ModelFLOWs-app: data-driven post-processing and reduced order modelling tools

This article presents an innovative open-source software named ModelFLOWs-app, written in Python, which has been created and tested to generate precise and robust hybrid reduced order models (ROMs) fully data-driven. By integrating modal decomposition and deep learning methods in diverse ways, the software uncovers the fundamental patterns in dynamic systems. This acquired knowledge is then employed to enrich the comprehension of the underlying physics, reconstruct databases from limited measurements, and forecast the progression of system dynamics. These hybrid models combine experimental and numerical database, and serve as accurate alternatives to numerical simulations, effectively diminishing computational expenses, and also as tools for optimization and control. The ModelFLOWs-app software has demonstrated in a wide range of applications its great capability to develop reliable data-driven hybrid ROMs, highlighting its potential in understanding complex non-linear dynamical systems and offering valuable insights into various applications. This article presents the mathematical background, review some examples of applications and introduces a short tutorial of ModelFLOWs-app

Antioxidant activity and characterization of whey protein-based beverages: Effect of shelf life and gastrointestinal transit on bioactivity

Whey proteins can exhibit antioxidant activity. The objectives of this study were to formulate model whey based beverages with well-established antioxidants (plant polyphenols, vitamins and astaxanthin) to investigate (1) the antioxidant shelf life over a 24-week period and (2) the antioxidant activity after upper gastrointestinal transit. Pilot scale processing (pasteurization, ultra-high temperature or spray drying) was used to prepare beverages which were representative of current product formats. In vitro gastrointestinal digestion of test samples was performed using the standardised INFOGEST method and antioxidant activity of samples was determined using ABTS, FRAP and ORAC. Results from the antioxidant shelf life study provided evidence that powder products functionality was preserved. Whey beverages (pasteurised or spray dried) increased or maintained antioxidant activity during gastrointestinal transit. Combination of whey with additional antioxidant ingredients increased the bioactivity of formulated products; however, this greater bioactivity was altered after gastrointestinal transit, depending on processing type and antioxidant methodology. Industrial relevance: Whey protein-based antioxidant beverages could benefit the elderly consumer to meet their increased protein requirements and boost their antioxidant status. Consumer's acceptance for whey protein-based beverages often improves with clear formulations. This work generated whey protein-based UHT beverages with greater stability and clarity than pasteurised formulations. A novel combination of plant and marine antioxidants increased antioxidant activity of whey protein-based formulations. Furthermore, to suit export markets this work generated spray dried whey protein formulations that did not alter antioxidant potentialThis work was funded by the Irish Department of Agriculture, Food and the Marine, FIRM 13F354-WheyGSH and 15F604-TOMI). A. R. Corrochano was in receipt of a Teagasc Walsh Fellowship. E. Arranz also received funding from Enterprise Ireland (MF2018-0151) and the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 71365

Approach to the Spanish continental Neogene synthesis and paleoclimatic interpretation

Integrated studies on Neogene geology have been scarce in Spain, but attemps to stratigraphic and sedimentological analysis of continental Tertiary basins have increased considerably lately. The large extent of Neogene basins in Spain, the good quality of the outcrops and the abundance of fossil provide an excellent basis for this kind of studies

Line geometry and camera autocalibration

We provide a completely new rigorous matrix formulation of the absolute quadratic complex (AQC), given by the set of lines intersecting the absolute conic. The new results include closed-form expressions for the camera intrinsic parameters in terms of the AQC, an algorithm to obtain the dual absolute quadric from the AQC using straightforward matrix operations, and an equally direct computation of a Euclidean-upgrading homography from the AQC. We also completely characterize the 6×6 matrices acting on lines which are induced by a spatial homography. Several algorithmic possibilities arising from the AQC are systematically explored and analyzed in terms of efficiency and computational cost. Experiments include 3D reconstruction from real images

The white collar complex is essential for sexual reproduction but dispensable for conidiation and invasive growth in Fusarium verticillioides

Fvwc1 and Fvwc2, orthologues of the wc-1 and wc-2 genes encoding for proteins of the white collar complex (WCC) in Neurospora crassa were cloned from Fusarium verticillioides and lack-of-function wc mutants were obtained by targeted gene disruption. Photo-conidiation was found to be absent in F. verticillioides, on the contrary, the wild type strain produced less conidia under continuous illumination than in the dark. Inactivation of any of the wc genes led to total female sterility, without affecting male fertility or asexual conidiation. No loss in colonization capability/invasive growth of the wc mutants was observed, when assessed on tomato fruits. Both Fvwc1 and Fvwc2 showed constitutive expression in the wild type cultures incubated in the dark and exposure to light caused only negligible increases in their transcription. Both Fvwc1 and Fvwc2 were down-regulated in a ΔFvmat1-2-1 gene disruption mutant, lacking a functional mating type (mat1-2-1) gene, suggesting that the MAT1-2-1 product has a positive regulatory effect on the white collar genes

Recent advances in understanding the roles of whole genome duplications in evolution

Ancient whole-genome duplications (WGDs)—paleopolyploidy events—are key to solving Darwin’s ‘abominable mystery’ of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life

Control of Cyclin C Levels during Development of Dictyostelium

Background: Cdk8 and its partner cyclin C form part of the mediator complex which links the basal transcription machinery to regulatory proteins. The pair are required for correct regulation of a subset of genes and have been implicated in control of development in a number of organisms including the social amoeba Dictyostelium discoideum. When feeding, Dictyostelium amoebae are unicellular but upon starvation they aggregate to form a multicellular structure which develops into a fruiting body containing spores. Cells in which the gene encoding Cdk8 has been deleted fail to enter aggregates due to a failure of early gene expression.Principal Findings: We have monitored the expression levels of cyclin C protein during development and find levels decrease after the multicellular mound is formed. This decrease is triggered by extracellular cAMP that, in turn, is working in part through an increase in intracellular cAMP. The loss of cyclin C is coincident with a reduction in the association of Cdk8 with a high molecular weight complex in the nucleus. Overexpression of cyclin C and Cdk8 lead to an increased rate of early development, consistent with the levels being rate limiting.Conclusions: Overall these results show that both cyclin C and Cdk8 are regulated during development in response to extracellular signals and the levels of these proteins are important in controlling the timing of developmental processes. These findings have important implications for the role of these proteins in controlling development, suggesting that they are targets for developmental signals to regulate gene expression.</p

α-Synuclein impairs macroautophagy: implications for Parkinson’s disease

α-Synuclein impairs autophagosome formation and mislocalizes Atg9 by inhibiting Rab1a

A LOV Protein Modulates the Physiological Attributes of Xanthomonas axonopodis pv. citri Relevant for Host Plant Colonization

Recent studies have demonstrated that an appropriate light environment is required for the establishment of efficient vegetal resistance responses in several plant-pathogen interactions. The photoreceptors implicated in such responses are mainly those belonging to the phytochrome family. Data obtained from bacterial genome sequences revealed the presence of photosensory proteins of the BLUF (Blue Light sensing Using FAD), LOV (Light, Oxygen, Voltage) and phytochrome families with no known functions. Xanthomonas axonopodis pv. citri is a Gram-negative bacterium responsible for citrus canker. The in silico analysis of the X. axonopodis pv. citri genome sequence revealed the presence of a gene encoding a putative LOV photoreceptor, in addition to two genes encoding BLUF proteins. This suggests that blue light sensing could play a role in X. axonopodis pv. citri physiology. We obtained the recombinant Xac-LOV protein by expression in Escherichia coli and performed a spectroscopic analysis of the purified protein, which demonstrated that it has a canonical LOV photochemistry. We also constructed a mutant strain of X. axonopodis pv. citri lacking the LOV protein and found that the loss of this protein altered bacterial motility, exopolysaccharide production and biofilm formation. Moreover, we observed that the adhesion of the mutant strain to abiotic and biotic surfaces was significantly diminished compared to the wild-type. Finally, inoculation of orange (Citrus sinensis) leaves with the mutant strain of X. axonopodis pv. citri resulted in marked differences in the development of symptoms in plant tissues relative to the wild-type, suggesting a role for the Xac-LOV protein in the pathogenic process. Altogether, these results suggest the novel involvement of a photosensory system in the regulation of physiological attributes of a phytopathogenic bacterium. A functional blue light receptor in Xanthomonas spp. has been described for the first time, showing an important role in virulence during citrus canker disease