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The EV-TRACK knowledgebase is developed to cope with the need for transparency and rigour to increase reproducibility and facilitate standardization of extracellular vesicle (EV) research. The knowledgebase includes a checklist for authors and editors intended to improve the transparency of methodological aspects of EV experiments, allows queries and meta-analysis of EV experiments and keeps track of the current state of the art. Widespread implementation by the EV research community is key to its success

Orthogonal rational functions and quadrature on an interval

AbstractRational functions with real poles and poles in the complex lower half-plane, orthogonal on the real line, are well known. Quadrature formulas similar to the Gauss formulas for orthogonal polynomials have been studied. We generalize to the case of arbitrary complex poles and study orthogonality on a finite interval. The zeros of the orthogonal rational functions are shown to satisfy a quadratic eigenvalue problem. In the case of real poles, these zeros are used as nodes in the quadrature formulas

Temperature dependent NIR emitting lanthanide-PMO/silica hybrid materials

Two materials - a mesoporous silica (MS) and a periodic mesoporous organosilica (PMO) functionalized with dipyridyl-pyridazine (dppz) units were grafted with near-infrared (NIR) emitting lanthanide (Nd3+, Er3+, Yb3+) complexes in an attempt to obtain hybrid NIR emitting materials. The parent materials: dppz-vSilica and dppz-ePMO were prepared by a hetero Diels-Alder reaction between 3,6-di(2-pyridyl)-1,2,4,5- tetrazine (dptz) and the double bonds of either ethenylene-bridged PMO (ePMO) or vinyl-silica (vSilica) and subsequent oxidation. The dppz-vSilica is reported here for the first time. The prepared lanthanide-PMO/silica hybrid materials were studied in depth for their luminescence properties at room temperature and chosen Nd3+ and Yb3+ samples also at low temperature (as low as 10 K). We show that both the dppz-vSilica and dppz-ePMO materials can be used as "platforms" for obtaining porous materials showing NIR luminescence. To obtain NIR emission these materials can be excited either in the UV or Vis region (into the pi -> pi* transitions of the ligands or directly into the f-f transitions of the Ln(3+) ions). More interestingly, when functionalized with Nd3+ or Yb3+ beta-diketonate complexes these materials showed interesting luminescence properties over a wide temperature range (10-360 K). The Yb3+ materials were investigated for their potential use as ratiometric temperature sensors

Near-infrared Fourier transform room-temperature photoluminescence of erbium complexes

A modified Fourier transform (FT) Raman bench spectrometer designed for the detection of weak light emission in the 800–1700 nm wavelength region has been used to demonstrate the advantages of FT spectroscopy for measuring near-infrared photoluminescence spectra of lanthanide complexes with a good resolution and very good sensitivity. This apparatus has been tested with an ultraviolet laser source (325 nm) on three standard erbium complexes. The 4I13/24I15/2 emission of tris-(acetylacetonato) (1,10 phenanthroline) erbium [Er(acac)3(phen)], tris-(4,4,4,-trifluoro-1-(2 thenoyl)-1,3-butenedione) (1,10 phenanthroline) erbium [Er(TTFA)3(phen)] and tris(8-hydroxyquinolinato) erbium [Erq3] has thus been recorded in solution and in the solid state and compared with literature. ©2003 American Institute of Physics

Joint mapping of genes and conditions via multidimensional unfolding analysis

<p>Abstract</p> <p>Background</p> <p>Microarray compendia profile the expression of genes in a number of experimental conditions. Such data compendia are useful not only to group genes and conditions based on their similarity in overall expression over profiles but also to gain information on more subtle relations between genes and conditions. Getting a clear visual overview of all these patterns in a single easy-to-grasp representation is a useful preliminary analysis step: We propose to use for this purpose an advanced exploratory method, called multidimensional unfolding.</p> <p>Results</p> <p>We present a novel algorithm for multidimensional unfolding that overcomes both general problems and problems that are specific for the analysis of gene expression data sets. Applying the algorithm to two publicly available microarray compendia illustrates its power as a tool for exploratory data analysis: The unfolding analysis of a first data set resulted in a two-dimensional representation which clearly reveals temporal regulation patterns for the genes and a meaningful structure for the time points, while the analysis of a second data set showed the algorithm's ability to go beyond a mere identification of those genes that discriminate between different patient or tissue types.</p> <p>Conclusion</p> <p>Multidimensional unfolding offers a useful tool for preliminary explorations of microarray data: By relying on an easy-to-grasp low-dimensional geometric framework, relations among genes, among conditions and between genes and conditions are simultaneously represented in an accessible way which may reveal interesting patterns in the data. An additional advantage of the method is that it can be applied to the raw data without necessitating the choice of suitable genewise transformations of the data.</p

Dye-sensitized Er3+-doped CaF2 nanoparticles for enhanced near-infrared emission at 1.5 μm

Lanthanide (Ln)-doped nanoparticles have shown potential for applications in various fields. However, the weak and narrow absorption bands of the Ln ions (Ln3+), hamper efficient optical pumping and severely limit the emission intensity. Dye sensitization is a promising way to boost the near-infrared (NIR) emission of Er3+, hence promoting possible application in optical amplification at 1.5 μm, a region that is much sought after for telecommunication technology. Herein, we introduce the fluorescein isothiocyanate (FITC) organic dye with large absorption cross section as energy donor of small-sized (∼3.6 nm) Er3+-doped CaF2 nanoparticles. FITC molecules on the surface of CaF2 work as antennas to efficiently absorb light, and provide the indirect sensitization of Er3+ boosting its emission. In this paper, we employ photoluminescence and transient absorption spectroscopy, as well as density functional theory calculations, to provide an in-depth investigation of the FITC → Er3+ energy transfer process. We show that an energy transfer efficiency of over 89% is achieved in CaF2:Er3+@FITC nanoparticles resulting in a 28 times enhancement of the Er3+ NIR emission with respect to bare CaF2:Er3+. Through the multidisciplinary approach used in our work, we are able to show that the reason for such high sensitization efficiency stems from the suitable size and geometry of the FITC dye with a localized transition dipole moment at a short distance from the surface of the nanoparticle

Performance of LED-Based Fluorescence Microscopy to Diagnose Tuberculosis in a Peripheral Health Centre in Nairobi.

Sputum microscopy is the only tuberculosis (TB) diagnostic available at peripheral levels of care in resource limited countries. Its sensitivity is low, particularly in high HIV prevalence settings. Fluorescence microscopy (FM) can improve performance of microscopy and with the new light emitting diode (LED) technologies could be appropriate for peripheral settings. The study aimed to compare the performance of LED-FM versus Ziehl-Neelsen (ZN) microscopy and to assess feasibility of LED-FM at a low level of care in a high HIV prevalence country

A flexible framework for sparse simultaneous component based data integration

<p>Abstract</p> <p>1 Background</p> <p>High throughput data are complex and methods that reveal structure underlying the data are most useful. Principal component analysis, frequently implemented as a singular value decomposition, is a popular technique in this respect. Nowadays often the challenge is to reveal structure in several sources of information (e.g., transcriptomics, proteomics) that are available for the same biological entities under study. Simultaneous component methods are most promising in this respect. However, the interpretation of the principal and simultaneous components is often daunting because contributions of each of the biomolecules (transcripts, proteins) have to be taken into account.</p> <p>2 Results</p> <p>We propose a sparse simultaneous component method that makes many of the parameters redundant by shrinking them to zero. It includes principal component analysis, sparse principal component analysis, and ordinary simultaneous component analysis as special cases. Several penalties can be tuned that account in different ways for the block structure present in the integrated data. This yields known sparse approaches as the lasso, the ridge penalty, the elastic net, the group lasso, sparse group lasso, and elitist lasso. In addition, the algorithmic results can be easily transposed to the context of regression. Metabolomics data obtained with two measurement platforms for the same set of <it>Escherichia coli </it>samples are used to illustrate the proposed methodology and the properties of different penalties with respect to sparseness across and within data blocks.</p> <p>3 Conclusion</p> <p>Sparse simultaneous component analysis is a useful method for data integration: First, simultaneous analyses of multiple blocks offer advantages over sequential and separate analyses and second, interpretation of the results is highly facilitated by their sparseness. The approach offered is flexible and allows to take the block structure in different ways into account. As such, structures can be found that are exclusively tied to one data platform (group lasso approach) as well as structures that involve all data platforms (Elitist lasso approach).</p> <p>4 Availability</p> <p>The additional file contains a MATLAB implementation of the sparse simultaneous component method.</p