Biclustering meets triadic concept analysis

Biclustering numerical data became a popular data-mining task at the beginning of 2000’s, especially for gene expression data analysis and recommender systems. A bicluster reflects a strong association between a subset of objects and a subset of attributes in a numerical object/attribute data-table. So-called biclusters of similar values can be thought as maximal sub-tables with close values. Only few methods address a complete, correct and non-redundant enumeration of such patterns, a well-known intractable problem, while no formal framework exists. We introduce important links between biclustering and Formal Concept Analysis (FCA). Indeed, FCA is known to be, among others, a methodology for biclustering binary data. Handling numerical data is not direct, and we argue that Triadic Concept Analysis (TCA), the extension of FCA to ternary relations, provides a powerful mathematical and algorithmic framework for biclustering numerical data. We discuss hence both theoretical and computational aspects on biclustering numerical data with triadic concept analysis. These results also scale to n-dimensional numerical datasets.     

A fast compound algorithm for mining generators,closed itemsets,and computing links between equivalence classes

In pattern mining and association rule mining, there is a variety of algorithms for mining frequent closed itemsets (FCIs) and frequent generators (FGs), whereas a smaller part further involves the precedence relation between FCIs. The interplay of these three constructs and their joint computation have been studied within the formal concept analysis (FCA) field yet none of the proposed algorithms is scalable. In frequent pattern mining, at least one suite of efficient algorithms has been designed that exploits basically the same ideas and follows the same overall computational schema. Based on an in-depth analysis of the aforementioned interplay that is rooted in a fundamental duality from hypergraph theory, we propose a new schema that should enable for a more parsimonious computation. We exemplify the new schema in the design of Snow-Touch, a concrete FCI/FG/precedence miner that reuses an existing algorithm, Charm, for mining FCIs, and completes it with two original methods for mining FGs and precedence, respectively. The performance of Snow-Touch and of its closest competitor, Charm-L, were experimentally compared using a large variety of datasets. The outcome of the experimental study suggests that our method outperforms Charm-L on dense data while on sparse one the trend is reversed. Furthermore, we demonstrate the usefulness of our method and the new schema through an application to the analysis of a genome dataset. The initial results reported here confirm the capacity of the method to focus on significant associations.     

Assessing T-Cell Immunity in Kidney Transplant Recipients with Absent Antibody Production after a 3rd Dose of the mRNA-1273 Vaccine

The vulnerable population of kidney transplant recipients (KTRs) are low responders to COVID-19 vaccines, so specific immune surveillance is needed. The interferon-gamma (IFN-γ) release assay (IGRA) is effective in assessing T cell-mediated immunity. We assessed SARS-CoV-2-directed T cell responses in KTRs with absent antibody production after a third dose of the mRNA-1273 vaccine, using two different IGRAs. A cohort of 57 KTRs, who were actively followed up, received a third dose of the mRNA-1273 vaccine. After the evaluation of humoral immunity to SARS-CoV-2, 14 seronegative patients were tested with two commercial IGRAs (SD Biosensor and Euroimmun). Out of 14 patients, one and three samples were positive by IGRAs with Euroimmun and SD Biosensor, respectively. The overall agreement between the two assays was 85.7% (κ = 0.444). In addition, multivariate linear regression analysis showed no statistically significant association between the IFN-γ concentration, and the independent variables analyzed (age, gender, years since transplant, total lymphocytes cells/mcl, CD3+ cells/mcl, CD3+ CD4+ cells/mcl, CD3+ CD8+ cells/mcl, CD19+ cells/mcl, CD3-CD16+CD56+ cells/mcl) (p > 0.01). In a vulnerable setting, assessing cellular immune response to complement the humoral response may be advantageous. Since the two commercial IGRAs showed a good agreement on negative samples, the three discordant samples highlight the need for further investigations.     

Germin-like protein Cit s 1 and profilin Cit s 2 are major allergens in orange (Citrus sinensis) fruits

Oranges are clinically relevant allergenic foods. To date, orange allergens have not been characterized in detail. The study is aimed at analyzing the sensitization profile in orange-sensitized subjects with and without clinical allergy, and to identify orange allergens. Fifty-six sensitized subjects with self-reported reactions to orange were grouped into reactors (anaphylaxis or multiple episodes of immediate reactions and/or positive challenge tests) and non-reactors (negative open food challenge tests). Allergens were characterized by IgE immunoblotting, N-terminal sequencing, IgE-inhibition assays, and mediator release assays were performed to determine the allergenic potency of orange profilin. Of 56 subjects, 23 were classified as orange allergic showing mainly an oral allergy syndrome. Of 23 subjects classified as orange allergic, 22 were sensitized to profilin, Cit s 2. In patients with mono-sensitization to profilin in vitro histamine releases up to 75% from basophils were induced using orange extract and purified plant profilins. Of the allergic patients 78% were sensitized to germin-like protein, Cit s 1. Both allergens showed retained IgE reactivity in heat-processed orange juice. Interestingly, subjects with and without clinical allergy showed a comparable sensitization profile. Profilin and germin-like proteins are major orange allergens. The potential clinical relevance of orange profilin was indicated by its strong capacity to release histamine from basophils. However, a predominant sensitization to both allergens in subjects without symptoms also indicates a high frequency of clinically insignificant sensitization.     

Improved design of a multifeedback bandpass filter

The multifeedback second-order RC active filter is of considerable interest and has been studied extensively. Nevertheless, its behaviour has been in general analysed without making allowance for the non-ideal characteristics of the embedded operational amplifier (OA). This paper presents some formulas that can be used for improving the design of such a filter. They were derived on the basis of an OA model that takes into account both input and output resistances, unity-gain frequency, and dc-gain. They make use of algorithms characterized by a relative simplicity and quite a good approximation. Their application makes the filter easy to tune and usable for high frequencies, while at the same time the dependence of the Q-value on temperature variations in the operational amplifier is minimized. Two universal graphs are given in the text. They simplify the use of the new formulas in obtaining the analysis and the synthesis of the multifeedback second order filter. Experimental results that check the validity of the proposed formulas are presented.     

Mycotoxin occurrence in beer produced in several European countries

The occurrence of ochratoxin A, trichothecenes, fumonisins and aflatoxins in a sample of 106 beers produced in several European countries, was investigated. The analyses were conducted using high-performance liquid chromatography with fluorimetric detection for ochratoxin A and aflatoxins, gas-chromatography and high-performance liquid chromatography, both coupled with mass spectrometer, for trichothecenes and fumonisins, respectively. Aflatoxins were not detected in any samples, whereas ochratoxin A, deoxynivalenol and fumonisins were found in a relatively high number of samples. Their presence was at low levels in all samples; however, some differences were observed between the European countries. As regards ochratoxin A, beer samples from southern Europe showed levels always lower than 0.040 μg l^?1, while the samples from other European countries showed significantly higher values, up to 0.189 μg l^?1 (P < 0.001). For fumonisins, the levels of Italian beers were significantly higher compared to the samples from other countries (P = 0.006).     

Kinetic and reaction mechanisms of calcium bisulfite catalytic oxidation

In this paper, the oxidation of calcium bisulfite in the presence of ferrous ions as a catalyst is studied in a laboratory scale apparatus at a fixed oxygen partial pressure (21.3 kPa) and at a temperature of 45 °C. The analysis of the experimental results, carried out by using the theory of mass transfer with chemical reaction, indicates that the slow reaction regime has been explored, and the transition from the kinetic to the diffusional subregime identified. A kinetic analysis allows to develop a reaction rate equation, assuming that the bisulfite oxidation in the presence of ferrous ions follows a parallel reaction mechanism; the resulting overall reaction rate has been found to be of first order with respect to ferrous ion concentration and of three halves with respect to bisulfite concentration. Moreover, the catalytic effect of ferrous ions has been compared with that of manganese ions previously studied, showing that ferrous is a catalyst more active than manganese.     

Solving job shop scheduling with setup times through constraint-based iterative sampling: an experimental analysis

This paper presents a heuristic algorithm for solving a job-shop scheduling problem with sequence dependent setup times and min/max separation constraints among the activities (SDST-JSSP/max). The algorithm relies on a core constraint-based search procedure, which generates consistent orderings of activities that require the same resource by incrementally imposing precedence constraints on a temporally feasible solution. Key to the effectiveness of the search procedure is a conflict sampling method biased toward selection of most critical conflicts and coupled with a non-deterministic choice heuristic to guide the base conflict resolution process. This constraint-based search is then embedded within a larger iterative-sampling search framework to broaden search space coverage and promote solution optimization. The efficacy of the overall heuristic algorithm is demonstrated empirically both on a set of previously studied job-shop scheduling benchmark problems with sequence dependent setup times and by introducing a new benchmark with setups and generalized precedence constraints.