Orbital-Free Molecular Dynamics Simulations of Melting in Na8 and Na20: Melting in Steps

The melting-like transitions of Na8 and Na20 are investigated by ab initio constant energy molecular dynamics simulations, using a variant of the Car-Parrinello method which employs an explicit electronic kinetic energy functional of the density, thus avoiding the use of one-particle orbitals. Several melting indicators are evaluated in order to determine the nature of the various transitions, and compared with other simulations. Both Na8 and Na20 melt over a wide temperature range. For Na8, a transition is observed to begin at approx. 110 K, between a rigid phase and a phase involving isomerizations between the different permutational isomers of the ground state structure. The ``liquid'' phase is completely established at approx. 220 K. For Na20, two transitions are observed: the first, at approx. 110 K, is associated with isomerization transitions between those permutational isomers of the ground state structure which are obtained by interchanging the positions of the surface-like atoms; the second, at approx. 160 K, involves a structural transition from the ground state isomer to a new set of isomers with the surface molten. The cluster is completely ``liquid'' at approx. 220 K.Comment: Revised version, accepted for publication in J. Chem. Phys. The changes include longer simulations for the Na20 microcluster, a more complete comparison to previous theoretical results, and the discussion of some technical details of the method applie

nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow

We present nsCouette, a highly scalable software tool to solve the Navier–Stokes equations for incompressible fluid flow between differentially heated and independently rotating, concentric cylinders. It is based on a pseudospectral spatial discretization and dynamic time-stepping. It is implemented in modern Fortran with a hybrid MPI-OpenMP parallelization scheme and thus designed to compute turbulent flows at high Reynolds and Rayleigh numbers. An additional GPU implementation (C-CUDA) for intermediate problem sizes and a version for pipe flow (nsPipe) are also provided

Improving the Antioxidant Protection of Packaged Food by Incorporating Natural Flavonoids into Ethylene-Vinyl Alcohol Copolymer (EVOH) Films

This document is the unedited Author s version of a Submitted Work that was subsequently accepted for publication in Journal of Agricultural and Food Chemistry, copyright © American Chemical Society after peer review. To access the final edited and published work see https://doi.org/10.1021/jf1022324[EN] Ethylene-vinyl alcohol copolymer (EVOH) films containing catechin or quercetin as antioxidant agents were successfully produced by extrusion. The addition of these bioactive compounds did not modify greatly their water and oxygen permeabilities, T-g, or crystallinity but improved their thermal resistance. Exposure of the films to different food simulants showed that both compounds were released, although the extent and kinetics of release were dependent on the type of food. In aqueous and alcoholic food simulants their release was greater in the case of the catechin-containing samples. Exposure of the films to isooctane and ethanol 95% (fatty food simulants) provided controversial results; no release was observed in isooctane, whereas both bioactive compounds were extracted by ethanol due to their high solubility in alcohol and the plasticizing effect of ethanol on the polymer. Packaging applications of these films can improve food stability and provide a method for adding such bioactive compounds.Received for review June 10, 2010. Revised manuscript received August 24, 2010. Accepted September 16, 2010. We acknowledge the financial support of the Spanish Ministry of Science and Innovation, Projects AGL2006-02176, AGL2009-08776, and Fun-C-Food CSD2007-00063, and the C.L.-d.-D. fellowship (FPU program).Lopez-De-Dicastillo, C.; Alonso, JM.; Catala Moragrega, R.; Gavara Clemente, R.; Hernandez-Muñoz, P. (2010). Improving the Antioxidant Protection of Packaged Food by Incorporating Natural Flavonoids into Ethylene-Vinyl Alcohol Copolymer (EVOH) Films. Journal of Agricultural and Food Chemistry. 58(20):10958-10964. https://doi.org/10.1021/jf1022324S1095810964582

Electrochemical and bioelectrocatalytical properties of novel block-copolymers containing interacting ferrocenyl units

The electrochemical characterization of three different polystyrene-b-polybutadiene block copolymers functionalized with ferrocenyl units electronically communicated, PSm-PBn(HSiMeFc2)p where m=615, n=53, p=39 (1), m=375, n=92, p=76 (2) and m=455, n=204, p=170 (3), has been carried out both in solution and electrochemically deposited onto platinum electrodes. The bioelectrocatalytical properties of electrodes modified with the polymers in the nicotinamide dinucleotide (NADH) and glucose oxidase (GOx) oxidations have been investigated as a function of the constitution and structure of the polymers. The analytical properties of electrodes modified with these polymers as sensors of NADH and GOx are described. In addition, an amperometric biosensor for glucose, prepared by electrostatic immobilization of glucose oxidase onto a platinum electrode modified with one of the ferrocenyl block copolymers as an example, has been developed. The results confirm that electrodes modified with the examined copolymers act as efficient redox mediators for the electrocatalytic oxidation of both reduced nicotinamide dinucleotide cofactor and glucose oxidase. The reaction with NADH proceeds via formation of a charge-transfer intermediate before yielding the reaction products. This is a novel example of electrodes modified with ferrocene derivatives that can be applied to the determination of NADH without the use of diaphorase. The redox copolymers co-immobilized with glucose-oxidase have been successfully used as amperometric biosensors for glucose determinations. As expected these compounds allow using lower working potentials. The sensitivities and detection limits obtained are comparable or even better than those of other ferrocene-modified polymers mediator electrodes

Structural evolution, optical gap and thermoelectric properties of CH3NH3SnBr3 hybrid perovskite, prepared by mechanochemistry

Direct bandgap semiconductors of the hybrid-perovskite family CH3NH3PbX3 (X = I, Br, Cl) exhibit outstanding light absorption properties and are the materials of choice for solar energy applications. As an alternative to poisonous Pb, tin-containing perovskites would show a lower effective mass thus exhibiting a higher charge carrier mobility. An auspicious candidate is CH3NH3SnBr3, with an estimated band gap of 1.902 eV, anticipating applications in photovoltaic devices for the visible to ultra-violet wavelength region. We describe that this perovskite can be prepared by ball milling in a straightforward way, yielding specimens with a superior crystallinity. A structural investigation from synchrotron X-ray powder diffraction (SXRD) data was essential to revisit the successive phase transitions this compound experiences down to 120 K, guided by specific heat capacity and DSC measurements. From the cubic structure identified at RT and 270 K, there is a gradual evolution of the patterns, analysed as a phase admixture between the cubic and the low-symmetry phase present at 160 K. This corresponds to an orthorhombic Pmc21 superstructure; this acentric space group enables polarization along the c-axis where there is a twofold screw axis, evidenced in the distribution of Sn-Br distances. Furthermore, there are two conspicuous changes in the orthorhombic framework, yet keeping the Pmc21 space group, which agree with the main calorimetric events (observed at 224 and 147 K). We interpret these changes as an interplay between the tilting of the SnBr6 octahedra of the inorganic framework and the breaking and reconstruction of H-bond interactions with the organic CH3NH+3 unit. The stereochemical effect of the lone electron pair of the Sn2+ ion is clear in the SnBr6 octahedral distortion. Diffuse reflectance UV/Vis spectroscopy yields an optical gap of ∼2.1 eV, in agreement with ab- initio calculations. A Seebeck coefficient of ∼2000 μV K-1 is determined near RT, which is one order of magnitude higher than those reported for other halide perovskites.Fil: Lopez, Carlos Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Investigaciones en Tecnología Química. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Instituto de Investigaciones en Tecnología Química; Argentina. Instituto de Ciencia de Materiales de Madrid; EspañaFil: Abia, Carmen. Institut Laue Langevin; Francia. Instituto de Ciencia de Materiales de Madrid; EspañaFil: Gainza, Javier. Instituto de Ciencia de Materiales de Madrid; EspañaFil: Kayser, Paula. Instituto de Ciencia de Materiales de Madrid; EspañaFil: Nemes, Norbert. Instituto de Ciencia de Materiales de Madrid; EspañaFil: Dura, Oscar J.. Universidad de Castilla-La Mancha; EspañaFil: Martinez, Jose L.. Instituto de Ciencia de Materiales de Madrid; EspañaFil: Fernandez Diaz, Maria Teresa. Institut Laue Langevin; FranciaFil: Alvarez Galvan, M. Consuelo. Consejo Superior de Investigaciones Científicas; EspañaFil: Alonso, José Antonio. Instituto de Ciencia de Materiales de Madrid; Españ

Vascular Inflammation in Subclinical Atherosclerosis Detected by Hybrid PET/MRI

BACKGROUND: Atherosclerosis is a chronic inflammatory disease, but data on arterial inflammation at early stages is limited. OBJECTIVES: The purpose of this study was to characterize vascular inflammation by hybrid 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography/magnetic resonance imaging (PET/MRI). METHODS: Carotid, aortic, and ilio-femoral 18F-FDG PET/MRI was performed in 755 individuals (age 40 to 54 years; 83.7% men) with known plaques detected by 2-/3-dimensional vascular ultrasound and/or coronary calcification in the PESA (Progression of Early Subclinical Atherosclerosis) study. The authors evaluated the presence, distribution, and number of arterial inflammatory foci (increased 18F-FDG uptake) and plaques with or without inflammation (coincident 18F-FDG uptake). RESULTS: Arterial inflammation was present in 48.2% of individuals (24.4% femorals, 19.3% aorta, 15.8% carotids, and 9.3% iliacs) and plaques in 90.1% (73.9% femorals, 55.8% iliacs, and 53.1% carotids). 18F-FDG arterial uptakes and plaques significantly increased with cardiovascular risk factors (p < 0.01). Coincident 18F-FDG uptakes were present in 287 of 2,605 (11%) plaques, and most uptakes were detected in plaque-free arterial segments (459 of 746; 61.5%). Plaque burden, defined by plaque presence, number, and volume, was significantly higher in individuals with arterial inflammation than in those without (p < 0.01). The number of plaques and 18F-FDG uptakes showed a positive albeit weak correlation (r = 0.25; p < 0.001). CONCLUSIONS: Arterial inflammation is highly prevalent in middle-aged individuals with known subclinical atherosclerosis. Large-scale multiterritorial PET/MRI allows characterization of atherosclerosis-related arterial inflammation and demonstrates 18F-FDG uptake in plaque-free arterial segments and, less frequently, within plaques. These findings suggest an arterial inflammatory state at early stages of atherosclerosis. (Progression of Early Subclinical Atherosclerosis [PESA]; NCT01410318).The PESA study is cofunded equally by the Centro Nacional de Investigaciones Cardiovasculares (CNIC) and Banco Santander. The study also receives funding from the Instituto de Salud Carlos III (PI15/02019) and the European Regional Development Fund (ERDF) “A way to make Europe.” The CNIC is supported by the Ministerio de Ciencia, Innovación y Universidades, and the Pro CNIC Foundation, and is a Severo Ochoa Center of Excellence (SEV-2015-0505). Dr. Sanchez-González is an employee of Philips Healthcare. Dr. Bueno has received research funding from the Instituto de Salud Carlos III, Spain (PIE16/00021 & PI17/01799), AstraZeneca, Bristol-Myers Squibb, Janssen, and Novartis; has received consulting fees from AstraZeneca, Bayer, Bristol-Myers Squibb-Pfizer, and Novartis; and has received speaking fees or support for attending scientific meetings from AstraZeneca, Bayer, Bristol-Myers Squibb-Pfizer, Novartis, and MEDSCAPE-the heart.org.S

Regulation of ovule initiation by gibberellins and brassinosteroids in tomato and Arabidopsis: two plant species, two molecular mechanisms

This is the peer reviewed version of the following article: Barro¿Trastoy, D., Carrera, E., Baños, J., Palau-Rodríguez, J., Ruiz-Rivero, O., Tornero, P., Alonso, J.M., López-Díaz, I., Gómez, M.D. and Pérez-Amador, M.A. (2020), Regulation of ovule initiation by gibberellins and brassinosteroids in tomato and Arabidopsis: two plant species, two molecular mechanisms. Plant J, 102: 1026-1041, which has been published in final form at https://doi.org/10.1111/tpj.14684. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.[EN] Ovule primordia formation is a complex developmental process with a strong impact on the production of seeds. In Arabidopsis this process is controlled by a gene network, including components of the signalling pathways of auxin, brassinosteroids (BRs) and cytokinins. Recently, we have shown that gibberellins (GAs) also play an important role in ovule primordia initiation, inhibiting ovule formation in both Arabidopsis and tomato. Here we reveal that BRs also participate in the control of ovule initiation in tomato, by promoting an increase on ovule primordia formation. Moreover, molecular and genetic analyses of the co-regulation by GAs and BRs of the control of ovule initiation indicate that two different mechanisms occur in tomato and Arabidopsis. In tomato, GAs act downstream of BRs. BRs regulate ovule number through the downregulation of GA biosynthesis, which provokes stabilization of DELLA proteins that will finally promote ovule primordia initiation. In contrast, in Arabidopsis both GAs and BRs regulate ovule number independently of the activity levels of the other hormone. Taken together, our data strongly suggest that different molecular mechanisms could operate in different plant species to regulate identical developmental processes even, as for ovule primordia initiation, if the same set of hormones trigger similar responses, adding a new level of complexity.We wish to thank B. Janssen (Horticulture and Food Research Institute, New Zealand) for the pBJ60 shuttle vector, C. Ferrandiz and M. Colombo (IBMCP, CSIC-UPV, Valencia, Spain) for their help in the generation of 35S:ANT lines and L.E.P. Peres (Universidade de Sao Paulo, Brazil) for the tomato mutant lines. Our thanks also go to C. Fuster for technical assistance. This work was supported by grants from the Spanish Ministry of Economy and Competitiveness-FEDER (BIO2017-83138R) to MAPA and from NSF (DBI-0820755, MCB-1158181, and IOS-1444561) to JMA.Barro-Trastoy, D.; Carrera, E.; Baños, J.; Palau-Rodríguez, J.; Ruiz-Rivero, O.; Tornero Feliciano, P.; Alonso, JM.... (2020). 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Nanoinformatics: developing new computing applications for nanomedicine

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others

Molecularly determined total tumour load in lymph nodes of stage I–II colon cancer patients correlates with high-risk factors. A multicentre prospective study

Stage I–II (pN0) colorectal cancer patients are surgically treated although up to 25 % will eventually die from disease recurrence. Lymph node (LN) status is an independent prognostic factor in colorectal cancer (CRC), and molecular tumour detection in LN of early-stage CRC patients is associated with an increased risk of disease recurrence and poor survival. This prospective multicentre study aimed to determine the relationship between LN molecular tumour burden and conventional high-risk factors in stage I–II colon cancer patients. A total of 1940 LN from 149 pathologically assessed pN0 colon cancer patients were analysed for the amount of tumour cytokeratin 19 (CK19) messenger RNA (mRNA) with the quantitative reverse transcription loop-mediated isothermal amplification molecular assay One-Step Nucleic Acid Amplification. Patient’s total tumour load (TTL) resulted from the sum of all CK19 mRNA tumour copies/μL of each positive LN from the colectomy specimen. A median of 15 LN were procured per case (IQR 12;20). Molecular positivity correlated with high-grade (p < 0.01), mucinous/signet ring type (p = 0.017), male gender (p = 0.02), number of collected LN (p = 0.012) and total LN weight per case (p < 0.01). The TTL was related to pT stage (p = 0.01) and tumour size (p < 0.01) in low-grade tumours. Multivariate logistic regression showed independent correlation of molecular positivity with gender, tumour grade and number of fresh LN [AUC = 0.71 (95 % CI = 0.62–0.79)]. Our results show that lymph node CK19 mRNA detection correlates with classical high-risk factors in stage I–II colon cancer patients. Total tumour load is a quantitative and objective measure that may help to better stage early colon cancer patients.Work supported by the Banc de Tumors-Biobanc Hospital Clinic-IDIBAPS and Xarxa de Bancs de Tumors de Catalunya (XBTC), and by grants from the Fundación Científica de la Asociación Española Contra el Cáncer (GCB13131592CAST), Ministerio de Economía y Competitividad (SAF2014–54,453-R), Agència de Gestió d’Ajuts Universitaris i de Recerca (2014SGR135), and by Sysmex Coorp Spain (Sant Just Desvern, Spain). CIBERehd is funded by the Instituto de Salud Carlos II