unbiased Dotaz Zobrazit nápovědu
Advanced methods
2nd ed. xvii, 277 s. : il.
- MeSH
- mikroskopie MeSH
- Konspekt
- Patologie. Klinická medicína
- NLK Obory
- chemie, klinická chemie
246 s.
- Konspekt
- Biochemie. Molekulární biologie. Biofyzika
- NLK Obory
- chemie, klinická chemie
- biologie
- biochemie
[1st ed.] x, 214 s. : il.
- MeSH
- mikroskopie MeSH
- Konspekt
- Patologie. Klinická medicína
- NLK Obory
- chemie, klinická chemie
Background: Many previous studies on mining prescription sequences are based only on frequency information, such as the number of prescriptions and the total number of patients issued the prescription. However, in cases where a very small number of doctors issue a prescription representative of a certain medication pattern to many patients many times, the prescribing intention of this very small number of doctors has a great influence on pattern extraction, which introduces bias into the final extracted frequent prescription sequence pattern. Objectives: We attempt to extract frequent prescription sequences from more diverse perspectives by considering factors other than frequency information to ensure highly reliable medication patterns. Methods: We propose the concept of unbiased frequent use by doctors as a factor in addition to frequency information based on the hypothesis that a prescription used by many doctors unbiasedly is a highly reliable prescription. We propose a medication pattern mining method that considers unbiased frequent use by doctors. We conducted an evaluation experiment using indicators based on clinical laboratory test results as a comparative evaluation of the existing method, which relied only on frequency, and included consideration of unbiased frequent use by doctors by the proposed method. Results: The weighted average value of the top k for two different evaluation methods is obtained. Conclusions: The study suggested that our medication pattern mining method considering unbiased frequent use by doctors is useful in certain situations such as when the clinical laboratory test value is outside of the normal value range.
Chloroplast number per cell is a frequently examined quantitative anatomical parameter, often estimated by counting chloroplast profiles in two-dimensional (2D) sections of mesophyll cells. However, a mesophyll cell is a three-dimensional (3D) structure and this has to be taken into account when quantifying its internal structure. We compared 2D and 3D approaches to chloroplast counting from different points of view: (i) in practical measurements of mesophyll cells of Norway spruce needles, (ii) in a 3D model of a mesophyll cell with chloroplasts, and (iii) using a theoretical analysis. We applied, for the first time, the stereological method of an optical disector based on counting chloroplasts in stacks of spruce needle optical cross-sections acquired by confocal laser-scanning microscopy. This estimate was compared with counting chloroplast profiles in 2D sections from the same stacks of sections. Comparing practical measurements of mesophyll cells, calculations performed in a 3D model of a cell with chloroplasts as well as a theoretical analysis showed that the 2D approach yielded biased results, while the underestimation could be up to 10-fold. We proved that the frequently used method for counting chloroplasts in a mesophyll cell by counting their profiles in 2D sections did not give correct results. We concluded that the present disector method can be efficiently used for unbiased estimation of chloroplast number per mesophyll cell. This should be the method of choice, especially in coniferous needles and leaves with mesophyll cells with lignified cell walls where maceration methods are difficult or impossible to use.
High-throughput sequencing has the power to reveal the nature of adaptive immunity as represented by the full complexity of T-cell receptor (TCR) and antibody (IG) repertoires, but is at present severely compromised by the quantitative bias, bottlenecks, and accumulated errors that inevitably occur in the course of library preparation and sequencing. Here we report an optimized protocol for the unbiased preparation of TCR and IG cDNA libraries for high-throughput sequencing, starting from thousands or millions of live cells in an investigated sample. Critical points to control are revealed, along with tips that allow researchers to minimize quantitative bias, accumulated errors, and cross-sample contamination at each stage, and to enhance the subsequent bioinformatic analysis. The protocol is simple, reliable, and can be performed in 1-2 days.
- Publikační typ
- časopisecké články MeSH
Stereological methods, using the principle of point counting and unbiased counting frames, for the estimation of muscle area, total fibre area, number of muscle fibres and mean fibre area are described in detail. Their practical application is demonstrated on cross-sections of the rat soleus muscles. It is shown that the efficiency of these methods is high and their results are comparable with those achieved by the conventional manual and image analysis methods. The main advantages of two-dimensional stereological methods in muscle morphometry are pointed out: measurements are made directly on specimens under the microscope and in the simplest implementation do not require sophisticated and expensive technical equipment. Furthermore, unbiased results are obtained, no segmentation and edge effect problems arise and the quantity of work invested in stereological estimation is reasonable. Based upon the study of the efficiency of used stereological methods, a suitable test system for muscle morphometry is proposed.
- MeSH
- histologické techniky MeSH
- kosterní svalová vlákna cytologie enzymologie MeSH
- kosterní svaly cytologie enzymologie MeSH
- krysa rodu rattus MeSH
- myosiny analýza metabolismus MeSH
- zkreslení výsledků (epidemiologie) MeSH
- zvířata MeSH
- Check Tag
- krysa rodu rattus MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
Recognition of single-stranded RNA (ssRNA) by RNA recognition motif (RRM) domains is an important class of protein-RNA interactions. Many such complexes were characterized using nuclear magnetic resonance (NMR) and/or X-ray crystallography techniques, revealing ensemble-averaged pictures of the bound states. However, it is becoming widely accepted that better understanding of protein-RNA interactions would be obtained from ensemble descriptions. Indeed, earlier molecular dynamics simulations of bound states indicated visible dynamics at the RNA-RRM interfaces. Here, we report the first atomistic simulation study of spontaneous binding of short RNA sequences to RRM domains of HuR and SRSF1 proteins. Using a millisecond-scale aggregate ensemble of unbiased simulations, we were able to observe a few dozen binding events. HuR RRM3 utilizes a pre-binding state to navigate the RNA sequence to its partially disordered bound state and then to dynamically scan its different binding registers. SRSF1 RRM2 binding is more straightforward but still multiple-pathway. The present study necessitated development of a goal-specific force field modification, scaling down the intramolecular van der Waals interactions of the RNA which also improves description of the RNA-RRM bound state. Our study opens up a new avenue for large-scale atomistic investigations of binding landscapes of protein-RNA complexes, and future perspectives of such research are discussed.
APMIS ; Suppl.079
34 s.
- MeSH
- nádory prsu MeSH
- Konspekt
- Gynekologie. Porodnictví
- NLK Obory
- gynekologie a porodnictví
- onkologie
Metastatic colorectal cancer (mCRC) is characterized by its extensive disease heterogeneity, suggesting that individualized analysis could be vital to improving patient outcomes. As a minimally invasive approach, the liquid biopsy has the potential to longitudinally monitor heterogeneous analytes. Current platforms primarily utilize enrichment-based approaches for epithelial-derived circulating tumor cells (CTC), but this subtype is infrequent in the peripheral blood (PB) of mCRC patients, leading to the liquid biopsy's relative disuse in this cancer type. In this study, we evaluated 18 PB samples from 10 mCRC patients using the unbiased high-definition single-cell assay (HDSCA). We first employed a rare-event (Landscape) immunofluorescence (IF) protocol, which captured a heterogenous CTC and oncosome population, the likes of which was not observed across 50 normal donor (ND) samples. Subsequent analysis was conducted using a colorectal-targeted IF protocol to assess the frequency of CDX2-expressing CTCs and oncosomes. A multi-assay clustering analysis isolated morphologically distinct subtypes across the two IF stains, demonstrating the value of applying an unbiased single-cell approach to multiple assays in tandem. Rare-event enumerations at a single timepoint and the variation of these events over time correlated with progression-free survival. This study supports the clinical utility of an unbiased approach to interrogating the liquid biopsy in mCRC, representing the heterogeneity within the CTC classification and warranting the further molecular characterization of the rare-event analytes with clinical promise.
- Publikační typ
- časopisecké články MeSH
