RS2-Net: An end-to-end deep learning framework for rodent skull stripping in multi-center brain MRI.

Skull stripping is a crucial preprocessing step in magnetic resonance imaging (MRI), where experts manually create brain masks. This labor-intensive process heavily relies on the annotator's expertise, as automation faces challenges such as low tissue contrast, significant variations in image resolution, and blurred boundaries between the brain and surrounding tissues, particularly in rodents. In this study, we have developed a lightweight framework based on Swin-UNETR to automate the skull stripping process in MRI scans of mice and rats. The primary objective of this framework is to eliminate the need for preprocessing, reduce the workload, and provide an out-of-the-box solution capable of adapting to various MRI image resolutions. By employing a lightweight neural network, we aim to lower the performance requirements of the framework. To validate the effectiveness of our approach, we trained and evaluated the network using publicly available multi-center data, encompassing 1,037 rodents and 1,142 images from 89 centers, resulting in a preliminary mean Dice coefficient of 0.9914. The framework, data, and pre-trained models can be found on the following link: https://github.com/VitoLin21/Rodent-Skull-Stripping.

Adaptive node feature extraction in graph-based neural networks for brain diseases diagnosis using self-supervised learning.

Electroencephalography (EEG) has demonstrated significant value in diagnosing brain diseases. In particular, brain networks have gained prominence as they offer additional valuable insights by establishing connections between EEG signal channels. While brain connections are typically delineated by channel signal similarity, there lacks a consistent and reliable strategy for ascertaining node characteristics. Conventional node features such as temporal and frequency domain properties of EEG signals prove inadequate for capturing the extensive EEG information. In our investigation, we introduce a novel adaptive method for extracting node features from EEG signals utilizing a distinctive task-induced self-supervised learning technique. By amalgamating these extracted node features with fundamental edge features constructed using Pearson correlation coefficients, we showed that the proposed approach can function as a plug-in module that can be integrated to many common GNN networks (e.g., GCN, GraphSAGE, GAT) as a replacement of node feature selections module. Comprehensive experiments are then conducted to demonstrate the consistently superior performance and high generality of the proposed method over other feature selection methods in various of brain disorder prediction tasks, such as depression, schizophrenia, and Parkinson's disease. Furthermore, compared to other node features, our approach unveils profound spatial patterns through graph pooling and structural learning, shedding light on pivotal brain regions influencing various brain disorder prediction based on derived features.

Comparative analysis of brain age prediction using structural and diffusion MRIs in neonates.

Using machine learning techniques to predict brain age from multimodal data has become a crucial biomarker for assessing brain development. Among various types of brain imaging data, structural magnetic resonance imaging (sMRI) and diffusion magnetic resonance imaging (dMRI) are the most commonly used modalities. sMRI focuses on depicting macrostructural features of the brain, while dMRI reveals the orientation of major white matter fibers and changes in tissue microstructure. However, their differential capabilities in reflecting newborn age and clinical implications have not been systematically studied. This study aims to explore the impact of sMRI and dMRI on brain age prediction. Comparing predictions based on T2-weighted(T2w) and fractional anisotropy (FA) images, we found their mean absolute errors (MAE) in predicting infant age to be similar. Exploratory analysis revealed for T2w images, areas such as the cerebral cortex and ventricles contribute most significantly to age prediction, whereas FA images highlight the cerebral cortex and regions of the main white matter tracts. Despite both modalities focusing on the cerebral cortex, they exhibit significant region-wise differences, reflecting developmental disparities in macro- and microstructural aspects of the cortex. Additionally, we examined the effects of prematurity, gender, and hemispherical asymmetry of the brain on age prediction for both modalities. Results showed significant differences (p<0.05) in age prediction biases based on FA images across gender and hemispherical asymmetry, whereas no significant differences were observed with T2w images. This study underscores the differences between T2w and FA images in predicting infant brain age, offering new perspectives for studying infant brain development and aiding more effective assessment and tracking of infant development.

Harmonizing three-dimensional MRI using pseudo-warping field guided GAN.

In pursuit of cultivating automated models for magnetic resonance imaging (MRI) to aid in diagnostics, an escalating demand for extensive, multisite, and heterogeneous brain imaging datasets has emerged. This potentially introduces biased outcomes when directly applied for subsequent analysis. Researchers have endeavored to address this issue by pursuing the harmonization of MRIs. However, most existing image-based harmonization methods for MRI are tailored for 2D slices, which may introduce inter-slice variations when they are combined into a 3D volume. In this study, we aim to resolve inconsistencies between slices by introducing a pseudo-warping field. This field is created randomly and utilized to transform a slice into an artificially warped subsequent slice. The objective of this pseudo-warping field is to ensure that generators can consistently harmonize adjacent slices to another domain, without being affected by the varying content present in different slices. Furthermore, we construct unsupervised spatial and recycle loss to enhance the spatial accuracy and slice-wise consistency across the 3D images. The results demonstrate that our model effectively mitigates inter-slice variations and successfully preserves the anatomical details of the images during the harmonization process. Compared to generative harmonization models that employ 3D operators, our model exhibits greater computational efficiency and flexibility.

The effect of preterm birth on thalamic development based on shape and structural covariance analysis.

Acting as a central hub in regulating brain functions, the thalamus plays a pivotal role in controlling high-order brain functions. Considering the impact of preterm birth on infant brain development, traditional studies focused on the overall development of thalamus other than its subregions. In this study, we compared the volumetric growth and shape development of the thalamic hemispheres between the infants born preterm and full-term (Left volume: P = 0.027, Left normalized volume: P < 0.0001; Right volume: P = 0.070, Right normalized volume: P < 0.0001). The ventral nucleus region, dorsomedial nucleus region, and posterior nucleus region of the thalamus exhibit higher vulnerability to alterations induced by preterm birth. The structural covariance (SC) between the thickness of thalamus and insula in preterm infants (Left: corrected P = 0.0091, Right: corrected P = 0.0119) showed significant increase as compared to full-term controls. Current findings suggest that preterm birth affects the development of the thalamus and has differential effects on its subregions. The ventral nucleus region, dorsomedial nucleus region, and posterior nucleus region of the thalamus are more susceptible to the impacts of preterm birth.

Hippocampal asymmetry of regional development and structural covariance in preterm neonates.

Premature birth is associated with a high prevalence of neurodevelopmental impairments in surviving infants. The hippocampus is known to be critical for learning and memory, yet the putative effects of hippocampal dysfunction remain poorly understood in preterm neonates. In particular, while asymmetry of the hippocampus has been well noted both structurally and functionally, how preterm birth impairs hippocampal development and to what extent the hippocampus is asymmetrically impaired by preterm birth have not been well delineated. In this study, we compared volumetric growth and shape development in the hippocampal hemispheres and structural covariance (SC) between hippocampal vertices and cortical thickness in cerebral cortex regions between two groups. We found that premature infants had smaller volumes of the right hippocampi only. Lower thickness was observed in the hippocampal head in both hemispheres for preterm neonates compared with full-term peers, though preterm neonates exhibited an accelerated age-related change of hippocampal thickness in the left hippocampi. The SC between the left hippocampi and the limbic lobe of the premature infants was severely impaired compared with the term-born neonates. These findings suggested that the development of the hippocampus during the third trimester may be altered following early extrauterine exposure with a high degree of asymmetry.

Morphological Development Trajectory and Structural Covariance Network of the Human Fetal Cortical Plate during the Early Second Trimester.

During the early second trimester, the cortical plate, or "the developing cortex", undergoes immensely complex and rapid development to complete its major complement of neurons. However, morphological development of the cortical plate and the precise patterning of brain structural covariance networks during this period remain unexplored. In this study, we used 7.0 T high-resolution magnetic resonance images of brain specimens ranging from 14 to 22 gestational weeks to manually segment the cortical plate. Thickness, area expansion, and curvature (i.e., folding) across the cortical plate regions were computed, and correlations of thickness values among different cortical plate regions were measured to analyze fetal cortico-cortical structural covariance throughout development of the early second trimester. The cortical plate displayed significant increases in thickness and expansions in area throughout all regions but changes of curvature in only certain major sulci. The topological architecture and network properties of fetal brain covariance presented immature and inefficient organizations with low degree of integration and high degree of segregation. Altogether, our results provide novel insight on the developmental patterning of cortical plate thickness and the developmental origin of brain network architecture throughout the early second trimester.

A probabilistic atlas of locus coeruleus pathways to transentorhinal cortex for connectome imaging in Alzheimer's disease.

According to the latest Braak staging of Alzheimer's disease (AD), tau pathology occurs earliest in the brain in the locus coeruleus (LC) of the brainstem, then propagates to the transentorhinal cortex (TEC), and later to other neocortical regions. Recent animal and in vivo human brain imaging research also support the trans-axonal propagation of tau pathology. In addition, neurochemical studies link norepinephrine to behavioral symptoms in AD. It is thus critical to examine the integrity of the LC-TEC pathway in studying the early development of the disease, but there has been limited work in this direction. By leveraging the high-resolution and multi-shell diffusion MRI data from the Human Connectome Project (HCP), in this work we develop a novel method for the reconstruction of the LC-TEC pathway in a cohort of 40 HCP subjects carefully selected based on rigorous quality control of the residual distortion artifacts in the brainstem. A probabilistic atlas of the LC-TEC pathway of both hemispheres is then developed in the MNI152 space and distributed publicly on the NITRC website. To apply our atlas on clinical imaging data, we develop an automated approach to calculate the medial core of the LC-TEC pathway for localized analysis of connectivity changes. In a cohort of 138 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI), we demonstrate the detection of the decreased fiber integrity in the LC-TEC pathways with increasing disease severity.

Morphometric development of the human fetal cerebellum during the early second trimester.

The protracted nature of development makes the cerebellum vulnerable to a broad spectrum of pathologic conditions, especially during the early fetal period. This study aims to characterize normal cerebellar growth in human fetuses during the early second trimester. We manually segmented the fetal cerebellum using 7.0-T high-resolution MR images obtained in 35 specimens with gestational ages ranging from 15 to 22 weeks. Volume measurements and shape analysis were performed to quantitatively evaluate global and regional cerebellar growth. The absolute volume of the fetal cerebellum showed a quadratic growth with increasing gestational age, while the pattern of relative volume changes revealed that the cerebellum grew at a greater pace than the cerebrum after 17 gestational weeks. Shape analysis was used to examine the distinctive development of subregions of the cerebellum. The extreme lateral portions of both cerebellar hemispheres showed the lowest rate of growth. The anterior lobe grew faster than most of the posterior lobe. These findings expand our understanding of the early growth pattern of the human cerebellum and could be further used to assess the developmental conditions of the fetal brain.

Development of the human fetal hippocampal formation during early second trimester.

Development of the fetal hippocampal formation has been difficult to fully describe because of rapid changes in its shape during the fetal period. The aims of this study were to: (1) segment the fetal hippocampal formation using 7.0 T MR images from 41 specimens with gestational ages ranging from 14 to 22 weeks and (2) reveal the developmental course of the fetal hippocampal formation using volume and shape analyses. Differences in hemispheric volume were observed, with the right hippocampi being larger than the left. Absolute volume changes showed a linear increase, while relative volume changes demonstrated an inverted-U shape trend during this period. Together these exhibited a variable developmental rate among different regions of the fetal brain. Different sub-regional growth of the fetal hippocampal formation was specifically observed using shape analysis. The fetal hippocampal formation possessed a prominent medial-lateral bidirectional shape growth pattern during its rotation process. Our results provide additional insight into 3D hippocampal morphology in the assessment of fetal brain development and can be used as a reference for future hippocampal studies.

Increasing breadth of the frontal lobe but decreasing height of the human brain between two Chinese samples from a Neolithic site and from living humans.

Morphological observation and measurements of endocasts have played a vital role in research on the evolution of the human brain. However, endocasts have never been used to investigate how the human brain has evolved since the Neolithic period. We investigated the evolution of the human brain during the Holocene by comparing virtual endocasts from Beiqian site (a Neolithic Chinese site) and a sample of Chinese modern-day humans. Standardized measurements and indices were taken to provide quantification of the overall endocast shape, including the length, breadth, height, frontal breadth, and the ratio of frontal breadth to breadth, as well as the cranial capacity. We found that the height of the endocasts and cranial capacity have decreased between our two samples, whereas the frontal breadth and sexual dimorphism have increased. We argue that these changes can be caused by random genetic mutation and epigenetic change in response to changes in the environment.

Enhanced prediction of cement raw meal oxides by near-infrared spectroscopy using machine learning combined with chemometric techniques.

The component analysis of raw meal is critical to the quality of cement. In recent years, near-infrared (NIR) has been emerged as an innovative and efficient analytical method to determine the oxide content of cement raw meal. This study aims to utilize NIR spectroscopy combined with machine learning and chemometrics to improve the prediction of oxide content in cement raw meal. The Savitzky-Golay convolution smoothing method is applied to eliminate noise interference for the analysis of calcium carbonate ( C a C O 3 ), silicon dioxide ( S i O 2 ), aluminum oxide ( A l 2 O 3 ), and ferric oxide ( F e 2 O 3 ) in cement raw materials. Different wavelength selection techniques are used to perform a comprehensive analysis of the model, comparing the performance of several wavelength selection techniques. The back-propagation neural network regression model based on particle swarm optimization algorithm was also applied to optimize the extracted and screened feature wavelengths, and the model prediction performance was checked and evaluated using R p and RMSE. In conclusion, the results indicate that NIR spectroscopy in combination with ML and chemometrics has great potential to effectively improve the prediction performance of oxide content in raw materials and highlight the importance of modeling and wavelength selection techniques. By enabling more accurate and efficient determination of oxide content in raw materials, NIR spectroscopy coupled with meta-modeling has the potential to revolutionize quality assurance practices in cement manufacturing.

Effects of Novel Nanoparticulate Bioceramic Endodontic Material on Human Dental Pulp Stem Cells In Vitro.

OBJECTIVES: This study aimed to investigate the in vitro effects of root canal filling and repair paste (nRoot BP) on human dental pulp stem cells (hDPSCs). METHODS: The effects of nRoot BP and iRoot BP Plus on the adhesion, proliferation, migration, and differentiation of hDPSCs were examined in vitro for 72 hours. The adhesion of cells was observed using immunofluorescence rhodamine ghost pen cyclic peptide staining and scanning electron microscopy (SEM). Cell density and changes in migration area were measured under a fluorescence inverted microscope. Fluorescent quantitative PCR was performed to detect genes related to odontogenesis and osteogenesis. RESULTS: Cells adhering to the surfaces of nRoot BP and iRoot BP Plus exhibited similar irregular polygonal morphologies, with cells extending irregular pseudopods to adhere to the materials. CCK-8 results indicated that the density of living cells for nRoot BP and iRoot BP Plus was lower than that of the blank control group at 3 and 5 days of culture. There was no significant difference in cell migration between the groups (P > .05). The migration ability of iRoot BP Plus and nRoot BP was similar to that of the control group. Both nRoot BP and iRoot BP Plus increased the expression of the RUNX2 gene, but there was no significant difference between the groups (P < .05). Furthermore, both nRoot BP and iRoot BP Plus downregulated the expression of the DSPP gene, with no significant difference between them (P > .05). CONCLUSIONS: nRoot BP exhibited a slight inhibition of hDPSC proliferation but did not affect the adhesion and migration of hDPSCs. The impact of nRoot BP on the osteogenic and odontogenic differentiation of hDPSCs was similar to that of iRoot BP Plus.

Deep-learning-based segmentation of perivascular spaces on T2-Weighted 3T magnetic resonance images.

Purpose: Studying perivascular spaces (PVSs) is important for understanding the pathogenesis and pathological changes of neurological disorders. Although some methods for automated segmentation of PVSs have been proposed, most of them were based on 7T MR images that were majorly acquired in healthy young people. Notably, 7T MR imaging is rarely used in clinical practice. Herein, we propose a deep-learning-based method that enables automatic segmentation of PVSs on T2-weighted 3T MR images. Method: Twenty patients with Parkinson's disease (age range, 42-79 years) participated in this study. Specifically, we introduced a multi-scale supervised dense nested attention network designed to segment the PVSs. This model fosters progressive interactions between high-level and low-level features. Simultaneously, it utilizes multi-scale foreground content for deep supervision, aiding in refining segmentation results at various levels. Result: Our method achieved the best segmentation results compared with the four other deep-learning-based methods, achieving a dice similarity coefficient (DSC) of 0.702. The results of the visual count of the PVSs in our model correlated extremely well with the expert scoring results on the T2-weighted images (basal ganglia: rs = 0.845, P < 0.001; rs = 0.868, P < 0.001; centrum semiovale: rs = 0.845, P < 0.001; rs = 0.823, P < 0.001 for raters 1 and 2, respectively). Experimental results show that the proposed method performs well in the segmentation of PVSs. Conclusion: The proposed method can accurately segment PVSs; it will facilitate practical clinical applications and is expected to replace the method of visual counting directly on T1-weighted images or T2-weighted images.

Cerebellopontine Angle Lipoma with Contralateral Sudden Deafness: A Case Report and Review of Literature.

BACKGROUND: Cerebellopontine angle lipoma is a rare tumor that composes less than 1% of all CPA tumors. There has been no recorded case of unilateral CPA/IAC lipoma with sudden contralateral deafness yet. CASE PRESENTATION: We report a 52-year-old man diagnosed with right cerebellopontine angle lipoma and combined left total deafness. Pure-tone audiometry revealed total sensorineural deafness in his left ear and moderate sensorineural deafness in the right ear. The patient was treated with glucocorticoids, batroxobin, and other symptomatic treatments. There was no substantial improvement in hearing after 14 days' treatment. DISCUSSION: We chose conservative treatment for him. It is advised to wear hearing aids in the right ear and to undergo regular imaging monitoring. CONCLUSION: Treatment options for such patients should be chosen by taking into account the degree of bilateral hearing loss, the size and location of the tumor, the possibility of preserving hearing during surgery, the functional level of the patient's facial nerve, and other factors.

An accurate green fruits detection method based on optimized YOLOX-m.

Fruit detection and recognition has an important impact on fruit and vegetable harvesting, yield prediction and growth information monitoring in the automation process of modern agriculture, and the actual complex environment of orchards poses some challenges for accurate fruit detection. In order to achieve accurate detection of green fruits in complex orchard environments, this paper proposes an accurate object detection method for green fruits based on optimized YOLOX_m. First, the model extracts features from the input image using the CSPDarkNet backbone network to obtain three effective feature layers at different scales. Then, these effective feature layers are fed into the feature fusion pyramid network for enhanced feature extraction, which combines feature information from different scales, and in this process, the Atrous spatial pyramid pooling (ASPP) module is used to increase the receptive field and enhance the network's ability to obtain multi-scale contextual information. Finally, the fused features are fed into the head prediction network for classification prediction and regression prediction. In addition, Varifocal loss is used to mitigate the negative impact of unbalanced distribution of positive and negative samples to obtain higher precision. The experimental results show that the model in this paper has improved on both apple and persimmon datasets, with the average precision (AP) reaching 64.3% and 74.7%, respectively. Compared with other models commonly used for detection, the model approach in this study has a higher average precision and has improved in other performance metrics, which can provide a reference for the detection of other fruits and vegetables.

Dual-Modal Information Bottleneck Network for Seizure Detection.

In recent years, deep learning has shown very competitive performance in seizure detection. However, most of the currently used methods either convert electroencephalogram (EEG) signals into spectral images and employ 2D-CNNs, or split the one-dimensional (1D) features of EEG signals into many segments and employ 1D-CNNs. Moreover, these investigations are further constrained by the absence of consideration for temporal links between time series segments or spectrogram images. Therefore, we propose a Dual-Modal Information Bottleneck (Dual-modal IB) network for EEG seizure detection. The network extracts EEG features from both time series and spectrogram dimensions, allowing information from different modalities to pass through the Dual-modal IB, requiring the model to gather and condense the most pertinent information in each modality and only share what is necessary. Specifically, we make full use of the information shared between the two modality representations to obtain key information for seizure detection and to remove irrelevant feature between the two modalities. In addition, to explore the intrinsic temporal dependencies, we further introduce a bidirectional long-short-term memory (BiLSTM) for Dual-modal IB model, which is used to model the temporal relationships between the information after each modality is extracted by convolutional neural network (CNN). For CHB-MIT dataset, the proposed framework can achieve an average segment-based sensitivity of 97.42%, specificity of 99.32%, accuracy of 98.29%, and an average event-based sensitivity of 96.02%, false detection rate (FDR) of 0.70/h. We release our code at https://github.com/LLLL1021/Dual-modal-IB.

Improving Alzheimer Diagnoses With An Interpretable Deep Learning Framework: Including Neuropsychiatric Symptoms.

Alzheimer's disease (AD) is a prevalent neurodegenerative disorder characterized by the progressive cognitive decline. Among the various clinical symptoms, neuropsychiatric symptoms (NPS) commonly occur during the course of AD. Previous researches have demonstrated a strong association between NPS and severity of AD, while the research methods are not sufficiently intuitive. Here, we report a hybrid deep learning framework for AD diagnosis using multimodal inputs such as structural MRI, behavioral scores, age, and gender information. The framework uses a 3D convolutional neural network to automatically extract features from MRI. The imaging features are passed to the Principal Component Analysis for dimensionality reduction, which fuse with non-imaging information to improve the diagnosis of AD. According to the experimental results, our model achieves an accuracy of 0.91 and an area under the curve of 0.97 in the task of classifying AD and cognitively normal individuals. SHapley Additive exPlanations are used to visually exhibit the contribution of specific NPS in the proposed model. Among all behavioral symptoms, apathy plays a particularly important role in the diagnosis of AD, which can be considered a valuable factor in further studies, as well as clinical trials.

YOLOF-Snake: An Efficient Segmentation Model for Green Object Fruit.

Accurate detection and segmentation of the object fruit is the key part of orchard production measurement and automated picking. Affected by light, weather, and operating angle, it brings new challenges to the efficient and accurate detection and segmentation of the green object fruit under complex orchard backgrounds. For the green fruit segmentation, an efficient YOLOF-snake segmentation model is proposed. First, the ResNet101 structure is adopted as the backbone network to achieve feature extraction of the green object fruit. Then, the C5 feature maps are expanded with receptive fields and the decoder is used for classification and regression. Besides, the center point in the regression box is employed to get a diamond-shaped structure and fed into an additional Deep-snake network, which is adjusted to the contours of the target fruit to achieve fast and accurate segmentation of green fruit. The experimental results show that YOLOF-snake is sensitive to the green fruit, and the segmentation accuracy and efficiency are significantly improved. The proposed model can effectively extend the application of agricultural equipment and provide theoretical references for other fruits and vegetable segmentation.

Enhanced Association of Tau Pathology and Cognitive Impairment in Mild Cognitive Impairment Subjects with Behavior Symptoms.

BACKGROUND: Mild cognitive impairment (MCI) individuals with neuropsychiatric symptoms (NPS) are more likely to develop dementia. OBJECTIVE: We sought to understand the relationship between neuroimaging markers such as tau pathology and cognitive symptoms both with and without the presence of NPS during the prodromal period of Alzheimer's disease. METHODS: A total of 151 MCI subjects with tau positron emission tomographic (PET) scanning with 18F AV-1451, amyloid-ß (Aß) PET scanning with florbetapir or florbetaben, magnetic resonance imaging, and cognitive and behavioral evaluations were selected from the Alzheimer's Disease Neuroimaging Initiative. A 4-group division approach was proposed using amyloid (A-/A+) and behavior (B-/B+) status: A-B-, A-B+, A+B-, and A+B+. Pearson's correlation test was conducted for each group to examine the association between tau deposition and cognitive performance. RESULTS: No statistically significant association between tau deposition and cognitive impairment was found for subjects without behavior symptoms in either the A-B-or A+B-groups after correction for false discovery rate. In contrast, tau deposition was found to be significantly associated with cognitive impairment in entorhinal cortex and temporal pole for the A-B+ group and nearly the whole cerebrum for the A+B+ group. CONCLUSION: Enhanced associations between tauopathy and cognitive impairment are present in MCI subjects with behavior symptoms, which is more prominent in the presence of elevated amyloid pathology. MCI individuals with NPS may thus be at greater risk for further cognitive decline with the increase of tau deposition in comparison to those without NPS.