Monte Carlo simulation of cluster growth in surface defects induced by the tip of a scanning tunnelling microscope

First steps are taken to model the electrochemical deposition of metals in nanometer-sized cavities. In the present work, the electrochemical deposition of Cu atoms in nanometer-sized holes dug on Au(111) is investigated through Monte Carlo simulations using the embedded atom method to represent particle interactions. By sweeping the chemical potential of Cu, a cluster is allowed to grow within the hole rising four atomic layers above the surface. Its lateral extension remains confined to the area defined by the borders of the original defect. (C) 2004 Elsevier B.V. All rights reserved.

A cluster randomised controlled trial to evaluate a policy of making hip protectors available to residents of nursing homes

Objectives: to evaluate the effectiveness of a policy of making hip protectors available to residents of nursing homes. Design: a cluster randomised controlled trial of the policy in nursing and residential homes, with the home as the unit of randomisation. Setting: 127 nursing and residential homes in the greater Belfast area of Northern Ireland. Participants: 40 homes in the intervention group (representing 1,366 occupied beds) and 87 homes in the control group (representing 2,751 occupied beds). Interventions: a policy of making hip protectors available free of charge to residents of nursing homes and supporting the implementation process by employing a nurse facilitator to encourage staff in the homes to promote their use, over a 72-week period. Main outcome measures: the rate of hip fractures in intervention and control homes, and the level of adherence to use of hip protectors. Results: there were 85 hip fractures in the intervention homes and 163 in the control homes. The mean fracture rate per 100 residents was 6.22 in the intervention homes and 5.92 in the control homes, giving an adjusted rate ratio for the intervention group compared to the control group of 1.05 (95% CI 0.77, 1.43, P = 0.76). Initial acceptance of the hip protectors was 37.2% (508/1,366) with adherence falling to 19.9% (272/1,366) at 72 weeks. Conclusions: making hip protectors available to residents of nursing and residential homes did not reduce the rate of hip fracture.

Characterization of White bream virus reveals a novel genetic cluster of nidoviruses.

The order Nidovirales comprises viruses from the families Coronaviridae (genera Coronavirus and Torovirus), Roniviridae (genus Okavirus), and Arteriviridae (genus Arterivirus). In this study, we characterized White bream virus (WBV), a bacilliform plus-strand RNA virus isolated from fish. Analysis of the nucleotide sequence, organization, and expression of the 26.6-kb genome provided conclusive evidence for a phylogenetic relationship between WBV and nidoviruses. The polycistronic genome of WBV contains five open reading frames (ORFs), called ORF1a, -1b, -2, -3, and -4. In WBV-infected cells, three subgenomic RNAs expressing the structural proteins S, M, and N were identified. The subgenomic RNAs were revealed to share a 42-nucleotide, 5' leader sequence that is identical to the 5'-terminal genome sequence. The data suggest that a conserved nonanucleotide sequence, CA(G/A)CACUAC, located downstream of the leader and upstream of the structural protein genes acts as the core transcription-regulating sequence element in WBV. Like other nidoviruses with large genomes (>26 kb), WBV encodes in its ORF1b an extensive set of enzymes, including putative polymerase, helicase, ribose methyltransferase, exoribonuclease, and endoribonuclease activities. ORF1a encodes several membrane domains, a putative ADP-ribose 1"-phosphatase, and a chymotrypsin-like serine protease whose activity was established in this study. Comparative sequence analysis revealed that WBV represents a separate cluster of nidoviruses that significantly diverged from toroviruses and, even more, from coronaviruses, roniviruses, and arteriviruses. The study adds to the amazing diversity of nidoviruses and appeals for a more extensive characterization of nonmammalian nidoviruses to better understand the evolution of these largest known RNA viruses.

Detection of the icaADBC gene cluster and biofilm formation in Staphylococcus epidermidis isolates from catheter-related urinary tract infections.

Cho SH, Naber K, Hacker J, Ziebuhr W. Institut für Molekulare Infektionsbiologie, Röntgenring 11, D-97070 Würzburg, Germany. Biofilm production in Staphylococcus epidermidis is an important virulence factor that is mediated by the expression of the icaADBC operon. In this study 41 S. epidermidis isolates obtained from catheter-related urinary tract infections were analyzed for the presence of the icaADBC operon and biofilm formation. Eighteen of 41 isolates (44%) were shown to carry ica-specific DNA, but only 11 isolates (27%) produced biofilms spontaneously under normal growth conditions. Upon induction by external stress or antibiotics, biofilm formation could be stimulated in five of seven ica-positive, biofilm-negative isolates, indicating that the icaADBC expression was down-regulated in these strains. Genetic analyses of the ica gene clusters of the remaining two ica-positive, biofilm-negative strains revealed a spontaneous ICAC::IS256 insertion in one strain. Insertion of the element caused a target site duplication of seven base pairs and a biofilm-negative phenotype. After repeated passages the insertion mutant was able to revert to a biofilm-forming phenotype which was due to the precise excision of IS256 from the icaC gene. The data show that icaC::IS256 integrations occur during S. epidermidis polymer-related infections and the results highlight the biological relevance of the IS256-mediated phase variation of biofilm production in S. epidermidis during an infection.

Expression of the phosphonoalanine-degradative gene cluster from Variovorax sp Pal2 is induced by growth on phosphonoalanine and phosphonopyruvate

The phosphonopyruvate hydrolase (PalA) found in Variovorax sp., Pal2, is a novel carbon-phosphorus bond cleavage enzyme, which is expressed even in the presence of high levels of phosphate, thus permitting phosphonopyruvate to be used as the sole carbon and energy source. Analysis of the regions adjacent to the palA gene revealed the presence of the five structural genes that constitute the 2-amino-3-phosphonopropionic acid (phosphonoalanine)-degradative operon. Reverse transcriptase-PCR (RT-PCR) experiments demonstrated that all five genes in the operon are transcribed as a single mRNA and that their transcription is induced by phosphonoalanine or phosphonopyruvate. Transcriptional fusions of the regulatory region of the phosphonoalanine degradative operon with the gfp gene were constructed. Expression analysis indicated that the presence of a LysR-type regulator (encoded by the palR gene) is essential for the transcription of the structural genes of the operon. Similar gene clusters were found in the sequenced genomes of six bacterial species from the Alpha-, Beta- and Gammaproteobacteria, and analysis of metagenomic libraries revealed that sequences related to palA are widely spread in the marine environment.

Ionography of nanostructures with the use of a laser plasma of cluster targets

It has been shown that a femtosecond plasma of cluster targets is an almost isotropic source of fast ions and, hence, can be used to obtain ionographic images with a wide field of view. The spatial resolution of the resulting ionographic images is no worse than 600 nm, which corresponds to a uniquely high value of about 105 of the ratio of the field of view to the resolution. The use of 100–300-keV ion fluxes ensures the sensitivity of the method to the sample thickness of no worse than 100 nm even for samples consisting of light chemical elements (C, H). The proposed method can be used to obtain images of low-contrast biological objects, thin films, membranes, and other nanostructured objects.

The human prion protein residue 129 polymorphism lies within a cluster of epitopes for T cell recognition.

T cell immune responses to central nervous system-derived and other self-antigens are commonly described in both healthy and autoimmune individuals. However, in the case of the human prion protein (PrP), it has been argued that immunologic tolerance is uncommonly robust. Although development of an effective vaccine for prion disease requires breaking of tolerance to PrP, the extent of immune tolerance to PrP and the identity of immunodominant regions of the protein have not previously been determined in humans. We analyzed PrP T cell epitopes both by using a predictive algorithm and by measuring functional immune responses from healthy donors. Interestingly, clusters of epitopes were focused around the area of the polymorphic residue 129, previously identified as an indicator of susceptibility to prion disease, and in the C-terminal region. Moreover, responses were seen to PrP peptide 121-134 containing methionine at position 129, whereas PrP 121-134 [129V] was not immunogenic. The residue 129 polymorphism was also associated with distinct patterns of cytokine response: PrP 128-141 [129M] inducing IL-4 and IL-6 production, which was not seen in response to PrP 128-141 [129V]. Our data suggest that the immunogenic regions of human PrP lie between residue 107 and the C-terminus and that, like with many other central nervous system antigens, healthy individuals carry responses to PrP within the T cell repertoire and yet do not experience deleterious autoimmune reactions.

Submicron ionography of nanostructures using a femtosecond-laser-driven-cluster-based source

An intense isotropic source of multicharged carbon and oxygen ions with energy above 300 keV and particle number >108 per shot was obtained by femtosecond Ti:Sa laser irradiation of submicron clusters. The source was employed for high-contrast contact ionography images with 600 nm spatial resolution. A variation in object thickness of 100 nm was well resolved for both Zr and polymer foils.

Sequential extracellular matrix-focused and baited-global cluster analysis of serial transcriptomic profiles identifies candidate modulators of renal tubulointerstitial fibrosis in murine adriamycin-induced nephropathy

Transcriptome analysis using microarray technology represents a powerful unbiased approach for delineating pathogenic mechanisms in disease. Here molecular mechanisms of renal tubulointerstitial fibrosis (TIF) were probed by monitoring changes in the renal transcriptome in a glomerular disease-dependent model of TIF ( adriamycin nephropathy) using Affymetrix (mu74av2) microarray coupled with sequential primary biological function-focused and secondary