Parareal in time 3D numerical solver for the LWR Benchmark neutron diffusion transient model

We present a parareal in time algorithm for the simulation of neutron diffusion transient model. The method is made efficient by means of a coarse solver defined with large time steps and steady control rods model. Using finite element for the space discretization, our implementation provides a good scalability of the algorithm. Numerical results show the efficiency of the parareal method on large light water reactor transient model corresponding to the Langenbuch-Maurer-Werner (LMW) benchmark [1]

Integrating Traditional and Scientific Knowledge through Collaborative Natural Science Field Research: Identifying Elements for Success

We discuss two recent projects to examine the role of collaborative environmental fieldwork both in research and in the interactions between academically trained researchers and experienced local residents. The Bidarki Project studied black leather chitons (Katharina tunicata) in the lower Kenai Peninsula, Alaska. Its conclusion that chiton declines are part of a serial decline of intertidal invertebrates drew on collaborative fieldwork, archaeological data, historical records, and interviews with local residents. The Siku-Inuit-Hila Project studied sea ice in Barrow, Alaska; Clyde River, Nunavut; and Qaanaaq, Greenland. Quantitative data from locally maintained observation sites were supplemented by knowledge exchanges among hunters from the communities and by discussion in local working groups to develop an understanding of the physical dynamics and human uses of sea ice at each locale. We conclude that careful planning and preparation, along with the effort to build strong personal relationships, can increase the likelihood that collaborative fieldwork will be productive, enjoyable, and rewarding.Nous discutons de deux récents projets ayant eu pour but d’examiner le rôle d’études environnementales collaboratives sur le terrain, tant sur le plan de la recherche que sur le plan des interactions entre les chercheurs universitaires et les résidents expérimentés des localités visées. Le projet Bidarki se penchait sur les chitons noirs (Katharina tunicata) de la basse péninsule Kenai, en Alaska. La conclusion selon laquelle le déclin des chitons fait partie d’un déclin en série d’invertébrés intertidaux s’appuie sur des études collaboratives sur le terrain, sur des données archéologiques, sur des dossiers historiques ainsi que sur des entrevues de résidents des localités. Pour sa part, le projet Siku-Inuit-Hila a eu comme objectif d’étudier la glace de mer à Barrow, en Alaska; à Clyde River, au Nunavut; et à Qaanaaq, au Groenland. Les données quantitatives provenant de lieux d’observation entretenus localement ont été supplémentées par les échanges de connaissances des chasseurs des collectivités et par les discussions de groupes de travail locaux visant à mieux comprendre la dynamique physique et l’utilisation humaine de la glace de mer à chaque endroit. Nous en concluons que des travaux de planification et de préparation attentionnés, accompagnés d’efforts visant à nouer des liens personnels étroits, peuvent accroître la possibilité que les études collaboratives sur le terrain soient productives, agréables et valorisantes

Ensiling and hydrothermal pretreatment of grass: Consequences for enzymatic biomass conversion and total monosaccharide yields

BACKGROUND: Ensiling may act as a pretreatment of fresh grass biomass and increase the enzymatic conversion of structural carbohydrates to fermentable sugars. However, ensiling does not provide sufficient severity to be a standalone pretreatment method. Here, ensiling of grass is combined with hydrothermal treatment (HTT) with the aim of improving the enzymatic biomass convertibility and decrease the required temperature of the HTT. RESULTS: Grass silage (Festulolium Hykor) was hydrothermally treated at temperatures of 170, 180, and 190°C for 10 minutes. Relative to HTT treated dry grass, ensiling increased the solubilization of dry matter (DM) during HTT and gave increased glucan content, but lower lignin in the insoluble fiber fraction. Ensiling improved glucose yields in the enzymatic hydrolysis of the washed solid fiber fraction at the lower HTT temperatures. At 170°C glucose yield improved from 17 to 24 (w/w)% (45 to 57% cellulose convertibility), and at 180°C glucose yield improved from 22 to 29 (w/w)% (54 to 69% cellulose convertibility). Direct HTT of grass at 190°C gave the same high glucose yield as for grass silage (35 (w/w)% (77% cellulose convertibility)) and improved xylan yields (27% xylan convertibility). The effect of ensiling of grass prior to HTT improved the enzymatic conversion of cellulose for HTT at 170 and 180°C, but the increased glucose release did not make up for the loss of water soluble carbohydrates (WSC) during ensiling. Overall, sugar yields (C6 + C5) were similar for HTT of grass and grass silage at both 170 and 180°C, but at 190°C the overall sugar yield was better for HTT of dry grass. CONCLUSIONS: This study unequivocally establishes that ensiling of grass as a biomass pretreatment method comes with a loss of WSC. The loss of WSC by ensiling is not necessarily compensated for by providing a lower temperature requirement for HTT for high enzymatic monosaccharide release. However, ensiling can be an advantageous storage method prior to grass processing

MRT-basierte Beurteilung der pulmonalen Vaskulatur in der Allgemeinbevölkerung. Die KORA-MRT-Studie

Inhaltszusammenfassung Ziel: Ziel der Studie war es die pulmonale Vaskulatur, sowie das Verhältnis von Truncus pulmonalis und der Aorta ascendens (rTP/AA) zueinander, mithilfe der Magnetresonanztomographie (MRT) zu bestimmen und deren Abhängigkeit von verschiedenen kardiovaskulären Risikofaktoren zu analysieren. Eine besondere Gewichtung lag hierbei auf Diabetes mellitus als Risikofaktor für erweiterte pulmonale Gefäße. Methodik: Der Truncus pulmonalis (TP), die Arteria pulmonalis dextra (Apd) und die Arteria pulmonalis sinistra (Aps) wurden manuell auf 400 MRT Datensätzen ausgemessen und die rTP/AA nachträglich berechnet. Diese Daten wurden für weitere statistische Analysen in Bezug auf kardiovaskuläre Risikofaktoren genutzt und sind im Rahmen der KORA Studie erhoben worden. Ergebnisse: In die finale Auswertung wurden 388 Probanden eingeschlossen, bei denen die Messungen mit hoher Reproduzierbarkeit durchgeführt werden konnten. Erweiterte TP hingen signifikant mit dem BMI (M = 2,59 cm bei Normalgewichtigen vs. M = 2,70 cm ab Adipositas Grad 1) und einem bestehenden aHT zusammen. Ebenso fanden sich erweiterte Pulmonalarterien vermehrt bei Probanden höheren Alters (Apd M = 1,76 cm bei den unter-60-Jährigen vs. Apd M = 1,95 cm bei den über-60-Jährigen). Die rTP/AA erhöhte sich signifikant in Kombination mit dem weiblichen Geschlecht (M = 0,84 bei Frauen vs M = 0,79 bei Männern) und mit Zunahme des BMI (M = 0,81 bei Normalgewichtigen vs. M = 0,92 bei Adipositas Grad 3). Paradoxerweise schien die rTP/AA mit zunehmendem Alter abzunehmen (M = 0,87 Altersgruppe 1 vs. M = 0,79 Altersgruppe 2-4). Fazit: Die MRT eignet sich gut zur Bewertung der pulmonalen Vaskulatur. Es konnten identische Risikofaktoren für erweiterte pulmonale Gefäße ermittelt werden, wie bereits in vorangegangenen Studien, die sich der Computertomographie bedienten. Probanden mit gestörten Glukosestoffwechsel zeigten zwar signifikante Unterschiede bezogen auf die Diameter der pulmonalen Vaskulatur, doch kann keine Aussage darüber getroffen werden, ob Diabetes mellitus selbst oder Faktoren, die diesen begünstigen ursächlich für die Gefäßerweiterungen sind

Les «sales bêtes» de la biodiversité urbaine

La nature en ville est généralement perçue comme bienfaisante et désirable. Certaines espèces peuvent pourtant engendrer des émotions moins positives. Parler de cette nature urbaine moins ou pas du tout souhaitée, mais qui mérite notre intérêt, est important

Multi-Omics Marker Analysis Enables Early Prediction of Breast Tumor Progression

Ductal carcinoma in situ (DCIS) is a preinvasive form of breast cancer with a highly variable potential of becoming invasive and affecting mortality of the patients. Due to the lack of accurate markers of disease progression, many women with detected DCIS are currently overtreated. To distinguish those DCIS cases who are likely to require therapy from those who should be left untreated, there is a need for robust and predictive biomarkers extracted from molecular or genetic profiles. We developed a supervised machine learning approach that implements multi-omics feature selection and model regularization for the identification of biomarker combinations that could be used to distinguish low-risk DCIS lesions from those with a higher likelihood of progression. To investigate the genetic heterogeneity of disease progression, we applied this approach to 40 pure DCIS and 259 invasive breast cancer (IBC) samples profiled with genome-wide transcriptomics, DNA methylation, and DNA copy number variation. Feature selection using the multi-omics Lasso-regularized algorithm identified both known genes involved in breast cancer development, as well as novel markers for early detection. Even though the gene expression-based model features led to the highest classification accuracy alone, methylation data provided a complementary source of features and improved especially the sensitivity of correctly classifying DCIS cases. We also identified a number of repeatedly misclassified DCIS cases when using either the expression or methylation markers. A small panel of 10 gene markers was able to distinguish DCIS and IBC cases with high accuracy in nested cross-validation (AU-ROC = 0.99). The marker panel was not specific to any of the established breast cancer subtypes, suggesting that the 10-gene signature may provide a subtype-agnostic and cost-effective approach for breast cancer detection and patient stratification. We further confirmed high accuracy of the 10-gene signature in an external validation cohort (AU-ROC = 0.95), profiled using distinct transcriptomic assay, hence demonstrating robustness of the risk signature.Peer reviewe

Expanded Consumer Niche Widths May Signal an Early Response to Spatial Protection

Marine management interventions are increasingly being implemented with the explicit goal of rebuilding ocean ecosystems, but early responses may begin with alterations in ecological interactions preceding detectable changes in population-level characteristics. To establish a baseline from which to monitor the effects of spatial protection on reef fish trophic ecology and track future ecosystem-level changes, we quantified temperate reef fish densities, size, biomass, diets and isotopic signatures at nine sites nested within two fished and one five-year old marine protected area (MPA) on the northwest coast of Canada. We calculated rockfish (Sebastes spp.) community and species-specific niche breadth for fished and protected areas based on δ13C and δ15N values. We found that rockfish community niche width was greater inside the MPA relative to adjacent fished reefs due to an expanded nitrogen range, possibly reflecting early changes in trophic interactions following five years of spatial protection. Our data also demonstrated that the MPA had a positive effect on the δ15N signature of rockfish (i.e., trophic position), but the effect of rockfish length on its own was not well-supported. In addition, we found a positive interaction between rockfish length and δ15N signature, such that δ15N signatures of rockfish caught within the MPA increased more rapidly with body size than those caught in fished areas. Differences in rockfish size structure and biomass among fished and unfished areas were not clearly evident. Species of rockfish and lingcod varied in trophic and size responses, indicating that life-history traits play an important role in predicting MPA effects. These results may suggest early changes in trophic behavior of slow-growing rockfish due to predation risk by faster growing higher trophic level predators such as lingcod inside MPAs established on temperate reefs. Consequently, spatial protection may restore both the trophic and behavioral roles of previously fished consumers earlier and in measurable ways sooner than observable changes in abundance and size

Results of a worldwide survey on the currently used histopathological diagnostic criteria for invasive lobular breast cancer

Invasive lobular carcinoma (ILC) represents the second most common subtype of breast cancer (BC), accounting for up to 15% of all invasive BC. Loss of cell adhesion due to functional inactivation of E-cadherin is the hallmark of ILC. Although the current world health organization (WHO) classification for diagnosing ILC requires the recognition of the dispersed or linear non-cohesive growth pattern, it is not mandatory to demonstrate E-cadherin loss by immunohistochemistry (IHC). Recent results of central pathology review of two large randomized clinical trials have demonstrated relative overdiagnosis of ILC, as only ~60% of the locally diagnosed ILCs were confirmed by central pathology. To understand the possible underlying reasons of this discrepancy, we undertook a worldwide survey on the current practice of diagnosing BC as ILC. A survey was drafted by a panel of pathologists and researchers from the European lobular breast cancer consortium (ELBCC) using the online tool SurveyMonkey®. Various parameters such as indications for IHC staining, IHC clones, and IHC staining procedures were questioned. Finally, systematic reporting of non-classical ILC variants were also interrogated. This survey was sent out to pathologists worldwide and circulated from December 14, 2020 until July, 1 2021. The results demonstrate that approximately half of the institutions use E-cadherin expression loss by IHC as an ancillary test to diagnose ILC and that there is a great variability in immunostaining protocols. This might cause different staining results and discordant interpretations. As ILC-specific therapeutic and diagnostic avenues are currently explored in the context of clinical trials, it is of importance to improve standardization of histopathologic diagnosis of ILC diagnosis