bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploiting advances in imaging technology to study biofilms by applying multiphoton laser scanning microscopy as an imaging and manipulation tool
Authors: LAKINS M.A. , MARRISON J.L. , O’TOOLE P.J. , VAN DER WOUDE M.W. 
Published: July 2009

SummaryBiofilms are an important element of the natural ecosystems but can be detrimental in health care and industrial settings. To improve our ability to combat biofilms, we need to understand the processes that facilitate their formation and dispersal. One approach that has proven to be invaluable is to image biofilms as they grow. Here we describe tools and protocols to visualize biofilms with multiphoton laser scanning microscopy, compare this with single photon laser scanning confocal microscopy and highlight best working procedures. Furthermore, we describe how with multiphoton laser scanning microscopy the laser can be used to manipulate the biofilm, specifically to achieve localized bleaching, killing or ablation within the biofilm biomass. These applications open novel ways to study the dynamics of biofilm formation, regeneration and dispersal.
Surface plasmon‐enhanced micro‐cylinder mode in photonic quasi‐crystal
Authors: FANG Z.Y. , DAI T. , FU Q. , ZHANG B. , ZHU X. 
Published: July 2009

SummaryTwo‐dimensional micro‐cylinder patterns of dodecagonal photonic quasi‐crystal (12‐PQC) and tetragonal photonic crystal (2‐PC) were fabricated on the top surface of a GaN light‐emitting diode (LED). The patterns were evaporated with a 10‐nm‐thick Ag film. Spatially resolved surface emission was recorded and analysed by scanning near‐field optical microscopy. Electromagnetic energy was confined and enhanced at the top surface when the surface plasmon (SP) resonated. The enhancement factor for 12‐PQC was 1.9 times that of 2‐PC, 8.6 times that of non‐patterned LED in the near field and 6.7 times in the far field, respectively. Finite‐difference time‐domain simulations are consistent with the experimental data. The results show that with a patterned structure on the top surface of an LED, the light emission can be greatly enhanced due to SP resonance.
Using conventional fluorescent markers for far‐field fluorescence localization nanoscopy allows resolution in the 10‐nm range
Authors: LEMMER P. , GUNKEL M. , WEILAND Y. , MÜLLER P. , BADDELEY D. , KAUFMANN R. , URICH A. , EIPEL H. , AMBERGER R. , HAUSMANN M. , CREMER C. 
Published: July 2009

SummaryWe present a novel technique of far‐field localization nanoscopy combining spectral precision distance microscopy with widely used fluorochromes like the Green Fluorescent Protein (GFP) derivatives eGFP, EmGFP, Yellow Fluorescent Protein (YFP) and eYFP, synthetic dyes like Alexa 488 and Alexa 568, as well as fluoresceine derivates. Spectral precision distance microscopy allows the surpassing of conventional resolution limits in fluorescence far‐field microscopy by precise object localization after the optical isolation of single signals in time. Based on the principles of this technique, our novel nanoscopic method was realized for laser optical precision localization and image reconstruction with highly enhanced optical resolution in intact cells. This allows for spatial assignment of individual fluorescent molecules with nanometre precision. The technique is based on excitation intensity dependent reversible photobleaching of the molecules used combined with fast time sequential imaging under appropriate focusing conditions. A meaningful advantage of the technique is the simple applicability as a universal tool for imaging and investigations to the major part of already available preparations according to standard protocols. Using the above mentioned fluorophores, the positions of single molecules within cellular structures were determined by visible light with an estimated localization precision down to 3 nm; hence distances in the range of 10–30 nm were resolved between individual fluorescent molecules allowing to apply different quantitative structure analysis tools.
Fabrication and evaluation of a near‐infrared hyperspectral imaging system
Authors: KATARI S. , WALLACK M. , HUEBSCHMAN M. , PANTANO P. , GARNER H. 
Published: July 2009

SummaryThis paper describes modifications to a hyperspectral imaging microscope that extend its capabilities into the near‐infrared (950–1300 nm). The major changes include installing a grating, charge‐coupled device camera, and lenses and filters appropriate for infrared wavelengths. Calibration of the system and validation with lead sulfide quantum dots of known emission wavelength is reported. Cells from the breast carcinoma cell line SkBr3 were scanned with lead sulfide quantum dots that emit at 1100 nm as the background and an image which contains the integrated spectral data is presented. We also demonstrate that this instrument is capable of detecting the photoluminescence spectra of single‐walled carbon nanotubes dispersed in aqueous solution.
Stereo soft X‐ray microscopy and elemental mapping of haematite and clay suspensions
Authors: GLEBER S.‐C. , THIEME J. , CHAO W. , FISCHER P. 
Published: July 2009

SummaryThe combination of high‐resolution chemically sensitive soft X‐ray microscopy with stereo imaging and processing techniques presented here forms a novel tool for the investigation of aqueous colloidal systems. Information about the spatial distribution within the sample is provided with small calculation effort processing just a pair of stereo micrographs. Thus, the extension towards investigation of dynamical behaviour is possible on the part of the experiment as well as of the processing.The potential of this technique is demonstrated with applications in aqueous soil and clay samples. Within these samples, haematite particles are identified taking advantage of the elemental contrast at the Fe‐L edge around E= 707 eV. In combination with stereo microscopy, information about spatial arrangements are revealed and correlated to electrostatic interactions of the different mixtures, addressing to an actual question of soil scientists. The technique allows in‐situ sample manipulation, which is demonstrated by a test specimen where particles were added during imaging.
Genome‐wide screens: novel mechanisms in colicin import and cytotoxicity
Authors: Sharma Onkar , Datsenko Kirill A. , Ess Sara C. , Zhalnina Mariya V. , Wanner Barry L. , Cramer William A. 
Published: July 2009

SummaryOnly two new genes (fkpA and lepB) have been identified to be required for colicin cytotoxicity in the last 25 years. Genome‐wide screening using the ‘Keio collection’ to test sensitivity to colicins (col) A, B, D, E1, E2, E3, E7 and N from groups A and B, allowed identification of novel genes affecting cytotoxicity and provided new information on mechanisms of action. The requirement of lipopolysaccharide for colN cytotoxicity resides specifically in the lipopolysaccharide inner‐core and first glucose. ColA cytotoxicity is dependent on gmhB and rffT genes, which function in the biosynthesis of lipopolysaccharide and enterobacterial common antigen. Of the tol genes that function in the cytoplasmic membrane translocon, colE1 requires tolA and tolR but not tolQ for activity. Peptidoglycan‐associated lipoprotein, which interacts with the Tol network, is not required for cytotoxicity of group A colicins. Except for TolQRA, no cytoplasmic membrane protein is essential for cytotoxicity of group A colicins, implying that TolQRA provides the sole pathway for their insertion into/through the cytoplasmic membrane. The periplasmic protease that cleaves between the receptor and catalytic domains of colE7 was not identified, implying either that the responsible gene is essential for cell viability, or that more than one gene product has the necessary proteolysis function.
Replication‐directed sister chromosome alignment in Escherichia coli
Authors: Liu Xun , Wang Xindan , Reyes‐Lamothe Rodrigo , Sherratt David 
Published: July 2009

SummaryNon‐replicating Escherichia coli chromosomes are organized as sausage‐shaped structures with the left (L) and the right (R) chromosome arms (replichores) on opposite cell halves and the replication origin (oriC) close to midcell. The replication termination region (ter) therefore passes between the two outer edges of the nucleoid. Four alignment patterns of the two <LR> sister chromosomes within a cell have been detected in an asynchronous population, with the <LRLR> pattern predominating. We test the hypothesis that the minority <LRRL> and <RLLR> patterns arise because of pausing of DNA replication on the right and left replichores respectively. The data resulting from transient pausing or longer‐term site‐specific blocking of replication show that paused/blocked loci remain close to midcell and the normally replicated‐segregated loci locate to the outer regions of the nucleoid, therefore providing experimental support for a direct mechanistic link between DNA replication and chromosome organization.
Analgesia before a spinal block for femoral neck fracture: fascia iliaca compartment block
Authors: YUN M. J. , KIM Y. H. , HAN M. K. , KIM J. H. , HWANG J. W. , DO S. H. 
Published: July 2009

Background: In this prospective randomized study, the authors compared the analgesic effect of a fascia iliaca compartment (FIC) block with that of intravenous (i.v.) alfentanil when administered to facilitate positioning for spinal anaesthesia in elderly patients undergoing surgery for a femoral neck fracture.Methods: The 40 patients were randomly assigned to one of two groups, namely, the FIC group (fascia iliaca compartment block, n=20) and the IVA group (intravenous analgesia with alfentanil, n=20). Group IVA patients received a bolus dose of i.v. alfentanil 10 μg/kg, followed by a continuous infusion of alfentanil 0.25 μg/kg/min starting 2 min before the spinal block, and group FIC patients received a FIC block with 30 ml of ropivacaine 3.75 mg/ml (112.5 mg) 20 min before the spinal block. Visual analogue pain scale (VAS) scores, time to achieve spinal anaesthesia, quality of patient positioning, and patient acceptance were compared.Results: VAS scores during positioning (mean and range) were lower in the FIC group than in the IVA group [2.0 (1–4) vs. 3.5 (2–6), P=0.001], and the mean (± SD) time to achieve spinal anaesthesia was shorter in the FIC group (6.9 ± 2.7 min vs. 10.8 ± 5.6 min; P=0.009). Patient acceptance (yes/no) was also better in the FIC group (19/1) than in the IVA group (12/8)(P=0.008).Conclusions: An FIC block is more efficacious than i.v. alfentanil in terms of facilitating the lateral position for spinal anaesthesia in elderly patients undergoing surgery for femoral neck fractures.
Introduction
Authors: Bertrand Paul P 
Published: July 2009

From the Editors‐in‐ChiefThis Introduction prefaces three minireviews that are being published under the aegis of our ‘Frontiers in Research’ series. The authors of these reviews recently presented their work at a symposium entitled ‘Inflammation and Innervation of the Intestine’ at the Australian Neuroscience Society meeting in Canberra, 2009. The symposium was supported by the Australian Neuroscience Society, Australasian Neurogastroenterology and Motility Association and this Journal via the present series of minireviews.Roger Evans and Ding‐Feng Su
Absolute quantification of Dehalococcoides proteins: enzyme bioindicators of chlorinated ethene dehalorespiration
Authors: Werner Jeffrey J. , Ptak A. Celeste , Rahm Brian G. , Zhang Sheng , Richardson Ruth E. 
Published: July 2009

SummaryThe quantification of trace proteins in complex environmental samples and mixed microbial communities would be a valuable monitoring tool in countless applications, including the bioremediation of groundwater contaminated with chlorinated solvents. Measuring the concentrations of specific proteins provides unique information about the activity and physiological state of organisms in a sample. We developed sensitive (< 5 fmol), selective bioindicator assays for the absolute quantification of select proteins used by Dehalococcoides spp. when reducing carbon atoms in the common pollutants trichloroethene (TCE) and tetrachloroethene (PCE). From complex whole‐sample digests of two different dechlorinating mixed communities, we monitored the chromatographic peaks of selected tryptic peptides chosen to represent 19 specific Dehalococcoides proteins. This was accomplished using multiple‐reaction monitoring (MRM) assays using nano‐liquid chromatography‐tandem mass spectrometry (nLC‐MS/MS), which provided the selectivity, sensitivity and reproducibility required to quantify Dehalococcoides proteins in complex samples. We observed reproducible peak areas (average CV = 0.14 over 4 days, n = 3) and linear responses in standard curves (n = 5, R2 > 0.98) using synthetic peptide standards spiked into a background matrix of sediment peptides. We detected and quantified TCE reductive dehalogenase (TceA) at 7.6 ± 1.7 × 103 proteins cell−1 in the KB1TM bioaugmentation culture, previously thought to be lacking TceA. Fragmentation data from MS/MS shotgun proteomics experiments were helpful in developing the MRM targets. Similar shotgun proteomics data are emerging in labs around the world for many environmentally relevant microbial proteins, and these data are a valuable resource for the future development of MRM assays. We expect targeted peptide quantification in environmental samples to be a useful tool in environmental monitoring.
Radiolabelled proteomics to determine differential functioning of Accumulibacter during the anaerobic and aerobic phases of a bioreactor operating for enhanced biological phosphorus removal
Authors: Wexler Margaret , Richardson David J. , Bond Philip L. 
Published: July 2009

SummaryProteins synthesized by the mixed microbial community of two sequencing batch reactors run for enhanced biological phosphorus removal (EBPR) during aerobic and anaerobic reactor phases were compared, using mass spectrometry‐based proteomics and radiolabelling. Both sludges were dominated by polyphosphate‐accumulating organisms belonging to Candidatis Accumulibacter and the majority of proteins identified matched closest to these bacteria. Enzymes from the Embden–Meyerhof–Parnas pathway were identified, suggesting this is the major glycolytic pathway for these Accumulibacter populations. Enhanced aerobic synthesis of glyoxylate cycle enzymes suggests this cycle is important during the aerobic phase of EBPR. In one sludge, several TCA cycle enzymes showed enhanced aerobic synthesis, suggesting this cycle is unimportant anaerobically. The second sludge showed enhanced synthesis of TCA cycle enzymes under anaerobic conditions, suggesting full or partial TCA cycle operation anaerobically. A phylogenetic analysis of Accumulibacter polyphosphate kinase genes from each sludge demonstrated different Accumulibacter populations dominated the two sludges. Thus, TCA cycle activity differences may be due to Accumulibacter strain differences. The major fatty acids present in Accumulibacter‐dominated sludge include palmitic, hexadecenoic and cis‐vaccenic acid and fatty acid content increased by approximately 20% during the anaerobic phase. We hypothesize that this is associated with increased anaerobic phospholipid membrane biosynthesis, to accommodate intracellular polyhydroxyalkanoate granules.
Effect of carvacrol on hepatic marker enzymes and antioxidant status in d‐galactosamine‐induced hepatotoxicity in rats
Authors: Aristatile Balakrishnan , Al‐Numair Khalid S. , Veeramani Chinnadurai , Pugalendi Kodukkur Viswanathan 
Published: July 2009

AbstractCarvacrol (2‐methyl‐5‐(1‐methylethyl)‐phenol) is a predominant monoterpenic phenol which occurs in many essential oils of the family Labiatae including Origanum, Satureja, Thymbra, Thymus, and Corydothymus species. This study was designed to investigate the hepatoprotective and antioxidant properties of carvacrol on d‐galactosamine (D‐GalN)‐induced hepatotoxicity and oxidative damage in male albino Wistar rats. D‐GalN hepatotoxic rats exhibited elevation in the activities of aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, gamma‐glutamyl transpeptidase, and lipidperoxidative markers such as thiobarbituric acid reactive substances (TBARS) and lipid hydroperoxides. Activities of enzymatic antioxidants (superoxide dismutase, catalase, and glutathione peroxidase) and the levels of non‐enzymatic antioxidants (vitamin C, vitamin E, and reduced glutathione) in the plasma, erythrocytes, liver, and kidney decreased in the hepatotoxic rats. Oral administration of carvacrol for 21 days brought these parameters towards normal. The biochemical observations were supported by histological studies of rat liver and kidney tissues. These results suggest that carvacrol could afford a significant hepatoprotective and antioxidant effect against D‐GalN‐induced rats.
Parametric models of local search progression
Authors: Oppen Johan , Woodruff David L. 
Published: July 2009

AbstractAlgorithms that search for good solutions to optimization problems present a trace of current best objective values over time. We describe an empirical study of parametric models of this progression that are both interesting as ways to characterize the search progression compactly and useful as means of predicting search behavior. In our computational experiments, we give examples of a variety of problems and algorithms where we are able to use the parametric models to make predictions of performance that cross instances and instance sizes.
Thymic involution, a co‐morbidity factor in amyotrophic lateral sclerosis
Authors: Seksenyan Akop , Ron‐Harel Noga , Azoulay David , Cahalon Liora , Cardon Michal , Rogeri Patricia , Ko Minhee K. , Weil Miguel , Bulvik Shlomo , Rechavi Gideon , Amariglio Ninette , Konen Eli , Koronyo‐Hamaoui Maya , Somech Raz , Schwartz Michal 
Published: July 2009

AbstractAmyotrophic lateral sclerosis (ALS) is a devastating disease, characterized by extremely rapid loss of motor neurons. Our studies over the last decade have established CD4+ T cells as important players in central nervous system maintenance and repair. Those results, together with recent findings that CD4+ T cells play a protective role in mouse models of ALS, led us to the current hypothesis that in ALS, a rapid T‐cell malfunction may develop in parallel to the motor neuron dysfunction. Here, we tested this hypothesis by assessing thymic function, which serves as a measure of peripheral T‐cell availability, in an animal model of ALS (mSOD1 [superoxide dismutase] mice; G93A) and in human patients. We found a significant reduction in thymic progenitor‐cell content, and abnormal thymic histology in 3–4‐month‐old mSOD1 mice. In ALS patients, we found a decline in thymic output, manifested in the reduction in blood levels of T‐cell receptor rearrangement excision circles, a non‐invasive measure of thymic function, and demonstrated a restricted T‐cell repertoire. The morbidity of the peripheral immune cells was also manifested in the increase of pro‐apoptotic BAX/BCXL2 expression ratio in peripheral blood mononuclear cells (PBMCs) of these patients. In addition, gene expression screening in the same PBMCs, revealed in the ALS patients a reduction in key genes known to be associated with T‐cell activity, including: CD80, CD86, IFNG and IL18. In light of the reported beneficial role of T cells in animal models of ALS, the present observation of thymic dysfunction, both in human patients and in an animal model, might be a co‐pathological factor in ALS, regardless of the disease aetiology. These findings may lead to the development of novel therapeutic approaches directed at overcoming the thymic defect and T‐cell deficiency.
Survival and complications of computer aided‐designing and computer‐aided manufacturing vs. conventionally fabricated implant‐supported reconstructions: a systematic review
Authors: Harder Sönke , Kern Matthias 
Published: July 2009

AbstractObjectives: The aim of this systematic review was to assess the internationally published survival and complication rates of implant‐supported computer‐aided designing (CAD) and computer‐aided manufacturing (CAM)‐fabricated restorations and to compare them with those of conventionally fabricated implant‐supported restorations.Methods: An electronic MEDLINE search was conducted to identify prospective and retrospective cohort studies on CAD–CAM fabricated implant‐supported restorations with a mean follow‐up time of at least 1 year. Failure and complication rates were evaluated and descriptive statistics were performed.Results: An electronic MEDLINE search revealed four studies reporting on implant‐supported CAD–CAM fabricated restorations. The cumulative 5‐year survival rate of implants supporting full‐arch‐fixed dental prostheses (FDPs) ranged from 81.4% to 95.6%. Reported survival rates of implants supporting all‐ceramic single crowns (SCs) were 100% [95% confidence interval (CI): 92.4–100]. The cumulative 5‐year survival rate for full‐arch FDPs ranged from 72.2% to 100%. Reported cumulative 5‐year survival rates for all‐ceramic SCs were 100% (95% CI: 92.4–100%). Technical complications were reported in two of the four selected studies and the estimated annual failure rate for chipping/fracture of the veneering material was 0.43 (95% CI: 0.06–3.06) for implant‐supported all‐ceramic SCs and 3.61 (95% CI: 2.05–6.36) for implant‐supported FDPs.Conclusions: Only a small number of clinical studies reporting on implant‐supported CAD–CAM fabricated restorations exists which makes a scientifically valid comparison with conventionally fabricated restorations impossible.
Biomechanics/risk management (Working Group 2)
Authors: Sanz Mariano , Naert Ignace 
Published: July 2009

AbstractIntroduction: The remit of this workgroup was to update the existing knowledge base in biomechanical factors, navigation systems and medications that may affect the outcome of implant therapy.Material and methods: The literature was systematically searched and critically reviewed. Five manuscripts were produced in five specific topics identified as areas where innovative approaches have been developed in biomechanical factors, navigation systems and medications that may affect the outcome of implant therapy.Results: The results and conclusions of the review process are presented in the following papers, together with the group consensus statements, clinical implications and directions for future research: • To what extent do cantilevers affect survival and complications of implant supported restorations in partially dentate patients? • To what extent does the crown–implant ratio affect survival and complications of implant supported restorations? • A systematic review on the accuracy and the clinical outcome of computer‐guided template based implant dentistry. • What is the impact of systemic bisphosphonates on patients undergoing oral implant therapy? • What is the impact of anticoagulants on patients undergoing oral implant therapy?