FreePSI: an alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome.

Alternative splicing plays an important role in many cellular processes of eukaryotic organisms. The exon-inclusion ratio, also known as percent spliced in, is often regarded as one of the most effective measures of alternative splicing events. The existing methods for estimating exon-inclusion ratios at the genome scale all require the existence of a reference transcriptome. In this paper, we propose an alignment-free method, FreePSI, to perform genome-wide estimation of exon-inclusion ratios from RNA-Seq data without relying on the guidance of a reference transcriptome. It uses a novel probabilistic generative model based on k-mer profiles to quantify the exon-inclusion ratios at the genome scale and an efficient expectation-maximization algorithm based on a divide-and-conquer strategy and ultrafast conjugate gradient projection descent method to solve the model. We compare FreePSI with the existing methods on simulated and real RNA-seq data in terms of both accuracy and efficiency and show that it is able to achieve very good performance even though a reference transcriptome is not provided. Our results suggest that FreePSI may have important applications in performing alternative splicing analysis for organisms that do not have quality reference transcriptomes. FreePSI is implemented in C++ and freely available to the public on GitHub

Genome-wide identification of long intergenic non-coding RNAs of responsive to powdery mildew stress in wheat (Triticum aestivum)

Wheat powdery mildew caused by Blumeria graminis f. sp. tritici is one of the most serious foliar diseases of wheat, causing grain yield and quality degradation by affecting plant photosynthesis. It is an effective method to improve the disease resistance of wheat plants by molecular breeding. With the continuous development of sequencing technology, long intergenic noncoding RNAs (lincRNAs) have been discovered in many eukaryotes and act as key regulators of many cellular processes. In this study, 12 sets of RNA-seq data from wheat leaves pre- and post-pathogen infection were analyzed and 2,266 candidate lincRNAs were identified. Consistent with previous findings, lincRNA has shorter length and fewer exons than mRNA. The results of differential expression analysis showed that 486 DE-lincRNAs were selected as lincRNAs that could respond to powdery mildew stress. Since lincRNAs may be functionally related to their adjacent target genes, the target genes of these lincRNAs were predicted, and the GO and KEGG functional annotations of the predicted target genes were performed. Integrating the functions of target genes and the biological processes in which they were involved uncovered 23 lincRNAs that may promote or inhibit the occurrence of wheat powdery mildew. Co-expression patterns of lincRNAs with their adjacent mRNAs showed that some lincRNAs showed significant correlation with the expression patterns of their potential target genes. These suggested an involvement of lincRNAs in pathogen stress response, which will provide a further understanding of the pathogenic mechanism of wheat powdery mildew

On the Measurements of Individual Particle Properties Via Compression and Crushing

An experimental study is presented to measure the elastic, yielding, and crushing properties of individual particles under compression using substrates made of aluminum alloy, stainless steel, and sapphire. Carefully selected, highly spherical individual Ottawa sand particles of 0.75-1.1 mm in nominal diameter were compressed between two smooth substrates, and the load-deformation curves were analyzed by Hertz elastic contact theory to derive their reduced modulus and Young\u27s modulus as well as yielding and crushing strengths, which vary significantly with the type of substrate materials. Further analysis of the yielding and plastic deformation at the particle-substrate contact shows that the yield strength or hardness of the substrate materials dominates the local contact behavior and hence affects the measured apparent yielding and crushing strengths. The two softer substrates (aluminum alloy and stainless steel) actually lead to underestimated apparent shear yield strengths of quartz particles by 60.4% and 54.2%, respectively, which are actually the yielding of substrates, while the true particle yielding occurs in the sapphire-particle contact. Moreover, the two softer substrates cause much overestimated crushing strengths of the quartz particles by 50.4% and 36.4%, respectively. Selection of inappropriate substrate materials and inappropriate interpretation of the particle-substrate contact can lead to significant errors in the measured yielding and crushing strengths. It is recommended that single particle compression testing uses substrates with yield strength greater than that of the tested particles and result interpretation also considers the elastic and yielding behaviors of the substrates. (C) 2021 Institute of Rock and Soil Mechanics, Chinese Academy of Sciences. Production and hosting by Elsevier B.V

Numerical study of acoustophoretic manipulation of particles in microfluidic channels

The microfluidic technology based on surface acoustic waves (SAW) has been developing rapidly, as it can precisely manipulate fluid flow and particle motion at microscales. We hereby present a numerical study of the transient motion of suspended particles in a microchannel. In conventional studies, only the microchannel’s bottom surface generates SAW and only the final positions of the particles are analyzed. In our study, the microchannel is sandwiched by two identical SAW transducers at both the bottom and top surfaces while the channel’s sidewalls are made of poly-dimethylsiloxane (PDMS). Based on the perturbation theory, the suspended particles are subject to two types of forces, namely the Acoustic Radiation Force (ARF) and the Stokes Drag Force (SDF), which correspond to the first-order acoustic field and the second-order streaming field, respectively. We use the Finite Element Method (FEM) to compute the fluid responses and particle trajectories. Our numerical model is shown to be accurate by verifying against previous experimental and numerical results. We have determined the threshold particle size that divides the SDF-dominated regime and the ARF-dominated regime. By examining the time scale of the particle movement, we provide guidelines on the device design and operation

Team Dynamics Theory: Nomological network among cohesion, team mental models, coordination, and collective efficacy

I put forth a theoretical framework, namely Team Dynamics Theory (TDT), to address the need for a parsimonious yet integrated, explanatory and systemic view of team dynamics. In TDT, I integrate team processes and outputs and explain their relationships within a systemic view of team dynamics. Specifically, I propose a generative nomological network linking cohesion, team mental models, coordination, collective efficacy, and team outcomes. From this nomological conceptualization, I illustrate how myriad alternative models can be derived to account for variance in different working teams, each comprised of unique members, and embedded in singular contexts. I outline TDT’s applied implications for team development, the enhancement of team functioning, and the profiling of team resilience. I conclude by discussing how TDT’s ontological and nomological propositions can be tested through various theoretical inquiries, methodological approaches, and intervention-based studies

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