A distributed-object infrastructure for corporate websites

A corporate website is the virtual representation of a cor-poration or organization on the Internet. Corporate web-sites face numerous problems due to their large size and complexity, and the nonscalability of the underlying Web infrastructure. Current solutions to these problems gener-ally rely on traditional scaling techniques such as caching and replication. These are usually too restrictive, however; taking a one-size-fits-all approach and applying the same solution to every document. We propose Globe as a founda-tion upon which to build scalable corporate websites, and introduce GlobeDoc, a website model based on Globe dis-tributed shared objects. This paper describes GlobeDoc, highlighting the design and technical details of the infras-tructure. 1

Statistical inference of the generation probability of T-cell receptors from sequence repertoires

Stochastic rearrangement of germline DNA by VDJ recombination is at the origin of immune system diversity. This process is implemented via a series of stochastic molecular events involving gene choices and random nucleotide insertions between, and deletions from, genes. We use large sequence repertoires of the variable CDR3 region of human CD4+ T-cell receptor beta chains to infer the statistical properties of these basic biochemical events. Since any given CDR3 sequence can be produced in multiple ways, the probability distribution of hidden recombination events cannot be inferred directly from the observed sequences; we therefore develop a maximum likelihood inference method to achieve this end. To separate the properties of the molecular rearrangement mechanism from the effects of selection, we focus on non-productive CDR3 sequences in T-cell DNA. We infer the joint distribution of the various generative events that occur when a new T-cell receptor gene is created. We find a rich picture of correlation (and absence thereof), providing insight into the molecular mechanisms involved. The generative event statistics are consistent between individuals, suggesting a universal biochemical process. Our distribution predicts the generation probability of any specific CDR3 sequence by the primitive recombination process, allowing us to quantify the potential diversity of the T-cell repertoire and to understand why some sequences are shared between individuals. We argue that the use of formal statistical inference methods, of the kind presented in this paper, will be essential for quantitative understanding of the generation and evolution of diversity in the adaptive immune system.Comment: 20 pages, including Appendi

KKF-Model Platform Coupling : summary report KKF01b

Nederland bereidt zich voor op een sneller stijgende zeespiegel en een veranderend klimaat. Hiervoor is het Deltaprogramma gestart. Dit deltaprogramma voorziet een serie beslissingen die grote gevolgen zullen hebben voor het beheer van het water in Nederland. Om deze beslissingen zorgvuldig te nemen is informatie nodig over hoe het klimaat en de stijgende zeespiegel dit waterbeheer zullen beïnvloeden. De modellen die de gevolgen van klimaatverandering berekenen zullen daarom met dezelfde klimaat forcering en gekoppeld aan elkaar moeten worden gebruikt. In dit onderzoek is gekeken naar het linken van hydrologische en hydrodynamische modellen – en daaraan gekoppelde modellen die de ontwikkelingen in natuur en landgebruik modelleren -- die het gebied van de Alpen tot en met de Noordzee inclusief Nederland beschrijven

Efficacy of natural antimicrobials in toothpaste formulations against oral biofilms in vitro

AbstractObjectivesTo evaluate the antimicrobial efficacies of two toothpaste formulations containing natural antimicrobials (herbal extracts and chitosan) against oral biofilms of different composition and maturational status.MethodsBacteria from a buffer suspension or fresh saliva were adhered for 2h to a salivary conditioning film and subsequently grown for 16h. Dual-species biofilms were prepared from Actinomyces naeslundii T14V-J1 and Streptococcus oralis J22, whilst multi-species biofilms were grown from freshly collected human saliva. Biofilms were exposed to 25wt% toothpaste supernatants. A chlorhexidine-containing mouthrinse and a buffer were used as positive- and negative-controls, respectively. Antibacterial efficacy was concluded from acute killing, bacterial removal, prevention of bacterial re-deposition and continued killing during re-deposition.ResultsThe herbal- and chitosan-based supernatants showed immediate killing of oral biofilm bacteria, comparable with chlorhexidine. Moreover, exposure of a biofilm to these supernatants or chlorhexidine, yielded ongoing killing of biofilm bacteria after exposure during re-deposition of bacteria to a matured 16h biofilm, but not to a much thinner initial biofilm formed by 2h adhesion only. This suggests that thicker, more matured biofilms can absorb and release oral antimicrobials.ConclusionsSupernatants based on herbal- and chitosan-based toothpastes have comparable immediate and ongoing antibacterial efficacies as chlorhexidine. Natural antimicrobials and chlorhexidine absorb in oral biofilms which contributes to their substantive action

A single center analysis of nucleophosmin in acute myeloid leukemia:value of combining immunohistochemistry with molecular mutation analysis

Mutations of nucleophosmin 1 are frequently found in acute myeloid leukemia and lead to aberrant cytoplasmic accumulation of nucleophosmin protein. Immunohistochemical staining is therefore recommended as the technique of choice in front-line screening. In this study, we assessed the sensitivity and specificity of immunohistochemistry on formalin-fixed bone marrow biopsies compared with gold standard molecular analysis to predict nucleophosmin 1 mutation status in 119 patients with acute myeloid leukemia. Discrepant cases were further characterized by gene expression analyses and fluorescence in situ hybridization. A large overlap between both methods was observed. Nevertheless, nine patients demonstrated discordant results at initial screening. Five cases demonstrated nuclear staining of nucleophosmin 1 by immunohistochemistry, but a nucleophosmin 1 mutation by molecular analysis. In two cases this could be attributed to technical issues and in three cases minor subpopulations of myeloblasts had not been discovered initially. All tested cases exhibited the characteristic nucleophosmin-mutated gene expression pattern. Four cases had cytoplasmic nucleophosmin 1 staining and a nucleophosmin-mutated gene expression pattern without a detectable nucleophosmin 1 mutation. In two of these cases we found the chromosomal translocation t(3;5)(q25;q35) encoding the NPM-MLF1 fusion protein. In the other discrepant cases the aberrant cytoplasmic nucleophosmin staining and gene expression could not be explained. In total six patients (5%) had true discordant results between immunohistochemistry and mutation analysis. We conclude that cytoplasmic nucleophosmin localization is not always caused by a conventional nucleophosmin 1 mutation and that in the screening for nucleophosmin 1 abnormalities, most information will be obtained by combining immunohistochemistry with molecular analysis

Development of a multiplexed bead-based immunoassay for the simultaneous detection of antibodies to 17 pneumococcal proteins

Presently, several pneumococcal proteins are being evaluated as potential vaccine candidates. Here, we gather novel insights in the immunogenicity of PLY, PsaA, PspA, PspC, NanA, Hyl, PpmA, SlrA, Eno, IgA1-protease, PdBD, BVH-3, SP1003, SP1633, SP1651, SP0189 and SP0376. We developed a multiplex bead-based immunoassay (xMAP® Technology, Luminex Corporation) to simultaneously quantify antibodies against these 17 pneumococcal proteins in serum. The median fluorescence intensity (MFI) values obtained for human pooled serum with the multiplex assay were between 82% and 111% (median 94%) of those obtained with the singleplex assays. For IgG, the coefficient of variation (CV) in serum ranged from 2% to 9%, for IgA, the CV ranged from 3% to 14% and for IgM, the CV ranged from 11% to 15%. Using this immunoassay, we showed that anti-pneumococcal antibody levels exhibited extensive inter-individual variability in young children suffering from invasive pneumococcal disease. All proteins, including the proteins with, as yet, unknown function, were immunogenic. In conclusion, the multiplex Streptococcus pneumoniae immunoassay based on proteins is reproducible. This assay can be used to monitor anti-S. pneumoniae antibody responses in a material- and time-saving manner

Altered neurodevelopmental DNA methylation status after fetal growth restriction with brain-sparing

It is under debate how preferential perfusion of the brain (brain-sparing) in fetal growth restriction (FGR) relates to long-term neurodevelopmental outcome. Epigenetic modification of neurotrophic genes by altered fetal oxygenation may be involved. To explore this theory, we performed a follow-up study of 21 FGR children, in whom we prospectively measured the prenatal cerebroplacental ratio (CPR) with Doppler sonography. At 4 years of age, we tested their neurodevelopmental outcome using the Wechsler Preschool and Primary Scale of Intelligence, the Child Behavior Checklist, and the Behavior Rating Inventory of Executive Function. In addition, we collected their buccal DNA to determine the methylation status at predefined genetic regions within the genes hypoxia-inducible factor-1 alpha (HIF1A), vascular endothelial growth factor A (VEGFA), erythropoietin (EPO), EPO-receptor (EPOR), brain-derived neurotrophic factor (BDNF), and neurotrophic tyrosine kinase, receptor, type 2 (NTRK2) by pyrosequencing. We found that FGR children with fetal brain-sparing (CPR <1, n = 8) demonstrated a trend (0.05 < p < 0.1) toward hypermethylation of HIF1A and VEGFA at their hypoxia-response element (HRE) compared with FGR children without fetal brain-sparing. Moreover, in cases with fetal brain-sparing, we observed statistically significant hypermethylation at a binding site for cyclic adenosine monophophate response element binding protein (CREB) of BDNF promoter exon 4 and hypomethylation at an HRE located within the NTRK2 promoter (both p <0.05). Hypermethylation of VEGFA was associated with a poorer Performance Intelligence Quotient, while hypermethylation of BDNF was associated with better inhibitory self-control (both p <0.05). These results led us to formulate the hypothesis that early oxygen-dependent epigenetic alterations due to hemodynamic alterations in FGR may be associated with altered neurodevelopmental outcome in later life. We recommend further studies to test this hypothesis