Risk factors and cognitive correlates of white matter hyperintensities in ethnically diverse populations without dementia: The COSMIC consortium.

INTRODUCTION: White matter hyperintensities (WMHs) are an important imaging marker for cerebral small vessel diseases, but their risk factors and cognitive associations have not been well documented in populations of different ethnicities and/or from different geographical regions. METHODS: We investigated how WMHs were associated with vascular risk factors and cognition in both Whites and Asians, using data from five population-based cohorts of non-demented older individuals from Australia, Singapore, South Korea, and Sweden (N = 1946). WMH volumes (whole brain, periventricular, and deep) were quantified with UBO Detector and harmonized using the ComBat model. We also harmonized various vascular risk factors and scores for global cognition and individual cognitive domains. RESULTS: Factors associated with larger whole brain WMH volumes included diabetes, hypertension, stroke, current smoking, body mass index, higher alcohol intake, and insufficient physical activity. Hypertension and stroke had stronger associations with WMH volumes in Whites than in Asians. No associations between WMH volumes and cognitive performance were found after correction for multiple testing. CONCLUSION: The current study highlights ethnic differences in the contributions of vascular risk factors to WMHs.

3 directional Inception-ResUNet: Deep spatial feature learning for multichannel singing voice separation with distortion.

Singing voice separation on robots faces the problem of interpreting ambiguous auditory signals. The acoustic signal, which the humanoid robot perceives through its onboard microphones, is a mixture of singing voice, music, and noise, with distortion, attenuation, and reverberation. In this paper, we used the 3D Inception-ResUNet structure in the U-shaped encoding and decoding network to improve the utilization of the spatial and spectral information of the spectrogram. Multiobjectives were used to train the model: magnitude consistency loss, phase consistency loss, and magnitude correlation consistency loss. We recorded the singing voice and accompaniment derived from the MIR-1K dataset with NAO robots and synthesized the 10-channel dataset for training the model. The experimental results show that the proposed model trained by multiple objectives reaches an average NSDR of 11.55 dB on the test dataset, which outperforms the comparison model.

Risk factors and cognitive correlates of white matter hyperintensities in ethnically diverse populations without dementia: the COSMIC consortium.

INTRODUCTION: White matter hyperintensities (WMH) are an important imaging marker for cerebral small vessel diseases, but their risk factors and cognitive associations have not been well-documented in populations of different ethnicities and/or from different geographical regions. METHOD: Magnetic resonance imaging data of five population-based cohorts of non-demented older individuals from Australia, Singapore, South Korea, and Sweden (N = 1,946) were examined for WMH and their associations with vascular risk factors and cognition. RESULT: Factors associated with larger whole brain WMH volumes included diabetes, hypertension, stroke, current smoking, body mass index, higher alcohol intake and insufficient physical activity. Participants with moderate or higher physical activity had less WMH than those who never exercised, but the former two groups did not differ. Hypertension and stroke had stronger associations with WMH volumes in the White, compared to Asian subsample. DISCUSSION: The current study highlighted the ethnic differences in the contributions of vascular risk factors to WMH.

Ordered growth of metal oxides in patterned multi-angle microstructures.

Herein, we report a facile method combining top-down patterning transfer and bottom-up nanorod growth for preparing large-area and ordered TiO2 nanorod arrays. Pre-crystallization seeding was patterned with nanostructured morphologies via interfacial tension-driven precursor solution scattering on various types and period templates. This is a widely applicable strategy for capillary force-driven interfacial patterns, which also shows great operability in complex substrate morphologies with multiple-angle mixing. Moreover, the customized patterned lithographic templates containing English words, Arabic numerals, and Chinese characters are used to verify the applicability and controllability of this hybrid method. In general, our work provides a versatile strategy for the low-cost and facile preparation of hydrothermally growable metal oxide (e.g., ZnO and MnO2) nanostructures with potential applications in the fields of microelectronic devices, photoelectric devices, energy storage, and photocatalysis.

A Multi-Scale Context Aware Attention Model for Medical Image Segmentation.

Medical image segmentation is critical for efficient diagnosis of diseases and treatment planning. In recent years, convolutional neural networks (CNN)-based methods, particularly U-Net and its variants, have achieved remarkable results on medical image segmentation tasks. However, they do not always work consistently on images with complex structures and large variations in regions of interest (ROI). This could be due to the fixed geometric structure of the receptive fields used for feature extraction and repetitive down-sampling operations that lead to information loss. To overcome these problems, the standard U-Net architecture is modified in this work by replacing the convolution block with a dilated convolution block to extract multi-scale context features with varying sizes of receptive fields, and adding a dilated inception block between the encoder and decoder paths to alleviate the problem of information recession and the semantic gap between features. Furthermore, the input of each dilated convolution block is added to the output through a squeeze and excitation unit, which alleviates the vanishing gradient problem and improves overall feature representation by re-weighting the channel-wise feature responses. The original inception block is modified by reducing the size of the spatial filter and introducing dilated convolution to obtain a larger receptive field. The proposed network was validated on three challenging medical image segmentation tasks with varying size ROIs: lung segmentation on chest X-ray (CXR) images, skin lesion segmentation on dermoscopy images and nucleus segmentation on microscopy cell images. Improved performance compared to state-of-the-art techniques demonstrates the effectiveness and generalisability of the proposed Dilated Convolution and Inception blocks-based U-Net (DCI-UNet).

Monitoring of Pigmented Skin Lesions Using 3D Whole Body Imaging.

BACKGROUND AND OBJECTIVES: Advanced artificial intelligence and machine learning have great potential to redefine how skin lesions are detected, mapped, tracked and documented. Here, we propose a 3D whole-body imaging system known as 3DSkin-mapper to enable automated detection, evaluation and mapping of skin lesions. METHODS: A modular camera rig arranged in a cylindrical configuration was designed to automatically capture images of the entire skin surface of a subject synchronously from multiple angles. Based on the images, we developed algorithms for 3D model reconstruction, data processing and skin lesion detection and tracking based on deep convolutional neural networks. We also introduced a customised, user-friendly, and adaptable interface that enables individuals to interactively visualise, manipulate, and annotate the images. The interface includes built-in features such as mapping 2D skin lesions onto the corresponding 3D model. RESULTS: The proposed system is developed for skin lesion screening, the focus of this paper is to introduce the system instead of clinical study. Using synthetic and real images we demonstrate the effectiveness of the proposed system by providing multiple views of a target skin lesion, enabling further 3D geometry analysis and longitudinal tracking. Skin lesions are identified as outliers which deserve more attention from a skin cancer physician. Our detector leverages expert annotated labels to learn representations of skin lesions, while capturing the effects of anatomical variability. It takes only a few seconds to capture the entire skin surface, and about half an hour to process and analyse the images. CONCLUSIONS: Our experiments show that the proposed system allows fast and easy whole body 3D imaging. It can be used by dermatological clinics to conduct skin screening, detect and track skin lesions over time, identify suspicious lesions, and document pigmented lesions. The system can potentially save clinicians time and effort significantly. The 3D imaging and analysis has the potential to change the paradigm of whole body photography with many applications in skin diseases, including inflammatory and pigmentary disorders. With reduced time requirements for recording and documenting high-quality skin information, doctors could spend more time providing better-quality treatment based on more detailed and accurate information.

Space-Confined seeding and growth of ordered arrays of TiO2 hierarchical nanostructures.

Here, we report a facile approach to fabricate large area ordered arrays of TiO2 hierarchical nanostructures through space-confined seeding and growth on inverted pyramid templates. The mechanisms of space-confined seeding and growth have been systematically explored and studied. The drying TiO2 seed precursor solution prefers to accumulate on the narrow structures including the centre and edges of the inverted pyramid structures, which facilitates to reduce the free energy of the precursor solution surface and form crystal seeds. Followed by hydrothermal treatment, selective growth of TiO2 hierarchical nanostructures on desirable locations, such as only on the centre, only on the edges, or on the entire surface of the inverted pyramid templates, can be achieved. In addition, the growth temperature, duration and solvents affect the morphology of TiO2 hierarchical nanostructures. This work may provide a universal approach to obtain ordered arrays of metal oxide (e.g. ZnO and MnO2, etc.) nanostructures for applications in optics, electrics, energy, and catalysis.

Detection and Visualisation of Pneumoconiosis Using an Ensemble of Multi-Dimensional Deep Features Learned from Chest X-rays.

Pneumoconiosis is a group of occupational lung diseases induced by mineral dust inhalation and subsequent lung tissue reactions. It can eventually cause irreparable lung damage, as well as gradual and permanent physical impairments. It has affected millions of workers in hazardous industries throughout the world, and it is a leading cause of occupational death. It is difficult to diagnose early pneumoconiosis because of the low sensitivity of chest radiographs, the wide variation in interpretation between and among readers, and the scarcity of B-readers, which all add to the difficulty in diagnosing these occupational illnesses. In recent years, deep machine learning algorithms have been extremely successful at classifying and localising abnormality of medical images. In this study, we proposed an ensemble learning approach to improve pneumoconiosis detection in chest X-rays (CXRs) using nine machine learning classifiers and multi-dimensional deep features extracted using CheXNet-121 architecture. There were eight evaluation metrics utilised for each high-level feature set of the associated cross-validation datasets in order to compare the ensemble performance and state-of-the-art techniques from the literature that used the same cross-validation datasets. It is observed that integrated ensemble learning exhibits promising results (92.68% accuracy, 85.66% Matthews correlation coefficient (MCC), and 0.9302 area under the precision-recall (PR) curve), compared to individual CheXNet-121 and other state-of-the-art techniques. Finally, Grad-CAM was used to visualise the learned behaviour of individual dense blocks within CheXNet-121 and their ensembles into three-color channels of CXRs. We compared the Grad-CAM-indicated ROI to the ground-truth ROI using the intersection of the union (IOU) and average-precision (AP) values for each classifier and their ensemble. Through the visualisation of the Grad-CAM within the blue channel, the average IOU passed more than 90% of the pneumoconiosis detection in chest radiographs.

Deep Ensemble Learning for the Automatic Detection of Pneumoconiosis in Coal Worker's Chest X-ray Radiography.

Globally, coal remains one of the natural resources that provide power to the world. Thousands of people are involved in coal collection, processing, and transportation. Particulate coal dust is produced during these processes, which can crush the lung structure of workers and cause pneumoconiosis. There is no automated system for detecting and monitoring diseases in coal miners, except for specialist radiologists. This paper proposes ensemble learning techniques for detecting pneumoconiosis disease in chest X-ray radiographs (CXRs) using multiple deep learning models. Three ensemble learning techniques (simple averaging, multi-weighted averaging, and majority voting (MVOT)) were proposed to investigate performances using randomised cross-folds and leave-one-out cross-validations datasets. Five statistical measurements were used to compare the outcomes of the three investigations on the proposed integrated approach with state-of-the-art approaches from the literature for the same dataset. In the second investigation, the statistical combination was marginally enhanced in the ensemble of multi-weighted averaging on a robust model, CheXNet. However, in the third investigation, the same model elevated accuracies from 87.80 to 90.2%. The investigated results helped us identify a robust deep learning model and ensemble framework that outperformed others, achieving an accuracy of 91.50% in the automated detection of pneumoconiosis.

Computer-aided extraction of select MRI markers of cerebral small vessel disease: A systematic review.

Cerebral small vessel disease (CSVD) is a major vascular contributor to cognitive impairment in ageing, including dementias. Imaging remains the most promising method for in vivo studies of CSVD. To replace the subjective and laborious visual rating approaches, emerging studies have applied state-of-the-art artificial intelligence to extract imaging biomarkers of CSVD from MRI scans. We aimed to summarise published computer-aided methods for the examination of three imaging biomarkers of CSVD, namely cerebral microbleeds (CMB), dilated perivascular spaces (PVS), and lacunes of presumed vascular origin. Seventy classical image processing, classical machine learning, and deep learning studies were identified. Transfer learning and weak supervision techniques have been applied to accommodate the limitations in the training data. While good performance metrics were achieved in local datasets, there have not been generalisable pipelines validated in different research and/or clinical cohorts. Future studies could consider pooling data from multiple sources to increase data size and diversity, and evaluating performance using both image processing metrics and associations with clinical measures.

Computer-Aided Diagnosis of Coal Workers' Pneumoconiosis in Chest X-ray Radiographs Using Machine Learning: A Systematic Literature Review.

Computer-aided diagnostic (CAD) systems can assist radiologists in detecting coal workers' pneumoconiosis (CWP) in their chest X-rays. Early diagnosis of the CWP can significantly improve workers' survival rate. The development of the CAD systems will reduce risk in the workplace and improve the quality of chest screening for CWP diseases. This systematic literature review (SLR) amis to categorise and summarise the feature extraction and detection approaches of computer-based analysis in CWP using chest X-ray radiographs (CXR). We conducted the SLR method through 11 databases that focus on science, engineering, medicine, health, and clinical studies. The proposed SLR identified and compared 40 articles from the last 5 decades, covering three main categories of computer-based CWP detection: classical handcrafted features-based image analysis, traditional machine learning, and deep learning-based methods. Limitations of this review and future improvement of the review are also discussed.

Weakly Supervised RGB-D Salient Object Detection With Prediction Consistency Training and Active Scribble Boosting.

RGB-D salient object detection (SOD) has attracted increasingly more attention as it shows more robust results in complex scenes compared with RGB SOD. However, state-of-the-art RGB-D SOD approaches heavily rely on a large amount of pixel-wise annotated data for training. Such densely labeled annotations are often labor-intensive and costly. To reduce the annotation burden, we investigate RGB-D SOD from a weakly supervised perspective. More specifically, we use annotator-friendly scribble annotations as supervision signals for model training. Since scribble annotations are much sparser compared to ground-truth masks, some critical object structure information might be neglected. To preserve such structure information, we explicitly exploit the complementary edge information from two modalities (i.e., RGB and depth). Specifically, we leverage the dual-modal edge guidance and introduce a new network architecture with a dual-edge detection module and a modality-aware feature fusion module. In order to use the useful information of unlabeled pixels, we introduce a prediction consistency training scheme by comparing the predictions of two networks optimized by different strategies. Moreover, we develop an active scribble boosting strategy to provide extra supervision signals with negligible annotation cost, leading to significant SOD performance improvement. Extensive experiments on seven benchmarks validate the superiority of our proposed method. Remarkably, the proposed method with scribble annotations achieves competitive performance in comparison to fully supervised state-of-the-art methods.

Deep Learning for Object Detection, Classification and Tracking in Industry Applications.

Object detection, classification and tracking are three important computer vision techniques [...].

Automatic detection of fish and tracking of movement for ecology.

Animal movement studies are conducted to monitor ecosystem health, understand ecological dynamics, and address management and conservation questions. In marine environments, traditional sampling and monitoring methods to measure animal movement are invasive, labor intensive, costly, and limited in the number of individuals that can be feasibly tracked. Automated detection and tracking of small-scale movements of many animals through cameras are possible but are largely untested in field conditions, hampering applications to ecological questions.Here, we aimed to test the ability of an automated object detection and object tracking pipeline to track small-scale movement of many individuals in videos. We applied the pipeline to track fish movement in the field and characterize movement behavior. We automated the detection of a common fisheries species (yellowfin bream, Acanthopagrus australis) along a known movement passageway from underwater videos. We then tracked fish movement with three types of tracking algorithms (MOSSE, Seq-NMS, and SiamMask) and evaluated their accuracy at characterizing movement.We successfully detected yellowfin bream in a multispecies assemblage (F1 score =91%). At least 120 of the 169 individual bream present in videos were correctly identified and tracked. The accuracies among the three tracking architectures varied, with MOSSE and SiamMask achieving an accuracy of 78% and Seq-NMS 84%.By employing this integrated object detection and tracking pipeline, we demonstrated a noninvasive and reliable approach to studying fish behavior by tracking their movement under field conditions. These cost-effective technologies provide a means for future studies to scale-up the analysis of movement across many visual monitoring systems.

Quantitative analysis of abnormalities in gynecologic cytopathology with deep learning.

Cervical cancer is one of the most frequent cancers in women worldwide, yet the early detection and treatment of lesions via regular cervical screening have led to a drastic reduction in the mortality rate. However, the routine examination of screening as a regular health checkup of women is characterized as time-consuming and labor-intensive, while there is lack of characteristic phenotypic profile and quantitative analysis. In this research, over the analysis of a privately collected and manually annotated dataset of 130 cytological whole-slide images, the authors proposed a deep-learning diagnostic system to localize, grade, and quantify squamous cell abnormalities. The system can distinguish abnormalities at the morphology level, namely atypical squamous cells of undetermined significance, low-grade squamous intraepithelial lesion, high-grade squamous intraepithelial lesion, and squamous cell carcinoma, as well as differential phenotypes of normal cells. The case study covered 51 positive and 79 negative digital gynecologic cytology slides collected from 2016 to 2018. Our automatic diagnostic system demonstrated its sensitivity of 100% at slide-level abnormality prediction, with the confirmation with three pathologists who performed slide-level diagnosis and training sample annotations. In the cellular-level classification, we yielded an accuracy of 94.5% in the binary classification between normality and abnormality, and the AUC was above 85% for each subtype of epithelial abnormality. Although the final confirmation from pathologists is often a must, empirically, computer-aided methods are capable of the effective extraction, interpretation, and quantification of morphological features, while also making it more objective and reproducible.

Automated detection of pneumoconiosis with multilevel deep features learned from chest X-Ray radiographs.

Early detection of pneumoconiosis in X-Rays has been a challenging task that leads to high inter- and intra-reader variability. Motivated by the success of deep learning in general and medical image classification, this paper proposes an approach to automatically detect pneumoconiosis using a deep feature based binary classifier. The features are extracted from X-rays using deep transfer learning, comprising both low and high-level feature sets. For this, a CNN model pre-trained with a transfer learning from a CheXNet model was initially used to extract deep features from the X-Ray images, then the deep features were mapped to higher-dimensional feature spaces for classification using Support Vector Machine (SVM) and CNN based feature aggregation methods. In order to cross validate the proposed method, the training and testing images were randomly split into three folds before each experiment. Nine evaluation metrics were employed to compare the performance of the proposed method and state-of-the-art methods from the literature that used the same datasets. The experimental results show that the proposed framework outperformed others, achieving an accuracy of 92.68% in the automated detection of pneumoconiosis.

Guidelines for establishing a 3-D printing biofabrication laboratory.

Advanced manufacturing and 3D printing are transformative technologies currently undergoing rapid adoption in healthcare, a traditionally non-manufacturing sector. Recent development in this field, largely enabled by merging different disciplines, has led to important clinical applications from anatomical models to regenerative bioscaffolding and devices. Although much research to-date has focussed on materials, designs, processes, and products, little attention has been given to the design and requirements of facilities for enabling clinically relevant biofabrication solutions. These facilities are critical to overcoming the major hurdles to clinical translation, including solving important issues such as reproducibility, quality control, regulations, and commercialization. To improve process uniformity and ensure consistent development and production, large-scale manufacturing of engineered tissues and organs will require standardized facilities, equipment, qualification processes, automation, and information systems. This review presents current and forward-thinking guidelines to help design biofabrication laboratories engaged in engineering model and tissue constructs for therapeutic and non-therapeutic applications.

Machine intelligence for nerve conduit design and production.

Nerve guidance conduits (NGCs) have emerged from recent advances within tissue engineering as a promising alternative to autografts for peripheral nerve repair. NGCs are tubular structures with engineered biomaterials, which guide axonal regeneration from the injured proximal nerve to the distal stump. NGC design can synergistically combine multiple properties to enhance proliferation of stem and neuronal cells, improve nerve migration, attenuate inflammation and reduce scar tissue formation. The aim of most laboratories fabricating NGCs is the development of an automated process that incorporates patient-specific features and complex tissue blueprints (e.g. neurovascular conduit) that serve as the basis for more complicated muscular and skin grafts. One of the major limitations for tissue engineering is lack of guidance for generating tissue blueprints and the absence of streamlined manufacturing processes. With the rapid expansion of machine intelligence, high dimensional image analysis, and computational scaffold design, optimized tissue templates for 3D bioprinting (3DBP) are feasible. In this review, we examine the translational challenges to peripheral nerve regeneration and where machine intelligence can innovate bottlenecks in neural tissue engineering.

CCND1 rs9344 polymorphism is associated with the risk of hepatocellular carcinoma in Caucasian population.

AIMS: Some studies investigated the association between CCND1 rs9344 polymorphism and hepatocellular carcinoma (HCC) risk. However, the results were inconclusive. Thus, we did a meta-analysis to determine this relationship. MATERIALS AND METHODS: Relevant studies were systematically searched using the PubMed, CNKI, and EMBASE databases. The strength of the association was calculated with the odds ratio (OR) and respective 95% confidence intervals (Cis). RESULTS: We investigated the association between CCND1 rs9344 polymorphism and HCC risk in the dominant models. The result of this meta-analysis showed that CCND1 rs9344 polymorphism did not significantly associated with HCC risk (OR = 1.09; 95% CI 0.88-1.34). In the stratified analysis by ethnicity, we found that this polymorphism was significantly associated with HCC risk in Caucasians (OR = 1.55; 95% CI, 1.05-2.29). However, we did not find any significant association between this polymorphism and HCC risk in Asians (OR = 0.91; 95% CI, 0.71-1.18). CONCLUSIONS: This meta-analysis suggested that CCND1 rs9344 polymorphism might be associated with the risk of HCC among Caucasians.

HEDD: the human epigenetic drug database.

Epigenetic drugs are chemical compounds that target disordered post-translational modification of histone proteins and DNA through enzymes, and the recognition of these changes by adaptor proteins. Epigenetic drug-related experimental data such as gene expression probed by high-throughput sequencing, co-crystal structure probed by X-RAY diffraction and binding constants probed by bio-assay have become widely available. The mining and integration of multiple kinds of data can be beneficial to drug discovery and drug repurposing. HEMD and other epigenetic databases store comprehensively epigenetic data where users can acquire segmental information of epigenetic drugs. However, some data types such as high-throughput datasets are not provide by these databases and they do not support flexible queries for epigenetic drug-related experimental data. Therefore, in reference to HEMD and other epigenetic databases, we developed a relatively comprehensive database for human epigenetic drugs. The human epigenetic drug database (HEDD) focuses on the storage and integration of epigenetic drug datasets obtained from laboratory experiments and manually curated information. The latest release of HEDD incorporates five kinds of datasets: (i) drug, (ii) target, (iii) disease, (vi) high-throughput and (v) complex. In order to facilitate data extraction, flexible search options were built in HEDD, which allowed an unlimited condition query for specific kinds of datasets using drug names, diseases and experiment types.Database URL: http://hedds.org/.