Integration of OpenCalphad thermo-chemical solver in PLEIADES/ALCYONE fuel performance code

International audienceThe ALCYONE fuel performance code, co-developed by CEA, EDF and Framatome, within the PLEIADES software environment provides a multidimensional modeling for detailed analysis of PWR fuel elements behavior under irradiation [1]. Iodine-Stress Corrosion Cracking is one of the physical phenomena of major interest for cladding design and long term operation of PWRs. In a first step towards I-SCC simulations, the thermochemical code ANGE was integrated in PLEIADES [2]. ANGE, a modified version of SOLGASMIX, enables to compute thermo-chemical equilibria using the TBASE database [3] and associate species description [4] but has some limitations and cannot be used to solve chemical systems based on the Compound Energy Formalism, such as the one proposed in the TAF-ID [5]. Consequently, a robust, efficient and free numerical tool, OpenCalphad [6], was introduced in PLEIADES. In this work, we focus our presentation on the calculation of complex multi-component systems representative of fuel elements behavior under irradiation. From the results of in-reactor power transient calculations (1D-2D-3D), we show that ALCYONE/OpenCalphad is much faster than ALCYONE/ANGE. We note a decrease of the CPU time by almost a factor 4 that can be explained by the OpenCalphad solver itself and by a set of numerical strategies implemented to start a thermodynamic calculation on a mesh node by using another calculated equilibrium as an initial solution. We also show through first results the capacity and the robustness of the ALCYONE/OpenCalphad coupling to do in-reactor power transients calculations (1D-2D-3D) using the TAF-ID. In the latter, the models are more complicated and the possible phases are greater in number than in the TBASE database. For calculations performed in the same conditions as those done with the TBASE database, we note a slight increase of the CPU time that can be reduced by calculating several thermodynamic equilibria simultaneously with a multithread approach.References[1] V. Marelle, et al. New developments in ALCYONE 2.0 fuel performance code, Top Fuel, Boise ID (2016)[2] B. Baurens, et al., J. Nucl. Mater. 452 (2014) 578[3] E.H.P. Cordfuncke, R.J.M. Konings, J. Phase Equilibria 14 [4] (1993)[4] T.M. Besmann, Comprehensive Nucl. Mater. 1.17 (2012)[5] C. Gueneau et al., J. Nucl. Mater. 419 (2011) 147[6] B. Sundman, et al, Integ. Mater. Manuf. Innov. 4 (2015)

Demonstrating MATE and COCOA for Data Discovery

One of the common use cases for data discovery is to enrich a given table with additional columns from related tables inside a data lake. We have recently introduced MATE and COCOA, two systems for joinability discovery and correlation calculation, respectively. By leveraging two novel index structures, a hash-based Super Key Index, and an Order Index, our system is capable of efficiently identifying tables that join on multiple columns and contain relevant features. We show how the data exploration and enrichment process benefits from our index structures by demonstrating MaCo, a unified system on top of open web and large table corpora

Commonsense Knowledge in Sentiment Analysis of Ordinance Reactions for Smart Governance

Smart Governance is an emerging research area which has attracted scientific as well as policy interests, and aims to improve collaboration between government and citizens, as well as other stakeholders. Our project aims to enable lawmakers to incorporate data driven decision making in enacting ordinances. Our first objective is to create a mechanism for mapping ordinances (local laws) and tweets to Smart City Characteristics (SCC). The use of SCC has allowed us to create a mapping between a huge number of ordinances and tweets, and the use of Commonsense Knowledge (CSK) has allowed us to utilize human judgment in mapping. We have then enhanced the mapping technique to link multiple tweets to SCC. In order to promote transparency in government through increased public participation, we have conducted sentiment analysis of tweets in order to evaluate the opinion of the public with respect to ordinances passed in a particular region. Our final objective is to develop a mapping algorithm in order to directly relate ordinances to tweets. In order to fulfill this objective, we have developed a mapping technique known as TOLCS (Tweets Ordinance Linkage by Commonsense and Semantics). This technique uses pragmatic aspects in Commonsense Knowledge as well as semantic aspects by domain knowledge. By reducing the sample space of big data to be processed, this method represents an efficient way to accomplish this task. The ultimate goal of the project is to see how closely a given region is heading towards the concept of Smart City

A comprehensive re-assessment of the association between vitamin D and cancer susceptibility using Mendelian randomization.

Previous Mendelian randomization (MR) studies on 25-hydroxyvitamin D (25(OH)D) and cancer have typically adopted a handful of variants and found no relationship between 25(OH)D and cancer; however, issues of horizontal pleiotropy cannot be reliably addressed. Using a larger set of variants associated with 25(OH)D (74 SNPs, up from 6 previously), we perform a unified MR analysis to re-evaluate the relationship between 25(OH)D and ten cancers. Our findings are broadly consistent with previous MR studies indicating no relationship, apart from ovarian cancers (OR 0.89; 95% C.I: 0.82 to 0.96 per 1 SD change in 25(OH)D concentration) and basal cell carcinoma (OR 1.16; 95% C.I.: 1.04 to 1.28). However, after adjustment for pigmentation related variables in a multivariable MR framework, the BCC findings were attenuated. Here we report that lower 25(OH)D is unlikely to be a causal risk factor for most cancers, with our study providing more precise confidence intervals than previously possible

A Tale of Two Tails: Exploring Stellar Populations in the Tidal Tails of NGC 3256

We have developed an observing program using deep, multiband imaging to probe the chaotic regions of tidal tails in search of an underlying stellar population, using NGC 3256's 400 Myr twin tidal tails as a case study. These tails have different colours of $u - g = 1.05 \pm 0.07$ and $r - i = 0.13 \pm 0.07$ for NGC 3256W, and $u - g = 1.26 \pm 0.07$ and $r - i = 0.26 \pm 0.07$ for NGC 3256E, indicating different stellar populations. These colours correspond to simple stellar population ages of $288^{+11}_{-54}$ Myr and $841^{+125}_{-157}$ Myr for NGC 3256W and NGC 3256E, respectively, suggesting NGC 3256W's diffuse light is dominated by stars formed after the interaction, while light in NGC 3256E is primarily from stars that originated in the host galaxy. Using a mixed stellar population model, we break our diffuse light into two populations: one at 10 Gyr, representing stars pulled from the host galaxies, and a younger component, whose age is determined by fitting the model to the data. We find similar ages for the young populations of both tails, ($195^{-13}_{+0}$ and $170^{-70}_{+44}$ Myr for NGC 3256W and NGC 3256E, respectively), but a larger percentage of mass in the 10 Gyr population for NGC 3256E ($98^{+1}_{-3}\%$ vs $90^{+5}_{-6}\%$). Additionally, we detect 31 star cluster candidates in NGC 3256W and 19 in NGC 2356E, with median ages of 141 Myr and 91 Myr, respectively. NGC 3256E contains several young (< 10 Myr), low mass objects with strong nebular emission, indicating a small, recent burst of star formation.Comment: Accepted for publication in MNRAS. 16 pages, 19 figure

Development of a mouse model for spontaneous oral squamous cell carcinoma in Fanconi anemia

Head and neck squamous cell carcinoma; Mouse model; Oral mucosaCarcinoma de células escamosas de cabeza y cuello; Modelo de ratón; Mucosa oralCarcinoma de cèl·lules escamoses de cap i coll; Model de ratolí; Mucosa oralFanconi anemia (FA) patients frequently develop oral squamous cell carcinoma (OSCC). This cancer in FA patients is diagnosed within the first 3–4 decades of life, very often preceded by lesions that suffer a malignant transformation. In addition, they respond poorly to current treatments due to toxicity or multiple recurrences. Translational research on new chemopreventive agents and therapeutic strategies has been unsuccessful partly due to scarcity of disease models or failure to fully reproduce the disease. Here we report that Fanca gene knockout mice (Fanca-/-) frequently display pre-malignant lesions in the oral cavity. Moreover, when these animals were crossed with animals having conditional deletion of Trp53 gene in oral mucosa (K14cre;Trp53F2-10/F2-10), they spontaneously developed OSCC with high penetrance and a median latency of less than ten months. Tumors were well differentiated and expressed markers of squamous differentiation, such as keratins K5 and K10. In conclusion, Fanca and Trp53 genes cooperate to suppress oral cancer in mice, and Fanca-/-;K14cre;Trp53F2-10/F2-10 mice constitute the first animal model of spontaneous OSCC in FA.This study has been funded by Instituto de Salud Carlos III (ISCIII) through the projects CB16/12/00228/CIBERONC, PI18/00263 and P121/00208 and co-funded by FEDER and the European Union; and grants from the Spanish Fundacion Anemia de Fanconi and Fanconi Anemia Research Fund USA. J.P. was supported by a FEDER co-funded grant (ref PEJ2018-002040-A) from the Ministerio de Ciencia, Innovación y Universidades. J.O. was supported by a FEDER co-funded grant (ref PEJ-2019-TL_BMD-12905) from the Comunidad de Madrid. The funding sources were not involved in study design; in the collection, analysis and interpretation of data; in the writing of the report; and in the decision to submit the article for publication

Development of a mouse model for spontaneous oral squamous cell carcinoma in Fanconi anemia

Altres ajuts: European Regional Development Fund (FEDER); the European Union; the Spanish Fundacion Anemia de Fanconi and Fanconi Anemia Research Fund USA; Comunidad de Madrid (ref PEJ-2019-TL_BMD-12905).Fanconi anemia (FA) patients frequently develop oral squamous cell carcinoma (OSCC). This cancer in FA patients is diagnosed within the first 3-4 decades of life, very often preceded by lesions that suffer a malignant transformation. In addition, they respond poorly to current treatments due to toxicity or multiple recurrences. Translational research on new chemopreventive agents and therapeutic strategies has been unsuccessful partly due to scarcity of disease models or failure to fully reproduce the disease. Here we report that Fanca gene knockout mice (Fanca ) frequently display pre-malignant lesions in the oral cavity. Moreover, when these animals were crossed with animals having conditional deletion of Trp53 gene in oral mucosa (K14cre;Trp53), they spontaneously developed OSCC with high penetrance and a median latency of less than ten months. Tumors were well differentiated and expressed markers of squamous differentiation, such as keratins K5 and K10. In conclusion, Fanca and Trp53 genes cooperate to suppress oral cancer in mice, and Fanca;K14cre;Trp53 mice constitute the first animal model of spontaneous OSCC in FA

Sequence Analysis of Novel Staphylococcus aureus Lineages from Wild and Captive Macaques

Staphylococcus aureus is a widespread and common opportunistic bacterium that can colonise or infect humans as well as a wide range of animals. There are a few studies of both methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) isolated from monkeys, apes, and lemurs, indicating a presence of a number of poorly or unknown lineages of the pathogen. In order to obtain insight into staphylococcal diversity, we sequenced strains from wild and captive individuals of three macaque species (Macaca mulatta, M. assamensis, and M. sylvanus) using Nanopore and Illumina technologies. These strains were previously identified by microarray as poorly or unknown strains. Isolates of novel lineages ST4168, ST7687, ST7688, ST7689, ST7690, ST7691, ST7692, ST7693, ST7694, ST7695, ST7745, ST7746, ST7747, ST7748, ST7749, ST7750, ST7751, ST7752, ST7753, and ST7754 were sequenced and characterised for the first time. In addition, isolates belonging to ST2990, a lineage also observed in humans, and ST3268, a MRSA strain already known from macaques, were also included into the study. Mobile genetic elements, genomic islands, and carriage of prophages were analysed. There was no evidence for novel host-specific virulence factors. However, a conspicuously high rate of carriage of a pathogenicity island harbouring edinB and etD2/etE as well as a higher number of repeat units within the gene sasG (encoding an adhesion factor) than in human isolates were observed. None of the strains harboured the genes encoding Panton–Valentine leukocidin. In conclusion, wildlife including macaques may harbour an unappreciated diversity of S. aureus lineages that may be of clinical relevance for humans, livestock, or for wildlife conservation, given the declining state of many wildlife populations

Sequence Analysis of Novel Staphylococcus aureus Lineages from Wild and Captive Macaques

Staphylococcus aureus is a widespread and common opportunistic bacterium that can colonise or infect humans as well as a wide range of animals. There are a few studies of both methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) isolated from monkeys, apes, and lemurs, indicating a presence of a number of poorly or unknown lineages of the pathogen. In order to obtain insight into staphylococcal diversity, we sequenced strains from wild and captive individuals of three macaque species (Macaca mulatta, M. assamensis, and M. sylvanus) using Nanopore and Illumina technologies. These strains were previously identified by microarray as poorly or unknown strains. Isolates of novel lineages ST4168, ST7687, ST7688, ST7689, ST7690, ST7691, ST7692, ST7693, ST7694, ST7695, ST7745, ST7746, ST7747, ST7748, ST7749, ST7750, ST7751, ST7752, ST7753, and ST7754 were sequenced and characterised for the first time. In addition, isolates belonging to ST2990, a lineage also observed in humans, and ST3268, a MRSA strain already known from macaques, were also included into the study. Mobile genetic elements, genomic islands, and carriage of prophages were analysed. There was no evidence for novel host-specific virulence factors. However, a conspicuously high rate of carriage of a pathogenicity island harbouring edinB and etD2/etE as well as a higher number of repeat units within the gene sasG (encoding an adhesion factor) than in human isolates were observed. None of the strains harboured the genes encoding Panton–Valentine leukocidin. In conclusion, wildlife including macaques may harbour an unappreciated diversity of S. aureus lineages that may be of clinical relevance for humans, livestock, or for wildlife conservation, given the declining state of many wildlife populations