567 results match your criteria Interface focus[Journal]


Glycan-decorated protocells: novel features for rebuilding cellular processes.

Interface Focus 2019 Apr 15;9(2):20180084. Epub 2019 Feb 15.

Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany.

In synthetic biology approaches, lipid vesicles are widely used as protocell models. While many compounds have been encapsulated in vesicles (e.g. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6388021PMC
April 2019
1 Read

Synthetic glycoscapes: addressing the structural and functional complexity of the glycocalyx.

Interface Focus 2019 Apr 15;9(2):20180080. Epub 2019 Feb 15.

Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0358, USA.

The glycocalyx is an information-dense network of biomacromolecules extensively modified through glycosylation that populates the cellular boundary. The glycocalyx regulates biological events ranging from cellular protection and adhesion to signalling and differentiation. Owing to the characteristically weak interactions between individual glycans and their protein binding partners, multivalency of glycan presentation is required for the high-avidity interactions needed to trigger cellular responses. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6388016PMC
April 2019
14 Reads

Serum IgA1 shows increased levels of 2,6-linked sialic acid in breast cancer.

Interface Focus 2019 Apr 15;9(2):20180079. Epub 2019 Feb 15.

School of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK.

The lectin agglutinin (HPA) recognizes altered glycosylation in solid cancers and the identification of HPA binding partners in tumour tissue and serum is an important aim. Among the many HPA binding proteins, IgA1 has been reported to be the most abundant in liver metastases. In this study, the glycosylation of IgA1 was evaluated using serum samples from patients with breast cancer (BCa) and the utility of IgA1 glycosylation as a biomarker was assessed. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6388022PMC
April 2019
1 Read

Prostate-specific antigen glycoprofiling as diagnostic and prognostic biomarker of prostate cancer.

Interface Focus 2019 Apr 15;9(2):20180077. Epub 2019 Feb 15.

Center for Advanced Materials, Qatar University, Doha 2713, Qatar.

The initial part of this review details the controversy behind the use of a serological level of prostate-specific antigen (PSA) for the diagnostics of prostate cancer (PCa). Novel biomarkers are in demand for PCa diagnostics, outperforming traditional PSA tests. The review provides a detailed and comprehensive summary that PSA glycoprofiling can effectively solve this problem, thereby considerably reducing the number of unnecessary biopsies. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6388024PMC
April 2019
1 Read

Cell type and receptor identity regulate cholera toxin subunit B (CTB) internalization.

Interface Focus 2019 Apr 15;9(2):20180076. Epub 2019 Feb 15.

Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Cholera toxin (CT) is a secreted bacterial toxin that binds to glycoconjugate receptors on the surface of mammalian cells, enters mammalian cells through endocytic mechanisms and intoxicates mammalian cells by activating cytosolic adenylate cyclase. CT recognizes cell surface receptors through its B subunit (CTB). While the ganglioside GM1 has been historically described as the sole receptor, CTB is also capable of binding to fucosylated glycoconjugates, and fucosylated molecules have been shown to play a functional role in host cell intoxication by CT. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6388018PMC
April 2019
1 Read

'Clickable lectins': bioorthogonal reactive handles facilitate the directed conjugation of lectins in a modular fashion.

Interface Focus 2019 Apr 15;9(2):20180072. Epub 2019 Feb 15.

Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria.

Lectins are carbohydrate-binding proteins with specificity for their target ligands. They play diverse roles in cellular recognition and signalling processes, as well as in infections and cancer metastasis. Owing to their specificity, lectins find application in biotechnology and medicine, e. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6388015PMC
April 2019
3 Reads

Harnessing glycoenzyme engineering for synthesis of bioactive oligosaccharides.

Interface Focus 2019 Apr 15;9(2):20180069. Epub 2019 Feb 15.

Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, 135, avenue de Rangueil, 31077 Toulouse cedex 04, France.

Combined with chemical synthesis, the use of glycoenzyme biocatalysts has shown great synthetic potential over recent decades owing to their remarkable versatility in terms of substrates and regio- and stereoselectivity that allow structurally controlled synthesis of carbohydrates and glycoconjugates. Nonetheless, the lack of appropriate enzymatic tools with requisite properties in the natural diversity has hampered extensive exploration of enzyme-based synthetic routes to access relevant bioactive oligosaccharides, such as cell-surface glycans or prebiotics. With the remarkable progress in enzyme engineering, it has become possible to improve catalytic efficiency and physico-chemical properties of enzymes but also considerably extend the repertoire of accessible catalytic reactions and tailor novel substrate specificities. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6388017PMC

Lectin engineering: the possible and the actual.

Interface Focus 2019 Apr 15;9(2):20180068. Epub 2019 Feb 15.

Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan.

Lectins are a widespread group of sugar-binding proteins occurring in all types of organisms including animals, plants, bacteria, fungi and even viruses. According to a recent report, there are more than 50 lectin scaffolds (∼Pfam), for which three-dimensional structures are known and sugar-binding functions have been confirmed in the literature, which far exceeds our view in the twentieth century (Fujimoto 2014 , 579-606 (doi:10.1007/978-1-4939-1292-6_46)). Read More

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http://www.royalsocietypublishing.org/doi/10.1098/rsfs.2018.
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http://dx.doi.org/10.1098/rsfs.2018.0068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6388023PMC
April 2019
17 Reads

Nonulosonic acids contribute to the pathogenicity of the oral bacterium .

Interface Focus 2019 Apr 15;9(2):20180064. Epub 2019 Feb 15.

Department of NanoBiotechnology, NanoGlycobiology unit, Universität für Bodenkultur Wien, Muthgasse 11, 1190 Vienna, Austria.

Periodontitis is a polymicrobial, biofilm-caused, inflammatory disease affecting the tooth-supporting tissues. It is not only the leading cause of tooth loss worldwide, but can also impact systemic health. The development of effective treatment strategies is hampered by the complicated disease pathogenesis which is best described by a polymicrobial synergy and dysbiosis model. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6388019PMC

Effect of calcium ions and pH on the morphology and mechanical properties of hyaluronan brushes.

Interface Focus 2019 Apr 15;9(2):20180061. Epub 2019 Feb 15.

CIC biomaGUNE, San Sebastian, Spain.

Hyaluronan (HA) is a linear, regular polysaccharide that plays as a chief structural and functional component in peri- and extracellular matrices, thus contributing significantly to many basic cellular processes. To understand more comprehensively the response of the supramolecular organization of HA polymers to changes in their aqueous environment, we study the effects of Ca concentration and pH on the morphology and rigidity of films of end-grafted HA polymers on planar supports (HA brushes), as a well-defined model system of HA-rich matrices, by reflection interference contrast microscopy and quartz crystal microbalance. The thickness and softness of HA brushes decrease significantly with Ca concentration but do not change with pH, within the physiological ranges of these parameters. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6388027PMC
April 2019
12 Reads

Structural features underlying recognition and translocation of extracellular polysaccharides.

Authors:
Jochen Zimmer

Interface Focus 2019 Apr 15;9(2):20180060. Epub 2019 Feb 15.

University of Virginia, 480 Ray C. Hunt Dr., Charlottesville, VA 22903, USA.

Essentially all living systems produce complex carbohydrates as an energy source, structural component, protective coat or adhesive for cell attachment. Many polysaccharides are displayed on the cell surface or are threaded through proteinaceous tunnels for degradation. Dictated by their chemical composition and mode of polymerization, the physical properties of complex carbohydrates differ substantially, from amphipathic water-insoluble polymers to highly hydrated hydrogel-forming macromolecules. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6388025PMC

Structural colours in the frond of .

Interface Focus 2019 Feb 14;9(1):20180055. Epub 2018 Dec 14.

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.

Blue and near-ultraviolet structural colours have often been reported in understorey plants living in deep shade. While this intense blue coloration is very catchy to the eye of a human observer, there are cases in which structural colours can be hidden either by the scattered light interacting with pigments or because they are found in unexpected positions in the plants. Here, we show that the fronds of produce structural coloration on both the adaxial and abaxial epidermal surface. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304010PMC
February 2019
6 Reads

I see your false colours: how artificial stimuli appear to different animal viewers.

Interface Focus 2019 Feb 14;9(1):20180053. Epub 2018 Dec 14.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

The use of artificially coloured stimuli, especially to test hypotheses about sexual selection and anti-predator defence, has been common in behavioural ecology since the pioneering work of Tinbergen. To investigate the effects of colour on animal behaviour, many researchers use paints, markers and dyes to modify existing colours or to add colour to synthetic models. Because colour perception varies widely across species, it is critical to account for the signal receiver's vision when performing colour manipulations. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304012PMC
February 2019
2 Reads

Nonlinear optical spectroscopy and two-photon excited fluorescence spectroscopy reveal the excited states of fluorophores embedded in a beetle's elytra.

Interface Focus 2019 Feb 14;9(1):20180052. Epub 2018 Dec 14.

Micro- and Nanophotonic Materials Group, University of Mons, Place du Parc 20, 7000 Mons, Belgium.

Upon illumination by ultraviolet light, many animal species emit light through fluorescence processes arising from fluorophores embedded within their biological tissues. Fluorescence studies in living organisms are however relatively scarce and so far limited to the linear regime. Multiphoton excitation fluorescence analyses as well as nonlinear optical techniques offer unique possibilities to investigate the effects of the local environment on the excited states of fluorophores. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304011PMC
February 2019
2 Reads

Coherent backscattering of light by an anisotropic biological network.

Interface Focus 2019 Feb 14;9(1):20180050. Epub 2018 Dec 14.

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.

The scattering strength of a random medium relies on the geometry and spatial distribution of its components as well as on their refractive index. Anisotropy can, therefore, play a major role in the optimization of the scattering efficiency in both biological and synthetic materials. In this study, we show that, by exploiting the coherent backscattering phenomenon, it is possible to characterize the optical anisotropy in beetle scales without the need to change their orientation or their thickness. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304008PMC
February 2019
1 Read

Quantitative characterization of iridescent colours in biological studies: a novel method using optical theory.

Interface Focus 2019 Feb 14;9(1):20180049. Epub 2018 Dec 14.

CEFE, Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France.

Iridescent colours are colours that change with viewing or illumination geometry. While they are widespread in many living organisms, most evolutionary studies on iridescence do not take into account their full complexity. Few studies try to precisely characterize what makes iridescent colours special: their angular dependency. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304013PMC
February 2019
2 Reads

Functional nanomaterials to augment photosynthesis: evidence and considerations for their responsible use in agricultural applications.

Interface Focus 2019 Feb 14;9(1):20180048. Epub 2018 Dec 14.

School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TL, UK.

At the current population growth rate, we will soon be unable to meet increasing food demands. As a consequence of this potential problem, considerable efforts have been made to enhance crop productivity by breeding, genetics and improving agricultural practices. While these techniques have traditionally been successful, their efficacy since the 'green revolution' has begun to significantly plateau. Read More

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http://www.royalsocietypublishing.org/doi/10.1098/rsfs.2018.
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http://dx.doi.org/10.1098/rsfs.2018.0048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304006PMC
February 2019
2 Reads

Phenotypic variation in crosses shows that iridescent structural colour is sex-linked and controlled by multiple genes.

Interface Focus 2019 Feb 14;9(1):20180047. Epub 2018 Dec 14.

Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK.

Bright, highly reflective iridescent colours can be seen across nature and are produced by the scattering of light from nanostructures. butterflies have been widely studied for their diversity and mimicry of wing colour patterns. Despite iridescence evolving multiple times in this genus, little is known about the genetic basis of the colour and the development of the structures which produce it. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304015PMC
February 2019
1 Read

Thin-film structural coloration from simple fused scales in moths.

Interface Focus 2019 Feb 14;9(1):20180044. Epub 2018 Dec 14.

Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland.

The metallic coloration of insects often originates from diverse nanostructures ranging from simple thin films to complex three-dimensional photonic crystals. In Lepidoptera, structural coloration is widely present and seems to be abundant in extant species. However, even some basal moths exhibit metallic coloration. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304009PMC
February 2019
1 Read

Reflections on iridescent neck and breast feathers of the peacock, .

Interface Focus 2019 Feb 14;9(1):20180043. Epub 2018 Dec 14.

Computational Physics, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.

The blue neck and breast feathers of the peacock are structurally coloured due to an intricate photonic crystal structure in the barbules consisting of a two-dimensionally ordered rectangular lattice of melanosomes (melanin rodlets) and air channels embedded in a keratin matrix. We here investigate the feather coloration by performing microspectrophotometry, imaging scatterometry and angle-dependent reflectance measurements. Using previously determined wavelength-dependent refractive indices of melanin and keratin, we interpret the spectral and spatial reflection characteristics by comparing the measured spectra to calculated spectra by effective-medium multilayer and full three-dimensional finite-difference time-domain modelling. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304014PMC
February 2019
2 Reads

Differences in the optical properties of valve and girdle band in a centric diatom.

Interface Focus 2019 Feb 14;9(1):20180031. Epub 2018 Dec 14.

Marine Biology Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark.

Diatoms are phototrophic single-celled microalgae encased in a cell wall (frustule) made of amorphous silicate. The frustule comprises two valves connected by a variable number of girdle bands, all exhibiting periodic micro/nanoporous structures. We studied the optical properties in water of girdle bands from the centric diatom , a frustule part that so far has received little attention by the scientific community. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304007PMC
February 2019
1 Read

Semantic information, autonomous agency and non-equilibrium statistical physics.

Interface Focus 2018 Dec 19;8(6):20180041. Epub 2018 Oct 19.

Santa Fe Institute, Santa Fe, NM 87501, USA.

Shannon information theory provides various measures of so-called syntactic information, which reflect the amount of statistical correlation between systems. By contrast, the concept of 'semantic information' refers to those correlations which carry significance or 'meaning' for a given system. Semantic information plays an important role in many fields, including biology, cognitive science and philosophy, and there has been a long-standing interest in formulating a broadly applicable and formal theory of semantic information. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227811PMC
December 2018
1 Read

Haematopoietic stem cells: entropic landscapes of differentiation.

Interface Focus 2018 Dec 19;8(6):20180040. Epub 2018 Oct 19.

Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund 223 62, Sweden.

The metaphor of a potential epigenetic differentiation landscape broadly suggests that during differentiation a stem cell approaches a stable equilibrium state from a higher free energy towards a stable equilibrium state which represents the final cell type. It has been conjectured that there is an analogy to the concept of entropy in statistical mechanics. In this context, in the undifferentiated state, the entropy would be large since fewer constraints exist on the gene expression programmes of the cell. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227807PMC
December 2018
1 Read

Intrinsic limits of information transmission in biochemical signalling motifs.

Interface Focus 2018 Dec 19;8(6):20180039. Epub 2018 Oct 19.

Center for Computational Biology, University of Kansas, Lawrence, KS 66047, USA.

All living things have evolved to sense changes in their environment in order to respond in adaptive ways. At the cellular level, these sensing systems generally involve receptor molecules at the cell surface, which detect changes outside the cell and relay those changes to the appropriate response elements downstream. With the advent of experimental technologies that can track signalling at the single-cell level, it has become clear that many signalling systems exhibit significant levels of 'noise,' manifesting as differential responses of otherwise identical cells to the same environment. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227803PMC
December 2018
1 Read

Computational modelling unravels the precise clockwork of cyanobacteria.

Interface Focus 2018 Dec 19;8(6):20180038. Epub 2018 Oct 19.

Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany.

Precisely timing the regulation of gene expression by anticipating recurring environmental changes is a fundamental part of global gene regulation. Circadian clocks are one form of this regulation, which is found in both eukaryotes and prokaryotes, providing a fitness advantage for these organisms. Whereas many different eukaryotic groups harbour circadian clocks, cyanobacteria are the only known oxygenic phototrophic prokaryotes to regulate large parts of their genes in a circadian fashion. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227802PMC
December 2018
2 Reads

A thermodynamically consistent model of finite-state machines.

Interface Focus 2018 Dec 19;8(6):20180037. Epub 2018 Oct 19.

Centre for Complex Systems, The University of Sydney, Sydney, New South Wales 2006, Australia.

Finite-state machines (FSMs) are a theoretically and practically important model of computation. We propose a general, thermodynamically consistent model of FSMs and characterize the resource requirements of these machines. We model FSMs as time-inhomogeneous Markov chains. Read More

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http://rsfs.royalsocietypublishing.org/lookup/doi/10.1098/rs
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http://dx.doi.org/10.1098/rsfs.2018.0037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227804PMC
December 2018
15 Reads

Thermodynamic efficiency of contagions: a statistical mechanical analysis of the SIS epidemic model.

Interface Focus 2018 Dec 19;8(6):20180036. Epub 2018 Oct 19.

Centre for Complex Systems, Faculty of Engineering and IT, University of Sydney, Sydney, New South Wales 2006, Australia.

We present a novel approach to the study of epidemics on networks as thermodynamic phenomena, quantifying the thermodynamic efficiency of contagions, considered as distributed computational processes. Modelling SIS dynamics on a contact network statistical-mechanically, we follow the maximum entropy (MaxEnt) principle to obtain steady-state distributions and derive, under certain assumptions, relevant thermodynamic quantities both analytically and numerically. In particular, we obtain closed-form solutions for some cases, while interpreting key epidemic variables, such as the reproductive ratio of a SIS model, in a statistical mechanical setting. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227806PMC
December 2018
2 Reads

Something has to give: scaling combinatorial computing by biological agents exploring physical networks encoding NP-complete problems.

Interface Focus 2018 Dec 19;8(6):20180034. Epub 2018 Oct 19.

Department of Bioengineering, McGill University, Montreal, Quebec, Canada H3A 0E9.

On-chip network-based computation, using biological agents, is a new hardware-embedded approach which attempts to find solutions to combinatorial problems, in principle, in a shorter time than the fast, but sequential electronic computers. This analytical review starts by describing the underlying mathematical principles, presents several types of combinatorial (including NP-complete) problems and shows current implementations of proof of principle developments. Taking the subset sum problem as example for in-depth analysis, the review presents various options of computing agents, and compares several possible operation 'run modes' of network-based computer systems. Read More

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http://rsfs.royalsocietypublishing.org/lookup/doi/10.1098/rs
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http://dx.doi.org/10.1098/rsfs.2018.0034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227808PMC
December 2018
15 Reads

From statistical inference to a differential learning rule for stochastic neural networks.

Interface Focus 2018 Dec 19;8(6):20180033. Epub 2018 Oct 19.

Italian Institute for Genomic Medicine, Torino, Italy.

Stochastic neural networks are a prototypical computational device able to build a probabilistic representation of an ensemble of external stimuli. Building on the relationship between inference and learning, we derive a synaptic plasticity rule that relies only on delayed activity correlations, and that shows a number of remarkable features. Our (DCM) rule satisfies some basic requirements for biological feasibility: finite and noisy afferent signals, Dale's principle and asymmetry of synaptic connections, locality of the weight update computations. Read More

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http://rsfs.royalsocietypublishing.org/lookup/doi/10.1098/rs
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http://dx.doi.org/10.1098/rsfs.2018.0033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227809PMC
December 2018
11 Reads

Towards fungal computer.

Authors:
Andrew Adamatzky

Interface Focus 2018 Dec 19;8(6):20180029. Epub 2018 Oct 19.

Unconventional Computing Lab, UWE, CSCT, Bristol, UK.

We propose that fungi Basidiomycetes can be used as computing devices: information is represented by spikes of electrical activity, a computation is implemented in a mycelium network and an interface is realized via fruit bodies. In a series of scoping experiments, we demonstrate that electrical activity recorded on fruits might act as a reliable indicator of the fungi's response to thermal and chemical stimulation. A stimulation of a fruit is reflected in changes of electrical activity of other fruits of a cluster, i. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227805PMC
December 2018
1 Read

Membrane remodelling by a lipidated endosomal sorting complex required for transport-III chimera, .

Interface Focus 2018 Oct 17;8(5):20180035. Epub 2018 Aug 17.

Department of Chemistry and Centre for Membrane Interactions and Dynamics, University of Sheffield, Sheffield, UK.

The complexity of eukaryotic cells is underscored by the compartmentalization of chemical signals by phospholipid membranes. A grand challenge of synthetic biology is building life from the 'bottom-up', for the purpose of generating systems simple enough to precisely interrogate biological pathways or for adapting biology to perform entirely novel functions. Achieving compartmentalization of chemistries in an addressable manner is a task exquisitely refined by nature and embodied in a unique membrane remodelling machinery that pushes membranes away from the cytosol, the ESCRT-III (endosomal sorting complex required for transport-III) complex. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227774PMC
October 2018
1 Read

Liquid-liquid phase separation in artificial cells.

Interface Focus 2018 Oct 17;8(5):20180032. Epub 2018 Aug 17.

Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.

Liquid-liquid phase separation (LLPS) in biology is a recently appreciated means of intracellular compartmentalization. Because the mechanisms driving phase separations are grounded in physical interactions, they can be recreated within less complex systems consisting of only a few simple components, to serve as artificial microcompartments. Within these simple systems, the effect of compartmentalization and microenvironments upon biological reactions and processes can be studied. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227770PMC
October 2018
2 Reads

Urea-mediated anomalous diffusion in supported lipid bilayers.

Interface Focus 2018 Oct 17;8(5):20180028. Epub 2018 Aug 17.

Department of Chemistry, Britannia House, King's College London, 7 Trinity Street, London SE1 1DB, UK.

Diffusion in biological membranes is seldom simply Brownian motion; instead, the rate of diffusion is dependent on the time scale of observation and so is often described as anomalous. In order to help better understand this phenomenon, model systems are needed where the anomalous diffusion of the lipid bilayer can be tuned and quantified. We recently demonstrated one such model by controlling the excluded area fraction in supported lipid bilayers (SLBs) through the incorporation of lipids derivatized with polyethylene glycol. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227775PMC
October 2018
1 Read

Human ubiquitin-like proteins as central coordinators in autophagy.

Interface Focus 2018 Oct 17;8(5):20180025. Epub 2018 Aug 17.

Membrane Biochemistry and Transport, Institute Pasteur, 28 rue du Dr Roux, 75015 Paris, France.

Autophagy is one of the most versatile recycling systems of eukaryotic cells. It degrades diverse cytoplasmic components such as organelles, protein aggregates, ribosomes and multi-enzyme complexes. Not surprisingly, any failure of autophagy or reduced activity of the pathway contributes to the onset of various pathologies, including neurodegeneration, cancer and metabolic disorders such as diabetes or immune diseases. Read More

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http://rsfs.royalsocietypublishing.org/lookup/doi/10.1098/rs
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http://dx.doi.org/10.1098/rsfs.2018.0025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227773PMC
October 2018
11 Reads

Functionalizing cell-mimetic giant vesicles with encapsulated bacterial biosensors.

Interface Focus 2018 Oct 17;8(5):20180024. Epub 2018 Aug 17.

Department of Chemistry, Imperial College London, London SW7 2AZ, UK.

The design of vesicle microsystems as artificial cells (bottom-up synthetic biology) has traditionally relied on the incorporation of molecular components to impart functionality. These cell mimics have reduced capabilities compared with their engineered biological counterparts (top-down synthetic biology), as they lack the powerful metabolic and regulatory pathways associated with living systems. There is increasing scope for using whole intact cellular components as functional modules artificial cells, as a route to increase the capabilities of artificial cells. Read More

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http://rsfs.royalsocietypublishing.org/lookup/doi/10.1098/rs
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http://dx.doi.org/10.1098/rsfs.2018.0024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227772PMC
October 2018
14 Reads

The hallmarks of living systems: towards creating artificial cells.

Interface Focus 2018 Oct 17;8(5):20180023. Epub 2018 Aug 17.

Eindhoven University of Technology, PO Box 513 (STO 3.31), Eindhoven, MB, The Netherlands.

Despite the astonishing diversity and complexity of living systems, they all share five common hallmarks: compartmentalization, growth and division, information processing, energy transduction and adaptability. In this review, we give not only examples of how cells satisfy these requirements for life and the ways in which it is possible to emulate these characteristics in engineered platforms, but also the gaps that remain to be bridged. The bottom-up synthesis of life-like systems continues to be driven forward by the advent of new technologies, by the discovery of biological phenomena through their transplantation to experimentally simpler constructs and by providing insights into one of the oldest questions posed by mankind, the origin of life on Earth. Read More

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http://rsfs.royalsocietypublishing.org/lookup/doi/10.1098/rs
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http://dx.doi.org/10.1098/rsfs.2018.0023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227776PMC
October 2018
9 Reads

A new approach to solving the feature-binding problem in primate vision.

Interface Focus 2018 Aug 15;8(4):20180021. Epub 2018 Jun 15.

Oxford Centre for Theoretical Neuroscience and Artificial Intelligence, University of Oxford, Oxford OX2 6GG, UK.

We discuss a recently proposed approach to solve the classic feature-binding problem in primate vision that uses neural dynamics known to be present within the visual cortex. Broadly, the feature-binding problem in the visual context concerns not only how a hierarchy of features such as edges and objects within a scene are represented, but also the hierarchical relationships between these features at every spatial scale across the visual field. This is necessary for the visual brain to be able to make sense of its visuospatial world. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015810PMC
August 2018
21 Reads

Image interpretation above and below the object level.

Interface Focus 2018 Aug 15;8(4):20180020. Epub 2018 Jun 15.

Center for Brains, Minds and Machines, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Computational models of vision have advanced in recent years at a rapid rate, rivalling in some areas human-level performance. Much of the progress to date has focused on analysing the visual scene at the object level-the recognition and localization of objects in the scene. Human understanding of images reaches a richer and deeper image understanding both 'below' the object level, such as identifying and localizing object parts and sub-parts, as well as 'above' the object level, such as identifying object relations, and agents with their actions and interactions. Read More

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http://rsfs.royalsocietypublishing.org/lookup/doi/10.1098/rs
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http://dx.doi.org/10.1098/rsfs.2018.0020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015807PMC
August 2018
4 Reads

Colour, contours, shading and shape: flow interactions reveal anchor neighbourhoods.

Interface Focus 2018 Aug 15;8(4):20180019. Epub 2018 Jun 15.

Department of Computer Science, Yale University, New Haven, CT, USA.

Two dilemmas arise in inferring shape information from shading. First, depending on the rendering physics, images can change significantly with (even) small changes in lighting or viewpoint, while the percept frequently does not. Second, brightness variations can be induced by material effects-such as pigmentation-as well as by shading effects. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015805PMC
August 2018
1 Read

Accurate and robust localization for walking robots fusing kinematics, inertial, vision and LIDAR.

Authors:
Maurice Fallon

Interface Focus 2018 Aug 15;8(4):20180015. Epub 2018 Jun 15.

Oxford Robotics Institute, University of Oxford, Oxford, UK.

In this article, we review methods for localization and situational awareness of biped and quadruped robotics. This type of robot is modelled as a free-floating mechanical system subject to external forces and constrained by whole-body distributed rigid contacts. Measurements of the state of the robot can be made using a variety of sensor information-such as kinematics (the sensing of the joint angles of the robot), contact force (pressure sensors in the robot's feet), accelerometers and gyroscopes as well as external sensors such as vision and LIDAR. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015814PMC
August 2018
1 Read

The functional neuroanatomy of face perception: from brain measurements to deep neural networks.

Interface Focus 2018 Aug 15;8(4):20180013. Epub 2018 Jun 15.

Department of Psychology, School of Medicine, Stanford University, Stanford, CA 94305, USA.

A central goal in neuroscience is to understand how processing within the ventral visual stream enables rapid and robust perception and recognition. Recent neuroscientific discoveries have significantly advanced understanding of the function, structure and computations along the ventral visual stream that serve as the infrastructure supporting this behaviour. In parallel, significant advances in computational models, such as hierarchical deep neural networks (DNNs), have brought machine performance to a level that is commensurate with human performance. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015811PMC
August 2018
6 Reads

The perception of colour and material in naturalistic tasks.

Interface Focus 2018 Aug 15;8(4):20180012. Epub 2018 Jun 15.

Department of Psychology, University of Pennsylvania, Philadelphia, PA 19104, USA.

Perceived object colour and material help us to select and interact with objects. Because there is no simple mapping between the pattern of an object's image on the retina and its physical reflectance, our perceptions of colour and material are the result of sophisticated visual computations. A long-standing goal in vision science is to describe how these computations work, particularly as they act to stabilize perceived colour and material against variation in scene factors extrinsic to object surface properties, such as the illumination. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015813PMC
August 2018
1 Read

Not-So-CLEVR: learning same-different relations strains feedforward neural networks.

Interface Focus 2018 Aug 15;8(4):20180011. Epub 2018 Jun 15.

Department of Cognitive, Linguistic & Psychological Sciences, Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA.

The advent of deep learning has recently led to great successes in various engineering applications. As a prime example, convolutional neural networks, a type of feedforward neural network, now approach human accuracy on visual recognition tasks like image classification and face recognition. However, here we will show that feedforward neural networks struggle to learn abstract visual relations that are effortlessly recognized by non-human primates, birds, rodents and even insects. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015812PMC
August 2018
21 Reads

Rotation invariant visual processing for spatial memory in insects.

Interface Focus 2018 Aug 15;8(4):20180010. Epub 2018 Jun 15.

School of Informatics, University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, UK.

Visual memory is crucial to navigation in many animals, including insects. Here, we focus on the problem of visual homing, that is, using comparison of the view at a current location with a view stored at the home location to control movement towards home by a novel shortcut. Insects show several visual specializations that appear advantageous for this task, including almost panoramic field of view and ultraviolet light sensitivity, which enhances the salience of the skyline. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015815PMC
August 2018
2 Reads

Control of gaze in natural environments: effects of rewards and costs, uncertainty and memory in target selection.

Interface Focus 2018 Aug 15;8(4):20180009. Epub 2018 Jun 15.

Center for Perceptual Systems, University of Texas Austin, Austin, TX, USA.

The development of better eye and body tracking systems, and more flexible virtual environments have allowed more systematic exploration of natural vision and contributed a number of insights. In natural visually guided behaviour, humans make continuous sequences of sensory-motor decisions to satisfy current goals, and the role of vision is to provide the relevant information in order to achieve those goals. This paper reviews the factors that control gaze in natural visually guided actions such as locomotion, including the rewards and costs associated with the immediate behavioural goals, uncertainty about the state of the world and prior knowledge of the environment. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015808PMC
August 2018
1 Read

Colour and illumination in computer vision.

Interface Focus 2018 Aug 15;8(4):20180008. Epub 2018 Jun 15.

School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK.

In computer vision, illumination is considered to be a problem that needs to be 'solved'. The colour cast due to illumination is removed to support colour-based image recognition and stable tracking (in and out of shadows), among other tasks. In this paper, I review historical and current algorithms for illumination estimation. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015817PMC
August 2018
24 Reads

Spiking neural networks for computer vision.

Interface Focus 2018 Aug 15;8(4):20180007. Epub 2018 Jun 15.

School of Computer Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.

State-of-the-art computer vision systems use frame-based cameras that sample the visual scene as a series of high-resolution images. These are then processed using convolutional neural networks using neurons with continuous outputs. Biological vision systems use a quite different approach, where the eyes (cameras) sample the visual scene continuously, often with a non-uniform resolution, and generate neural spike events in response to changes in the scene. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015816PMC
August 2018
19 Reads

Improving the glial differentiation of human Schwann-like adipose-derived stem cells with graphene oxide substrates.

Interface Focus 2018 Jun 20;8(3):20180002. Epub 2018 Apr 20.

School of Materials and National Graphene Institute, University of Manchester, Manchester M13 9PL, UK.

There is urgent need to improve the clinical outcome of peripheral nerve injury. Many efforts are directed towards the fabrication of bioengineered conduits, which could deliver stem cells to the site of injury to promote and guide peripheral nerve regeneration. The aim of this study is to assess whether graphene and related nanomaterials can be useful in the fabrication of such conduits. Read More

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http://dx.doi.org/10.1098/rsfs.2018.0002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5915665PMC
June 2018
5 Reads