327 research outputs found

    Octagonal defects at carbon nanotube junctions

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    We investigate knee-shaped junctions of semiconductor zigzag carbon nanotubes. Two dissimilar octagons appear at such junctions; one of them can reconstruct into a pair of pentagons. The junction with two octagons presents two degenerate localized states at Fermi energy (EF). The reconstructed junction has only one state near EF, indicating that these localized states are related to the octagonal defects. The inclusion of Coulomb interaction splits the localized states in the junction with two octagons, yielding an antiferromagnetic system

    Effects of stiffness and cell shape on cellular mechanosensing

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    Cellular mechanosensing is the process of converting mechanical signals into biological responses. Stem cells are self-renewing cells with the potential to transform into specialized cell types - this differentiation process is influenced by cellular mechanosensing. Cells sense material stiffness, and stiffer environments result in increased cellular mechanosensing and preferential differentiation into bone-producing osteoblasts. Cell shape also plays an important role due to its influence on cytoskeletal contractility, and photopatterning can be used to study the effects of cell shape on cellular mechanosensing. Although the effects of material stiffness and cell shape have been studied, little is known about the joint effects of these factors on stem cell mechanosensing. Taken together, the goal of this research is to develop a biomaterial system to study the combinatorial effects of shape and stiffness on mesenchymal stem cell (MSC) mechanosensing. Hydrogels of three stiffness (5 kPa, 10 kPa, 20 kPa) were photopatterned with shapes (circle, square, octagon) that cause a range of contractile forces in cells. These shapes were made into patterns on a glass photomask, allowing hydrogels placed under the photomask to be photopatterned. Photopatterns were found to over 90% accurate. Highly angular shapes, such as the octagon, and increased stiffness were both seen to influence an increased nuclear localization of mechanosensing protein YAP, with stiffness having a greater influence than shape

    Vinculin binding angle in podosomes revealed by high resolution microscopy

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    Podosomes are highly dynamic actin-rich adhesive structures formed predominantly by cells of the monocytic lineage, which degrade the extracellular matrix. They consist of a core of F-actin and actin-regulating proteins, surrounded by a ring of adhesion-associated proteins such as vinculin. We have characterised the structure of podosomes in macrophages, particularly the structure of the ring, using three super-resolution fluorescence microscopy techniques: stimulated emission depletion microscopy, structured illumination microscopy and localisation microscopy. Rather than being round, as previously assumed, we found the vinculin ring to be created from relatively straight strands of vinculin, resulting in a distinctly polygonal shape. The strands bind preferentially at angles between 116° and 135°. Furthermore, adjacent vinculin strands are observed nucleating at the corners of the podosomes, suggesting a mechanism for podosome growth

    A large scale survey reveals that chromosomal copy-number alterations significantly affect gene modules involved in cancer initiation and progression

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    Background Recent observations point towards the existence of a large number of neighborhoods composed of functionally-related gene modules that lie together in the genome. This local component in the distribution of the functionality across chromosomes is probably affecting the own chromosomal architecture by limiting the possibilities in which genes can be arranged and distributed across the genome. As a direct consequence of this fact it is therefore presumable that diseases such as cancer, harboring DNA copy number alterations (CNAs), will have a symptomatology strongly dependent on modules of functionally-related genes rather than on a unique "important" gene. Methods We carried out a systematic analysis of more than 140,000 observations of CNAs in cancers and searched by enrichments in gene functional modules associated to high frequencies of loss or gains. Results The analysis of CNAs in cancers clearly demonstrates the existence of a significant pattern of loss of gene modules functionally related to cancer initiation and progression along with the amplification of modules of genes related to unspecific defense against xenobiotics (probably chemotherapeutical agents). With the extension of this analysis to an Array-CGH dataset (glioblastomas) from The Cancer Genome Atlas we demonstrate the validity of this approach to investigate the functional impact of CNAs. Conclusions The presented results indicate promising clinical and therapeutic implications. Our findings also directly point out to the necessity of adopting a function-centric, rather a gene-centric, view in the understanding of phenotypes or diseases harboring CNAs.Spanish Ministry of Science and Innovation (grant BIO2008-04212)Spanish Ministry of Science and Innovation (grant FIS PI 08/0440)GVA-FEDER (PROMETEO/2010/001)Red Temática de Investigación Cooperativa en Cáncer (RTICC) (grant RD06/0020/1019)Instituto de Salud Carlos III (ISCIII)Spanish Ministry of Science and InnovationSpanish Ministry of Health (FI06/00027

    Monitoring Active Sites for Hydrogen Evolution Reaction at Model Carbon Surfaces

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    Carbon is ubiquitous as an electrode material in electrochemical energy conversion devices. If used as support material, the evolution of H2 is undesired on carbon. However, recently carbon-based materials are of high interest as economic and eco-conscious alternative to noble metal catalysts. The targeted design of improved carbon electrode materials requires atomic scale insight into the structure of the sites that catalyse H2 evolution. This work demonstrates that electrochemical scanning tunnelling microscopy under reaction conditions (n-EC-STM) can monitor active sites of highly oriented pyrolytic graphite for the hydrogen evolution reaction. With down to atomic resolution, the most active sites in acidic medium are pinpointed near edge sites and defects, whereas the basal planes remain inactive. Density functional theory calculations support these findings and reveal that only specific defects on graphite are active. Motivated by these results, the extensive usage of n-EC-STM on doped carbon-based materials is encouraged to locate their active sites and guide the synthesis of enhanced electrocatalysts.The authors thank Prof. Plamen Atanassov (University of California, Irvine, USA) and Dr. Jun Maruyama (Osaka Research Institute of Industrial Science and Technology, Japan) for fruitful discussion regarding some experimental results. RMK, RWH and ASB acknowledge the financial support from the German Research Foundation (DFG), in the framework of the projects BA 5795/4-1 and BA 5795/3-1, and under Germany's Excellence Strategy–EXC 2089/1–390776260, cluster of excellence ‘e-conversion’. ASB acknowledges the funding from the European Union's Horizon 2020 research and innovation programme under grant agreement HERMES No. 952184. FCV acknowledges financial support from Spanish MICIUN through RTI2018-095460-B-I00 and María de Maeztu (MDM-2017-0767) grants and a Ramón y Cajal research contract (RYC-2015-18996), and also from Generalitat de Catalunya (grants 2017SGR13 and XRQTC). The use of supercomputing facilities at SURFsara was sponsored by NWO Physical Sciences, with financial support from NWO

    Octagonal defects at carbon nanotube junctions,”

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    We investigate knee-shaped junctions of semiconductor zigzag carbon nanotubes. Two dissimilar octagons appear at such junctions; one of them can reconstruct into a pair of pentagons. The junction with two octagons presents two degenerate localized states at Fermi energy ( ). The reconstructed junction has only one state near , indicating that these localized states are related to the octagonal defects. The inclusion of Coulomb interaction splits the localized states in the junction with two octagons, yielding an antiferromagnetic system

    Matter-Wave Diffraction from a Quasicrystalline Optical Lattice.

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    Quasicrystals are long-range ordered and yet nonperiodic. This interplay results in a wealth of intriguing physical phenomena, such as the inheritance of topological properties from higher dimensions, and the presence of nontrivial structure on all scales. Here, we report on the first experimental demonstration of an eightfold rotationally symmetric optical lattice, realizing a two-dimensional quasicrystalline potential for ultracold atoms. Using matter-wave diffraction we observe the self-similarity of this quasicrystalline structure, in close analogy to the very first discovery of quasicrystals using electron diffraction. The diffraction dynamics on short timescales constitutes a continuous-time quantum walk on a homogeneous four-dimensional tight-binding lattice. These measurements pave the way for quantum simulations in fractal structures and higher dimensions

    Closing the Performance Gap between Doubles and Rationals for Octagons

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    Octagons have enduring appeal because their domain opera- tions are simple, readily mapping to for-loops which apply max, min and sum to the entries of a Difference Bound Matrix (DBM). In the quest for efficiency, arithmetic is often realised with double-precision floating- point, albeit at the cost of the certainty provided by arbitrary-precision rationals. In this paper we show how Compact DBMs (CoDBMs), which have recently been proposed as a memory refinement for DBMs, enable arithmetic calculation to be short-circuited in various domain operations. We also show how comparisons can be avoided by changing the tables which underpin CoDBMs. From the perspective of implementation, the optimisations are attractive because they too are conceptually simple, following the ethos of Octagons. Yet they can halve the running time on rationals, putting CoDBMs on rationals on a par with DBMs on doubles

    Control of the Mitotic Cleavage Plane by Local Epithelial Topology

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    For nearly 150 years, it has been recognized that cell shape strongly influences the orientation of the mitotic cleavage plane (e.g. Hofmeister, 1863). However, we still understand little about the complex interplay between cell shape and cleavage plane orientation in epithelia, where polygonal cell geometries emerge from multiple factors, including cell packing, cell growth, and cell division itself. Here, using mechanical simulations, we show that the polygonal shapes of individual cells can systematically bias the long axis orientations of their adjacent mitotic neighbors. Strikingly, analysis of both animal epithelia and plant epidermis confirm a robust and nearly identical correlation between local cell topology and cleavage plane orientation in vivo. Using simple mathematics, we show that this effect derives from fundamental packing constraints. Our results suggest that local epithelial topology is a key determinant of cleavage plane orientation, and that cleavage plane bias may be a widespread property of polygonal cell sheets in plants and animals.Engineering and Applied Science

    MorphDB : prioritizing genes for specialized metabolism pathways and gene ontology categories in plants

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    Recent times have seen an enormous growth of "omics" data, of which high-throughput gene expression data are arguably the most important from a functional perspective. Despite huge improvements in computational techniques for the functional classification of gene sequences, common similarity-based methods often fall short of providing full and reliable functional information. Recently, the combination of comparative genomics with approaches in functional genomics has received considerable interest for gene function analysis, leveraging both gene expression based guilt-by-association methods and annotation efforts in closely related model organisms. Besides the identification of missing genes in pathways, these methods also typically enable the discovery of biological regulators (i.e., transcription factors or signaling genes). A previously built guilt-by-association method is MORPH, which was proven to be an efficient algorithm that performs particularly well in identifying and prioritizing missing genes in plant metabolic pathways. Here, we present MorphDB, a resource where MORPH-based candidate genes for large-scale functional annotations (Gene Ontology, MapMan bins) are integrated across multiple plant species. Besides a gene centric query utility, we present a comparative network approach that enables researchers to efficiently browse MORPH predictions across functional gene sets and species, facilitating efficient gene discovery and candidate gene prioritization. MorphDB is available at http://bioinformatics.psb.ugent.be/webtools/morphdb/morphDB/index/. We also provide a toolkit, named "MORPH bulk" (https://github.com/arzwa/morph-bulk), for running MORPH in bulk mode on novel data sets, enabling researchers to apply MORPH to their own species of interest
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