Integrative bioinformatics and omics data source interoperability in the next-generation sequencing era-Editorial

With the advent of high-throughput and next-generation sequencing (NGS) technologies [1], huge amounts of \u2018omics\u2019 data (i.e. data from genomics, proteomics, pharmacogenomics, metagenomics, etc.) are continuously produced. Combining and integrating diverse omics data types is important in order to investigate the molecular machinery of complex diseases, with the hope for better disease prevention and treatment [2]. Experimental data repositories of omics data are publicly available, with the main aim of fostering the cooperation among research groups and laboratories all over the world. However, despite their openness, the effective integrated use of available public sources is hampered by the heterogeneity, complexity and large size of data stored therein

Causality estimates among brain cortical areas by Partial Directed Coherence: simulations and application to real data

The problem of the definition and evaluation of brain connectivity has become a central one in neuroscience during the latest years, as a way to understand the organization and interaction of cortical areas during the execution of cognitive or motor tasks. Among various methods established during the years, the Partial Directed Coherence (PDC) is a frequency-domain approach to this problem, based on a multivariate autoregressive modeling of time series and on the concept of Granger causality. In this paper we propose the use of the PDC method on cortical signals estimated from high resolution EEG recordings, a non invasive method which exhibits a higher spatial resolution than conventional cerebral electromagnetic measures. The principle contributions of this work are the results of a simulation study, testing the performances of PDC, and a statistical analysis (via the ANOVA, analysis of variance) of the influence of different levels of Signal to Noise Ratio and temporal length, as they have been systematically imposed on simulated signals. An application to high resolution EEG recordings during a foot movement is also presented

Vegetation changes and water cycle in a changing environment

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Studying the WHIM with Gamma Ray Bursts

We assess the possibility to detect and characterize the physical state of the missing baryons at low redshift by analyzing the X-ray absorption spectra of the Gamma Ray Burst [GRB] afterglows, measured by a micro calorimeters-based detector with 3 eV resolution and 1000 cm2 effective area and capable of fast re-pointing, similar to that on board of the recently proposed X-ray satellites EDGE and XENIA. For this purpose we have analyzed mock absorption spectra extracted from different hydrodynamical simulations used to model the properties of the Warm Hot Intergalactic Medium [WHIM]. These models predict the correct abundance of OVI absorption lines observed in UV and satisfy current X-ray constraints. According to these models space missions like EDGE and XENIA should be able to detect about 60 WHIM absorbers per year through the OVII line. About 45 % of these have at least two more detectable lines in addition to OVII that can be used to determine the density and the temperature of the gas. Systematic errors in the estimates of the gas density and temperature can be corrected for in a robust, largely model-independent fashion. The analysis of the GRB absorption spectra collected in three years would also allow to measure the cosmic mass density of the WHIM with about 15 % accuracy, although this estimate depends on the WHIM model. Our results suggest that GRBs represent a valid, if not preferable, alternative to Active Galactic Nuclei to study the WHIM in absorption. The analysis of the absorption spectra nicely complements the study of the WHIM in emission that the spectrometer proposed for EDGE and XENIA would be able to carry out thanks to its high sensitivity and large field of view.Comment: 16 pages, 16 figures, accepted for publication by Ap

Role of perfusion CT in the evaluation of metastatic nodal tumor response after radiochemotherapy in head and neck cancer: preliminary findings

OBJECTIVE: To assess changes of CT perfusion parameters (ΔPCTp) of cervical lymph node metastases from head and neck cancer (HNC) before and after radiochemotherapy (RT-CT) and their association with nodal tumor persistence. PATIENTS AND METHODS: Eligibility criteria included HNC (Stage III-IV) candidates for RT-CT. Patients underwent perfusion CT (PCT) at baseline 3 weeks and 3 months after RT-CT. Blood volume (BV), blood flow (BF), mean transit time (MTT) and permeability surface (PS) were calculated. PET/CT examination was also performed at baseline and 3 months after treatment for metabolic assessment. RESULTS: Between July 2012 and May 2016, 27 patients were evaluated. Overall, only 3 patients (11%) experienced tumor persistence in the largest metastatic lymph node. A significant reduction of all PCTp values (p<0.0001), except MTT (from 6.3 to 5.7 s; p=0.089), was observed at 3 weeks post-RT-CT compared to baseline. All PCTp values including MTT were significantly lower at 3-month follow-up compared to baseline (p<0.05). Moreover, a statistical significant association was observed between nodal tumor persistence and high BF values (p=0.045) at 3 months after treatment that did not occur for the other parameters. CONCLUSIONS: Our preliminary findings show that all PCTp except MTT are significantly reduced after RT-CT. High BF values at 3 months post-RTCT are predictive of nodal tumor persistence

Xmm-Newton Observations of the Diffuse X-ray Background

We analyzed two XMM-Newton observations in the direction of the high density, high latitude, neutral hydrogen cloud MBM20 and of a nearby low density region that we called the Eridanus hole. The cloud MBM20 is at a distance evaluated between 100 and 200 pc from the Sun and its density is sufficiently high to shield about 75% of the foreground emission in the 3/4 keV energy band.The combination of the two observations makes possible an evaluation of the OVII and OVIII emission both for the foreground component due to the Local Bubble,and the background one, due primary to the galactic halo.The two observations are in good agreement with each other and with ROSAT observations of the same part of the sky and the OVII and OVIII fluxes are OVII=3.89+/-0.56 photons cm^-2 s^-1 sr^-1, OVIII=0.68+/-0.24 photons cm^-2 s^-1 sr^-1 for MBM20 and OVII=7.26+/-0.34 photons cm^-2 s^-1 sr^-1,OVIII=1.63+/-0.17 photons cm^-2 s^-1 sr^-1 for the Eridanus hole. The spectra are in agreement with a simple three component model, one unabsorbed and one absorbed plasma component, and a power law, without evidence for any strong contamination from ion exchange in the solar system. Assuming that the two plasma components are in thermal equilibrium we obtain a temperature of 0.096 keV for the foreground component and 0.197 keV for the background one. Assuming the foreground component is due solely to Local Bubble emission we obtain a lower and upper limit for the plasma density of 0.0079 cm^-3 and 0.0095 cm^-3 and limits of 16,200 cm^-3 K and 19,500 cm^-3 K for the plasma pressure, in good agreement with theoretical predictions. Similarly, assuming that the absorbed plasma component is due to Galactic halo emission, we obtain a plasma density ranging from 0.0009 cm^-3 to 0.0016 cm^-3, and a pressure ranging from 3.0*10^3 to 6.7*10^3 cm^-3 K.Comment: 31 pages, 5 figures, Accepted for publication in Ap