A Fast Reconstruction Algorithm for Gene Networks

This paper deals with gene networks whose dynamics is assumed to be generated by a continuous-time, linear, time invariant, finite dimensional system (LTI) at steady state. In particular, we deal with the problem of network reconstruction in the typical practical situation in which the number of available data is largely insufficient to uniquely determine the network. In order to try to remove this ambiguity, we will exploit the biologically a priori assumption of network sparseness, and propose a new algorithm for network reconstruction having a very low computational complexity (linear in the number of genes) so to be able to deal also with very large networks (say, thousands of genes). Its performances are also tested both on artificial data (generated with linear models) and on real data obtained by Gardner et al. from the SOS pathway in Escherichia coli.Comment: 12 pages, 3 figure

Time resolved diffuse optical spectroscopy with geometrically accurate models for bulk parameter recovery

A novel straightforward, accessible and efficient approach is presented for performing hyperspectral time-domain diffuse optical spectroscopy to determine the optical properties of samples accurately using geometry specific models. To allow bulk parameter recovery from measured spectra, a set of libraries based on a numerical model of the domain being investigated is developed as opposed to the conventional approach of using an analytical semi-infinite slab approximation, which is known and shown to introduce boundary effects. Results demonstrate that the method improves the accuracy of derived spectrally varying optical properties over the use of the semi-infinite approximation

Discrimination of thermal baths by single qubit probes

Non-equilibrium states of quantum systems in contact with thermal baths help telling environments with different temperatures or different statistics apart. We extend these studies to a more generic problem that consists in discriminating between two baths with disparate constituents at unequal temperatures. Notably there exist temperature regimes in which the presence of coherence in the initial state preparation is beneficial for the discrimination capability. We also find that non-equilibrium states are not universally optimal, and detail the conditions in which it becomes convenient to wait for complete thermalisation of the probe. These concepts are illustrated in a linear optical simulation.Comment: Few typos corrected, bibliography expande

Biological Notes and Distribution in Southern Europe of Aclees taiwanensis Kono, 1933 (Coleoptera: Curculionidae): A New Pest of the Fig Tree

Ficus carica L. is one of the earliest cultivated fruit trees, and figs are a typical fruit of the Mediterranean diet and traditional medicine as well. In recent years, a new pest, the black weevil Aclees taiwanensis Kono, 1933 (Coleoptera: Curculionidae) native to Asia, has been recorded in France and Italy. Aclees taiwanensis causes the rapid death of the fig tree by its larvae that dig alimentation galleries in the trunk and surface roots, compromising the phloem flux. In Italy, from 2005, the year of the first detection of A. taiwanensis, the fig production has nearly halved, decreasing from 20.09 t to 10.65 t. To date, no specific EU regulation has been applied to prevent the A. taiwanensis spread, and we can reasonably expect a rapid diffusion of this pest all over the Mediterranean area. To avoid the loss of the Mediterranean fig orchards, effective strategies to detect and control the black weevil are required. Such strategies need a detailed knowledge of A. taiwanensis distribution, biology, and physiology. This paper updates the known distribution of this species in Southern Europe, using a citizen science approach, and describes, under laboratory and field conditions, its main biological traits

Diffuse optical characterization of collagen absorption from 500 to 1700 nm

Reduction in scattering, high absorption, and spectral features of tissue constituents above 1000 nm could help in gaining higher spatial resolution, penetration depth, and specificity for in vivo studies, opening possibilities of near-infrared diffuse optics in tissue diagnosis. We present the characterization of collagen absorption over a broadband range (500 to 1700 nm) and compare it with spectra presented in the literature. Measurements were performed using a time-domain diffuse optical technique. The spectrum was extracted by carefully accounting for various spectral distortion effects, due to sample and system properties. The contribution of several tissue constituents (water, lipid, collagen, oxy, and deoxy-hemoglobin) to the absorption properties of a collagen-rich in vivo bone location, such as radius distal in the 500-to 1700-nm wavelength region, is also discussed, suggesting bone diagnostics as a potential area of interest

Time-Resolved Diffuse Optical Spectroscopy up to 1700 nm by Means of a Time-Gated InGaAs/InP Single-Photon Avalanche Diode

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Early peripheral clearance of leukemia-associated immunophenotypes in AML: centralized analysis of a randomized trial

Although genetics is a relevant risk factor in acute myeloid leukemia (AML), it can be minimally informative and/or not readily available for the early identification of patients at risk for treatment failure. In a randomized trial comparing standard vs high-dose induction (ClinicalTrials.gov 64NCT00495287), we studied early peripheral blast cell clearance (PBC) as a rapid predictive assay of chemotherapy response to determine whether it correlates with the achievement of complete remission (CR), as well as postremission outcome, according to induction intensity. Individual leukemia-associated immunophenotypes (LAIPs) identified pretherapy by flow cytometry were validated and quantified centrally after 3 days of treatment, expressing PBC on a logarithmic scale as the ratio of absolute LAIP1 cells on day 1 and day 4. Of 178 patients, 151 (84.8%) were evaluable. Patients in CR exhibited significantly higher median PBC (2.3 log) compared with chemoresistant patients (1.0 log; P<.0001). PBC<1.0 predicted the worst outcome (CR, 28%). With 1.5 log established as the most accurate cutoff predicting CR, 87.5% of patients with PBC .1.5 (PBChigh, n = 96) and 43.6% of patients with PBC 641.5 (PBClow, n = 55) achieved CR after single-course induction (P<.0001). CR and PBChigh rates were increased in patients randomized to the high-dose induction arm (P 5 .04) and correlated strongly with genetic/cytogenetic risk. In multivariate analysis, PBC retained significant predictive power for CR, relapse risk, and survival. Thus, PBC analysis can provide a very early prediction of outcome, correlates with treatment intensity and disease subset, and may support studies of customized AML therapy

In-vivo multilaboratory investigation of the optical properties of the human head

The in-vivo optical properties of the human head are investigated in the 600–1100 nm range on different subjects using continuous wave and time domain diffuse optical spectroscopy. The work was performed in collaboration with different research groups and the different techniques were applied to the same subject. Data analysis was carried out using homogeneous and layered models and final results were also confirmed by Monte Carlo simulations. The depth sensitivity of each technique was investigated and related to the probed region of the cerebral tissue. This work, based on different validated instruments, is a contribution to fill the existing gap between the present knowledge and the actual in-vivo values of the head optical properties

Performance assessment of time-domain optical brain imagers, part 1: basic instrumental performance protocol

open21siAbstract.  Performance assessment of instruments devised for clinical applications is of key importance for validation and quality assurance. Two new protocols were developed and applied to facilitate the design and optimization of instruments for time-domain optical brain imaging within the European project nEUROPt. Here, we present the “Basic Instrumental Performance” protocol for direct measurement of relevant characteristics. Two tests are discussed in detail. First, the responsivity of the detection system is a measure of the overall efficiency to detect light emerging from tissue. For the related test, dedicated solid slab phantoms were developed and quantitatively spectrally characterized to provide sources of known radiance with nearly Lambertian angular characteristics. The responsivity of four time-domain optical brain imagers was found to be of the order of 0.1  m2 sr. The relevance of the responsivity measure is demonstrated by simulations of diffuse reflectance as a function of source-detector separation and optical properties. Second, the temporal instrument response function (IRF) is a critically important factor in determining the performance of time-domain systems. Measurements of the IRF for various instruments were combined with simulations to illustrate the impact of the width and shape of the IRF on contrast for a deep absorption change mimicking brain activation.H. Wabnitz; D. R. Taubert; M. Mazurenka; O. Steinkellner; A. Jelzow;R. Macdonald;D. Milej;P. Sawosz;M. Kacprzak;A. Liebert;R. Cooper;J. Hebden;A. Pifferi;A. Farina;I. Bargigia;D. Contini;M. Caffini;L. Zucchelli;L. Spinelli;R. Cubeddu;A. TorricelliH., Wabnitz; D. R., Taubert; M., Mazurenka; O., Steinkellner; A., Jelzow; R., Macdonald; D., Milej; P., Sawosz; M., Kacprzak; A., Liebert; R., Cooper; J., Hebden; Pifferi, ANTONIO GIOVANNI; Farina, Andrea; Bargigia, Ilaria; Contini, Davide; Caffini, Matteo; Zucchelli, LUCIA MARIA GRAZIA; Spinelli, Lorenzo; Cubeddu, Rinaldo; Torricelli, Alessandr

Twenty questions from the surgeon to the radiologist to better plan an open partial horizontal laryngectomy

Open partial horizontal laryngectomies (OPHLs) represent a valuable therapeutic option for tumors of the intermediate T-category and, in selected cases, for locally advanced tumors with low-volume extra-laryngeal extension. The eligibility of patients treated with this type of surgery has increased with the introduction of the modular approach to OPHL planning. This strategy follows the introduction of the classification proposed by the European Laryngological Society, based on the extent of horizontal resection. Optimization of the selection is the result of a meticulous work-up process involving close cooperation between experienced surgeons and radiologists, followed by final quality control by pathologists. Computed tomography and magnetic resonance imaging are study methods whose pearls and pitfalls are well known, especially when performed at a high level of expertise. In this paper, based on the experience of two high-volume centers, a checklist of 20 questions addressed by the surgeon to the radiologist before planning an OPHL was proposed. Considerations regarding case selection are reported for each of the questioned parameters. A very simple question-and-answer process is easy to understand and mainly addressed by less experienced colleagues who wish to increase their knowledge and skills in performing this type of surgery