Montera: A Framework for Efficient Execution of Monte Carlo Codes on Grid Infrastructures

he objective of this work is to improve the performance of Monte Carlo codes on Grid production infrastructures. To do so, the codes and the grid sites are characterized with simple parameters to model their behaviors. Then, a new performance model for grid infrastructures is proposed, and an algorithm that employs this information is described. This algorithm dynamically calculates the number and size of tasks to execute on each site to maximize the performance and reduce makespan. Finally, a newly developed framework called Montera is presented. Montera deals with the execution of Monte Carlo codes in an unattended way, isolating the complexity of the problem from the final user. By employing two fusion Monte Carlo codes as example cases, along with the described characterizations and scheduling algorithm, a performance improvement up to 650 % over current best results is obtained on a real production infrastructure, together with enhanced stability and robustness

Study of the fetal and maternal microbiota in pregnant women with intrauterine growth restriction and its relationship with inflammatory biomarkers: A case-control study protocol (SPIRIT compliant)

In general terms, fetal growth restriction (FGR) is considered the impossibility of achieving the genetically determined potential size. In the vast majority of cases, it is related to uteroplacental insufficiency. Although its origin remains unknown and causes are only known in 30% of cases, it is believed to be related to an interaction of environmental and genetic factors with either a fetal or maternal origin. One hypothesis is that alterations in the gastrointestinal microbiota composition, and thus alteration in the immune response, could play a role in FGR development. We performed an observational, prospective study in a subpopulation affected with FGR to elucidate the implications of this microbiota on the FGR condition. A total of 63 fetuses with FGR diagnosed in the third trimester as defined by the Delphi consensus, and 63 fetuses with fetal growth appropriate for gestational age will be recruited. Obstetric and nutritional information will be registered by means of specific questionnaires. We will collect maternal fecal samples between 30 to 36 weeks, intrapartum samples (maternal feces, maternal and cord blood) and postpartum samples (meconium and new-born feces at 6 weeks of life). Samples will be analyzed in the Department of Biochemistry and Molecular Biology II, Nutrition and Food Technology Institute of the University of Granada (UGR), for the determination of the gastrointestinal microbiota composition and its relationship with inflammatory biomarkers. This study will contribute to a better understanding of the influence of gastrointestinal microbiota and related inflammatory biomarkers in the development of FGR. Trial registration: NCT04047966. Registered August 7, 2019, during the recruitment stage. Retrospectively registered. Ongoing research. Keywords: fetal growth restriction, gastrointestinal microbiota, inflammatory biomarker

Desarrollo de bioherramientas para la remediación de agua y suelos contaminados con cobre

Motivación: La contaminación por cobre es uno de los principales problemas mediambientales en Andalucía. Diversos estudios señalan el estuario conjunto de los ríos Tinto y Odiel como uno de los ecosistemas más contaminados del mundo (Sáinz et al., 2004). El objetivo de este trabajo es diseñar bioherramientas útiles para la descontaminación de suelos y aguas residuales contaminadas con cobre. Métodos: Se ha caracterizado un operón copABCD de resistencia a cobre de la cepa Pseudomonas sp. Az13 , aislada de la rizosfera de leguminosas que crecían de forma espontánea en la zona de Aznalcóllar afectada por el vertido tóxico de 1998 (Dary et al., 2010). Diversos genes de dicho operón se han transferido a rizobios y a plantas, con el propósito de aumentar su resistencia y/o capacidad de acumulación de Cu. Resultados: Con el objetivo de mejorar la respuesta de la simbiosis Sinorhizobium medicae-Medicago truncatula en suelos contaminados con Cu (lo que permitiría su enriquecimiento en nitrógeno), se obtuvo una cepa de S. medicae modificada genéticamente que expresaba parte del operón resistencia a Cu (genes copAB). Las plantas inoculadas con esta bacteria tienen parámetros de crecimiento y nodulación similares en sustratos contaminados con 300 µM de Cu y sin contaminar. El microsimbionte obtenido por ingeniería genética parece dirigir la acumulación de Cu de forma preferente al nódulo. Por otro lado, el gen copC (cuyo producto es capaz de unir dos átomos de Cu) se introdujo en plantas de Arabidopsis thaliana y en raíces pilosas de tabaco. En plantas transgénicas que expresaban dicho gen se incrementó hasta 5 veces su capacidad de acumulación de Cu, si bien su tolerancia al metal disminuía (Rodríguez-Llorente et al., 2012). Por su parte, las raíces transgénicas que expresan el mismo gen se han mostrado como el sistema vivo capaz de acumular los niveles de Cu más altos descritos hasta la fecha, alcanzando valores de 30.000 ppm, sin mostrar síntomas aparentes de toxicidad. Conclusiones: La cepa de S. medicae que expresa los genes copAB tiene un gran potencial como herramienta para la fitoestabilización de Cu utilizando plantas del género Medicago. La expresión de copC tanto en plantas como en raíces permite aumentar su capacidad de acumulación de Cu, haciendo esta herramienta útil en biorremediación de suelos y aguas contaminadas por Cu

Knowledge and perceptions of food sustainability in a Spanish university population

In 2015, the United Nations adopted the 2030 Agenda for Sustainable Development, with 17 Sustainable Development Goals (SDGs) at its core. Besides tackling climate change and the fight to reduce inequality, the SDG number 12 is specifically focused to develop strategies toward food sustainability. The aim of this study, aligned with SDG number 12, was to analyze the level of knowledge and perceptions of food sustainability in a university community from Spain. A descriptive cross-sectional study, based on an online questionnaire, was carried out between July and November 2021 with convenience sampling. The survey included 28 items and was distributed among students, teachers, researchers and administrative staff from a Spanish university. A total of 1,220 participants completed the survey. 70.4% of the respondents heard about the environmental impact of food and more than 50% were aware of the existence of the SDGs. The different aspects related to diet that concerned them the most were food waste, plastic usage, and environmental impact. They reported that a sustainable diet should be mainly based on local and seasonal products and with a low environmental impact as well as no or the minimum food waste. When asked if they were following a sustainable diet, 77% answered affirmatively. Moreover, the food groups more involved in a sustainable diet should be vegetables and fruits, olive oil, legumes, and whole grains. Regarding food waste, 60% of the surveyed population claimed to generate it at home, with the use of leftovers and planning shopping and meals being some of the most important domestic actions to avoid it. Further initiatives must be implemented to increase the level of knowledge as well as to raise the awareness on the importance to translate it into individual and collective actions that allow a shift toward more sustainable practices

Characterisation of the Immunophenotype of Dogs with Primary Immune-Mediated Haemolytic Anaemia

Immune-mediated haemolytic anaemia (IMHA) is reported to be the most common autoimmune disease of dogs, resulting in significant morbidity and mortality in affected animals. Haemolysis is caused by the action of autoantibodies, but the immunological changes that result in their production have not been elucidated.To investigate the frequency of regulatory T cells (Tregs) and other lymphocyte subsets and to measure serum concentrations of cytokines and peripheral blood mononuclear cell expression of cytokine genes in dogs with IMHA, healthy dogs and dogs with inflammatory diseases.19 dogs with primary IMHA, 22 dogs with inflammatory diseases and 32 healthy control dogs.Residual EDTA-anti-coagulated blood samples were stained with fluorophore-conjugated monoclonal antibodies and analysed by flow cytometry to identify Tregs and other lymphocyte subsets. Total RNA was also extracted from peripheral blood mononuclear cells to investigate cytokine gene expression, and concentrations of serum cytokines (interleukins 2, 6 10, CXCL-8 and tumour necrosis factor α) were measured using enhanced chemiluminescent assays. Principal component analysis was used to investigate latent variables that might explain variability in the entire dataset.There was no difference in the frequency or absolute numbers of Tregs among groups, nor in the proportions of other lymphocyte subsets. The concentrations of pro-inflammatory cytokines were greater in dogs with IMHA compared to healthy controls, but the concentration of IL-10 and the expression of cytokine genes did not differ between groups. Principal component analysis identified four components that explained the majority of the variability in the dataset, which seemed to correspond to different aspects of the immune response.The immunophenotype of dogs with IMHA differed from that of dogs with inflammatory diseases and from healthy control dogs; some of these changes could suggest abnormalities in peripheral tolerance that permit development of autoimmune disease. The frequency of Tregs did not differ between groups, suggesting that deficiency in the number of these cells is not responsible for development of IMHA

Interplay of Mre11 Nuclease with Dna2 plus Sgs1 in Rad51-Dependent Recombinational Repair

The Mre11/Rad50/Xrs2 complex initiates IR repair by binding to the end of a double-strand break, resulting in 5′ to 3′ exonuclease degradation creating a single-stranded 3′ overhang competent for strand invasion into the unbroken chromosome. The nuclease(s) involved are not well understood. Mre11 encodes a nuclease, but it has 3′ to 5′, rather than 5′ to 3′ activity. Furthermore, mutations that inactivate only the nuclease activity of Mre11 but not its other repair functions, mre11-D56N and mre11-H125N, are resistant to IR. This suggests that another nuclease can catalyze 5′ to 3′ degradation. One candidate nuclease that has not been tested to date because it is encoded by an essential gene is the Dna2 helicase/nuclease. We recently reported the ability to suppress the lethality of a dna2Δ with a pif1Δ. The dna2Δ pif1Δ mutant is IR-resistant. We have determined that dna2Δ pif1Δ mre11-D56N and dna2Δ pif1Δ mre11-H125N strains are equally as sensitive to IR as mre11Δ strains, suggesting that in the absence of Dna2, Mre11 nuclease carries out repair. The dna2Δ pif1Δ mre11-D56N triple mutant is complemented by plasmids expressing Mre11, Dna2 or dna2K1080E, a mutant with defective helicase and functional nuclease, demonstrating that the nuclease of Dna2 compensates for the absence of Mre11 nuclease in IR repair, presumably in 5′ to 3′ degradation at DSB ends. We further show that sgs1Δ mre11-H125N, but not sgs1Δ, is very sensitive to IR, implicating the Sgs1 helicase in the Dna2-mediated pathway

Identifying future research directions for biodiversity, ecosystem services and sustainability: perspectives from early-career researchers

We aimed to identify priority research questions in the field of biodiversity, ecosystem services and sustainability (BESS), based on a workshop held during the NRG BESS Conference for Early Career Researchers on BESS, and to compare these to existing horizon scanning exercises. This work highlights the need for improved data availability through collaboration and knowledge exchange, which, in turn, can support the integrated valuation and sustainable management of ecosystems in response to global change. In addition, clear connectivity among different research themes in this field further emphasizes the need to consider a wider range of topics simultaneously to ensure the sustainable management of ecosystems for human wellbeing. In contrast to other horizon scanning exercises, our focus was more interdisciplinary and more concerned with the limits of sustainability and dynamic relationships between social and ecological systems. The identified questions could provide a framework for researchers, policy makers, funding agencies and the private sector to advance knowledge in biodiversity and ES research and to develop and implement policies to enable sustainable future development

Experiences of assessment in data and security courses using personal response systems

This paper details an experience report of two interventions which explored the use of a audience response system in summative assessment in two different ways within a conversion Masters degree programme. One course explored students understanding of topics and self-assessment of ability through small multiple-choice quizzes. The other course was based around cyber security and used the audience response system to ensure engagement with the pre-class reading material. Both interventions were designed in an attempt to encourage students to engage more effectively with the material. This paper aims to identify and contrast the ways in which the audience response system was used in assessment in higher education computing science with a view to suggesting key considerations for implementing such an intervention