A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?

Motivation: Survival prediction of breast cancer (BC) patients independently of treatment, also known as prognostication, is a complex task since clinically similar breast tumors, in addition to be molecularly heterogeneous, may exhibit different clinical outcomes. In recent years, the analysis of gene expression profiles by means of sophisticated data mining tools emerged as a promising technology to bring additional insights into BC biology and to improve the quality of prognostication. The aim of this work is to assess quantitatively the accuracy of prediction obtained with state-of-the-art data analysis techniques for BC microarray data through an independent and thorough framework

The motor cortex of the sheep: laminar organization, projections and diffusion tensor imaging of the intracranial pyramidal and extrapyramidal tracts

The laminar organization of the motor cortex of the sheep and other large domestic herbivores received scarce attention and is generally considered homologous to that of rodents and primates. Thickness of the cortex, subdivision into layers and organization are scarcely known. In the present study, we applied different modern morphological, mathematical and image-analyses techniques to the study of the motor area that controls movements of the forelimb in the sheep. The thickness of the cortex resulted comparable to that of other terrestrial Cetartiodactyls (but thicker than in marine Cetartiodactyls of similar body mass). The laminar organization showed marked development of layer 1, virtual absence of layer 4, and image analysis suggested prevalence of large irregular neural cells in the deeper layers. Diffusion tensor imaging revealed robust projections from the motor cortex to the pyramids in the brainstem, and well evident tracts descending to the tegmentum of the mesencephalon and dorsal pons. Our data contrast the general representation of the motor system of this species, considered to be predominantly based on extra-pyramidal tracts that originate from central pattern generators in the brainstem. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature

Thermo-mechanical behavior of surface acoustic waves in ordered arrays of nanodisks studied by near infrared pump-probe diffraction experiments

The ultrafast thermal and mechanical dynamics of a two-dimensional lattice of metallic nano-disks has been studied by near infrared pump-probe diffraction measurements, over a temporal range spanning from 100 fs to several nanoseconds. The experiments demonstrate that, in these systems, a two-dimensional surface acoustic wave (2DSAW), with a wavevector given by the reciprocal periodicity of the array, can be excited by ~120 fs Ti:sapphire laser pulses. In order to clarify the interaction between the nanodisks and the substrate, numerical calculations of the elastic eigenmodes and simulations of the thermodynamics of the system are developed through finite-element analysis. At this light, we unambiguously show that the observed 2DSAW velocity shift originates from the mechanical interaction between the 2DSAWs and the nano-disks, while the correlated 2DSAW damping is due to the energy radiation into the substrate.Comment: 13 pages, 10 figure

A computer simulation protocol to assess the accuracy of a Radio Stereometric Analysis (RSA) image processor according to the ISO-5725

Radio-Stereometric-Analysis and x-ray fluoroscopy are radiological techniques that require dedicated software to process data. The accurate calibration of these software is therefore critical. The aim of this work is to produce a protocol for evaluating the softwares' accuracy according to the ISO-5725. A series of computer simulations of the radiological setup and images were employed. The noise level of the images was also changed to evaluate the accuracy with different image qualities. The protocol was tested on a custom software developed by the authors. Radiological scene reconstruction accuracy was of (0.092 +- 0.14) mm for tube position, and (0.38 +- 0.31) mm / (2.09 +- 1.39) deg for detectors oriented in a direction other than the source-detector direction. In the source-detector direction the accuracy was of (2.68 +- 3.08) mm for tube position, and of (0.16 +- 0.27) mm / (0.075 +- 1.16) deg for the detectors. These disparate results are widely discussed in the literature. Model positioning and orientation was also highly accurate: (0.22 +- 0.46) mm / (0.26 +- 0.22) deg. Accuracy was not affected by the noise level. The protocol was able to assess the accuracy of the RSA system. It was also useful to detect and fix hidden bugs. It was also useful to detect and resolve hidden bugs in the software, and in optimizing the algorithms

Very Large Baseline Array observations of Mrk 6 : probing the jet-lobe connection

We present the results of high-resolution VLBI (very long baseline interferometry) observations at 1.6 and 4.9 GHz of the radio-loud Seyfert galaxy, Mrk 6. These observations are able to detect a compact radio core in this galaxy for the first time. The core has an inverted spectral index (α1.6 4.9 = +1.0 ± 0.2) and a brightness temperature of 1 × 108 K. Three distinct radio components, which resemble jet elements and/or hotspots, are also detected. The position angles of these elongated jet elements point not only to a curved jet in Mrk 6, but also towards a connection between the AGN and the kpc-scale radio lobes/bubbles in this galaxy. Firmer constraints on the star formation rate provided by new Herschel observations (SFR <0.8 M⊙ yr-1) make the starburst-wind-powered bubble scenario implausible. From plasma speeds, obtained via prior Chandra X-ray observations, and ram pressure balance arguments for the interstellar medium and radio bubbles, the north-south bubbles are expected to take 7.5 × 106 yr to form, and the east-west bubbles 1.4 × 106 yr. We suggest that the jet axis has changed at least once in Mrk 6 within the last ≈107 yr. A comparison of the nuclear radio-loudness of Mrk 6 and a small sample of Seyfert galaxies with a subset of low-luminosity FR I radio galaxies reveals a continuum in radio properties.Peer reviewe

The plankton, aerosol, cloud, ocean ecosystem mission status, science, advances

The Plankton, Aerosol, Cloud, Ocean Ecosystem (PACE) mission represents the National Aeronautics and Space Administration\u27s (NASA) next investment in satellite ocean color and the study of Earth\u27s ocean-atmosphere system, enabling new insights into oceanographic and atmospheric responses to Earth\u27s changing climate. PACE objectives include extending systematic cloud, aerosol, and ocean biological and biogeochemical data records, making essential ocean color measurements to further understand marine carbon cycles, food-web processes, and ecosystem responses to a changing climate, and improving knowledge of how aerosols influence ocean ecosystems and, conversely, how ocean ecosystems and photochemical processes affect the atmosphere. PACE objectives also encompass management of fisheries, large freshwater bodies, and air and water quality and reducing uncertainties in climate and radiative forcing models of the Earth system. PACE observations will provide information on radiative properties of land surfaces and characterization of the vegetation and soils that dominate their reflectance. The primary PACE instrument is a spectrometer that spans the ultraviolet to shortwave-infrared wavelengths, with a ground sample distance of 1 km at nadir. This payload is complemented by two multiangle polarimeters with spectral ranges that span the visible to near-infrared region. Scheduled for launch in late 2022 to early 2023, the PACE observatory will enable significant advances in the study of Earth\u27s biogeochemistry, carbon cycle, clouds, hydrosols, and aerosols in the ocean-atmosphere-land system. Here, we present an overview of the PACE mission, including its developmental history, science objectives, instrument payload, observatory characteristics, and data products

Multiple-input multiple-output causal strategies for gene selection

Traditional strategies for selecting variables in high dimensional classification problems aim to find sets of maximally relevant variables able to explain the target variations. If these techniques may be effective in generalization accuracy they often do not reveal direct causes. The latter is essentially related to the fact that high correlation (or relevance) does not imply causation. In this study, we show how to efficiently incorporate causal information into gene selection by moving from a single-input single-output to a multiple-input multiple-output setting.Journal ArticleResearch Support, N.I.H. ExtramuralResearch Support, Non-U.S. Gov'tSCOPUS: ar.jinfo:eu-repo/semantics/publishe

Red Tides In the Gulf of Mexico: Where, When, and Why?

Independent data from the Gulf of Mexico are used to develop and test the hypothesis that the same sequence of physical and ecological events each year allows the toxic dinoflagellate Karenia brevis to become dominant. A phosphorus-rich nutrient supply initiates phytoplankton succession, once deposition events of Saharan iron-rich dust allow Trichodesmium blooms to utilize ubiquitous dissolved nitrogen gas within otherwise nitrogen-poor sea water. They and the co-occurring K. brevis are positioned within the bottom Ekman layers, as a consequence of their similar diel vertical migration patterns on the middle shelf. Upon onshore upwelling of these near-bottom seed populations to CDOM-rich surface waters of coastal regions, light-inhibition of the small red tide of similar to 1 ug chl l(-1) of ichthytoxic K. brevis is alleviated. Thence, dead fish serve as a supplementary nutrient source, yielding large, self-shaded red tides of similar to 10 ug chl l(-1). The source of phosphorus is mainly of fossil origin off west Florida, where past nutrient additions from the eutrophied Lake Okeechobee had minimal impact. In contrast, the P-sources are of mainly anthropogenic origin off Texas, since both the nutrient loadings of Mississippi River and the spatial extent of the downstream red tides have increased over the last 100 years. During the past century and particularly within the last decade, previously cryptic Karenia spp. have caused toxic red tides in similar coastal habitats of other western boundary currents off Japan, China, New Zealand, Australia, and South Africa, downstream of the Gobi, Simpson, Great Western, and Kalahari Deserts, in a global response to both desertification and eutrophication