MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings

Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we developed MyROOT, a software for the semiautomatic quantification of root growth of seedlings growing directly on agar plates. Our method automatically determines the scale from the image of the plate, and subsequently measures the root length of the individual plants. To this aim, MyROOT combines a bottom‐up root tracking approach with a hypocotyl detection algorithm. At the same time as providing accurate root measurements, MyROOT also significantly minimizes the user intervention required during the process. Using Arabidopsis, we tested MyROOT with seedlings from different growth stages and experimental conditions. When comparing the data obtained from this software with that of manual root measurements, we found a high correlation between both methods (R² = 0.997). When compared with previous developed software with similar features (BRAT and EZ‐Rhizo), MyROOT offered an improved accuracy for root length measurements. Therefore, MyROOT will be of great use to the plant science community by permitting high‐throughput root length measurements while saving both labor and time.     

Optical coherence tomography to detect acute esophageal radiation‐induced damage in mice: A validation study

Radiation therapy for patients with non‐small‐cell lung cancer is hampered by acute radiation‐induced toxicity in the esophagus. This study aims to validate that optical coherence tomography (OCT), a minimally invasive imaging technique with high resolution (~10 μm), is able to visualize and monitor acute radiation‐induced esophageal damage (ARIED) in mice. We compare our findings with histopathology as the gold standard. Irradiated mice receive a single dose of 40 Gy at proximal and distal spots of the esophagus of 10.0 mm in diameter. We scan mice using OCT at two, three, and seven days post‐irradiation. In OCT analysis, we define ARIED as a presence of distorted esophageal layering, change in backscattering signal properties, or change in the esophageal wall thickness. The average esophageal wall thickness is 0.53 mm larger on OCT when ARIED is present based on histopathology. The overall sensitivity and specificity of OCT to detect ARIED compared to histopathology are 94% and 47%, respectively. However, the overall sensitivity of OCT to assess ARIED is 100% seven days post‐irradiation. We validate the capability of OCT to detect ARIED induced by high doses in mice. Nevertheless, clinical studies are required to assess the potential role of OCT to visualize ARIED in humans.      

In vivo detection of endotracheal tube biofilms in intubated critical care patients using catheter‐based optical coherence tomography

The formation of biofilms in the endotracheal tubes (ETTs) of intubated patients on mechanical ventilation is associated with a greater risk of ventilator‐associated pneumonia and death. New technologies are needed to detect and monitor ETTs in vivo for the presence of these biofilms. Longitudinal OCT imaging was performed in mechanically ventilated subjects at 24‐hour intervals until extubation to detect the formation and temporal changes of in vivo ETT biofilms. OCT‐derived attenuation coefficient images were used to differentiate between mucus and biofilm. Extubated ETTs were examined with optical and electron microscopy, and all imaging results were correlated with standard‐of‐care clinical test reports. OCT and attenuation coefficient images from four subjects were positive for ETT biofilms and were negative for two subjects. The processed and stained extubated ETTs and clinical reports confirmed the presence/absence of biofilms in all subjects. Our findings confirm that OCT can detect and differentiate between biofilm‐positive and biofilm‐negative groups (P < 10^?5). OCT image‐based features may serve as biomarkers for direct in vivo detection of ETT biofilms and help drive investigation of new management strategies to reduce the incidence of VAP.      

Large‐depth‐of‐field full‐field optical angiography

A large‐depth‐of‐field full‐field optical angiography (LD‐FFOA) method is developed to expand the depth‐of‐field (DOF) using a contrast pyramid fusion algorithm (CPFA). The absorption intensity fluctuation modulation effect is utilized to obtain full‐field optical angiography (FFOA) images at different focus positions. The CPFA is used to process these FFOA images with different focuses. By selecting high‐contrast areas, the CPFA can highlight the characteristics and details of blood vessels to obtain LD‐FFOA images. In the optimal case of the proposed method, the DOF for FFOA is more than tripled using 10 differently focused FFOA images. Both the phantom and animal experimental results show that the LD‐FFOA resolves FFOA defocusing issues induced by surface and thickness inhomogeneities in biological samples. The proposed method can be potentially applied to practical biological experiments.      

Use of image analysis to understand enzyme stability in an aerated stirred reactor

Efficient regeneration of NAD(P)⁺ cofactors is essential for large-scale application of alcohol dehydrogenases due to the high cost and chemical instability of these cofactors. NAD(P)⁺ can be regenerated effectively using NAD(P)H oxidases (NOXs) that require molecular oxygen as a cosubstrate. In large-scale biocatalytic processes, agitation and aeration are needed for sufficient oxygen transfer into the liquid phase, both of which have been shown to significantly increase the rate of enzyme deactivation. As such, the aim of this study was to identify the existence of a correlation between enzyme stability and gas–liquid interfacial area inside the bioreactor. This was done by measuring gas–liquid interfacial areas inside an aerated stirred reactor, using an in situ optical probe, and simultaneously measuring the kinetic stability of NOXs. Following enzyme incubation at various power inputs and gas-phase compositions, the residual activity was assessed and video samples were analyzed through an image processing algorithm. Enzyme deactivation was found to be proportional to an increase in interfacial area up to a certain limit, where power input appears to have a higher impact. Furthermore, the presence of oxygen increased enzyme deactivation rates at low interfacial areas. The areas were validated with defined glass beads and found to be in the range of those in large-scale bioreactors. Finally, a correlation between the enzyme half-life and specific interfacial area was obtained. Therefore, we conclude that the method developed in this contribution can help to predict the behavior of biocatalyst stability under industrially relevant conditions, concerning specific gas–liquid interfacial areas.     

Robustness of neural codes and its implication on natural image processing

In this study, based on the view of statistical inference, we investigate the robustness of neural codes, i.e., the sensitivity of neural responses to noise, and its implication on the construction of neural coding. We first identify the key factors that influence the sensitivity of neural responses, and find that the overlap between neural receptive fields plays a critical role. We then construct a robust coding scheme, which enforces the neural responses not only to encode external inputs well, but also to have small variability. Based on this scheme, we find that the optimal basis functions for encoding natural images resemble the receptive fields of simple cells in the striate cortex. We also apply this scheme to identify the important features in the representation of face images and Chinese characters.

The effect of obesity management on body image in patients seeking treatment at medical centers

Objective: Body image dissatisfaction is common in treatment‐seeking patients with obesity. We aimed to investigate the effects of obesity management on body image in patients with obesity attending Italian medical centers for weight loss programs. Research Methods and Procedures: A total of 473 obese patients seeking treatment in 13 Italian medical centers (80% females; age, 45.9 ± standard deviation 11.0 years; BMI, 36.8 ± 5.7 kg/m²) were evaluated at baseline and after a 6‐month weight loss treatment. Body uneasiness, psychiatric distress, and binge eating were tested by Body Uneasiness Test (BUT, Part A), Symptom CheckList‐90 (SCL‐90), and Binge Eating Scale (BES), respectively. Results: At 6‐month follow‐up, the percentage weight loss was significantly higher in men (9.0 ± 6.3%) than in women (6.8 ± 7.3%; p = 0.010). Both men and women had a significant improvement in BUT Global Severity Index and in all of the BUT subscales with the exception of the Compulsive Self‐Monitoring subscale. Linear regression analysis selected baseline psychological and behavioral measures (global score of BUT and SCL‐90) and improved psychiatric distress and binge eating as independent predictors of changes in basal body dissatisfaction in females, whereas in males, changes were associated only with baseline BUT‐Global Severity Index score, binge eating, and its treatment‐associated improvement. Pre‐treatment BMI and BMI changes did not enter the regression. Discussion: Obesity treatment, even with a modest degree of weight loss, is associated with a significant improvement of body image, in both females and males. This effect depends mainly on psychological factors, not on the amount of weight loss.     

中国植物标本馆数字化发展的缩影——江苏省中国科学院植物研究所标本馆(NAS)

江苏省中国科学院植物研究所标本馆(NAS)是中国最早的植物标本馆之一,也是国内最早开展植物标本数字化的标本馆,其标本数字化发展经历了4个阶段: 20世纪80年代后期尝试的标本文字信息数字化的起步阶段; 20世纪90年代末的标本图像数字化和文字信息数字化规范阶段; 2004年以后的标本批量数字化与信息网络共享快速发展阶段; 2018年后的标本数字化信息维护与优化阶段。这一过程集中代表和反映了中国植物标本数字化的发展历程。此外,近年来开始了发掘和利用江苏植物标本的数字化信息工作,包括建设江苏省级数字植物标本馆、开发江苏省维管植物标本时空分布可视化系统、开展标本采集-入库过程数字化等。今后,将不断深化标本数字化的工作,以期形成有NAS特色的数字化植物标本馆。     

Tomographic PIV in a model of the left ventricle: 3D flow past biological and mechanical heart valves

Left ventricular flow is intrinsically complex, three-dimensional and unsteady. Its features are susceptible to cardiovascular pathology and treatment, in particular to surgical interventions involving the valves (mitral valve replacement). To improve our understanding of intraventricular fluid mechanics and the impact of various types of prosthetic valves thereon, we have developed a custom-designed versatile left ventricular phantom with anatomically realistic moving left ventricular membrane. A biological, a tilting disc and a bileaflet valve (in two different orientations) were mounted in the mitral position and tested under the same settings. To investigate 3D flow within the phantom, a four-view tomographic particle image velocimetry setup has been implemented. The results compare side-by-side the evolution of the 3D flow topology, vortical structures and kinetic energy in the left ventricle domain during the cardiac cycle. Except for the tilting disc valve, all tested prosthetic valves induced a crossed flow path, where the outflow crosses the inflow path, passing under the mitral valve. The biological valve shows a strong jet with a peak velocity about twice as high compared to all mechanical heart valves, which makes it easier to penetrate deeply into the cavity. Accordingly, the peak kinetic energy in the left ventricle in case of the biological valve is about four times higher than the mechanical heart valves. We conclude that the tomographic particle imaging velocimetry setup provides a useful ground truth measurement of flow features and allows a comparison of the effects of different valve types on left ventricular flow patterns.