Recent Progress in Transformer-based Medical Image Analysis

The transformer is primarily used in the field of natural language processing. Recently, it has been adopted and shows promise in the computer vision (CV) field. Medical image analysis (MIA), as a critical branch of CV, also greatly benefits from this state-of-the-art technique. In this review, we first recap the core component of the transformer, the attention mechanism, and the detailed structures of the transformer. After that, we depict the recent progress of the transformer in the field of MIA. We organize the applications in a sequence of different tasks, including classification, segmentation, captioning, registration, detection, enhancement, localization, and synthesis. The mainstream classification and segmentation tasks are further divided into eleven medical image modalities. A large number of experiments studied in this review illustrate that the transformer-based method outperforms existing methods through comparisons with multiple evaluation metrics. Finally, we discuss the open challenges and future opportunities in this field. This task-modality review with the latest contents, detailed information, and comprehensive comparison may greatly benefit the broad MIA community.Comment: Computers in Biology and Medicine Accepte

Modeling seismic wave propagation in the Loess Plateau using a viscoacoustic wave equation with explicitly expressed quality factor

The thick Quaternary loess on the Loess Plateau of China produces strong seismic attenuation, resulting in weak reflections from subsurface exploration targets. Accurately simulating seismic wavefield in the Loess Plateau is important for guiding subsequent data processing and interpretation. We present a 2D/3D wavefield simulation method for the Loess Plateau using a viscoacoustic wave equation with explicitly expressed quality factor. To take into account the effect of irregular surface, we utilize a vertically deformed grid to represent the topography, and solve the viscoacoustic wave equation in a regular computational domain that conforms to topographic surface. Grid deformation introduces the partial derivatives such as ∂vx/∂z and ∂vy/∂z in the wave equation, which is difficult to be accurately computed using traditional staggered-grid finite-difference method. To mitigate this issue, a finite-difference scheme based on a fully staggered-grid is adopted to solve the viscoacoustic wave equation. Numerical experiments for a simple layer model and 2D/3D realistic Loess Plateau models demonstrate the feasibility and adaptability of the proposed method. The 3D modeling results show comparable amplitude and waveform characteristics to the field data acquired from the Chinese Loess Plateau, suggesting a good performance of the proposed modeling method

Global Effects of Catecholamines on Actinobacillus pleuropneumoniae Gene Expression

Bacteria can use mammalian hormones to modulate pathogenic processes that play essential roles in disease development. Actinobacillus pleuropneumoniae is an important porcine respiratory pathogen causing great economic losses in the pig industry globally. Stress is known to contribute to the outcome of A. pleuropneumoniae infection. To test whether A. pleuropneumoniae could respond to stress hormone catecholamines, gene expression profiles after epinephrine (Epi) and norepinephrine (NE) treatment were compared with those from untreated bacteria. The microarray results showed that 158 and 105 genes were differentially expressed in the presence of Epi and NE, respectively. These genes were assigned to various functional categories including many virulence factors. Only 18 genes were regulated by both hormones. These genes included apxIA (the ApxI toxin structural gene), pgaB (involved in biofilm formation), APL_0443 (an autotransporter adhesin) and genes encoding potential hormone receptors such as tyrP2, the ygiY-ygiX (qseC-qseB) operon and narQ-narP (involved in nitrate metabolism). Further investigations demonstrated that cytotoxic activity was enhanced by Epi but repressed by NE in accordance with apxIA gene expression changes. Biofilm formation was not affected by either of the two hormones despite pgaB expression being affected. Adhesion to host cells was induced by NE but not by Epi, suggesting that the hormones affect other putative adhesins in addition to APL_0443. This study revealed that A. pleuropneumoniae gene expression, including those encoding virulence factors, was altered in response to both catecholamines. The differential regulation of A. pleuropneumoniae gene expression by the two hormones suggests that this pathogen may have multiple responsive systems for the two catecholamines

Conversion of solid organic wastes into oil via Boettcherisca peregrine (Diptera: Sarcophagidae) larvae and optimization of parameters for biodiesel production.

The feedstocks for biodiesel production are predominantly from edible oils and the high cost of the feedstocks prevents its large scale application. In this study, we evaluated the oil extracted from Boettcherisca peregrine larvae (BPL) grown on solid organic wastes for biodiesel production. The oil contents detected in the BPL converted from swine manure, fermentation residue and the degreased food waste, were 21.7%, 19.5% and 31.1%, respectively. The acid value of the oil is 19.02 mg KOH/g requiring a two-step transesterification process. The optimized process of 12∶1 methanol/oil (mol/mol) with 1.5% H(2)SO(4) reacted at 70°C for 120 min resulted in a 90.8% conversion rate of free fatty acid (FFA) by esterification, and a 92.3% conversion rate of triglycerides into esters by alkaline transesterification. Properties of the BPL oil-based biodiesel are within the specifications of ASTM D6751, suggesting that the solid organic waste-grown BPL could be a feasible non-food feedstock for biodiesel production

Development of CAR T Cell Therapy in Children—A Comprehensive Overview

CAR T cell therapy has revolutionized immunotherapy in the last decade with the successful establishment of chimeric antigen receptor (CAR)-expressing cellular therapies as an alternative treatment in relapsed and refractory CD19-positive leukemias and lymphomas. There are fundamental reasons why CAR T cell therapy has been approved by the Food and Drug administration and the European Medicines Agency for pediatric and young adult patients first. Commonly, novel therapies are developed for adult patients and then adapted for pediatric use, due to regulatory and commercial reasons. Both strategic and biological factors have supported the success of CAR T cell therapy in children. Since there is an urgent need for more potent and specific therapies in childhood malignancies, efforts should also include the development of CAR therapeutics and expand applicability by introducing new technologies. Basic aspects, the evolution and the drawbacks of childhood CAR T cell therapy are discussed as along with the latest clinically relevant information

Development of CAR T Cell Therapy in Children—A Comprehensive Overview

CAR T cell therapy has revolutionized immunotherapy in the last decade with the successful establishment of chimeric antigen receptor (CAR)-expressing cellular therapies as an alternative treatment in relapsed and refractory CD19-positive leukemias and lymphomas. There are fundamental reasons why CAR T cell therapy has been approved by the Food and Drug administration and the European Medicines Agency for pediatric and young adult patients first. Commonly, novel therapies are developed for adult patients and then adapted for pediatric use, due to regulatory and commercial reasons. Both strategic and biological factors have supported the success of CAR T cell therapy in children. Since there is an urgent need for more potent and specific therapies in childhood malignancies, efforts should also include the development of CAR therapeutics and expand applicability by introducing new technologies. Basic aspects, the evolution and the drawbacks of childhood CAR T cell therapy are discussed as along with the latest clinically relevant information

Optimization of four esterification parameters.

<p>A) methanol to oil molar ratio (1.0% catalyst, 65°C, 60 min, 200 rpm); B) catalyst amount (12∶1 methanol to oil molar ratio, 65°C, 60 min, 200 rpm); C) temperature (1.5% catalyst, 12∶1methanol to oil molar ratio, 60 min, 200 rpm); D) reaction time (1.5% catalyst, 12∶1methanol to oil molar ratio, 70°C, 200 rpm). Each experiment was repeated for three times.</p

Crude oil content in BPL biomass grown on solid organic wastes.

<p>Crude oil content in BPL biomass grown on solid organic wastes.</p

Properties of <i>B. peregrine</i> larvae oil and three known oils.

<p>n/a stands for not reported;</p>a<p>data from literature <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045940#pone.0045940-Zheng1" target="_blank">[10]</a>;</p>b<p>data from literature <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045940#pone.0045940-Li3" target="_blank">[11]</a>;</p>c<p>data from literature <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045940#pone.0045940-Demirbas1" target="_blank">[20]</a>.</p