Pore-size dependence of the thermal conductivity of porous silicon : a phonon hydrodynamic approach

Phononhydrodynamics is used to analyze the influence of porosity and of pore size on reduction in thermal conductivity in porous silicon, with respect to crystalline silicon. The expressions predict that the thermal conductivity is lower for higher porosity and for smaller pore radius, as a consequence of phononballisticeffects. The theoretical results describe experimental data better than the assumption that they only depend on porosity

Ground State Vortex Lattice Structures in d-wave Superconductors

We show in a realistic $d_{x^{2}-y^{2}}$ symmetry gap model for a cuprate superconductor that the clean vortex lattice has discontinuous structural transitions (at and near T=0), as a function of the magnetic field $B$ along the c-axis. The transitions arise from the singular nonlocal and anisotropic susceptibility of the $d_{x^{2}-y^{2}}$ superconductor to the perturbation caused by supercurrents associated with vortices. The susceptibility, due to virtual Dirac quasiparticle-hole excitation, is calculated carefully, and leads to a ground state transition for the triangular lattice from an orientation along one of the crystal axis to one at 45$^o$ to them, i.e, along the gap zero direction. The field scale is seen to be 5 Tesla $\sim (\Delta_{0}/ta)^{2}\Phi_{0}$, where $\Delta_{0}$ is the gap maximum, $t$ is the nearest neighbour hopping, $a$ is the lattice constant, and $\Phi_{0}$ is the flux quantum. At much higher fields ($\sim 28T$) there is a discontinuous transition to a centred square structure. The source of the differences from existing calculations, and experimental observability are discussed, the latter especially in view of the very small (a few degrees $K$ per vortex) differences in the ground state energy.Comment: To be published in Phys. Rev.

Climate adaptation and speciation : particular focus on reproductive barriers in Ficedula flycatchers

Climate adaptation is surprisingly rarely reported as a cause for the build-up of reproductive isolation between diverging populations. In this review, we summarize evidence for effects of climate adaptation on pre- and postzygotic isolation between emerging species with a particular focus on pied (Ficedula hypoleuca) and collared (Ficedula albicollis) flycatchers as a model for research on speciation. Effects of climate adaptation on prezygotic isolation or extrinsic selection against hybrids have been documented in several taxa, but the combined action of climate adaptation and sexual selection is particularly well explored in Ficedula flycatchers. There is a general lack of evidence for divergent climate adaptation causing intrinsic postzygotic isolation. However, we argue that the profound effects of divergence in climate adaptation on the whole biochemical machinery of organisms and hence many underlying genes should increase the likelihood of genetic incompatibilities arising as side effects. Fast temperature-dependent co-evolution between mitochondrial and nuclear genomes may be particularly likely to lead to hybrid sterility. Thus, how climate adaptation relates to reproductive isolation is best explored in relation to fast-evolving barriers to gene flow, while more research on later stages of divergence is needed to achieve a complete understanding of climate-driven speciation.Peer reviewe

Primary skin fibroblasts as a model of Parkinson's disease

Parkinson's disease is the second most frequent neurodegenerative disorder. While most cases occur sporadic mutations in a growing number of genes including Parkin (PARK2) and PINK1 (PARK6) have been associated with the disease. Different animal models and cell models like patient skin fibroblasts and recombinant cell lines can be used as model systems for Parkinson's disease. Skin fibroblasts present a system with defined mutations and the cumulative cellular damage of the patients. PINK1 and Parkin genes show relevant expression levels in human fibroblasts and since both genes participate in stress response pathways, we believe fibroblasts advantageous in order to assess, e.g. the effect of stressors. Furthermore, since a bioenergetic deficit underlies early stage Parkinson's disease, while atrophy underlies later stages, the use of primary cells seems preferable over the use of tumor cell lines. The new option to use fibroblast-derived induced pluripotent stem cells redifferentiated into dopaminergic neurons is an additional benefit. However, the use of fibroblast has also some drawbacks. We have investigated PARK6 fibroblasts and they mirror closely the respiratory alterations, the expression profiles, the mitochondrial dynamics pathology and the vulnerability to proteasomal stress that has been documented in other model systems. Fibroblasts from patients with PARK2, PARK6, idiopathic Parkinson's disease, Alzheimer's disease, and spinocerebellar ataxia type 2 demonstrated a distinct and unique mRNA expression pattern of key genes in neurodegeneration. Thus, primary skin fibroblasts are a useful Parkinson's disease model, able to serve as a complement to animal mutants, transformed cell lines and patient tissues

Pilot performance of a dedicated prostate PET suitable for diagnosis and biopsy guidance

[EN] Background: Prostate cancer (PCa) represents one of the most common types of cancers facing the male population. Nowadays, to confirm PCa, systematic or multiparametric MRI-targeted transrectal or transperineal biopsies of the prostate are required. However, due to the lack of an accurate imaging technique capable to precisely locate cancerous cells in the prostate, ultrasound biopsies sample random parts of the prostate and, therefore, it is possible to miss regions where those cancerous cells are present. In spite of the improvement with multiparametric MRI, the low reproducibility of its reading undermines the specificity of the method. Recent development of prostatespecific radiotracers has grown the interest on using positron emission tomography (PET) scanners for this purpose, but technological improvements are still required (current scanners have resolutions in the range of 4¿5 mm). Results: The main goal of this work is to improve state-of-the-art PCa imaging and diagnosis. We have focused our efforts on the design of a novel prostate-dedicated PET scanner, named ProsPET. This system has small scanner dimensions defined by a ring of just 41 cm inner diameter. In this work, we report the design, implementation, and evaluation (both through simulations and real data) of the ProsPET scanner. We have been able to achieve < 2 mm resolution in reconstructed images and high sensitivity. In addition, we have included a comparison with the Philips Gemini-TF scanner, which is used for routine imaging of PCa patients. The ProsPET exhibits better contrast, especially for rod sizes as small as 4.5 mm in diameter. Finally, we also show the first reconstructed image of a PCa patient acquired with the ProsPET. Conclusions: We have designed and built a prostate specific PET system, with a small footprint and improved spatial resolution when compared to conventional whole-body PET scanners. The gamma ray impact within each detector block includes accurate DOI determination, correcting for the parallax error. The potential role of combined organdedicated prostate-specific membrane antigen (PSMA) PET and ultrasound devices, as a prebiopsy diagnostic tool, could be used to guide sampling of the most aggressive sites in the prostate.The work presented in this article has been partially funded by a research grant from the regional government of the Comunitat Valenciana (Spain), co-funded by the European Union ERDF funds (European Regional Development Fund) of the Comunitat Valenciana 2014-2020, with reference IDIFEDER/2018/032 (High-Performance Algorithms for the Modelling, Simulation and early Detection of diseases in Personalized Medicine). This project has also received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 695536). It has also been supported by the EU Grant 603002 under the FP7 program and by the Spanish Ministerio de Economia, Industria y Competitividad under Grant e and through PROSPET (DTS15/00152) funded by the Ministerio de Economia y Competitividad.Cañizares-Ledo, G.; Gonzalez-Montoro, A.; Freire, M.; Lamprou, E.; Barrio, J.; Sánchez Martínez, F.; Benlloch Baviera, JM.... (2020). Pilot performance of a dedicated prostate PET suitable for diagnosis and biopsy guidance. EJNMMI Physics. 7(1):1-17. https://doi.org/10.1186/s40658-020-00305-yS11771GLOBOCAN 2018. http://www.gco.iarc.fr/today/ datasources-methods. Accessed 26 Dec 2019.Ferlay J, et al. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN. Int J Cancer. 2012;2015:136–E359.Rawla P. Epidemiology of prostate cancer. 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MR-guided focused ultrasound: enhancement of intratumoral uptake of [H]-docetaxel in vivo. Phys Med Biol. 2010;55(24):–7399.Osborne JR, et al. Prostate-specific membrane antigen-based imaging. Seminars and Original Investigations: Urologic Oncology; 2012.Gonzalez AJ, et al. Organ-dedicated molecular imaging systems. IEEE Trans. Rad. Plasma Med. Scie. 2018;2:388.Majewski S, Proffitt J. Dedicated mobile high resolution prostate PET imager with an insertable transrectal probe. US Patent. 2010;7:858–944.Weinberg IN, et al. Flexible geometries for hand-held PET and SPECT cameras. IEEE NSS-MIC Conference Record. 2002.Weinberg I. Dedicated apparatus and method for positron emission tomography of the prostate. US Patent. 2006;7:102–34.Gonzalez-Montoro A, et al. Performance study of a large monolithic LYSO PET detector with accurate photon DOI using retroreflector layers. IEEE Trans. Rad. Plasma Med. Scie. 2017;1:229.Gonzalez-Montoro A, et al. Detector block performance based on a monolithic LYSO crystal using a novel signal multiplexing method. Nucl Instrum Meth. 2018;912:372-77.Gonzalez-Montoro A, et al. Performance comparison of large-area SiPM arrays suitable for gamma ray detectors. Biomed Phys Eng Express. 2019;5:045013.Seimetz M, et al. Correction algorithms for signal reduction in insensitive areas of a small gamma camera. J Instrum. 2014;9(05):C05042.Freire M, et al. Calibration of gamma ray impacts in monolithic-based detectors using Voronoi diagrams. In IEEE Transactions on Radiation and Plasma Medical Sciences. 2019. https://doi.org/10.1109/TRPMS.2019.2947716 .Jan S, et al. GATE: a simulation toolkit for PET and SPECT. Phys Med Biol. 2004;49:4543–61.Merlin T, et al. CASToR: a generic data organization and processing code framework for multi-modal and multi-dimensional tomographic reconstruction. Phys Med Biol. 2018;63(18):5505.Jacobs F, et al. A fast algorithm to calculate the exact radiological path through a pixel or voxel space. J Comput Inf Technol. 1998;6(1).Gonzalez-Montoro A, et al. Novel method to measure the intrinsic spatial resolution in PET detectors based on monolithic crystals. Nucl. Instrum. Meth. A. 2019;920:39(9).Vicente E, et al. Normalization in 3D PET: dependence on the activity distribution of the source. IEEE Nuclear Science Symposium Conference Record. 2006:M06–379.Soriano A, et al. Attenuation correction without transmission scan for the MAMMI breast PET. Nucl Instrum Meth A. 2011;648:S75.Yushkevich PA, et al. User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability. Neuroimage. 2006;34(3):1116-28.Gonzalez AJ, et al. Initial results of the MINDView PET insert inside the 3T mMR. IEEE Trans Rad Plasma Med Scie. 2019;3:343.Suti S, et al. 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Eur J Nucl Med Mol Imaging. 2017;44(6):941-49.Koerber SA, et al. 68Ga-PSMA-11 PET/CT in newly diagnosed carcinoma of the prostate: correlation of intraprostatic PSMA uptake with several clinical parameters. J Nucl Med. 2017;58(12):1943–8

The mutational impact of culturing human pluripotent and adult stem cells

Genetic changes acquired during in vitro culture pose a risk for the successful application of stem cells in regenerative medicine. To assess the genetic risks induced by culturing, we determined all mutations in individual human stem cells by whole genome sequencing. Individual pluripotent, intestinal, and liver stem cells accumulate 3.5 ± 0.5, 7.2 ± 1.1 and 8.3 ± 3.6 base substitutions per population doubling, respectively. The annual in vitro mutation accumulation rate of adult stem cells is nearly 40-fold higher than the in vivo mutation accumulation rate. Mutational signature analysis reveals that in vitro induced mutations are caused by oxidative stress. Reducing oxygen tension in culture lowers the mutational load. We use the mutation rates, spectra, and genomic distribution to model the accumulation of oncogenic mutations during typical in vitro expansion, manipulation or screening experiments using human stem cells. Our study provides empirically defined parameters to assess the mutational risk of stem cell based therapies

Optimized Trigger for Ultra-High-Energy Cosmic-Ray and Neutrino Observations with the Low Frequency Radio Array

When an ultra-high energy neutrino or cosmic ray strikes the Lunar surface a radio-frequency pulse is emitted. We plan to use the LOFAR radio telescope to detect these pulses. In this work we propose an efficient trigger implementation for LOFAR optimized for the observation of short radio pulses.Comment: Submitted to Nuclear Instruments and Methods in Physics Research Section

Semiparametrically Efficient Inference Based on Signs and Ranks for Median Restricted Models

Since the pioneering work of Koenker and Bassett (1978), econometric models involving median and quantile rather than the classical mean or conditional mean concepts have attracted much interest.Contrary to the traditional models where the noise is assumed to have mean zero, median-restricted models enjoy a rich group-invariance structure.In this paper, we exploit this invariance structure in order to obtain semiparametrically efficient inference procedures for these models.These procedures are based on residual signs and ranks, and therefore insensitive to possible misspecification of the underlying innovation density, yet semiparametrically efficient at correctly specified densities.This latter combination is a definite advantage of these procedures over classical quasi-likelihood methods.The techniques we propose can be applied, without additional technical difficulties, to both cross-sectional and time-series models.They do not require any explicit tangent space calculation nor any projections on these.

Structure of vortex liquid phase in irradiated BSCCO(2212) crystals

The c-axis resistivity in irradiated and in pristine BSCCO(2212) crystals is measured as a function of the in-plane magnetic field component at fixed out-of-plane component B_\perp in the vortex liquid phase at T=67 K. From this data we extract the dependence of the phase difference correlation length inside layers on B_\perp and estimate the average length of pieces of vortex lines confined inside columnar defects as a function of the filling factor f=B_\perp / B_\phi. The maximum length, about 15 interlayer distances, is reached near f=0.35.Comment: 4 pages, 4 figure

PCR-GLOBWB 2: a 5 arcmin global hydrological and water resources model

We present PCR-GLOBWB 2, a global hydrology and water resources model. Compared to previous versions of PCR-GLOBWB, this version fully integrates water use. Sector-specific water demand, groundwater and surface water withdrawal, water consumption, and return flows are dynamically calculated at every time step and interact directly with the simulated hydrology. PCR-GLOBWB 2 has been fully rewritten in Python and PCRaster Python and has a modular structure, allowing easier replacement, maintenance, and development of model components. PCR-GLOBWB 2 has been implemented at 5 arcmin resolution, but a version parameterized at 30 arcmin resolution is also available. Both versions are available as open-source codes on https://github.com/UU-Hydro/PCR-GLOBWB_model (Sutanudjaja et al., 2017a). PCR-GLOBWB 2 has its own routines for groundwater dynamics and surface water routing. These relatively simple routines can alternatively be replaced by dynamically coupling PCR-GLOBWB 2 to a global two-layer groundwater model and 1-D–2-D hydrodynamic models. Here, we describe the main components of the model, compare results of the 30 and 5 arcmin versions, and evaluate their model performance using Global Runoff Data Centre discharge data. Results show that model performance of the 5 arcmin version is notably better than that of the 30 arcmin version. Furthermore, we compare simulated time series of total water storage (TWS) of the 5 arcmin model with those observed with GRACE, showing similar negative trends in areas of prevalent groundwater depletion. Also, we find that simulated total water withdrawal matches reasonably well with reported water withdrawal from AQUASTAT, while water withdrawal by source and sector provide mixed results