Transfer Learning for Domain Adaptation in MRI: Application in Brain Lesion Segmentation

Magnetic Resonance Imaging (MRI) is widely used in routine clinical diagnosis and treatment. However, variations in MRI acquisition protocols result in different appearances of normal and diseased tissue in the images. Convolutional neural networks (CNNs), which have shown to be successful in many medical image analysis tasks, are typically sensitive to the variations in imaging protocols. Therefore, in many cases, networks trained on data acquired with one MRI protocol, do not perform satisfactorily on data acquired with different protocols. This limits the use of models trained with large annotated legacy datasets on a new dataset with a different domain which is often a recurring situation in clinical settings. In this study, we aim to answer the following central questions regarding domain adaptation in medical image analysis: Given a fitted legacy model, 1) How much data from the new domain is required for a decent adaptation of the original network?; and, 2) What portion of the pre-trained model parameters should be retrained given a certain number of the new domain training samples? To address these questions, we conducted extensive experiments in white matter hyperintensity segmentation task. We trained a CNN on legacy MR images of brain and evaluated the performance of the domain-adapted network on the same task with images from a different domain. We then compared the performance of the model to the surrogate scenarios where either the same trained network is used or a new network is trained from scratch on the new dataset.The domain-adapted network tuned only by two training examples achieved a Dice score of 0.63 substantially outperforming a similar network trained on the same set of examples from scratch.Comment: 8 pages, 3 figure

The 3-Band Hubbard-Model versus the 1-Band Model for the high-Tc Cuprates: Pairing Dynamics, Superconductivity and the Ground-State Phase Diagram

One central challenge in high-$T_c$ superconductivity (SC) is to derive a detailed understanding for the specific role of the $Cu$-$d_{x^2-y^2}$ and $O$-$p_{x,y}$ orbital degrees of freedom. In most theoretical studies an effective one-band Hubbard (1BH) or t-J model has been used. Here, the physics is that of doping into a Mott-insulator, whereas the actual high-$T_c$ cuprates are doped charge-transfer insulators. To shed light on the related question, where the material-dependent physics enters, we compare the competing magnetic and superconducting phases in the ground state, the single- and two-particle excitations and, in particular, the pairing interaction and its dynamics in the three-band Hubbard (3BH) and 1BH-models. Using a cluster embedding scheme, i.e. the variational cluster approach (VCA), we find which frequencies are relevant for pairing in the two models as a function of interaction strength and doping: in the 3BH-models the interaction in the low- to optimal-doping regime is dominated by retarded pairing due to low-energy spin fluctuations with surprisingly little influence of inter-band (p-d charge) fluctuations. On the other hand, in the 1BH-model, in addition a part comes from "high-energy" excited states (Hubbard band), which may be identified with a non-retarded contribution. We find these differences between a charge-transfer and a Mott insulator to be renormalized away for the ground-state phase diagram of the 3BH- and 1BH-models, which are in close overall agreement, i.e. are "universal". On the other hand, we expect the differences - and thus, the material dependence to show up in the "non-universal" finite-T phase diagram ($T_c$-values).Comment: 17 pages, 9 figure

Optical Sum Rule in Finite Bands

In a single finite electronic band the total optical spectral weight or optical sum carries information on the interactions involved between the charge carriers as well as on their band structure. It varies with temperature as well as with impurity scattering. The single band optical sum also bears some relationship to the charge carrier kinetic energy and, thus, can potentially provide useful information, particularly on its change as the charge carriers go from normal to superconducting state. Here we review the considerable advances that have recently been made in the context of high $T_c$ oxides, both theoretical and experimental.Comment: Review article accepted for publication in J. Low Temp. Phys. 29 pages, 33 figure

The KASCADE-Grande Experiment and the LOPES Project

KASCADE-Grande is the extension of the multi-detector setup KASCADE to cover a primary cosmic ray energy range from 100 TeV to 1 EeV. The enlarged EAS experiment provides comprehensive observations of cosmic rays in the energy region around the knee. Grande is an array of 700 x 700 sqm equipped with 37 plastic scintillator stations sensitive to measure energy deposits and arrival times of air shower particles. LOPES is a small radio antenna array to operate in conjunction with KASCADE-Grande in order to calibrate the radio emission from cosmic ray air showers. Status and capabilities of the KASCADE-Grande experiment and the LOPES project are presented.Comment: To appear in Nuclear Physics B, Proceedings Supplements, as part of the volume for the CRIS 2004, Cosmic Ray International Seminar: GZK and Surrounding

Software engineering techniques for the development of systems of systems

This paper investigates how existing software engineering techniques can be employed, adapted and integrated for the development of systems of systems. Starting from existing system-of-systems (SoS) studies, we identify computing paradigms and techniques that have the potential to help address the challenges associated with SoS development, and propose an SoS development framework that combines these techniques in a novel way. This framework addresses the development of a class of IT systems of systems characterised by high variability in the types of interactions between their component systems, and by relatively small numbers of such interactions. We describe how the framework supports the dynamic, automated generation of the system interfaces required to achieve these interactions, and present a case study illustrating the development of a data-centre SoS using the new framework

Macroscopic limits and phase transition in a system of self-propelled particles

We investigate systems of self-propelled particles with alignment interaction. Compared to previous work, the force acting on the particles is not normalized and this modification gives rise to phase transitions from disordered states at low density to aligned states at high densities. This model is the space inhomogeneous extension of a previous work by Frouvelle and Liu in which the existence and stability of the equilibrium states were investigated. When the density is lower than a threshold value, the dynamics is described by a non-linear diffusion equation. By contrast, when the density is larger than this threshold value, the dynamics is described by a hydrodynamic model for self-alignment interactions previously derived in Degond and Motsch. However, the modified normalization of the force gives rise to different convection speeds and the resulting model may lose its hyperbolicity in some regions of the state space

Improved constraints on the expansion rate of the Universe up to z~1.1 from the spectroscopic evolution of cosmic chronometers

We present new improved constraints on the Hubble parameter H(z) in the redshift range 0.15 < z < 1.1, obtained from the differential spectroscopic evolution of early-type galaxies as a function of redshift. We extract a large sample of early-type galaxies (\sim11000) from several spectroscopic surveys, spanning almost 8 billion years of cosmic lookback time (0.15 < z < 1.42). We select the most massive, red elliptical galaxies, passively evolving and without signature of ongoing star formation. Those galaxies can be used as standard cosmic chronometers, as firstly proposed by Jimenez & Loeb (2002), whose differential age evolution as a function of cosmic time directly probes H(z). We analyze the 4000 {\AA} break (D4000) as a function of redshift, use stellar population synthesis models to theoretically calibrate the dependence of the differential age evolution on the differential D4000, and estimate the Hubble parameter taking into account both statistical and systematical errors. We provide 8 new measurements of H(z) (see Tab. 4), and determine its change in H(z) to a precision of 5-12% mapping homogeneously the redshift range up to z \sim 1.1; for the first time, we place a constraint on H(z) at z \neq 0 with a precision comparable with the one achieved for the Hubble constant (about 5-6% at z \sim 0.2), and covered a redshift range (0.5 < z < 0.8) which is crucial to distinguish many different quintessence cosmologies. These measurements have been tested to best match a \Lambda CDM model, clearly providing a statistically robust indication that the Universe is undergoing an accelerated expansion. This method shows the potentiality to open a new avenue in constrain a variety of alternative cosmologies, especially when future surveys (e.g. Euclid) will open the possibility to extend it up to z \sim 2.Comment: 34 pages, 15 figures, 6 tables, published in JCAP. It is a companion to Moresco et al. (2012b, http://arxiv.org/abs/1201.6658) and Jimenez et al. (2012, http://arxiv.org/abs/1201.3608). The H(z) data can be downloaded at http://www.physics-astronomy.unibo.it/en/research/areas/astrophysics/cosmology-with-cosmic-chronometer

Quantifying Between-Cohort and Between-Sex Genetic Heterogeneity in Major Depressive Disorder

Major depressive disorder (MDD) is clinically heterogeneous with prevalence rates twice as high in women as in men. There are many possible sources of heterogeneity in MDD most of which are not measured in a sufficiently comparable way across study samples. Here, we assess genetic heterogeneity based on two fundamental measures, between-cohort and between-sex heterogeneity. First, we used genome-wide association study (GWAS) summary statistics to investigate between-cohort genetic heterogeneity using the 29 research cohorts of the Psychiatric Genomics Consortium (PGC; N cases = 16,823, N controls = 25,632) and found that some of the cohort heterogeneity can be attributed to ascertainment differences (such as recruitment of cases from hospital vs community sources). Second, we evaluated between-sex genetic heterogeneity using GWAS summary statistics from the PGC, Kaiser Permanente GERA, UK Biobank and the Danish iPSYCH studies but did not find convincing evidence for genetic differences between the sexes. We conclude that there is no evidence that the heterogeneity between MDD data sets and between sexes reflects genetic heterogeneity. Larger sample sizes with detailed phenotypic records and genomic data remain the key to overcome heterogeneity inherent in assessment of MDD

Long-term quality of life in adult survivors of pediatric differentiated thyroid carcinoma

Context: Little is known about long-term quality of life (QoL) of survivors of pediatric differentiated thyroid carcinoma. Therefore, this study aimed to evaluate generic health-related QoL (HRQoL), fatigue, anxiety, and depression in these survivors compared with matched controls, and to evaluate thyroid cancer–specific HRQoL in survivors only. Design: Survivors diagnosed between 1970 and 2013 at age #18 years, were included. Exclusion criteria were a follow-up ,5 years, attained age ,18 years, or diagnosis of DTC as a second malignant neoplasm (SMN). Controls were matched by age, sex, and socioeconomic status. Survivors and controls were asked to complete 3 questionnaires [Short-Form 36 (HRQoL), Multidimensional Fatigue Inventory 20 (fatigue), and Hospital Anxiety and Depression Scale (anxiety/depression)]. Survivors completed a thyroid cancer–specific HRQoL questionnaire. Results: Sixty-seven survivors and 56 controls. Median age of survivors at evaluation was 34.2 years (range, 18.8 to 61.7). Median follow-up was 17.8 years (range, 5.0 to 44.7). On most QoL subscales, scores of survivors and controls did not differ significantly. However, survivors had more physical problems (P = 0.031), role limitations due to physical problems (P = 0.021), and mental fatigue (P = 0.016) than controls. Some thyroid cancer–specific complaints (e.g., sensory complaints and chilliness) were present in survivors. Unemployment and more extensive disease or treatment characteristics were most frequently associated with worse QoL. Conclusions: Overall, long-term QoL in survivors of pediatric DTC was normal. Survivors experienced mild impairment of QoL in some domains (physical problems, mental fatigue, and various thyroid cancer–specific complaints). Factors possibly affecting QoL need further exploration