Spatial clustering and common regulatory elements correlate with coordinated gene expression

Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can generate coordinated gene expression. In eukaryotic cells, transcriptional activity of a gene is affected by not only transcription factors but also the epigenetic modifications and three-dimensional chromosome structure of the gene. To examine how local gene environment and transcription factor regulation are coupled, we performed a combined analysis of time-course RNA-seq data of TGF-\b{eta} treated MCF10A cells and related epigenomic and Hi-C data. Using Dynamic Regulatory Events Miner (DREM), we clustered differentially expressed genes based on gene expression profiles and associated transcription factors. Genes in each class have similar temporal gene expression patterns and share common transcription factors. Next, we defined a set of linear and radial distribution functions, as used in statistical physics, to measure the distributions of genes within a class both spatially and linearly along the genomic sequence. Remarkably, genes within the same class despite sometimes being separated by tens of million bases (Mb) along genomic sequence show a significantly higher tendency to be spatially close despite sometimes being separated by tens of Mb along the genomic sequence than those belonging to different classes do. Analyses extended to the process of mouse nervous system development arrived at similar conclusions. Future studies will be able to test whether this spatial organization of chromosomes contributes to concerted gene expression.Comment: 30 pages, 9 figures, accepted in PLoS Computational Biolog

Depositing boron on Cu(111): Borophene or boride?

Large-area single-crystal surface structures were successfully prepared on Cu(111) substrate with boron deposition, which is critical for prospective applications. However, the proposed borophene structures do not match the scanning tunneling microscopy (STM) results very well, while the proposed copper boride is at odds with the traditional knowledge that ordered copper-rich borides normally do not exist due to small difference in electronegativity and large difference in atomic size. To clarify the controversy and elucidate the formation mechanism of the unexpected copper boride, we conducted systematic STM, X-ray photoelectron spectroscopy and angle-resolved photoemission spectroscopy investigations, confirming the synthesis of two-dimensional copper boride rather than borophene on Cu(111) after boron deposition under ultrahigh vacuum. First-principles calculations with defective surface models further indicate that boron atoms tend to react with Cu atoms near terrace edges or defects, which in turn shapes the intermediate structures of copper boride and leads to the formation of stable Cu-B monolayer via large-scale surface reconstruction eventually.Comment: 15 pages, 4 figure

A novel Li(2)FeSiO(4)/C composite: Synthesis, characterization and high storage capacity

A Li(2)FeSiO(4)/C composite material has been prepared via a solution-polymerization approach. The composite is characterized by X-ray diffraction (XRD), X-ray absorption near edge structure (XANES), scanning electron microscope (SEM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and superconducting quantum interference device (SQUID). The electrochemical performance of the Li(2)FeSiO(4) is greatly enhanced and the initial discharge capacity is similar to 220 mA h g(-1), when it is cycled between 1.5-4.8 V. This indicates that more than one lithium ion can be extracted out of the Li(2)FeSiO(4) lattice. At high current densities, the Li(2)FeSiO(4)/C also exhibits excellent rate capability and cycling stability. This indicates that it is a very promising cathode material for next generation lithium-ion batteries.National Natural Science Foundation of China[20873115, 20473068, 29925310]; National Basic Research Program[2007CB209702, 2011CB905903

Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

Funder: European Society of Intensive Care Medicine; doi: http://dx.doi.org/10.13039/501100013347Funder: Flemish Society for Critical Care NursesAbstract: Purpose: Intensive care unit (ICU) patients are particularly susceptible to developing pressure injuries. Epidemiologic data is however unavailable. We aimed to provide an international picture of the extent of pressure injuries and factors associated with ICU-acquired pressure injuries in adult ICU patients. Methods: International 1-day point-prevalence study; follow-up for outcome assessment until hospital discharge (maximum 12 weeks). Factors associated with ICU-acquired pressure injury and hospital mortality were assessed by generalised linear mixed-effects regression analysis. Results: Data from 13,254 patients in 1117 ICUs (90 countries) revealed 6747 pressure injuries; 3997 (59.2%) were ICU-acquired. Overall prevalence was 26.6% (95% confidence interval [CI] 25.9–27.3). ICU-acquired prevalence was 16.2% (95% CI 15.6–16.8). Sacrum (37%) and heels (19.5%) were most affected. Factors independently associated with ICU-acquired pressure injuries were older age, male sex, being underweight, emergency surgery, higher Simplified Acute Physiology Score II, Braden score 3 days, comorbidities (chronic obstructive pulmonary disease, immunodeficiency), organ support (renal replacement, mechanical ventilation on ICU admission), and being in a low or lower-middle income-economy. Gradually increasing associations with mortality were identified for increasing severity of pressure injury: stage I (odds ratio [OR] 1.5; 95% CI 1.2–1.8), stage II (OR 1.6; 95% CI 1.4–1.9), and stage III or worse (OR 2.8; 95% CI 2.3–3.3). Conclusion: Pressure injuries are common in adult ICU patients. ICU-acquired pressure injuries are associated with mainly intrinsic factors and mortality. Optimal care standards, increased awareness, appropriate resource allocation, and further research into optimal prevention are pivotal to tackle this important patient safety threat

Correction to: Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

The original version of this article unfortunately contained a mistake