Understanding spatial data usability

In recent geographical information science literature, a number of researchers have made passing reference to an apparently new characteristic of spatial data known as 'usability'. While this attribute is well-known to professionals engaged in software engineering and computer interface design and testing, extension of the concept to embrace information would seem to be a new development. Furthermore, while notions such as the use and value of spatial information, and the diffusion of spatial information systems, have been the subject of research since the late-1980s, the current references to usability clearly represent something which extends well beyond that initial research. Accordingly, the purposes of this paper are: (1) to understand what is meant by spatial data usability; (2) to identify the elements that might comprise usability; and (3) to consider what the related research questions might be

Shark tooth regeneration reveals common stem cell characters in both human rested lamina and ameloblastoma

The human dentition is a typical diphyodont mammalian system with tooth replacement of most positions. However, after dental replacement and sequential molar development, the dental lamina undergoes apoptosis and fragments, leaving scattered epithelial units (dental lamina rests; DLRs). DLRs in adult humans are considered inactive epithelia, thought to possess limited capacity for further regeneration. However, we show that these tissues contain a small proportion of proliferating cells (assessed by both Ki67 and PCNA) but also express a number of common dental stem cell markers (Sox2, Bmi1, β-catenin and PH3) similar to that observed in many vertebrates that actively, and continuously regenerate their dentition. We compared these human tissues with the dental lamina of sharks that regenerate their dentition throughout life, providing evidence that human tissues have the capacity for further and undocumented regeneration. We also assessed cases of human ameloblastoma to characterise further the proliferative signature of dental lamina rests. Ameloblastomas are assumed to derive from aberrant lamina rests that undergo changes, which are not well understood, to form a benign tumour. We suggest that dental lamina rests can offer a potential source of important dental stem cells for future dental regenerative therapy. The combined developmental genetic data from the shark dental lamina and ameloblastoma may lead to the development of novel methods to utilise these rested populations of adult lamina stem cells for controlled tooth replacement in humans

Non-intrusive measurement of strip thickness and roll-bite length in metal rolling

It is important to monitor the rolled strip thickness standard to minimize material waste and loss of profit due to strip flatness defects, and also to maintain the product’s size and dimensional homogeneity. Several online measurement techniques are available but none of this can give an in situ measurement within the roll bite. Due to this, a novice experimental method utilizing ultrasonic reflection sensor mounted on one roll was developed for in situ measurement of strip thickness and roll-bite length during cold rolling process. A pitch–catch method was used whereby a piezoelectric element generated an ultrasonic pulse and transmitted to the contact interface evaluated on a pilot mill. The reflected signal was captured by a second piezoelectric element and analysed to determine the condition at the strip–roll interface. This approach was implemented on a pilot mill and reflections from various locations in the roll bite during the rolling were recorded. Recorded signals were used to estimate the rolled strip thickness and roll-bite length after the rolling process

Direct Imaging of Protein Organization in an Intact Bacterial Organelle Using High-Resolution Atomic Force Microscopy

The function of bioenergetic membranes is strongly influenced by the spatial arrangement of their constituent membrane proteins. Atomic force microscopy (AFM) can be used to probe protein organization at high resolution, allowing individual proteins to be identified. However, previous AFM studies of biological membranes have typically required that curved membranes are ruptured and flattened during sample preparation, with the possibility of disruption of the native protein arrangement or loss of proteins. Imaging native, curved membranes requires minimal tip–sample interaction in both lateral and vertical directions. Here, long-range tip–sample interactions are reduced by optimizing the imaging buffer. Tapping mode AFM with high-resonance-frequency small and soft cantilevers, in combination with a high-speed AFM, reduces the forces due to feedback error and enables application of an average imaging force of tens of piconewtons. Using this approach, we have imaged the membrane organization of intact vesicular bacterial photosynthetic “organelles”, chromatophores. Despite the highly curved nature of the chromatophore membrane and lack of direct support, the resolution was sufficient to identify the photosystem complexes and quantify their arrangement in the native state. Successive imaging showed the proteins remain surprisingly static, with minimal rotation or translation over several-minute time scales. High-order assemblies of RC-LH1-PufX complexes are observed, and intact ATPases are successfully imaged. The methods developed here are likely to be applicable to a broad range of protein-rich vesicles or curved membrane systems, which are an almost ubiquitous feature of native organelles

Interference lithographic nanopatterning of plant and bacterial light-harvesting complexes on gold substrates

We describe a facile approach for nanopatterning of photosynthetic light-harvesting complexes over macroscopic areas, and use optical spectroscopy to demonstrate retention of native properties by both site-specifically and non-specifically attached photosynthetic membrane proteins. A Lloyd's mirror dual-beam interferometer was used to expose self-assembled monolayers of amine-terminated alkylthiolates on gold to laser irradiation. Following exposure, photo-oxidized adsorbates were replaced by oligo(ethylene glycol) terminated thiols, and the remaining intact amine-functionalized regions were used for attachment of the major light-harvesting chlorophyll–protein complex from plants, LHCII. These amine patterns could be derivatized with nitrilotriacetic acid (NTA), so that polyhistidine-tagged bacteriochlorophyll–protein complexes from phototrophic bacteria could be attached with a defined surface orientation. By varying parameters such as the angle between the interfering beams and the laser irradiation dose, it was possible to vary the period and widths of NTA and amine-functionalized lines on the surfaces; periods varied from 1200 to 240 nm and linewidths as small as 60 nm (λ/4) were achieved. This level of control over the surface chemistry was reflected in the surface topology of the protein nanostructures imaged by atomic force microscopy; fluorescence imaging and spectral measurements demonstrated that the surface-attached proteins had retained their native functionality

Are Causality Violations Undesirable?

Causality violations are typically seen as unrealistic and undesirable features of a physical model. The following points out three reasons why causality violations, which Bonnor and Steadman identified even in solutions to the Einstein equation referring to ordinary laboratory situations, are not necessarily undesirable. First, a space-time in which every causal curve can be extended into a closed causal curve is singularity free--a necessary property of a globally applicable physical theory. Second, a causality-violating space-time exhibits a nontrivial topology--no closed timelike curve (CTC) can be homotopic among CTCs to a point, or that point would not be causally well behaved--and nontrivial topology has been explored as a model of particles. Finally, if every causal curve in a given space-time passes through an event horizon, a property which can be called "causal censorship", then that space-time with event horizons excised would still be causally well behaved.Comment: Accepted in October 2008 by Foundations of Physics. Latex2e, 6 pages, no figures. Presented at a seminar at the Universidad Nacional Autonoma de Mexico. Version 2 was co-winner of the QMUL CTC Essay Priz

From Monochrome to Technicolor: Simple Generic Approaches to Multicomponent Protein Nanopatterning Using Siloxanes with Photoremovable Protein-Resistant Protecting Groups.

We show that sequential protein deposition is possible by photodeprotection of films formed from a tetraethylene-glycol functionalized nitrophenylethoxycarbonyl-protected aminopropyltriethoxysilane (NPEOC-APTES). Exposure to near-UV irradiation removes the protein-resistant protecting group, and allows protein adsorption onto the resulting aminated surface. The protein resistance was tested using proteins with fluorescent labels and microspectroscopy of two-component structures formed by micro- and nanopatterning and deposition of yellow and green fluorescent proteins (YFP/GFP). Nonspecific adsorption onto regions where the protecting group remained intact was negligible. Multiple component patterns were also formed by near-field methods. Because reading and writing can be decoupled in a near-field microscope, it is possible to carry out sequential patterning steps at a single location involving different proteins. Up to four different proteins were formed into geometric patterns using near-field lithography. Interferometric lithography facilitates the organization of proteins over square cm areas. Two-component patterns consisting of 150 nm streptavidin dots formed within an orthogonal grid of bars of GFP at a period of ca. 500 nm could just be resolved by fluorescence microscopy

Time-reversal violating rotation of polarization plane of light in gas placed in electric field

Rotation of polarization plane of light in gas placed in electric field is considered. Different factors causing this phenomenon are investigated. Angle of polarization plane rotation for transition 6S_{1/2} - 7S_{1/2} in cesium (lambda=539 nm) is estimated. The possibility to observe this effect experimentally is discussed.Comment: 10 pages, Late

Turning the challenge of quantum biology on its head: biological control of quantum optical systems

When light-harvesting complex II (LHCII), isolated from spinach, is adsorbed onto arrays of gold nanostructures formed by interferometric lithography, a pronounced splitting of the plasmon band is observed that is attributable to strong coupling of the localised surface plasmon resonance to excitons in the pigment-protein complex. The system is modelled as coupled harmonic oscillators, yielding an exciton energy of 2.24 ± 0.02 eV. Analysis of the dispersion curves yields a Rabi energy of 0.25 eV. Extinction spectra of the strongly coupled system yield a resonance at 1.43 eV that varies as a function of the density of nanostructures in the array. The enhanced intensity of this feature is attributed to strong plasmon-exciton coupling. Comparison of data for a large number of light-harvesting complexes indicates that by control of the protein structure and/or pigment compliment it is possible to manipulate the strength of plasmon-exciton coupling. In strongly coupled systems, ultra-fast exchange of energy occurs between pigment molecules: coherent coupling between non-local excitons can be manipulated via selection of the protein structure enabling the observation of transitions that are not seen in the weak coupling regime. Synthetic biology thus provides a means to control quantum-optical interactions in the strong coupling regime

Augmenting light coverage for photosynthesis through YFP-enhanced charge separation at the Rhodobacter sphaeroides reaction centre.

Photosynthesis uses a limited range of the solar spectrum, so enhancing spectral coverage could improve the efficiency of light capture. Here, we show that a hybrid reaction centre (RC)/yellow fluorescent protein (YFP) complex accelerates photosynthetic growth in the bacterium Rhodobacter sphaeroides. The structure of the RC/YFP-light-harvesting 1 (LH1) complex shows the position of YFP attachment to the RC-H subunit, on the cytoplasmic side of the RC complex. Fluorescence lifetime microscopy of whole cells and ultrafast transient absorption spectroscopy of purified RC/YFP complexes show that the YFP-RC intermolecular distance and spectral overlap between the emission of YFP and the visible-region (QX) absorption bands of the RC allow energy transfer via a Förster mechanism, with an efficiency of 40±10%. This proof-of-principle study demonstrates the feasibility of increasing spectral coverage for harvesting light using non-native genetically-encoded light-absorbers, thereby augmenting energy transfer and trapping in photosynthesis