Beyond position weight matrices: nucleotide correlations in transcription factor binding sites and their description

The identification of transcription factor binding sites (TFBSs) on genomic DNA is of crucial importance for understanding and predicting regulatory elements in gene networks. TFBS motifs are commonly described by Position Weight Matrices (PWMs), in which each DNA base pair independently contributes to the transcription factor (TF) binding, despite mounting evidence of interdependence between base pairs positions. The recent availability of genome-wide data on TF-bound DNA regions offers the possibility to revisit this question in detail for TF binding {\em in vivo}. Here, we use available fly and mouse ChIPseq data, and show that the independent model generally does not reproduce the observed statistics of TFBS, generalizing previous observations. We further show that TFBS description and predictability can be systematically improved by taking into account pairwise correlations in the TFBS via the principle of maximum entropy. The resulting pairwise interaction model is formally equivalent to the disordered Potts models of statistical mechanics and it generalizes previous approaches to interdependent positions. Its structure allows for co-variation of two or more base pairs, as well as secondary motifs. Although models consisting of mixtures of PWMs also have this last feature, we show that pairwise interaction models outperform them. The significant pairwise interactions are found to be sparse and found dominantly between consecutive base pairs. Finally, the use of a pairwise interaction model for the identification of TFBSs is shown to give significantly different predictions than a model based on independent positions

Advantages of gated silicon single photon detectors

We present a gated silicon single photon detector based on a commercially available avalanche photodiode. Our detector achieves a photon detection efficiency of 45\pm5% at 808 nm with 2x 10^-6 dark count per ns at -30V of excess bias and -30{\deg}C. We compare gated and free-running detectors and show that this mode of operation has significant advantages in two representative experimental scenarios: detecting a single photon either hidden in faint continuous light or after a strong pulse. We also explore, at different temperatures and incident light intensities, the "charge persistence" effect, whereby a detector clicks some time after having been illuminated

Diseño y desarrollo de la domótica de una casa bioclimática

La idea de este proyecto es la de llevar a cabo la domótica de la casa bioclimática Sumbiosi, para lo cual he ido cumpliendo una serie de pasos. En primer lugar, tuve que comprender tanto los planos como los aparatos de la casa y entender las necesidades que tenía la misma. Una vez comprendido esto, pasé a estudiar el tipo de sensores que eran necesarios en la casa, con el fin de recuperar toda la información necesaria, y la ubicación que debían tener los mismos. Esta labor, la lleve a cabo conjuntamente con el siguiente paso, ver las relaciones de los diferentes elementos de la casa, desarrollando varios organigramas con todas ellas y con los diferentes modos de actuación que podían utilizar la casa (calor, frío, ventilación, humedad, electricidad, riego, seguridad, iluminación, confort de la casa…), estos dos procesos fueron realizados a la vez puesto que se iban retroalimentando, cuando hacia un organigrama, veía las necesidades que tenía la vivienda, por lo que en ese momento sabía el tipo de sensor que necesitaba y viceversa, cuando veía un sensor con más capacidades de las que necesitaba en ese momento, proyectaba el resto de los organigramas para ver si serían necesarias en un futuro y merecía la pena obtener un sensor más complejo o no. Una vez conseguido todo esto, pasé a utilizar el programa ETS4, con el cual configure todos los dispositivos y sensores que habíamos instalado en la casa para controlar y monitorizar todos los datos en la pantalla del ordenador. Para ello, en primer lugar tuve que introducir todos los sensores, en este proceso conté con la ayuda del técnico instalador. Una vez que el programa detectaba el sensor, automáticamente aparecían todas las informaciones que se podían obtener provenientes del mismo, por lo que se podían empezar a crear las direcciones de grupo para organizarlos. En este proceso se iban intercalando las tareas, puesto que dependía de las fechas de recibo de los distintos pedidos y de la disponibilidad del técnico para instalarlo. Una vez que se pudo visualizar todos los datos en el ordenador se pasó a instalar y configurar el programa Domovea, en el cual introduje toda la lógica de control que había diseñado previamente mediante los organigramas. Para la utilización del Domovea, también tuve que configurar los sensores exportando las bases de datos que había creado anteriormente con el programa ETS4. El penúltimo paso fue configurar todos los aparatos y los escenarios en el Domovea, ordenándolos y simplificándolos de cara al usuario con el fin de que fuera un interfaz intuitivo y manejable para que una persona, que nunca haya trabajado con él, lo pueda utilizar. Se diseñaron y comprobaron el funcionamiento de los escenarios y de todos los sensores. Por último y también relacionado con la domótica de la vivienda, se realizaron una serie de estudios energéticos con el fin de facilitar las decisiones a tomar en la parte domótica del Domovea, tanto con los datos obtenidos del Domovea (monitoring) como con las previsiones de consumo de la vivienda en los diferentes momentos del año con el fin de identificar los aspectos potenciales de la vivienda a reducir para optimizar al máximo el consumo energético de la vivienda Sumbiosi

Vegetation shadow casts impact remotely sensed reflectance from permafrost thaw ponds in the subarctic forest-tundra zone

Thermokarst lakes and ponds are a common landscape feature resulting from permafrost thaw, but their intense greenhouse gas emissions are still poorly constrained as a feedback mechanism for global warming because of their diversity, abundance, and remoteness. Thermokarst waterbodies may be small and optically diverse, posing specifc challenges for optical remote sensing regarding detection, classifcation, and monitoring. This is especially relevant when accounting for external factors that afect water refectance, such as scattering and vegetation shadow casts. In this study, we evaluated the efects of shadowing across optically diverse waterbodies located in the forest–tundra zone of northern Canada. We used ultra-high spatial resolution multispectral data and digital surface models obtained from unmanned aerial systems for modeling and analyzing shadow efects on water refectance at Earth Observation satellite overpass time. Our results show that shadowing causes variations in refectance, reducing the usable area of remotely sensed pixels for waterbody analysis in small lakes and ponds. The efects were greater on brighter and turbid inorganic thermokarst lakes embedded in post-glacial silt–clay marine deposits and littoral sands, where the mean refectance decrease was from -51 to -70%, depending on the wavelength. These efects were also dependent on lake shape and vegetation height and were amplifed in the cold season due to low solar elevations. Remote sensing will increasingly play a key role in assessing thermokarst lake responses and feedbacks to global change, and this study shows the magnitude and sources of optical variations caused by shading that need to be considered in future analyses.info:eu-repo/semantics/publishedVersio

Lung transplantation for interstitial lung disease in idiopathic inflammatory myositis: A cohort study

Connective tissue disease; Idiopathic inflammatory myopathy; Interstitial lung diseaseEnfermedad del tejido conectivo; Miopatía inflamatoria idiopática; Enfermedad pulmonar intersticialMalaltia del teixit conjuntiu; Miopatia inflamatòria idiopàtica; Malaltia pulmonar intersticialIn patients with interstitial lung disease (ILD) complicating classical or amyopathic idio-pathic inflammatory myopathy (IIM), lung transplantation outcomes might be affected by the disease and treatments. Here, our objective was to assess survival and prog-nostic factors in lung transplant recipients with IIM-ILD. We retrospectively reviewed data for 64 patients who underwent lung transplantation between 2009 and 2021 at 19 European centers. Patient survival was the primary outcome. At transplantation, the median age was 53 [46–59] years, 35 (55%) patients were male, 31 (48%) had clas-sical IIM, 25 (39%) had rapidly progressive ILD, and 21 (33%) were in a high- priority transplant allocation program. Survival rates after 1, 3, and 5 years were 78%, 73%, and 70%, respectively. During follow-up (median, 33 [7–63] months), 23% of patients developed chronic lung allograft dysfunction. Compared to amyopathic IIM, classical IIM was characterized by longer disease duration, higher-intensity immunosuppres-sion before transplantation, and significantly worse posttransplantation survival. Five (8%) patients had a clinical IIM relapse, with mild manifestations. No patient expe-rienced ILD recurrence in the allograft. Posttransplantation survival in IIM-ILD was similar to that in international all- cause- transplantation registries. The main factor as-sociated with worse survival was a history of muscle involvement (classical IIM). In lung transplant recipients with idiopathic inflammatory myopathy, survival was similar to that in all-cause transplantation and was worse in patients with muscle involvement compared to those with the amyopathic disease

Los efectos de la crisis económica en la brecha salarial

Jornada de promoción y difusión del SIMA dedicada a "Los salarios durante la crisis económica y su incidencia en el ASAC y los sistemas de solución de conflictos". Celebrada el día 16 de noviembre de 2016 y organizada por CCOO

Sectoral specialisation in the EU a macroeconomic perspective

This paper analyses trends in sectoral specialisation in the EU and concludes the following: 1) The European production structure appears more homogenous than that of the US. 2) While sectoral specialisation has shown a slight increase in some smaller euro area countries towards the end-1990s, it is too early to detect any potential impact of EMU. 3) Despite some changes in sectoral composition, the business cycles of euro area countries became more synchronised over the 1990s, which may be seen as reassuring from the point of view of the single monetary policy. 4) Sectoral re-allocation accounts for as much as 50% of the increase in labour productivity growth in business sector services in the euro area. 5) The slowdown of European labour productivity growth relative to the US since the mid-1990s is explained by a stronger performance in the US wholesale and retail trade, financial intermediation and high-tech manufacturing sectors.

Elevated Plasma Endothelin-1 and Pulmonary Arterial Pressure in Children Exposed to Air Pollution

BackgroundControlled exposures of animals and humans to particulate matter (PM) or ozone air pollution cause an increase in plasma levels of endothelin-1, a potent vasoconstrictor that regulates pulmonary arterial pressure.ObjectivesThe primary objective of this field study was to determine whether Mexico City children, who are chronically exposed to levels of PM and O3 that exceed the United States air quality standards, have elevated plasma endothelin-1 levels and pulmonary arterial pressures.MethodsWe conducted a study of 81 children, 7.9 ± 1.3 years of age, lifelong residents of either northeast (n = 19) or southwest (n = 40) Mexico City or Polotitlán (n = 22), a control city with PM and O3 levels below the U.S. air quality standards. Clinical histories, physical examinations, and complete blood counts were done. Plasma endothelin-1 concentrations were determined by immunoassay, and pulmonary arterial pressures were measured by Doppler echocardiography.ResultsMexico City children had higher plasma endothelin-1 concentrations compared with controls (p < 0.001). Mean pulmonary arterial pressure was elevated in children from both northeast (p < 0.001) and southwest (p < 0.05) Mexico City compared with controls. Endothelin-1 levels in Mexico City children were positively correlated with daily outdoor hours (p = 0.012), and 7-day cumulative levels of PM air pollution < 2.5 μm in aerodynamic diameter (PM2.5) before endothelin-1 measurement (p = 0.03).ConclusionsChronic exposure of children to PM2.5 is associated with increased levels of circulating endothelin-1 and elevated mean pulmonary arterial pressure