163 results on '"Foulquié P"'
Search Results
2. Classical discrete multiple orthogonal polynomials: hypergeometric and integral representations
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Branquinho, Amílcar, Díaz, Juan E. F., Foulquié-Moreno, Ana, Mañas, Manuel, and Wolfs, Thomas
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Mathematics - Classical Analysis and ODEs ,Mathematical Physics ,42C05, 33C45, 33C47 - Abstract
This work explores classical discrete multiple orthogonal polynomials, including Hahn, Meixner of the first and second kinds, Kravchuk, and Charlier polynomials, with an arbitrary number of weights. Explicit expressions for the recursion coefficients of Hahn multiple orthogonal polynomials are derived. By leveraging the multiple Askey scheme and the recently discovered explicit hypergeometric representation of type I multiple Hahn polynomials, corresponding explicit hypergeometric representations are provided for the type I polynomials and recursion coefficients of all the aforementioned descendants within the Askey scheme. Additionally, integral representations for these families within the Hahn class in the Askey scheme are presented. The multiple Askey scheme is further completed by providing the corresponding limits for the weights, polynomials, and recurrence coefficients., Comment: 37 pages, 5 figures
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- 2024
3. Integral and hypergeometric representations for multiple orthogonal polynomials
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Branquinho, Amílcar, Díaz, Juan EF, Foulquié-Moreno, Ana, Mañas, Manuel, and Wolfs, Thomas
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Mathematics - Classical Analysis and ODEs ,Mathematical Physics ,42C05, 33C45, 33C47 - Abstract
This paper addresses two primary objectives in the realm of classical multiple orthogonal polynomials with an arbitrary number of weights. Firstly, it establishes new and explicit hypergeometric expressions for type I Hahn multiple orthogonal polynomials. Secondly, applying the residue theorem and the Mellin transform, the paper derives contour integral representations for several families of orthogonal polynomials. Specifically, it presents contour integral formulas for both type I and type II multiple orthogonal polynomials in the Laguerre of the first kind, Jacobi-Pi\~neiro, and Hahn families. The evaluation of these integrals leads to explicit hypergeometric representations., Comment: 21 pages
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- 2024
4. Semiclassical orthogonal polynomials on the unit circle: A Riemann-Hilbert perspective
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Branquinho, Amí lcar, Foulquié-Moreno, Ana, and Rampazzi, Karina
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Mathematics - Classical Analysis and ODEs ,42C05 and 33C45 and 33C47 and 47A56 and 47A75 - Abstract
In this work we apply Riemann-Hilbert problem to study two families of orthogonal polynomials on the unit circle, named of modified Jacobi and Bessel. We derive first and second order differential equations, for these families of orthogonal polynomials and functions of second kind, as well as nonlinear equations that the Verblunsky coefficients satisfy.
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- 2024
5. Banded totally positive matrices and normality for mixed multiple orthogonal polynomials
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Branquinho, Amílcar, Foulquié-Moreno, Ana, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,Mathematical Physics ,42C05, 33C45, 33C47, 47B39, 47B36 - Abstract
This paper serves as an introduction to banded totally positive matrices, exploring various characterizations and associated properties. A significant result within is the demonstration that the collection of such matrices forms a semigroup, notably including a subset permitting positive bidiagonal factorization. Moreover, the paper applies this concept to investigate step line normality concerning the degrees of associated recursion polynomials. It presents a spectral Favard theorem, ensuring the existence of measures, thereby guaranteeing that these recursion polynomials represent mixed multiple orthogonal polynomials that maintain normality on the step line indices.
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- 2024
6. Classical multiple orthogonal polynomials for arbitrary number of weights and their explicit representation
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Branquinho, Amílcar, Díaz, Juan EF, Foulquié-Moreno, Ana, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,Mathematical Physics ,42C05, 33C45, 33C47, 47B39, 47B36 - Abstract
This paper delves into classical multiple orthogonal polynomials with an arbitrary number of weights, including Jacobi-Pi\~neiro, Laguerre of both first and second kinds, as well as multiple orthogonal Hermite polynomials. Novel explicit expressions for nearest-neighbor recurrence coefficients, as well as the step line case, are provided for all these polynomial families. Furthermore, new explicit expressions for type I multiple orthogonal polynomials are derived for Laguerre of the second kind and also for multiple Hermite polynomials.
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- 2024
7. Lax-type pairs in the theory of bivariate orthogonal polynomials
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Branquinho, Amílcar, Foulquié-Moreno, Ana, Pérez, Teresa E., and Piñar, Miguel A.
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Mathematics - Classical Analysis and ODEs ,42C05, 33C50, 35Q53 - Abstract
Sequences of bivariate orthogonal polynomials written as vector polynomials of increasing size satisfy a couple of three term relations with matrix coefficients. In this work, introducing a time-dependent parameter, we analyse a Lax-type pair system for the coefficients of the three term relations. We also deduce several characterizations relating the Lax-type pair, the shape of the weight, Stieltjes function, moments, a differential equation for the weight, and the bidimensional Toda-type systems.
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- 2023
8. Hypergeometric Expressions for Type I Jacobi-Pi\~neiro Orthogonal Polynomials with Arbitrary Number of Weights
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Branquinho, Amílcar, Díaz, Juan EF, Moreno, Ana Foulquié, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,33C45, 33C47, 42C05, 47A56 - Abstract
For a general number $p\geq 2$ of measures, we provide explicit expressions for the Jacobi-Pi\~neiro and Laguerre of the first kind multiple orthogonal polynomials of type I, presented in terms of multiple hypergeometric functions.
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- 2023
9. Population status of the Critically Endangered fan mussel Pinna nobilis in Thau Lagoon (France)
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M Foulquié, S Coupé, N Vicente, and R Bunet
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Zoology ,QL1-991 ,Botany ,QK1-989 - Abstract
Since 2016, the noble pen shell Pinna nobilis, a unique and emblematic giant bivalve endemic to the Mediterranean Sea, has been affected by mass mortality events (MMEs), primarily due to the pathogen Haplosporidium pinnae. To date, all known populations located in the open sea have been decimated by epizootics, and P. nobilis is currently classified as a Critically Endangered species. The last refuge areas with P. nobilis populations are now in coastal lagoons. This study assesses the status, size, density, and spatial distributions of P. nobilis populations in Thau Lagoon (Occitany, France). At the end of January 2024, 1931 live individuals were recorded at 30 different surveyed sites. Our surveys indicate various size-class distributions ranging from young recruits to adults. Examining the spatial distribution of P. nobilis revealed high-density populations in specific areas (up to 25 ind. 100 m-2). P. nobilis is present from the edges of the lagoon to the central and deeper zones (up to 9 m deep). Although Thau Lagoon experienced a localized MME at the end of 2020, driven by the presence of H. pinnae, this study reveals the occurrence of new individuals in previously infected areas, indicating signs of population recovery and potential resilience. All these observations suggest that Thau Lagoon represents one of the very last sanctuaries for P. nobilis in the Mediterranean Sea.
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- 2024
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10. Bidiagonal factorization of the recurrence matrix for the Hahn multiple orthogonal polynomials
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Branquinho, Amílcar, Díaz, Juan E. F., Foulquié-Moreno, Ana, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,Mathematical Physics ,42C05, 33C45, 33C47, 47B39, 47B36 - Abstract
This paper explores a factorization using bidiagonal matrices of the recurrence matrix of Hahn multiple orthogonal polynomials. The factorization is expressed in terms of ratios involving the generalized hypergeometric function ${}_3F_2$ and is proven using recently discovered contiguous relations. Moreover, employing the multiple Askey scheme, a bidiagonal factorization is derived for the Hahn descendants, including Jacobi-Pi\~neiro, multiple Meixner (kinds I and II), multiple Laguerre (kinds I and II), multiple Kravchuk, and multiple Charlier, all represented in terms of hypergeometric functions. For the cases of multiple Hahn, Jacobi-Pi\~neiro, Meixner of kind II, and Laguerre of kind I, where there exists a region where the recurrence matrix is nonnegative, subregions are identified where the bidiagonal factorization becomes a positive bidiagonal factorization., Comment: 14 pages, 2 figures
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- 2023
11. Finite Markov chains and multiple orthogonal polynomials
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Branquinho, Amílcar, Díaz, Juan EF, Foulquié-Moreno, Ana, and Mañas, Manuel
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Mathematics - Probability ,Mathematical Physics ,Mathematics - Classical Analysis and ODEs ,42C05, 33C45, 33C47, 47B39, 47B36, 60J10, 60J22 - Abstract
This paper investigates stochastic finite matrices and the corresponding finite Markov chains constructed using recurrence matrices for general families of orthogonal polynomials and multiple orthogonal polynomials. The paper explores the spectral theory of transition matrices, utilizing both orthogonal and multiple orthogonal polynomials. Several properties are derived, including classes, periodicity, recurrence, stationary states, ergodicity, expected recurrence times, time-reversed chains, and reversibility. Furthermore, the paper uncovers factorization in terms of pure birth and pure death processes. The case study focuses on hypergeometric orthogonal polynomials, where all the computations can be carried out effectively. Particularly within the Askey scheme, all descendants under Hahn (excluding Bessel), such as Hahn, Jacobi, Meixner, Kravchuk, Laguerre, Charlier, and Hermite, present interesting examples of recurrent reversible birth and death finite Markov chains. Additionally, the paper considers multiple orthogonal polynomials, including multiple Hahn, Jacobi-Pi\~neiro, Laguerre of the first kind, and Meixner of the second kind, along with their hypergeometric representations and derives the corresponding recurrent finite Markov chains and time-reversed chains., Comment: 40 pages, 3 figures
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- 2023
12. Banded matrices and their orthogonality
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Branquinho, Amílcar, Foulquié-Moreno, Ana, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,42C05, 33C45, 33C47, 60J10, 60Gxx - Abstract
Banded bounded matrices, which represent non normal operators, of oscillatory type that admit a positive bidiagonal factorization are considered. To motivate the relevance of the oscillatory character the Favard theorem for Jacobi matrices is revisited and it is shown that after an adequate shift of the Jacobi matrix one gets an oscillatory matrix. In this work we present a spectral theorem for this type of operators and show how the theory of multiple orthogonal polynomials apply., Comment: arXiv admin note: substantial text overlap with arXiv:2203.13578
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- 2023
13. New biomarkers underlying acetic acid tolerance in the probiotic yeast Saccharomyces cerevisiae var. boulardii
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Samakkarn, Wiwan, Vandecruys, Paul, Moreno, Maria Remedios Foulquié, Thevelein, Johan, Ratanakhanokchai, Khanok, and Soontorngun, Nitnipa
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- 2024
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14. Matrix Orthogonal Polynomials: A Riemann--Hilbert approach
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Branquinho, Amílcar, Foulquié-Moreno, Ana, Fradi, Assil, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs - Abstract
In this work we show how to get advantage from the Riemann--Hilbert analysis in order to obtain information about the matrix orthogonal polynomials and functions of second kind associated with a weight matrix. We deduce properties for the recurrence relation coefficients from differential properties of the weight matrix. We take the matrix polynomials of Hermite, Laguerre and Jacobi type as a case study.
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- 2023
15. Markov Chains and Multiple Orthogonality
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Branquinho, Amílcar, Díaz, Juan E. F., Foulquié-Moren, Ana, and Mañas, Manuel
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Mathematics - Probability ,Mathematics - Classical Analysis and ODEs ,42C05, 33C45, 33C47, 60J10, 60Gxx - Abstract
In this work we survey on connections of Markov chains and the theory of multiple orthogonality. Here we mainly concentrate on give a procedure to generate stochastic tetra diagonal Hessenberg matrices, coming from some specific families of multiple orthogonal, such as the ones of Jacobi--Pi\~neiro and Hypergeometric Lima--Loureiro. We show that associated with a positive tetra diagonal nonnegative bounded Hessenberg matrix we can construct two stochastic tetra diagonal ones. These two stochastic tridiagonal nonnegative Hessenberg matrices are shown to be, enlightened by the Poincar\'e theorem, limit transpose of each other.
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- 2023
16. Language Brokering in Healthcare in Spain: Insight Based on Testimonies
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Almudena Nevado Llopis, Ana Isabel Foulquié Rubio, and Alina Pelea
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linguistic and cultural mediation ,healthcare services ,children ,young adults ,Language and Literature - Abstract
There were 6,491,502 foreign residents living in Spain in January 2024, a number that indicates a significant increase since the beginning of the 21st century. Among this foreign population, the largest communities are Moroccans, Romanians and British, whose mother tongue is not Spanish. According to the results from several studies conducted over the last decades, when these allophone residents use the Spanish healthcare services, they frequently ask their children to help them communicate with healthcare providers through linguistic and cultural mediation, even when professional interpreting or mediation services are available. How did these children feel while mediating for their parents in this context? Did they have any negative experiences? We intend to provide answers to these questions through semi-structured individual interviews with adults who had mediated for their parents in healthcare settings in Spain when they were children or young adults. These answers contribute to a clear understanding of the consequences of language brokering, thus promoting the use of professional interpreting and mediation services in these settings.
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- 2024
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17. Hahn multiple orthogonal polynomials of type I: Hypergeometrical expressions
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Branquinho, Amílcar, Díaz, Juan E. F., Foulquié-Moreno, Ana, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,Mathematical Physics ,42C05, 33C45, 33C47 - Abstract
Explicit expressions for the Hahn multiple polynomials of type I, in terms of Kamp\'e de F\'eriet hypergeometric series, are given. Orthogonal and biorthogonal relations are proven. Then, part of the Askey scheme for multiple orthogonal polynomials type I is completed. In particular, explicit expressions in terms of generalized hypergeometric series and Kamp\'e de F\'eriet hypergeometric series, are given for the multiple orthogonal polynomials of type I for the Jacobi-Pi\~neiro, Meixner I, Meixner II, Kravchuk, Laguerre I, Laguerre II and Charlier families., Comment: 27 pages. Minor typos corrected
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- 2022
18. Spectral theory for bounded banded matrices with positive bidiagonal factorization and mixed multiple orthogonal polynomials
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Branquinho, Amílcar, Foulquié-Moreno, Ana, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,Mathematical Physics ,Mathematics - Functional Analysis ,42C05, 33C45, 33C47, 47B39, 47B36 - Abstract
Spectral and factorization properties of oscillatory matrices leads to a spectral Favard theorem for bounded banded matrices, that admit a positive bidiagonal factorization, in terms of sequences of mixed multiple orthogonal polynomials with respect to a set positive Lebesgue-Stieltjes measures. A mixed multiple Gauss quadrature formula with corresponding degrees of precision is given., Comment: 33 pages
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- 2022
19. Positive bidiagonal factorization of tetradiagonal Hessenberg matrices
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Branquinho, Amílcar, Foulquié-Moreno, Ana, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,Mathematics - Functional Analysis ,42C05, 33C45, 33C47, 15B48, 47B39, 47B28, 47B36 - Abstract
Recently a spectral Favard theorem for bounded banded lower Hessenberg matrices that admit a positive bidiagonal factorization was presented. In this paper conditions, in terms of continued fractions, for an oscillatory tetradiagonal Hessenberg matrix to have such positive bidiagonal factorization are found. Oscillatory tetradiagonal Toeplitz matrices are taken as a case study of matrix that admits a positive bidiagonal factorization. Moreover, it is proved that oscillatory banded Hessenberg matrices are organized in rays, with the origin of the ray not having the positive bidiagonal factorization and all the interior points of the ray having such positive bidiagonal factorization., Comment: 20 pages This is the second part of the splitting of the paper arXiv:2203.13578 into three
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- 2022
20. Bidiagonal factorization of tetradiagonal matrices and Darboux transformations
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Branquinho, Amílcar, Foulquié-Moreno, Ana, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,Nonlinear Sciences - Exactly Solvable and Integrable Systems ,42C05, 33C45, 33C47 - Abstract
Recently a spectral Favard theorem for bounded banded lower Hessenberg matrices that admit a positive bidiagonal factorization was presented. These type of matrices are oscillatory. In this paper the Lima-Loureiro hypergeometric multiple orthogonal polynomials and the Jacobi-Pi\~neiro multiple orthogonal polynomials are discussed at the light of this bidiagonal factorization for tetradiagonal matrices. The Darboux transformations of tetradiagonal Hessenberg matrices is studied and Christoffel formulas for the elements of the bidiagonal factorization are given, i.e., the bidiagonal factorization is given in terms of the recursion polynomials evaluated at the origin., Comment: This is the third part of the splitting of the paper arXiv:2203.13578 into three. 15 pages and 1 figure
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- 2022
21. Matrix Jacobi Biorthogonal Polynomials via Riemann-Hilbert problem
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Branquinho, Amílcar, Foulquié-Moreno, Ana, Fradi, Assil, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,33C45, 33C47, 42C05, 47A56 - Abstract
We consider matrix orthogonal polynomials related to Jacobi type matrices of weights that can be defined in terms of a given matrix Pearson equation. Stating a Riemann-Hilbert problem we can derive first and second order differential relations that these matrix orthogonal polynomials and the second kind functions associated to them verify. For the corresponding matrix recurrence coefficients, non-Abelian extensions of a family of discrete Painlev\'e d-PIV equations are obtained for the three term recurrence relation coefficients.
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- 2022
22. Monomial and Rodrigues orthogonal polynomials on the cone
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Aktas, Rabia, Branquinho, Amilcar, Foulquie-Moreno, Ana, and Xu, Yuan
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Mathematics - Classical Analysis and ODEs - Abstract
We study two families of orthogonal polynomials with respect to the weight function $w(t)(t^2-\|x\|^2)^{\mu-\frac12}$, $\mu > -\frac 12$, on the cone $\{(x,t): \|x\| \le t, \, x \in \mathbb{R}^d, t >0\}$ in $\mathbb{R}^{d+1}$. The first family consists of monomial polynomials $\mathsf{V}_{\mathbf{k},n}(x,t) = t^{n-|\mathbf{k}|} x^\mathbf{k} + \cdots$ for $\mathbf{k} \in \mathbb{N}_0^d$ with $|\mathbf{k}| \le n$, which has the least $L^2$ norm among all polynomials of the form $t^{n-|\mathbf{k}|} x^\mathbf{k} + \mathsf{P}$ with $\deg \mathsf{P} \le n-1$, and we will provide an explicit construction for $\mathsf{V}_{\mathbf{k},n}$. The second family consists of orthogonal polynomials defined by the Rodrigues type formulas when $w$ is either the Laguerre weight or the Jacobi weight, which satisfies a generating function in both cases. The two families of polynomials are partially biorthogonal., Comment: 24 pp
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- 2022
23. Oscillatory banded Hessenberg matrices, multiple orthogonal polynomials and random walks
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Branquinho, Amilcar, Foulquié-Moreno, Ana, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,Mathematical Physics ,Mathematics - Functional Analysis ,Mathematics - Probability ,42C05, 33C45, 33C47, 60J10, 47B39, 47B36 - Abstract
A spectral Favard theorem for bounded banded lower Hessenberg matrices that admit a positive bidiagonal factorization is found. The large knowledge on the spectral and factorization properties of oscillatory matrices leads to this spectral Favard theorem in terms of sequences of multiple orthogonal polynomials of types I and II with respect to a set of positive Lebesgue-Stieltjes~measures. Also a multiple Gauss quadrature is proven and corresponding degrees of precision are found. This spectral Favard theorem is applied to Markov chains with $(p+2)$-diagonal transition matrices, i.e. beyond birth and death, that admit a positive stochastic bidiagonal factorization. In the finite case, the Karlin-McGregor spectral representation is given. It is shown that the Markov chains are recurrent and explicit expressions in terms of the orthogonal polynomials for the stationary distributions are given. Similar results are obtained for the countable infinite Markov chain. Now the Markov chain is not necessarily recurrent, and it is characterized in terms of the first measure. Ergodicity of the Markov chain is discussed in terms of the existence of a mass at $1$, which is an eigenvalue corresponding to the right and left eigenvectors., Comment: 38 pages. This a very much improved version of the initial one. We have divided the original paper in three parts. Two more parts to follow: arXiv:2210.10728, Positive bidiagonal factorization of tetradiagonal Hessenberg matrices arXiv:2210.10727, Bidiagonal factorization of tetradiagonal matrices and Darboux transformations
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- 2022
24. Quadratic decomposition of bivariate orthogonal polynomials
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Branquinho, Amílcar, Moreno, Ana Foulquié, and Pérez, Teresa E.
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Mathematics - Classical Analysis and ODEs ,42C05, 33C50 - Abstract
We describe bivariate polynomial sequences orthogonal to a symmetric weight function in terms of several bivariate polynomial sequences orthogonal with respect to Christoffel transformations of the initial weight under a quadratic transformation. We analyze the construction of a symmetric bivariate orthogonal polynomial sequence from a given one, orthogonal to a weight function defined on the positive plane. In this description plays an important role a sort of Backlund type matrix transformations for the involved three term matrix coefficients. We take as a case study relations between symmetric orthogonal polynomials defined on the ball and on the simplex.
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- 2022
25. Jacobi–Piñeiro Markov chains
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Branquinho, Amílcar, Díaz, Juan E. F., Foulquié-Moreno, Ana, Mañas, Manuel, and Álvarez-Fernández, Carlos
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- 2024
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26. Hypergeometric Multiple Orthogonal Polynomials and Random Walks
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Branquinho, Amílcar, Fernández-Díaz, Juan E., Foulquié-Moreno, Ana, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,Mathematical Physics ,Mathematics - Probability - Abstract
The recently found hypergeometric multiple orthogonal polynomials on the step-line by Lima and Loureiro are shown to be random walk polynomials. It is proven that the corresponding Jacobi matrix and its transpose, which are nonnegative matrices and describe higher recurrence relations, can be normalized to two stochastic matrices, dual to each other. Using the Christoffel-Darboux formula on the step-line and the Poincar\'e theory for non-homogeneous recurrence relations it is proven that both stochastic matrices are related by transposition in the large $n$ limit. These random walks are beyond birth and death, as they describe a chain in where transitions to the two previous states are allowed, or in the dual to the two next states.The corresponding Karlin-McGregor representation formula is given for these new Markov chains. The regions of hypergeometric parameters where the Markov chains are recurrent or transient are given. Stochastic factorizations, in terms of pure birth and of pure death factors, for the corresponding Markov matrices of types I and II, are provided.Twelve uniform Jacobi matrices and the corresponding random walks, related to a Jacobi matrix of Toeplitz type, and theirs stochastic or semi-stochastic matrices (with sinks and sources), that describe Markov chains beyond birth and death, are found and studied. One of these uniform stochastic cases, which is a recurrent random walk, is the only hypergeometric multiple random walk having a uniform stochastic factorization. The corresponding weights, Jacobi and Markov transition matrices and sequences of type II multiple orthogonal polynomials are provided. Chain of Christoffel transformations connecting the stochastic uniform tuples between them, and the semi-stochastic uniform tuples, between them, are presented., Comment: In the revision we added explicit expressions for the type I multiple orthogonal polynomials associated with the uniform tuples
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- 2021
27. Multiple orthogonal polynomials: Pearson equations and Christoffel formulas
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Branquinho, Amilcar, Foulquié-Moreno, Ana, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,Mathematical Physics ,42C05, 33C45, 33C47 - Abstract
Multiple orthogonal polynomials with respect to two weights on the step-line are considered. A connection between different dual spectral matrices, one banded (recursion matrix) and one Hessenberg, respectively, and the Gauss-Borel factorization of the moment matrix is given. It is shown a hidden freedom exhibited by the spectral system related to the multiple orthogonal polynomials. Pearson equations are discussed, a Laguerre-Freud matrix is considered, and differential equations for type I and II multiple orthogonal polynomials, as well as for the corresponding linear forms are given. The Jacobi-Pi\~neiro multiple orthogonal polynomials of type I and type II are used as an illustrating case and the corresponding differential relations are presented. A permuting Christoffel transformation is discussed, finding the connection between the different families of multiple orthogonal polynomials. The Jacobi-Pi\~neiro case provides a convenient illustration of these symmetries, giving linear relations between different polynomials with shifted and permuted parameters. We also present the general theory for the perturbation of each weight by a different polynomial or rational function aka called Christoffel and Geronimus transformations. The connections formulas between the type II multiple orthogonal polynomials, the type I linear forms, as well as the vector Stieltjes-Markov vector functions is also presented. We illustrate these findings by analyzing the special case of modification by an even polynomial., Comment: Revised version, completely new section on general Christoffel and Geronimus for multiple orthogonal polynomials on the stepline
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- 2021
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28. Multiple Orthogonal Polynomials and Random Walks
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Branquinho, Amílcar, Foulquié-Moreno, Ana, Mañas, Manuel, Álvarez-Fernández, Carlos, and Fernández-Díaz, Juan E.
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Mathematics - Classical Analysis and ODEs ,Mathematical Physics ,Mathematics - Probability ,42C05, 33C45, 33C47, 60J10, 60Gxx - Abstract
Given a non-negative Jacobi matrix describing higher order recurrence relations for multiple orthogonal polynomials of type~II and corresponding linear forms of type I, a general strategy for constructing a pair of stochastic matrices, dual to each other, is provided. The corresponding Markov chains (or 1D random walks) allow, in one transition, to reach for the N-th previous states, to remain in the state or reach for the immediately next state. The dual Markov chains allow, in one transition, to reach for the N-th next states, to remain in the state or reach for immediately previous state. The connection between both dual Markov chains is discussed at the light of the Poincar\'e's theorem on ratio asymptotics for homogeneous linear recurrence relations and the Christoffel-Darboux formula within the sequence of multiple orthogonal polynomials and linear forms of type I. The Karlin-McGregor representation formula is extended to both dual random walks, and applied to the discussion of the corresponding generating functions and first-passage distributions. Recurrent or transient character of the Markov chain is discussed. Steady state and some conjectures on its existence and the relation with mass points are also given. The Jacobi-Pi\~neiro multiple orthogonal polynomials are taken as a case study of the described results. For the first time in the literature, an explicit formula for the type~I Jacobi--Pi\~neiro polynomials is determined. The region of parameters where the Markov chains are recurrent or transient is given, and it is conjectured that when recurrent, the Markov chains are null recurrent and, consequently, the expected return times are infinity. Examples of recurrent and transient Jacobi--Pi\~neiro random walks are constructed explicitly.
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- 2021
29. Riemann-Hilbert Problem for the Matrix Laguerre Biorthogonal Polynomials: Eigenvalue Problems and the Matrix Discrete Painlev\'e IV
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Branquinho, Amilcar, Moreno, Ana Foulquié, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,Mathematical Physics ,33C45, 33C47, 42C05, 47A56 - Abstract
In this paper the Riemann-Hilbert problem, with jump supported on a appropriate curve on the complex plane with a finite endpoint at the origin, is used for the study of corresponding matrix biorthogonal polynomials associated with Laguerre type matrices of weights ---which are constructed in terms of a given matrix Pearson equation. First and second order differential systems for the fundamental matrix, solution of the mentioned Riemann-Hilbert problem are derived. An explicit and general example is presented to illustrate the theoretical results of the work. Related matrix eigenvalue problems for second order matrix differential operators and non-Abelian extensions of a family of discrete Painlev\'e IV equations are discussed., Comment: arXiv admin note: text overlap with arXiv:1807.07119
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- 2019
30. Quadratic Decomposition of Bivariate Orthogonal Polynomials
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Branquinho, Amílcar, Foulquié-Moreno, Ana, and Pérez, Teresa E.
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- 2023
- Full Text
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31. Bidiagonal factorization of tetradiagonal matrices and Darboux transformations
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Branquinho, Amílcar, Foulquié-Moreno, Ana, and Mañas, Manuel
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- 2023
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32. Development of an industrial yeast strain for efficient production of 2,3-butanediol
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Guangxin Huo, María R. Foulquié-Moreno, and Johan M. Thevelein
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Yeast cell factory ,Bio-based chemical ,Metabolic engineering ,2,3-Butanediol ,Alternative oxidase ,NADH oxidase ,Microbiology ,QR1-502 - Abstract
Abstract As part of the transition from a fossil resources-based economy to a bio-based economy, the production of platform chemicals by microbial cell factories has gained strong interest. 2,3-butanediol (2,3-BDO) has various industrial applications, but its production by microbial fermentation poses multiple challenges. We have engineered the bacterial 2,3-BDO synthesis pathway, composed of AlsS, AlsD and BdhA, in a pdc-negative version of an industrial Saccharomyces cerevisiae yeast strain. The high concentration of glycerol caused by the excess NADH produced in the pathway from glucose to 2,3-BDO was eliminated by overexpression of NoxE and also in a novel way by combined overexpression of NDE1, encoding mitochondrial external NADH dehydrogenase, and AOX1, encoding a heterologous alternative oxidase expressed inside the mitochondria. This was combined with strong downregulation of GPD1 and deletion of GPD2, to minimize glycerol production while maintaining osmotolerance. The HGS50 strain produced a 2,3-BDO titer of 121.04 g/L from 250 g/L glucose, the highest ever reported in batch fermentation, with a productivity of 1.57 g/L.h (0.08 g/L.h per gCDW) and a yield of 0.48 g/g glucose or with 96% the closest to the maximum theoretical yield ever reported. Expression of Lactococcus lactis NoxE, encoding a water-forming NADH oxidase, combined with similar genetic modifications, as well as expression of Candida albicans STL1, also minimized glycerol production while maintaining high osmotolerance. The HGS37 strain produced 130.64 g/L 2,3-BDO from 280 g/L glucose, with productivity of 1.58 g/L.h (0.11 g/L.h per gCDW). Both strains reach combined performance criteria adequate for industrial implementation.
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- 2022
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33. The characterization of toll‐like receptor repertoire in Pinna nobilis after mass mortality events suggests adaptive introgression
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Stéphane Coupé, Ioannis A. Giantsis, Maite Vázquez Luis, Fabio Scarpa, Mathieu Foulquié, Jean‐Marc Prévot, Marco Casu, Athanasios Lattos, Basile Michaelidis, Daria Sanna, José Rafa García‐March, José Tena‐Medialdea, Nardo Vicente, and Robert Bunet
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adaptation ,critically endangered ,fan mussel ,genetic diversity ,Haplosporidium pinnae ,hybrids ,Ecology ,QH540-549.5 - Abstract
Abstract The fan mussel Pinna nobilis is currently on the brink of extinction due to a multifactorial disease mainly caused to the highly pathogenic parasite Haplosporidium pinnae, meaning that the selection pressure outweighs the adaptive potential of the species. Hopefully, rare individuals have been observed somehow resistant to the parasite, stretching the need to identify the traits underlying this better fitness. Among the candidate to explore at first intention are fast‐evolving immune genes, of which toll‐like receptor (TLR). In this study, we examined the genetic diversity at 14 TLR loci across P. nobilis, Pinna rudis and P. nobilis × P. rudis hybrid genomes, collected at four physically distant regions, that were found to be either resistant or sensitive to the parasite H. pinnae. We report a high genetic diversity, mainly observed at cell surface TLRs compared with that of endosomal TLRs. However, the endosomal TLR‐7 exhibited unexpected level of diversity and haplotype phylogeny. The lack of population structure, associated with a high genetic diversity and elevated dN/dS ratio, was interpreted as balancing selection, though both directional and purifying selection were detected. Interestingly, roughly 40% of the P. nobilis identified as resistant to H. pinnae were introgressed with P. rudis TLR. Specifically, they all carried a TLR‐7 of P. rudis origin, whereas sensitive P. nobilis were not introgressed, at least at TLR loci. Small contributions of TLR‐6 and TLR‐4 single‐nucleotide polymorphisms to the clustering of resistant and susceptible individuals could be detected, but their specific role in resistance remains highly speculative. This study provides new information on the diversity of TLR genes within the P. nobilis species after MME and additional insights into adaptation to H. pinnae that should contribute to the conservation of this Mediterranean endemic species.
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- 2023
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34. Matrix Biorthogonal Polynomials: eigenvalue problems and non-Abelian discrete Painlev\'e equations
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Branquinho, Amilcar, Moreno, Ana Foulquié, and Mañas, Manuel
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Mathematics - Classical Analysis and ODEs ,Mathematical Physics ,Nonlinear Sciences - Exactly Solvable and Integrable Systems - Abstract
In this paper we use the Riemann-Hilbert problem, with jumps supported on appropriate curves in the complex plane, for matrix biorthogonal polynomials and apply it to find Sylvester systems of differential equations for the orthogonal polynomials and its second kind functions as well. For this aim, Sylvester type differential Pearson equations for the matrix of weights are shown to be instrumental. Several applications are given, in order of increasing complexity. First, a general discussion of non-Abelian Hermite biorthogonal polynomials in the real line, understood as those whose matrix of weights is a solution of a Sylvester type Pearson equation with coefficients first order matrix polynomials, is given. All these is applied to the discussion of possible scenarios leading to eigenvalue problems for second order linear differential operators with matrix eigenvalues. Nonlinear matrix difference equations are discussed next. Firstly, for the general Hermite situation a general non linear relation (non trivial because the non commutativity features of the setting) for the recursion coefficients is gotten. In the next case of higher difficulty, degree two polynomials are allowed in the Pearson equation, but the discussion is simplified by considering only a left Pearson equation. In the case, the support of the measure is on an appropriate branch of an hyperbola. The recursion coefficients are shown to fulfill a non-Abelian extension of the alternate discrete Painlev\'e I equation. Finally, a discussion is given for the case of degree three polynomials as coefficients in the left Pearson equation characterizing the matrix of weights. However, for simplicity only odd polynomials are allowed. In this case, a new and more general matrix extension of the discrete Painlev\'e I equation is found., Comment: 38 pages, 1 figure
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- 2018
35. Genome-wide analyses reveal a strong association between LEPR gene variants and body fat reserves in ewes
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Tiphaine Macé, Eliel González-García, Didier Foulquié, Fabien Carrière, Julien Pradel, Christian Durand, Sebastien Douls, Charlotte Allain, Sara Parisot, and Dominique Hazard
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Animal genomics ,Adaptation ,Adipose tissue ,Ruminants ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Among the adaptive capacities of animals, the management of energetic body reserves (BR) through the BR mobilization and accretion processes (BR dynamics, BRD) has become an increasingly valuable attribute for livestock sustainability, allowing animals to cope with more variable environments. BRD has previously been reported to be heritable in ruminants. In the present work, we conducted genome-wide studies (GWAS) in sheep to determine genetic variants associated with BRD. BR (i.e. levels) and BRD (i.e. changes over time) were obtained through body condition score measurements at eight physiological stages throughout each productive cycle in Romane ewes (n = 1034) and were used as phenotypes for GWAS. After quality controls and imputation, 48,593 single nucleotide polymorphisms (SNP) were included in the GWAS. Results Among the 23 QTL regions identified, a major QTL associated with BR during pregnancy and lactation was identified on chromosome 1. In this region, several significant SNPs mapped to the leptin receptor gene (LEPR), among which one SNP mapped to the coding sequence. The point mutation induces the p.P1019S substitution in the cytoplasmic domain, close to tyrosine phosphorylation sites. The frequency of the SNP associated with increased BR levels was 32%, and the LEPR genotype explained up to 5% of the variance of the trait. Higher fatness levels in ewes carrying the LEPR p.P1019S mutation were observed all along the productive cycle. Conclusions These results provide strong evidences for involvement of LEPR in the regulation of BR in sheep and highlight it as a major candidate gene for improving adaptive capacities by genetic selection.
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- 2022
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36. Patient and Caregiver Perceptions of Advanced Bladder Cancer Systemic Treatments: Infodemiology Study Based on Social Media Data
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Simon Renner, Paul Loussikian, Pierre Foulquié, Alexia Marrel, Valentin Barbier, Adel Mebarki, Stéphane Schück, and Murtuza Bharmal
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
BackgroundIn 2022, it was estimated that more than 80,000 new cases of bladder cancer (BC) were diagnosed in the United States, 12% of which were locally advanced or metastatic BC (advanced BC). These forms of cancer are aggressive and have a poor prognosis, with a 5-year survival rate of 7.7% for metastatic BC. Despite recent therapeutic advances for advanced BC, little is known about patient and caregiver perceptions of different systemic treatments. To further explore this topic, social media can be used to collect the perceptions of patients and caregivers when they discuss their experiences on forums and online communities. ObjectiveThe aim of this study was to assess patient and caregiver perceptions of chemotherapy and immunotherapy for treating advanced BC from social media–posted data. MethodsPublic posts on social media in the United States between January 2015 and April 2021 from patients with advanced BC and their caregivers were collected. The posts included in this analysis were geolocalized to the United States; collected from publicly available domains and sites, including social media sites such as Twitter and forums such as patient association forums; and were written in English. Posts mentioning any line of chemotherapy or immunotherapy were qualitatively analyzed by two researchers to classify perceptions of treatments (positive, negative, mixed, or without perception). ResultsA total of 80 posts by 69 patients and 142 posts by 127 caregivers mentioning chemotherapy, and 42 posts by 31 patients and 35 posts by 32 caregivers mentioning immunotherapy were included for analysis. These posts were retrieved from 39 public social media sites. Among patients with advanced BC and their caregivers, treatment perceptions of chemotherapy were more negative (36%) than positive (7%). Most of the patients’ posts (71%) mentioned chemotherapy factually without expressing a perception of the treatment. The caregivers’ perceptions of treatment were negative in 44%, mixed in 8%, and positive in 7% of posts. In combined patient and caregiver posts, immunotherapy was perceived positively in 47% of posts and negatively in 22% of posts. Caregivers also posted more negative perceptions (37%) of immunotherapy than patients (9%). Negative perceptions of both chemotherapy and immunotherapy were mainly due to side effects and perceived lack of effectiveness. ConclusionsDespite chemotherapy being standard first-line therapy for advanced BC, negative perceptions were identified on social media, particularly among caregivers. Addressing these negative perceptions of treatment may improve treatment adoption. Strengthening support for patients receiving chemotherapy and their caregivers to help them manage side effects and understand the role of chemotherapy in the treatment of advanced BC would potentially enable a more positive experience.
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- 2023
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37. Development of an industrial yeast strain for efficient production of 2,3-butanediol
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Huo, Guangxin, Foulquié-Moreno, María R., and Thevelein, Johan M.
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- 2022
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38. Genome-wide analyses reveal a strong association between LEPR gene variants and body fat reserves in ewes
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Macé, Tiphaine, González-García, Eliel, Foulquié, Didier, Carrière, Fabien, Pradel, Julien, Durand, Christian, Douls, Sebastien, Allain, Charlotte, Parisot, Sara, and Hazard, Dominique
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- 2022
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39. Multiple orthogonal polynomials: Pearson equations and Christoffel formulas
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Branquinho, Amílcar, Foulquié-Moreno, Ana, and Mañas, Manuel
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- 2022
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40. Identifying Profiles and Symptoms of Patients With Long COVID in France: Data Mining Infodemiology Study Based on Social Media
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Amélia Déguilhem, Joelle Malaab, Manissa Talmatkadi, Simon Renner, Pierre Foulquié, Guy Fagherazzi, Paul Loussikian, Tom Marty, Adel Mebarki, Nathalie Texier, and Stephane Schuck
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Computer applications to medicine. Medical informatics ,R858-859.7 - Abstract
BackgroundLong COVID—a condition with persistent symptoms post COVID-19 infection—is the first illness arising from social media. In France, the French hashtag #ApresJ20 described symptoms persisting longer than 20 days after contracting COVID-19. Faced with a lack of recognition from medical and official entities, patients formed communities on social media and described their symptoms as long-lasting, fluctuating, and multisystemic. While many studies on long COVID relied on traditional research methods with lengthy processes, social media offers a foundation for large-scale studies with a fast-flowing outburst of data. ObjectiveWe aimed to identify and analyze Long Haulers’ main reported symptoms, symptom co-occurrences, topics of discussion, difficulties encountered, and patient profiles. MethodsData were extracted based on a list of pertinent keywords from public sites (eg, Twitter) and health-related forums (eg, Doctissimo). Reported symptoms were identified via the MedDRA dictionary, displayed per the volume of posts mentioning them, and aggregated at the user level. Associations were assessed by computing co-occurrences in users’ messages, as pairs of preferred terms. Discussion topics were analyzed using the Biterm Topic Modeling; difficulties and unmet needs were explored manually. To identify patient profiles in relation to their symptoms, each preferred term’s total was used to create user-level hierarchal clusters. ResultsBetween January 1, 2020, and August 10, 2021, overall, 15,364 messages were identified as originating from 6494 patients of long COVID or their caregivers. Our analyses revealed 3 major symptom co-occurrences: asthenia-dyspnea (102/289, 35.3%), asthenia-anxiety (65/289, 22.5%), and asthenia-headaches (50/289, 17.3%). The main reported difficulties were symptom management (150/424, 35.4% of messages), psychological impact (64/424,15.1%), significant pain (51/424, 12.0%), deterioration in general well-being (52/424, 12.3%), and impact on daily and professional life (40/424, 9.4% and 34/424, 8.0% of messages, respectively). We identified 3 profiles of patients in relation to their symptoms: profile A (n=406 patients) reported exclusively an asthenia symptom; profile B (n=129) expressed anxiety (n=129, 100%), asthenia (n=28, 21.7%), dyspnea (n=15, 11.6%), and ageusia (n=3, 2.3%); and profile C (n=141) described dyspnea (n=141, 100%), and asthenia (n=45, 31.9%). Approximately 49.1% of users (79/161) continued expressing symptoms after more than 3 months post infection, and 20.5% (33/161) after 1 year. ConclusionsLong COVID is a lingering condition that affects people worldwide, physically and psychologically. It impacts Long Haulers’ quality of life, everyday tasks, and professional activities. Social media played an undeniable role in raising and delivering Long Haulers’ voices and can potentially rapidly provide large volumes of valuable patient-reported information. Since long COVID was a self-titled condition by patients themselves via social media, it is imperative to continuously include their perspectives in related research. Our results can help design patient-centric instruments to be further used in clinical practice to better capture meaningful dimensions of long COVID.
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- 2022
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41. Perceived Unmet Needs in Patients Living With Advanced Bladder Cancer and Their Caregivers: Infodemiology Study Using Data From Social Media in the United States
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Simon Renner, Paul Loussikian, Pierre Foulquié, Benoit Arnould, Alexia Marrel, Valentin Barbier, Adel Mebarki, Stéphane Schück, and Murtuza Bharmal
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
BackgroundLocally advanced or metastatic bladder cancer (BC), which is generally termed advanced BC (aBC), has a very poor prognosis, and in addition to its physical symptoms, it is associated with emotional and social challenges. However, few studies have assessed the unmet needs and burden of aBC from patient and caregiver perspectives. Infodemiology, that is, epidemiology based on internet health-related content, can help obtain more insights on patients’ and caregivers’ experiences with aBC. ObjectiveThe study aimed to identify the main discussion themes and the unmet needs of patients with aBC and their caregivers through a mixed methods analysis of social media posts. MethodsSocial media posts were collected between January 2015 and April 2021 from US geolocalized sites using specific keywords for aBC. Automatic natural language processing (regular expressions and machine learning) methods were used to filter out irrelevant content and identify verbatim posts from patients and caregivers. The verbatim posts were analyzed to identify main discussion themes using biterm topic modeling. Difficulties or unmet needs were further explored using qualitative research methods by 2 independent annotators until saturation of concepts. ResultsA total of 688 posts from 262 patients and 1214 posts from 679 caregivers discussing aBC were identified. Analysis of 340 randomly selected patient posts and 423 randomly selected caregiver posts uncovered 33 unique unmet need categories among patients and 36 among caregivers. The main unmet patient needs were related to challenges regarding adverse events (AEs; 28/95, 29%) and the psychological impact of aBC (20/95, 21%). Other patient unmet needs identified were prognosis or diagnosis errors (9/95, 9%) and the need for better management of aBC symptoms (9/95, 9%). The main unmet caregiver needs were related to the psychological impacts of aBC (46/177, 26.0%), the need for support groups and to share experiences between peers (28/177, 15.8%), and the fear and management of patient AEs (22/177, 12.4%). ConclusionsThe combination of manual and automatic methods allowed the extraction and analysis of several hundreds of social media posts from patients with aBC and their caregivers. The results highlighted the emotional burden of cancer for both patients and caregivers. Additional studies on patients with aBC and their caregivers are required to quantitatively explore the impact of this disease on quality of life.
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- 2022
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42. In-situ muconic acid extraction reveals sugar consumption bottleneck in a xylose-utilizing Saccharomyces cerevisiae strain
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Thomas Nicolaï, Quinten Deparis, María R. Foulquié-Moreno, and Johan M. Thevelein
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Yeast cell factory ,Muconic acid ,Xylose ,PDC negative ,In-situ product removal ,Lignocellulosic biomass ,Microbiology ,QR1-502 - Abstract
Abstract Background The current shift from a fossil-resource based economy to a more sustainable, bio-based economy requires development of alternative production routes based on utilization of biomass for the many chemicals that are currently produced from petroleum. Muconic acid is an attractive platform chemical for the bio-based economy because it can be converted in chemicals with wide industrial applicability, such as adipic and terephthalic acid, and because its two double bonds offer great versatility for chemical modification. Results We have constructed a yeast cell factory converting glucose and xylose into muconic acid without formation of ethanol. We consecutively eliminated feedback inhibition in the shikimate pathway, inserted the heterologous pathway for muconic acid biosynthesis from 3-dehydroshikimate (DHS) by co-expression of DHS dehydratase from P. anserina, protocatechuic acid (PCA) decarboxylase (PCAD) from K. pneumoniae and oxygen-consuming catechol 1,2-dioxygenase (CDO) from C. albicans, eliminated ethanol production by deletion of the three PDC genes and minimized PCA production by enhancing PCAD overexpression and production of its co-factor. The yeast pitching rate was increased to lower high biomass formation caused by the compulsory aerobic conditions. Maximal titers of 4 g/L, 4.5 g/L and 3.8 g/L muconic acid were reached with glucose, xylose, and a mixture, respectively. The use of an elevated initial sugar level, resulting in muconic acid titers above 2.5 g/L, caused stuck fermentations with incomplete utilization of the sugar. Application of polypropylene glycol 4000 (PPG) as solvent for in situ product removal during the fermentation shows that this is not due to toxicity by the muconic acid produced. Conclusions This work has developed an industrial yeast strain able to produce muconic acid from glucose and also with great efficiency from xylose, without any ethanol production, minimal production of PCA and reaching the highest titers in batch fermentation reported up to now. Utilization of higher sugar levels remained conspicuously incomplete. Since this was not due to product inhibition by muconic acid or to loss of viability, an unknown, possibly metabolic bottleneck apparently arises during muconic acid fermentation with high sugar levels and blocks further sugar utilization.
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- 2021
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43. Identification of the major fermentation inhibitors of recombinant 2G yeasts in diverse lignocellulose hydrolysates
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Gert Vanmarcke, Mekonnen M. Demeke, Maria R. Foulquié-Moreno, and Johan M. Thevelein
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Bioethanol production ,Lignocellulose hydrolysates ,Fermentation inhibitors ,2G yeast strains ,Fuel ,TP315-360 ,Biotechnology ,TP248.13-248.65 - Abstract
Abstract Background Presence of inhibitory chemicals in lignocellulose hydrolysates is a major hurdle for production of second-generation bioethanol. Especially cheaper pre-treatment methods that ensure an economical viable production process generate high levels of these inhibitory chemicals. The effect of several of these inhibitors has been extensively studied with non-xylose-fermenting laboratory strains, in synthetic media, and usually as single inhibitors, or with inhibitor concentrations much higher than those found in lignocellulose hydrolysates. However, the relevance of individual inhibitors in inhibitor-rich lignocellulose hydrolysates has remained unclear. Results The relative importance for inhibition of ethanol fermentation by two industrial second-generation yeast strains in five lignocellulose hydrolysates, from bagasse, corn cobs and spruce, has now been investigated by spiking higher concentrations of each compound in a concentration range relevant for industrial hydrolysates. The strongest inhibition was observed with industrially relevant concentrations of furfural causing partial inhibition of both D-glucose and D-xylose consumption. Addition of 3 or 6 g/L furfural strongly reduced the ethanol titer obtained with strain MD4 in all hydrolysates evaluated, in a range of 34 to 51% and of 77 to 86%, respectively. This was followed by 5-hydroxymethylfurfural, acetic acid and formic acid, for which in general, industrially relevant concentrations caused partial inhibition of D-xylose fermentation. On the other hand, spiking with levulinic acid, 4-hydroxybenzaldehyde, 4-hydroxybenzoic acid or vanillin caused little inhibition compared to unspiked hydrolysate. The further evolved MD4 strain generally showed superior performance compared to the previously developed strain GSE16-T18. Conclusion The results highlight the importance of individual inhibitor evaluation in a medium containing a genuine mix of inhibitors as well as the ethanol that is produced by the fermentation. They also highlight the potential of increasing yeast inhibitor tolerance for improving industrial process economics.
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- 2021
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44. Mechanisms underlying lactic acid tolerance and its influence on lactic acid production in Saccharomyces cerevisiae
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Arne Peetermans, María R. Foulquié-Moreno, and Johan M. Thevelein
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lactic acid tolerance ,saccharomyces cerevisiae ,lactic acid production ,yeast cell factory ,lactic acid stress response ,Biology (General) ,QH301-705.5 - Abstract
One of the major bottlenecks in lactic acid production using microbial fermentation is the detrimental influence lactic acid accumulation poses on the lactic acid producing cells. The accumulation of lactic acid results in many negative effects on the cell such as intracellular acidification, anion accumulation, membrane perturbation, disturbed amino acid trafficking, increased turgor pressure, ATP depletion, ROS accumulation, metabolic dysregulation and metal chelation. In this review, the manner in which Saccharomyces cerevisiae deals with these issues will be discussed extensively not only for lactic acid as a singular stress factor but also in combination with other stresses. In addition, different methods to improve lactic acid tolerance in S. cerevisiae using targeted and non-targeted engineering methods will be discussed.
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- 2021
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45. PCR24 Patient and Caregiver Perceptions of Systemic Anticancer Treatments in Advanced Bladder Cancer (aBC): Results of a Social Media Listening (SML) Study Conducted in 5 European Countries (Eu5)
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Schück, S., primary, Loussikian, P., additional, Mebarki, A., additional, Malaab, J., additional, Foulquié, P., additional, Talmatkadi, M., additional, and Kearney, M., additional
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- 2023
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46. Polygenic analysis of very high acetic acid tolerance in the yeast Saccharomyces cerevisiae reveals a complex genetic background and several new causative alleles
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Marija Stojiljkovic, María R. Foulquié-Moreno, and Johan M. Thevelein
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Bioethanol production ,Acetic acid tolerance ,Polygenic analysis ,Industrial yeast ,Fuel ,TP315-360 ,Biotechnology ,TP248.13-248.65 - Abstract
Abstract Background High acetic acid tolerance is of major importance in industrial yeast strains used for second-generation bioethanol production, because of the high acetic acid content of lignocellulose hydrolysates. It is also important in first-generation starch hydrolysates and in sourdoughs containing significant acetic acid levels. We have previously identified snf4 E269* as a causative allele in strain MS164 obtained after whole-genome (WG) transformation and selection for improved acetic acid tolerance. Results We have now performed polygenic analysis with the same WG transformant MS164 to identify novel causative alleles interacting with snf4 E269* to further enhance acetic acid tolerance, from a range of 0.8–1.2% acetic acid at pH 4.7, to previously unmatched levels for Saccharomyces cerevisiae. For that purpose, we crossed the WG transformant with strain 16D, a previously identified strain displaying very high acetic acid tolerance. Quantitative trait locus (QTL) mapping with pooled-segregant whole-genome sequence analysis identified four major and two minor QTLs. In addition to confirmation of snf4 E269* in QTL1, we identified six other genes linked to very high acetic acid tolerance, TRT2, MET4, IRA2 and RTG1 and a combination of MSH2 and HAL9, some of which have never been connected previously to acetic acid tolerance. Several of these genes appear to be wild-type alleles that complement defective alleles present in the other parent strain. Conclusions The presence of several novel causative genes highlights the distinct genetic basis and the strong genetic background dependency of very high acetic acid tolerance. Our results suggest that elimination of inferior mutant alleles might be equally important for reaching very high acetic acid tolerance as introduction of rare superior alleles. The superior alleles of MET4 and RTG1 might be useful for further improvement of acetic acid tolerance in specific industrial yeast strains.
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- 2020
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47. Repeated batches as a strategy for high 2G ethanol production from undetoxified hemicellulose hydrolysate using immobilized cells of recombinant Saccharomyces cerevisiae in a fixed-bed reactor
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Thais S. Milessi, Caroline L. Perez, Teresa C. Zangirolami, Felipe A. S. Corradini, Juliana P. Sandri, Maria R. Foulquié-Moreno, Roberto C. Giordano, Johan M. Thevelein, and Raquel L. C. Giordano
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Hemicellulose utilization ,Cell immobilization ,Inhibitor tolerance ,Bioethanol ,Recombinant yeast ,Fixed-bed reactor ,Fuel ,TP315-360 ,Biotechnology ,TP248.13-248.65 - Abstract
Abstract Background The search for sustainable energy sources has become a worldwide issue, making the development of efficient biofuel production processes a priority. Immobilization of second-generation (2G) xylose-fermenting Saccharomyces cerevisiae strains is a promising approach to achieve economic viability of 2G bioethanol production from undetoxified hydrolysates through operation at high cell load and mitigation of inhibitor toxicity. In addition, the use of a fixed-bed reactor can contribute to establish an efficient process because of its distinct advantages, such as high conversion rate per weight of biocatalyst and reuse of biocatalyst. Results This work assessed the influence of alginate entrapment on the tolerance of recombinant S. cerevisiae to acetic acid. Encapsulated GSE16-T18SI.1 (T18) yeast showed an outstanding performance in repeated batch fermentations with cell recycling in YPX medium supplemented with 8 g/L acetic acid (pH 5.2), achieving 10 cycles without significant loss of productivity. In the fixed-bed bioreactor, a high xylose fermentation rate with ethanol yield and productivity values of 0.38 gethanol/gsugars and 5.7 g/L/h, respectively were achieved in fermentations using undetoxified sugarcane bagasse hemicellulose hydrolysate, with and without medium recirculation. Conclusions The performance of recombinant strains developed for 2G ethanol production can be boosted strongly by cell immobilization in alginate gels. Yeast encapsulation allows conducting fermentations in repeated batch mode in fixed-bed bioreactors with high xylose assimilation rate and high ethanol productivity using undetoxified hemicellulose hydrolysate.
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- 2020
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48. A New Method to Extract Health-Related Quality of Life Data From Social Media Testimonies: Algorithm Development and Validation
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Simon Renner, Tom Marty, Mickaïl Khadhar, Pierre Foulquié, Paméla Voillot, Adel Mebarki, Ilaria Montagni, Nathalie Texier, and Stéphane Schück
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Computer applications to medicine. Medical informatics ,R858-859.7 ,Public aspects of medicine ,RA1-1270 - Abstract
BackgroundMonitoring social media has been shown to be a useful means to capture patients’ opinions and feelings about medical issues, ranging from diseases to treatments. Health-related quality of life (HRQoL) is a useful indicator of overall patients’ health, which can be captured online. ObjectiveThis study aimed to describe a social media listening algorithm able to detect the impact of diseases or treatments on specific dimensions of HRQoL based on posts written by patients in social media and forums. MethodsUsing a web crawler, 19 forums in France were harvested, and messages related to patients’ experience with disease or treatment were specifically collected. The SF-36 (Short Form Health Survey) and EQ-5D (Euro Quality of Life 5 Dimensions) HRQoL surveys were mixed and adapted for a tailored social media listening system. This was carried out to better capture the variety of expression on social media, resulting in 5 dimensions of the HRQoL, which are physical, psychological, activity-based, social, and financial. Models were trained using cross-validation and hyperparameter optimization. Oversampling was used to increase the infrequent dimension: after annotation, SMOTE (synthetic minority oversampling technique) was used to balance the proportions of the dimensions among messages. ResultsThe training set was composed of 1399 messages, randomly taken from a batch of 20,000 health-related messages coming from forums. The algorithm was able to detect a general impact on HRQoL (sensitivity of 0.83 and specificity of 0.74), a physical impact (0.67 and 0.76), a psychic impact (0.82 and 0.60), an activity-related impact (0.73 and 0.78), a relational impact (0.73 and 0.70), and a financial impact (0.79 and 0.74). ConclusionsThe development of an innovative method to extract health data from social media as real time assessment of patients’ HRQoL is useful to a patient-centered medical care. As a source of real-world data, social media provide a complementary point of view to understand patients’ concerns and unmet needs, as well as shedding light on how diseases and treatments can be a burden in their daily lives.
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- 2022
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49. Social Media Platforms Listening Study on Atopic Dermatitis: Quantitative and Qualitative Findings
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Paméla Voillot, Brigitte Riche, Michel Portafax, Pierre Foulquié, Anaïs Gedik, Sébastien Barbarot, Laurent Misery, Stéphane Héas, Adel Mebarki, Nathalie Texier, and Stéphane Schück
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Computer applications to medicine. Medical informatics ,R858-859.7 ,Public aspects of medicine ,RA1-1270 - Abstract
BackgroundAtopic dermatitis (AD) is a chronic, pruritic, inflammatory disease that occurs most frequently in children but also affects many adults. Social media have become key tools for finding and disseminating medical information. ObjectiveThe aims of this study were to identify the main themes of discussion, the difficulties encountered by patients with respect to AD, the impact of the pathology on quality of life (QoL; physical, psychological, social, or financial), and to study the perception of patients regarding their treatment. MethodsA retrospective study was carried out by collecting social media posts in French language written by internet users mentioning their experience with AD, their QoL, and their treatments. Messages related to AD discomfort posted between July 1, 2010, and October 23, 2020, were extracted from French-speaking publicly available online forums. Automatic and manual extractions were implemented to create a general corpus and 2 subcorpuses depending on the level of control of the disease. ResultsA total of 33,115 messages associated with AD were included in the analysis corpus after extraction and cleaning. These messages were posted by 15,857 separate web users, most of them being women younger than 40 years. Tips to manage AD and everyday hygiene/treatments were among the most discussed topics for controlled AD subcorpus, while baby-related topics and therapeutic failure were among the most discussed topics for insufficiently controlled AD subcorpus. QoL was discussed in both subcorpuses with a higher proportion in the controlled AD subcorpus. Treatments and their perception were also discussed by web users. ConclusionsMore than just emotional or peer support, patients with AD turn to online forums to discuss their health. Our findings show the need for an intersection between social media and health care and the importance of developing new approaches such as the Atopic Dermatitis Control Tool, which is a patient-related disease severity assessment tool focused on patients with AD.
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- 2022
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50. Natural Saccharomyces cerevisiae Strain Reveals Peculiar Genomic Traits for Starch-to-Bioethanol Production: the Design of an Amylolytic Consolidated Bioprocessing Yeast
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Nicoletta Gronchi, Nicola De Bernardini, Rosemary A. Cripwell, Laura Treu, Stefano Campanaro, Marina Basaglia, Maria R. Foulquié-Moreno, Johan M. Thevelein, Willem H. Van Zyl, Lorenzo Favaro, and Sergio Casella
- Subjects
Saccharomyces cerevisiae ,delta integration ,CRISPR/Cas9 ,starch ,Ethanol Red ,consolidated bioprocessing ,Microbiology ,QR1-502 - Abstract
Natural yeast with superior fermentative traits can serve as a platform for the development of recombinant strains that can be used to improve the sustainability of bioethanol production from starch. This process will benefit from a consolidated bioprocessing (CBP) approach where an engineered strain producing amylases directly converts starch into ethanol. The yeast Saccharomyces cerevisiae L20, previously selected as outperforming the benchmark yeast Ethanol Red, was here subjected to a comparative genomic investigation using a dataset of industrial S. cerevisiae strains. Along with Ethanol Red, strain L20 was then engineered for the expression of α-amylase amyA and glucoamylase glaA genes from Aspergillus tubingensis by employing two different approaches (delta integration and CRISPR/Cas9). A correlation between the number of integrated copies and the hydrolytic abilities of the recombinants was investigated. L20 demonstrated important traits for the construction of a proficient CBP yeast. Despite showing a close relatedness to commercial wine yeast and the benchmark Ethanol Red, a unique profile of gene copy number variations (CNVs) was found in L20, mainly encoding membrane transporters and secretion pathway proteins but also the fermentative metabolism. Moreover, the genome annotation disclosed seven open reading frames (ORFs) in L20 that are absent in the reference S288C genome. Genome engineering was successfully implemented for amylase production. However, with equal amylase gene copies, L20 proved its proficiency as a good enzyme secretor by exhibiting a markedly higher amylolytic activity than Ethanol Red, in compliance to the findings of the genomic exploration. The recombinant L20 dT8 exhibited the highest amylolytic activity and produced more than 4 g/L of ethanol from 2% starch in a CBP setting without the addition of supplementary enzymes. Based on the performance of this strain, an amylase/glucoamylase ratio of 1:2.5 was suggested as baseline for further improvement of the CBP ability. Overall, L20 showed important traits for the future construction of a proficient CBP yeast. As such, this work shows that natural S. cerevisiae strains can be used for the expression of foreign secreted enzymes, paving the way to strain improvement for the starch-to-bioethanol route.
- Published
- 2022
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