Not proper ROC curves as new tool for the analysis of differentially expressed genes in microarray experiments

<p>Abstract</p> <p>Background</p> <p>Most microarray experiments are carried out with the purpose of identifying genes whose expression varies in relation with specific conditions or in response to environmental stimuli. In such studies, genes showing similar mean expression values between two or more groups are considered as not differentially expressed, even if hidden subclasses with different expression values may exist. In this paper we propose a new method for identifying differentially expressed genes, based on the area between the ROC curve and the rising diagonal (<it>ABCR</it>). <it>ABCR </it>represents a more general approach than the standard area under the ROC curve (<it>AUC</it>), because it can identify both proper (<it>i.e.</it>, concave) and not proper ROC curves (NPRC). In particular, NPRC may correspond to those genes that tend to escape standard selection methods.</p> <p>Results</p> <p>We assessed the performance of our method using data from a publicly available database of 4026 genes, including 14 normal B cell samples (NBC) and 20 heterogeneous lymphomas (namely: 9 follicular lymphomas and 11 chronic lymphocytic leukemias). Moreover, NBC also included two sub-classes, <it>i.e.</it>, 6 heavily stimulated and 8 slightly or not stimulated samples. We identified 1607 differentially expressed genes with an estimated False Discovery Rate of 15%. Among them, 16 corresponded to NPRC and all escaped standard selection procedures based on <it>AUC </it>and <it>t </it>statistics. Moreover, a simple inspection to the shape of such plots allowed to identify the two subclasses in either one class in 13 cases (81%).</p> <p>Conclusion</p> <p>NPRC represent a new useful tool for the analysis of microarray data.</p

The automation of the \"Welding Machine\" for the DUs integration in the KM3NeT experiment

This note describes some technical aspects, in particular the control system, of one of the tools used during Process-1 of the integration of the Detection Units (DUs) in the KM3NeT experiment. In particular, the device is designed to seal the Break-out-box (BOB). The BOB is a box interface between a Digital Optical Module (DOM) and the electro-optical cable (VEOC) for power and optical connection of each optical module (DOM) to the DU. The original manual version of the tool developed by NIKHEF was then automatized by INFN-LNS in order to guarantee a replicable operation in the recursive process of the DU integration and two samples have been developed for the integration sites at LNS and Genova respectively. The general principle and performances of the automated welding machine will be presented shortly in a dedicated INFN report. Here we summarize the cycle of the operations performed by the machine and how they are managed by corresponding control program and related electronics boards

The integration of the detection units of KM3NET in Genova

The KM3NeT experiment (1) for the detection of high energy cosmic neutrinos is being built in two sites of the Mediterranean Sea: Capo Passero in Sicily and Toulon in the French coast. The full detection system includes 3 building blocks of Detection Units (DU) (2), each block of 115 DUs. The DU accommodates up to 18 digital optical modules (DOMs) (3). In this note we describe the facility to integrate the DOMs to the vertical cable of the line (VEOC) as realized in our ground floor laboratory of the INFN Institute in Genova

Effect of the ingestion in the WRF model of different Sentinel-derived and GNSS-derived products: analysis of the forecasts of a high impact weather event

This paper presents the first experimental results of a study on the ingestion in the Weather Research and Forecasting (WRF) model, of Sentinel satellites and Global Navigation Satellite Systems (GNSS) derived products. The experiments concern a flash-floodevent occurred in Tuscany (Central Italy) in September 2017. The rationale is that numerical weather prediction (NWP) models are presently able to produce forecasts with a km scale spatial resolution, but the poor knowledge of the initial state of the atmosphere may imply an inaccurate simulation of the weather phenomena. Hence, to fully exploit the advances in numerical weather modelling, it is necessary to feed them with high spatiotemporal resolution information over the surface boundary and the atmospheric column. In this context, the Copernicus Sentinel satellites represent an important source of data, because they can provide a set of high-resolution observations of physical variables (e.g. soil moisture, land/sea surface temperature, wind speed) used in NWP models runs. The possible availability of a spatially dense network of GNSS stations is also exploited to assimilate water vapour content. Results show that the assimilation of Sentinel-1 derived wind field and GNSS-derivedwater vapour data produce the most positive effects on the performance of the forecast

The new "Welding Machine" for the DUs integration in the KM3NeT experiment: Mechanical and Pneumatic parts

This note describes one of the tools used during Process-1 of the integration of the Detection Units (DUs) in the KM3NeT experiment. In particular, the device is designed to seal the Break-out-box (BOB). The BOB is a box interface between a Digital Optical Module (DOM) and the electro-optical cable (VEOC) for power and optical connection of each optical module (DOM) to the DU. The original manual version of the tool developed by NIKHEF was then automatized by INFN-LNS in order to guarantee a reproducible operation in the recursive process of the DU integration and two samples have been realized for the integration sites at LNS and Genova respectively

Time-course of plasma NT-proc-type natriuretic peptide in end-stage heart failure patients supported by left ventricular assist device implant

Purpose: Atrial natriuretic peptide (ANP) and B-type natriuretic peptide (BNP) as well as the respective amino-terminal NT-proANP and NT-proBNP have now been well established as predictors of outcome in patients with heart failure (HF). C-type natriuretic peptide (CNP) and NT-proCNP are increased in HF patients as a function of disease severity, supporting a role for these peptides in the pathophysiology of HF, but their modifications during left ventricular assist device (LVAD) implant are lacking. Aim of this study was to evaluate the time-course of natriuretic peptides in end-stage HF patients undergoing LVAD implant in order to recognize new reliable predictive biomakers of cardiac recovery during LVAD. Methods: Five end-stage HF patients (NYHA class III and IV; age: 57?11 yrs; LVEF%<20) undergoing LVAD implantation were studied. Clinical hemodynamic evaluation and blood samples were obtained at admission (T1) and at 4, 24, 72 hrs and 1, 2, 4 weeks (T2-T7) after LVAD implant. NT-proANP and NT-proCNP were measured in plasma EDTA and aprotinin samples by a direct ELISA () while NT-proBNP by the Elecsys? 2010 analyzer. Results: The NT-proCNP time-course during LVAD was the following: T1=88.8?12.8 pg/ml; T2=144?29.8; T3=241.6?86.8 (p<0.05 vs T1); T4=229.7?66.4; T5=162.3?66.5; T6=175.3?47.7; T7=76.9?8 (p=ns vs T1). NT-proANP showed a similar pathway while NT-proBNP is reduced after LVAD implant (T1=4.1?2.2 ng/ml; T3=3.0?0.4), remaining lower than at baseline until 4 weeks (T7=3.1?0.9 ng/ml). NT-proCNP positively correlated with NT-proANP (p=0.03) while no correlation was found with NT-proBNP. Conclusions: This study reports for the first time original data on NT-proCNP levels after LVAD as a function of the time. The natriuretic peptides are differently modulated by LVAD, although all peptides resulted reduced after 4 weeks from implantation. The parallel determination of these effectors could allow us to obtain an integrated description of pathophysiological changes occurring during mechanical support

Smart environments and context-awareness for lifestyle management in a healthy active ageing framework

Health trends of elderly in Europe motivate the need for technological solutions aimed at preventing the main causes of morbidity and premature mortality. In this framework, the DOREMI project addresses three important causes of morbidity and mortality in the elderly by devising an ICT-based home care services for aging people to contrast cognitive decline, sedentariness and unhealthy dietary habits. In this paper, we present the general architecture of DOREMI, focusing on its aspects of human activity recognition and reasoning

A Fatal Case of Nosocomial Legionnaires' Disease: Implications From an Extensive Environmental Investigation and Isolation of the Bacterium From Blood Culture

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Road traffic pollution and childhood leukemia: a nationwide case-control study in Italy

Background The association of childhood leukemia with traffic pollution was considered in a number of studies from 1989 onwards, with results not entirely consistent and little information regarding subtypes. Aim of the study We used the data of the Italian SETIL case-control on childhood leukemia to explore the risk by leukemia subtypes associated to exposure to vehicular traffic. Methods We included in the analyses 648 cases of childhood leukemia (565 Acute lymphoblastic–ALL and 80 Acute non lymphoblastic-AnLL) and 980 controls. Information on traffic exposure was collected from questionnaire interviews and from the geocoding of house addresses, for all periods of life of the children. Results We observed an increase in risk for AnLL, and at a lower extent for ALL, with indicators of exposure to traffic pollutants. In particular, the risk was associated to the report of closeness of the house to traffic lights and to the passage of trucks (OR: 1.76; 95% CI 1.03–3.01 for ALL and 6.35; 95% CI 2.59–15.6 for AnLL). The association was shown also in the analyses limited to AML and in the stratified analyses and in respect to the house in different period of life. Conclusions Results from the SETIL study provide some support to the association of traffic related exposure and risk for AnLL, but at a lesser extent for ALL. Our conclusion highlights the need for leukemia type specific analyses in future studies. Results support the need of controlling exposure from traffic pollution, even if knowledge is not complete