Efficient Hybrid Transformer: Learning Global-local Context for Urban Scene Segmentation

Semantic segmentation of fine-resolution urban scene images plays a vital role in extensive practical applications, such as land cover mapping, urban change detection, environmental protection and economic assessment. Driven by rapid developments in deep learning technologies, the convolutional neural network (CNN) has dominated the semantic segmentation task for many years. Convolutional neural networks adopt hierarchical feature representation, demonstrating strong local information extraction. However, the local property of the convolution layer limits the network from capturing global context that is crucial for precise segmentation. Recently, Transformer comprise a hot topic in the computer vision domain. Transformer demonstrates the great capability of global information modelling, boosting many vision tasks, such as image classification, object detection and especially semantic segmentation. In this paper, we propose an efficient hybrid Transformer (EHT) for real-time urban scene segmentation. The EHT adopts a hybrid structure with and CNN-based encoder and a transformer-based decoder, learning global-local context with lower computation. Extensive experiments demonstrate that our EHT has faster inference speed with competitive accuracy compared with state-of-the-art lightweight models. Specifically, the proposed EHT achieves a 66.9% mIoU on the UAVid test set and outperforms other benchmark networks significantly. The code will be available soon

Scale-aware neural network for semantic segmentation of multi-resolution remote sensing images

Assigning geospatial objects with specific categories at the pixel level is a fundamental task in remote sensing image analysis. Along with the rapid development of sensor technologies, remotely sensed images can be captured at multiple spatial resolutions (MSR) with information content manifested at different scales. Extracting information from these MSR images represents huge opportunities for enhanced feature representation and characterisation. However, MSR images suffer from two critical issues: (1) increased scale variation of geo-objects and (2) loss of detailed information at coarse spatial resolutions. To bridge these gaps, in this paper, we propose a novel scale-aware neural network (SaNet) for the semantic segmentation of MSR remotely sensed imagery. SaNet deploys a densely connected feature network (DCFFM) module to capture high-quality multi-scale context, such that the scale variation is handled properly and the quality of segmentation is increased for both large and small objects. A spatial feature recalibration (SFRM) module was further incorporated into the network to learn intact semantic content with enhanced spatial relationships, where the negative effects of information loss are removed. The combination of DCFFM and SFRM allows SaNet to learn scale-aware feature representation, which outperforms the existing multi-scale feature representation. Extensive experiments on three semantic segmentation datasets demonstrated the effectiveness of the proposed SaNet in cross-resolution segmentation

The lightest organic radical cation for charge storage in redox flow batteries

In advanced electrical grids of the future, electrochemically rechargeable fluids of high energy density will capture the power generated from intermittent sources like solar and wind. To meet this outstanding technological demand there is a need to understand the fundamental limits and interplay of electrochemical potential, stability, and solubility in low-weight redox-active molecules. By generating a combinatorial set of 1,4-dimethoxybenzene derivatives with different arrangements of substituents, we discovered a minimalistic structure that combines exceptional long-term stability in its oxidized form and a record-breaking intrinsic capacity of 161 mAh/g. The nonaqueous redox flow battery has been demonstrated that uses this molecule as a catholyte material and operated stably for 100 charge/discharge cycles. The observed stability trends are rationalized by mechanistic considerations of the reaction pathways.United States. Dept. of Energy. Office of Basic Energy Sciences. Chemical Sciences, Geosciences, & Biosciences Division (Contract DE-AC02-06CH11357

Annulated Dialkoxybenzenes as Catholyte Materials for Non‐aqueous Redox Flow Batteries: Achieving High Chemical Stability through Bicyclic Substitution

1,4‐Dimethoxybenzene derivatives are materials of choice for use as catholytes in non‐aqueous redox flow batteries, as they exhibit high open‐circuit potentials and excellent electrochemical reversibility. However, chemical stability of these materials in their oxidized form needs to be improved. Disubstitution in the arene ring is used to suppress parasitic reactions of their radical cations, but this does not fully prevent ring‐addition reactions. By incorporating bicyclic substitutions and ether chains into the dialkoxybenzenes, a novel catholyte molecule, 9,10‐bis(2‐methoxyethoxy)‐1,2,3,4,5,6,7,8‐octahydro‐1,4:5,8‐dimethanenoanthracene (BODMA), is obtained and exhibits greater solubility and superior chemical stability in the charged state. A hybrid flow cell containing BODMA is operated for 150 charge–discharge cycles with a minimal loss of capacity.A novel bicyclical substituted dialkoxy‐benzene molecule, 9,10‐bis(2‐methoxy‐ethoxy)‐1,2,3,4,5,6,7,8‐octahydro‐1,4:5,8‐dimethanenoanthracene (BODMA), is developed for use as catholyte materials in non‐aqueous redox flow batteries with greater solubility (in their neutral state) and improved chemical stability (in their charged state). A hybrid flow cell using BODMA demonstrates stable efficiencies and capacity over 150 cycles. The molecular design approach of BODMA can be inspirational for future development of redox active molecules.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/139992/1/aenm201701272.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/139992/2/aenm201701272-sup-0001-S1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/139992/3/aenm201701272_am.pd

Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients

Circulating tumor cells (CTCs) enter peripheral blood from primary tumors and seed metastases. The genome sequencing of CTCs could offer noninvasive prognosis or even diagnosis, but has been hampered by low single-cell genome coverage of scarce CTCs. Here, we report the use of the recently developed multiple annealing and looping-based amplification cycles for whole-genome amplification of single CTCs from lung cancer patients. We observed characteristic cancer-associated single-nucleotide variations and insertions/deletions in exomes of CTCs. These mutations provided information needed for individualized therapy, such as drug resistance and phenotypic transition, but were heterogeneous from cell to cell. In contrast, every CTC from an individual patient, regardless of the cancer subtypes, exhibited reproducible copy number variation (CNV) patterns, similar to those of the metastatic tumor of the same patient. Interestingly, different patients with the same lung cancer adenocarcinoma (ADC) shared similar CNV patterns in their CTCs. Even more interestingly, patients of small-cell lung cancer have CNV patterns distinctly different from those of ADC patients. Our finding suggests that CNVs at certain genomic loci are selected for the metastasis of cancer. The reproducibility of cancer-specific CNVs offers potential for CTC-based cancer diagnostics.Chemistry and Chemical Biolog

Identification of alternative splicing associated with clinical features: from pan-cancers to genitourinary tumors

BackgroundAlternative splicing events (ASEs) are vital causes of tumor heterogeneity in genitourinary tumors and many other cancers. However, the clinicopathological relevance of ASEs in cancers has not yet been comprehensively characterized.MethodsBy analyzing splicing data from the TCGA SpliceSeq database and phenotype data for all TCGA samples from the UCSC Xena database, we identified differential clinical feature-related ASEs in 33 tumors. CIBERSORT immune cell infiltration data from the TIMER2.0 database were used for differential clinical feature-related immune cell infiltration analysis. Gene function enrichment analysis was used to analyze the gene function of ASEs related to different clinical features in tumors. To reveal the regulatory mechanisms of ASEs, we integrated race-related ASEs and splicing quantitative trait loci (sQTLs) data in kidney renal clear cell carcinoma (KIRC) to comprehensively assess the impact of SNPs on ASEs. In addition, we predicted regulatory RNA binding proteins in bladder urothelial carcinoma (BLCA) based on the enrichment of motifs around alternative exons for ASEs.ResultsAlternative splicing differences were systematically analyzed between different groups of 58 clinical features in 33 cancers, and 30 clinical features in 24 cancer types were identified to be associated with more than 50 ASEs individually. The types of immune cell infiltration were found to be significantly different between subgroups of primary diagnosis and disease type. After integrating ASEs with sQTLs data, we found that 63 (58.9%) of the race-related ASEs were significantly SNP-correlated ASEs in KIRC. Gene function enrichment analyses showed that metastasis-related ASEs in KIRC mainly enriched Rho GTPase signaling pathways. Among those ASEs associated with metastasis, alternative splicing of GIT2 and TUBB3 might play key roles in tumor metastasis in KIRC patients. Finally, we identified several RNA binding proteins such as PCBP2, SNRNP70, and HuR, which might contribute to splicing differences between different groups of neoplasm grade in BLCA.ConclusionWe demonstrated the significant clinical relevance of ASEs in multiple cancer types. Furthermore, we identified and validated alternative splicing of TUBB3 and RNA binding proteins such as PCBP2 as critical regulators in the progression of urogenital cancers

A Survey of Chinese Pig Farms and Human Healthcare Isolates Reveals Separate Human and Animal Methicillin-Resistant Staphylococcus aureus Populations.

There has been increasing concern that the overuse of antibiotics in livestock farming is contributing to the burden of antimicrobial resistance in people. Farmed animals in Europe and North America, particularly pigs, provide a reservoir for livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA ST398 lineage) found in people. This study is designed to investigate the contribution of MRSA from Chinese pig farms to human infection. A collection of 483 MRSA are isolated from 55 farms and 4 hospitals in central China, a high pig farming density area. CC9 MRSA accounts for 97.2% of all farm isolates, but is not present in hospital isolates. ST398 isolates are found on farms and hospitals, but none of them formed part of the "LA-MRSA ST398 lineage" present in Europe and North America. The hospital ST398 MRSA isolate form a clade that is clearly separate from the farm ST398 isolates. Despite the presence of high levels of MRSA found on Chinese pig farms, the authors find no evidence of them spilling over to the human population. Nevertheless, the ST398 MRSA obtained from hospitals appear to be part of a widely distributed lineage in China. The new animal-adapted ST398 lineage that has emerged in China is of concern

Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homo-dimers, 3 homo-trimers, 13 hetero-dimers including 3 antibody-antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their 5 best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% for the targets compared to 8% two years earlier, a remarkable improvement resulting from the wide use of the AlphaFold2 and AlphaFold-Multimer software. Creative use was made of the deep learning inference engines affording the sampling of a much larger number of models and enriching the multiple sequence alignments with sequences from various sources. Wide use was also made of the AlphaFold confidence metrics to rank models, permitting top performing groups to exceed the results of the public AlphaFold-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem

A Limited Memory BFGS Method for Solving Large-Scale Symmetric Nonlinear Equations

A limited memory BFGS (L-BFGS) algorithm is presented for solving large-scale symmetric nonlinear equations, where a line search technique without derivative information is used. The global convergence of the proposed algorithm is established under some suitable conditions. Numerical results show that the given method is competitive to those of the normal BFGS methods