Useful ‘junk': Alu RNAs in the human transcriptome

Abstract.: Alu elements are the most abundant repetitive elements in the human genome; they have amplified by retrotransposition to reach the present number of more than one million copies. Alu elements can be transcribed in two different ways, by two independent polymerases. ‘Free Alu RNAs' are transcribed by Pol III from their own promoter, while ‘embedded Alu RNAs' are transcribed by Pol II as part of protein- and non-protein-coding RNAs. Recent studies have demonstrated that both free and embedded Alu RNAs play a major role in post transcriptional regulation of gene expression, for example by affecting protein translation, alternative splicing and mRNA stability. These discoveries illustrate how a part of the ‘junk DNA' content of the human genome has been recruited to important functions in regulation of gene expressio

Neural Collaborative Filtering

In recent years, deep neural networks have yielded immense success on speech recognition, computer vision and natural language processing. However, the exploration of deep neural networks on recommender systems has received relatively less scrutiny. In this work, we strive to develop techniques based on neural networks to tackle the key problem in recommendation -- collaborative filtering -- on the basis of implicit feedback. Although some recent work has employed deep learning for recommendation, they primarily used it to model auxiliary information, such as textual descriptions of items and acoustic features of musics. When it comes to model the key factor in collaborative filtering -- the interaction between user and item features, they still resorted to matrix factorization and applied an inner product on the latent features of users and items. By replacing the inner product with a neural architecture that can learn an arbitrary function from data, we present a general framework named NCF, short for Neural network-based Collaborative Filtering. NCF is generic and can express and generalize matrix factorization under its framework. To supercharge NCF modelling with non-linearities, we propose to leverage a multi-layer perceptron to learn the user-item interaction function. Extensive experiments on two real-world datasets show significant improvements of our proposed NCF framework over the state-of-the-art methods. Empirical evidence shows that using deeper layers of neural networks offers better recommendation performance.Comment: 10 pages, 7 figure

Seasonal Climatology of Hydrographic Conditions in the Upwelling Region Off Northern Chile

Over 30 years of hydrographic data from the northern Chile (18 degreesS-24 degreesS) upwelling region are used to calculate the surface and subsurface seasonal climatology extending 400 km offshore. The data are interpolated to a grid with sufficient spatial resolution to preserve cross-shelf gradients and then presented as means within four seasons: austral winter (July-September), spring (October-December), summer (January-March), and fall (April-June). Climatological monthly wind forcing, surface temperature, and sea level from three coastal stations indicate equatorward (upwelling favorable) winds throughout the year, weakest in the north. Seasonal maximum alongshore wind stress is in late spring and summer (December-March). Major water masses of the region are identified in climatological T-S plots and their sources and implied circulation discussed. Surface fields and vertical transects of temperature and salinity confirm that upwelling occurs year-round, strongest in summer and weakest in winter, bringing relatively fresh water to the surface nearshore. Surface geostrophic flow nearshore is equatorward throughout the year. During summer, an anticyclonic circulation feature in the north which extends to at least 200 m depth is evident in geopotential anomaly and in both temperature and geopotential variance fields. Subsurface fields indicate generally poleward flow throughout the year, strongest in an undercurrent near the coast. This undercurrent is strongest in summer and most persistent and organized in the south (south of 21 degreesS), A subsurface oxygen minimum, centered at similar to 250 m, is strongest at lower latitudes. Low-salinity subsurface water intrudes into the study area near 100 m, predominantly in offshore regions, strongest during summer and fall and in the southernmost portion of the region. The climatological fields are compared to features off Baja within the somewhat analogous California Current and to measurements from higher latitudes within the Chile-Peru Current system

Gene induction during differentiation of human monocytes into dendritic cells: an integrated study at the RNA and protein levels

Changes in gene expression occurring during differentiation of human monocytes into dendritic cells were studied at the RNA and protein levels. These studies showed the induction of several gene classes corresponding to various biological functions. These functions encompass antigen processing and presentation, cytoskeleton, cell signalling and signal transduction, but also an increase in mitochondrial function and in the protein synthesis machinery, including some, but not all, chaperones. These changes put in perspective the events occurring during this differentiation process. On a more technical point, it appears that the studies carried out at the RNA and protein levels are highly complementary.Comment: website publisher: http://www.springerlink.com/content/ha0d2c351qhjhjdm

Seasonal Climatology of Hydrographic Conditions in the Upwelling Region Off Northern Chile

Over 30 years of hydrographic data from the northern Chile (18°S-24°S) upwelling region are used to calculate the surface and subsurface seasonal climatology extending 400 km offshore. The data are interpolated to a grid with sufficient spatial resolution to preserve crossshelf gradients and then presented as means within four seasons: austral winter (JulySeptember), spring (October-December), summer (January-March), and fall (April-June). Climatological monthly wind forcing, surface temperature, and sea level from three coastal stations indicate equatorward (upwelling favorable) winds throughout the year, weakest in the north. Seasonal maximum alongshore wind stress is in late spring and summer (DecemberMarch). Major water masses of the region are identified in climatological T-S plots and their sources and implied circulation discussed. Surface fields and vertical transects of temperature and salinity confirm that upwelling occurs year-round, strongest in summer and weakest in winter, bringing relatively fresh water to the surface nearshore. Surface geostrophic flow nearshore is equatorward throughout the year. During summer, an anticyclonic circulation feature in the north which extends to at least 200 rn depth is evident in geopotential anomaly and in both temperature and geopotential variance fields. Subsurface fields indicate generally poleward flow throughout the year, strongest in an undercurrent near the coast. This undercurrent is strongest in summer and most persistent and organized in the south (south of 21°S). A subsurface oxygen minimum, centered at ~250 m, is strongest at lower latitudes. Low-salinity subsurface water intrudes into the study area near 100 m, predominantly in offshore regions, strongest during summer and fall and in the southernmost portion of the region. The climatological fields are compared to features off Baja within the somewhat analogous California Current and to measurements from higher latitudes within the Chile-Peru Current system. Copyright 2001 by the American Geophysiccal Union

Sea level anomaly on the Patagonian continental shelf: Trends, annual patterns and geostrophic flows

We study the annual patterns and linear trend of satellite sea level anomaly (SLA) over the southwest South Atlantic continental shelf (SWACS) between 54S and 36S. Results show that south of 42°S the thermal steric effect explains nearly 100% of the annual amplitude of the SLA, while north of 42°S it explains less than 60%. This difference is due to the halosteric contribution. The annual wind variability plays a minor role over the whole continental shelf. The temporal linear trend in SLA ranges between 1 and 5 mm/yr (95% confidence level). The largest linear trends are found north of 39°S, at 42°S and at 50°S. We propose that in the northern region the large positive linear trends are associated with local changes in the density field caused by advective effects in response to a southward displacement of the South Atlantic High. The causes of the relative large SLA trends in two southern coastal regions are discussed as a function meridional wind stress and river discharge. Finally, we combined the annual cycle of SLA with the mean dynamic topography to estimate the absolute geostrophic velocities. This approach provides the first comprehensive description of the seasonal component of SWACS circulation based on satellite observations. The general circulation of the SWACS is northeastward with stronger/weaker geostrophic currents in austral summer/winter. At all latitudes, geostrophic velocities are larger (up to 20 cm/s) close to the shelf-break and decrease toward the coast. This spatio-temporal pattern is more intense north of 45°S.Fil: Ruiz Etcheverry, Laura Agustina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Centro de Investigaciones del Mar y la Atmósfera. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Centro de Investigaciones del Mar y la Atmósfera; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ciencias de la Atmósfera y los Océanos; Argentina. University of Hawaii at Manoa; Estados UnidosFil: Saraceno, Martin. Universidad de Buenos Aires; Argentina. Instituto Franco Argentino para el Estudio del Clima y sus Impactos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Centro de Investigaciones del Mar y la Atmósfera. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Centro de Investigaciones del Mar y la Atmósfera; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Centro de Investigaciones del Mar y la Atmósfera; ArgentinaFil: Piola, Alberto Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Ministerio de Defensa. Armada Argentina. Servicio de Hidrografía Naval; ArgentinaFil: Strub, P. T.. State University of Oregon; Estados Unido

Satellite-Measured Chlorophyll and Temperature Variability Off Northern Chile During the 1996-1998 La Niña and El Niño

Time series of satellite measurements are used to describe patterns of surface temperature and chlorophyll associated with the 1996 cold La Nina phase and the 1997-1998 warm El Nino phase of the El Nino - Southern Oscillation cycle in the upwelling region off northern Chile. Surface temperature data are available through the entire study period. Sea-viewing Wide Field-of-view Sensor (SeaWiFS) data first became available in September 1997 during a relaxation in El Nino conditions identified by in situ hydrographic data. Over the time period of coincident satellite data, chlorophyll patterns closely track surface temperature patterns. Increases both in nearshore chlorophyll concentration and in cross-shelf extension of elevated concentrations are associated with decreased coastal temperatures during both the relaxation in El Nino conditions in September-November 1997 and the recovery from EI Nino conditions after March 1998. Between these two periods during austral summer (December 1997 to March 1998) and maximum El Nino temperature anomalies, temperature patterns normally associated with upwelling were absent and chlorophyll concentrations were minimal. Cross-shelf chlorophyll distributions appear to be modulated by surface temperature frontal zones and are positively correlated with a satellite-derived upwelling index. Frontal zone patterns and the upwelling index in 1996 imply an austral summer nearshore chlorophyll maximum, consistent with SeaWiFS data from I 1998-1999, after the El Nino. SeaWiFS retrievals in the data set used here are higher than in situ measurements by a factor of 2-4; however, consistency in the offset suggests relative patterns are valid

Blended sea level anomaly fields with enhanced coastal coverage along the U.S. West Coast

We form a new ‘blended’ data set of sea level anomaly (SLA) fields by combining gridded daily fields derived from altimeter data with coastal tide gauge data. Within approximately 55–70 km of the coast, the altimeter data are discarded and replaced by a linear interpolation between the tide gauge and remaining offshore altimeter data. To create a common reference height for altimeter and tide gauge data, a 20-year mean is subtracted from each time series (from each tide gauge and altimeter grid point) before combining the data sets to form a blended mean sea level anomaly (SLA) data set. Daily mean fields are produced for the 22-year period 1 January 1993–31 December 2014. The primary validation compares geostrophic velocities calculated from the height fields and velocities measured at four moorings covering the north-south range of the new data set. The blended data set improves the alongshore (meridional) component of the currents, indicating an improvement in the cross-shelf gradient of the mean SLA data set.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Nature Publishing Group. The published article can be found at: http://www.nature.com/articles/sdata201613. The dataset described by this publication is available in ScholarsArchive@OSU at: https://ir.library.oregonstate.edu/xmlui/handle/1957/57170. Metadata associated with this Data Descriptor is available at http://www.nature.com/sdata/ and is released under the CC0 waiver to maximize reus