Artificial Intelligence Analysis of Gene Expression Data Predicted the Prognosis of Patients with Diffuse Large B-Cell Lymphoma

OBJECTIVE: We aimed to identify new biomarkers in Diffuse Large B-cell Lymphoma (DLBCL) using the deep learning technique. METHODS AND RESULTS: The multilayer perceptron (MLP) analysis was performed in the GSE10846 series, divided into discovery (n = 100) and validation (n = 414) sets. The top 25 gene-probes from a total of 54,614 were selected based on their normalized importance for outcome prediction (dead/alive). By Gene Set Enrichment Analysis (GSEA) the association to unfavorable prognosis was confirmed. In the validation set, by univariate Cox regression analysis, high expression of ARHGAP19, MESD, WDCP, DIP2A, CACNA1B, TNFAIP8, POLR3H, ENO3, SERPINB8, SZRD1, KIF23 and GGA3 associated to poor, and high SFTPC, ZSCAN12, LPXN and METTL21A to favorable outcome. A multivariate analysis confirmed MESD, TNFAIP8 and ENO3 as risk factors and ZSCAN12 and LPXN as protective factors. Using a risk score formula, the 25 genes identified two groups of patients with different survival that was independent to the cell-of-origin molecular classification (5-year OS, low vs. high risk): 65% vs. 24%, respectively (Hazard Risk = 3.2, P < 0.000001). Finally, correlation with known DLBCL markers showed that high expression of all MYC, BCL2 and ENO3 associated to the worst outcome. CONCLUSION: By artificial intelligence we identified a set of genes with prognostic relevance

Hydrological connectivity inferred from diatom transport through the riparian-stream system

Funding for this research was provided by the Luxembourg National Research Fund (FNR) in the framework of the BIGSTREAM (C09/SR/14), ECSTREAM (C12/SR/40/8854) and CAOS (INTER/DFG/11/01) projects. We are most grateful to the Administration des Services Techniques de l’Agriculture (ASTA) for providing meteorological data. We also acknowledge Delphine Collard for technical assistance in diatom sample treatment and preparation, François Barnich for the water chemistry analyses, and Jean-François Iffly, Christophe Hissler, Jérôme Juilleret, Laurent Gourdol and Julian Klaus for their constructive comments on the project and technical assistance in the field.Peer reviewedPublisher PD

Using particle size distributions to fingerprint suspended sediment sources Evaluation at laboratory and catchment scales

Applications of sediment source fingerprinting studies are growing globally despite the high costs and workloads associated with the analyses of conventional fingerprint properties on target sediment samples collected using traditional methods. To this end, there is a need to test new fingerprint properties that can overcome these challenges. Sediment particle size could potentially contribute here since it is relatively easy to measure but, until now, has rarely been deployed as a fingerprint itself. Instead, particle size has been used to ensure that source and target sediment samples are more directly comparable on the basis of the fingerprints used. Accordingly, this work examined whether particle size distributions (PSDs) could be used as a reliable fingerprint for apportioning sediment sources, in combination with a grain size un-mixing model. Application of PSDs as a fingerprint was tested at two scales: (i) in a laboratory setting where soil samples with known PSDs were used to generate artificial mixtures to evaluate un-mixing model results, and (ii) a catchment setting comparing PSDs in a confluence-based approach to test if downstream target sediment PSDs could be un-mixed into the contributions of sediment coming from an upstream and a tributary sampling site. Laboratory results showed that the known proportions of the two, three and four soil samples in the artificial mixtures were predicted accurately using the AnalySize grain size un-mixing model, giving average absolute errors of 9%, 8% and 6%, respectively. Catchment results showed variable performances when comparing un-mixing results with sediment budget estimations, with the best results obtained at higher discharge values during storm runoff events. Overall, our results suggest the potential of using PSDs for estimating contributions of sediment sources delivering SS with distinct PSDs when sources are located at short distance to the downstream sampling site

An Intervention-AUV learns how to perform an underwater valve turning

Intervention autonomous underwater vehicles (I-AUVs) are a promising platform to perform intervention task in underwater environments, replacing current methods like remotely operate underwater vehicles (ROVs) and manned sub-mersibles that are more expensive. This article proposes a complete system including all the necessary elements to perform a valve turning task using an I-AUV. The knowledge of an operator to perform the task is transmitted to an I-AUV by a learning by demonstration (LbD) algorithm. The algorithm learns the trajectory of the vehicle and the end-effector to accomplish the valve turning. The method has shown its feasibility in a controlled environment repeating the learned task with different valves and configurations

High frequency un-mixing of soil samples using a submerged spectrophotometer in a laboratory setting—implications for sediment fingerprinting

Purpose This study tests the feasibility of using a submersible spectrophotometer as a novel method to trace and apportion suspended sediment sources in situ and at high temporal frequency. Methods Laboratory experiments were designed to identify how absorbance at different wavelengths can be used to un-mix artificial mixtures of soil samples (i.e. sediment sources). The experiment consists of a tank containing 40 L of water, to which the soil samples and soil mixtures of known proportions were added in suspension. Absorbance measurements made using the submersible spectrophotometer were used to elucidate: (i) the effects of concentrations on absorbance, (ii) the relationship between absorbance and particle size and (iii) the linear additivity of absorbance as a prerequisite for un-mixing. Results The observed relationships between soil sample concentrations and absorbance in the ultraviolet visible (UV–VIS) wavelength range (200–730 nm) indicated that differences in absorbance patterns are caused by soil-specific properties and particle size. Absorbance was found to be linearly additive and could be used to predict the known soil sample proportions in mixtures using the MixSIAR Bayesian tracer mixing model. Model results indicate that dominant contributions to mixtures containing two and three soil samples could be predicted well, whilst accuracy for four-soil sample mixtures was lower (with respective mean absolute errors of 15.4%, 12.9% and 17.0%). Conclusion The results demonstrate the potential for using in situ submersible spectrophotometer sensors to trace suspended sediment sources at high temporal frequency

Fractional generalization of Fick's law: a microscopic approach

In the study of transport in inhomogeneous systems it is common to construct transport equations invoking the inhomogeneous Fick law. The validity of this approach requires that at least two ingredients be present in the system. First, finite characteristic length and time scales associated to the dominant transport process must exist. Secondly, the transport mechanism must satisfy a microscopic symmetry: global reversibility. Global reversibility is often satisfied in nature. However, many complex systems exhibit a lack of finite characteristic scales. In this Letter we show how to construct a generalization of the inhomogeneous Fick law that does not require the existence of characteristic scales while still satisfying global reversibility.Comment: 4 pages. Published versio

Use of a submersible spectrophotometer probe to fingerprint spatial suspended sediment sources at catchment scale

Sediment fingerprinting is used to identify catchment sediment sources. Traditionally, it has been based on the collection and analysis of potential soil sources and target sediment. Differences between soil source properties (i.e., fingerprints) are then used to discriminate between sources, allowing the quantification of the relative source contributions to the target sediment. The traditional approach generally requires substantial resources for sampling and fingerprint analysis, when using conventional laboratory procedures. In pursuit of reducing the resources required, several new fingerprints have been tested and applied. However, despite the lower resource demands for analysis, most recently proposed fingerprints still require resource intensive sampling and laboratory analysis. Against this background, this study describes the use of UV-VIS absorbance spectra for sediment fingerprinting, which can be directly measured by submersible spectrophotometers on water samples in a rapid and non-destructive manner. To test the use of absorbance to estimate spatial source contributions to the target suspended sediment (SS), water samples were collected from a series of confluences during three sampling campaigns in which a confluence-based approach to source fingerprinting was undertaken. Water samples were measured in the laboratory and, after compensation for absorbance influenced by dissolved components and SS concentration, absorbance readings were used in combination with the MixSIAR Bayesian mixing model to quantify spatial source contributions. The contributions were compared with the sediment budget, to evaluate the potential use of absorbance for sediment fingerprinting at catchment scale. Overall deviations between the spatial source contributions using source fingerprinting and sediment budgeting were 18 % for all confluences (n = 11), for all events (n = 3). However, some confluences showed much higher deviations (up to 52 %), indicating the need for careful evaluation of the results using the spectrophotometer probe. Overall, this study shows the potential of using absorbance, directly obtained from grab water samples, for sediment fingerprinting in natural environments