Almost Perfect Spin Filtering in Graphene-Based Magnetic Tunnel Junctions.

We report on large spin-filtering effects in epitaxial graphene-based spin valves, strongly enhanced in our specific multilayer case. Our results were obtained by the effective association of chemical vapor deposited (CVD) multilayer graphene with a high quality epitaxial Ni(111) ferromagnetic spin source. We highlight that the Ni(111) spin source electrode crystallinity and metallic state are preserved and stabilized by multilayer graphene CVD growth. Complete nanometric spin valve junctions are fabricated using a local probe indentation process, and spin properties are extracted from the graphene-protected ferromagnetic electrode through the use of a reference Al2O3/Co spin analyzer. Strikingly, spin-transport measurements in these structures give rise to large negative tunnel magneto-resistance TMR = -160%, pointing to a particularly large spin polarization for the Ni(111)/Gr interface PNi/Gr, evaluated up to -98%. We then discuss an emerging physical picture of graphene-ferromagnet systems, sustained both by experimental data and ab initio calculations, intimately combining efficient spin filtering effects arising (i) from the bulk band structure of the graphene layers purifying the extracted spin direction, (ii) from the hybridization effects modulating the amplitude of spin polarized scattering states over the first few graphene layers at the interface, and (iii) from the epitaxial interfacial matching of the graphene layers with the spin-polarized Ni surface selecting well-defined spin polarized channels. Importantly, these main spin selection effects are shown to be either cooperating or competing, explaining why our transport results were not observed before. Overall, this study unveils a path to harness the full potential of low Resitance.Area (RA) graphene interfaces in efficient spin-based devices.

Spin filtering by proximity effects at hybridized interfaces in spin-valves with 2D graphene barriers.

We report on spin transport in state-of-the-art epitaxial monolayer graphene based 2D-magnetic tunnel junctions (2D-MTJs). In our measurements, supported by ab-initio calculations, the strength of interaction between ferromagnetic electrodes and graphene monolayers is shown to fundamentally control the resulting spin signal. In particular, by switching the graphene/ferromagnet interaction, spin transport reveals magneto-resistance signal MR > 80% in junctions with low resistance × area products. Descriptions based only on a simple K-point filtering picture (i.e. MR increase with the number of layers) are not sufficient to predict the behavior of our devices. We emphasize that hybridization effects need to be taken into account to fully grasp the spin properties (such as spin dependent density of states) when 2D materials are used as ultimately thin interfaces. While this is only a first demonstration, we thus introduce the fruitful potential of spin manipulation by proximity effect at the hybridized 2D material / ferromagnet interface for 2D-MTJs.

The ONETEP linear-scaling density functional theory program.

We present an overview of the onetep program for linear-scaling density functional theory (DFT) calculations with large basis set (plane-wave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the density matrix and the NGWFs are optimized with localization constraints. By taking advantage of localization, onetep is able to perform calculations including thousands of atoms with computational effort, which scales linearly with the number or atoms. The code has a large and diverse range of capabilities, explored in this paper, including different boundary conditions, various exchange-correlation functionals (with and without exact exchange), finite electronic temperature methods for metallic systems, methods for strongly correlated systems, molecular dynamics, vibrational calculations, time-dependent DFT, electronic transport, core loss spectroscopy, implicit solvation, quantum mechanical (QM)/molecular mechanical and QM-in-QM embedding, density of states calculations, distributed multipole analysis, and methods for partitioning charges and interactions between fragments. Calculations with onetep provide unique insights into large and complex systems that require an accurate atomic-level description, ranging from biomolecular to chemical, to materials, and to physical problems, as we show with a small selection of illustrative examples. onetep has always aimed to be at the cutting edge of method and software developments, and it serves as a platform for developing new methods of electronic structure simulation. We therefore conclude by describing some of the challenges and directions for its future developments and applications.

Universal Spin Diffusion Length in Polycrystalline Graphene.

Graphene grown by chemical vapor deposition (CVD) is the most promising material for industrial-scale applications based on graphene monolayers. It also holds promise for spintronics; despite being polycrystalline, spin transport in CVD graphene has been measured over lengths up to 30 µm, which is on par with the best measurements made in single-crystal graphene. These results suggest that grain boundaries (GBs) in CVD graphene, while impeding charge transport, may have little effect on spin transport. However, to date very little is known about the true impact of disordered networks of GBs on spin relaxation. Here, by using first-principles simulations, we derive an effective tight-binding model of graphene GBs in the presence of spin-orbit coupling (SOC), which we then use to evaluate spin transport in realistic morphologies of polycrystalline graphene. The spin diffusion length is found to be independent of the grain size, and it is determined only by the strength of the substrate-induced SOC. This result is consistent with the D'yakonov-Perel' mechanism of spin relaxation in the diffusive regime, but we find that it also holds in the presence of quantum interference. These results clarify the role played by GBs and demonstrate that the average grain size does not dictate the upper limit for spin transport in CVD-grown graphene, a result of fundamental importance for optimizing large-scale graphene-based spintronic devices.

Label free noninvasive spatially resolved NaCl concentration measurements using Coherent Anti-Stokes Raman Scattering microscopy applied to butter.

Imaging the microstructure of opaque composite foodstuffs and extracting quantitative chemical information about specific localized components is challenging. Herein, a method has been developed to determine spatially resolved concentrations of aqueous salt and applied to measure salt concentrations of water droplets in butter samples. This was done using Coherent Anti-Stokes Raman Scattering (CARS) microscopy which achieves non-invasive label free imaging based on visualization of specific chemical-bond vibrations. The concentration of salt in the dispersed water droplets in butter was determined based on the relative change in intensity of the CARS-signal at two distinct wavenumbers, which have been shown to be dependent on the inter-molecular coupling of water molecules and salt. The results provide the size and salt concentration distribution of the droplets in the samples. It is further shown that the average salt concentration in the whole sample can correctly be inferred from the concentration measured within the water droplets.

A missense mutation in Katnal1 underlies behavioural, neurological and ciliary anomalies.

Microtubule severing enzymes implement a diverse range of tissue-specific molecular functions throughout development and into adulthood. Although microtubule severing is fundamental to many dynamic neural processes, little is known regarding the role of the family member Katanin p60 subunit A-like 1, KATNAL1, in central nervous system (CNS) function. Recent studies reporting that microdeletions incorporating the KATNAL1 locus in humans result in intellectual disability and microcephaly suggest that KATNAL1 may play a prominent role in the CNS; however, such associations lack the functional data required to highlight potential mechanisms which link the gene to disease symptoms. Here we identify and characterise a mouse line carrying a loss of function allele in Katnal1. We show that mutants express behavioural deficits including in circadian rhythms, sleep, anxiety and learning/memory. Furthermore, in the brains of Katnal1 mutant mice we reveal numerous morphological abnormalities and defects in neuronal migration and morphology. Furthermore we demonstrate defects in the motile cilia of the ventricular ependymal cells of mutants, suggesting a role for Katnal1 in the development of ciliary function. We believe the data we present here are the first to associate KATNAL1 with such phenotypes, demonstrating that the protein plays keys roles in a number of processes integral to the development of neuronal function and behaviour.

Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP.

Density functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFT-MD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in the understanding and assignment of experimental peaks and bands at finite temperature, particularly in the case of floppy molecules. Linear-scaling DFT methods can be used to study large and complex systems, such as peptides, DNA strands, amorphous solids, and molecules in solution. Here, we present the implementation of DFT-MD IR spectroscopy in the ONETEP linear-scaling code. In addition, two methods for partitioning the dipole moment within the ONETEP framework are presented. Dipole moment partitioning allows us to compute spectra of molecules in solution, which fully include the effects of the solvent, while at the same time removing the solvent contribution from the spectra.

Achievements of DFT for the investigation of graphene-related nanostructures.

CONSPECTUS: Graphene-related nanostructures stand out as exceptional materials due to both their wide range of properties and their expanse of interest in both applied and fundamental research. They are good examples of nanoscale materials for which the properties do not necessarily replicate those of the bulk. For the description and the understanding of their properties, it is clear that a general quantum-mechanical approach is mandatory. The remarkable result of density functional theory (DFT) is that the quantum-mechanical description of materials at the ground state is made amenable to simulations at a relatively low computational cost. The knowledge of materials has undergone a revolution after the introduction of DFT as an unrivaled instrument for the investigation of materials properties through computer experiments. Their deeper understanding comes from a variety of tools developed from concepts intrinsically present in DFT, notably the total energy and the charge density. Such tools allow the prediction of a diverse set of physicochemical properties relevant for material scientists. This Account lays out an example-driven tour through the achievements of ground-state DFT applied to the description of graphene-related nanostructures and to the deep understanding of their outstanding properties. After a brief introduction to DFT, the survey starts with the determination of the most basic properties that can be obtained from DFT, that is, band structures, lattice parameters, and spin ground state. Next follows an exploration of how total energies of different systems can give information about relative stability, formation energies, and reaction paths. Exploiting the derivatives of the energy with respect to displacements leads the way toward the extraction of vibrational and mechanical properties. In addition, a close examination of the charge density gives information about charge transfer mechanisms, which can be linked to chemical reactivity. The ground state density and Hamiltonian finally connect to the concepts behind transport phenomena, which drive much of the application-oriented research on graphene and graphene-related nanostructures. In each section, a selection of cases that are of current importance are used to illustrate the use and relevance of DFT-based techniques. In summary, this Account presents an introductory landscape of the possibilities of ground-state DFT for the study of graphene-related nanostructures. The prospect is rich, and the use of DFT for the study of graphene-related nanostructures will continue to be fruitful for the advancement of these and other materials.

A chronological expression profile of gene activity during embryonic mouse brain development.

The brain is a functionally complex organ, the patterning and development of which are key to adult health. To help elucidate the genetic networks underlying mammalian brain patterning, we conducted detailed transcriptional profiling during embryonic development of the mouse brain. A total of 2,400 genes were identified as showing differential expression between three developmental stages. Analysis of the data identified nine gene clusters to demonstrate analogous expression profiles. A significant group of novel genes of as yet undiscovered biological function were detected as being potentially relevant to brain development and function, in addition to genes that have previously identified roles in the brain. Furthermore, analysis for genes that display asymmetric expression between the left and right brain hemispheres during development revealed 35 genes as putatively asymmetric from a combined data set. Our data constitute a valuable new resource for neuroscience and neurodevelopment, exposing possible functional associations between genes, including novel loci, and encouraging their further investigation in human neurological and behavioural disorders.

Apoptosis induced by the fungal pathogen gliotoxin requires a triple phosphorylation of Bim by JNK.

We previously reported that gliotoxin (GT), the major virulence factor of the mold Aspergillus fumigatus causing invasive aspergillosis (IA) in immunocompromised patients, induces apoptosis in a Bak-dependent manner. The signaling pathway leading to Bak activation and subsequent mitochondrial outer membrane permeabilization (MOMP) is elusive. Here, we show that GT and the supernatant of A. fumigatus (but not its GT-defective mutant) activate the JNK pathway and require a co-operative JNK-mediated BimEL phosphorylation at three sites (S100, T112 and S114) to induce apoptosis in mouse fibroblasts, human bronchial and mouse alveolar epithelial cells. Cells (i) treated with the JNK inhibitor SP600125, (ii) deleted or knocked down for JNK1/2 or Bim or (iii) carrying the BimEL triple phosphomutant S100A/T112A/S114A instead of wild-type BimEL are similarly resistant to GT-induced apoptosis. Triple-phosphorylated BimEL is more stable, redistributes from a cytoskeletal to a membrane fraction, better interacts with Bcl-2 and Bcl-xL and more effectively activates Bak than the unphosphorylated mutant. These data indicate that JNK-mediated BimEL phosphorylation at S100, T112 and S114 constitutes a novel regulatory mechanism to activate Bim in response to apoptotic stimuli.

Viscum album agglutinin-I (VAA-I) increases cell surface expression of cytoskeletal proteins in apoptotic human neutrophils: moesin and ezrin are two novel targets of VAA-I.

Viscum album agglutinin-I (VAA-I) is a plant lectin, which possesses anti-inflammatory properties, including the ability to induce neutrophil apoptosis by a mechanism that is not completely understood. Among the three actin-binding membrane-anchoring proteins ezrin/radixin/moesin (ERM), neutrophils are known to express ezrin and moesin. The behavior of these proteins in apoptotic neutrophils is not well established. In the present study, the expression and localization of ezrin and moesin by Western blot and immunofluorescence revealed a clear degradation and relocalization of both the proteins during VAA-I-induced apoptosis. Also, flow cytometry analysis revealed that VAA-I markedly and significantly induced the cell surface expression of ezrin and moesin and this was reversed when cells were pretreated with the Syk inhibitor piceatannol. The expression of ezrin and moesin on the cell surface of apoptotic neutrophils may represent a mechanism responsible for the appearance of autoantibodies directed against ERM proteins, which have been found in the serum of patients suffering from autoimmune diseases. Therefore, the ability of VAA-I to increase cell surface expression of cytoskeletal proteins in apoptotic neutrophils provides important insight into a possible toxic mechanism of this plant lectin and this has to be considered for its potential utilization for in vivo treatment.

MAGUKs, scaffolding proteins at cell junctions, are substrates of different proteases during apoptosis.

A major feature of apoptotic cell death is gross structural changes, one of which is the loss of cell-cell contacts. The caspases, executioners of apoptosis, were shown to cleave several proteins involved in the formation of cell junctions. The membrane-associated guanylate kinases (MAGUKs), which are typically associated with cell junctions, have a major role in the organization of protein-protein complexes at plasma membranes and are therefore potentially important caspase targets during apoptosis. We report here that MAGUKs are cleaved and/or degraded by executioner caspases, granzyme B and several cysteine cathepsins in vitro. When apoptosis was induced by UV-irradiation and staurosporine in different epithelial cell lines, caspases were found to efficiently cleave MAGUKs in these cell models, as the cleavages could be prevented by a pan-caspase inhibitor N-benzyloxycarbonyl-Val-Ala-Asp(OMe)fluoromethylketone. Using a selective lysosomal disrupting agent L-leucyl-L-leucine methyl ester, which induces apoptosis through the lysosomal pathway, it was further shown that MAGUKs are also cleaved by the cathepsins in HaCaT and CaCo-2 cells. Immunohistological data showed rapid loss of MAGUKs at the sites of cell-cell contacts, preceding actual cell detachment, suggesting that cleavage of MAGUKs is an important step in fast and efficient cell detachment.

Two-dimensional graphene with structural defects: elastic mean free path, minimum conductivity, and Anderson transition.

Quantum transport properties of disordered graphene with structural defects (Stone-Wales and divacancies) are investigated using a realistic π-π* tight-binding model elaborated from ab initio calculations. Mean free paths and semiclassical conductivities are then computed as a function of the nature and density of defects (using an order-N real-space Kubo-Greenwood method). By increasing the defect density, the decay of the semiclassical conductivities is predicted to saturate to a minimum value of 4e2/πh over a large range (plateau) of carrier density (>0.5×10(14) cm(-20). Additionally, strong contributions of quantum interferences suggest that the Anderson localization regime could be experimentally measurable for a defect density as low as 1%.

Mouse granzyme K has pro-inflammatory potential.

Granzymes (gzms) are key components of T-killer (Tc) cells believed to mediate pro-apoptotic activities. Recent evidence suggests that gzms also possess non-cytotoxic activities that contribute to host defense. In this study, we show that Tc cells from lymphocytic choriomeningitis virus (LCMV)-infected wild-type (wt) and gzm A/B-deficient mice express similar levels of gzmK protein, with both mouse strains efficiently controlling infection. GzmK, in recombinant form or secreted by ex vivo-derived LCMV-immune gzmAxB(-/-) Tc cells, lacks pro-apoptotic activity. Instead, gzmK induces primary mouse macrophages to process and secrete interleukin-1ß, independent of the ATP receptor P2X(7). Together with the finding that IL-1Ra (Anakinra) treatment inhibits virus elimination but not generation of cytotoxic Tc cells in wt mice, the data suggest that Tc cells control LCMV through non-cytotoxic processes that involve gzmK.

Quantum transport in graphene nanoribbons: effects of edge reconstruction and chemical reactivity.

We present first-principles transport calculations of graphene nanoribbons with chemically reconstructed edge profiles. Depending on the geometry of the defect and the degree of hydrogenation, spectacularly different transport mechanisms are obtained. In the case of monohydrogenated pentagon (heptagon) defects, an effective acceptor (donor) character results in strong electron-hole conductance asymmetry. In contrast, weak backscattering is obtained for defects that preserve the benzenoid structure of graphene. Based on a tight-binding model derived from ab initio calculations, evidence for large conductance scaling fluctuations are found in disordered ribbons with lengths up to the micrometer scale.

The serum metabolite response to diet intervention with probiotic acidified milk in irritable bowel syndrome patients is indistinguishable from that of non-probiotic acidified milk by 1H NMR-based metabonomic analysis.

The effects of a probiotic acidified milk product on the blood serum metabolite profile of patients suffering from Irritable Bowel Syndrome (IBS) compared to a non-probiotic acidified milk product was investigated using (1)H NMR metabonomics. For eight weeks, IBS patients consumed 0.4 L per day of a probiotic fermented milk product or non-probiotic acidified milk. Both diets resulted in elevated levels of blood serum L-lactate and 3-hydroxybutyrate. Our results showed identical effects of acidified milk consumption independent of probiotic addition. A similar result was previously obtained in a questionnaire-based evaluation of symptom relief. A specific probiotic effect is thus absent both in the patient subjective symptom evaluations and at the blood serum metabolite level. However, there was no correspondence between symptom relief and metabolite response on the patient level.

[Lyme borreliosis: research gaps and research approaches. Results from an interdisciplinary expert meeting at the Robert Koch Institute]. / Lyme-Borreliose: Forschungsbedarf und Forschungsansätze. Ergebnisse eines interdisziplinären Expertentreffens am Robert Koch-Institut.

Lyme borreliosis is currently the most frequent tick-transmitted zoonosis in the northern hemisphere. Germany and other European countries are regarded as highly endemic areas; therefore the burden of disease and consequently the costs for the health systems are considered to be high. This report summarises the results of an interdisciplinary workshop on Lyme borreliosis which aimed to identify research deficits and to prioritise areas which need to be addressed. Research needs have been recognised for different areas: diagnosis, epidemiology, immunology, clinics, ecology and health services research. Examples of research areas which have priority are the standardisation of diagnostic tests, the development of markers to detect an active infection, the improvement of the epidemiological database and the analysis of the burden of disease.

Assessment of total arsenic and arsenic species stability in alga samples and their aqueous extracts.

In order to achieve reliable information on speciation analysis, it is necessary to assess previously the species stability in the sample to analyse. Furthermore, in those cases where the sample treatment for species extraction is time-consuming, an assessment of the species integrity in the extracts is of paramount importance. Thus, the present paper reports total arsenic and arsenic species stability in alga samples (Sargassum fulvellum and Hizikia fusiformis), as well as in their aqueous extracts, which were stored in amber glass and polystyrene containers at different temperatures. Total arsenic determination was carried out by inductively coupled plasma atomic emission spectroscopy (ICP-AES), after sample acid digestion in a microwave oven, while arsenic speciation was conducted by anion exchange high performance liquid chromatography on-line coupled to ICP-AES, with and without sample introduction by hydride generation (HPLC-ICP-AES and HPLC-HG-ICP-AES), after aqueous microwave-assisted extraction. The results obtained for solid alga samples showed that total arsenic (for Hijiki alga) and arsenic species present (As(V) for Hijiki and NIES No. 9 Sargasso) are stable for at least 12 months when samples are stored in polystyrene containers at +20 degrees C. On the other hand, a different behaviour was observed in the stability of total arsenic and As(V) species in aqueous extracts for both samples, being the best storage conditions for Sargasso extracts a temperature of -18 degrees C and polystyrene containers, under which they are stable for at least 15 days, while Hijiki extracts must be stored in polystyrene containers at +4 degrees C in order to ensure the stability for 10 days.