The Phylogenetic Likelihood Library

[Abstract] We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2–10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required).DFG, German Research Foundation; STA/860-4. F.I.-C.DFG, German Research Foundation; STA/860-3DFG, German Research Foundation; STA/860-2. L.-T.N.University of Vienna; I059-NAustrian Science Fund; I760-B1

ViCTree: an automated framework for taxonomic classification from protein sequences

Motivation: The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualisation tool that enables the tree to be explored interactively in the context of pairwise distance data. Results: To demonstrate utility, ViCTree was applied to subfamily Densovirinae of family Parvoviridae. This led to the identification of six new species of insect virus. Availability: ViCTree is open-source and can be run on any Linux- or Unix-based computer or cluster. A tutorial, the documentation and the source code are available under a GPL3 license, and can be accessed at http://bioinformatics.cvr.ac.uk/victree_web/

Evaluación de tres soluciones nutritivas para el cultivo de lechuga (Lactuca sativa L.) en el sistema hidropónico popular de raíz flotante.

Resumen (Spanish, English)122 p.Se evaluó el efecto de distintos contenidos de N, Mg, y Fe en la solución nutritiva Huerta Hidropónica Popular (HHP), las que fueron denominadas para el estudio como: HHP (254,5 ppm de N-NO3; 30,801 ppm de N-NH4; 76,348 ppm de Mg y 0,254 ppm de Fe) y las soluciones derivadas de la misma HHP, (222,3 ppm de N-NO3;30,801 ppm de N-NH4; 30,348 ppm de Mg y 0,254 ppm de Fe) y HHP2 (222,3ppm de N-NO3; 30801 ppm de N-NH4; 30,348 ppm de Mg y 1,5 ppm de Fe), sobre parámetros de rendimiento, nutrición y calidad de lechugas tipo mantecosa (Lactusa sartiva L. var. capitata cv. “Española”) producidas en el sistema hidropónico popular de raíz flotante. Este estudio se realizó bajo invernadero, en la Estación Experimental Panguilemo de la universidad de Talca (35º26´L.S.; 71º4º´L.W. y 90 m.s.n.m.), entre los meses de agosto y octubre de 1995. La menor disponibilidad de N en las soluciones HHP1 y Hhp2 permitieron una mayor eficiencia del uso del agua en la etapa de activo crecimiento, roseta. La tasa de asimilación neta, por su parte, no se vio afectada por la distinta disponibilidad de N, Mg, y Fe en cada solución nutritiva. Al considerar el rendimiento similar, junto al adecuado estado nutricional de las plantas obteniendo en las tres soluciones nutritivas estudiadas y pese a que la solución HHP1 resultó ser la más económica, la alidad superior otorgada al cultivo por la solución HHP2, hacen de ésta una alternativa atractiva, de menos costo y sugerible para ser empleada en hidroponía popular, presumiblemente en todas aquellas hortalizas preferidas por sus hojas, y en reemplazo de la solución HHP hasta hoy utilizada. Por otra parte, la exclusión de la sal fertilizante Nitrato de Magnesio (MgNO3) de la solución nutritiva HHP es relevante, sin embargo, debería ir acompañada de un aumento en la concentración de Fe pues mejora la calidad de la lechuga. La disminución en los costos de solución nutritiva en hidroponía popular es significativo al momento de considerar el objetivo final de esta técnica de cultivo

Latin Americans and Caribbeans in Europe. A cross-country analysis

With the beginning of the 21st century, there has been an acceleration of migratory flows from Latin America and the Caribbean (LAC) to Europe. As a result, and despite the negative impact of the economic crisis, 4.6 million Latin American and Caribbean immigrants reside in Europe, half of them in Spain. This article analyses the recent evolution of these migratory flows, their territorial distribution, and their demographic profiles according to the 2011 European census data disseminated by a new tool -the Census Hub- implemented by the European Statistical System. The analysis shows the existence of a high LAC immigrant concentration in Spain and in certain European cities, a marked young and feminized demographic profile, a great variety of educational levels and a different insertion in each European labour market, although many LAC immigrants work in low-skill occupations, being overqualified and underemployed in most of the countries

Social times, reproduction and social inequality at work : contrasts and comparative perspectives between countries

Production of INCASI Project H2020-MSCA-RISE-2015 GA 691004If the focus is placed specifically on the problem of work and family, the daily life of people and their use of time are a main problem. This time is expressed in both freely available time, which is related to activities, and time of the productive and reproductive sphere. This chapter considers work in a broad sense and takes into account the sexual division of labour. Specifically, this chapter will explore transformations in time use and social inequality in unpaid work. For this purpose, a comparative analysis of time-use surveys will be used, analysing the time spent, and the time dedicated to household chores in Chile, Argentina, Uruguay and Spain. From an analytical viewpoint, the analysis will place social reproduction at the centre of the socio-economic system, showing that the economic crisis has affected women and men differently, and that in both Europe and Latin America the family pattern is being replaced by a dominant family model of a male provider and a double presence of women. The large-scale incorporation of women into the labour market has emphasised the role that women assume in the domestic sphere perpetuating gender segregation in employment and in domestic and care work

Riesgo quirúrgico tras resección pulmonar anatómica en cirugía torácica. Modelo predictivo a partir de una base de datos nacional multicéntrica

Introduction: the aim of this study was to develop a surgical risk prediction model in patients undergoing anatomic lung resections from the registry of the Spanish Video-Assisted Thoracic Surgery Group (GEVATS). Methods: data were collected from 3,533 patients undergoing anatomic lung resection for any diagnosis between December 20, 2016 and March 20, 2018. We defined a combined outcome variable: death or Clavien Dindo grade IV complication at 90 days after surgery. Univariate and multivariate analyses were performed by logistic regression. Internal validation of the model was performed using resampling techniques. Results: the incidence of the outcome variable was 4.29% (95% CI 3.6-4.9). The variables remaining in the final logistic model were: age, sex, previous lung cancer resection, dyspnea (mMRC), right pneumonectomy, and ppo DLCO. The performance parameters of the model adjusted by resampling were: C-statistic 0.712 (95% CI 0.648-0.750), Brier score 0.042 and bootstrap shrinkage 0.854. Conclusions: the risk prediction model obtained from the GEVATS database is a simple, valid, and reliable model that is a useful tool for establishing the risk of a patient undergoing anatomic lung resection

Association of a single nucleotide polymorphism combination pattern of the Klotho gene with non-cardiovascular death in patients with chronic kidney disease

Chronic kidney disease (CKD) is associated with an elevated risk of all-cause mortality, with cardiovascular death being extensively investigated. However, non-cardiovascular mortality represents the biggest percentage, showing an evident increase in recent years. Klotho is a gene highly expressed in the kidney, with a clear influence on lifespan. Low levels of Klotho have been linked to CKD progression and adverse outcomes. Single nucleotide polymorphisms (SNPs) of the Klotho gene have been associated with several diseases, but studies investigating the association of Klotho SNPs with noncardiovascular death in CKD populations are lacking. The main aim of this study was to assess whether 11 Klotho SNPs were associated with non-cardiovascular death in a subpopulation of the National Observatory of Atherosclerosis in Nephrology (NEFRONA) study (n ¼ 2185 CKD patients). After 48 months of follow-up, 62 cardiovascular deaths and 108 non-cardiovascular deaths were recorded. We identified a high non-cardiovascular death risk combination of SNPs corresponding to individuals carrying the most frequent allele (G) at rs562020, the rare allele (C) at rs2283368 and homozygotes for the rare allele (G) at rs2320762 (rs562020 GG/AG þ rs2283368 CC/CT þ rs2320762 GG). Among the patients with the three SNPs genotyped (n ¼ 1016), 75 (7.4%) showed this combination. Furthermore, 95 (9.3%) patients showed a low-risk combination carrying all the opposite genotypes (rs562020 AA þ rs2283368 TT þ rs2320762 GT/TT). All the other combinations [n ¼ 846 (83.3%)] were considered as normal risk. Using competing risk regression analysis, we confirmed that the proposed combinations are independently associated with a higher fhazard ratio [HR] 3.28 [confidence interval (CI) 1.51-7.12]g and lower [HR 6 × 10- (95% CI 3.3 × 10--1.1 × 10-)] risk of suffering a non-cardiovascular death in the CKD population of the NEFRONA cohort compared with patients with the normal-risk combination. Determination of three SNPs of the Klotho gene could help in the prediction of non-cardiovascular death in CKD

Grupo español de cirugía torácica asistida por videoimagen: método, auditoría y resultados iniciales de una cohorte nacional prospectiva de pacientes tratados con resecciones anatómicas del pulmón

Introduction: our study sought to know the current implementation of video-assisted thoracoscopic surgery (VATS) for anatomical lung resections in Spain. We present our initial results and describe the auditing systems developed by the Spanish VATS Group (GEVATS). Methods: we conducted a prospective multicentre cohort study that included patients receiving anatomical lung resections between 12/20/2016 and 03/20/2018. The main quality controls consisted of determining the recruitment rate of each centre and the accuracy of the perioperative data collected based on six key variables. The implications of a low recruitment rate were analysed for '90-day mortality' and 'Grade IIIb-V complications'. Results: the series was composed of 3533 cases (1917 VATS; 54.3%) across 33 departments. The centres' median recruitment rate was 99% (25-75th:76-100%), with an overall recruitment rate of 83% and a data accuracy of 98%. We were unable to demonstrate a significant association between the recruitment rate and the risk of morbidity/mortality, but a trend was found in the unadjusted analysis for those centres with recruitment rates lower than 80% (centres with 95-100% rates as reference): grade IIIb-V OR=0.61 (p=0.081), 90-day mortality OR=0.46 (p=0.051). Conclusions: more than half of the anatomical lung resections in Spain are performed via VATS. According to our results, the centre's recruitment rate and its potential implications due to selection bias, should deserve further attention by the main voluntary multicentre studies of our speciality. The high representativeness as well as the reliability of the GEVATS data constitute a fundamental point of departure for this nationwide cohort

Policy and Practice in Language Support for Newly Arrived Migrant Children in Ireland and Spain

To cite this article: Rosa M Rodríguez-Izquierdo & Merike Darmody (2017): Policy and Practice in Language Support for Newly Arrived Migrant Children in Ireland and Spain, British Journal of Educational Studies, DOI: 10.1080/00071005.2017.1417973Over the last decades migration across Europe has continued to increase. Consequently, the issue of offering appropriate educational support for migrant students has been extensively debated across Europe and further afield, especially in countries with a history of immigration. However, less is known about how education systems in the ¿new¿ immigration countries have responded to the needs of newly arrived migrants (NAMs). While various research and policy documents have highlighted the importance of proficiency in the language of instruction for social and academic outcomes of migrant children and youth: how language support is provided varies significantly from one jurisdiction to another. This article focuses on language support measures set up for migrant students in statefunded schools in the Republic of Ireland and Spain ¿ both multilingual countries with more than one official language and with heterogeneous migrant population. In both countries, there is also a mismatch between an increasingly diverse student cohort and a homogenous teacher population.. Reviewing educational policy and practice in these jurisdictions in the areas of language support for migrants and how diversity is addressed in initial teacher education, the paper seeks to contribute to the debate on how to address the needs of migrant students in multi-lingual settings.Educación y Psicología SocialPreprin

Association of Candidate Gene Polymorphisms With Chronic Kidney Disease: Results of a Case-Control Analysis in the Nefrona Cohort

Chronic kidney disease (CKD) is a major risk factor for end-stage renal disease, cardiovascular disease and premature death. Despite classical clinical risk factors for CKD and some genetic risk factors have been identified, the residual risk observed in prediction models is still high. Therefore, new risk factors need to be identified in order to better predict the risk of CKD in the population. Here, we analyzed the genetic association of 79 SNPs of proteins associated with mineral metabolism disturbances with CKD in a cohort that includes 2, 445 CKD cases and 559 controls. Genotyping was performed with matrix assisted laser desorption ionizationtime of flight mass spectrometry. We used logistic regression models considering different genetic inheritance models to assess the association of the SNPs with the prevalence of CKD, adjusting for known risk factors. Eight SNPs (rs1126616, rs35068180, rs2238135, rs1800247, rs385564, rs4236, rs2248359, and rs1564858) were associated with CKD even after adjusting by sex, age and race. A model containing five of these SNPs (rs1126616, rs35068180, rs1800247, rs4236, and rs2248359), diabetes and hypertension showed better performance than models considering only clinical risk factors, significantly increasing the area under the curve of the model without polymorphisms. Furthermore, one of the SNPs (the rs2248359) showed an interaction with hypertension, being the risk genotype affecting only hypertensive patients. We conclude that 5 SNPs related to proteins implicated in mineral metabolism disturbances (Osteopontin, osteocalcin, matrix gla protein, matrix metalloprotease 3 and 24 hydroxylase) are associated to an increased risk of suffering CKD