pinecone/core-2020-05-10-deduplication huggingface dataset:
Outcome-based determination of optimal pyrosequencing assay for MGMT methylation detection in glioblastoma patients.

Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited. The online version of this article (doi:10.​1007/​s11060-013-1332-y) contains supplementary material, which is available to authorized users.International audienceThe methylation of O(6)-methylguanine DNA methyltransferase (MGMT) gene promoter is a key biological marker in clinical neuro-oncology. Nevertheless, there is no consensus concerning the best technique for its assessment. In a recent study comparing five methods to analyze MGMT status, we found that the best prediction of survival was obtained with a pyrosequencing (PSQ) test assessing methylation of 5 CpGs (CpGs 74-78). In the present study we extended our PSQ analysis to 16 CpGs (CpGs 74-89) identified as critical for transcriptional control of the gene. The predictive value of the methylation levels at each CpG, as well as the mean methylation levels of selected sets of consecutive CpGs was tested in a cohort of 89 de novo glioblastoma patients who had received standard of care treatment (Stupp protocol). Using an optimal risk cut-off, each CpG or combination of CpGs, was associated with overall survival (OS) and progression free survival. The best predictive models for OS after stratification on performance score and age were obtained with CpG 89, CpG 84 and mean methylation of CpG 84-88 (Hazard ratio (HR), 0.31; p < 0.0001). The improvement compared to the predictive value of the test analyzing average methylation of CpG 74-78 (HR, 0.32; p < 0.0001) was however marginal. We recommend to test CpGs 74-78 when analyzing MGMT methylation status by PSQ because a commercial kit that has successfully been used in several studies is available, allowing reproducible and comparable results from one laboratory to another
Using 2D inversion of magnetic resonance soundings to locate a water-filled karst conduit

A new methodology for magnetic resonance sounding (MRS) data acquisition and interpretation was developed for locating water-filled karst cavities. This methodology was used to investigate the Ouysse karst system in the Poumeyssens shaft in the Causse de Gramat (France). A new 2D numerical MRS response model was designed for improved accuracy over the previous 1D MRS approach. A special survey performed by cave divers confirmed the accuracy of the MRS results. Field results demonstrated that in favourable conditions (a low EM noise environment and a relatively shallow, large target) the MRS method, used with a coincident transmitter/receiver loop, can be an effective tool for locating a water-filled karst conduit. It was shown numerically that because an a priori orientation of the MRS profile with the karst conduit is used in the inversion scheme (perpendicular for instance), any error in this assumption introduces an additional error in locating the karst. However, the resulting error is within acceptable limits when the deviation is less than 30°. The MRS results were compared with an electrical resistivity tomography (ERT) survey. It was found that in Poumeyssens, ERT is not able to locate the water-filled karst. On the other hand, ERT provides additional information about heterogeneities in the limestone
Breaking the dimensionality curse in multi-server queues

International audiencePh/Ph/c and and Ph/Ph/c/N queues can be viewed as a common model of multi-server facilities. We propose a simple approximate solution for the equilibrium probabilities in such queues based on a reduced state description in order to circumvent the well-known and dreaded combinatorial growth of the number of states inherent in the classical state description. The number of equations to solve in our approach increases linearly with the number of servers and phases in the service time distribution. A simple fixed-point iteration is used to solve these equations. Our approach applies both to open models with unrestricted buffer size and to queues with finite-size buffers. The results of a large number of empirical studies indicate that the overall accuracy of the proposed approximation appears very good. For instance, the median relative error for the mean number in the queue over thousands of examples is below 0.1% and the relative error exceeds 5% in less than 1.5% of cases explored. The accuracy of the proposed approximation becomes particularly good for systems with more than 8 servers, and tends to become excellent as the number of servers increases
Fluid circulation pattern inside La Soufrière volcano (Guadeloupe) inferred from combined electrical resistivity tomography, self-potential, soil temperature and diffuse degassing measurements

International audienceAfter a drastic decline in 1983, hydrothermal activity at La Soufrière lava dome (Guadeloupe, Lesser Antilles) has been progressively increasing in the summit area since 1992, raising the threat of a renewed eruptive activity. To better constrain the geometry of the hydrothermal system, an extensive high-resolution self-potential survey was performed on the dome and three multi-method profiles combining electrical resistivity tomography, self-potential, ground thermometry and soil CO 2 diffuse degassing measurements were carried out to cover its southern periphery in January 2011. Results indicate that hydrothermal ascending flows are currently restricted to a proximal area including the dome and its very vicinity. The extension of hydrothermal alteration inferred from electrical resistivity tomography reflects the presence of a heat source just below the dome. A first-order correction of topography-related self-potential variations allows the identification of major hydrothermal fluid circulations pathways, as well as significant meteoric infiltration zones. Local shifting of hydrothermal fluids towards the dome periphery is favored by the presence of major axes. The regional La Ty fault appears as the major axis draining large volumes of hydrothermal and magmatic fluids. However hydrothermal activity remains confined inside a collapse structure surrounding the dome, that formed in the last 9000 years as a result of recurrent edifice collapses, the latest occurring at the onset of the 1530 AD eruption. The combination of these qualitative results with structural analysis leads to a synthetic model of magmatic and hydrothermal fluids circulation inside the dome, which may be useful for the assessment of potential hazards associated with a renewal of fluid pres-surization, and a possibly associated partial flank-failure
The role of organic anion-transporting polypeptides and their common genetic variants in mycophenolic acid pharmacokinetics.

International audienceThe goal of this study was to determine the roles of the organic anion-transporting polypeptides (OATPs) OATP1A2, OATP1B1, and OATP1B3 and their genetic variants in the pharmacokinetics of the immunosuppressive drug mycophenolate mofetil (MMF). Using OATP-transfected human embryonic kidney (HEK) cells, we measured the uptake of mycophenolic acid (MPA) and its glucuronide (MPAG). MPAG, but not MPA, significantly accumulated in cells expressing OATP1B3 or OATP1B1 (P < 0.05). The pharmacokinetics of both MPA and MPAG were significantly influenced by the OATP1B3 polymorphism 334T>G/699G>A in 70 renal transplant patients receiving combination treatment of MMF with either tacrolimus or sirolimus, but not in 115 patients receiving MMF and cyclosporine. The decrease in dose-normalized (dn) MPA exposure and the concomitant increase in the MPAG/MPA metabolic ratio are consistent with reduced enterohepatic cycling in patients carrying the OATP1B3 334G-699A haplotype. Further studies demonstrated that this variant of OATP1B3 exhibited a reduced maximal velocity (V(max)) in transfected HEK cells, thereby providing functional evidence to support our clinical findings
On the stress-wave imaging of cavities in a semi-infinite solid

The problem of mapping underground cavities from surface seismic measurements is investigated within the framework of a regularized boundary integral equation (BIE) method. With the ground modeled as a uniform elastic half-space, the inverse analysis of elastic waves scattered by a three-dimensional void is formulated as a task of minimizing the misfit between experimental observations and theoretical predictions for an assumed void geometry. For an accurate treatment of the gradient search technique employed to solve the inverse problem, sensitivities of the predictive BIE model with respect to cavity parameters are evaluated semi-analytically using an adjoint problem approach and a continuum kinematics description. Several key features of the formulation, including the rigorous treatment of the radiation condition for semi-infinite solids, modeling of an illuminating seismic wave field, and treatment of the prior information, are highlighted. A set of numerical examples with spherical and ellipsoidal cavity geometries is included to illustrate the performance of the method. It is shown that the featured adjoint problem approach reduces the computational requirements by an order of magnitude relative to conventional finite-difference estimates, thus rendering the three-dimensional elastic-wave imaging of solids tractable for engineering applications
New predictive scheme for the control of LTI systems with input delay and unknown disturbances

International audienceA new predictive scheme is proposed for the control of Linear Time Invariant (LTI) systems with a constant and known delay in the input and unknown disturbances. It has been achieved to include disturbances effect in the prediction even though there are completely unknown. The Artstein reduction is thenrevisited thanks to the computation of this new prediction. An extensive comparison with the standard scheme is presented throughout the article. It is proved that the new scheme leads to feedback controllers that are able to reject perfectly constant disturbances. For time-varying ones, a better attenuation is achieved for a wide range of perturbations and for both linear and nonlinear controllers. A criterion is given to characterize this class of perturbations. Finally, some simulations illustrate the results
Bulgarian relative and factive clauses with an invariant complementizer

The paper offers an analysis of Bulgarian relative clauses introduced by the invariant complementizer deto ‘that’, whose\ud
distribution also extends to factive contexts. Using reconstruction as primary evidence for movement, I review the basic facts for its\ud
presence (amount readings, idiom interpretation, binding and scope) and absence (Principle C) and argue that both a raising and a\ud
matching analysis must be available for the derivation of deto-relatives. I also discuss the distribution and structural properties of\ud
resumptive clitics which are shown to block reconstruction in all types of contexts and hence to be compatible with a matching\ud
derivation only. Given the structural ambiguity in the derivation of Bulgarian complementizer relatives and in search of a unified\ud
treatment of their potentially ambivalent behavior, the paper applies Cinque’s (2003, 2008) analysis of relative clauses, which\ud
postulates two identical copies of the relativized Head (internal and external) and exploits different movement options to account for\ud
the raising and the matching derivations. It is then argued that such a proposal, which also exploits distinct CP positions, can\ud
successfully accommodate all of the observed reconstruction effects (or lack thereof), including the option of resumption. The paper\ud
also offers a discussion of factive clauses introduced by the same complementizer and proposes that they are best treated as hidden\ud
relatives embedded under a more complex structure involving a PP projection and a silent D head
Comparative EPMA and μ-XRF methods for mapping micro-scale distribution of iodine in biocarbonates of the Callovian-Oxfordian clayey formation at Bure, Eastern part of the Paris Basin

International audienceA pluridisciplinary approach was used to define iodine immobilization mechanisms by biocarbonates in a natural marine carbonate-bearing clayey formation. For this purpose, different techniques of observation (optical microscope, scanning electron microscope (SEM), cathodoluminescence (CL)) and of analyses (infrared spectrometry (IR), electron microprobe (EPMA), spatially resolved synchrotron-based X-ray fluorescence (μ-XRF) and X-ray diffraction (μ-XRD)) were performed on two entire and centimeter-sized carbonate shells of the Callovian-Oxfordian (160 Ma) clayey formation from the ANDRA (French Radioactive Waste Management Agency) Underground Research Laboratory (Meuse/Haute Marne, France), in the Eastern part of the Paris Basin. Combined (SEM, CL, IR and μ-XRD) data indicates that the biostructure of the Rhynchonella shell is relatively well-preserved but bio-aragonite slowly transforms into calcite, whereas the bivalve shell is entirely recrystallized into diagenetic calcite and celestite. EPMA and μ-XRF data show bioaccumulation of iodine in carbonate shells, confirming previous work on present-day mollusks. EPMA analyses give evidence of iodine content up to 1200 ppm in the preserved Rhynchonella shell and up to 2000 ppm in recrystallized bivalve shell. μ-XRF elemental mapping shows that iodine is more homogeneously distributed in bio-calcite of the Rhynchonella shell than in recrystallized calcite of the bivalve shell, suggesting a loss of iodine during re-crystallization processes, but not a total exclusion of iodine from the carbonate structure. Combined EPMA data and μ-XRF elemental maps do not give evidence of any correlation between the iodine location and the distribution of other elements
An Emerging Role of mTOR in Lipid Biosynthesis

Lipid biosynthesis is essential for the maintenance of cellular homeostasis. The lipids produced by cells (glycerolipids, fatty acids, phospholipids, cholesterol, and sphingolipids) are used as an energy source/reserve, as building blocks for membrane biosynthesis, as precursor molecules for the synthesis of various cellular products, and as signaling molecules. Defects in lipid synthesis or processing contribute to the development of many diseases, including obesity, insulin resistance, type 2 diabetes, non-alcoholic fatty liver disease, and cancer. Studies published over the last few years have shown that the target of rapamycin (TOR), a conserved serine/threonine kinase with an important role in regulating cell growth, controls lipid biosynthesis through various mechanisms. Here, we review these findings and briefly discuss their potential relevance for human health and disease
Progression of coronary artery calcification and cardiac events in patients with chronic renal disease not receiving dialysis

We tested for the presence of coronary calcifications in patients with chronic renal disease not on dialysis and studied its progression in 181 consecutive non-dialyzed patients who were followed for a median of 745 days. Coronary calcifications (calcium score) were tallied in Agatston units by computed tomography, and the patients were stratified into two groups by their baseline calcium score (100U or less and over 100U). Survival was measured by baseline calcium score and its progression. Cardiac death and myocardial infarction occurred in 29 patients and were significantly more frequent in those patients with calcium scores over 100U (hazard ratio of 4.11). With a calcium score of 100U or less, the hazard ratio for cardiac events was 0.41 and 3.26 in patients with absent and accelerated progression, respectively. Thus, in non-dialyzed patients, the extent of coronary calcifications was associated to cardiac events, and progression was an independent predictive factor of cardiac events mainly in less calcified patients. Hence, assessment of coronary calcifications and progression might be useful for earlier management of risk factors and guiding decisions for prevention of cardiac events in this patient population
New results on lower bounds for the number of k-facets

In this paper we present three different results dealing with the number of (≤ k)- facets of a set of points: (i) We give structural properties of sets in the plane that achieve the optimal lower bound 3_k+2 2 _ of (≤ k)-edges for a fixed k ≤ [n/3 ]− 1; (ii) We show that the new lower bound 3((k+2) 2 ) + 3((k−(n/ 3)+2) 2 ) for the number of (≤ k)-edges of a planar point set  is optimal in the range [n/3] ≤ k ≤ [5n/12] − 1; (iii) We show that for k < n/4 the number of (≤ k)-facets of a set of n points in R3 in general position is at least 4((k+3 )3 ), and that this bound is tight in that range
A Genetic Algorithm Approach for the TV Self-Promotion Assignment Problem

We report on the development of a Genetic Algorithm (GA), which has been integrated into a Decision Support System to plan the best assignment of the weekly self-promotion space for a TV station. The problem addressed consists on deciding which shows to advertise and when such that the number of viewers, of an intended group or target, is maximized. The GA proposed incorporates a greedy heuristic to find good initial solutions. These solutions, as well as the solutions later obtained through the use of the GA, go then through a repair procedure. This is used with two objectives, which are addressed in turn. Firstly, it checks the solution feasibility and if unfeasible it is fixed by removing some shows. Secondly, it tries to improve the solution by adding some extra shows. Since the problem faced by the commercial TV station is too big and has too many features it cannot be solved exactly. Therefore, in order to test the quality of the solutions provided by the proposed GA we have randomly generated some smaller problem instances. For these problems we have obtained solutions on average within 1% of the optimal solution value
Opinion formation in multiplex networks with general initial distributions

We study opinion dynamics over multiplex networks where agents interact with bounded confidence. Namely, two neighbouring individuals exchange opinions and compromise if their opinions do not differ by more than a given threshold. In literature, agents are generally assumed to have a homogeneous confidence bound. Here, we study analytically and numerically opinion evolution over structured networks characterised by multiple layers with respective confidence thresholds and general initial opinion distributions. Through rigorous probability analysis, we show analytically the critical thresholds at which a phase transition takes place in the long-term consensus behaviour, over multiplex networks with some regularity conditions. Our results reveal the quantitative relation between the critical threshold and initial distribution. Further, our numerical simulations illustrate the consensus behaviour of the agents in network topologies including lattices and, small-world and scale-free networks, as well as for structure-dependent convergence parameters accommodating node heterogeneity. We find that the critical thresholds for consensus tend to agree with the predicted upper bounds in Theorems 4 and 5 in this paper. Finally, our results indicate that multiplexity hinders consensus formation when the initial opinion configuration is within a bounded range and, provide insight into information diffusion and social dynamics in multiplex systems modeled by networks
Bias dependence of tunneling-electron-induced molecular fluorescence from porphyrin films on noble-metal substrates

We investigated scanning tunneling microscope (STM)-excited luminescence from porphyrin (PhTPP and H2TPP) thin films on metal substrate (Au and Ag) under ambient conditions. Molecular fluorescence similar to the corresponding photoluminescence was observed from PhTPP/Au and H2TPP/Ag at both STM bias polarities. We found that at the same experimental condition and parameters, the STM-induced luminescence intensities of maxima peak are similar for PhTPP and H2TPP but weaker by a factor of about 4 than that for H2TBPP which we studied previously, probably due to fluorescence quenching by aggregation. The polarity dependence and the bias voltage dependence of the fluorescence intensity for the PhTPP/Au were similar to that for the respective pristine metal. These facts support our proposal that intense molecular fluorescence from porphyrin film on the noble metals is a result of the enhancement of molecular excitation by substrate surface plasmons
Real-time registration of paper watermarks

The aim of this article is to outline the issues involved in the application of machine vision to the automatic extraction and registration of watermarks from continuous web paper. The correct identiﬁcation and localisation of watermarks are key issues in paper manufacturing. As well as requiring the position of the watermark for defect detection and classiﬁcation, it is necessary to insure its position on the paper prior to the cutting process. Two paper types are discussed, with and without laid and chain lines(these lines appear as a complex periodic background to the watermark and further complicate the segmentation process). We will examine both morphological and Fourier approaches to the watermark segmentation process, concentrating speciﬁcally on those images with complex backgrounds. Finally we detail a system design suitable for real-time implementation
Personalisation of intelligent homecare services adapted to children with motor impairments

Ambient Intelligence could support innovative application domains like motor impairments' detection at the home environment. This research aims to prevent neurodevelopmental disorders through the natural interaction of the children with embedded intelligence daily life objects, like home furniture and toys. Designed system uses an interoperable platform to provide two intelligent interrelated home healthcare services: monitoring of children¿s abilities and completion of early stimulation activities. A set of sensors, which are embedded within the rooms, toys and furniture, allows private data gathering about the child's interaction with the environment. This information feeds a reasoning subsystem, which encloses an ontology of neurodevelopment items, and adapts the service to the age and acquisition of expected abilities. Next, the platform proposes customized stimulation services by taking advantage of the existing facilities at the child's environment. The result integrates Embedded Sensor Systems for Health at Mälardalen University with UPM Smart Home, for adapted services delivery