Showing papers by "Chalmers University of Technology published in 2006"

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

Abstract: A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

Structural mechanism of plant aquaporin gating

Abstract: Plants counteract fluctuations in water supply by regulating all aquaporins in the cell plasma membrane. Channel closure results either from the dephosphorylation of two conserved serine residues under conditions of drought stress, or from the protonation of a conserved histidine residue following a drop in cytoplasmic pH due to anoxia during flooding. Here we report the X-ray structure of the spinach plasma membrane aquaporin SoPIP2; 1 in its closed conformation at 2.1 angstrom resolution and in its open conformation at 3.9 angstrom resolution, and molecular dynamics simulations of the initial events governing gating. In the closed conformation loop D caps the channel from the cytoplasm and thereby occludes the pore. In the open conformation loop D is displaced up to 16 angstrom and this movement opens a hydrophobic gate blocking the channel entrance from the cytoplasm. These results reveal a molecular gating mechanism which appears conserved throughout all plant plasma membrane aquaporins.

Translating Pseudo-Boolean Constraints into SAT

Abstract: In this paper, we describe and evaluate three dieren t techniques for translating pseudoboolean constraints (linear constraints over boolean variables) into clauses that can be handled by a standard SAT-solver. We show that by applying a proper mix of translation techniques, a SAT-solver can perform on a par with the best existing native pseudo-boolean solvers. This is particularly valuable in those cases where the constraint problem of interest is naturally expressed as a SAT problem, except for a handful of constraints. Translating those constraints to get a pure clausal problem will take full advantage of the latest improvements in SAT research. A particularly interesting result of this work is the eciency of sorting networks to express pseudo-boolean constraints. Although tangential to this presentation, the result gives a suggestion as to how synthesis tools may be modied to produce arithmetic circuits more suitable for SAT based reasoning.

In vivo biocompatibility of bacterial cellulose

Abstract: The biocompatibility of a scaffold for tissue engineered constructs is essential for the outcome. Bacterial cellulose (BC) consists of completely pure cellulose nanofibrils synthesized by Acetobacter xylinum. BC has high mechanical strength and can be shaped into three-dimensional structures. Cellulose-based materials induce negligible foreign body and inflammatory responses and are considered as biocompatible. The in vivo biocompatibility of BC has never been evaluated systematically. Thus, in the development of tissue engineered constructs with a BC scaffold, it is necessary to evaluate the in vivo biocompatibility. BC was implanted subcutaneously in rats for 1, 4, and 12 weeks. The implants were evaluated in aspects of chronic inflammation, foreign body responses, cell ingrowth, and angiogenesis, using histology, immunohistochemistry, and electron microscopy. There were no macroscopic signs of inflammation around the implants. There were no microscopic signs of inflammation either (i.e., a high number of small cells around the implants or the blood vessels). No fibrotic capsule or giant cells were present. Fibroblasts infiltrated BC, which was well integrated into the host tissue, and did not elicit any chronic inflammatory reactions. The biocompatibility of BC is good and the material has potential to be used as a scaffold in tissue engineering.

Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective.

Abstract: Background DNA sequences are increasingly seen as one of the primary information sources for species identification in many organism groups. Such approaches, popularly known as barcoding, are underpinned by the assumption that the reference databases used for comparison are sufficiently complete and feature correctly and informatively annotated entries. Methodology/Principal Findings The present study uses a large set of fungal DNA sequences from the inclusive International Nucleotide Sequence Database to show that the taxon sampling of fungi is far from complete, that about 20% of the entries may be incorrectly identified to species level, and that the majority of entries lack descriptive and up-to-date annotations. Conclusions The problems with taxonomic reliability and insufficient annotations in public DNA repositories form a tangible obstacle to sequence-based species identification, and it is manifest that the greatest challenges to biological barcoding will be of taxonomical, rather than technical, nature.

Plasmonic Properties of Supported Pt and Pd Nanostructures

Abstract: The plasmonic properties of nanodisk arrays of Pt, Pd, and, for comparison, Ag are studied over a large size and spectral range and analyzed theoretically by an electrostatic model. Pt and Pd nanodisks exhibit broad localized surface plasmons with a higher sensitivity of the plasmon to the disk aspect ratio compared to Ag. Extinction cross-sections are generally about 50% smaller for Pt and Pd. The spectral plasmon positions, line-widths, and extinction cross-sections are well reproduced by the model.

Influence of solvent mixing on the morphology and performance of solar cells based on polyfluorene copolymer/fullerene blends

Abstract: The influence of the solvent on the morphol. and performance of polymer solar cells was studied in devices based on blends of the polyfluorene copolymer, poly(2,7-(9,9-dioctyl-fluorene)-alt-5,5-(4',7'-di-2-thienyl-2', 1',3'-benzothiadiazole)), and [6,6]-phenyl-C61-butyric acid Me ester. The blends are spin-coated from CHCl3 or from CHCl3 mixed with small amts. of xylene, toluene, or chlorobenzene. The devices are characterized under monochromatic light and AM1.5 solar illumination. An enhancement of the photocurrent d. was obsd. in diodes made from CHCl3 mixed with chlorobenzene, and a decreased photocurrent d. is obsd. in diodes made from CHCl3 mixed with xylene or toluene, compared to diodes made from neat CHCl3. The open-circuit voltages are almost the same for all diodes. The surfaces of the active layers were imaged with AFM. Height images indicate that a finer and more uniform distribution of domains corresponds to the diodes with enhanced photocurrent that are made from CHCl3 mixed with chlorobenzene, while a structure with larger domains is assocd. with the lower photocurrents in the diodes made from CHCl3 mixed with xylene or toluene. The influence of the morphol. on the excited-state dynamics and charge generation was studied using time-resolved spectroscopy. Fast formation of bound charge pairs followed by their conversion into free charge carriers was resolved, and excitation-intensity-dependent non-geminate recombination of free charges was obsd. A significant enhancement in free-charge-carrier generation was obsd. on introducing chlorobenzene into CHCl3. Imaging photocurrent generation from the solar cells with a light-pulse technique shows an inhomogeneous photocurrent distribution, which is related to the undulations in the thickness of the active layer. Thicker parts of the diodes yield higher photocurrent values. [on SciFinder (R)]

Thermal Analysis of Chemical-Looping Combustion

Abstract: In chemical-looping combustion, a gaseous fuel is burnt with inherent separation of the greenhouse gas CO2. Oxygen is transferred from the combustion air to the fuel by an oxygen carrier, which is usually a metal oxide, and therefore direct contact between the fuel and the combustion air is avoided. Thus, the products of combustion, i.e., CO2 and H2O, are not mixed with the rest of the flue gases and after condensation almost pure CO2 is obtained, without any energy lost for the separation. A thermal analysis of the process using a large number of possible oxygen carriers was performed by simulating reactions using the HSC Chemistry 5.0 software. Three fuels were used in the investigation, CH4, CO and H2. Based on the ability of the oxygen carriers to convert the fuel to the combustion products CO2 and H2O, stability in air and the melting temperatures of the solid material some metal oxides based on Ni, Cu, Fe, Mn, Co, W and sulphates of Ba and Sr showed good ther-modynamic properties and could be feasible oxygen carriers. Only a few of these possible oxygen carrier systems, based on Cu, Fe and Mn, showed complete conversion of the fuel gas, but still the other systems had limited equilibrium restrictions, with only small and acceptable amounts of unreacted CO and H2 released from the fuel reactor. The promising systems were investigated further with respect to temperature changes in the fuel reactor as well as possible carbon, sulphide and sulphate formation in the fuel reactor. For some systems the reactions in the fuel reactor were endothermic, resulting in a temperature drop in the fuel reactor. However, this drop can be limited by applying a sufficient circulation of particles from the air reactor to the fuel reactor. When Ni or Co is used as oxygen carrier the fuel may need to be desulphurized prior to combustion to avoid formation of solid or liquid sulphides or sulphates. On the other hand, to prevent decomposition of the sulphates BaSO4 and SrSO4, in the fuel reactor, to sulphur-containing gases and metal oxides, it is necessary that some sulphur is present in the fuel and that high temperatures are avoided. Formation of carbon should not be a problem as long as the process is run under conditions of high fuel conversion.

Separation of human adipocytes by size: hypertrophic fat cells display distinct gene expression

Abstract: Enlarged adipocytes are associated with insulin resistance and are an independent predictor of type 2 diabetes. To understand the molecular link between these diseases and adipocyte hypertrophy, we developed a technique to separate human adipocytes from an adipose tissue sample into populations of small cells (mean 57.6+-3.54 um) and large cells (mean 100.1+-3.94 um). Microarray analysis of the cell populations separated from adipose tissue from three subjects identified 14 genes, of which five immune-related, with more than fourfold higher expression in large cells than small cells. Two of these genes were serum amyloid A (SAA) and transmembrane 4 L six family member 1 (TM4SF1). Real-time RT-PCR analysis of SAA and TM4SF1 expression in adipocytes from seven subjects revealed 19-fold and 22-fold higher expression in the large cells, respectively, and a correlation between adipocyte size and both SAA and TM4SF1 expression. The results were verified using immunohistochemistry. In comparison with 17 other human tissues and cell types by microarray, large adipocytes displayed by far the highest SAA and TM4SF1 expression. Thus, we have identified genes with markedly higher expression in large, compared with small, human adipocytes. These genes may link hypertrophic obesity to insulin resistance/type 2 diabetes.

Premature mortality in patients with Addison's disease: a population-based study.

Abstract: Background: The survival rate of patients with primary adrenal insufficiency (Addison’s disease) undergoing currently accepted replacement therapy is not known, although well-informed patients are considered to have a normal survival rate. In this study, we evaluated the mortality of patients with Addison’s disease in Sweden. Methods: A population-based, retrospective, observational study was performed, using the National Swedish Hospital and Cause of Death Registers, covering the period from 1987–2001. After a diagnosis of Addison’s disease, each patient was followed until the end of follow-up or death. Mortality was compared with that of the Swedish background population. Findings: We identified 1675 patients (995 women and 680 men) diagnosed with primary adrenal insufficiency. The average follow-up from initial diagnosis was 6.5 yr. Five hundred seven patients died during the study period compared with an expected 199. The risk ratio for all-cause mortality was 2.19 (confidence interval 1.91–2.51) for ...

Divide and protect : Capping gold nanoclusters with molecular gold-thiolate rings

Abstract: Density functional theory calculations are used to explore phosphine- and thiolate-protected gold nanoclusters, namely, Au39(PH3)14Cl6 and Au38(SCH3)24. For Au38(SCH3)24, a novel structural motif is predicted, consisting of ringlike (AuSCH3)4 units protecting a central Au14 core. The calculated optical spectrum of this species features a large optical gap (about 1.5 eV) and a prominently peaked structure, correlating with experimental findings of “molecular-like spectra” of thiolate-protected 1.1 nm gold nanoparticles. Ligand−ligand interactions and steric effects in the ligand shell are suggested as possible driving forces toward an ordered gold core structure. A novel mechanism for ligand-exchange reactions on gold clusters is proposed.

Application of van der Waals Density Functional to an Extended System: Adsorption of Benzene and Naphthalene on Graphite

Abstract: It is shown that it is now possible to include van der Waals (vdW) interactions via a nonempirical implementation of density functional (DF) theory to describe the correlation energy in electronic structure calculations on infinite systems of no particular symmetry. The vdW-DF theory [Phys. Rev. Lett. 92, 246401 (2004)] is applied to the adsorption of benzene and naphthalene on an infinite sheet of graphite, as well as the binding between two graphite sheets. A comparison with recent thermal-desorption data [Phys. Rev. B 69, 155406 (2004)] shows great promise for the vdW-DF method.

Low-Bandgap Alternating Fluorene Copolymer/Methanofullerene Heterojunctions in Efficient Near-Infrared Polymer Solar Cells

Abstract: Efficient near-IR polymer solar cells based on the low-bandgap alternating fluorene copolymer APFO-Green 5 exhibit a photoresponse up to 800 nm. The copolymer performs well in combination with the common electron acceptor [6,6]-phenyl-C61-butyric acid Me ester (PCBM), reaching a power-conversion efficiency of 2.2% with a lower PCBM content in the active layer than previous devices based on low-bandgap polymers. [on SciFinder (R)]

Silicon carbide and diamond for high temperature device applications

Abstract: The physical and chemical properties of wide bandgap semiconductors silicon carbide and diamond make these materials an ideal choice for device fabrication for applications in many different areas, e.g. light emitters, high temperature and high power electronics, high power microwave devices, micro-electromechanical system (MEMS) technology, and substrates. These semiconductors have been recognized for several decades as being suitable for these applications, but until recently the low material quality has not allowed the fabrication of high quality devices. Silicon carbide and diamond based electronics are at different stages of their development. An overview of the status of silicon carbide's and diamond's application for high temperature electronics is presented.

Collaborative logistics management and the role of third‐party service providers

Abstract: Purpose – This paper aims to derive and verify a collaborative framework that specifies the role of different parties in contemporary logistics setups. Methodology/Approach – To prepare this paper, a study of the logistics literature has been conducted together with several case studies. The empirical evidence has been collected in Europe as well as in the US. Different aspects of collaboration between organizations in logistics setups have been studied where the services and the activities have been analyzed to understand the characteristics of the role of third-party service providers. Findings – The results from the work cluster the different third-party service providers in three different groups: Carriers, Logistics Service Providers and Logistics Service Intermediaries. All of these parties have different roles and provide various services in outsourced logistics setups. A Collaborative Logistics Management (CLM) model has been derived that embraces the role of the different parties, the information and material flows between them, the interface attributes and the information systems architecture. In this paper, a focus is mainly on the part of the model that reveals the role of the third-party service providers. Practical implications – The practical implications of the work has its foundation in that activities, performed by two parties, can be adapted to each other so that their combined efficiency is improved. The CLM model can be applied when designing and negotiating third-party services for specific logistics assignments. Originality/value – The paper offers a model of logistics collaboration between the different parties in contemporary, outsourced logistics setups.

Risk factors for failure after treatment of a periprosthetic fracture of the femur

Abstract: Periprosthetic fracture of the femur is an uncommon complication after total hip replacement, but appears to be increasing. We undertook a nationwide observational study to determine the risk factors for failure after treatment of these fractures, examining patient- and implant-related factors, the classification of the fractures and the outcome. Between 1979 and 2000, 1049 periprosthetic fractures of the femur were reported to the Swedish National Hip Arthroplasty Register. Of these, 245 had a further operation after failure of their initial management. Data were collected from the Register and hospital records. The material was analysed by the use of Poisson regression models. It was found that the risk of failure of treatment was reduced for Vancouver type B2 injuries (p = 0.0053) if revision of the implant was undertaken (p = 0.0033) or revision and open reduction and internal fixation (p = 0.0039) were performed. Fractures classified as Vancouver type B1 had a significantly higher risk of failure (p = 0.0001). The strongest negative factor was the use of a single plate for fixation (p = 0.001). The most common reasons for failure in this group were loosening of the femoral prosthesis, nonunion and re-fracture. It is probable that many fractures classified as Vancouver type B1 (n = 304), were in reality type B2 fractures with a loose stem which were not recognised. Plate fixation was inadequate in these cases. The difficulty in separating type B1 from type B2 fractures suggests that the prosthesis should be considered as loose until proven otherwise.

Creating Hot Nanoparticle Pairs for Surface-Enhanced Raman Spectroscopy through Optical Manipulation

Abstract: We use optical tweezers to move single silver nanoparticles into near-field contact with immobilized particles, forming isolated surface-enhanced Raman spectroscopy (SERS) active Ag particle dimers. The surface-averaged SERS intensity increases by a factor ∼20 upon dimerization. Electrodynamics calculations indicate that the final approach between the particles is due to “optical binding”. The described methodology may facilitate controlled single molecule SERS analysis.