Fast feature selection aimed at high-dimensional data via hybrid-sequential-ranked searches

We address the feature subset selection problem for classification tasks. We examine the performance of two hybrid strategies that directly search on a ranked list of features and compare them with two widely used algorithms, the fast correlation based filter (FCBF) and sequential forward selection (SFS). The pro-posed hybrid approaches provide the possibility of efficiently applying any subset evaluator, with a wrap-per model included, to large and high-dimensional domains. The experiments performed show that our two strategies are competitive and can select a small subset of features without degrading the classifica-tion error or the advantages of the strategies under study

Evolutionary feature selection to estimate forest stand variablesusing LiDAR

Light detection and ranging (LiDAR) has become an important tool in forestry. LiDAR-derived models are mostly developed by means of multiple linear regression (MLR) after stepwise selection of predictors. An increasing interest in machine learning and evolutionary computation has recently arisen to improve regression use in LiDAR data processing. Although evolutionary machine learning has already proven to be suitable for regression, evolutionary computation may also be applied to improve parametric models such as MLR. This paper provides a hybrid approach based on joint use of MLR and a novel genetic algorithm for the estimation of the main forest stand variables. We show a comparison between our genetic approach and other common methods of selecting predictors. The results obtained from several LiDAR datasets with different pulse densities in two areas of the Iberian Peninsula indicate that genetic algorithms perform better than the other methods statistically. Preliminary studies suggest that a lack of parametric conditions in field data and possible misuse of parametric tests may be the main reasons for the better performance of the genetic algorithm. This research confirms the findings of previous studies that outline the importance of evolutionary computation in the context of LiDAR analisys of forest data, especially when the size of fieldwork datatasets is reduced.Ministerio de Ciencia y Tecnología TIN2007- 68084-C-00Ministerio de Ciencia y Tecnología TIN2011-28956-C02Xunta de Galicia 09MRU022291PXunta de Galicia CGL2011-30285-C02-02Xunta de Galicia FP7-SME-2011-BS

Influencia del riego deficitario controlado precosecha sobre la calidad de la cereza ´Prime Giant`

El uso de redes de sensores para el manejo del riego deficitario controlado (RDC) en cerezo puede incidir en la mejora de la productividad del agua, calidad de la fruta y en su comportamiento poscosecha, al permitir el conocimiento y control del estado hídrico del suelo y árbol en todo momento. En el primer año de ensayo, el riego deficitario aplicado en precosecha para satisfacer el 85% de las necesidades máximas del cultivo (ETcg) permitió un ahorro de agua del 17% (380 m3 ha-1) respecto al tratamiento control, que se regó al 110% de la ETcg. Este déficit hídrico ligero no afectó a la producción (16,13 t ha-1) e incluso mejoró la calidad del fruto. Así, en el momento de la cosecha (t0) los frutos bajo déficit ligero presentaron matices más rojos y mayor acidez que los de riego completo. Esta mayor acidez no afectó al índice de madurez debido a la compensación por sólidos solubles totales (SST). El carácter de mayor acidez perduró tras 30 días de conservación en frio (t1) y 5 días de simulación de las condiciones de comercialización (t2). Igualmente, los frutos bajo déficit hídrico presentaron una tendencia a menores pérdidas de peso por deshidratación a finales de los periodos de conservación en frio y de simulación de la comercialización.Ministerio de Economía y Competitividad AGL2013-49047-C2-1

A functional IL1RL1 variant regulates corticosteroid-induced sST2 expression in ulcerative colitis

Indexación: Web of Science; Scopus.The ST2/IL33 signalling pathway has been associated with ulcerative colitis (UC). ST2, encoded by the IL1RL1 gene, is expressed as both a membrane-anchored receptor (ST2L) activated by IL33 and as a soluble receptor (sST2) with anti-inflammatory properties. In UC patients, sST2 is further increased by corticosteroid treatment; however, the glucocorticoid-mediated molecular regulation remains unknown. We therefore tested whether genetic variants in the IL1RL1 distal promoter are involved in UC and affect glucocorticoid-mediated ST2 expression. Serum ST2 levels and genetic variants in the IL1RL1 distal promoter were examined by ELISA and PCR sequencing in UC patients receiving corticosteroids. Glucocorticoid-mediated ST2 production was evaluated in intestinal mucosa cultures. Molecular regulation of glucocorticoid-mediated ST2 was assessed by RT-qPCR, ChIP assay and luciferase reporter assay. Dexamethasone effect on ST2 transcript expression was analyzed in leukocytes and related to IL1RL1 variants. Sequencing of a distal IL1RL1 promoter region demonstrated that SNPs rs6543115(C) and rs6543116(A) are associated with increased sST2 in UC patients on corticosteroids. Dexamethasone up-regulated sST2 transcription through interaction with the glucocorticoid-response element (GRE) carrying rs6543115(C) variant. Our data indicate that IL1RL1 SNPs rs6543115(C) confer susceptibility to UC and is contained in the GRE, which may modulate glucocorticoid-induced sST2 expression.https://www.nature.com/articles/s41598-017-10465-

Factors structuring microbial communities in highly impacted coastal marine sediments (Mar Menor lagoon, SE Spain)

Coastal marine lagoons are environments highly vulnerable to anthropogenic pressures such as agriculture nutrient loading or runoff from metalliferous mining. Sediment microorganisms, which are key components in the biogeochemical cycles, can help attenuate these impacts by accumulating nutrients and pollutants. The Mar Menor, located in the southeast of Spain, is an example of a coastal lagoon strongly altered by anthropic pressures, but the microbial community inhabiting its sediments remains unknown. Here, we describe the sediment prokaryotic communities along a wide range of environmental conditions in the lagoon, revealing that microbial communities were highly heterogeneous among stations, although a core microbiome was detected. The microbiota was dominated by Delta- and Gammaproteobacteria and members of the Bacteroidia class. Additionally, several uncultured groups such as Asgardarchaeota were detected in relatively high proportions. Sediment texture, the presence of Caulerpa or Cymodocea, depth, and geographic location were among the most important factors structuring microbial assemblages. Furthermore, microbial communities in the stations with the highest concentrations of potentially toxic elements (Fe, Pb, As, Zn, and Cd) were less stable than those in the non-contaminated stations. This finding suggests that bacteria colonizing heavily contaminated stations are specialists sensitive to change.The study of the microbial communities has been carried out within the project “Metafluidics” and it was funded by the European Union’s framework program Horizon 2020 (LEIT-BIO-2015-685474 to JA). Samplings were supported by the projects MEMM (financed by the Spanish Institute of Oceanography), 19-ESMARES2-ANG (financed by the Spanish Ministry of Ecological Transition and Demographic Challenge), and BIOFOM (Ref. TEC0004869 financed by the Regional Government of Murcia). M-DB and JB-E were supported by a contract within the Program Personal Técnico de Apoyo funded by the Ministerio de Economía y Competitividad. BA-R was also supported by the ACIF fellow of the Generalitat Valenciana government

Dense Gas in Nearby Galaxies: XVII. The Distribution of Ammonia in NGC253, Maffei2 and IC342

The central few 100 pc of galaxies often contain large amounts of molecular gas. The chemical and physical properties of these extragalactic star formation regions differ from those in galactic disks, but are poorly constrained. This study aims to develop a better knowledge of the spatial distribution and kinetic temperature of the dense neutral gas associated with the nuclear regions of three prototypical spiral galaxies, NGC253, IC342, and Maffei2. VLA CnD and D configuration measurements have been made of three ammonia (NH3) inversion transitions. The (J,K)=(1,1) and (2,2) transitions of NH3 were imaged toward IC342 and Maffei2. The (3,3) transition was imaged toward NGC253. The entire flux obtained from single-antenna measurements is recovered for all three galaxies observed. Derived lower limits to the kinetic temperatures determined for the giant molecular clouds in the centers of these galaxies are between 25 and 50K. There is good agreement between the distributions of NH3 and other H2 tracers, such as rare CO isotopologues or HCN, suggesting that NH3 is representative of the distribution of dense gas. The "Western Peak" in IC342 is seen in the (6,6) line but not in lower transitions, suggesting maser emission in the (6,6) transition.Comment: 13 pages, 8 figures, latex format, accepted by A&

Dynamics of the MRSA Population in a Chilean Hospital: a Phylogenomic Analysis (2000-2016)

La diseminación mundial de Staphylococcus aureus resistente a meticilina (SARM) está asociada a la aparición y el establecimiento de clones en zonas geográficas específicas. El clon chileno-cordobés (ChC) (ST5-SCCmecI) ha sido el clon de SARM predominante en Chile desde su primera descripción en 1998, a pesar del informe de otros clones de SARM emergentes en los últimos años. Aquí, caracterizamos la historia evolutiva de MRSA desde 2000 hasta 2016 en un centro de salud terciario chileno utilizando análisis filogenómicos. Secuenciamos 469 aislamientos de SARM recogidos entre 2000 y 2016. Evaluamos las tendencias temporales de los clones circulantes y realizamos una reconstrucción filogenómica para caracterizar la dinámica clonal. Encontramos un aumento significativo en la diversidad y riqueza de tipos de secuencia (STs; Spearman r = 0,8748, P , 0,0001) con un índice de diversidad de Shannon que aumentó de 0,221 en el año 2000 a 1,33 en 2016, y una diversidad efectiva (número de Hill; q = 2) que aumentó de 1,12 a 2,71. El análisis de la tendencia temporal reveló que en el periodo de 2000 a 2003 la mayoría de los aislados (94,2%; n = 98) pertenecían al clon ChC. Sin embargo, desde entonces, la frecuencia del clon ChC ha disminuido con el tiempo, representando el 52% de la colección en el período de 2013 a 2016. Este descenso estuvo acompañado por el aumento de dos linajes emergentes de SARM, ST105-SCCmecII y ST72-SCCmecVI. En conclusión, el clon ChC sigue siendo el linaje MRSA más frecuente, pero este linaje está siendo reemplazado gradualmente por varios clones emergentes, el más importante de los cuales es el clon ST105-SCCmecII. Hasta donde sabemos, éste es el mayor estudio de la dinámica clonal del SARM realizado en Sudamérica. © 2023 Martínez et al.The global dissemination of methicillin-resistant Staphylococcus aureus (MRSA) is associated with the emergence and establishment of clones in specific geographic areas. The Chilean-Cordobes clone (ChC) (ST5-SCCmecI) has been the predominant MRSA clone in Chile since its first description in 1998, despite the report of other emerging MRSA clones in recent years. Here, we characterize the evolutionary history of MRSA from 2000 to 2016 in a Chilean tertiary health care center using phylogenomic analyses. We sequenced 469 MRSA isolates collected between 2000 and 2016. We evaluated the temporal trends of the circulating clones and performed a phylogenomic reconstruction to characterize the clonal dynamics. We found a significant increase in the diversity and richness of sequence types (STs; Spearman r = 0.8748, P , 0.0001) with a Shannon diversity index increasing from 0.221 in the year 2000 to 1.33 in 2016, and an effective diversity (Hill number; q = 2) increasing from 1.12 to 2.71. The temporal trend analysis revealed that in the period 2000 to 2003 most of the isolates (94.2%; n = 98) belonged to the ChC clone. However, since then, the frequency of the ChC clone has decreased over time, accounting for 52% of the collection in the 2013 to 2016 period. This decline was accompanied by the rise of two emerging MRSA lineages, ST105-SCCmecII and ST72-SCCmecVI. In conclusion, the ChC clone remains the most frequent MRSA lineage, but this lineage is gradually being replaced by several emerging clones, the most important of which is clone ST105-SCCmecII. To the best of our knowledge, this is the largest study of MRSA clonal dynamics performed in South America. © 2023 Martínez et al

Dynamics of the Mrsa Population in a Chilean Hospital: a Phylogenomic analysis (2000-2016)

The global dissemination of methicillin-resistant Staphylococcus aureus (MRSA) is associated with the emergence and establishment of clones in specific geographic areas. The Chilean-Cordobes clone (ChC) (ST5-SCCmecI) has been the predominant MRSA clone in Chile since its first description in 1998, despite the report of other emerging MRSA clones in recent years. Here, we characterize the evolutionary history of MRSA from 2000 to 2016 in a Chilean tertiary health care center using phylogenomic analyses. We sequenced 469 MRSA isolates collected between 2000 and 2016. We evaluated the temporal trends of the circulating clones and performed a phylogenomic reconstruction to characterize the clonal dynamics. We found a significant increase in the diversity and richness of sequence types (STs; Spearman r = 0.8748, P \u3c 0.0001) with a Shannon diversity index increasing from 0.221 in the year 2000 to 1.33 in 2016, and an effective diversity (Hill number; q = 2) increasing from 1.12 to 2.71. The temporal trend analysis revealed that in the period 2000 to 2003 most of the isolates (94.2%; n = 98) belonged to the ChC clone. However, since then, the frequency of the ChC clone has decreased over time, accounting for 52% of the collection in the 2013 to 2016 period. This decline was accompanied by the rise of two emerging MRSA lineages, ST105-SCCmecII and ST72-SCCmecVI. In conclusion, the ChC clone remains the most frequent MRSA lineage, but this lineage is gradually being replaced by several emerging clones, the most important of which is clone ST105-SCCmecII. to the best of our knowledge, this is the largest study of MRSA clonal dynamics performed in South America. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health pathogen that disseminates through the emergence of successful dominant clones in specific geographic regions. Knowledge of the dissemination and molecular epidemiology of MRSA in Latin America is scarce and is largely based on small studies or more limited typing techniques that lack the resolution to represent an accurate description of the genomic landscape. We used whole-genome sequencing to study 469 MRSA isolates collected between 2000 and 2016 in Chile providing the largest and most detailed study of clonal dynamics of MRSA in South America to date. We found a significant increase in the diversity of MRSA clones circulating over the 17-year study period. Additionally, we describe the emergence of two novel clones (ST105-SCCmecII and ST72-SCCmecVI), which have been gradually increasing in frequency over time. Our results drastically improve our understanding of the dissemination and update our knowledge about MRSA in Latin America

Kinematics of Galactic Centre clouds shaped by shear-seeded solenoidal turbulence

The Central Molecular Zone (CMZ; the central ~ 500 pc of the Galaxy) is a kinematically unusual environment relative to the Galactic disc, with high velocity dispersions and a steep size-linewidth relation of the molecular clouds. In addition, the CMZ region has a significantly lower star formation rate (SFR) than expected by its large amount of dense gas. An important factor in explaining the low SFR is the turbulent state of the star-forming gas, which seems to be dominated by rotational modes. However, the turbulence driving mechanism remains unclear. In this work, we investigate how the Galactic gravitational potential affects the turbulence in CMZ clouds. We focus on the CMZ cloud G0.253+0.016 (`the Brick'), which is very quiescent and unlikely to be kinematically dominated by stellar feedback. We demonstrate that several kinematic properties of the Brick arise naturally in a cloud-scale hydrodynamics simulation that takes into account the Galactic gravitational potential. These properties include the line-of-sight velocity distribution, the steepened size-linewidth relation, and the predominantly solenoidal nature of the turbulence. Within the simulation, these properties result from the Galactic shear in combination with the cloud's gravitational collapse. This is a strong indication that the Galactic gravitational potential plays a crucial role in shaping the CMZ gas kinematics, and is a major contributor to suppressing the SFR by inducing predominantly solenoidal turbulent modes.Comment: 7 pages, 8 figures; accepted to MNRAS (July 24th 2023