Search results for " enumeration."
showing 10 items of 10 documents
Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo
2019
This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs. Viroids are small, non-coding, circular RNA molecules that infect plants. Different hypotheses for their evolutionary origin have been put forward, such as an early emergence in a precellular RNA World or several de novo independent evolutionary origins in plants. Here, we discuss the plausibility of de novo emergence of viroid-like replicons by giving theoretical support to the likelihood of different steps along a parsimonious evolutionary pathway. While Avsunviroidae-like structures are relatively easy to obtain through evolution of a population of random RNA sequences of fixe…
A modified culture medium for improved isolation of marine vibrios
2019
Abstract Marine Vibrio members are of great interest for both ecological and biotechnological research, which often relies on their isolation. Whereas many efforts have been made for the detection of food‐borne pathogenic species, much less is known about the performances of standard culture media toward environmental vibrios. We show that the isolation/enumeration of marine vibrios using thiosulfate‐citrate‐bile salts‐sucrose agar (TCBS) as selective medium may be hampered by the variable adaptability of different taxa to the medium, which may result even in isolation failure and/or in substantial total count underestimation. We propose a modified TCBS as isolation medium, adjusted for mar…
Open and Closed Words
2017
Combinatorics on words aims at finding deep connections between properties of sequences. The resulting theoretical findings are often used in the design of efficient combinatorial algorithms for string processing, but may also have independent interest, especially in connection with other areas of discrete mathematics. The property we discuss here is, for a given finite word, that of being closed. A finite word is called closed if it has length ≤ 1 or it contains a proper factor (substring) that occurs both as a prefix and as a suffix but does not have internal occurrences. Otherwise the word is called open. We illustrate several aspects of open and closed words and factors, and propose som…
The Linear Ordering Polytope
2010
So far we developed a general integer programming approach for solving the LOP. It was based on the canonical IP formulation with equations and 3-dicycle inequalities which was then strengthened by generating mod-k-inequalities as cutting planes. In this chapter we will add further ingredients by looking for problem- specific inequalities. To this end we will study the convex hull of feasible solutions of the LOP: the so-called linear ordering polytope.
Polyhedral results for a vehicle routing problem
1991
Abstract The Vehicle Routing Problem is a well known, and hard, combinatorial problem, whose polyhedral structure has deserved little attention. In this paper we consider the particular case in which all the demands are equal (since in the general case the associated polytope may be empty). From a known formulation of the problem we obtain the dimension of the corresponding polytope and we study the facetial properties of every inequality in it.
On prefix normal words and prefix normal forms
2016
A $1$-prefix normal word is a binary word with the property that no factor has more $1$s than the prefix of the same length; a $0$-prefix normal word is defined analogously. These words arise in the context of indexed binary jumbled pattern matching, where the aim is to decide whether a word has a factor with a given number of $1$s and $0$s (a given Parikh vector). Each binary word has an associated set of Parikh vectors of the factors of the word. Using prefix normal words, we provide a characterization of the equivalence class of binary words having the same set of Parikh vectors of their factors. We prove that the language of prefix normal words is not context-free and is strictly contai…
Robust Conditional Independence maps of single-voxel Magnetic Resonance Spectra to elucidate associations between brain tumours and metabolites.
2020
The aim of the paper is two-fold. First, we show that structure finding with the PC algorithm can be inherently unstable and requires further operational constraints in order to consistently obtain models that are faithful to the data. We propose a methodology to stabilise the structure finding process, minimising both false positive and false negative error rates. This is demonstrated with synthetic data. Second, to apply the proposed structure finding methodology to a data set comprising single-voxel Magnetic Resonance Spectra of normal brain and three classes of brain tumours, to elucidate the associations between brain tumour types and a range of observed metabolites that are known to b…
Circulating monocyte subsets and heart failure prognosis
2018
Altres ajuts: Fundacio' La MARATO' de TV3 (201502 to ABG, 201516), AdvanceCat with the support of ACCIÓ [Catalonia Trade & Investment, Generalitat de Catalunya], Fundació Bancària La Caixa. Monocytes are a heterogeneous population of effector cells with key roles in tissue integrity restoration and maintenance. Here, we explore the association of monocyte subsets and prognosis in patients with ambulatory heart failure (HF). Monocyte subsets were classified as classical (CD14 ++ /CD16 -), intermediate (CD14 ++ /CD16 +), or non-classical (CD14 + /CD16 ++). Percentage distribution and absolute cell count were assessed in each subset, and multivariable Cox regression analyses were performed wit…
PML nuclear body-residing proteins sequentially associate with HPV genome after infectious nuclear delivery.
2019
Subnuclear promyelocytic leukemia (PML) nuclear bodies (NBs) are targeted by many DNA viruses after nuclear delivery. PML protein is essential for formation of PML NBs. Sp100 and Small Ubiquitin-Like Modifier (SUMO) are also permanently residing within PML NBs. Often, large DNA viruses disassemble and reorganize PML NBs to counteract their intrinsic antiviral activity and support establishment of infection. However, human papillomavirus (HPV) requires PML protein to retain incoming viral DNA in the nucleus for subsequent efficient transcription. In contrast, Sp100 was identified as a restriction factor for HPV. These findings suggested that PML NBs are important regulators of early stages o…
Normal, Abby Normal, Prefix Normal
2014
A prefix normal word is a binary word with the property that no substring has more 1s than the prefix of the same length. This class of words is important in the context of binary jumbled pattern matching. In this paper we present results about the number \(\textit{pnw}(n)\) of prefix normal words of length n, showing that \(\textit{pnw}(n) =\Omega\left(2^{n - c\sqrt{n\ln n}}\right)\) for some c and \(\textit{pnw}(n) = O \left(\frac{2^n (\ln n)^2}{n}\right)\). We introduce efficient algorithms for testing the prefix normal property and a “mechanical algorithm” for computing prefix normal forms. We also include games which can be played with prefix normal words. In these games Alice wishes t…