$, a finite set of AVGs describe all parsimonious interpretations of $G$, and this set can be explored with a few sampling moves.Comment: 52 pages, 24 figure

One-Step Laparoscopic Management of a Female Adnexal Tumor of Wolffian Origin

We report a case of female adnexal tumor of Wolffian origin (FATWO), a rare neoplasm arising from the mesonephric ducts. A 48-year-old woman came first to our center for a recent discovery of a pelvic mass. Transvaginal ultrasonographic findings suggested a solid right para-ovarian mass suspected to be malignant. After thorough counseling, the patient underwent operative laparoscopy for excision of the para-ovarian mass with frozen section (FS) examination resulting in the diagnosis of a poorly differentiated adenocarcinoma. In this case, FS results allowed performing a comprehensive oncological staging, through a totally laparoscopic extrafascial hysterectomy, bilateral adnexectomy, total omentectomy, pelvic wall peritonectomy, and pelvic, parasacral and para-aortic lymphadenectomy. Final pathological and immunohistochemical results confirmed the diagnosis of FATWO. To our knowledge, this is the first case of FATWO managed entirely by a minimally invasive laparoscopic approach in a single surgical session

National variation in prophylactic antibiotic use for elective primary total joint replacement an analysis of guidelines across hospitals and trusts in the UK

Aims Prophylactic antibiotic regimens for elective primary total hip and knee arthroplasty vary widely across hospitals and trusts in the UK. This study aimed to identify antibiotic prophylaxis regimens currently in use for elective primary arthroplasty across the UK, establish variations in antibiotic prophylaxis regimens and their impact on the risk of periprosthetic joint infection (PJI) in the first-year post-index procedure, and evaluate adherence to current international consensus guidance. Methods The guidelines for the primary and alternative recommended prophylactic antibiotic regimens in clean orthopaedic surgery (primary arthroplasty) for 109 hospitals and trusts across the UK were sought by searching each trust and hospital’s website (intranet webpages), and by using the MicroGuide app. The mean cost of each antibiotic regimen was calculated using price data from the British National Formulary (BNF). Regimens were then compared to the 2018 Philadelphia Consensus Guidance, to evaluate adherence to international guidance. Results The primary choice and dosing of the prophylactic antimicrobial regimens varied widely. The two most used regimens were combined teicoplanin and gentamicin, and cefuroxime followed by two or three doses of cefuroxime eight-hourly, recommended by 24 centres (22.02%) each. The alternative choice and dosing of the prophylactic antimicrobial regimen also varied widely across the 83 centres with data available. Prophylaxis regimens across some centres fail to cover the likeliest causes of surgical site infection (SSI). Five centres (4.59%) recommend co-amoxiclav, which confers no Staphylococcus coverage, while 33 centres (30.28%) recommend cefuroxime, which confers no Enterococcus coverage. Limited adherence to 2018 Philadelphia Consensus Guidance was observed, with 67 centres (61.50%) not including a cephalosporin in their guidance. Conclusion This analysis of guidance on antimicrobial prophylaxis in primary arthroplasty across 109 hospitals and trusts in the UK has identified widespread variation in primary and alternative antimicrobial regimens currently recommended