Monomial generators of complete planar ideals

We provide an algorithm that computes a set of generators for any complete ideal in a smooth complex surface. More interestingly, these generators admit a presentation as monomials in a set of maximal contact elements associated to the minimal log-resolution of the ideal. Furthermore, the monomial expression given by our method is an equisingularity invariant of the ideal. As an outcome, we provide a geometric method to compute the integral closure of a planar ideal and we apply our algorithm to some families of complete idealsPeer ReviewedPostprint (author's final draft

Water aging and the quality of organic carbon sources drive niche partitioning of the active bathypelagic prokaryotic microbiome

Due to the scarcity of organic matter (OM) sources in the bathypelagic (1000–4000 m depth), prokaryotic metabolism is believed to be concentrated on particles originating from the surface. However, the structure of active bathypelagic prokaryotic communities and how it changes across environmental gradients remains unexplored. Using a combination of 16S rRNA gene and transcripts sequencing, metagenomics, and substrate uptake potential measurements, here we aimed to explore how water masses aging and the quality of OM influence the structure of the active microbiome, and the potential implications for community function. We found that the relative contribution of taxa with a free-living lifestyle to the active microbiome increased in older water masses that were enriched in recalcitrant OM, suggesting that these prokaryotes may also play a substantial role in the bathypelagic metabolism of vast areas of the ocean. In comparison to particle-associated prokaryotes, free-living prokaryotes exhibited lower potential metabolic rates, and harbored a limited number of twocomponent sensory systems, suggesting they have less ability to sense and respond to environmental cues. In contrast, particle-associated prokaryotes carried genes for particle colonization and carbohydrate utilization that were absent in prokaryotes with a free-living lifestyle. Consistently, we observed that prokaryotic communities inhabiting older waters displayed reduced abilities to colonize particles, and higher capabilities to use complex carbon sources, compared to communities in waters with a higher proportion of labile OM. Our results provide evidence of regionalization of the bathypelagic active prokaryotic microbiome, unveiling a niche partitioning based on the quality of OM.Spanish Ministry of Economy and Competitiveness Science and Innovation through the Consolider-Ingenio programme (project Malaspina 2010 Expedition, ref. CSD2008-00077)Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231Spanish Ministry of Economy and Competitivity grants MAGGY (CTM2017-87736-R), MALASPINOMICS (CTM2011-15461-E), DOREMI (CTM2012-34294), ANIMA (CTM2015-65720-R), MIAU (RTI2018-101025-B-I00

Carbon dioxide (CO2) emissions and adherence to Mediterranean diet in an adult population: the Mediterranean diet index as a pollution level index

Background Research related to sustainable diets is is highly relevant to provide better understanding of the impact of dietary intake on the health and the environment. Aim To assess the association between the adherence to an energy-restricted Mediterranean diet and the amount of CO2 emitted in an older adult population. Design and population Using a cross-sectional design, the association between the adherence to an energy-reduced Mediterranean Diet (erMedDiet) score and dietary CO2 emissions in 6646 participants was assessed. Methods Food intake and adherence to the erMedDiet was assessed using validated food frequency questionnaire and 17-item Mediterranean questionnaire. Sociodemographic characteristics were documented. Environmental impact was calculated through greenhouse gas emissions estimations, specifically CO2 emissions of each participant diet per day, using a European database. Participants were distributed in quartiles according to their estimated CO2 emissions expressed in kg/day: Q1 (= 2.80 kg CO2). Results More men than women induced higher dietary levels of CO2 emissions. Participants reporting higher consumption of vegetables, fruits, legumes, nuts, whole cereals, preferring white meat, and having less consumption of red meat were mostly emitting less kg of CO2 through diet. Participants with higher adherence to the Mediterranean Diet showed lower odds for dietary CO2 emissions: Q2 (OR 0.87; 95%CI: 0.76-1.00), Q3 (OR 0.69; 95%CI: 0.69-0.79) and Q4 (OR 0.48; 95%CI: 0.42-0.55) vs Q1 (reference). Conclusions The Mediterranean diet can be environmentally protective since the higher the adherence to the Mediterranean diet, the lower total dietary CO2 emissions. Mediterranean Diet index may be used as a pollution level index

Systematic Collaborative Reanalysis of Genomic Data Improves Diagnostic Yield in Neurologic Rare Diseases

Altres ajuts: Generalitat de Catalunya, Departament de Salut; Generalitat de Catalunya, Departament d'Empresa i Coneixement i CERCA Program; Ministerio de Ciencia e Innovación; Instituto Nacional de Bioinformática; ELIXIR Implementation Studies (CNAG-CRG); Centro de Investigaciones Biomédicas en Red de Enfermedades Raras; Centro de Excelencia Severo Ochoa; European Regional Development Fund (FEDER).Many patients experiencing a rare disease remain undiagnosed even after genomic testing. Reanalysis of existing genomic data has shown to increase diagnostic yield, although there are few systematic and comprehensive reanalysis efforts that enable collaborative interpretation and future reinterpretation. The Undiagnosed Rare Disease Program of Catalonia project collated previously inconclusive good quality genomic data (panels, exomes, and genomes) and standardized phenotypic profiles from 323 families (543 individuals) with a neurologic rare disease. The data were reanalyzed systematically to identify relatedness, runs of homozygosity, consanguinity, single-nucleotide variants, insertions and deletions, and copy number variants. Data were shared and collaboratively interpreted within the consortium through a customized Genome-Phenome Analysis Platform, which also enables future data reinterpretation. Reanalysis of existing genomic data provided a diagnosis for 20.7% of the patients, including 1.8% diagnosed after the generation of additional genomic data to identify a second pathogenic heterozygous variant. Diagnostic rate was significantly higher for family-based exome/genome reanalysis compared with singleton panels. Most new diagnoses were attributable to recent gene-disease associations (50.8%), additional or improved bioinformatic analysis (19.7%), and standardized phenotyping data integrated within the Undiagnosed Rare Disease Program of Catalonia Genome-Phenome Analysis Platform functionalities (18%)

Co-limitation towards lower latitudes shapes global forest diversity gradients

The latitudinal diversity gradient (LDG) is one of the most recognized global patterns of species richness exhibited across a wide range of taxa. Numerous hypotheses have been proposed in the past two centuries to explain LDG, but rigorous tests of the drivers of LDGs have been limited by a lack of high-quality global species richness data. Here we produce a high-resolution (0.025° × 0.025°) map of local tree species richness using a global forest inventory database with individual tree information and local biophysical characteristics from ~1.3 million sample plots. We then quantify drivers of local tree species richness patterns across latitudes. Generally, annual mean temperature was a dominant predictor of tree species richness, which is most consistent with the metabolic theory of biodiversity (MTB). However, MTB underestimated LDG in the tropics, where high species richness was also moderated by topographic, soil and anthropogenic factors operating at local scales. Given that local landscape variables operate synergistically with bioclimatic factors in shaping the global LDG pattern, we suggest that MTB be extended to account for co-limitation by subordinate drivers

Effective computation of base points of ideals in two-dimensional local rings

© 2018 Elsevier Ltd. We provide an algorithm that allows to describe the minimal log-resolution of an ideal in a smooth complex surface from the minimal log-resolution of its generators. In order to make this algorithm effective we present a modified version of the Newton-Puiseux algorithm that computes the Puiseux decomposition of a product of not necessarily reduced or irreducible elements together with their algebraic multiplicity in each factor.Peer ReviewedPostprint (author's final draft

Adversarial models for priority-based networks

We propose several variations of the adversarial queueing model. The priority model takes into account the case in which the packets can have different priorities, assigned by the adversary at injection time. The variable priority model is an extension of the priority model in which the adversary may change the priority of packets at each time step. The failure and reliable models are designed to cope with dynamic networks in which the adversary controls, under different constraints, the edge failures. We address stability issues in the proposed adversarial models. We show that the set of universally stable networks in the adversarial model remains the same in the priority, variable priority, failure and reliable models. From the point of view of queueing policies we show that several queueing policies that are universally stable in the adversarial model remain so in the priority, failure and reliable models. However, we show that LIS, a universally stable queueing policy in the adversarial model, is not universally stable in any of the other models. Moreover, we show that no greedy queueing policy is universally stable in the variable priority model. Finally we analyze the problem of deciding stability of a given network under a fixed protocol. We provide a characterization of the networks that are stable under FIFO and LIS in the failure model (and therefore in the reliable and priority models). This characterization allows us to show that the stability problem under FIFO and LIS in the failure model can be solved in polynomial time.Postprint (published version

The Complexity of deciding stability under FFS in the adversarial model

In this paper we show the polynomial time decidability of the stability property under FFS in the case that the adversary can solve ties arbitrarily. This results follows from a characterization of the stability property in terms of a family of forbidden subgraphs.Postprint (published version