The importance of detailed epigenomic profiling of different cell types within organs.

The human body consists of hundreds of kinds of cells specified from a single genome overlaid with cell type-specific epigenetic information. Comprehensively profiling the body's distinct epigenetic landscapes will allow researchers to verify cell types used in regenerative medicine and to determine the epigenetic effects of disease, environmental exposures and genetic variation. Key marks/factors that should be investigated include regions of nucleosome-free DNA accessible to regulatory factors, histone marks defining active enhancers and promoters, DNA methylation levels, regulatory RNAs, and factors controlling the three-dimensional conformation of the genome. Here we use the lung to illustrate the importance of investigating an organ's purified cell epigenomes, and outline the challenges and promise of realizing a comprehensive catalog of primary cell epigenomes

Transcriptomic profiling of primary alveolar epithelial cell differentiation in human and rat

AbstractCell-type specific gene regulation is a key to gaining a full understanding of how the distinct phenotypes of differentiated cells are achieved and maintained. Here we examined how changes in transcriptional activation during alveolar epithelial cell (AEC) differentiation determine phenotype. We performed transcriptomic profiling using in vitro differentiation of human and rat primary AEC. This model recapitulates in vitro an in vivo process in which AEC transition from alveolar type 2 (AT2) cells to alveolar type 1 (AT1) cells during normal maintenance and regeneration following lung injury. Here we describe in detail the quality control, preprocessing, and normalization of microarray data presented within the associated study (Marconett et al., 2013). We also include R code for reproducibility of the referenced data and easily accessible processed data tables

Towards Discriminative Representation with Meta-learning for Colonoscopic Polyp Re-Identification

Colonoscopic Polyp Re-Identification aims to match the same polyp from a large gallery with images from different views taken using different cameras and plays an important role in the prevention and treatment of colorectal cancer in computer-aided diagnosis. However, traditional methods for object ReID directly adopting CNN models trained on the ImageNet dataset usually produce unsatisfactory retrieval performance on colonoscopic datasets due to the large domain gap. Additionally, these methods neglect to explore the potential of self-discrepancy among intra-class relations in the colonoscopic polyp dataset, which remains an open research problem in the medical community. To solve this dilemma, we propose a simple but effective training method named Colo-ReID, which can help our model to learn more general and discriminative knowledge based on the meta-learning strategy in scenarios with fewer samples. Based on this, a dynamic Meta-Learning Regulation mechanism called MLR is introduced to further boost the performance of polyp re-identification. To the best of our knowledge, this is the first attempt to leverage the meta-learning paradigm instead of traditional machine learning to effectively train deep models in the task of colonoscopic polyp re-identification. Empirical results show that our method significantly outperforms current state-of-the-art methods by a clear margin.Comment: arXiv admin note: text overlap with arXiv:2307.1062

Förster Resonance Energy Transfer (FRET) Correlates of Altered Subunit Stoichiometry in Cys-Loop Receptors, Exemplified by Nicotinic α4β2

We provide a theory for employing Förster resonance energy transfer (FRET) measurements to determine altered heteropentameric ion channel stoichiometries in intracellular compartments of living cells. We simulate FRET within nicotinic receptors (nAChRs) whose α4 and β2 subunits contain acceptor and donor fluorescent protein moieties, respectively, within the cytoplasmic loops. We predict FRET and normalized FRET (NFRET) for the two predominant stoichiometries, (α4)3(β2)2 vs. (α4)2(β2)3. Studying the ratio between FRET or NFRET for the two stoichiometries, minimizes distortions due to various photophysical uncertainties. Within a range of assumptions concerning the distance between fluorophores, deviations from plane pentameric geometry, and other asymmetries, the predicted FRET and NFRET for (α4)3(β2)2 exceeds that of (α4)2(β2)3. The simulations account for published data on transfected Neuro2a cells in which α4β2 stoichiometries were manipulated by varying fluorescent subunit cDNA ratios: NFRET decreased monotonically from (α4)3(β2)2 stoichiometry to mostly (α4)2(β2)3. The simulations also account for previous macroscopic and single-channel observations that pharmacological chaperoning by nicotine and cytisine increase the (α4)2(β2)3 and (α4)3(β2)2 populations, respectively. We also analyze sources of variability. NFRET-based monitoring of changes in subunit stoichiometry can contribute usefully to studies on Cys-loop receptors

QCD Multipole Expansion and Hadronic Transitions in Heavy Quarkonium Systems

We review the developments of QCD multipole expansion and its applications to hadronic transitions and some radiative decays of heavy quarkonia. Theoretical predictions are compsred with updated experimental results.Comment: 23 pages, 7 figures. Some typos corrected, and 3 references adde

Tranßcripting: playful subversion with Chinese characters

This article discusses a relatively under-explored phenomenon that we call Tranßcripting - writing, designing and digitally generating new scripts with elements from different scriptal and semiotic systems. The data are drawn from examples of such scripts created by multilingual Chinese users in everyday online social interaction. We analyse the dynamic processes of how such scripts are created that transcend language boundaries as well as transforming the subjectivities of the writer and the reader. We are particularly interested in the playful subversiveness of such practices, and discuss it against the background of uni-scriptal language ideology in China. We are also interested in the methodological challenges of researching such practices, including the challenge of drawing distinctions between the ‘ordinary’ and the ‘unordinary’. We analyse the data from a translanguaging perspective