Publications by authors named "Tian Liu"

531 Publications

Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omics.

Genomics Proteomics Bioinformatics 2021 Jun 9. Epub 2021 Jun 9.

BGI-Shenzhen, Shenzhen 518083, China.

The vagina contains at least a billion microbial cells, dominated by lactobacilli. Here we perform metagenomic shotgun sequencing on cervical and fecal samples from a cohort of 516 Chinese women of reproductive age, and cervical, fecal, and salivary samples from a second cohort of 632 women. Factors such as pregnancy, delivery histories, cesarean section, and breast-feeding were all more important than menstrual cycle in shaping the microbiome, and such information would be necessary before trying to interpret differences between vagino-cervical microbiome data. Greater proportion of Bifidobacterium breve was seen with older age at sexual debut. The relative abundance of lactobacilli especially Lactobacillus crispatus was negatively associated with pregnancy history. Potential markers for lack of menstrual regularity, heavy flow, dysmenorrhea, and contraceptives were also identified. Lactobacilli were rare during breast-feeding or post-menopause. Other features such as mood fluctuations and facial speckles could potentially be predicted from the vagino-cervical microbiome. Gut and salivary microbiome, plasma vitamins, metals, amino acids, and hormones showed associations with the vagino-cervical microbiome. Our results offer an unprecedented glimpse into the microbiota of the female reproductive tract and call for international collaborations to better understand its long-term health impact other than in the settings of infection or pre-term birth.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gpb.2021.01.005DOI Listing
June 2021

[Effects of noise, bright light and mechanical stimulation on sleep, blood-brain barrier and cognitive function in septic rats].

Zhonghua Wei Zhong Bing Ji Jiu Yi Xue 2021 May;33(5):529-534

Department of Critical Care Medicine, Xiaogan Hospital Affiliated to Wuhan University of Science and Technology (Xiaogan Central Hospital), Xiaogan 432000, Hubei, China. Corresponding author: Yao Peng, Email:

Objective: To evaluate the effects of noise, bright light and mechanical stimulation on sleep, blood-brain barrier and cognitive function in septic rats.

Methods: Forty male Sprague-Dawley (SD) rats were selected and intraperitoneal injection of 10 mg/kg lipopolysaccharide (LPS) was used to establish sepsis model. 0, 30, 45, 60, 75 dB noise stimulation or 0, 50, 100, 200, 400 Lux light stimulation were given to rats (all n = 4). The serum levels of cortisol and melatonin, and the cerebral content of Evans blue (EB) were measured 96 hours after the stimulation to determine the optimal intensity of intervention. The other 40 SD rats were randomly divided into control group (Con group), LPS group, noise intervention group (LPS+60 dB group), 200 Lux light intervention group (LPS+200 Lux group) and mechanical stimulation group (LPS+MS group), with 8 rats in each group. The open fields test and fear conditioning test were used to evaluate the exploratory behavior and cognitive function 96 hours after corresponding stimulation. The enzyme linked immunosorbent assay (ELISA) was used to detect cerebral level of interleukin-6 (IL-6) and serum levels of cortisol and melatonin. The blood-brain barrier integrity was assessed by EB staining. The protein levels of ZO-1, Claudin-5 and caspase-3 in the hippocampus were detected by Western blotting to assess the blood-brain barrier integrity and neuronal apoptosis.

Results: Compared with 0 dB group or 0 Lux group, the serum melatonin concentration in 60 dB group and 200 Lux group were significantly reduced, while the serum cortisol concentration and cerebral EB content were significantly increased. Therefore, 60 dB noise and 200 Lux light were selected in the subsequent experiments. Compared with Con group, the horizontal score and vertical score in the open field test in LPS group were significantly decreased. There were no significant differences in the proportion of freezing time, the cerebral contents of EB and IL-6, the serum levels of melatonin and cortisol, and the hippocampal expressions of ZO-1, Claudin-5 and caspase-3. Compared with LPS group, the horizontal score, vertical score and the percentage of freezing time in LPS+60 dB group, LPS+200 Lux group and LPS+MS group were significantly reduced [horizontal score: 73.8±9.7, 80.3±9.4, 64.5±8.3 vs. 103.6±15.5; vertical score: 9.4±1.7, 11.2±1.9, 6.8±0.9 vs. 15.9±2.8; the percentage of freezing time: (45.3±4.7)%, (53.3±5.8)%, (42.1±5.1)% vs. (66.1±6.3)%], the serum level of melatonin was significantly decreased (ng/L: 53.62±6.20, 44.25±6.41, 45.33±5.84 vs. 74.39±7.54), the serum level of cortisol was significantly increased (nmol/L: 818.34±95.53, 710.04±65.41, 989.73±91.63 vs. 398.82±72.59), the levels of EB, IL-6 in the brain tissue were significantly increased [EB (μg/g): 2.80±0.35, 2.38±0.31, 3.24±0.42 vs. 1.59±0.26; IL-6 (ng/g): 31.56±4.11, 26.69±3.75, 37.47±4.56 vs. 16.28±2.69], the expressions of ZO-1 and Claudin-5 were significantly decreased (ZO-1/β-actin: 0.37±0.04, 0.32±0.05, 0.24±0.04 vs. 0.80±0.09; Claudin-5/β-actin: 0.62±0.08, 0.47±0.06, 0.35±0.05 vs. 0.97±0.20), and the expression of cleaved caspase-3 was significantly increased (caspase-3/β-actin: 0.56±0.06, 0.39±0.04, 0.72±0.12 vs. 0.20±0.03), with statistically significant differences (all P < 0.05).

Conclusions: 60 dB noise, 200 Lux light or mechanical stimulation for 96 hours could inhibit the secretion of serum melatonin, promote the secretion of cortisol, and activate neuroinflammation in septic rats, and lead to neuronal apoptosis in hippocampus and hyper-permeability of blood-brain barrier, which in turn could cause sleep disturbance and cognitive impairment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3760/cma.j.cn121430-20200630-00514DOI Listing
May 2021

Fully Automated Segmentation of Brain Tumor from Multiparametric MRI Using 3D Context Deep Supervised U-Net.

Med Phys 2021 Jun 8. Epub 2021 Jun 8.

Department of Radiation Oncology and Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA.

Purpose: Owing to histologic complexities of brain tumors, its diagnosis requires the use of multi-modalities to obtain valuable structural information so that brain tumor subregions can be properly delineated. In current clinical workflow, physicians typically perform slice by slice delineation of brain tumor subregions, which is a time-consuming process and also more susceptible to intra- and inter-rater variabilities possibly leading to misclassification. To deal with this issue, this study aims to develop an automatic segmentation of brain tumor in MR images using deep learning.

Method: In this study, we develop a context deep-supervised U-Net to segment brain tumor subregions. A context block which aggregates multiscale contextual information for dense segmentation was proposed. This approach enlarges the effective receptive field of convolutional neural networks, which, in turn, improves the segmentation accuracy of brain tumor subregions. We performed the 5-fold cross-validation on the Brain Tumor Segmentation Challenge (BraTS) 2020 training dataset. The BraTS 2020 testing datasets were obtained via BraTS online website as a hold-out test. For BraTS, the evaluation system divides the tumor into three regions: whole tumor (WT), tumor core (TC) and enhancing tumor (ET). The performance of our proposed method was compared against two state-of-the-arts CNN networks in terms of segmentation accuracy via Dice similarity coefficient (DSC) and Hausdorff distance (HD). The tumor volumes generated by our proposed method were compared with manually contoured volumes via Bland-Altman plots and Pearson analysis.

Results: The proposed method achieved the segmentation results with a DSC of 0.923 ± 0.047, 0.893 ± 0.176, and 0.846 ± 0.165 and a 95% HD95 of 3.946 ± 7.041 mm, 3.981 ± 6.670 mm, and 10.128 ± 51.136 mm on WT, TC and ET, respectively. Experimental results demonstrate that our method achieved comparable to significantly (P < 0.05) better segmentation accuracies than other two state-of-the-arts CNN networks. Pearson correlation analysis showed a high positive correlation between the tumor volumes generated by proposed method and manual contour.

Conclusion: Overall qualitative and quantitative results of this work demonstrate the potential of translating proposed technique into clinical practice for segmenting brain tumor subregions, and further facilitate brain tumor radiotherapy workflow.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mp.15032DOI Listing
June 2021

The length of disulfide bond-containing linkages impacts the oral absorption and antitumor activity of paclitaxel prodrug-loaded nanoemulsions.

Nanoscale 2021 Jun 8. Epub 2021 Jun 8.

Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China.

The rational design of oral paclitaxel (PTX) preparations is still a challenge. Many studies focus on developing PTX-loaded nanoemulsions (NEs) for oral administration. Unfortunately, PTX has poor affinity with the commonly used oil phases, leading to low encapsulation efficiency, poor colloidal stability, and premature drug leakage of PTX-loaded NEs. Herein, three lipophilic PTX prodrugs are synthesized by conjugating PTX with citronellol (CIT), using different lengths of disulfide bond-containing linkages. Interestingly, compared with PTX, the prodrugs exhibit higher affinity with the oil phase, effectively improving the encapsulation efficiency, colloidal stability, and sustained-release behavior of NEs. In addition, the disulfide bond-bridged prodrugs could specifically release PTX in tumor cells, reducing unnecessary systemic exposure of PTX. As a result, all three prodrug NEs exhibited improved oral bioavailability and antitumor effects compared to oral Taxol. Moreover, the length of disulfide bond-containing linkages exhibits great impacts on the oral absorption, drug release, and antitumor behaviors of NEs. It is found that the prodrug NEs with the shortest linkages show comparable antitumor effects with intravenous Taxol, but with less systemic and gastrointestinal toxicity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1039/d1nr01359aDOI Listing
June 2021

Learning-based dose prediction for pancreatic stereotactic body radiation therapy using dual pyramid adversarial network.

Phys Med Biol 2021 Jun 4. Epub 2021 Jun 4.

Department of Radiology and Sciences Imaging Department of Radiology Oncology, Emory University, Atlanta, Georgia, UNITED STATES.

Treatment planning for pancreatic cancer stereotactic body radiation therapy (SBRT) is very challenging owing to vast spatial variations and close proximity of many organs-at-risk. Recently, deep learning (DL)-based methods have been applied in dose prediction tasks of various treatment sites with the aim of relieving planning challenges. Limited investigations, however, have been reported on DL-based dose prediction for pancreatic cancer SBRT. This study aims to further current knowledge in DL-based dose prediction tasks by implementing and demonstrating the feasibility of a new dual pyramid networks (DPNs) integrated DL-model for predicting dose distributions of pancreatic SBRT. The proposed framework is composed of four parts: CT-only feature pyramid network (FPN), contour-only FPN, late fusion network and adversarial network. Combination of mean absolute error, gradient difference error, histogram matching, and adversarial loss is used for supervision. The performance of proposed model was demonstrated for pancreatic cancer SBRT plans for doses prescribed between 33 and 50 Gy over five fractions to up to three planning target volumes (PTV). Five-fold cross-validation was performed on 30 patients and another 20 patients were used as holdout tests. Predicted plans were compared with clinically approved plans through dose-volume parameters. The proposed framework was able to predict 87% and 91% of clinically relevant dose parameters for cross-validation sets and holdout sets, respectively, without any significant differences (P > 0.05). For the parameters with significant differences (P < 0.05), the predicted doses to the duodenum and spinal cord were lower in comparison to the clinical plans. The proposed model was also able to predict the intentional hotspots as feature characteristics of SBRT plans. Overall, the proposed model was able to predict doses to cases with both single and multiple PTVs. In conclusion, the DPN integrated DL-model demonstrated good overall plan quality and dose prediction accuracy for pancreatic cancer SBRT.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1088/1361-6560/ac0856DOI Listing
June 2021

FSTL1 aggravates OVA-induced inflammatory responses by activating the NLRP3/IL-1β signaling pathway in mice and macrophages.

Inflamm Res 2021 Jun 2. Epub 2021 Jun 2.

Department of Respiratory, Shandong Provincial Qianfoshan Hospital, Shandong University, The First Affiliated Hospital of Shandong First Medical University, Shandong Institute of Respiratory Diseases, Jinan, China.

Objective: Asthma, a well-known disease with high morbidity, is characterized by chronic airway inflammation. However, the allergic inflammation mechanisms of follistatin-like protein 1 (FSTL1) have not been elucidated. This study aims to investigate the effects of FSTL1 in ovalbumin (OVA)-induced mice and macrophages on nucleotide-binding domain and leucine-rich repeat protein 3 (NLRP3)/interleukin-1β (IL-1β) signaling pathway.

Methods: Mice were randomly divided into control-WT, OVA-WT, control-Fstl1, OVA-Fstl1. Histological changes were assessed by HE and PAS staining. The protein levels of Muc-5AC, FSTL1, NLRP3, and IL-1β in lung tissue were detected by immunohistochemistry and ELISA. The bronchoalveolar lavage fluid (BALF) in mice and human serum samples were detected by ELISA. Then, mice were grouped into control, FSTL1, MCC950 + FSTL1 to further investigate the relationship between FSTL1 and NLRP3/IL-1β. Alveolar macrophage cells (MH-S cells) were separated into control, OVA, FSTL1, OVA + FSTL1, OVA + siNC, OVA + siFSTL1, MCC950, and FSTL1 + MCC950 groups to explore the effect of FSTL1 on the NLRP3/IL-1β signaling. The protein expression of NLRP3 and IL-1β in MH-S cells was detected by Western blot analysis.

Results: The present results uncovered that Fstl1 significantly ameliorated OVA-induced Muc-5AC production and mucus hypersecretion. Fstl1 was also found to decrease the production of inflammatory cytokines and inflammatory cell infiltration in OVA-induced asthmatic mice. Meanwhile, the serum concentrations of FSTL1 and IL-1β were higher in  asthma subjects than the health subjects, and Fstl1 ameliorated the production of NLRP3 and IL-1β in OVA-induced asthmatic mice. Furthermore, mice by injected FSTL1 substantially stimulated the expression of NLRP3 and IL-1β, while pretreatment with MCC950 in mice significantly weakened the production of NLRP3 and IL-1β induced by injection FSTL1. Pretreatment with siFSTL1 or MCC950 significantly reduced the production of NLRP3 and IL-1β induced by OVA or FSTL1 in MH-S cells.

Conclusions: The study results showed that FSTL1 played an important role in allergic airway inflammation by activating NLRP3/IL-1β. Hence, inhibition FSTL1 could be applied as a therapeutic agent against asthma.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00011-021-01475-wDOI Listing
June 2021

High through-plane resolution CT imaging with self-supervised deep learning.

Phys Med Biol 2021 May 28. Epub 2021 May 28.

Department of Radiology and Sciences Imaging Department of Radiology Oncology, Emory University, Atlanta, Georgia, UNITED STATES.

CT images for radiotherapy planning are usually acquired in thick slice to reduce imaging dose, especially for pediatric patients, and to lessen the need for contouring and treatment planning on more slices. However, low through-plane resolution may degrade the accuracy of dose calculations. In this paper, a self-supervised deep learning workflow is proposed to synthesize high through-plane resolution CT images by learning from their high in-plane resolution features. The proposed workflow was designed to facilitate the neural networks to learn the mapping from low resolution (LR) to high resolution (HR) images in the axial plane. During the inference step, the HR sagittal and coronal images were generated by feeding two parallelly trained neural networks with the respective LR sagittal and coronal images to the trained neural networks. The CT simulation images of a cohort of 75 head and neck (HN) cancer patients (1 mm slice thickness) and 200 CT images of a cohort of 20 lung cancer patients (3 mm slice thickness) were retrospectively investigated with a cross validation manner. The generated HR images with the proposed method were qualitatively (visual quality, image intensity profiles and preliminary observer study) and quantitatively (Mean Absolute Error (MAE), Edge Keeping Index (EKI), Structural Similarity Index Measurement (SSIM), Information Fidelity Criterion (IFC) and Visual Information Fidelity in Pixel domain (VIFP)) inspected, while taking the original HN and lung cancer patients' CT images as the reference. The qualitative results have shown the capability of the proposed method for generating high through-plane resolution CT images with data of the HN and lung cancer patients. All the improvements of the measure metrics are confirmed to be statistically significant with paired two-sample t-test analysis. The innovative point of the work is that the proposed deep learning workflow for CT image generation with high through-plane resolution in radiotherapy is self-supervised, which means it does not rely on ground truth CT images to train the network. In addition, the assumption that the in-plane HR information can supervise the through-plane HR generation is confirmed and anticipated to potentially inspire more researches on this topic to further improve the through-plane resolution of medical images.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1088/1361-6560/ac0684DOI Listing
May 2021

Physicochemical characterizations of starches isolated from Tetrastigma hemsleyanum Diels et Gilg.

Int J Biol Macromol 2021 May 18;183:1540-1547. Epub 2021 May 18.

Horticulture Department, University of Arkansas, 309 Plant Science Building, Fayetteville, AR 72701, USA. Electronic address:

Physicochemical characteristics of starch isolated from Tetrastigma hemsleyanum Diels et Gilg (T. hemsleyanum) tuber root of 4 different origins were firstly analyzed in this study. The starch granules of T. hemsleyanum tuber root were oval or globular, showed unimodal distribution with average size of 21.66-28.79 μm. T. hemsleyanum starch had typical B-type diffraction pattern. T. hemsleyanum root was rich in starch, and apparent amylose content ranged from 39.82% to 47.67%. The amylopectin chain profiles showed that over 50% of the total detectable chains had degree of polymerization (DP) with 13-24. T. hemsleyanum tuber root had high RS content, which reached up to 61.44% in flour and 68.81% in isolated starch. After cooking, the RS content decreased, but was still high up to 7.52% in flour and 9.93% in isolated starch. The peak gelatinization temperature of T. hemsleyanum starch ranged from 68.12 to 74.42 °C. The peak viscosity of T. hemsleyanum flour and starch ranged from 778 to 1258 cP and 1577 to 2009 cP respectively. The results indicate that T. hemsleyanum is a potential source for novel starch with high resistant starch and provide some guides for comprehensive utilization of T. hemsleyanum starch in food and pharmaceuticals industry.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ijbiomac.2021.05.117DOI Listing
May 2021

Biosynthesis of Polydatin in .

J Agric Food Chem 2021 Jun 21;69(21):5917-5925. Epub 2021 May 21.

Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

Polydatin, with better structural stability and biological activities than resveratrol, is mainly extracted from the traditional Chinese medicinal plant . In this study, based on the transcriptome analysis of , we identified the key glycosyltransferase of resveratrol and achieved the biosynthesis of polydatin from glucose by incorporation with the resveratrol biosynthesis module, UDP-glucose supply module, and glycosyltransferase expression module. Through metabolic engineering and fermentation optimization, the production of polydatin reached 545 mg/L, and the dry cell weight was 27.83 mg/g DCW, which was about twice that of extracted from the root (11.404 mg/g DCW). Therefore, it is possible to replace the production mode of polydatin from plant extraction to microbial chassis in the future.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jafc.1c01557DOI Listing
June 2021

Self-supervised learning for accelerated 3D high-resolution ultrasound imaging.

Med Phys 2021 May 16. Epub 2021 May 16.

Department of Radiation Oncology and Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA.

Purpose: Ultrasound (US) imaging has been widely used in diagnosis, image-guided intervention, and therapy, where high-quality three-dimensional (3D) images are highly desired from sparsely acquired two-dimensional (2D) images. This study aims to develop a deep learning-based algorithm to reconstruct high-resolution (HR) 3D US images only reliant on the acquired sparsely distributed 2D images.

Methods: We propose a self-supervised learning framework using cycle-consistent generative adversarial network (cycleGAN), where two independent cycleGAN models are trained with paired original US images and two sets of low-resolution (LR) US images, respectively. The two sets of LR US images are obtained through down-sampling the original US images along the two axes, respectively. In US imaging, in-plane spatial resolution is generally much higher than through-plane resolution. By learning the mapping from down-sampled in-plane LR images to original HR US images, cycleGAN can generate through-plane HR images from original sparely distributed 2D images. Finally, HR 3D US images are reconstructed by combining the generated 2D images from the two cycleGAN models.

Results: The proposed method was assessed on two different datasets. One is automatic breast ultrasound (ABUS) images from 70 breast cancer patients, the other is collected from 45 prostate cancer patients. By applying a spatial resolution enhancement factor of 3 to the breast cases, our proposed method achieved the mean absolute error (MAE) value of 0.90 ± 0.15, the peak signal-to-noise ratio (PSNR) value of 37.88 ± 0.88 dB, and the visual information fidelity (VIF) value of 0.69 ± 0.01, which significantly outperforms bicubic interpolation. Similar performances have been achieved using the enhancement factor of 5 in these breast cases and using the enhancement factors of 5 and 10 in the prostate cases.

Conclusions: We have proposed and investigated a new deep learning-based algorithm for reconstructing HR 3D US images from sparely acquired 2D images. Significant improvement on through-plane resolution has been achieved by only using the acquired 2D images without any external atlas images. Its self-supervision capability could accelerate HR US imaging.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mp.14946DOI Listing
May 2021

A review of deep learning based methods for medical image multi-organ segmentation.

Phys Med 2021 May 13;85:107-122. Epub 2021 May 13.

Department of Radiation Oncology and Winship Cancer Institute, Emory University, Atlanta, GA, USA. Electronic address:

Deep learning has revolutionized image processing and achieved the-state-of-art performance in many medical image segmentation tasks. Many deep learning-based methods have been published to segment different parts of the body for different medical applications. It is necessary to summarize the current state of development for deep learning in the field of medical image segmentation. In this paper, we aim to provide a comprehensive review with a focus on multi-organ image segmentation, which is crucial for radiotherapy where the tumor and organs-at-risk need to be contoured for treatment planning. We grouped the surveyed methods into two broad categories which are 'pixel-wise classification' and 'end-to-end segmentation'. Each category was divided into subgroups according to their network design. For each type, we listed the surveyed works, highlighted important contributions and identified specific challenges. Following the detailed review, we discussed the achievements, shortcomings and future potentials of each category. To enable direct comparison, we listed the performance of the surveyed works that used thoracic and head-and-neck benchmark datasets.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ejmp.2021.05.003DOI Listing
May 2021

Mitochondrial CHCHD2: Disease-Associated Mutations, Physiological Functions, and Current Animal Models.

Front Aging Neurosci 2021 22;13:660843. Epub 2021 Apr 22.

USF Health Byrd Alzheimer's Center and Research Institute, Tampa, FL, United States.

Rare mutations in the mitochondrial protein coiled-coil-helix-coiled-coil-helix domain containing 2 (CHCHD2) are associated with Parkinson's disease (PD) and other Lewy body disorders. CHCHD2 is a bi-organellar mediator of oxidative phosphorylation, playing crucial roles in regulating electron flow in the mitochondrial electron transport chain and acting as a nuclear transcription factor for a cytochrome c oxidase subunit (COX4I2) and itself in response to hypoxic stress. CHCHD2 also regulates cell migration and differentiation, mitochondrial cristae structure, and apoptosis. In this review, we summarize the known disease-associated mutations of CHCHD2 in Asian and Caucasian populations, the physiological functions of CHCHD2, how CHCHD2 mutations contribute to α-synuclein pathology, and current animal models of CHCHD2. Further, we discuss the necessity of continued investigation into the divergent functions of CHCHD2 and CHCHD10 to determine how mutations in these similar mitochondrial proteins contribute to different neurodegenerative diseases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fnagi.2021.660843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8100248PMC
April 2021

Tumour-derived substrate-adherent cells promote neuroblastoma survival through secreted trophic factors.

Mol Oncol 2021 May 1. Epub 2021 May 1.

School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.

Neuroblastoma (NB) is the most common extracranial solid tumour in children. NB is highly heterogeneous and is comprised of a mixture of neuroblastic cancer cells and stromal cells. We previously reported that N-type cells (neuroblastic cells) and S-type cells (substrate-adherent cells) in the SK-N-SH cell line shared almost identical genetic backgrounds. Sublines of N- and S-type cells were isolated from an early passage (P35) of SK-N-SH. Sequencing analysis revealed that all sublines harboured the anaplastic lymphoma kinase (ALK) F1174L mutation, indicating that they were tumour derived. Surprisingly, over 74% resembled S-type cells. In coculture experiments, S-type cells protected N-type cells from apoptosis induced by the oncogenic ALK inhibitor TAE684. Western blotting analyses showed that ALK, protein kinase A (AKT) and STAT3 signalling were stimulated in the cocultures. Furthermore, the conditioned medium from S-type cells activated these downstream signalling molecules in the N-type cells. The activation of STAT3 in the N-type cells was ALK-independent, while AKT was regulated by the ALK activation status. To identify the responsible soluble factors, we used a combination of transcriptomic and proteomic analysis and found that plasminogen activator inhibitor 1, secreted protein acidic and cysteine rich, periostin and galectin-1 were potential mediators of STAT3 signalling. The addition of recombinant proteins to the tumour cells treated with the ALK inhibitor partially enhanced cell viability. Overall, the tumour-derived S-type cells prevented apoptosis in the N-type cells via ALK-independent STAT3 activation triggered by secreted factors. The inhibition of these factors in combination with ALK inhibition could provide a new direction for targeted therapies to treat high-risk NB.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/1878-0261.12969DOI Listing
May 2021

Head and neck multi-organ segmentation on dual-energy CT using dual pyramid convolutional neural networks.

Phys Med Biol 2021 May 20;66(11). Epub 2021 May 20.

Department of Radiation Oncology and Winship Cancer Institute, Emory University, Atlanta, GA 30322, United States of America.

Organ delineation is crucial to diagnosis and therapy, while it is also labor-intensive and observer-dependent. Dual energy CT (DECT) provides additional image contrast than conventional single energy CT (SECT), which may facilitate automatic organ segmentation. This work aims to develop an automatic multi-organ segmentation approach using deep learning for head-and-neck region on DECT. We proposed a mask scoring regional convolutional neural network (R-CNN) where comprehensive features are firstly learnt from two independent pyramid networks and are then combined via deep attention strategy to highlight the informative ones extracted from both two channels of low and high energy CT. To perform multi-organ segmentation and avoid misclassification, a mask scoring subnetwork was integrated into the Mask R-CNN framework to build the correlation between the class of potential detected organ's region-of-interest (ROI) and the shape of that organ's segmentation within that ROI. We evaluated our model on DECT images from 127 head-and-neck cancer patients (66 training, 61 testing) with manual contours of 19 organs as training target and ground truth. For large- and mid-sized organs such as brain and parotid, the proposed method successfully achieved average Dice similarity coefficient (DSC) larger than 0.8. For small-sized organs with very low contrast such as chiasm, cochlea, lens and optic nerves, the DSCs ranged between around 0.5 and 0.8. With the proposed method, using DECT images outperforms using SECT in almost all 19 organs with statistical significance in DSC (<0.05). Meanwhile, by using the DECT, the proposed method is also significantly superior to a recently developed FCN-based method in most of organs in terms of DSC and the 95th percentile Hausdorff distance. Quantitative results demonstrated the feasibility of the proposed method, the superiority of using DECT to SECT, and the advantage of the proposed R-CNN over FCN on the head-and-neck patient study. The proposed method has the potential to facilitate the current head-and-neck cancer radiation therapy workflow in treatment planning.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1088/1361-6560/abfce2DOI Listing
May 2021

Discovery of Kasugamycin as a Potent Inhibitor of Glycoside Hydrolase Family 18 Chitinases.

Front Mol Biosci 2021 7;8:640356. Epub 2021 Apr 7.

School of Bioengineering, Dalian University of Technology, Dalian, China.

Kasugamycin, a well-known aminoglycoside antibiotic, has been used widely in agriculture and medicine to combat microbial pathogens by binding the ribosome to inhibit translation. Here, kasugamycin was discovered to be a competitive inhibitor of glycoside hydrolase family 18 (GH18) chitinases from three different organisms (bacterium, insect and human). Results from tryptophan fluorescence spectroscopy and molecular docking revealed that kasugamycin binds to the substrate-binding clefts in a similar mode as the substrate. An electrostatic interaction between the amino group of kasugamycin and the carboxyl group of a conserved aspartate in GH18 chitinase (one of the catalytic triad residues) was found to be vital for the inhibitory activity. This paper not only reports new molecular targets of kasugamycin, but also expands our thinking about GH inhibitor design by using a scaffold unrelated to the substrate.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmolb.2021.640356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8058351PMC
April 2021

Male pelvic multi-organ segmentation on transrectal ultrasound using anchor-free mask CNN.

Med Phys 2021 Apr 24. Epub 2021 Apr 24.

Department of Radiation Oncology and Winship Cancer Institute, Emory University, Atlanta, GA, USA.

Purpose: Current prostate brachytherapy uses transrectal ultrasound images for implant guidance, where contours of the prostate and organs-at-risk are necessary for treatment planning and dose evaluation. This work aims to develop a deep learning-based method for male pelvic multi-organ segmentation on transrectal ultrasound images.

Methods: We developed an anchor-free mask convolutional neural network (CNN) that consists of three subnetworks, that is, a backbone, a fully convolutional one-state object detector (FCOS), and a mask head. The backbone extracts multi-level and multi-scale features from an ultrasound (US) image. The FOCS utilizes these features to detect and label (classify) the volume-of-interests (VOIs) of organs. In contrast to the design of a previously investigated mask regional CNN (Mask R-CNN), the FCOS is anchor-free, which can capture the spatial correlation of multiple organs. The mask head performs segmentation on each detected VOI, where a spatial attention strategy is integrated into the mask head to focus on informative feature elements and suppress noise. For evaluation, we retrospectively investigated 83 prostate cancer patients by fivefold cross-validation and a hold-out test. The prostate, bladder, rectum, and urethra were segmented and compared with manual contours using the Dice similarity coefficient (DSC), 95% Hausdorff distance (HD ), mean surface distance (MSD), center of mass distance (CMD), and volume difference (VD).

Results: The proposed method visually outperforms two competing methods, showing better agreement with manual contours and fewer misidentified speckles. In the cross-validation study, the respective DSC and HD results were as follows for each organ: bladder 0.75 ± 0.12, 2.58 ± 0.7 mm; prostate 0.93 ± 0.03, 2.28 ± 0.64 mm; rectum 0.90 ± 0.07, 1.65 ± 0.52 mm; and urethra 0.86 ± 0.07, 1.85 ± 1.71 mm. For the hold-out tests, the DSC and HD results were as follows: bladder 0.76 ± 0.13, 2.93 ± 1.29 mm; prostate 0.94 ± 0.03, 2.27 ± 0.79 mm; rectum 0.92 ± 0.03, 1.90 ± 0.28 mm; and urethra 0.85 ± 0.06, 1.81 ± 0.72 mm. Segmentation was performed in under 5 seconds.

Conclusion: The proposed method demonstrated fast and accurate multi-organ segmentation performance. It can expedite the contouring step of prostate brachytherapy and potentially enable auto-planning and auto-evaluation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mp.14895DOI Listing
April 2021

Cost benefit analysis of portable chest radiography through glass: Initial experience at a tertiary care centre during COVID-19 pandemic.

J Med Imaging Radiat Sci 2021 Apr 8. Epub 2021 Apr 8.

Department of Radiology, St. Michael's Hospital, University of Toronto, 30 Bond Street, Toronto, ON, Canada. M5B 1W8.

Introduction: Portable chest radiography through glass (TG-CXR) is a novel technique, particularly useful during the COVID-19 (Coronavirus disease 2019) pandemic. The purpose of this study was to understand the cost and benefit of adopting TG-CXR in quantifiable terms.

Methods: Portable or bedside radiographs are typically performed by a team of two technologists. The TG-CXR method has the benefit of allowing one technologist to stay outside of the patient room while operating the portable radiography machine, reducing PPE use, decreasing the frequency of radiography machine sanitization and decreasing technologists' exposures to potentially infectious patients. The cost of implementing this technique during the current COVID-19 pandemic was obtained from our department's operational database. The direct cost of routinely used PPE and sanitization materials and the cost of the time taken by the technologists to clean the machine was used to form a quantitative picture of the benefit associated with TG-CXR technique.

Results: Technologists were trained on the TG-CXR method during a 15 min shift change briefing. This translated to a one-time cost of $424.88 USD. There was an average reduction of portable radiography machine downtime of 4 min and 48 s per study. The benefit of adopting the TG-CXR technique was $9.87 USD per patient imaged. This will result in a projected net cost savings of $51,451.84 USD per annum.

Conclusion: Adoption of the TG-CXR technique during the COVID-19 pandemic involved minimal one-time cost, but is projected to result in a net-benefit of over $51,000 USD per annum in our emergency department.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmir.2021.03.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8026266PMC
April 2021

Expression of the Testis-Specific Serine/Threonine Kinases Suggests Their Role in Spermiogenesis of Bay Scallop .

Front Physiol 2021 30;12:657559. Epub 2021 Mar 30.

MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.

Members of the testis-specific serine/threonine kinases (Tssk) family play critical roles in spermatogenesis in vertebrates. But in mollusks, research on Tssk family is still lagging. In this study, we systematically identified Tssk family based on the genomic and transcriptomic data from a commercially important scallop and detected the spatiotemporal expression in adult gonads. Five members were identified, with the gene length varying from 1,068 to 10,729 bp and the protein length ranging from 294 to 731 aa. All the Tssks possess a serine/threonine protein kinase catalytic (S_TKc) domain. Phylogenetic analysis revealed existence of four homologs of vertebrate Tssk1/2, Tssk3, Tssk4, Tssk5, and absence of Tssk6 in the scallop. The remaining gene (Tssk7) formed an independent clade with Tssks of other mollusks and arthropods, indicating that it may be a new member of Tssk family unique to protostomes. By investigating the expression of in four developmental stages of testes and ovaries, we found all five were primarily expressed in mature testis. hybridization experiment revealed the five were localized in the spermatids and spermatozoa. The testis-predominant expression of Tssk family suggests Tssks may play pivotal roles in spermiogenesis in the scallop. Our study provides basic information on the characteristics and expression profiles of Tssk family of . To our knowledge, it represents the first comprehensive analysis of Tssk family in mollusks.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fphys.2021.657559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8042308PMC
March 2021

Transforaminal epidural steroid injection combined with radio frequency for the treatment of lumbar disc herniation: a 2-year follow-up.

BMC Musculoskelet Disord 2021 Apr 12;22(1):347. Epub 2021 Apr 12.

The Key Laboratory of Biomedical Information Engineering of Ministry of Education, The Key Laboratory of Neuro-informatics & Rehabilitation Engineering of Ministry of Civil Affairs, and Institute of Health and Rehabilitation Science, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P. R. China.

Background: To assess the therapeutic efficacy of transforaminal epidural steroid injection (TFESI) combined with radio frequency (RF) for the treatment of lumbar disc herniation (LDH).

Methods: A total of 230 patients participated in the study: TFESI (Group T, n = 110), TFESI combined with RF (Group TR, n = 120). Visual analogue scale (VAS), Oswestry disability index (ODI) and Global perceived effect (GPE) scale were measured pre-operation, 1, 3, 6, 12 and 24 months after the operation. Hospitalization time, treatment time, complications, and recurrence were compared between the two groups.

Results: The VAS and ODI at each observation point of the post-operation were significantly decreased compared with the pre-operation in both groups (P < 0.05). There was no statistically difference of VAS and ODI between the two groups at 1 and 3 months of the post-operation (P > 0.05). However, The VAS and ODI scores in Group TR were significantly lower than that in Group T at 6, 12 and 24 months of the post-operation (P < 0.05). The GPE in group TR was high in the early days, while that at 1 and 3 months after treatment was significantly higher than that in group T (P < 0.05). The recurrence rate in Group TR was lower than that in Group T (P = 0.002). There was no significant difference in hospitalization time, complications, VAS and ODI score at the pre-operation between the two groups (P > 0.05).

Conclusion: These findings suggest that TFESI combined with RF could effectively improve the pain and function, and had a long-term satisfactory effect for the treatment of LDH.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12891-021-04209-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8042724PMC
April 2021

Bracovirus-mediated innexin hemichannel closure in cell disassembly.

iScience 2021 Apr 8;24(4):102281. Epub 2021 Mar 8.

School of Life Sciences, Yunnan University, Kunming 650500, P.R. China.

Cell-cell communication is necessary for cellular immune response. Hemichannel closure disrupts communication between intracellular and extracellular environments during polydnavirus-induced immunosuppression in invertebrates. However, the effects of hemichannel closure on cellular immune response are unclear. Here, we examined apoptotic body formation triggered by hemichannel closure in hemocytes of infected with bracovirus from the parasitic wasp, . We showed that Microplitis bicoloratus bracovirus (MbBV) induced apoptotic cell disassembly, accompanied by hemichannel closure. Hemocyte apoptotic body formation was caused by the dysregulation of the innexins (Inxs), Inx1, Inx2, Inx3, and Inx4, during the MbBV-mediated inhibition of pI3K/AKT signaling and activation of caspase-3, which cleaved gap junction Inx proteins. Our results showed that hemichannel opening or closure in response to various stimuli, which induces the modulation of Inx levels, could inhibit or activate apoptotic body formation, respectively. Therefore, the "hemichannel open and close" model may regulate the cellular immune response.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.isci.2021.102281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8008186PMC
April 2021

Sexual Development of the Hermaphroditic Scallop Revealed by Morphological, Endocrine and Molecular Analysis.

Front Cell Dev Biol 2021 16;9:646754. Epub 2021 Mar 16.

MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.

Simultaneous or functional hermaphrodites possessing both ovary and testis at the same time are good materials for studying sexual development. However, previous research on sex determination and differentiation was mainly conducted in gonochoristic species and studies on simultaneous hermaphrodites are still limited. In this study, we conducted a combined morphological, endocrine and molecular study on the gonadal development of a hermaphroditic scallop aged 2-10 month old. Morphological analysis showed that sex differentiation occurred at 6 months of age. By examining the dynamic changes of progesterone, testosterone and estradiol, we found testosterone and estradiol were significantly different between the ovaries and testes almost throughout the whole process, suggesting the two hormones may be involved in scallop sex differentiation. In addition, we identified two critical sex-related genes FoxL2 and Dmrt1L, and investigated their spatiotemporal expression patterns. Results showed that and were female- and male-biased, respectively, and mainly localized in the germ cells and follicular cells, indicating their feasibility as molecular markers for early identification of sex. Further analysis on the changes of and expression in juveniles showed that significant sexual dimorphic expression of occurred at 2 months of age, earlier than that of . Moreover, expression was significantly correlated with estradiol/testosterone ratio (E/T). All these results indicated that molecular sex differentiation occurs earlier than morphological sex differentiation, and may be a key driver that functions through regulating sex steroid hormones in the scallop. This study will deepen our understanding of the molecular mechanism underlying sex differentiation and development in spiralians.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fcell.2021.646754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8007870PMC
March 2021

Regulation of Nrf2 by phosphorylation: Consequences for biological function and therapeutic implications.

Free Radic Biol Med 2021 May 29;168:129-141. Epub 2021 Mar 29.

State Key Laboratory of Natural Medicines, And Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China. Electronic address:

The transcription factor nuclear factor erythroid-derived 2-like 2 (NRF2) participates in the activation of the antioxidant cytoprotective pathway and other important physiological processes to maintain cellular homeostasis. The dysregulation of NRF2 activity plays a role in various diseases, such as cardiovascular diseases, neurodegenerative diseases, and cancer. Thus, NRF2 activity is tightly regulated through multiple mechanisms, among which phosphorylation by kinases is critical in the posttranslational regulation of NRF2. For instance, PKC, casein kinase 2, and AMP-activated kinase positively, while GSK-3 negatively regulates NRF2 activity through phosphorylation of different sites. Here, we provide an overview of the phosphorylation regulation pattern of NRF2 and discuss the therapeutic potential of interventions targeting NRF2 phosphorylation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.freeradbiomed.2021.03.034DOI Listing
May 2021

Male pelvic CT multi-organ segmentation using synthetic MRI-aided dual pyramid networks.

Phys Med Biol 2021 Apr 16;66(8). Epub 2021 Apr 16.

Department of Radiation Oncology and Winship Cancer Institute, Emory University, Atlanta, GA 30322, United States of America.

The delineation of the prostate and organs-at-risk (OARs) is fundamental to prostate radiation treatment planning, but is currently labor-intensive and observer-dependent. We aimed to develop an automated computed tomography (CT)-based multi-organ (bladder, prostate, rectum, left and right femoral heads (RFHs)) segmentation method for prostate radiation therapy treatment planning. The proposed method uses synthetic MRIs (sMRIs) to offer superior soft-tissue information for male pelvic CT images. Cycle-consistent adversarial networks (CycleGAN) were used to generate CT-based sMRIs. Dual pyramid networks (DPNs) extracted features from both CTs and sMRIs. A deep attention strategy was integrated into the DPNs to select the most relevant features from both CTs and sMRIs to identify organ boundaries. The CT-based sMRI generated from our previously trained CycleGAN and its corresponding CT images were inputted to the proposed DPNs to provide complementary information for pelvic multi-organ segmentation. The proposed method was trained and evaluated using datasets from 140 patients with prostate cancer, and were then compared against state-of-art methods. The Dice similarity coefficients and mean surface distances between our results and ground truth were 0.95 ± 0.05, 1.16 ± 0.70 mm; 0.88 ± 0.08, 1.64 ± 1.26 mm; 0.90 ± 0.04, 1.27 ± 0.48 mm; 0.95 ± 0.04, 1.08 ± 1.29 mm; and 0.95 ± 0.04, 1.11 ± 1.49 mm for bladder, prostate, rectum, left and RFHs, respectively. Mean center of mass distances was within 3 mm for all organs. Our results performed significantly better than those of competing methods in most evaluation metrics. We demonstrated the feasibility of sMRI-aided DPNs for multi-organ segmentation on pelvic CT images, and its superiority over other networks. The proposed method could be used in routine prostate cancer radiotherapy treatment planning to rapidly segment the prostate and standard OARs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1088/1361-6560/abf2f9DOI Listing
April 2021

Electrochemical recovery and high value-added reutilization of heavy metal ions from wastewater: Recent advances and future trends.

Environ Int 2021 07 21;152:106512. Epub 2021 Mar 21.

National-Local Joint Engineering Research Center of Heavy Metals Pollutants Control and Resource Utilization, Nanchang Hangkong University, Nanchang 330063, PR China; Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang 330063, PR China. Electronic address:

Wastewater treatment for heavy metals is currently transitioning from pollution remediation towards resource recovery. As a controllable and environment-friendly method, electrochemical technologies have recently gained significant attention. However, there is a lack of systematic and goal oriented summarize of electrochemical metal recovery techniques, which has inhibited the optimized application of these methods. This review aims at recent advances in electrochemical metal recovery techniques, by comparing different electrochemical recovery methods, attempts to target recycling heavy metal resources with minimize energy consumption, boost recovery efficiency and realize the commercial application. In this review, different electrochemical recovery methods (including E-adsorption recovery, E-oxidation recovery, E-reduction recovery, and E-precipitation recovery) for recovering heavy metals are introduced, followed an analysis of their corresponding mechanisms, influencing factors, and recovery efficiencies. In addition, the mass transfer efficiency can be promoted further through optimizing electrodes and reactors, and multiple technologies (photo-electrochemical and sono-electrochemical) could to be used synergistically improve recovery efficiencies. Finally, the most promising directions for electrochemical recovery of heavy metals are discussed along with the challenges and future opportunities of electrochemical technology in recycling heavy metals from wastewater.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.envint.2021.106512DOI Listing
July 2021

Additional Effects of Xbox Kinect Training on Upper Limb Function in Chronic Stroke Patients: A Randomized Control Trial.

Healthcare (Basel) 2021 Feb 24;9(3). Epub 2021 Feb 24.

The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Institute of Health and Rehabilitation Science, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.

Background: Xbox Kinect-based virtual reality, being a novel approach, has therapeutic benefits in rehabilitation and its use is encouraged in stroke rehabilitation of upper extremities.

Objective: Primary aim of the current study is to investigate the additional effects of Xbox Kinect training in combination with routine physiotherapy exercises based on each component of Fugl-Meyer Assessment Scale for Upper Extremity (FMA-UE). Moreover, effect of upper limb rehabilitation on cognitive functions was also assessed.

Methods: This study was a parallel arm randomized control trial. Fifty-six participants were recruited and randomly allocated to either an Xbox Kinect training group (XKGT) or exercise training group (ETG). Measures of concern were recorded using FMA-UE, Box and Block Test (BBT), and Montreal Cognitive Assessment (MOCA). Evaluation was conducted at baseline and after completion of intervention at the sixth week.

Results: There were significant differences from pre- to post-intervention scores of FMA-UE and BBT ( < 0.001) in both groups, whereas no difference was observed for MOCA (XKTG p value 0.417, ETG p value 0.113). At six-week follow-up there were significant differences between both groups in FMA-UE total score ( < 0.001), volitional movement within synergies ( < 0.001), wrist ( = 0.021), hand ( = 0.047), grasp ( = 0.006) and coordination/speed ( = 0.004), favoring the Xbox Kinect training group.

Conclusion: To conclude, results indicate repetitive use of the hemiparetic upper extremity by Xbox Kinect-based upper limb rehabilitation training in addition to conventional therapy has a promising potential to enhance upper limb motor function for stroke patients.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/healthcare9030242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7996301PMC
February 2021

Echocardiographic image multi-structure segmentation using Cardiac-SegNet.

Med Phys 2021 May 1;48(5):2426-2437. Epub 2021 Apr 1.

Department of Radiation Oncology and Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA.

Purpose: Cardiac boundary segmentation of echocardiographic images is important for cardiac function assessment and disease diagnosis. However, it is challenging to segment cardiac ventricles due to the low contrast-to-noise ratio and speckle noise of the echocardiographic images. Manual segmentation is subject to interobserver variability and is too slow for real-time image-guided interventions. We aim to develop a deep learning-based method for automated multi-structure segmentation of echocardiographic images.

Methods: We developed an anchor-free mask convolutional neural network (CNN), termed Cardiac-SegNet, which consists of three subnetworks, that is, a backbone, a fully convolutional one-state object detector (FCOS) head, and a mask head. The backbone extracts multi-level and multi-scale features from endocardium image. The FOCS head utilizes these features to detect and label the region-of-interests (ROIs) of the segmentation targets. Unlike the traditional mask regional CNN (Mask R-CNN) method, the FCOS head is anchor-free and can model the spatial relationship of the targets. The mask head utilizes a spatial attention strategy, which allows the network to highlight salient features to perform segmentation on each detected ROI. For evaluation, we investigated 450 patient datasets by a five-fold cross-validation and a hold-out test. The endocardium (LV ) and epicardium (LV ) of the left ventricle and left atrium (LA) were segmented and compared with manual contours using the Dice similarity coefficient (DSC), Hausdorff distance (HD), mean absolute distance (MAD), and center-of-mass distance (CMD).

Results: Compared to U-Net and Mask R-CNN, our method achieved higher segmentation accuracy and fewer erroneous speckles. When our method was evaluated on a separate hold-out dataset at the end diastole (ED) and the end systole (ES) phases, the average DSC were 0.952 and 0.939 at ED and ES for the LV , 0.965 and 0.959 at ED and ES for the LV , and 0.924 and 0.926 at ED and ES for the LA. For patients with a typical image size of 549 × 788 pixels, the proposed method can perform the segmentation within 0.5 s.

Conclusion: We proposed a fast and accurate method to segment echocardiographic images using an anchor-free mask CNN.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mp.14818DOI Listing
May 2021

Automatic delineation of cardiac substructures using a region-based fully convolutional network.

Med Phys 2021 Mar 2. Epub 2021 Mar 2.

Department of Radiation Oncology and Winship Cancer Institute, Emory University, Atlanta, GA, USA.

Purpose: Radiation dose to specific cardiac substructures, such as the atria and ventricles, has been linked to post-treatment toxicity and has shown to be more predictive of these toxicities than dose to the whole heart. A deep learning-based algorithm for automatic generation of these contours is proposed to aid in either retrospective or prospective dosimetric studies to better understand the relationship between radiation dose and toxicities.

Methods: The proposed method uses a mask-scoring regional convolutional neural network (RCNN) which consists of five major subnetworks: backbone, regional proposal network (RPN), RCNN head, mask head, and mask-scoring head. Multiscale feature maps are learned from computed tomography (CT) via the backbone network. The RPN utilizes these feature maps to detect the location and region-of-interest (ROI) of all substructures, and the final three subnetworks work in series to extract structural information from these ROIs. The network is trained using 55 patient CT datasets, with 22 patients having contrast scans. Threefold cross validation (CV) is used for evaluation on 45 datasets, and a separate cohort of 10 patients are used for holdout evaluation. The proposed method is compared to a 3D UNet.

Results: The proposed method produces contours that are qualitatively similar to the ground truth contours. Quantitatively, the proposed method achieved average Dice score coefficients (DSCs) for the whole heart, chambers, great vessels, coronary arteries, the valves of the heart of 0.96, 0.94, 0.93, 0.66, and 0.77 respectively, outperforming the 3D UNet, which achieved DSCs of 0.92, 0.87, 0.88, 0.48, and 0.59 for the corresponding substructure groups. Mean surface distances (MSDs) between substructures segmented by the proposed method and the ground truth were <2 mm except for the left anterior descending coronary artery and the mitral and tricuspid valves, and <5 mm for all substructures. When dividing results into noncontrast and contrast datasets, the model performed statistically significantly better in terms of DSC, MSD, centroid mean distance (CMD), and volume difference for the chambers and whole heart with contrast. Notably, the presence of contrast did not statistically significantly affect coronary artery segmentation DSC or MSD. After network training, all substructures and the whole heart can be segmented on new datasets in less than 5 s.

Conclusions: A deep learning network was trained for automatic delineation of cardiac substructures based on CT alone. The proposed method can be used as a tool to investigate the relationship between cardiac substructure dose and treatment toxicities.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mp.14810DOI Listing
March 2021

Multifunctional Batteries: Flexible, Transient, and Transparent.

ACS Cent Sci 2021 Feb 26;7(2):231-244. Epub 2021 Jan 26.

Laboratory for Multifunctional Materials, Department of Materials, ETH Zurich, Vladimir-Prelog-Weg 5, 8093 Zurich, Switzerland.

The primary task of a battery is to store energy and to power electronic devices. This has hardly changed over the years despite all the progress made in improving their electrochemical performance. In comparison to batteries, electronic devices are continuously equipped with new functions, and they also change their physical appearance, becoming flexible, rollable, stretchable, or maybe transparent or even transient or degradable. Mechanical flexibility makes them attractive for wearable electronics or for electronic paper; transparency is desired for transparent screens or smart windows, and degradability or transient properties have the potential to reduce electronic waste. For fully integrated and self-sufficient systems, these devices have to be powered by batteries with similar physical characteristics. To make the currently used rigid and heavy batteries flexible, transparent, and degradable, the whole battery architecture including active materials, current collectors, electrolyte/separator, and packaging has to be redesigned. This requires a fundamental paradigm change in battery research, moving away from exclusively addressing the electrochemical aspects toward an interdisciplinary approach involving chemists, materials scientists, and engineers. This Outlook provides an overview of the different activities in the field of flexible, transient, and transparent batteries with a focus on the challenges that have to be faced toward the development of such multifunctional energy storage devices.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acscentsci.0c01318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7908028PMC
February 2021

PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment.

Nat Commun 2021 02 26;12(1):1167. Epub 2021 Feb 26.

Department of Computer Science, Rice University, Houston, Texas, 77005, United States.

With advances in synthetic biology and genome engineering comes a heightened awareness of potential misuse related to biosafety concerns. A recent study employed machine learning to identify the lab-of-origin of DNA sequences to help mitigate some of these concerns. Despite their promising results, this deep learning based approach had limited accuracy, was computationally expensive to train, and wasn't able to provide the precise features that were used in its predictions. To address these shortcomings, we developed PlasmidHawk for lab-of-origin prediction. Compared to a machine learning approach, PlasmidHawk has higher prediction accuracy; PlasmidHawk can successfully predict unknown sequences' depositing labs 76% of the time and 85% of the time the correct lab is in the top 10 candidates. In addition, PlasmidHawk can precisely single out the signature sub-sequences that are responsible for the lab-of-origin detection. In summary, PlasmidHawk represents an explainable and accurate tool for lab-of-origin prediction of synthetic plasmid sequences. PlasmidHawk is available at https://gitlab.com/treangenlab/plasmidhawk.git .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-021-21180-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7910462PMC
February 2021

Mortality Risk After Radioiodine Therapy for Hyperthyroidism: A Systematic Review and Meta-Analysis.

Endocr Pract 2021 Apr 14;27(4):362-369. Epub 2020 Dec 14.

Department of Pathology, Renmin Hospital of Wuhan University, 238 Jiefang-Road, Wuchang District, Wuhan, 430060, P.R. China. Electronic address:

Objective: Radioiodine has been increasingly used to treat hyperthyroidism for many years. Although widely regarded as an effective therapy, radioiodine treatment for hyperthyroidism has been suspected to be associated with the risk of mortality. This study aimed to quantify the mortality outcomes in patients who were treated for hyperthyroidism with radioiodine.

Methods: Systematic search and meta-analysis were performed to determine the risk of mortality in patients treated with radioiodine for hyperthyroidism. Relevant studies were searched through August 2020 and selected in accordance with the inclusion criteria.

Results: A total of 13 studies were identified. The summary odds ratios (ORs) showed an increased risk of all-cause mortality in patients who were treated with radioiodine for hyperthyroidism (OR = 1.20; 95% CI = 1.07-1.35). The risk of death attributed to all forms of circulatory, respiratory, and endocrine and metabolic diseases was significantly increased, with summary ORs of 1.23 (95% CI, 1.12-1.35), 1.43 (95% CI, 1.17-1.75), and 2.38 (95% CI, 1.85-3.06), respectively. The summary ORs revealed no significant association between radioiodine treatment for hyperthyroidism and the risk of cancer mortality (OR = 1.03; 95% CI, 0.98-1.09). Radioiodine treatment for hyperthyroidism was not associated with the risk of mortality from breast, respiratory system, gastrointestinal, and genitourinary cancers.

Conclusion: Radioiodine treatment for hyperthyroidism is associated with the risk of all-cause mortality but not cancer mortality. Future research needs to address the causes of hyperthyroidism, effects of radioiodine therapy, and potential effects of confounding to identify causality.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.eprac.2020.10.018DOI Listing
April 2021