Interpretable CNN-Multilevel Attention Transformer for Rapid Recognition of Pneumonia from Chest X-Ray Images

Chest imaging plays an essential role in diagnosing and predicting patients with COVID-19 with evidence of worsening respiratory status. Many deep learning-based approaches for pneumonia recognition have been developed to enable computer-aided diagnosis. However, the long training and inference time makes them inflexible, and the lack of interpretability reduces their credibility in clinical medical practice. This paper aims to develop a pneumonia recognition framework with interpretability, which can understand the complex relationship between lung features and related diseases in chest X-ray (CXR) images to provide high-speed analytics support for medical practice. To reduce the computational complexity to accelerate the recognition process, a novel multi-level self-attention mechanism within Transformer has been proposed to accelerate convergence and emphasize the task-related feature regions. Moreover, a practical CXR image data augmentation has been adopted to address the scarcity of medical image data problems to boost the model's performance. The effectiveness of the proposed method has been demonstrated on the classic COVID-19 recognition task using the widespread pneumonia CXR image dataset. In addition, abundant ablation experiments validate the effectiveness and necessity of all of the components of the proposed method.Comment: Accepted by the IEEE Journal of Biomedical and Health Informatic, doi: 10.1109/JBHI.2023.324794

Cognitive impairment in diffuse axonal injury patients with favorable outcome

Background and purposeTraumatic brain injury (TBI), especially the severe TBI are often followed by persistent cognitive sequalae, including decision-making difficulties, reduced neural processing speed and memory deficits. Diffuse axonal injury (DAI) is classified as one of the severe types of TBI. Part of DAI patients are marginalized from social life due to cognitive impairment, even if they are rated as favorable outcome. The purpose of this study was to elucidate the specific type and severity of cognitive impairment in DAI patients with favorable outcome.MethodsThe neurocognition of 46 DAI patients with favorable outcome was evaluated by the Chinese version of the Montreal Cognitive Assessment Basic (MoCA-BC), and the differences in the domains of cognitive impairment caused by different grades of DAI were analyzed after data conversion of scores of nine cognitive domains of MoCA-BC by Pearson correlation analysis.ResultsAmong the 46 DAI patients with favorable outcome, eight had normal cognitive function (MoCA-BC ≥ 26), and 38 had cognitive impairment (MoCA-BC < 26). The MoCA-BC scores were positively correlated with pupillary light reflex (r = 0.361, p = 0.014), admission Glasgow Coma Scale (GCS) (r = 0.402, p = 0.006), and years of education (r = 0.581, p < 0.001). Return of consciousness (r = −0.753, p < 0.001), Marshall CT (r = −0.328, p = 0.026), age (r = −0.654, p < 0.001), and DAI grade (r = −0.403, p = 0.006) were found to be negatively correlated with the MoCA-BC scores. In patients with DAI grade 1, the actually deducted scores (Ads) of memory (r = 0.838, p < 0.001), abstraction (r = 0.843, p < 0.001), and calculation (r = 0.782, p < 0.001) were most related to the Ads of MoCA-BC. The Ads of nine cognitive domains and MoCA-BC were all proved to be correlated, among patients with DAI grade 2. However, In the DAI grade 3 patients, the highest correlation with the Ads of MoCA-BC were the Ads of memory (r = 0.904, p < 0.001), calculation (r = 0.799, p = 0.006), orientation (r = 0.801, p = 0.005), and executive function (r = 0.869, p = 0.001).ConclusionDAI patients with favorable outcome may still be plagued by cognitive impairment, and different grades of DAI cause different domains of cognitive impairment

Transcriptomic Analysis Comparing Tumor-Associated Neutrophils with Granulocytic Myeloid-Derived Suppressor Cells and Normal Neutrophils

The role of myeloid cells in supporting cancer growth is well established. Most work has focused on myeloid-derived suppressor cells (MDSC) that accumulate in tumor-bearing animals, but tumor-associated neutrophils (TAN) are also known to be capable of augmenting tumor growth. However, little is known about their evolution, phenotype, and relationship to naïve neutrophils (NN) and to the granulocytic fraction of MDSC (G-MDSC)

Comparative analysis of the transcriptome across distant species

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters

Nitrogen Fertilization Weakly Influences the Anatomy and Chemical Composition of Rice Leaves

In this paper, four rice genotypes showing different leaf mass per area (LMA) are used to explore the effects of nitrogen (N) supplies on rice leaf anatomy and leaf chemical composition as well as their impacts on leaf gas exchange parameters. The results showed that the mass-based and area-based leaf N contents as well as the net photosynthetic rate (A) under high N supply (HN) were all higher than those under a low N supply (LN). However, N supplies had no effect on stomatal conductance, mesophyll conductance, and photosynthetic N use efficiency. Moreover, N supplies had no significant effect on LMA and cell wall thickness. Leaf thickness and leaf density responses to N supplies were inconsistent in different genotypes. Except for the soluble sugar in Huanghuazhan and non-structural carbohydrates (NSC) in Sab Ini, N supplies showed no significant effects on mass-based leaf chemical components (pectic substance, hemicellulose, cellulose, lignin, total cell wall, soluble sugar, starch and NSC) content. The area-based leaf chemical components content showed significant differences between HN and LN in some occasions. The soluble sugar, NSC, hemicellulose, and lignin contents of Sab Ini under HN were higher than those under LN. The pectic substance, hemicellulose, and lignin contents of Huanghuazhan under LN were higher than those under HN. The cellulose and cell wall contents of Yongyou 12 under LN were higher than those under HN. Therefore, we conclude that nitrogen fertilization weakly influences the anatomy and chemical composition of rice leaves with a few exceptions

Maintenance Role of a Glutathionyl-Hydroquinone Lyase (PcpF) in Pentachlorophenol Degradation by Sphingobium chlorophenolicum ATCC 39723

Pentachlorophenol (PCP) is a toxic pollutant. Its biodegradation has been extensively studied in Sphingobium chlorophenolicum ATCC 39723. All enzymes required to convert PCP to a common metabolic intermediate before entering the tricarboxylic acid cycle have been characterized. One of the enzymes is tetrachloro- p -hydroquinone (TeCH) reductive dehalogenase (PcpC), which is a glutathione (GSH) S -transferase (GST). PcpC catalyzes the GSH-dependent conversion of TeCH to trichloro- p -hydroquinone (TriCH) and then to dichloro- p -hydroquinone (DiCH) in the PCP degradation pathway. PcpC is susceptible to oxidative damage, and the damaged PcpC produces glutathionyl (GS) conjugates, GS-TriCH and GS-DiCH, which cannot be further metabolized by PcpC. The fate and effect of GS-hydroquinone conjugates were unknown. A putative GST gene ( pcpF ) is located next to pcpC on the bacterial chromosome. The pcpF gene was cloned, and the recombinant PcpF was purified. The purified PcpF was able to convert GS-TriCH and GS-DiCH conjugates to TriCH and DiCH, respectively. The GS-hydroquinone lyase reactions catalyzed by PcpF are rather unusual for a GST. The disruption of pcpF in S. chlorophenolicum made the mutant lose the GS-hydroquinone lyase activities in the cell extracts. The mutant became more sensitive to PCP toxicity and had a significantly decreased PCP degradation rate, likely due to the accumulation of the GS-hydroquinone conjugates inside the cell. Thus, PcpF played a maintenance role in PCP degradation and converted the GS-hydroquinone conjugates back to the intermediates of the PCP degradation pathway

Nitrogen Fertilization Weakly Influences the Anatomy and Chemical Composition of Rice Leaves

In this paper, four rice genotypes showing different leaf mass per area (LMA) are used to explore the effects of nitrogen (N) supplies on rice leaf anatomy and leaf chemical composition as well as their impacts on leaf gas exchange parameters. The results showed that the mass-based and area-based leaf N contents as well as the net photosynthetic rate (A) under high N supply (HN) were all higher than those under a low N supply (LN). However, N supplies had no effect on stomatal conductance, mesophyll conductance, and photosynthetic N use efficiency. Moreover, N supplies had no significant effect on LMA and cell wall thickness. Leaf thickness and leaf density responses to N supplies were inconsistent in different genotypes. Except for the soluble sugar in Huanghuazhan and non-structural carbohydrates (NSC) in Sab Ini, N supplies showed no significant effects on mass-based leaf chemical components (pectic substance, hemicellulose, cellulose, lignin, total cell wall, soluble sugar, starch and NSC) content. The area-based leaf chemical components content showed significant differences between HN and LN in some occasions. The soluble sugar, NSC, hemicellulose, and lignin contents of Sab Ini under HN were higher than those under LN. The pectic substance, hemicellulose, and lignin contents of Huanghuazhan under LN were higher than those under HN. The cellulose and cell wall contents of Yongyou 12 under LN were higher than those under HN. Therefore, we conclude that nitrogen fertilization weakly influences the anatomy and chemical composition of rice leaves with a few exceptions

Columnar structure deposition regulation and surface modification of PS-PVD thermal barrier coatings

Plasma spray-physical vapor deposition(PS-PVD) technology which has many characteristics of the multi-structure regulation, provides the possibility for the preparation of thermal barrier coatings with high thermal insulation and long life. It is one of the key technology to realize the development of high performance aero-engine. The unique microstructure of PS-PVD columnar structure coatings has dual advantages of high thermal insulation and long thermal cycle life, and has broad application prospects in the field of thermal barrier coatings for aircraft engines. However, the process control of PS-PVD columnar structure coating is achieved on the basis of a large number of experiments, and there is a lack of relevant theoretical research. Moreover, the CaO-MgO-Al2O3-SiO2(CMAS) corrosion failure problem faced by the columnar structure coating with high porosity restricts the use of the coating. The influence of deposition unit phase states on the coating structure was described from the structural characteristics of the coating, and the vapor deposition mechanism of columnar coating was revealed. Based on the phase transition of coating material in the jet, the essence of process parameters regulation was clarified. In addition, the corrosion mechanism of CMAS and the corrosion resistance mechanism of Al-modified coating were investigated. Finally, the structure control and performance improvement of PS-PVD coating and the application of PS-PVD technology in environmental barrier coatings and functional films were prospected

Leaf Photosynthesis and Its Temperature Response Are Different between Growth Stages and N Supplies in Rice Plants

Leaf photosynthesis is highly correlated with CO2-diffusion capacities, which are determined by both leaf anatomical traits and environmental stimuli. In the present study, leaf photosynthetic rate (A), stomatal conductance (gs), mesophyll conductance (gm) and the related leaf anatomical traits were studied on rice plants at two growth stages and with two different N supplies, and the response of photosynthesis to temperature (T) was also studied. We found that gm was significantly higher at mid-tillering stage and at high N treatment. The larger gm was related to a larger chloroplast surface area facing intercellular air spaces and a thinner cell wall in comparison with booting stage and zero N treatment. At mid-tillering stage and at high N treatment, gm showed a stronger temperature response. The modelling of the gm-T relationships suggested that, in comparison with booting stage and zero N treatment, the stronger temperature response of gm was related to the higher activation energy of the membrane at mid-tillering stage and at high N treatment. The findings in the present study can enhance our knowledge on the physiological and environmental determinants of photosynthesis