Personalized automatic sleep staging with single-night data: a pilot study with Kullback-Leibler divergence regularization.

OBJECTIVE: Brain waves vary between people. This work aims to improve automatic sleep staging for longitudinal sleep monitoring via personalization of algorithms based on individual characteristics extracted from sleep data recorded during the first night. APPROACH: As data from a single night are very small, thereby making model training difficult, we propose a Kullback-Leibler (KL) divergence regularized transfer learning approach to address this problem. We employ the pretrained SeqSleepNet (i.e. the subject independent model) as a starting point and finetune it with the single-night personalization data to derive the personalized model. This is done by adding the KL divergence between the output of the subject independent model and it of the personalized model to the loss function during finetuning. In effect, KL-divergence regularization prevents the personalized model from overfitting to the single-night data and straying too far away from the subject independent model. MAIN RESULTS: Experimental results on the Sleep-EDF Expanded database consisting of 75 subjects show that sleep staging personalization with single-night data is possible with help of the proposed KL-divergence regularization. On average, we achieve a personalized sleep staging accuracy of 79.6%, a Cohen's kappa of 0.706, a macro F1-score of 73.0%, a sensitivity of 71.8%, and a specificity of 94.2%. SIGNIFICANCE: We find both that the approach is robust against overfitting and that it improves the accuracy by 4.5 percentage points compared to the baseline method without personalization and 2.2 percentage points compared to it with personalization but without regularization

Segmented simultaneous multi-slice diffusion-weighted imaging with navigated 3D rigid motion correction

Purpose To improve the robustness of diffusion-weighted imaging (DWI) data acquired with segmented simultaneous multi-slice (SMS) echo-planar imaging (EPI) against in-plane and through-plane rigid motion.Theory and Methods The proposed algorithm incorporates a 3D rigid motion correction and wavelet denoising into the image reconstruction of segmented SMS-EPI diffusion data. Low-resolution navigators are used to estimate shot-specific diffusion phase corruptions and 3D rigid motion parameters through SMS-to-volume registration. The shot-wise rigid motion and phase parameters are integrated into a SENSE-based full-volume reconstruction for each diffusion direction. The algorithm is compared to a navigated SMS reconstruction without gross motion correction in simulations and in vivo studies with four-fold interleaved 3-SMS diffusion tensor acquisitions.Results Simulations demonstrate high fidelity was achieved in the SMS-to-volume registration, with submillimeter registration errors and improved image reconstruction quality. In vivo experiments validate successful artifact reduction in 3D motion-compromised in vivo scans with a temporal motion resolution of approximately 0.3 s.Conclusion This work demonstrates the feasibility of retrospective 3D rigid motion correction from shot navigators for segmented SMS DWI.Radiolog

X-ray magneto-optics of lanthanide materials: principles and applications

Lanthanide metals are a particular class of magnetic materials in which the magnetic moments are carried mainly by the localized electrons of the 4f shell. They are frequently found in technically relevant systems, to achieve, e.g., high magnetic anisotropy. Magneto-optical methods in the x-ray range are well suited to study complex magnetic materials in an element-specific way. In this work, we report on recent progress on the quantitative determination of magneto-optical constants of several lanthanides in the soft x-ray region and we show some examples of applications of magneto-optics to hard-magnetic interfaces and exchange-coupled layered structures containing lanthanide elements.Comment: 7 pages, 6 figures, invited contribution to the Symposium "X-ray magneto-optics" of the Spring Meeting of the German Physical Society held in Regensburg, Germany, 8-12 March 2004. Revised version, minor change

The SCF/KIT axis in human mast cells: capicua acts as potent KIT repressor and ERK predominates PI3K

BACKGROUND: The SCF/KIT axis regulates nearly all aspects of mast cell (MC) biology. A comprehensive view of SCF-triggered phosphorylation dynamics is lacking. The relationship between signaling modules and SCF-supported functions likewise remains ill-defined. METHODS: MCs were isolated from human skin; upon stimulation by SCF, global phosphoproteomic changes were analyzed by LC-MS/MS and selectively validated by immunoblotting. MC survival was inspected by YoPro; BrdU incorporation served to monitor proliferation. Gene expression was quantified by RT-qPCR and cytokines by ELISA. Pharmacological inhibitors were supplemented by ERK1 and/or ERK2 knock-down. CIC translocation and degradation were studied in nuclear and cytoplasmic fractions. CIC's impact on KIT signaling and function was assessed following RNA interference. RESULTS: ≈5,400 out of ≈10,500 phosphosites experienced regulation by SCF. The MEK/ERK cascade was strongly induced surpassing STAT5>PI3K/Akt>p38>JNK. Comparison between MEK/ERK's and PI3K's support of basic programs (apoptosis, proliferation) revealed equipotency between modules. In functional outputs (gene expression, cytokines), ERK was the most influential kinase. OSM and LIF production was identified in skin MCs. Strikingly, SCF triggered massive phosphorylation of a protein not associated with KIT previously: CIC. Phosphorylation was followed by CIC's cytoplasmic appearance and degradation, the latter sensitive to protease- but not preoteasome-inhibition. Both shuttling and degradation were ERK-dependent. Conversely, CIC-siRNA facilitated KIT-signaling, functional outputs and survival. CONCLUSION: The SCF/KIT axis shows notable strength in MCs, and MEK/ERK as most prominent module. An inhibitory circuit exists between KIT and CIC. CIC stabilization in MCs may turn out as a therapeutic option to interfere with allergic and MC-driven diseases

Mapping the unique and shared functions of oncogenic KRAS and RIT1 with proteome and transcriptome profiling

Aberrant activation of RAS oncogenes is prevalent in lung adenocarcinoma, with somatic mutation of KRAS occurring in ∼30% of tumors. Recently, we identified somatic mutation of the RAS-family GTPase RIT1 in lung adenocarcinoma, but relatively little is known about the biological pathways regulated by RIT1 and how these relate to the oncogenic KRAS network. Here we present quantitative proteomic and transcriptomic profiles from KRAS-mutant and RIT1-mutant isogenic lung epithelial cells and globally characterize the signaling networks regulated by each oncogene. We find that both mutant KRAS and mutant RIT1 promote S6 kinase, AKT, and RAF/MEK signaling, and promote epithelial-to-mesenchymal transition and immune evasion via HLA protein loss. However, KRAS and RIT1 diverge in regulation of phosphorylation sites on EGFR, USO1, and AHNAK proteins. The majority of the proteome changes are related to altered transcriptional regulation, but a small subset of proteins are differentially regulated by both oncoproteins at the post-transcriptional level, including intermediate filament proteins, metallothioneins, and MHC Class I proteins. These data provide the first global, unbiased characterization of oncogenic RIT1 network and identify the shared and divergent functions of oncogenic RIT1 and KRAS GTPases in lung cancer

Prediction of huge X-ray Faraday rotation at the Gd N_4,5 threshold

X-ray absorption spectra in a wide energy range around the 4d-4f excitation threshold of Gd were recorded by total electron yield from in-plane magnetized Gd metal films. Matching the experimental spectra to tabulated absorption data reveals unprecedented short light absorption lengths down to 3 nm. The associated real parts of the refractive index for circularly polarized light propagating parallel or antiparallel to the Gd magnetization, determined through the Kramers-Kronig transformation, correspond to a magneto-optical Faraday rotation of 0.7 degrees per atomic layer. This finding shall allow the study of magnetic structure and magnetization dynamics of lanthanide elements in nanosize systems and dilute alloys.Comment: 4 pages, 2 figures, final version resubmitted to Phys. Rev. B, Brief Reports. Minor change

Review of biorthogonal coupled cluster representations for electronic excitation

Single reference coupled-cluster (CC) methods for electronic excitation are based on a biorthogonal representation (bCC) of the (shifted) Hamiltonian in terms of excited CC states, also referred to as correlated excited (CE) states, and an associated set of states biorthogonal to the CE states, the latter being essentially configuration interaction (CI) configurations. The bCC representation generates a non-hermitian secular matrix, the eigenvalues representing excitation energies, while the corresponding spectral intensities are to be derived from both the left and right eigenvectors. Using the perspective of the bCC representation, a systematic and comprehensive analysis of the excited-state CC methods is given, extending and generalizing previous such studies. Here, the essential topics are the truncation error characteristics and the separability properties, the latter being crucial for designing size-consistent approximation schemes. Based on the general order relations for the bCC secular matrix and the (left and right) eigenvector matrices, formulas for the perturbation-theoretical (PT) order of the truncation errors (TEO) are derived for energies, transition moments, and property matrix elements of arbitrary excitation classes and truncation levels. In the analysis of the separability properties of the transition moments, the decisive role of the so-called dual ground state is revealed. Due to the use of CE states the bCC approach can be compared to so-called intermediate state representation (ISR) methods based exclusively on suitably orthonormalized CE states. As the present analysis shows, the bCC approach has decisive advantages over the conventional CI treatment, but also distinctly weaker TEO and separability properties in comparison with a full (and hermitian) ISR method

Self-consistent Green's function approaches

We present the fundamental techniques and working equations of many-body Green's function theory for calculating ground state properties and the spectral strength. Green's function methods closely relate to other polynomial scaling approaches discussed in chapters 8 and 10. However, here we aim directly at a global view of the many-fermion structure. We derive the working equations for calculating many-body propagators, using both the Algebraic Diagrammatic Construction technique and the self-consistent formalism at finite temperature. Their implementation is discussed, as well as the inclusion of three-nucleon interactions. The self-consistency feature is essential to guarantee thermodynamic consistency. The pairing and neutron matter models introduced in previous chapters are solved and compared with the other methods in this book.Comment: 58 pages, 14 figures, Submitted to Lect. Notes Phys., "An advanced course in computational nuclear physics: Bridging the scales from quarks to neutron stars", M. Hjorth-Jensen, M. P. Lombardo, U. van Kolck, Editor