440 research outputs found
SAPHO syndrome in an adult with ulcerative colitis responsive to intravenous pamidronate: a case report and review of the literature
pGQL: A probabilistic graphical query language for gene expression time courses
<p>Abstract</p> <p>Background</p> <p>Timeboxes are graphical user interface widgets that were proposed to specify queries on time course data. As queries can be very easily defined, an exploratory analysis of time course data is greatly facilitated. While timeboxes are effective, they have no provisions for dealing with noisy data or data with fluctuations along the time axis, which is very common in many applications. In particular, this is true for the analysis of gene expression time courses, which are mostly derived from noisy microarray measurements at few unevenly sampled time points. From a data mining point of view the robust handling of data through a sound statistical model is of great importance.</p> <p>Results</p> <p>We propose probabilistic timeboxes, which correspond to a specific class of Hidden Markov Models, that constitutes an established method in data mining. Since HMMs are a particular class of probabilistic graphical models we call our method Probabilistic Graphical Query Language. Its implementation was realized in the free software package pGQL. We evaluate its effectiveness in exploratory analysis on a yeast sporulation data set.</p> <p>Conclusions</p> <p>We introduce a new approach to define dynamic, statistical queries on time course data. It supports an interactive exploration of reasonably large amounts of data and enables users without expert knowledge to specify fairly complex statistical models with ease. The expressivity of our approach is by its statistical nature greater and more robust with respect to amplitude and frequency fluctuation than the prior, deterministic timeboxes.</p
Quantitative Analysis of Protein Phosphorylations and Interactions by Multi-Colour IP-FCM as an Input for Kinetic Modelling of Signalling Networks
BACKGROUND: To understand complex biological signalling mechanisms, mathematical modelling of signal transduction pathways has been applied successfully in last few years. However, precise quantitative measurements of signal transduction events such as activation-dependent phosphorylation of proteins, remains one bottleneck to this success. METHODOLOGY/PRINCIPAL FINDINGS: We use multi-colour immunoprecipitation measured by flow cytometry (IP-FCM) for studying signal transduction events to unrivalled precision. In this method, antibody-coupled latex beads capture the protein of interest from cellular lysates and are then stained with differently fluorescent-labelled antibodies to quantify the amount of the immunoprecipitated protein, of an interaction partner and of phosphorylation sites. The fluorescence signals are measured by FCM. Combining this procedure with beads containing defined amounts of a fluorophore allows retrieving absolute numbers of stained proteins, and not only relative values. Using IP-FCM we derived multidimensional data on the membrane-proximal T-cell antigen receptor (TCR-CD3) signalling network, including the recruitment of the kinase ZAP70 to the TCR-CD3 and subsequent ZAP70 activation by phosphorylation in the murine T-cell hybridoma and primary murine T cells. Counter-intuitively, these data showed that cell stimulation by pervanadate led to a transient decrease of the phospho-ZAP70/ZAP70 ratio at the TCR. A mechanistic mathematical model of the underlying processes demonstrated that an initial massive recruitment of non-phosphorylated ZAP70 was responsible for this behaviour. Further, the model predicted a temporal order of multisite phosphorylation of ZAP70 (with Y319 phosphorylation preceding phosphorylation at Y493) that we subsequently verified experimentally. CONCLUSIONS/SIGNIFICANCE: The quantitative data sets generated by IP-FCM are one order of magnitude more precise than Western blot data. This accuracy allowed us to gain unequalled insight into the dynamics of the TCR-CD3-ZAP70 signalling network
Direct Visualization of Dislocation Dynamics in Grain Boundary Scars
Mesoscale objects with unusual structural features may serve as the analogues
of atoms in the design of larger-scale materials with novel optical, electronic
or mechanical behaviour. In this paper we investigate the structural features
and the equilibrium dynamics of micron-scale spherical crystals formed by
polystyrene particles adsorbed on the surface of a spherical water droplet. The
ground state of sufficiently large crystals possesses finite-length grain
boundaries (scars). We determine the elastic response of the crystal by
measuring single-particle diffusion and quantify the fluctuations of individual
dislocations about their equilibrium positions within a scar determining the
dislocation spring constants. We observe rapid dislocation glide with
fluctuations over the barriers separating one local Peierls minimum from the
next and rather weak binding of dislocations to their associated scars. The
long-distance (renormalised) dislocation diffusion glide constant is extracted
directly from the experimental data and is found to be moderately faster than
single particle diffusion. We are also able to determine the parameters of the
Peierls potential induced by the underlying crystalline lattice.Comment: 11 pages, 4 figures, pdf forma
Human CD34+/CD90+ ASCs Are Capable of Growing as Sphere Clusters, Producing High Levels of VEGF and Forming Capillaries
Background: Human adult adipose tissue is an abundant source of mesenchymal stem cells (MSCs). Moreover, it is an easily
accessible site producing a considerable amount of stem cells.
Methodology/Principal Findings: In this study, we have selected and characterized stem cells within the stromal vascular
fraction (SVF) of human adult adipose tissue with the aim of understanding their differentiation capabilities and
performance. We have found, within the SVF, different cell populations expressing MSC markers – including CD34, CD90,
CD29, CD44, CD105, and CD117 – and endothelial-progenitor-cell markers – including CD34, CD90, CD44, and CD54.
Interestingly, CD34+/CD90+ cells formed sphere clusters, when placed in non-adherent growth conditions. Moreover, they
showed a high proliferative capability, a telomerase activity that was significantly higher than that found in differentiated
cells, and contained a fraction of cells displaying the phenotype of a side population. When cultured in adipogenic medium,
CD34+/CD90+ quickly differentiated into adipocytes. In addition, they differentiated into endothelial cells (CD31+/VEGF+/Flk-
1+) and, when placed in methylcellulose, were capable of forming capillary-like structures producing a high level of VEGF, as
substantiated with ELISA tests.
Conclusions/Significance: Our results demonstrate, for the first time, that CD34+/CD90+ cells of human adipose tissue are
capable of forming sphere clusters, when grown in free-floating conditions, and differentiate in endothelial cells that form
capillary-like structures in methylcellulose. These cells might be suitable for tissue reconstruction in regenerative medicine,
especially when patients need treatments for vascular disease
Recycled gabbro signature in hotspot magmas unveiled by plume–ridge interactions
Lavas erupted within plate interiors above upwelling mantle
plumes have chemical signatures that are distinct from midocean
ridge lavas. When a plume interacts with a mid-ocean
ridge, the compositions of both their lavas changes, but there
is no consensus as to how this interaction occurs1–3. For the
past 15 Myr, the Pacific–Antarctic mid-ocean ridge has been
approaching the Foundation hotspot4 and erupted lavas have
formed seamounts. Here we analyse the noble gas isotope
and trace element signature of lava samples collected from
the seamounts. We find that both intraplate and on-axis
lavas have noble gas isotope signatures consistent with the
contribution from a primitive plume source. In contrast, nearaxis
lavas show no primitive noble gas isotope signatures, but
are enriched in strontium and lead, indicative of subducted
former oceanic lower crust melting within the plume source5–7.
We propose that, in a near-ridge setting, primitive, plumesourced
magmas formed deep in the plume are preferentially
channelled to and erupted at the ridge-axis. The remaining
residue continues to rise and melt, forming the near-axis
seamounts. With the deep melts removed, the geochemical
signature of subduction contained within the residue becomes
apparent. Lavas with strontium and lead enrichments are found
worldwide where plumes meet mid-ocean ridges6–8, suggesting
that subducted lower crust is an important but previously
unrecognised plume component
FishNet: an online database of zebrafish anatomy
Background: Over the last two decades, zebrafish have been established as a genetically versatile model system for investigating many different aspects of vertebrate developmental biology. With the credentials of zebrafish as a developmental model now well recognized, the emerging new opportunity is the wider application of zebrafish biology to aspects of human disease modelling. This rapidly increasing use of zebrafish as a model for human disease has necessarily generated interest in the anatomy of later developmental phases such as the larval, juvenile, and adult stages, during which many of the key aspects of organ morphogenesis and maturation take place. Anatomical resources and references that encompass these stages are non-existent in zebrafish and there is therefore an urgent need to understand how different organ systems and anatomical structures develop throughout the life of the fish. Results: To overcome this deficit we have utilized the technique of optical projection tomography to produce three-dimensional (3D) models of larval fish. In order to view and display these models we have created FishNet http://www.fishnet.org.au, an interactive reference of zebrafish anatomy spanning the range of zebrafish development from 24 h until adulthood. Conclusion: FishNet contains more than 36 000 images of larval zebrafish, with more than 1 500 of these being annotated. The 3D models can be manipulated on screen or virtually sectioned. This resource represents the first complete embryo to adult atlas for any species in 3D
Image Texture Characterization Using the Discrete Orthonormal S-Transform
We present a new efficient approach for characterizing image texture based on a recently published discrete, orthonormal space-frequency transform known as the DOST. We develop a frequency-domain implementation of the DOST in two dimensions for the case of dyadic frequency sampling. Then, we describe a rapid and efficient approach to obtain local spatial frequency information for an image and show that this information can be used to characterize the horizontal and vertical frequency patterns in synthetic images. Finally, we demonstrate that DOST components can be combined to obtain a rotationally invariant set of texture features that can accurately classify a series of texture patterns. The DOST provides the computational efficiency and multi-scale information of wavelet transforms, while providing texture features in terms of Fourier frequencies. It outperforms leading wavelet-based texture analysis methods
A search for the decay modes B+/- to h+/- tau l
We present a search for the lepton flavor violating decay modes B+/- to h+/-
tau l (h= K,pi; l= e,mu) using the BaBar data sample, which corresponds to 472
million BBbar pairs. The search uses events where one B meson is fully
reconstructed in one of several hadronic final states. Using the momenta of the
reconstructed B, h, and l candidates, we are able to fully determine the tau
four-momentum. The resulting tau candidate mass is our main discriminant
against combinatorial background. We see no evidence for B+/- to h+/- tau l
decays and set a 90% confidence level upper limit on each branching fraction at
the level of a few times 10^-5.Comment: 15 pages, 7 figures, submitted to Phys. Rev.
Observation and study of baryonic B decays: B -> D(*) p pbar, D(*) p pbar pi, and D(*) p pbar pi pi
We present a study of ten B-meson decays to a D(*), a proton-antiproton pair,
and a system of up to two pions using BaBar's data set of 455x10^6 BBbar pairs.
Four of the modes (B0bar -> D0 p anti-p, B0bar -> D*0 p anti-p, B0bar -> D+ p
anti-p pi-, B0bar -> D*+ p anti-p pi-) are studied with improved statistics
compared to previous measurements; six of the modes (B- -> D0 p anti-p pi-, B-
-> D*0 p anti-p pi-, B0bar -> D0 p anti-p pi- pi+, B0bar -> D*0 p anti-p pi-
pi+, B- -> D+ p anti-p pi- pi-, B- -> D*+ p anti-p pi- pi-) are first
observations. The branching fractions for 3- and 5-body decays are suppressed
compared to 4-body decays. Kinematic distributions for 3-body decays show
non-overlapping threshold enhancements in m(p anti-p) and m(D(*)0 p) in the
Dalitz plots. For 4-body decays, m(p pi-) mass projections show a narrow peak
with mass and full width of (1497.4 +- 3.0 +- 0.9) MeV/c2, and (47 +- 12 +- 4)
MeV/c2, respectively, where the first (second) errors are statistical
(systematic). For 5-body decays, mass projections are similar to phase space
expectations. All results are preliminary.Comment: 28 pages, 90 postscript figures, submitted to LP0
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