Integrating sequence and structural biology with DAS.

BACKGROUND: The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence. RESULTS: Here we present several extensions to the current DAS 1.5 protocol. These provide new commands to share alignments, three dimensional molecular structure data, add the possibility for registration and discovery of DAS servers, and provide a convention how to provide different types of data plots. We present examples of web sites and applications that use the new extensions. We operate a public registry of DAS sources, which now includes entries for more than 250 distinct sources. CONCLUSION: Our DAS extensions are essential for the management of the growing number of services and exchange of diverse biological data sets. In addition the extensions allow new types of applications to be developed and scientific questions to be addressed. The registry of DAS sources is available at http://www.dasregistry.org.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Requirements for Receptor Engagement during Infection by Adenovirus Complexed with Blood Coagulation Factor X

Human adenoviruses from multiple species bind to coagulation factor X (FX), yet the importance of this interaction in adenovirus dissemination is unknown. Upon contact with blood, vectors based on adenovirus serotype 5 (Ad5) binds to FX via the hexon protein with nanomolar affinity, leading to selective uptake of the complex into the liver and spleen. The Ad5:FX complex putatively targets heparan sulfate proteoglycans (HSPGs). The aim of this study was to elucidate the specific requirements for Ad5:FX-mediated cellular uptake in this high-affinity pathway, specifically the HSPG receptor requirements as well as the role of penton base-mediated integrin engagement in subsequent internalisation. Removal of HS sidechains by enzymatic digestion or competition with highly-sulfated heparins/heparan sulfates significantly decreased FX-mediated Ad5 cell binding in vitro and ex vivo. Removal of N-linked and, in particular, O-linked sulfate groups significantly attenuated the inhibitory capabilities of heparin, while the chemical inhibition of endogenous HSPG sulfation dose-dependently reduced FX-mediated Ad5 cellular uptake. Unlike native heparin, modified heparins lacking O- or N-linked sulfate groups were unable to inhibit Ad5 accumulation in the liver 1h after intravascular administration of adenovirus. Similar results were observed in vitro using Ad5 vectors possessing mutations ablating CAR- and/or αv integrin binding, demonstrating that attachment of the Ad5:FX complex to the cell surface involves HSPG sulfation. Interestingly, Ad5 vectors ablated for αv integrin binding showed markedly delayed cell entry, highlighting the need for an efficient post-attachment internalisation signal for optimal Ad5 uptake and transport following surface binding mediated through FX. This study therefore integrates the established model of αv integrin-dependent adenoviral infection with the high-affinity FX-mediated pathway. This has important implications for mechanisms that define organ targeting following contact of human adenoviruses with blood

A room-temperature fabrication method for microwave dielectric Li₂MoO₄ ceramics and their applicability for antennas

Abstract This work presents a method for the fabrication of Li₂MoO₄ ceramics at room-temperature based on utilizing a small amount of water with Li₂MoO₄ powder. The densification of the ceramic takes place during pressing. Thus the shape and size of the final ceramic compact can easily be managed by controlling the mould dimensions and the amount of material. Post-processing at 120 °C is applied to remove residual water from the compact. This post-processing temperature can be chosen to be suitable to the other materials integrated, such as the substrate or electrodes, as long as the post-processing time is adequate to remove the residual water. The dielectric properties (relative permittivity of 5.1 and a loss tangent value of 0.00035 at 9.6 GHz) after optimization of the powder particle size, sample pressing pressure, and post-processing time were similar to those achieved for Li₂MoO₄ ceramics fabricated by sintering at 540 °C. The dielectric properties of Li₂MoO₄ ceramics were also modified using composite methods. For example, an addition of 10 volume-% of BaTiO₃ increased the relative permittivity from 6.4 to 9.7 and the loss tangent value from 0.0006 to 0.011 at 1 GHz. To investigate the thermal dependence of the permittivity, different amounts of rutile TiO₂ were incorporated into a Li₂MoO₄ ceramic matrix fabricated with the method described in this work. As the amount of TiO₂ increased from 10 to 30 volume-%, the thermal coefficient of permittivity decreased from 180 ppm/°C to -170 ppm/°C. The low processing temperature made the fabrication approach introduced here feasible for silver electrode integration without the formation of extra phases, which were observed in sintered samples with similar compositions in another study. A patch antenna was realized utilizing a Li₂MoO₄ ceramic disk fabricated by the room-temperature method. The antenna operating at ~4 GHz showed reasonably good performance. A relative humidity of 80% lowered the resonant frequency by 3.25% from the initial value, and reduced the total and radiation efficiencies of the antenna by ~2 dB. The changes were slowly reversible. Use of a silicone conformal coating reduced the shift of the resonant frequency to 1.26% from the initial value and also reduced the effect on efficiencies to ~1 dB. The use of the coating also speeded up the reversibility of the changes when the humidity was decreased.Tiivistelmä Tässä työssä esitellään menetelmä, jolla Li₂MoO₄-keraameja voidaan valmistaa huoneenlämpötilassa. Menetelmä hyödyntää pientä määrää Li₂MoO₄-vesiliuosta ja sen kiteytymistä. Keraami tiivistyy kappaletta puristettaessa, joten sen koko ja muoto ovat sama kuin muotilla riippuen vain keraamin määrästä. Kappaleeseen jäänyt vesi poistetaan lämpökäsittelyllä yleensä 120 celsiusasteessa. Jälkikäsittelylämpötila voidaan valita muiden integroitavien materiaalien mukaan, kuten alusta- tai elektrodimateriaalin, kunhan jälkikäsittelyaikaa muokataan vastaavasti, jotta kaikki vesi poistuu. Optimoimalla Li₂MoO₄-jauheen partikkelikokoa, puristuspainetta ja jälkikäsittelyaikaa saavutettiin samankaltaiset dielektriset ominaisuudet taajuudella 9,6 GHz (suhteellinen permittiivisyys 5,1 ja häviötangentti 0,00035) kuin Li₂MoO₄-keraameilla, jotka on sintrattu 540 celsiusasteessa. Li₂MoO₄-keraamien dielektrisiä ominaisuuksia muokattiin myös lisäaineilla. Esimerkiksi 10 tilavuus-% BaTiO₃-jauhetta kasvatti suhteellista permittiivisyyttä taajuudella 1 GHz arvosta 6,4 arvoon 9,7 ja häviötangenttia arvosta 0,0006 arvoon 0,011. Myös eri määriä TiO₂-jauhetta (rutiili) lisättiin Li₂MoO₄-matriisiin permittiivisyyden lämpötilariippuvuuden tutkimiseksi. TiO₂-jauheen määrän kasvaessa 10 tilavuusprosentista 30 tilavuusprosenttiin laski permittiivisyyden lämpötilariippuvuus arvosta 180 ppm/°C arvoon -170 ppm/°C. Matalan käsittelylämpötilan ansiosta työssä esitelty valmistusmenetelmä soveltui käytettäväksi hopeaelektrodien kanssa. Aiemman tutkimuksen mukaan nämä komposiittimateriaalit muodostivat ei-toivottuja faaseja sintrattaessa hopean kanssa. Menetelmällä valmistettua Li₂MoO₄-keraamikiekkoa käytettiin mikroliuska-antennin valmistuksessa. Taajuudella 4 GHz toimivan antennin suorituskyky oli suunnitellun kaltainen. 80 prosentin suhteellinen ilmankosteus laski resonanssitaajuutta 3,25 % alkuperäisestä arvosta ja vähensi antennin kokonais- ja säteilytehokkuutta noin 2 dB. Muutokset palautuivat hitaasti. Silikonisuojalakan käyttö vähensi taajuuden laskua 1,26 prosenttiin alkuperäisestä arvosta ja tehokkuudet laskivat vain noin 1 dB. Suojalakan käyttö nopeutti muutosten palautuvuutta ilmankosteuden laskiessa

Li₂MoO₄-based composite ceramics fabricated from temperature- and atmosphere-sensitive MnZn ferrite at room temperature

Abstract The first magnetic ceramic composites manufactured, using the room-temperature densification method are reported. The samples were prepared at room temperature using Li₂MoO₄ as a matrix and MnZn ferrite with loading levels of 10–30 vol-% followed by postprocessing at 120°C. The method utilizes the water solubility of the dielectric Li₂MoO₄ and compression pressure instead of high temperatures typical of conventional solid-state sintering. Hence, composite manufacturing using temperature- and atmosphere-sensitive materials is possible without special conditions. This was demonstrated with MnZn ferrite, which is prone to oxidation when heat treated in air. Samples manufactured with room-temperature densification showed no signs of reactivity during processing, whereas reference samples sintered at 685°C suffered from oxidation and formation of an additional reaction phase. The densities achieved with different loading levels of MnZn ferrite with both methods were very similar. Measurements up to 1 GHz showed relatively high values of relative permittivity (21.7 at 1 GHz) and permeability (2.6 at 1 GHz) with 30 vol-% loading of MnZn ferrite in the samples manufactured by room-temperature densification. In addition, pre-granulation is proposed to improve the processability of the composite powders in room-temperature densification

Direct integration of dielectric all-ceramic thick films on a polymer substrate using room temperature fabrication

Abstract Direct integration of all-ceramic thick films and a polymer substrate has been realized for the first time without high temperature processing using the Room Temperature Fabrication method. Printable Li2MoO4-BaTiO3 composite pastes with 0, 10, and 20 vol.% of BaTiO3 were fabricated from the respective ceramic powders and water without organic additives or vehicles. The pastes were stencil printed on a polyimide substrate and dried at 120 °C without pressing or lamination. Using scanning electron microscopy, the films were observed to be in seamless contact with the substrate and to have a uniform microstructure. Relative permittivities of the ceramic films increased from 4.2 to 7.2 (at 2.5 GHz) and 4.5 to 7.5 (at 9.9 GHz) according to the vol.% content of the added BaTiO3, with corresponding dielectric losses from 10−3 to 10-2. The results show that the room temperature fabrication method enables 2D printing of all-ceramic thick films on temperature-sensitive substrates

3D printed dielectric ceramic without a sintering stage

Abstract This paper presents for the first time the fabrication of dielectric ceramic parts by 3D printing without sintering. The printable paste was prepared by mixing a carefully selected amount of water-soluble Li₂MoO₄ powder with water. A viscous mixture of solid ceramic particles and saturated aqueous phase was formed with a solid content of 60.0 vol.%. Printing of the sample discs was conducted with material extrusion using a low-cost syringe-style 3D printer. The consolidation and densification of the printed parts occurred during both printing and drying of the paste due to extrusion pressure, capillary forces, and recrystallization of the dissolved Li₂MoO₄. Complete drying of the paste was ensured by heating at 120 °C. The microstructure showed no delamination of the printed layers. Relatively high densities and good dielectric properties were obtained, especially when considering that no sintering and only pressure from the extrusion was employed. This approach is expected to be feasible for similar ceramics and ceramic composites

Characterization of Li₂MoO₄/BaTiO₃ all-ceramic films on organic substrate printed capacitors at 45 MHz–10 GHz

Abstract This article presents novel all-ceramic composite films used as a screen-printed capacitors on polymer surface and their characterization at 45-MHz to 10-GHz frequency range. All-ceramic composite paste is based on lithium molybdate (Li₂MoO₄), barium titanate (BaTiO₃), and water manufactured by the room temperature fabrication (RTF) method. For the determination of the permittivity and the loss tangent of the materials, ceramic thick films are printed on the top of an interdigital-shaped microwave capacitors using pastes with 0, 10, and 20 vol.% of BaTiO₃ filler in Li₂MoO₄ followed by a drying process at 120 °C. The electrical properties of the capacitors, capacitance, and quality value are derived from measured S-parameter results, whereas the electrical properties of the ceramic thick-film materials, real, and imaginary values of permittivity are derived from the measured results through computer simulations. The electrical properties of the ceramic material, such as moderate permittivity and moderately low-loss tangent, could be adjusted by changing the volume fraction of the BaTiO₃ filler to match the demands of different areas of applications. The obtained results are verified with five samples of each ceramic composition. The results show the capacitance values of 0.30 pF for an uncoated capacitor and 0.55, 0.67, and 0.95 pF with coatings of Li₂MoO₄ with 0, 10, and 20 vol.% of BaTiO₃ composites, respectively, at 2.5-GHz frequency. The calculated relative permittivity (εr) values for the same materials are 3.70, 5.23, and 6.43, and loss tangent values are 0.035, 0.027, and 0.036 at 2.5 GHz. These novel all-ceramic capacitor composite materials are applicable for the RF components used in telecommunication applications in the frequency range of 45 MHz–10 GHz, thus widening the technology roadmap in terms of material choices for different applications, especially high thermal resistant materials

Upside - down composites:fabricating piezoceramics at room temperature

Abstract Piezoelectric materials have a multi-billion dollar impact on the electromechanical transducers market. Their conventional synthesis includes a sintering step (at over 1000 °C) that often hampers direct integration into monolithic devices and confines their applications to heterostructures made using tedious multi-step assembly or to composites with poor electromechanical behavior. Here, we demonstrate a new and easy to scale method for the integration of piezoelectric ceramics at ultra-low temperatures without compromising their functionality. We show that all-ceramic “upside-down” composites with exceptionally high fractions of piezoelectric filler (−75 vol. %) and low porosity can be achieved using aqueous dispersion of lithium molybdate as a binder. The method is based only on coating, mixing, moulding and drying sequences. The measured piezoelectric charge coefficient, d33 −84 pC·N−1, outperforms any other known composite, whereas the voltage constant, g33 -33 mV m·N−1, competes with bulk materials, thus paving the way for versatile applications not previously considered