PubMed · 10625345
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B Lambolez, J Rossier. 2000. Quantitative RT-PCR.. https://doi.org/10.1038/71936
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MOTIVATION: 10x Genomics VisiumHD enables spatial transcriptomics at 2 µm × 2 µm resolution but exhibits slide-specific, non-periodic striping artifacts due to lane-width variability. These multiplicative row/column effects distort bin total counts and can bias downstream analyses. The state-of-the-art destriping approach is the normalization procedure used as a preprocessing step in bin2cell; it applies sequential high-quantile row- then column-wise normalization, which is asymmetric and can introduce edge effects/macro-stripes and distortions of large-scale total-count structure. RESULTS: We propose a statistical destriping approach that leverages nuclei segmentation from the co-registered H&E image. Assuming transcript abundance is constant within each nucleus, we model bin counts with a negative binomial distribution whose mean is a product of a nucleus-specific concentration and row- and column-specific stripe-factors reflecting lane-width variation. We fit all parameters in a generalized linear modeling framework with cross-validated regularization on stripe-factors and iterative dispersion estimation, and use the fitted parameters to correct the observed counts into a destriped image. On synthetic data with known ground truth, our method improves stripe-factor estimation accuracy and reduces error in corrected counts relative to bin2cell and bin2cell-derived baselines. Across four public VisiumHD slides, it consistently lowers striping intensity while substantially better preserving biological signal present in the large-scale global count structure and avoiding the artifacts introduced by other methods. AVAILABILITY AND IMPLEMENTATION: All source code and links to publicly available data used for this study are available at https://github.com/paolamalsot/destriping-GLM.
The chemical changes and artifact formation in daidai (Citrus aurantium L. var. Cyathifera Y. Tanaka) cold-pressed peel oil upon storage at 20, 5, and -21 degrees C for 3, 6, and 12 months were investigated using capillary gas chromatography (GC) and GC-MS. Major changes occurred in the oil stored at 20 and 5 degrees C. No changes were found at -21 degrees C. Monoterpene hydrocarbons decreased from 98.0 to 66.4% upon 12 months at 20 degrees C, while sesquiterpene hydrocarbons and alcohols increased from 0.1 to 2.4% and from 0.3 to 7.9%, respectively. Notable decreases of germacrene D, myrcene, linalyl acetate, and limonene occurred. Prominent increases of cis-carveol, trans-beta-farnesene, trans-p-2,8-menthadien-1-ol, linalool, and beta-caryophyllene were found. Thirty-four artifact compounds constituting 17.0% of the total volatile compounds were formed upon 12 months at 20 degrees C. The artifacts consisted of 13 alcohols (6.0%), five carbonyl compounds (5.3%), seven esters (4.9%), three epoxides (0.4%), four hydrocarbons (0.3%), and two unidentified. The prominent artifact compounds were (+)-carvone, trans,trans-farnesyl acetate, sabinene hydrate, 1-octen-3-ol, cis,cis-farnesyl acetate, and dihydrocarveol acetate. The results could be applied for monitoring and control of the flavor quality of daidai essential oil and related products.
Glycerol has been shown to cross the plasma membrane of Saccharomyces cerevisiae through (1) a H(+)/symport detected in cells grown on non-fermentable carbon sources, (2) the constitutively expressed Fps1p channel and (3) by passive diffusion. The Fps1p channel has been named a facilitator for mediating glycerol low affinity transport of the facilitated diffusion type. We present experimental evidence that this kinetic is an artefact created by glycerol kinase activity. Instead, the channel is shown to mediate the major part of glycerol's passive diffusion. This is not incompatible with Fps1p's major role in vivo, which has been previously shown to be the control of glycerol export under osmotic stress or in reaction to turgor changes. We also verified that FPS1 overexpression caused an increase in H(+)/symport V(max). Furthermore, yfl054c and fps1 mutants were equally affected by exogenously added ethanol, being the correspondent passive diffusion stimulated. For the first time, to our knowledge, a phenotype attributed to the functioning of YFL054c gene is presented. Glycerol passive diffusion is thus apparently channel-mediated. This is discussed according to glycerol's chemical properties, which contradict the widely spread concept of glycerol's liposoluble nature. The discussion considers the multiple roles that the intracellular levels of glycerol and its pathway regulation might play as a central key to metabolism control.