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

Phosphorus recovery from a pilot-scale grate furnace: influencing factors beyond wet chemical leaching conditions

Phosphorus is a non-renewable resource going to exhaustion in the future. Sewage sludge ash is a promising secondary raw material due to its high phosphorus content. In this work, the distribution of 19 elements in bottom and cyclone ashes from pilot-scale grate furnace have been monitored to determine the suitability for the phosphorus acid extraction. Moreover, the influence of some parameters beyond wet chemical leaching conditions were investigated. Experimental results showed that bottom ash presented lower contamination in comparison to cyclone ash and low co-dissolution of heavy metals (especially Cr, Pb and Ni), while high phosphorus extraction efficiencies (76-86%) were achieved. High Al content in the bottom ash (9.4%) negatively affected the phosphorus extraction efficiency as well as loss on ignition, while the particle size reduction was necessary for ensuring a suitable contact surface. The typology of precipitating agents did not strongly affect the phosphorus precipitation, while pH was the key parameter. At pH 3.5-5, phosphorus precipitation efficiencies higher than 90% were achieved, with a mean phosphorus content in the recovered material equal to 16-17%, comparable to commercial fertilizers. Instead, the co-precipitation of Fe and Al had a detrimental effect on the recovered material, indicating the need for additional treatments

Affine arithmetic-based methodology for energy hub operation-scheduling in the presence of data uncertainty

In this study, the role of self-validated computing for solving the energy hub-scheduling problem in the presence of multiple and heterogeneous sources of data uncertainties is explored and a new solution paradigm based on affine arithmetic is conceptualised. The benefits deriving from the application of this methodology are analysed in details, and several numerical results are presented and discussed

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

Knee position at the moment of bone bruise could reflect the late phase of non-contact anterior cruciate ligament injury rather than the mechanisms leading to ligament failure

Purpose: The aim of the present study was to trace knee position at the time of bone bruise (BB) and investigate how much this position departed from the knee biomechanics of an in vivo flexion–extension. Methods: From an original cohort of 62 patients, seven (11%) presented bicompartmental edemas and were included in the study. 3D models of bones and BB were obtained from MRI. Matching bone edemas, a reconstruction of the knee at the moment of BB was obtained. For the same patients, knee kinematics of a squat was calculated using dynamic Roentgen sterephotogrammetric analysis (RSA). Data describing knee position at the moment of BB were compared to kinematics of the same knee extrapolated from RSA system. Results: Knee positions at the moment of BB was significantly different from the kinematics of the squat. In particular, all the patients’ positions were out of squat range for both anterior and proximal tibial translation, varus–valgus rotation (five in valgus and two in varus), tibial internal–external rotation (all but one, five externally and one internally). A direct comparison at same flexion angle between knee at the moment of BB (average 46.1° ± 3.8°) and knee during squat confirmed that tibia in the former was significantly more anterior (p < 0.0001), more externally rotated (6.1 ± 3.7°, p = 0.04), and valgus (4.1 ± 2.4°, p = 0.03). Conclusion: Knee position at the moment of Bone bruise position was out of physiological in-vivo knee range of motion and could reflect a locked anterior subluxation occurring in the late phase of ACL injury rather than the mechanism leading to ligament failure. Level of evidence: Level I

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

Prospective assessment of integrating the existing emergency medical system with automated external defibrillators fully operated by volunteers and laypersons for out-of-hospital cardiac arrest: the Brescia Early Defibrillation Study (BEDS)

AIMS: There are few data on the outcomes of cardiac arrest (CA) victims when the defibrillation capability of broad rural and urban territories is fully operated by volunteers and laypersons. METHODS AND RESULTS: In this study, we investigated whether a programme based on diffuse deployment of automated external defibrillators (AEDs) operated by 2186 trained volunteers and laypersons across the County of Brescia, Italy (area: 4826 km(2); population: 1 112 628), would safely and effectively impact the current survival among victims of out-of-hospital CA. Forty-nine AEDs were added to the former emergency medical system that uses manual EDs in the emergency department of 10 county hospitals and in five medically equipped ambulances. The primary endpoint was survival free of neurological impairment at 1-year follow-up. Data were analysed in 692 victims before and in 702 victims after the deployment of the AEDs. Survival increased from 0.9% (95% CI 0.4-1.8%) in the historical cohort to 3.0% (95% CI 1.7-4.3%) (P=0.0015), despite similar intervals from dispatch to arrival at the site of collapse [median (quartile range): 7 (4) min vs. 6 (6) min]. Increase of survival was noted both in the urban [from 1.4% (95% CI 0.4-3.4 %) to 4.0% (95% CI 2.0-6.9 %), P=0.024] and in the rural territory [from 0.5% (95% CI 0.1-1.6%) to 2.5% (95% CI 1.3-4.2%), P=0.013]. The additional costs per quality-adjusted life year saved amounted to euro39 388 (95% CI euro16 731-49 329) during the start-up phase of the study and to euro23 661 (95% CI euro10 327-35 528) at steady state. CONCLUSION: Diffuse implementation of AEDs fully operated by trained volunteers and laypersons within a broad and unselected environment proved safe and was associated with a significantly higher long-term survival of CA victims

Heavy Metals in Soil and Salad in the Proximity of Historical Ferroalloy Emission

Emissions of manganese (Mn), lead (Pb), iron (Fe), zinc (Zn), copper (Cu) from ferro-alloy operations has taken place in Valcamonica, a pre-Alp valley in the province of Brescia, Italy, for about a century until 2001. Metal concentrations were measured in the soil of local home gardens and in the cultivated vegetables. Soil analysis was carried out using a portable X-Ray Fluorescence (XRF) spectrometer in both surface soil and at 10 cm depth. A subset of soil samples (n = 23) additionally was analysed using the modified BCR sequential extraction method and ICP-OES for intercalibration with XRF (XRF Mn = 1.33 * total OES Mn – 71.8; R = 0.830, p < 0.0001). Samples of salads (Lactuca sativa and Chichorium spp.) were analyzed with a Total Reflection X-Ray Fluorescence (TXRF) technique. Vegetable and soil metal measurements were performed in 59 home gardens of Valcamonica, and compared with 23 gardens from the Garda Lake reference area. Results indicate significantly higher levels of soil Mn (median 986 ppm vs 416 ppm), Pb (median 46.1 ppm vs 30.2 ppm), Fe (median 19,800 ppm vs 13,100 ppm) in the Valcamonica compared to the reference area. Surface soil levels of all metals were significantly higher in surface soil compared to deeper soil, consistent with atmospheric deposition. Significantly higher levels of metals were shown also in lettuce from Valcamonica for Mn (median 53.6 ppm vs 30.2) and Fe (median 153 vs 118). Metals in Chichorium spp. did not differ between the two areas. Surface soil metal levels declined with increasing distance from the closest ferroalloy plant, consistent with plant emis- sions as the source of elevated soil metal levels. A correlation between Mn concentrations in soil and lettuce was also observed. These data show that historic ferroalloy plant activity, which ended nearly a decade before this study, has contributed to the persistence of increased Mn levels in locally grown vegetables. Further research is needed to assess whether this increase can lead to adverse effects in humans and plants especially for Mn, an essential element that can be toxic in humans when exceeding the homeostatic ranges

Dual-encoded magnetization transfer and diffusion imaging and its application to tract-specific microstructure mapping

We present a novel dual-encoded magnetization transfer (MT) and diffusion-weighted sequence and demonstrate its potential to resolve distinct properties of white matter fiber tracts at the sub-voxel level. The sequence was designed and optimized for maximal MT contrast efficiency. The resulting whole brain 2.6 mm isotropic protocol to measure tract-specific MT ratio (MTR) has a scan time under 7 minutes. Ten healthy subjects were scanned twice to assess repeatability. Two different analysis methods were contrasted: a technique to extract tract-specific MTR using Convex Optimization Modeling for Microstructure Informed Tractography (COMMIT), a global optimization technique; and conventional MTR tractometry. The results demonstrate that the tract-specific method can reliably resolve the MT ratios of major white matter fiber pathways and is less affected by partial volume effects than conventional multi-modal tractometry. Dual-encoded MT and diffusion is expected to both increase the sensitivity to microstructure alterations of specific tracts due to disease, ageing or learning, as well as lead to weighted structural connectomes with more anatomical specificity.Comment: 26 pages, 7 figure