Robust analysis of allele-specific copy number alterations from scRNA-seq data with XClone.

Somatic copy number alterations (CNAs) are major mutations that contribute to the development and progression of various cancers. Despite a few computational methods proposed to detect CNAs from single-cell transcriptomic data, the technical sparsity of such data makes it challenging to identify allele-specific CNAs, particularly in complex clonal structures. In this study, we present a statistical method, XClone, that strengthens the signals of read depth and allelic imbalance by effective smoothing on cell neighborhood and gene coordinate graphs to detect haplotype-aware CNAs from scRNA-seq data. By applying XClone to multiple datasets with challenging compositions, we demonstrated its ability to robustly detect different types of allele-specific CNAs and potentially indicate whole genome duplication, therefore enabling the discovery of corresponding subclones and the dissection of their phenotypic impacts.

PhosMap: An ensemble bioinformatic platform to empower interactive analysis of quantitative phosphoproteomics.

BACKGROUND: Liquid chromatography-mass spectrometry (LC-MS)-based quantitative phosphoproteomics has been widely used to detect thousands of protein phosphorylation modifications simultaneously from the biological specimens. However, the complicated procedures for analyzing phosphoproteomics data has become a bottleneck to widening its application. METHODS: Here, we develop PhosMap, a versatile and scalable tool to accomplish phosphoproteomics data analysis. A standardized phosphorylation data format was created for data analyses, from data preprocessing to downstream bioinformatic analyses such as dimension reduction, differential phosphorylation analysis, kinase activity, survival analysis, and so on. For better usability, we distribute PhosMap as a Docker image for easy local deployment upon any of Windows, Linux, and Mac system. RESULTS: The source code is deposited at https://github.com/BADD-XMU/PhosMap. A free PhosMap webserver (https://huggingface.co/spaces/Bio-Add/PhosMap), with easy-to-follow fashion of dashboards, is curated for interactive data analysis. CONCLUSIONS: PhosMap fills the technical gap of large-scale phosphorylation research by empowering researchers to process their own phosphoproteomics data expediently and efficiently, and facilitates better data interpretation.

Nanopatterning of beaded poly(lactic acid) nanofibers for highly electroactive, breathable, UV-shielding and antibacterial protective membranes.

Despite great potential in fabrication of biodegradable protective membranes by electrospinning of poly(lactic acid) (PLA) nanofibers, it is still thwarted by smooth surfaces and poor electroactivity that challenge the promotion of electret properties and long-term air filtration performance. Here, a microwave-assisted synthetic method was used to customize dielectric TiO2 nanocrystals of ultrasmall and uniform dimensions (∼30 nm), which were homogeneously embedded at beaded PLA nanofibers (PLA@TiO2, diameter of around 280 nm) by the combined "electrospinning-electrospray" approach. With small amounts of TiO2 (2, 4 and 6 wt%), the nanopatterned PLA@TiO2 nanofibrous membranes (NFMs) were characterized by largely increased dielectric constants (nearly 1.9), surface potential (up to 1.63 kV) and triboelectric properties (output voltage of 12.2 V). Arising from the improved electroactivity and self-charging mechanisms, the nanopatterned PLA@TiO2 NFMs exhibited remarkable PM0.3 filtration properties (97.9 %, 254.6 Pa) even at the highest airflow rate of 85 L/min, surpassing those of pure PLA membranes (86.2 %, 483.7 Pa). This was moreover accompanied by inhibition rates of 100 % against both E. coli and S. aureus, as well as excellent UV-blocking properties (UPF as high as 3.8, TUVA of 50.9 % and TUVB of 20.1 %). The breathable and electroactive nanopatterned PLA NFMs permit promising applications in multifunctional protective membranes toward excellent UV shielding and high-efficiency removal of both PMs and pathogens.

Influence of environmental parameters on workers' dust inhalation in underground mines.

Much dust is generated in underground coal mining processes, posing threats to workers' health and safety production. Dust enters the human body mainly through inhalation, primarily determined by the dust concentration around workers. In this study, the airflow field and dust distribution in the tunnel are simulated with FLUENT software. The breathing zone for a worker was defined to clarify the extent of external dust distribution influencing dust inhalation. The effects of human respiration, dust production rates, air supply velocities, and workers' positions on dust concentration in the breathing zone were investigated. The results show that there is upward airflow around the worker standing in the center of the air circulation. Human breath barely influences the airflow distribution and respirable dust concentrations in the breathing zone. Reducing the dust production rate in the tunnel can decrease the respirable dust concentration in the breathing zone by almost the same proportion. While increasing the air supply velocity by 50% would reduce only 20% of dust in the breathing zone. The dust concentrations vary along the roadway, in which the low concentration zone is located in the middle, more than 1.0 m away from the dust-producing surface and the wind surface. The research contributes to reducing workers' dust exposure with suggestions regarding ventilation optimization and working position selection.

Effects of various wet environments on the characteristics of the dust cake deposited on the surface of filter media.

The effect of wet environments on the dust cake of filter media was studied. The collapse angles of dust particles and the collapse angles between dust particles and filter media increase with increasing dust moisture content, relative humidity, and spray rate. The smallest growth rate of collapse was observed under dust moisture content, while the largest growth rate occurred under the spray rate condition. The collapse angles between dust particles and filter media of coated filter media were smaller compared to those of mechanical filter media under different wet environments. The dust cake drag coefficients of both filter media initially increase and then decrease with an increase in the dust moisture content, decrease with the acceleration of the relative humidity, and show a pattern of first decreasing and then increasing as the spray rate increases. The dust loading capacity of both filter media follows an opposite trend to that of the dust cake drag coefficients.

Activating C-H Bonds by Tuning Fe Sites and an Interfacial Effect for Enhanced Methanol Oxidation.

The interaction mechanism between the reacting species and the active site of α-Fe2 O3 -based photoanodes in photoelectrochemical methanol conversion reaction is still ambiguous. Herein, a simple two-step strategy is demonstrated to fabricate a porous α-Fe2 O3 /CoFe2 O4 heterojunction for the methanol conversion reaction. The influence of the electronic structure of active site and interfacial effect on the reaction are investigated by constructing two different FeO6 octahedral configurations and heterogeneous structures. The optimal sample ZnFeCo-2 affords high photocurrent density of 1.17 mA cm-2 at 0.5 V vs Ag/AgCl, which is 3.2 times than that of ZnFe (0.37 mA cm-2 ). Meanwhile, the ZnFeCo-2 also exhibits 97.8% Faraday efficiency of CH3 OH to HCHO, and long-term stability over 40 h. Furthermore, density functional theory calculations reveal that the heterostructured α-Fe2 O3 /CoFe2 O4 with favorable electron transfer effectively lowers methanol adsorption, C-H bond activation, and HCHO desorption energy relative to the pristine α-Fe2 O3 , resulting in excellent methanol conversion efficiency.

MQuad enables clonal substructure discovery using single cell mitochondrial variants.

Mitochondrial mutations are increasingly recognised as informative endogenous genetic markers that can be used to reconstruct cellular clonal structure using single-cell RNA or DNA sequencing data. However, identifying informative mtDNA variants in noisy and sparse single-cell sequencing data is still challenging with few computation methods available. Here we present an open source computational tool MQuad that accurately calls clonally informative mtDNA variants in a population of single cells, and an analysis suite for complete clonality inference, based on single cell RNA, DNA or ATAC sequencing data. Through a variety of simulated and experimental single cell sequencing data, we showed that MQuad can identify mitochondrial variants with both high sensitivity and specificity, outperforming existing methods by a large extent. Furthermore, we demonstrate its wide applicability in different single cell sequencing protocols, particularly in complementing single-nucleotide and copy-number variations to extract finer clonal resolution.

Investigation on condensable particulate matter emission characteristics in wet ammonia-based desulfurization system.

Particulate matter emissions from ammonia-based wet flue gas desulfurization (Ammonia-WFGD) systems are composed of a filterable particulate matter and a condensable particulate matter (CPM) portion. However, the CPM part has been ignored for a long time, which results in an underestimation of the aerosol problems caused by Ammonia-WFGD systems. In our research, the characteristics of the CPM that emits from an Ammonia-WFGD system are investigated experimentally for the first time, with the US Environmental Protection Agency Method 202 employed as the primary measurement. The influences of some essential desulfurizing parameters are evaluated based on the experimental data. The results show that CPM contributes about 68.8% to the total particulate matter emission. CPM consists mainly of ammonium sulfates/sulfites, with the organic part accounting for less than 4%. CPM is mostly in the submicron fraction, about 71.1% of which originates from the NH3-H2O-SO2 reactions. The appropriate adjustments for the parameters of the flue gas and the desulfurizing solution can inhibit CPM formation to different extents. This indicates that the parameter optimizations are promising in solving CPM emission problems in Ammonia-WFGD systems, in which the pH adjustment alone can abate CPM emission by around 49%. The opposite variations of the parameters need attention because they can cause tremendous CPM emission increase.

Crosstalk of intracellular post-translational modifications in cancer.

Post-translational modifications (PTMs) have been reported to play pivotal roles in numerous cellular biochemical and physiological processes. Multiple PTMs can influence the actions of each other positively or negatively, termed as PTM crosstalk or PTM code. During recent years, development of identification strategies for PTMs co-occurrence has revealed abundant information of interplay between PTMs. Increasing evidence demonstrates that deregulation of PTMs crosstalk is involved in the genesis and development of various diseases. Insight into the complexity of PTMs crosstalk will help us better understand etiology and provide novel targets for drug therapy. In the present review, we will discuss the important functional roles of PTMs crosstalk in proteins associated with cancer diseases.

Systematic characterization and prediction of post-translational modification cross-talk between proteins.

MOTIVATION: Protein post-translational modifications (PTMs) regulate a wide range of cellular protein functions. Many PTM sites from the same (intra) or different (inter) proteins often cooperate with each other to perform a function, which is defined as PTM cross-talk. PTM cross-talk within proteins attracted great attentions in the past a few years. However, the inter-protein PTM cross-talk is largely under studied due to its large protein pair space and lack of a gold standard dataset, even though the PTM interplay between proteins is a key element in cell signaling and regulatory networks. RESULTS: In this study, 199 inter-protein PTM cross-talk pairs in 82 pairs of human proteins were collected from literature, which to our knowledge is the first effort in compiling such dataset. By comparing with background PTM pairs from the same protein pairs, we found that inter-protein cross-talk PTM pairs have higher sequence co-evolution at both PTM residue and motif levels. Also, we found that cross-talk PTMs have higher co-modification across multiple species and 88 human tissues or conditions. Furthermore, we showed that these features are predictive for PTM cross-talk between proteins, and applied a random forest model to integrate these features with achieving an area under the receiver operating characteristic curve of 0.81 in 10-fold cross-validation, prevailing over using any single feature alone. Therefore, this method would be a valuable tool to identify inter-protein PTM cross-talk at proteome-wide scale. AVAILABILITY AND IMPLEMENTATION: A web server for prioritization of both intra- and inter-protein PTM cross-talk candidates is at http://bioinfo.bjmu.edu.cn/ptm-x/. Python code for local computer is also freely available at https://github.com/huangyh09/PTM-X. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Removal characteristics of sulfuric acid aerosols from coal-fired power plants.

With increasing attention on sulfuric acid emission, investigations on the removal characteristics of sulfuric acid aerosols by the limestone gypsum wet flue gas desulfurization (WFGD) system and the wet electrostatic precipitator (WESP) were carried out in two coal-fired power plants, and the effects of the WFGD scrubber type and the flue gas characteristics were discussed. The results showed that it was necessary to install the WESP device after desulfurization, as the WFGD system was inefficient to remove sulfuric acid aerosols from the flue gas. The removal efficiency of sulfuric acid aerosols in the WFGD system with double scrubbers ranged from 50% to 65%, which was higher than that with a single scrubber, ranging from 30% to 40%. Furthermore, the removal efficiency of WESP on the sulfuric acid aerosols was from 47.9% to 52.4%. With increased concentrations of SO3 and particles in the flue gas, the removal efficiencies of the WFGD and the WESP on the sulfuric acid aerosols were increased. IMPLICATIONS: Investigations on removal of sulfuric acid aerosols by the WFGD and the WESP in the power plants were aimed at the control of sulfuric acid emission. The results showed that the improvement of the WFGD system was beneficial for the reduction of sulfuric acid emission, while the WESP system was essential to control the final sulfuric acid aerosol concentration.

Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana.

BACKGROUND: Messenger RNA polyadenylation is an essential step for the maturation of most eukaryotic mRNAs. Accurate determination of poly(A) sites helps define the 3'-ends of genes, which is important for genome annotation and gene function research. Genomic studies have revealed the presence of poly(A) sites in intergenic regions, which may be attributed to 3'-UTR extensions and novel transcript units. However, there is no systematically evaluation of intergenic poly(A) sites in plants. RESULTS: Approximately 16,000 intergenic poly(A) site clusters (IPAC) in Arabidopsis thaliana were discovered and evaluated at the whole genome level. Based on the distributions of distance from IPACs to nearby sense and antisense genes, these IPACs were classified into three categories. About 70 % of them were from previously unannotated 3'-UTR extensions to known genes, which would extend 6985 transcripts of TAIR10 genome annotation beyond their 3'-ends, with a mean extension of 134 nucleotides. 1317 IPACs were originated from novel intergenic transcripts, 37 of which were likely to be associated with protein coding transcripts. 2957 IPACs corresponded to antisense transcripts for genes on the reverse strand, which might affect 2265 protein coding genes and 39 non-protein-coding genes, including long non-coding RNA genes. The rest of IPACs could be originated from transcriptional read-through or gene mis-annotations. CONCLUSIONS: The identified IPACs corresponding to novel transcripts, 3'-UTR extensions, and antisense transcription should be incorporated into current Arabidopsis genome annotation. Comprehensive characterization of IPACs from this study provides insights of alternative polyadenylation and antisense transcription in plants.