Hyperspectral phase imaging based on denoising in complex-valued eigensubspace

A new denoising algorithm for hyperspectral complex domain data has been developed and studied. This algorithm is based on the complex domain block-matching 3D filter including the 3D Wiener filtering stage. The developed algorithm is applied and tuned to work in the singular value decomposition (SVD) eigenspace of reduced dimension. The accuracy and quantitative advantage of the new algorithm are demonstrated in simulation tests and in the processing of the experimental data. It is shown that the algorithm is effective and provides reliable results even for highly noisy data

Enhanced release of IgE-dependent early phase mediators from nasal polyp tissue

Background: The mast cell is a crucial effector cell in allergic rhinitis and other inflammatory diseases. During the acute allergic reaction preformed mediators such as histamine, but also de novo produced mediators such as leukotrienes (LTC4/D-4/E-4) and prostaglandins (PGD(2)) are released. Mast cells represent targets for therapeutic intervention, and thus a human ex-vivo model to stimulate mast cells taken from mucosal sites would be instrumental for drug intervention studies. We have aimed to activate mast cells within ex-vivo human nasal tissue by IgE/anti-IgE specific (epsilon chain specific) stimulations and in this respect to test the usability of nasal polyps versus inferior turbinates Methods: Biopsy samples were collected from patients with nasal polyps and inferior turbinates from patients who underwent sinus or septal surgery. Tissue fragments were primed with IgE 1 mu g/ml for 60 minutes and then stimulated for 30 minutes with tissue culture medium (negative control), anti-IgE 10 mu g/ml, anti-IgE 30 mu g/ml and ionomycin 10 mu M (positive control). Histamine, leukotrienes and PGD2 were measured in supernatants. To help provide an understanding of the extent of the response, the number of tryptase and Fc epsilon RI alpha positive cells was evaluated by means of immunohistochemistry and the Fc epsilon RI alpha-chain was measured by means of quantitative PCR in the nasal polyp and inferior turbinate tissues. Finally, the correlation between IgE concentrations in the nasal tissue and the release of mediators was analysed. Results: Stimulations with anti-IgE on IgE-primed nasal tissue fragments lead to a concentration-dependent release of histamine, leukotrienes and PGD(2). The release of these early phase mediators was significantly higher in nasal polyps compared to inferior turbinates, although tryptase, Fc epsilon RI alpha positive cells and Fc epsilon RI alpha-chain transcripts were equally present in both groups. No correlation was found between baseline concentrations of IgE, and the release of histamine, LTC4/LTD4/LTE4 and PGD2 after stimulation. Conclusion: This human nasal challenge model mimics the allergic early phase reaction. The release of histamine, cys-leukotrienes and PGD(2) was significantly higher in nasal polyps versus inferior turbinates, however, this observation could not be explained by differences in mast cell or Fc epsilon RI+ cell numbers

Lack of systematicity in research prioritisation processes - a scoping review of evidence syntheses

BACKGROUND: A systematically and transparently prepared research priority-setting process within a specific scientific area is essential in order to develop a comprehensive and progressive evidence-based approach that will have a substantial societal impact on the site of interest. On the basis of two consensus workshops, the authors suggest the following methods for all such processes: use of experts, stakeholder involvement, literature review, and ranking. OBJECTIVES: The identification, categorisation, and discussion of methods for preparing a research prioritisation process. METHODS: Eligibility criteria: Evidence synthesis includes original studies presenting a research prioritisation process and which listed the methods used to create a research prioritisation process. Only evidence syntheses related to health research were included. Data sources: We searched the following electronic databases, without limiting by date or language: MEDLINE Ovid, Embase Ovid, Epistemonikos, and CINAHL EBSCO. Charting methods: The methods used were mapped and broken down into different elements, and the use of the elements was determined. To support the mapping, (A) all of the elements were collapsed into unique categories, and (B) four essential categories were selected as crucial to a successful research prioritisation process. RESULTS: Twelve evidence syntheses were identified, including 416 original studies. The identification and categorisation of methods used resulted in 13 unique categories of methods used to prepare a research agenda. CONCLUSION: None of the identified categories was used in all of the original studies. Surprisingly, all four of the essential categories were used in only one of the 416 original studies identified. There is seemingly no international consensus on which methods to use when preparing a research prioritisation process. PROTOCOL REGISTRATION: The protocol was registered in Open Science Framework (https://osf.io/dygz8/). SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13643-022-02149-2

Functional genomics of mountain pine beetle (Dendroctonus ponderosae) midguts and fat bodies

<p>Abstract</p> <p>Background</p> <p>The mountain pine beetle (<it>Dendroctonus ponderosae</it>) is a significant coniferous forest pest in western North America. It relies on aggregation pheromones to colonize hosts. Its three major pheromone components, <it>trans</it>-verbenol, <it>exo</it>-brevicomin, and frontalin, are thought to arise via different metabolic pathways, but the enzymes involved have not been identified or characterized. We produced ESTs from male and female midguts and associated fat bodies and used custom oligonucleotide microarrays to study gene expression patterns and thereby made preliminary identification of pheromone-biosynthetic genes.</p> <p>Results</p> <p>Clones from two un-normalized cDNA libraries were directionally sequenced from the 5' end to yield 11,775 ESTs following sequence cleansing. The average read length was 550 nt. The ESTs clustered into 1,201 contigs and 2,833 singlets (4,034 tentative unique genes). The ESTs are broadly distributed among GO functional groups, suggesting they reflect a broad spectrum of the transcriptome. Among the most represented genes are representatives of sugar-digesting enzymes and members of an apparently Scolytid-specific gene family of unknown function. Custom NimbleGen 4-plex arrays representing the 4,034 tentative unique genes were queried with RNA from eleven different biological states representing larvae, pupae, and midguts and associated fat bodies of unfed or fed adults. Quantitative (Real-Time) RT-PCR (qRT-PCR) experiments confirmed that the microarray data accurately reflect expression levels in the different samples. Candidate genes encoding enzymes involved in terminal steps of biosynthetic pathways for <it>exo</it>-brevicomin and frontalin were tentatively identified.</p> <p>Conclusions</p> <p>These EST and microarray data are the first publicly-available functional genomics resources for this devastating forestry pest.</p