Research on nonlinear and quantum optics at the photonics and quantum information group of the University of Valladolid

We outline the main research lines in Nonlinear and Quantum Optics of the Group of Photonics and Quantum Information at the University of Valladolid. These works focus on Optical Solitons, Quantum Information using Photonic Technologies and the development of new materials for Nonlinar Optics. The investigations on optical solitons cover both temporal solitons in dispersion managed fiber links and nonparaxial spatial solitons as described by the Nonlinear Helmholtz Equation. Within the Quantum Information research lines of the group, the studies address new photonic schemes for quantum computation and the multiplexing of quantum data. The investigations of the group are, to a large extent, based on intensive and parallel computations. Some associated numerical techniques for the development of the activities described are briefly sketched

Importance sampling and Bayesian model comparison in ecology and evolution

This is the final version. Available on open access from Wiley via the DOI in this record. Data availability statement: All code and data presented in this manuscript are available via Zenodo (Hudson, 2023).Bayesian approaches to the modelling of ecological systems are increasingly popular, but there are competing methods for formal model comparisons. Here, we focus on the task of performing multimodel inference through estimating posterior model weights, which encompasses uncertainties in the choice of competing model structure into the inference outputs. Model-based approaches such as reversible-jump Markov chain Monte Carlo (RJ-MCMC) are flexible and allow multimodel inference, but can be complex to implement and optimise, and so we translate a model-based approach for ecological applications using Importance Sampling to estimate the marginal likelihood of the data given a particular model. This approach allows for model comparison through the estimation of Bayes' Factors or interpretable posterior model probabilities, yielding model weights that facilitate multimodel inference through Bayesian model averaging. We demonstrate Importance Sampling with two case study investigations in animal demography: censused analysis of banded mongoose (Mungos mungo) survival where missing data are uncommon, and capture–mark–recapture analysis of European badger (Meles meles) survival where data are commonly missing. We compare outcomes of the model comparison using the Importance Sampling approach to those obtained through single-model inference approaches using Deviance information criteria and the Watanabe–Akaike information criteria. The results of the Importance Sampling method aligns with RJ-MCMC model comparisons while often being more straightforward to fit and optimise, particularly if the competing models are non-nested.Natural Environment Research Council (NERC)Animal and Plant Health AgencyUniversity of Exete

Selective targeting of activating and inhibitory Smads by distinct WWP2 ubiquitin ligase isoforms differentially modulates TGFβ signalling and EMT

Ubiquitin-dependent mechanisms have emerged as essential regulatory elements controlling cellular levels of Smads and TGFß-dependent biological outputs such as epithelial–mesenchymal transition (EMT). In this study, we identify a HECT E3 ubiquitin ligase known as WWP2 (Full-length WWP2-FL), together with two WWP2 isoforms (N-terminal, WWP2-N; C-terminal WWP2-C), as novel Smad-binding partners. We show that WWP2-FL interacts exclusively with Smad2, Smad3 and Smad7 in the TGFß pathway. Interestingly, the WWP2-N isoform interacts with Smad2 and Smad3, whereas WWP2-C interacts only with Smad7. In addition, WWP2-FL and WWP2-C have a preference for Smad7 based on protein turnover and ubiquitination studies. Unexpectedly, we also find that WWP2-N, which lacks the HECT ubiquitin ligase domain, can also interact with WWP2-FL in a TGFß-regulated manner and activate endogenous WWP2 ubiquitin ligase activity causing degradation of unstimulated Smad2 and Smad3. Consistent with our protein interaction data, overexpression and knockdown approaches reveal that WWP2 isoforms differentially modulate TGFß-dependent transcription and EMT. Finally, we show that selective disruption of WWP2 interactions with inhibitory Smad7 can stabilise Smad7 protein levels and prevent TGFß-induced EMT. Collectively, our data suggest that WWP2-N can stimulate WWP2-FL leading to increased activity against unstimulated Smad2 and Smad3, and that Smad7 is a preferred substrate for WWP2-FL and WWP2-C following prolonged TGFß stimulation. Significantly, this is the first report of an interdependent biological role for distinct HECT E3 ubiquitin ligase isoforms, and highlights an entirely novel regulatory paradigm that selectively limits the level of inhibitory and activating Smads

Leaf Morphology, Taxonomy and Geometric Morphometrics: A Simplified Protocol for Beginners

Taxonomy relies greatly on morphology to discriminate groups. Computerized geometric morphometric methods for quantitative shape analysis measure, test and visualize differences in form in a highly effective, reproducible, accurate and statistically powerful way. Plant leaves are commonly used in taxonomic analyses and are particularly suitable to landmark based geometric morphometrics. However, botanists do not yet seem to have taken advantage of this set of methods in their studies as much as zoologists have done. Using free software and an example dataset from two geographical populations of sessile oak leaves, we describe in detailed but simple terms how to: a) compute size and shape variables using Procrustes methods; b) test measurement error and the main levels of variation (population and trees) using a hierachical design; c) estimate the accuracy of group discrimination; d) repeat this estimate after controlling for the effect of size differences on shape (i.e., allometry). Measurement error was completely negligible; individual variation in leaf morphology was large and differences between trees were generally bigger than within trees; differences between the two geographic populations were small in both size and shape; despite a weak allometric trend, controlling for the effect of size on shape slighly increased discrimination accuracy. Procrustes based methods for the analysis of landmarks were highly efficient in measuring the hierarchical structure of differences in leaves and in revealing very small-scale variation. In taxonomy and many other fields of botany and biology, the application of geometric morphometrics contributes to increase scientific rigour in the description of important aspects of the phenotypic dimension of biodiversity. Easy to follow but detailed step by step example studies can promote a more extensive use of these numerical methods, as they provide an introduction to the discipline which, for many biologists, is less intimidating than the often inaccessible specialistic literature

Fecal microbiota transplant mitigates adverse outcomes in patients colonized with multidrug-resistant organisms undergoing allogeneic hematopoietic cell transplantation

The gut microbiome can be adversely affected by chemotherapy and antibiotics prior to hematopoietic cell transplantation (HCT). This affects graft success and increases susceptibility to multidrug-resistant organism (MDRO) colonization and infection. We performed an initial retrospective analysis of our use of fecal microbiota transplantation (FMT) from healthy donors as therapy for MDRO-colonized patients with hematological malignancy. FMT was performed on eight MDRO-colonized patients pre-HCT (FMT-MDRO group), and outcomes compared with 11 MDRO colonized HCT patients from the same period. At 12 months, survival was significantly higher in the FMT-MDRO group (70% versus 36% p = 0.044). Post-HCT, fewer FMT-MDRO patients required intensive care (0% versus 46%, P = 0.045) or experienced fever (0.29 versus 0.11 days, P = 0.027). Intestinal MDRO decolonization occurred in 25% of FMT-MDRO patients versus 11% non-FMT MDRO patients. Despite the significant difference and statistically comparable patient/transplant characteristics, as the sample size was small, a matched-pair analysis to non-MDRO colonized control cohorts (2:1 matching) was performed. At 12 months, the MDRO group who did not have an FMT had significantly lower survival (36.4% versus 61.9% respectively, p=0.012), and higher non relapse mortality (NRM; 60.2% versus 16.7% respectively, p=0.009) than their paired non-colonized cohort. There was no difference in survival (70% versus 43.4%, p=0.14) or NRM (12.5% versus 31.2% respectively, p=0.24) between the FMT-MDRO group and their paired cohort. Negative outcomes, including mortality associated with MDRO colonization, may be ameliorated by pre-HCT FMT, despite lack of intestinal decolonization. Further work is needed to explore the observed benefit

Tetraspanin (TSP-17) Protects Dopaminergic Neurons against 6-OHDA-Induced Neurodegeneration in <i>C. elegans</i>

Parkinson's disease (PD), the second most prevalent neurodegenerative disease after Alzheimer's disease, is linked to the gradual loss of dopaminergic neurons in the substantia nigra. Disease loci causing hereditary forms of PD are known, but most cases are attributable to a combination of genetic and environmental risk factors. Increased incidence of PD is associated with rural living and pesticide exposure, and dopaminergic neurodegeneration can be triggered by neurotoxins such as 6-hydroxydopamine (6-OHDA). In C. elegans, this drug is taken up by the presynaptic dopamine reuptake transporter (DAT-1) and causes selective death of the eight dopaminergic neurons of the adult hermaphrodite. Using a forward genetic approach to find genes that protect against 6-OHDA-mediated neurodegeneration, we identified tsp-17, which encodes a member of the tetraspanin family of membrane proteins. We show that TSP-17 is expressed in dopaminergic neurons and provide genetic, pharmacological and biochemical evidence that it inhibits DAT-1, thus leading to increased 6-OHDA uptake in tsp-17 loss-of-function mutants. TSP-17 also protects against toxicity conferred by excessive intracellular dopamine. We provide genetic and biochemical evidence that TSP-17 acts partly via the DOP-2 dopamine receptor to negatively regulate DAT-1. tsp-17 mutants also have subtle behavioral phenotypes, some of which are conferred by aberrant dopamine signaling. Incubating mutant worms in liquid medium leads to swimming-induced paralysis. In the L1 larval stage, this phenotype is linked to lethality and cannot be rescued by a dop-3 null mutant. In contrast, mild paralysis occurring in the L4 larval stage is suppressed by dop-3, suggesting defects in dopaminergic signaling. In summary, we show that TSP-17 protects against neurodegeneration and has a role in modulating behaviors linked to dopamine signaling

GlycoForm and Glycologue: two software applications for the rapid construction and display of N-glycans from mammalian sources

<p>Abstract</p> <p>Background</p> <p>The display of <it>N</it>-glycan carbohydrate structures is an essential part of glycoinformatics. Several tools exist for building such structures graphically, by selecting from a palette of symbols or sugar names, or else by specifying a structure in one of the chemical naming schemes currently available.</p> <p>Findings</p> <p>In the present work we present two tools for displaying <it>N</it>-glycans found in the mammalian CHO (Chinese hamster ovary) cell line, both of which take as input a 9-digit identifier that uniquely defines each structure. The first of these, GlycoForm, is designed to display a single structure automatically from an identifier entered by the user. The display is updated in real time, using symbols for the sugar residues, or in text-only form. Structures can be added to a library, which is recorded in a preference file and loaded automatically at start. Individual structures can be saved in a variety of bitmap image formats. The second program, Glycologue, reads a file containing columnar data of nine-digit codes, which can be displayed on-screen and printed at high resolution.</p> <p>Conclusion</p> <p>A key advantage of both programs is the speed and facility with which carbohydrate structures can be drawn. It is anticipated that these programs will be useful to glycobiologists, systems biologists and biotechnologists interested in <it>N</it>-glycosylation systems in mammalian cells.</p

The chronic pain coping inventory: Confirmatory factor analysis of the French version

BACKGROUND: Coping strategies are among the psychosocial factors hypothesized to contribute to the development of chronic musculoskeletal disability. The Chronic Pain Coping Inventory (CPCI) was developed to assess eight behavioral coping strategies targeted in multidisciplinary pain treatment (Guarding, Resting, Asking for Assistance, Task Persistence, Relaxation, Exercise/Stretch, Coping Self-Statements and Seeking Social Support). The present study had two objectives. First, it aimed at measuring the internal consistency and the construct validity of the French version of the CPCI. Second, it aimed to verify if, as suggested by the CPCI authors, the scales of this instrument can be grouped according to the following coping families: Illness-focused coping and Wellness-focused coping. METHOD: The CPCI was translated into French with the forward and backward translation procedure. To evaluate internal consistency, Cronbach's alphas were computed. Construct validity of the inventory was estimated through confirmatory factor analysis (CFA) in two samples: a group of 439 Quebecois workers on sick leave in the sub-acute stage of low back pain (less than 84 days after the work accident) and a group of 388 French chronic pain patients seen in a pain clinic. A CFA was also performed to evaluate if the CPCI scales were grouped into two coping families (i.e. Wellness-focused and Illness-focused coping). RESULTS: The French version of the CPCI had adequate internal consistency in both samples. The CFA confirmed the eight-scale structure of the CPCI. A series of second-order CFA confirmed the composition of the Illness-focused family of coping (Guarding, Resting and Asking for Assistance). However, the composition of the Wellness-focused family of coping (Relaxation, Exercise/Stretch, Coping Self-Statements and Seeking Social Support) was different than the one proposed by the authors of the CPCI. Also, a positive correlation was observed between Illness and Wellness coping families. CONCLUSION: The present study indicates that the internal consistency and construct validity of the French version of the CPCI were adequate, but the grouping and labeling of the CPCI families of coping are debatable and deserve further analysis in the context of musculoskeletal and pain rehabilitation

Stress related epigenetic changes may explain opportunistic success in biological invasions in Antipode mussels

Different environmental factors could induce epigenetic changes, which are likely involved in the biological invasion process. Some of these factors are driven by humans as, for example, the pollution and deliberate or accidental introductions and others are due to natural conditions such as salinity. In this study, we have analysed the relationship between different stress factors: time in the new location, pollution and salinity with the methylation changes that could be involved in the invasive species tolerance to new environments. For this purpose, we have analysed two different mussels’ species, reciprocally introduced in antipode areas: the Mediterranean blue mussel Mytilus galloprovincialis and the New Zealand pygmy mussel Xenostrobus securis, widely recognized invaders outside their native distribution ranges. The demetylathion was higher in more stressed population, supporting the idea of epigenetic is involved in plasticity process. These results can open a new management protocols, using the epigenetic signals as potential pollution monitoring tool. We could use these epigenetic marks to recognise the invasive status in a population and determine potential biopollutants

Demonstration of the event identification capabilities of the NEXT-White detector

In experiments searching for neutrinoless double-beta decay, the possibility of identifying the two emitted electrons is a powerful tool in rejecting background events and therefore improving the overall sensitivity of the experiment. In this paper we present the first measurement of the efficiency of a cut based on the different event signatures of double and single electron tracks, using the data of the NEXT-White detector, the first detector of the NEXT experiment operating underground. Using a 228Th calibration source to produce signal-like and background-like events with energies near 1.6 MeV, a signal efficiency of 71.6 ± 1.5 stat± 0.3 sys% for a background acceptance of 20.6 ± 0.4 stat± 0.3 sys% is found, in good agreement with Monte Carlo simulations. An extrapolation to the energy region of the neutrinoless double beta decay by means of Monte Carlo simulations is also carried out, and the results obtained show an improvement in background rejection over those obtained at lower energies. [Figure not available: see fulltext.