Corrigendum: Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli

The definition of bacterial essential genes has been widely pursued using different approaches. Their study has impacted several fields of research such as synthetic biology, the construction of bacteria with minimal chromosomes, the search for new antibiotic targets, or the design of strains with biotechnological applications. Bacterial genomes are mosaics that only share a small subset of gene-sequences (core genome) even among members of the same species. It has been reported that the presence of essential genes is highly variable between closely related bacteria and even among members of the same species, due to the phenomenon known as “non-orthologous gene displacement” that refers to the coding for an essential function by genes with no sequence homology due to horizontal gene transfer (HGT). The existence of dormant forms among bacteria and the high incidence of HGT have been proposed to be driving forces of bacterial evolution, and they might have a role in the low level of conservation of essential genes among related bacteria by non-orthologous gene displacement, but this correlation has not been recognized. The aim of this mini-review is to give a brief overview of the approaches that have been taken to define and study essential genes, and the implications of non-orthologous gene displacement in bacterial evolution, focusing mainly in the case of Escherichia coli. To this end, we reviewed the available literature, and we searched for the presence of the essential genes defined by mutagenesis in the genomes of the 63 best-sequenced E. coli genomes that are available in NCBI database. We could not document specific cases of non-orthologous gene displacement among the E. coli strains analyzed, but we found that the quality of the genome-sequences in the database is not enough to make accurate predictions about the conservation of essential-genes among members of this bacterial species

MEGsim: A Novel methodology for efficient simulation of graphics workloads in GPUs

An important drawback of cycle-accurate microarchitectural simulators is that they are several orders of magnitude slower than the system they model. This becomes an important issue when simulations have to be repeated multiple times sweeping over the desired design space. In the specific context of graphics workloads, performing cycle-accurate simulations are even more demanding due to the high number of triangles that have to be shaded, lighted and textured to compose a single frame. As a result, simulating a few minutes of a video game sequence is extremely time-consuming.In this paper, we make the observation that collecting information about the vertices and primitives that are processed, along with the times that shader programs are invoked, allows us to characterize the activity performed on a given frame. Based on that, we propose a novel methodology for the efficient simulation of graphics workloads called MEGsim, an approach that is capable of accurately characterizing entire video sequences by using a small subset of selected frames which substantially drops the simulation time. For a set of popular Android games, we show that MEGsim achieves an average simulation speedup of 126×, achieving remarkably accurate results for the estimated final statistics, e.g., with average relative errors of just 0.84% for the total number of cycles, 0.99% for the number of DRAM accesses, 1.2% for the number of L2 cache accesses, and 0.86% for the number of L1 (tile cache) accesses.This work has been supported by the CoCoUnit ERC Advanced Grant of the EU’s Horizon 2020 program (grant No 833057), the Spanish State Research Agency (MCIN/AEI) under grant PID2020-113172RB-I00, and the ICREA Academia program.Peer ReviewedPostprint (author's final draft

RSSI-Based direction-of-departure estimation in bluetooth low energy using an array of frequency-steered leaky-wave antennas

This paper presents a novel advanced Bluetooth Low Energy (BLE) beacon, which is based on an array of frequency-steered leaky-wave antennas (LWAs), as a transmitter for a Direction-of-Departure (DoD) estimation system. The LWA array is completely passive, fabricated in a low-cost FR4 printed-circuit board and designed to multiplex to different angular directions in space each one of the three associated BLE advertising channels that are used for periodically transmitting the ID of the beacon. This way, the use of more expensive hardware associated to electronic phased-array steering/beam-switching is avoided. Four commercial BLE modules are connected to the four ports of the array, producing an advanced BLE beacon that synthesizes twelve directive beams (one per each port and advertising channel) distributed over a wide Field of View (FoV) of 120 degrees in the azimuthal plane. Then, any BLE enabled IoT device located within this FoV can scan the messages from the beacon and obtain the corresponding Received Signal Strength Indicator (RSSI) of these twelve beams to estimate the relative DoD by using amplitude-monopulse signal processing, thus dispensing from complex In-phase/Quadrature (IQ) data acquisition or high computational load.We propose an angular windowing technique to eliminate angular ambiguities and increase the angular resolution, reporting a root mean squared angular error of 3.7º in a wide FoV of 120º.This work was supported in part by the Spanish National projects TEC2016-75934-C4-4-R and TEC2016-76465-C2-1-R, and in part by the 2018 UPCT Santander Research Grant

Triangle Dropping: An occluded-geometry predictor for energy-efficient mobile GPUs

This article proposes a novel micro-architecture approach for mobile GPUs aimed at early removing the occluded geometry in a scene by leveraging frame-to-frame coherence, thus reducing the overall energy consumption. Mobile GPUs commonly implement a Tile-Based Rendering (TBR) architecture that differentiates two main phases: the Geometry Pipeline, where all the geometry of a scene is processed; and the Raster Pipeline, where primitives are rendered in a framebuffer. After the Geometry Pipeline, only non-culled primitives inside the camera’s frustum are stored into the Parameter Buffer, a data structure stored in DRAM. However, among the non-culled primitives there is a significant amount that are rendered but non-visible at all, resulting in useless computations. On average, 60% of those primitives are completely occluded in our benchmarks. Despite TBR architectures use on-chip caches for the Parameter Buffer, about 46% of the DRAM traffic still comes from accesses to such buffer. The proposed Triangle Dropping technique leverages the visibility information computed along the Raster Pipeline to predict the primitives’ visibility in the next frame to early discard those that will be totally occluded, drastically reducing Parameter Buffer accesses. On average, our approach achieves overall 14.5% energy savings, 28.2% energy-delay product savings, and a speedup of 20.2%.This work has been supported by the CoCoUnit ERC Advanced Grant of the EU’s Horizon 2020 program (grant no. 833057), the Spanish State Research Agency (MCIN/AEI) under grant PID2020-113172RB-I00 (AEI/FEDER, EU), and the ICREA Academia program. D. Corbalán-Navarro has been also supported by a PhD research fellowship from the University of Murcia’s “Plan Propio de Investigación.Peer ReviewedPostprint (author's final draft

Effects of water pollution and river fragmentation on population genetic structure of invasive mosquitofish

We analyzed variation at the GPI-2 locus and eleven microsatellite loci of eastern mosquitofish Gambusia holbrooki populations introduced to the Ebro River (Spain), sampling above and below a dam (Flix Reservoir) where severe chronic pollution has been well documented. Allele frequency changes at the GPI-2 locus in the sites nearest to the polluted sediments agree with previous results from studies in mercury-exposed populations of this highly invasive fish. Genetic distinction of the mosquitofish collected close to the polluted sediments was detected at the GPI locus but also at the presumptive neutral microsatellite loci. Recent migration rates estimated from microsatellites indicated that around 30% of fish collected in a specific location were immigrants from upstream and downstream sources. Such high migration rates probably contribute to the mosquitofish's invasive success and suggest that the consequences on the mosquitofish regional genetic structured of high levels of water toxicants could be mediated by immigration from other sites, but the effect of pollutants on local diversity might be higher than observed here.info:eu-repo/semantics/acceptedVersio

The International Summer School on Land Cover Change and Hydroclimate of the La Plata Basin

The La Plata Basin (LPB) in southern South America has been subject to land cover and land use changes (LCLUCs) since colonial times and with an accelerated rate in the last decades and over extensive areas. The work of Ameghino even suggested that there were relations between those land use changes and the frequency of droughts and floods in the region. Despite this early knowledge, not much is known of the potential impacts of LCLUC on the hydroclimate of the La Plata basin. Besides, over the last century much of the La Plata Basin has had a reported increase in precipitation and heavy rains, and these changes along with an increase in population growth - have resulted in more adverse effects from flooding. To draw attention to these issues, during two weeks in November 2009 the International Summer School on Land Cover Change and Hydroclimate of the La Plata Basin was organized at the grounds of the Itaip Hydropower Plant in Brazil. The school was the result of the combination of interests between the La Plata Basin Regional Hydroclimate Project, the Inter-American Institute for Global Change Research (IAI), and the International Hydroinformatics Center (IHC) in Itaip . LPB is an umbrella project endorsed by the Global Energy and Water Cycle Experiment (GEWEX) and the Climate Prediction and Variability (CLIVAR), both of the World Climate Research Programme (WCRP). LPB has made a priority to train young scientists and promote interdisciplinary collaborations in areas related to Climate, Hydrology, Ecology and Agriculture. The IAI, with a similar agenda, was a natural partner to develop this Summer School, which in turn benefited from Itaipu s interest in relating with the scientific community of neighboring countries. The choice of location (Itaip Technological Park) was made so that participants could relate research usually done at academic institutions to applications and operations at one of the largest hydropower plants in the world. The school was attended by 45 advanced graduate students and young scientists with different backgrounds from seven countries, including less technically advanced ones in the region.

Quaternary fossil horses within the Prados-Guatén Depression (Pantoja de La Sagra, Toledo)

Durante la primera reunión de campo del Grupo Madrileño de Cuaternario (GQM-AEQUA) se localizaron restos fragmentarios de dentición de caballos fósiles en los antiguos areneros de Pantoja de La Sagra (Toledo), actualmente en proceso de desmantelamiento y relleno. Ante la posibilidad de deterioro y pérdida los restos fueron recolectados y trasladados al Museo Nacional de Ciencias Naturales (CSIC, Madrid) donde se ha procedido a su análisis. Las piezas fósiles analizadas responden a un maxilar izquierdo con tres piezas dentales in situ (molares y premolares), y otras siete más aisladas. Todos los dientes aislados, junto con el fragmento de maxilar existente, corresponden a un adulto joven. Los restos fósiles se encontraban asociados a un nivel de arenas fluviales situado unos cuatro metros por debajo de la superficie de la Terraza de +15 m de la Depresión Prados-Guatén definida como un nivel perteneciente al tránsito Pleistoceno inferior-medio, del antiguo Sistema fluvial Manzanares-Guatén por Silva (1988). En concreto los niveles superiores de esta terraza han sido interpretados como resultado de la superposición de los últimos depósitos del antiguo sistema fluvial y los primeros asociados al relleno de la Depresión por tributarios de área fuente más local tras su abandono como consecuencia del proceso de captura del valle inferior del Manzanares por parte del Río Jarama al SW de la Ciudad de Madrid (Silva et al., 1988). Los caracteres morfológicos y morfométricos de las piezas dentarias permiten identificarlos como Equus ferus cf. mosbachensis cuya distribución bioestratigráfica abarca la parte final del Pleistoceno Medio (c.a. 500-200 ka B.P.). Junto a los restos fósiles aparecieron también escasos fragmentos líticos correspondientes a productos de lascado en sílex de difícil atribución tecnológica. Los restos fósiles analizados, indican que el depósito extensivo de arenas fluviales en el eje de la Depresión, culminó durante el final del Pleistoceno medio, y que la dinámica fluvial de la Depresión tras su proceso de abandono fue de hecho más activa de lo que se pensaba con la instalación de sistemas de arroyos relevantes alimentados por cabeceras locales antes del encajamiento definitivo actual de los arroyos Prados y Guatén.During the first field-meeting of the Madrid Quaternary Research Group (GQM-AEQUA) several fossil teeth remnants of horses were localised at the ancient sand-quarries of Pantoja de La Sagra (Toledo), which presently are abandoned and refilling in progress. The possibility of deterioration and loss of the localised fossils remnants induced by the quarry works, they were collected and taken away to the Museo Nacional de Ciencias Naturales (CSIC, Madrid) for their preservation and analysis. Fossil remains correspond to a left maxilla with two in situ molars, another one inset on its alveolar cavity, fragments of premolar cavities, as well as other seven more isolated teeth. These fossils were outcropping in a sandy level at four meters below the +15 m fluvial terrace surface of the axial sector of de Prados-Guatén Depression, which is considered the last fluvial level belonging to the ancient Manzanares-Guatén fluvial system during the Lower-Middle Pleistocene transit (Silva, 1988). In detail, the upper fluvial sediments of this particular terrace level were interpreted as the result of the overlapping between the last materials deposited by the ancient Manzanares-Guatén fluvial system and the first ones resulting from the readjustment of former tributaries after the abandonment of the Depression caused by fluvial capture of the Lower Manzanares Valley SW Madrid City. The morphological features of the oclusal surface of the horse teeth and morphometric comparative analyses indicate that they belong to the specie Equus ferus, and probably to the subspecie mosbachensis. However due to the bad definition of this group in Europe and the few individuals analysed the better classification is Equus ferus cf. mosbachensis. The bioestratigraphic distribution of this fossil horse group in Europe extends on the upper part of the Middle Pleistocene (c.a. 500-200 ka B.P.). Few lithic artefacts outcropped also associated to the fossil remains, constituted by laminar flakes of hard technological classification. Fossil remains analysed in this work joint to the unique previous quaternary fossil mammal described for the Prados-Guatén Depression constituted by Mammuthus meridionalis NESTI of the former quarry of Esquivias adjacent to the AVE railway line (Silva et al., 1988b; 1999). The chronostratigraphic attribution of the fossil horses (Upper Middle Pleistocene) described here indicate that fluvial sedimentary activity within the Depression was relevant after its abandonment. Ancient tributaries of the former Manzanares-Guatén fluvial system, feed by local-intrabasinal headwaters, reworked the previous sandy sediments triggering multiepisodic deposition during the upper part of the Middle Pleistocene, before the more recent eventual incision of present streams dissecting the Depression

Atención a mujeres inmigrantes en un programa de mediación intercultural en salud

Creative Commons: Atribución-NoComercial-SinDerivadas 3.0 Unported (CC BY-NC-ND 3.0)Fundamentos: la mediación intercultural es una estrategia para una atención sanitaria de calidad orientada a la disminución de desigualdades en población inmigrante. El objetivo fue analizar los principales motivos de consulta con el servicio de mediación, el perfil de las mujeres atendidas y las características de la intervención realizada. Métodos: Estudio transversal de 339 episodios de atención de dos mediadoras interculturales (MI) desde febrero de 2008 a octubre de 2011 en Valencia. Se analizaron las variables de los registros individuales de las consultas de mediación: motivos de derivación a MI y profesionales que remitieron, motivos y problemas detectados por MI, tipo de intervención, tipo de derivación de MI y variables socioeconómicas. Para evaluar las diferencias entre países de origen se utilizó el test chi2 en las variables cualitativas y el test de Anova de un factor en las cuantitativas. Resultados: 123 (36,3%) mujeres fueron remitidas a las MI por el Centro de Salud Sexual y Reproductiva y 98 (28,9%) por la matrona. 272 (80,24%) fueron remitidas para información y demanda de métodos anticonceptivos. Las MI realizaron educación para la salud y detectaron problemas sociales en 67 (19,7%) mujeres y en 38 (11,21%) violencia de género. 142 (27%) eran bolivianas. Conclusiones: Las mujeres atendidas fueron inmigrantes latinoamericanas y fueron remitidas principalmente para anticoncepción. Las mujeres bolivianas presentan más factores de vulnerabilidad como irregularidad, trabajo precario y poco tiempo de residencia.Alcaraz Quevedo, M.; Paredes Carbonell, JJ.; Sancho Mestre, C.; López Sánchez, P.; García Moreno, JL.; Vivas Consuelo, DJJ. (2014). Atención a mujeres inmigrantes en un programa de mediación intercultural en salud. Revista Española de Salud Pública. 88(2):301-310. doi:10.4321/S1135-57272014000200012S30131088