De Baets Research Articles

Characterizations for convolution lattices based on non-distributive lattices

Recently, De Miguel, Bustince and De Baets have conducted a systematic study on convolution lattices based on distributive lattices. There have been few reports on applying non-distributive lattices to a domain of functions. As a complement to their work, in this paper, we carry out an in-depth investigation of convolution operations of the functions between a non-distributive lattice (domain) and a frame (co-domain). We first present an equivalence characterization between non-distributive lattices and idempotent functions and further show that a subset of the set of idempotent functions is closed under convolution operations. We demonstrate that this subset also is a bisemilattice and satisfies the Birkhoff equation under join- and meet-convolution operations. Finally, we analyze and study the lattice structure related to the obtained algebraic structure.

On linear combinations of binomial OWA functions

We consider the binomial decomposition of ordered weighted averaging (OWA) functions proposed by Calvo and De Baets (1998) in the framework of Choquet integration. Our aim in the paper is to further investigate the equivalence between the two representations of OWA functions involved in the binomial decomposition: the usual canonical representation in terms of the order statistics, and the binomial representation in terms of the binomial OWA functions. We describe and discuss in detail the linear transformations that relate the coefficients of these two equivalent representations: the original expression of the weights in terms of the coefficients of the binomial representation, and its inverse, the expression of those coefficients in terms of the weights. In both cases simple and direct proofs are presented. Moreover, we consider the linear transformations between the two representations in the general linear algebra framework of unconstrained linear combinations of binomial OWA functions. In this perspective we obtain compact matrix expressions for the linear transformations, which also offer new insight on the geometry of the coefficient constraints in the binomial representation of OWA functions.

Onion lattices and an answer to an open problem on convolution lattices

We develop a new class of lattices called Onion lattices, analyse the properties of Onion lattices and further prove that the set of idempotent lattice functions on a bounded lattice L is closed under convolution operations if and only if L is an Onion lattice. This solves the second open problem posed by De Miguel, Bustince and De Baets (2018) [1]. Furthermore, we study in depth the lattice function algebraic system with the properties of the Birkhoff system proposed in [1]. We obtain that the set of idempotent lattice functions under the operations ⊓ and ⊔ constitutes a Birkhoff system if and only if the domain of the idempotent lattice functions is the Onion lattice. And we explore some algebraic properties of Birkhoff systems consisting of sets of idempotent lattice functions.

W obronie historii. Piotr Kowalewski Jahromi rozmawia z Antoonem De Baetsem

In this interview, conducted at the XXIII International Congress of Historical Sciences in Poznan, Antoon De Baets (emeritus professor of History, Ethics and Human Rights at the University of Groningen, the Netherlands) addresses key issues for historians and other produ-cers of history. His remarks about the scientific status of historiography and the range of different threats to history seem particularly important. He talks not only about the most direct crimes against historians and history, but also about issues like hindsight bias and fake news. The professional duties of historians and the issue of ethical codes for historians are also discussed.

SNPeffect 5.0: large-scale structural phenotyping of protein coding variants extracted from next-generation sequencing data using AlphaFold models

BackgroundNext-generation sequencing technologies yield large numbers of genetic alterations, of which a subset are missense variants that alter an amino acid in the protein product. These variants can have a potentially destabilizing effect leading to an increased risk of misfolding and aggregation. Multiple software tools exist to predict the effect of single-nucleotide variants on proteins, however, a pipeline integrating these tools while starting from an NGS data output list of variants is lacking.ResultsThe previous version SNPeffect 4.0 (De Baets in Nucleic Acids Res 40(D1):D935–D939, 2011) provided an online database containing pre-calculated variant effects and low-throughput custom variant analysis. Here, we built an automated and parallelized pipeline that analyzes the impact of missense variants on the aggregation propensity and structural stability of proteins starting from the Variant Call Format as input. The pipeline incorporates the AlphaFold Protein Structure Database to achieve high coverage for structural stability analyses using the FoldX force field. The effect on aggregation-propensity is analyzed using the established predictors TANGO and WALTZ. The pipeline focuses solely on the human proteome and can be used to analyze proteome stability/damage in a given sample based on sequencing results.ConclusionWe provide a bioinformatics pipeline that allows structural phenotyping from sequencing data using established stability and aggregation predictors including FoldX, TANGO, and WALTZ; and structural proteome coverage provided by the AlphaFold database. The pipeline and installation guide are freely available for academic users on https://github.com/vibbits/snpeffect and requires a computer cluster.

Construction of non-direct product triangular norms on product lattices

In this paper, we focus on the construction of non-direct product triangular norms on product lattices. First, we give one class of non-direct product triangular norms on more general product lattices, which generalizes the previous results. Subsequently, we provide another class of non-direct product triangular norms on product lattices, which differ from others. Our work gives an alternative answer to an open problem proposed by Jenei and De Baets.

MP18-04 TESTICULAR DEVELOPMENT IN HEALTHY BOYS WITH AND WITHOUT VARICOCELE AND THE INFLUENCE OF VARICOCELE PARAMETERS: LONGITUDINAL FOLLOW UP

You have accessJournal of UrologyCME1 Apr 2023MP18-04 TESTICULAR DEVELOPMENT IN HEALTHY BOYS WITH AND WITHOUT VARICOCELE AND THE INFLUENCE OF VARICOCELE PARAMETERS: LONGITUDINAL FOLLOW UP Gunter de Win, Judith Janssen, Judith Klein, Donald Vaganee, Stefan de Wachter, Karen de Baets, and Stefan van Dongen Gunter de WinGunter de Win More articles by this author , Judith JanssenJudith Janssen More articles by this author , Judith KleinJudith Klein More articles by this author , Donald VaganeeDonald Vaganee More articles by this author , Stefan de WachterStefan de Wachter More articles by this author , Karen de BaetsKaren de Baets More articles by this author , and Stefan van DongenStefan van Dongen More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003238.04AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Main goal of this study was to construct longitudinal testicular growth charts for healthy adolescent boys with and without a varicocele, and evaluate the effect of varicocele grade, peak retrograde flow, and spontaneous reflux in standing position on testicular development. METHODS: Between march 2015 and January 2022, after local ethical approval, 775 adolescent boys were recruited for 6 monthly longitudinal follow up with testicular ultrasound. During each measurement, Tanner stage was assessed and testicular volume was calculated using the Lambert formula. In varicocele boys, the clinical grade was assessed, the peak retrograde flow (PRF) (during Valsalva in supine position) was measured as well as the spontaneous reflux in standing position. Boys with one measurement or with a medical condition (except varicocele) affecting testicular growth were excluded. (Generalized) Linear Mixed models were used to construct longitudinal growth charts and evaluate the effect of varicoceles with low PRF (<38.4 cm/s) and high PRF (>38.4 cm/s) on testicular development. A separate analysis was performed for the different varicocele grades and for the spontaneous reflux in standing position (SR>20 cm/s and SR<20 cm/s). RESULTS: After exclusion we analyzed 857 measurements of 399 healthy boys and 453 measurements of 143 varicocele boys. Varicocele boys tend to have a slower testicular development compared to healthy boys, however only the right testicular volume in varicocele boys with high PRF grew significantly slower compared to healthy boys during pubertal development. At Tanner 5 no significant difference in testicular volume was seen between the 3 groups. Similar results (significant slower right testicular growth) were found for grade 3 varicoceles as well as for SR>20 cm/s. When combing the different parameters only boys with grade 3 varicocele together with a high PRF had a significant slower growth curve, higher testicular volume in the earlier tanner stages and lower at the later tanner stages compared to healthy adolescent boys. The growth curves from those boys with grade 3 varicocele and low PRF and those with grade 2 varicocele with high or low PRF were not significantly different from the healthy boys CONCLUSIONS: The developed growth charts can be used as reference curves in clinical practice. A grade 3 varicocele combined with a high PRF is a negative prognostic factor for testicular development. Source of Funding: No funding © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e223 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Gunter de Win More articles by this author Judith Janssen More articles by this author Judith Klein More articles by this author Donald Vaganee More articles by this author Stefan de Wachter More articles by this author Karen de Baets More articles by this author Stefan van Dongen More articles by this author Expand All Advertisement PDF downloadLoading ...

Fuzzy compatibility relations and pseudo-monometrics: Some correspondences

De Baets and Mesiar in a seminal work showed that Fuzzy Compatibility Relations (FCR) - reflexive and symmetric fuzzy relations - that are also T-transitive w.r.t. an Archimedean t-norm are in a one-to-one correspondence with pseudo-metrics. However, FCRs that are not T-transitive have not merited as much scrutiny. Recently, ternary relations on a set known as betweenness relations and monometrics on the obtained betweenness set, or a B-set, have garnered a lot of attention, especially for their role in decision making and penalty based data aggregation. In this work we show that there is a one-to-one correspondence between FCRs and distance functions, not necessarily metrics, through these betweenness relations. Through interesting correspondences between FCRs and pseudo-monometrics on a given B-set, we also give some pointers to one of the major challenges in this field - that of obtaining pseudo-monometrics on a given B-set.

Index to Titles and Authors/Editors of Books Reviewed

Index to Titles and Authors/Editors of Books Reviewed

THE TWICE UNEARTHED: THE TROPE OF CENSORSHIP AND THE SENSE OF HISTORY

ABSTRACTIn this review essay occasioned by Antoon De Baets's short book Crimes against History, I argue that the censorship of a historical work can produce narrative effects. Drawing on Hayden White's method of examining the literary tropes that shape historical narratives and determine much of their meaning, I suggest that the reception of works (including their censorship and even the murder or repression of history workers) can act like a second layer of tropes. When we tell stories about formerly repressed historians or formerly censored interpretations of the past, we add layers of meaning so that an original work of history that has been “rescued” comes to mean something new. The result is what I call the trope of the twice unearthed, and I suggest that one of its primary effects is to yield a particular moral sense of the meaning of the past. However, any serious consideration of the problem of censorship will show us something troubling: as Leo Strauss once argued, censorship of a less dramatic kind affects us even in liberal democracies because the political, social, and cultural systems in which we live and work act with censorious effect. Censorship is not a “crime against history” but rather one of the forces that creates history in the first place.

Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains.

SUMMARYAcidic activation domains are intrinsically disordered regions of the transcription factors that bind coactivators. The intrinsic disorder and low evolutionary conservation of activation domains have made it difficult to identify the sequence features that control activity. To address this problem, we designed thousands of variants in seven acidic activation domains and measured their activities with a high-throughput assay in human cell culture. We found that strong activation domain activity requires a balance between the number of acidic residues and aromatic and leucine residues. These findings motivated a predictor of acidic activation domains that scans the human proteome for clusters of aromatic and leucine residues embedded in regions of high acidity. This predictor identifies known activation domains and accurately predicts previously unidentified ones. Our results support a flexible acidic exposure model of activation domains in which the acidic residues solubilize hydrophobic motifs so that they can interact with coactivators. A record of this paper’s transparent peer review process is included in the supplemental information.

Preideals in EQ-algebras

EQ-algebras were introduced by Novak (2006) as an algebraic structure of truth values for fuzzy-type theory (FFT). Novák and De Baets (2009) introduced various kinds of EQ-algebras such as good, residuated, and IEQ-algebras. In this paper, we define the notion of (pre)ideal in bounded EQ-algebras (BEQ-algebras) and investigate some properties. Then, we introduce a congruence relation on good BEQ-algebras by using ideals, and then, we solve an open problem in Paad (2019). Moreover, we show that in IEQ-algebras, there is a one-to-one correspondence between congruence relations and the set of ideals. In the following, we characterize the generated preideal in BEQ-algebras, and by using this, we prove that the family of all preideals of a BEQ-algebra is a complete lattice. Then, we show that the family of all preideals of a prelinear IEQ-algebras is a distributive lattice and becomes a Heyting algebra. Finally, we show that we can construct an MV-algebra from the family of all preideals of a prelinear IEQ-algebra.

Constructing some logical algebras from EQ-algebras

EQ-algebras were introduced by Nov?ak in [16] as an algebraic structure of truth values for fuzzy type theory (FTT). Nov?k and De Baets in [18] introduced various kinds of EQ-algebras such as good, residuated, and lattice ordered EQ-algebras. In any logical algebraic structures, by using various kinds of filters, one can construct various kinds of other logical algebraic structures. With this inspirations, by means of fantastic filters of EQ-algebras we construct MV-algebras. Also, we study prelinear EQ-algebras and introduce a new kind of filter and named it prelinear filter. Then, we show that the quotient structure which is introduced by a prelinear filter is a distributive lattice-ordered EQ-algebras and under suitable conditions, is a De Morgan algebra, Stone algebra and Boolean algebra.

Plasma C3d levels as a diagnostic marker for complete complement factor I deficiency

Plasma C3d levels as a diagnostic marker for complete complement factor I deficiency

Dominance on continuous Archimedean triangular norms and generalized Mulholland inequality

As a preceding result, it has been shown that the dominance relation is not transitive on the set of strict triangular norms. This result has been achieved thanks to new results on Mulholland inequality. Recently, Saminger-Platz, De Baets, and De Meyer have introduced the generalized Mulholland inequality which characterizes the dominance on all continuous Archimedean triangular norms in an analogous way as does Mulholland inequality on the strict triangular norms. Based on these new results, the present paper shows that the dominance relation is not transitive on the set of nilpotent triangular norms and, consequently, on the set of continuous Archimedean triangular norms. This result is achieved by introducing a new sufficient condition under which a given function solves the generalized Mulholland inequality and by showing that the set of the functions that solve the inequality is not closed with respect to compositions.

On the Compatibility of a Ternary Relation with a Binary Fuzzy Relation

Recently, De Baets et al. have characterized the fuzzy tolerance relations that a given strict order relation is compatible with. In general, the compatibility of a strict order relation with a binary fuzzy relation guarantees also the compatibility of its associated betweenness relation with that binary fuzzy relation. In this paper, we study the compatibility of an arbitrary ternary relation with a binary fuzzy relation. We prove that this compatibility can be expressed in terms of inclusions of the binary fuzzy relation in the traces of the given ternary relation.

A note on an idempotent transformation of absolutely continuous Archimedean copulas

In De Baets et al. [6] the authors define, for a copula C, an idempotent transformation D[C] which, in some cases, generates new copulas. In this note we give a (negative) answer to a question posed in [6], showing that D[C] is not necessarily a copula when C is an absolutely continuous Archimedean copula.

On the decomposability of aggregation functions on direct products of posets

Based on results concerning equivalences on direct products of sets, a representation of aggregation functions acting on products of ordered structures by means of aggregation functions acting component-wise is obtained and discussed. In particular, t-norms and t-conorms on direct products of bounded lattices are considered, generalizing some earlier results of De Baets and Mesiar.

Finite direct products of EQ-algebras

The aim of this paper is to improve the filters of EQ-algebras proposed by V. Novak and B. De Baets. We give a new class of EQ-algebras, namely multiplicatively relative EQ-algebras, and investigate their properties. Particularly, following the work “The lattice of prefilters of an EQ-algebra,” we give a characterization of filter generated by a nonempty subset of multiplicatively relative EQ-algebras. In addition, we give the concrete forms of Spec(E) and Max(E) in an EQ-algebra E, which are finite direct products of special types of EQ-algebras.

Dissection of Influenza Infection InVivo by Single-Cell RNA Sequencing.

SummaryThe influenza virus is a major cause of morbidity and mortality worldwide. Yet, both the impact of intracellular viral replication and the variation in host response across different cell types remain uncharacterized. Here we used single-cell RNA sequencing to investigate the heterogeneity in the response of lung tissue cells to in vivo influenza infection. Analysis of viral and host transcriptomes in the same single cell enabled us to resolve the cellular heterogeneity of bystander (exposed but uninfected) as compared with infected cells. We reveal that all major immune and non-immune cell types manifest substantial fractions of infected cells, albeit at low viral transcriptome loads relative to epithelial cells. We show that all cell types respond primarily with a robust generic transcriptional response, and we demonstrate novel markers specific for influenza-infected as opposed to bystander cells. These findings open new avenues for targeted therapy aimed exclusively at infected cells.