Theoretical Study of Molecular Electronic and Rotational Coherences by High-Harmonic Generation

The detection of electron motion and electronic wavepacket dynamics is one of the core goals of attosecond science. Recently, choosing the nitric oxide (NO) molecule as an example, we have introduced and demonstrated a new experimental approach to measure coupled valence electronic and rotational wavepackets using high-harmonic generation (HHG) spectroscopy [Kraus et al., Phys. Rev. Lett. 111, 243005 (2013)]. A short outline of the theory to describe the combination of the pump and HHG probe process was published together with an extensive discussion of experimental results [Baykusheva et al., Faraday Discuss 171, 113 (2014)]. The comparison of theory and experiment showed good agreement on a quantitative level. Here, we present the generalized theory in detail, which is based on a generalized density matrix approach that describes the pump process and the subsequent probing of the wavepackets by a semiclassical quantitative rescattering approach. An in-depth analysis of the different Raman scattering contributions to the creation of the coupled rotational and electronic spin-orbit wavepackets is made. We present results for parallel and perpendicular linear polarizations of the pump and probe laser pulses. Furthermore, an analysis of the combined rotational-electronic density matrix in terms of irreducible components is presented, that facilitates interpretation of the results.Comment: 14 figure

Active split-ring metamaterial slabs for magnetic resonance imaging

In this work, it is analyzed the ability of split-ring metamaterial slabs with zero/high permeability to reject/confine the radiofrequency magnetic field in magnetic resonance imaging systems. Using an homogenization procedure, split-ring slabs have been designed and fabricated to work in a 1.5T system. Active elements consisting of pairs of crossed diodes are inserted in the split-rings. With these elements, the permeability of the slabs can be automatically switched between a unity value when interacting with the strong excitation field of the transmitting body coil, and zero or high values when interacting with the weak field produced by protons in tissue. Experiments are shown for different configurations where these slabs can help to locally increase the signal-to-noise-ratio.Comment: 6 pages, 4 figure

Undersampling reconstruction in parallel and single coil imaging with COMPaS -- COnvolutional Magnetic Resonance Image Prior with Sparsity regularization

Purpose: To propose COMPaS, a learning-free Convolutional Network, that combines Deep Image Prior (DIP) with transform-domain sparsity constraints to reconstruct undersampled Magnetic Resonance Imaging (MRI) data without previous training of the network. Methods: COMPaS uses a U-Net as DIP for undersampledMRdata in the image domain. Reconstruction is constrained by data fidelity to k-space measurements and transform-domain sparsity, such as Total Variation (TV) or Wavelet transform sparsity. Two-dimensional MRI data from the public FastMRI dataset with Cartesian undersampling in phase-encoding direction were reconstructed for different acceleration rates (R) from R = 2 to R = 8 for single coil and multicoil data. Performance of the proposed architecture was compared to Parallel Imaging with Compressed Sensing (PICS). Results: COMPaS outperforms standard PICS algorithms by reducing ghosting artifacts and yielding higher quantitative reconstruction quality metrics in multicoil imaging settings and especially in single coil k-space reconstruction. Furthermore, COMPaS can reconstruct multicoil data without explicit knowledge of coil sensitivity profiles. Conclusion: COMPaS utilizes a training-free convolutional network as a DIP in MRI reconstruction and transforms it with transform-domain sparsity regularization. It is a competitive algorithm for parallel imaging and a novel tool for accelerating single coil MRI.Comment: 13 pages, 8 figures, 2 table

Comparing reverse complementary genomic words based on their distance distributions and frequencies

In this work we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance distributions are considered, and it is found that the peak dissimilarity works best in this setting. We report the existence of reverse complementary word pairs with very dissimilar distance distributions, as well as word pairs with very similar distance distributions even when both distributions are irregular and contain strong peaks. The association between distribution dissimilarity and frequency discrepancy is explored also, and it is speculated that symmetric pairs combining low and high values of each measure may uncover features of interest. Taken together, our results suggest that some asymmetries in the human genome go far beyond Chargaff's rules. This study uses both the complete human genome and its repeat-masked version.Comment: Post-print of a paper accepted to publication in "Interdisciplinary Sciences: Computational Life Sciences" (ISSN: 1913-2751, ESSN: 1867-1462

Dissimilar Symmetric Word Pairs in the Human Genome

In this work we explore the dissimilarity between symmetric word pairs, by comparing the inter-word distance distribution of a word to that of its reversed complement. We propose a new measure of dissimilarity between such distributions. Since symmetric pairs with different patterns could point to evolutionary features, we search for the pairs with the most dissimilar behaviour. We focus our study on the complete human genome and its repeat-masked version.Comment: Submitted 13-Feb-2017; accepted, after a minor revision, 17-Mar-2017; 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2017, Porto, Portugal, 21-23 June, 201

Control groups in recent septic shock trials : a systematic review

The interpretation of septic shock trial data is profoundly affected by patients, control intervention, co-interventions and selected outcome measures. We evaluated the reporting of control groups in recent septic shock trials. We searched for original articles presenting randomized clinical trials (RCTs) in adult septic shock patients from 2006 to 2016. We included RCTs focusing on septic shock patients with at least two parallel groups and at least 50 patients in the control group. We selected and evaluated data items regarding patients, control group characteristics, and mortality outcomes, and calculated a data completeness score to provide an overall view of quality of reporting. A total of 24 RCTs were included (mean n = 287 patients and 71 % of eligible patients were randomized). Of the 24 studies, 14 (58 %) presented baseline data on vasopressors and 58 % the proportion of patients with elevated lactate values. Five studies (21 %) provided data to estimate the proportion of septic shock patients fulfilling the Sepsis-3 definition. The mean data completeness score was 19 out of 36 (range 8-32). Of 18 predefined control group characteristics, a mean of 8 (range 2-17) were reported. Only 2 (8 %) trials provided adequate data to confirm that their control group treatment represented usual care. Recent trials in septic shock provide inadequate data on the control group treatment and hemodynamic values. We propose a standardized trial dataset to be created and validated, comprising characteristics of patient population, interventions administered, hemodynamic values achieved, surrogate organ dysfunction, and mortality outcomes, to allow better analysis and interpretation of future trial results.Peer reviewe

Dysregulation of Glucagon Secretion by Hyperglycemia-Induced Sodium-Dependent Reduction of ATP Production

© 2018 The Author(s). Published by Elsevier Inc.Diabetes is a bihormonal disorder resulting from combined insulin and glucagon secretion defects. Mice lacking fumarase (Fh1) in their β cells (Fh1βKO mice) develop progressive hyperglycemia and dysregulated glucagon secretion similar to that seen in diabetic patients (too much at high glucose and too little at low glucose). The glucagon secretion defects are corrected by low concentrations of tolbutamide and prevented by the sodium-glucose transport (SGLT) inhibitor phlorizin. These data link hyperglycemia, intracellular Na+ accumulation, and acidification to impaired mitochondrial metabolism, reduced ATP production, and dysregulated glucagon secretion. Protein succination, reflecting reduced activity of fumarase, is observed in α cells from hyperglycemic Fh1βKO and β-V59M gain-of-function KATP channel mice, diabetic Goto-Kakizaki rats, and patients with type 2 diabetes. Succination is also observed in renal tubular cells and cardiomyocytes from hyperglycemic Fh1βKO mice, suggesting that the model can be extended to other SGLT-expressing cells and may explain part of the spectrum of diabetic complications.Peer reviewe

A modeling study of functional magnetic resonance imaging to individualize target definition of seminal vesicles for external beam radiotherapy

Background Pre-treatment magnetic resonance imaging (MRI) can give patient-specific evaluation of 25 suspected pathologically-involved volumes in the seminal vesicles (SV) in prostate cancer patients. By 26 targeting this suspicious volume we hypothesize that radiotherapy is more efficient without introducing more 27 toxicity. In this study we evaluate the concept of using MRI-defined target volumes in terms of tumor 28 control probability (TCP) and rectal normal tissue complication probability (NTCP). Materials and methods Twenty-one high-risk prostate cancer patients were included. Pre-treatment CT 30 images, T2 weighted (T2w) MRI and two multi-parametric MRI were acquired. Overlap between a 31 suspicious volume in the SV observed on T2w images and a suspicious volume observed on either multi-32 parametric MRI was assumed to reflect a true malignant region (named “MRI positive”). In addition the 33 entire SV on the CT-scan was delineated. Three treatment plans of 2Gyx39 fractions were generated per 34 patient: one covering the MRI positive volume in SV and prostate with margin of 11 mm to the MRI positive 35 in the SV and two plans covering prostate and SV using 11mm and 7mm SV margin, respectively. All plans 36 prescribed the same PTV mean dose. Rectal NTCP grade≥2 was evaluated with the Lyman-Kutcher-Burman 37 model and TCP was estimated by a logistic model using the combined MRI positive volume in SV and 38 prostate as region-of-interest. Results 14/21 patients were classified as MRI positive, 6 of which had suspicious volumes in all three MRI 40 modalities. On average TCP for the plan covering prostate and the MRI positive volume was 3% higher (up 41 to 11%) than the two other plans which was statistically significant. The increased TCP was obtained without 42 increasing rectal NTCP grade≥2. Conclusion Using functional MRI for individualized target delineation in the seminal vesicles may improve 44 the treatment outcome in radiotherapy of prostate cancer without increasing the rectal toxicity.</p