Evaluation of measures for assessing time-saving of automatic organ-at-risk segmentation in radiotherapy

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Automatic delineation software shows promising results in terms of time-saving.

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Standard geometry measures do not have a high correlation with delineation time.

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New evaluation measures were introduced: added path length (APL) and surface DSC.

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(Added) path length showed the highest correlation with time-recordings.

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This makes APL the most representative measure for clinical usefulness.

Background and purpose

In radiotherapy, automatic organ-at-risk segmentation algorithms allow faster delineation times, but clinically relevant contour evaluation remains challenging. Commonly used measures to assess automatic contours, such as volumetric Dice Similarity Coefficient (DSC) or Hausdorff distance, have shown to be good measures for geometric similarity, but do not always correlate with clinical applicability of the contours, or time needed to adjust them. This study aimed to evaluate the correlation of new and commonly used evaluation measures with time-saving during contouring.

Materials and methods

Twenty lung cancer patients were used to compare user-adjustments after atlas-based and deep-learning contouring with manual contouring. The absolute time needed (s) of adjusting the auto-contour compared to manual contouring was recorded, from this relative time-saving (%) was calculated. New evaluation measures (surface DSC and added path length, APL) and conventional evaluation measures (volumetric DSC and Hausdorff distance) were correlated with time-recordings and time-savings, quantified with the Pearson correlation coefficient, R.

Results

The highest correlation (R = 0.87) was found between APL and absolute adaption time. Lower correlations were found for APL with relative time-saving (R = −0.38), for surface DSC with absolute adaption time (R = −0.69) and relative time-saving (R = 0.57). Volumetric DSC and Hausdorff distance also showed lower correlation coefficients for absolute adaptation time (R = −0.32 and 0.64, respectively) and relative time-saving (R = 0.44 and −0.64, respectively).

Conclusion

Surface DSC and APL are better indicators for contour adaptation time and time-saving when using auto-segmentation and provide more clinically relevant and better quantitative measures for automatically-generated contour quality, compared to commonly-used geometry-based measures.

Plane wave imaging combined with eigenspace-based minimum variance beamforming using a ring array in ultrasound computed tomography

BACKGROUND

Ultrasound computed tomography (USCT) is usually realized with a ring array. It can provide better imaging performance and more tissue information by emitting and receiving the ultrasound signal in different directions simultaneously. However, USCT imaging is usually applied with the synthetic aperture (SA) emission method, which leads to a long scanning time with a large number of elements on the ring array. The echo image can provide the structural information, and has a higher resolution than maps of other parameters in USCT. Hence, we proposed plane wave (PW) imaging for ring array to acquire the echo wave and reduce the scanning time considerably.

RESULTS

In this paper, an emitting and receiving process was proposed to realize plane wave imaging with a ring array. With the proposed scanning method, the number of emission events can be reduced greatly. A beamforming method based on the eigenspace-based minimum variance (ESBMV) was also combined with the scanning method. With ESBMV beamformer, the resolution and contrast ratio of reconstruction result can be maintained or even improved under a fewer-emissions condition. We validated the method using both computer simulations with Field II and phantom experiments with a ring array of 512 elements. The Verasonics^® system was used to transmit and receive the ultrasound signal in the phantom experiments.

CONCLUSIONS

According to the results of the experiments, the imaging results will have a better contrast ratio with a higher emitting energy. Additionally, the scanning time with the proposed method can be only one-tenth of that with the SA emission method, while the echo imaging performance still remains at a similar level or even better.

A Simple, Time-Saving Dye Staining of Proteins in Sodium Dodecyl Sulfate-Polyacrylamide Gel Using Coomassie Blue

Most traditional post-electrophoretic processes need several hours to several days to finish the whole staining process and traditional staining solutions all contain methanol, acetic acid, or phosphoric acid, which not only produce the unpleasant smell but also cause environmental pollution. Here a fixation-free, fast protein staining method in sodium dodecyl sulfate-polyacrylamide gel electrophoresis using Coomassie blue is described. The protocol includes only staining and quick washing steps, can be completed in 0.5 h. It has a sensitivity of 10 ng. In addition, the dye stain does not contain any acid or methanol.

Patulin removal from apple juice using a novel cysteine-functionalized metal-organic framework adsorbent

Patulin (PAT) is one of the most common toxic contaminants of apple juice, which causes severe food safety issues throughout the apple industry. In order to remove PAT efficiently, a metal-organic framework-based adsorbent (UiO-66(NH₂)@Au-Cys) was successfully synthesized and used for PAT removal from juice-pH simulation solution and real apple juice. Batch adsorption experiments were systematically performed to study the adsorption behavior for PAT. The results showed that adsorption process could be well described by the Pseudo-second order model and Freundlich isotherm model. The maximum adsorption capacity (4.38 µg/mg) was 10 times higher than the microbe-based biosorbents. Thermodynamic investigation demonstrated that adsorption process was spontaneous and endothermic. Furthermore, no marked cytotoxicity on NIH 3T3 cell lines was observed when the concentration of the adsorbent was lower than 10 μg/mL. Therefore, UiO-66(NH₂)@Au-Cys is a potential adsorbent for PAT removal from apple juice with little quality changes.

Simple, time saving pulsed-field gel electrophoresis protocol for the typing of Stenotrophomonas maltophilia

We developed a time-saving and cost-efficient Pulsed Field Gel Electrophoresis (PFGE) method for the typing of Stenotrophomonas maltophilia by modifying the conventional procedures. Our modifications related to the cell suspension preparation, lysis of bacterial cells in plugs, washing steps, and consumption of restriction enzyme. Although few rapid PFGE protocols on Gram-negative bacteria are available, the use of comparatively large amounts of costly reagents prompted us to look for other alternative. Hence, by considering the speed, simplicity, and relatively low cost, the modified protocol may be of more practical value than other established protocols in investigating S. maltophilia nosocomial outbreaks.