From impact to recovery: tracking mild traumatic brain injury with MRI-a pilot study and case series.

Background: Diagnosis and recovery tracking of mild traumatic brain injury (mTBI) is often challenging due to the lack of clear findings on routine imaging techniques. This also complicates defining safe points for returning to activities. Hypothesis/purpose: Quantitative susceptibility mapping (QSM) can provide information about cerebral venous oxygen saturation (CSvO2) in the context of brain injury. We tested the prediction that these imaging modalities would enable the detection of changes and recovery patterns in the brains of patients with mTBI. Study design: In a case-control study, we recruited a cohort of 24 contact sport athletes for baseline QSM and resting-state functional MRI (rs-fMRI) scanning. Two of those who subsequently experienced head impact with significant post-injury symptoms underwent scans at 3, 7, 14 and 28 days post-injury; one had a boxing match without classical mTBI symptoms were also followed-up on. Results: The cohort baseline QSM measurements of the straight sinus were established. The two injured athletes with post-impact symptoms consistent with mTBI had susceptibility results at days 3 and 7 post-impact that fell below the 25th percentile of the baseline values. The per cent amplitude fluctuation quantified from rs-fMRI agreed with the susceptibility trends in the straight sinus. Conclusion: QSM holds promise as a diagnostic tool for tracking mTBI progression or recovery in contact sport head injury.

Long-Term Improvement in Hippocampal-Dependent Learning Ability in Healthy, Aged Individuals Following High Intensity Interval Training.

Physical exercise may reduce dementia risk in aging, but varying reports on its effectiveness make it challenging to ascribe what level of exercise will have significant longer-term effects on important functions such as hippocampal-based learning and memory. This study compared the effect of three different 6-month exercise regimens on hippocampal-dependent cognition in healthy, elderly individuals. Participants, aged 65-85 with no cognitive deficits, were randomly assigned to one of three exercise interventions (low (LIT), medium (MIT), and High intensity interval training (HIIT), respectively). Each participant attended 72 supervised exercise sessions over a 6-month period. A total of 151 participants completed all sessions. Cognitive testing for hippocampal performance occurred monthly, as did blood collection, and continued for up to 5 years following initiation of the study. Multimodal 7 Tesla MRI scans were taken at commencement, 6 and 12 months. After 6 months, only the HIIT group displayed significant improvement in hippocampal function, as measured by paired associative learning (PAL). MRI from the HIIT group showed abrogation of the age-dependent volumetric decrease within several cortical regions including the hippocampus and improved functional connectivity between multiple neural networks not seen in the other groups. HIIT-mediated changes in the circulating levels of brain-derived neurotrophic factor (BDNF) and cortisol correlated to improved hippocampal-dependent cognitive ability. These findings demonstrate that HIIT significantly improves and prolongs the hippocampal-dependent cognitive health of aged individuals. Importantly, improvement was retained for at least 5 years following initiation of HIIT, suggesting that the changes seen in hippocampal volume and connectivity underpin this long-term maintenance. Sustained improvement in hippocampal function to this extent confirms that such exercise-based interventions can provide significant protection against hippocampal cognitive decline in the aged population. The changes in specific blood factor levels also may provide useful biomarkers for choosing the optimal exercise regimen to promote cognitive improvement.

Scanning ultrasound-mediated memory and functional improvements do not require amyloid-ß reduction.

A prevalent view in treating age-dependent disorders including Alzheimer's disease (AD) is that the underlying amyloid plaque pathology must be targeted for cognitive improvements. In contrast, we report here that repeated scanning ultrasound (SUS) treatment at 1 MHz frequency can ameliorate memory deficits in the APP23 mouse model of AD without reducing amyloid-ß (Aß) burden. Different from previous studies that had shown Aß clearance as a consequence of blood-brain barrier (BBB) opening, here, the BBB was not opened as no microbubbles were used. Quantitative SWATH proteomics and functional magnetic resonance imaging revealed that ultrasound induced long-lasting functional changes that correlate with the improvement in memory. Intriguingly, the treatment was more effective at a higher frequency (1 MHz) than at a frequency within the range currently explored in clinical trials in AD patients (286 kHz). Together, our data suggest frequency-dependent bio-effects of ultrasound and a dissociation of cognitive improvement and Aß clearance, with important implications for the design of trials for AD therapies.

Characteristics of Resting-State Electroencephalogram Network in α-Band of Table Tennis Athletes.

BACKGROUND: Table tennis athletes have been extensively studied for their cognitive processing advantages and brain plasticity. However, limited research has focused on the resting-state function of their brains. This study aims to investigate the network characteristics of the resting-state electroencephalogram in table tennis athletes and identify specific brain network biomarkers. METHODS: A total of 48 healthy right-handed college students participated in this study, including 24 table tennis athletes and 24 controls with no exercise experience. Electroencephalogram data were collected using a 64-conductive active electrode system during eyes-closed resting conditions. The analysis involved examining the average power spectral density and constructing brain functional networks using the weighted phase-lag index. Network topological characteristics were then calculated. RESULTS: The results revealed that table tennis athletes exhibited significantly higher average power spectral density in the α band compared to the control group. Moreover, athletes not only demonstrated stronger functional connections, but they also exhibited enhanced transmission efficiency in the brain network, particularly at the local level. Additionally, a lateralization effect was observed, with more potent interconnected hubs identified in the left hemisphere of the athletes' brain. CONCLUSIONS: Our findings imply that the α band may be uniquely associated with table tennis athletes and their motor skills. The brain network characteristics of athletes during the resting state are worth further attention to gain a better understanding of adaptability of and changes in their brains during training and competition.

Evidence of Ongoing Cerebral Microstructural Reorganization in Children With Persisting Symptoms Following Mild Traumatic Brain Injury: A NODDI DTI Analysis.

Approximately 300-550 children per 100,000 sustain a mild traumatic brain injury (mTBI) each year, of whom ∼25-30% have long-term cognitive problems. Following mTBI, free water (FW) accumulation occurs in white matter (WM) tracts. Diffusion tensor imaging (DTI) can be used to investigate structural integrity following mTBI. Compared with conventional DTI, neurite orientation dispersion and density imaging (NODDI) orientation dispersion index (ODI) and fraction of isolated free water (FISO) metrics may allow a more advanced insight into microstructural damage following pediatric mTBI. In this longitudinal study, we used NODDI to explore whole-brain and tract-specific differences in ODI and FISO in children with persistent symptoms after mTBI (n = 80) and in children displaying clinical recovery (n = 32) at 1 and 2-3 months post-mTBI compared with healthy controls (HCs) (n = 21). Two-way repeated measures analysis of variance (ANOVA) and voxelwise two-sample t tests were conducted to compare whole-brain and tract-specific diffusion across groups. All results were corrected at positive false discovery rate (pFDR) <0.05. We also examined the association between NODDI metrics and clinical outcomes, using logistical regression to investigate the value of NODDI metrics in predicting future recovery from mTBI. Whole-brain ODI was significantly increased in symptomatic participants compared with HCs at both 1 and 2 months post-injury, where the uncinate fasciculus (UF) and inferior fronto-occipital fasciculus (IFOF) were particularly implicated. Using region of interest (ROI) analysis in significant WM, bilateral IFOF and UF voxels, symptomatic participants had the highest ODI in all ROIs. ODI was lower in asymptomatic participants, and HCs had the lowest ODI in all ROIs. No changes in FISO were found across groups or over time. WM ODI was moderately correlated with a higher youth-reported post-concussion symptom inventory (PCSI) score. With 87% predictive power, ODI (1 month post-injury) and clinical predictors (age, sex, PCSI score, attention scores) were a more sensitive predictor of recovery at 2-3 months post-injury than fractional anisotropy (FA) and clinical predictors, or clinical predictors alone. FISO could not predict recovery at 2-3 months post-injury. Therefore, we found that ODI was significantly increased in symptomatic children following mTBI compared with HCs at 1 month post-injury, and progressively decreased over time alongside clinical recovery. We found no significant differences in FISO between groups or over time. WM ODI at 1 month was a more sensitive predictor of clinical recovery at 2-3 months post-injury than FA, FISO, or clinical measures alone. Our results show evidence of ongoing microstructural reorganization or neuroinflammation between 1 and 2-3 months post-injury, further supporting delayed return to play in children who remain symptomatic. We recommend future research examining the clinical utility of NODDI following mTBI to predict recovery or persistence of post-concussion symptoms and thereby inform management of mTBI.

Toward hippocampal volume measures on ultra-high field magnetic resonance imaging: a comprehensive comparison study between deep learning and conventional approaches.

The hippocampus is a complex brain structure that plays an important role in various cognitive aspects such as memory, intelligence, executive function, and path integration. The volume of this highly plastic structure is identified as one of the most important biomarkers of specific neuropsychiatric and neurodegenerative diseases. It has also been extensively investigated in numerous aging studies. However, recent studies on aging show that the performance of conventional approaches in measuring the hippocampal volume is still far from satisfactory, especially in terms of delivering longitudinal measures from ultra-high field magnetic resonance images (MRIs), which can visualize more boundary details. The advancement of deep learning provides an alternative solution to measuring the hippocampal volume. In this work, we comprehensively compared a deep learning pipeline based on nnU-Net with several conventional approaches including Freesurfer, FSL and DARTEL, for automatically delivering hippocampal volumes: (1) Firstly, we evaluated the segmentation accuracy and precision on a public dataset through cross-validation. Results showed that the deep learning pipeline had the lowest mean (L = 1.5%, R = 1.7%) and the lowest standard deviation (L = 5.2%, R = 6.2%) in terms of volume percentage error. (2) Secondly, sub-millimeter MRIs of a group of healthy adults with test-retest 3T and 7T sessions were used to extensively assess the test-retest reliability. Results showed that the deep learning pipeline achieved very high intraclass correlation coefficients (L = 0.990, R = 0.986 for 7T; L = 0.985, R = 0.983 for 3T) and very small volume percentage differences (L = 1.2%, R = 0.9% for 7T; L = 1.3%, R = 1.3% for 3T). (3) Thirdly, a Bayesian linear mixed effect model was constructed with respect to the hippocampal volumes of two healthy adult datasets with longitudinal 7T scans and one disease-related longitudinal dataset. It was found that the deep learning pipeline detected both the subtle and disease-related changes over time with high sensitivity as well as the mild differences across subjects. Comparison results from the aforementioned three aspects showed that the deep learning pipeline significantly outperformed the conventional approaches by large margins. Results also showed that the deep learning pipeline can better accommodate longitudinal analysis purposes.

A cross-comparative analysis of in vivo versus ex vivo MRI indices in a mouse model of concussion.

BACKGROUND: We present a cross-sectional, case-matched, and pair-wise comparison of structural magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), and neurite orientation dispersion and density imaging (NODDI) measures in vivo and ex vivo in a mouse model of concussion, thus aiming to establish the concordance of structural and diffusion imaging findings in living brain and after fixation. METHODS: We allocated 28 male mice aged 3-4 months to sham injury and concussion (CON) groups. CON mice had received a single concussive impact on day 0 and underwent MRI at day 2 (n = 9) or 7 (n = 10) post-impact, and sham control mice likewise underwent imaging at day 2 (n = 5) or 7 (n = 4). Immediately after the final scanning, we collected the perfusion-fixed brains, which were stored for imaging ex vivo 6-12 months later. We then compared the structural imaging, DTI, and NODDI results between different methods. RESULTS: In vivo to ex vivo structural and DTI/NODDI findings were in notably poor agreement regarding the effects of concussion on structural integrity of the brain. COMPARISON WITH EXISTING METHODS: ex vivo imaging was frequently done to study the effects of diseases and treatments, but our results showed that ex vivo and in vivo imaging can detect completely opposite and contradictory results. This is also the first study that compares in vivo and ex vivo NODDI. CONCLUSION: Our findings call for caution in extrapolating translational capabilities obtained ex vivo to physiological measurements in vivo. The divergent findings may reflect fixation artefacts and the contribution of the glymphatic system changes.

Anti-inflammatory interleukin 1 receptor antagonist concentration in plasma correlates with blood-brain barrier integrity in the primary lesion area in traumatic brain injury patients.

Purpose: Blood-brain barrier (BBB) dysregulation and pro-inflammatory signalling molecules are secondary factors that have been associated with injury severity and long-term clinical outcome following traumatic brain injury (TBI). However, the association between BBB permeability and inflammation is unknown in human TBI patients. In this study, we investigated whether BBI integrity as measured by Dynamic Contrast-Enhanced (DCE) Magnetic Resonance Imaging (MRI) correlates with plasma levels of immunological markers following TBI. Methods: Thirty-two TBI patients recruited from a neurosurgical unit were included in the study. Structural three-dimensional T1-weighted and DCE-MRI images were acquired on a 3T MRI at the earliest opportunity once the participant was sufficiently stable after patient admission to hospital. Blood sampling was performed on the same day as the MRI. The location and extents of the haemorrhagic and contusional lesions were identified. Immunological biomarkers were quantified from the participants' plasma using a multiplex immunoassay. Demographic and clinical information, including age and Glasgow Coma Scale (GCS) were also collected and the immunological biomarker profiles were compared across controls and the TBI severity sub-groups. Contrast agent leakiness through blood-brain barriers (BBB) in the contusional lesions were assessed by fitting DCE-MRI using Patlak model and BBB leakiness characteristics of the participants were correlated with the immunological biomarker profiles. Results: TBI patients showed reduced plasma levels of interleukin (IL)-1ß, IFN-γ, IL-13, and chemokine (C-C motif) ligands (CCL)2 compared to controls and significantly higher levels of platelet-derived growth factor (PDGF-BB), IL-6, and IL-8. BBB leakiness of the contusional lesions did not significantly differ across different TBI severity sub-groups. IL-1ra levels significantly and positively correlated with the contusional lesion's BBB integrity as measured with DCE-MRI via an exponential curve relationship. Discussion: This is the first study to combine DCE-MRI with plasma markers of inflammation in acute TBI patients. Our finding that plasma levels of the anti-inflammatory cytokine IL-1ra correlated negatively with increased leakiness of the BBB.

Cascaded Multi-Modal Mixing Transformers for Alzheimer's Disease Classification with Incomplete Data.

Accurate medical classification requires a large number of multi-modal data, and in many cases, different feature types. Previous studies have shown promising results when using multi-modal data, outperforming single-modality models when classifying diseases such as Alzheimer's Disease (AD). However, those models are usually not flexible enough to handle missing modalities. Currently, the most common workaround is discarding samples with missing modalities which leads to considerable data under-utilisation. Adding to the fact that labelled medical images are already scarce, the performance of data-driven methods like deep learning can be severely hampered. Therefore, a multi-modal method that can handle missing data in various clinical settings is highly desirable. In this paper, we present Multi-Modal Mixing Transformer (3MT), a disease classification transformer that not only leverages multi-modal data but also handles missing data scenarios. In this work, we test 3MT for AD and Cognitively normal (CN) classification and mild cognitive impairment (MCI) conversion prediction to progressive MCI (pMCI) or stable MCI (sMCI) using clinical and neuroimaging data. The model uses a novel Cascaded Modality Transformers architecture with cross-attention to incorporate multi-modal information for more informed predictions. We propose a novel modality dropout mechanism to ensure an unprecedented level of modality independence and robustness to handle missing data scenarios. The result is a versatile network that enables the mixing of arbitrary numbers of modalities with different feature types and also ensures full data utilization in missing data scenarios. The model is trained and evaluated on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset with the state-of-the-art performance and further evaluated with The Australian Imaging Biomarker & Lifestyle Flagship Study of Ageing (AIBL) dataset with missing data.

Self-reported Fatigue was Associated with Increased White-matter Alterations in Long-term Traumatic Brain Injury and Posttraumatic Stress Disorder Patients.

Fatigue is a long-lasting problem in traumatic brain injury (TBI) and post-traumatic stress disorder (PTSD), with limited research that investigated the fatigue-related white-matter changes within TBI and/or PTSD cohorts. This exploratory cross-sectional study used diffusion tensor imaging (DTI) and neuropsychological data collected from 153 male Vietnam War veterans, as part of the Alzheimer's Disease Neuroimaging Initiative - Department of Defense, and were divided clinically into control veterans, PTSD, TBI, and with both TBI and PTSD (TBI + PTSD). The existence of fatigue was defined by the question "Do you often feel tired, fatigued, or sleepy during the daytime?". DTI data were compared between fatigue and non-fatigue subgroups in each clinical group using tract-based spatial statistics voxel-based differences. Fatigue was reported in controls (29.55%), slightly higher in TBI (52.17%, PBenf = 0.06), and significantly higher in both TBI + PTSD (66.67%, PBenf = 0.001) and PTSD groups (79.25%, PBenf < 0.001). Compared to non-fatigued subgroups, no white-matter differences were observed in the fatigued subgroups of control or TBI, while the fatigued PTSD subgroup only showed increased diffusivity measures (i.e., radial and axial), and the fatigued TBI + PTSD subgroup showed decreased fractional anisotropy and increased diffusivity measures (PFWE ≤ 0.05). The results act as preliminary findings suggesting fatigue to be significantly reported in TBI + PTSD and PTSD decades post-trauma with a possible link to white-matter microstructural differences in both PTSD and TBI + PTSD. Future studies with larger cohorts and detailed fatigue assessments would be required to identify the white-matter changes associated with fatigue in these cohorts.

Hippocampal demyelination is associated with increased magnetic susceptibility in a mouse model of concussion.

Structural and functional deficits in the hippocampus are a prominent feature of moderate-severe traumatic brain injury (TBI). In this work, we investigated the potential of Quantitative Susceptibility Imaging (QSM) to reveal the temporal changes in myelin integrity in a mouse model of concussion (mild TBI). We employed a cross-sectional design wherein we assigned 43 mice to cohorts undergoing either a concussive impact or a sham procedure, with QSM imaging at day 2, 7, or 14 post-injury, followed by Luxol Fast Blue (LFB) myelin staining to assess the structural integrity of hippocampal white matter (WM). We assessed spatial learning in the mice using the Active Place Avoidance Test (APA), recording their ability to use visual cues to locate and avoid zone-dependent mild electrical shocks. QSM and LFB staining indicated changes in the stratum lacunosum-molecular layer of the hippocampus in the concussion groups, suggesting impairment of this key relay between the entorhinal cortex and the CA1 regions. These imaging and histology findings were consistent with demyelination, namely increased magnetic susceptibility to MR imaging and decreased LFB staining. In the APA test, sham animals showed fewer entries into the shock zone compared to the concussed cohort. Thus, we present radiological, histological, and behavioral findings that concussion can induce significant and alterations in hippocampal integrity and function that evolve over time after the injury.

PREdiction and Diagnosis using Imaging and Clinical biomarkers Trial in Traumatic Brain Injury (PREDICT-TBI) study protocol: an observational, prospective, multicentre cohort study for the prediction of outcome in moderate-to-severe TBI.

INTRODUCTION: Traumatic brain injury (TBI) is a heterogeneous condition with a broad spectrum of injury severity, pathophysiological processes and variable outcomes. For moderate-to-severe TBI survivors, recovery is often protracted and outcomes can range from total dependence to full recovery. Despite advances in medical treatment options, prognosis remains largely unchanged. The objective of this study is to develop a machine learning predictive model for neurological outcomes at 6 months in patients with a moderate-to-severe TBI, incorporating longitudinal clinical, multimodal neuroimaging and blood biomarker predictor variables. METHODS AND ANALYSIS: A prospective, observational, cohort study will enrol 300 patients with moderate-to-severe TBI from seven Australian hospitals over 3 years. Candidate predictors including demographic and general health variables, and longitudinal clinical, neuroimaging (CT and MRI), blood biomarker and patient-reported outcome measures will be collected at multiple time points within the acute phase of injury. The predictor variables will populate novel machine learning models to predict the Glasgow Outcome Scale Extended 6 months after injury. The study will also expand on current prognostic models by including novel blood biomarkers (circulating cell-free DNA), and the results of quantitative neuroimaging such as Quantitative Susceptibility Mapping and Dynamic Contrast Enhanced MRI as predictor variables. ETHICS AND DISSEMINATION: Ethical approval has been obtained by the Royal Brisbane and Women's Hospital Human Research Ethics Committee, Queensland. Participants or their substitute decision-maker/s will receive oral and written information about the study before providing written informed consent. Study findings will be disseminated by peer-review publications and presented at national and international conferences and clinical networks. TRIAL REGISTRATION NUMBER: ACTRN12620001360909.

An end-end deep learning framework for lesion segmentation on multi-contrast MR images-an exploratory study in a rat model of traumatic brain injury.

Traumatic brain injury (TBI) engenders traumatic necrosis and penumbra-areas of secondary neural injury which are crucial targets for therapeutic interventions. Segmenting manually areas of ongoing changes like necrosis, edema, hematoma, and inflammation is tedious, error-prone, and biased. Using the multi-parametric MR data from a rodent model study, we demonstrate the effectiveness of an end-end deep learning global-attention-based UNet (GA-UNet) framework for automatic segmentation and quantification of TBI lesions. Longitudinal MR scans (2 h, 1, 3, 7, 14, 30, and 60 days) were performed on eight Sprague-Dawley rats after controlled cortical injury was performed. TBI lesion and sub-regions segmentation was performed using 3D-UNet and GA-UNet. Dice statistics (DSI) and Hausdorff distance were calculated to assess the performance. MR scan variations-based (bias, noise, blur, ghosting) data augmentation was performed to develop a robust model.Training/validation median DSI for U-Net was 0.9368 with T2w and MPRAGE inputs, whereas GA-UNet had 0.9537 for the same. Testing accuracies were higher for GA-UNet than U-Net with a DSI of 0.8232 for the T2w-MPRAGE inputs.Longitudinally, necrosis remained constant while oligemia and penumbra decreased, and edema appearing around day 3 which increased with time. GA-UNet shows promise for multi-contrast MR image-based segmentation/quantification of TBI in large cohort studies.

Diffusion tensor imaging and plasma immunological biomarker panel in a rat traumatic brain injury (TBI) model and in human clinical TBI.

Introduction: Neuroinflammatory reactions play a significant role in the pathology and long-term consequences of traumatic brain injury (TBI) and may mediate salutogenic processes that white matter integrity. This study aimed to investigate the relationship between inflammatory markers and white matter integrity following TBI in both a rat TBI model and clinical TBI cases. Methods: In the rat model, blood samples were collected following a controlled cortical impact (CCI) to assess a panel of inflammatory markers; MR-based diffusion tensor imaging (DTI) was employed to evaluate white matter integrity 60 days post-injury. 15 clinical TBI patients were similarly assessed for a panel of inflammatory markers and DTI post-intensive care unit discharge. Blood samples from healthy controls were used for comparison of the inflammatory markers. Results: Time-dependent elevations in immunological markers were observed in TBI rats, with a correlation to preserved fractional anisotropy (FA) in white matter. Specifically, TBI-induced increased plasma levels of IL-1ß, IL-6, G-CSF, CCL3, CCL5, and TNF-α were associated with higher white matter integrity, as measured by FA. Clinical cases had similar findings: elevated inflammatory markers (relative to controls) were associated with preservation of FA in vulnerable white matter regions. Discussion: Inflammatory markers in post-TBI plasma samples are ambivalent with respect to prediction of favourable outcome versus a progression to more pervasive pathology and morbidity.

Escalation of Tau Accumulation after a Traumatic Brain Injury: Findings from Positron Emission Tomography.

Traumatic brain injury (TBI) has come to be recognized as a risk factor for Alzheimer's disease (AD), with poorly understood underlying mechanisms. We hypothesized that a history of TBI would be associated with greater tau deposition in elders with high-risk for dementia. A Groups of 20 participants with self-reported history of TBI and 100 without any such history were scanned using [18F]-AV1451 positron emission tomography as part of the Alzheimer's Disease Neuroimaging Initiative (ADNI). Scans were stratified into four groups according to TBI history, and by clinical dementia rating scores into cognitively normal (CDR = 0) and those showing cognitive decline (CDR ≥ 0.5). We pursued voxel-based group comparison of [18F]-AV1451 uptake to identify the effect of TBI history on brain tau deposition, and for voxel-wise correlation analyses between [18F]-AV1451 uptake and different neuropsychological measures and cerebrospinal fluid (CSF) biomarkers. Compared to the TBI-/CDR ≥ 0.5 group, the TBI+/CDR ≥ 0.5 group showed increased tau deposition in the temporal pole, hippocampus, fusiform gyrus, and inferior and middle temporal gyri. Furthermore, the extent of tau deposition in the brain of those with TBI history positively correlated with the extent of cognitive decline, CSF-tau, and CSF-amyloid. This might suggest TBI to increase the risk for tauopathies and Alzheimer's disease later in life.

A mice resting-state functional magnetic resonance imaging dataset on the effects of medetomidine dosages and prior-stimulation on functional connectivity.

Nine 8 C57Bl6 mice (9 ± 0.5 months) were utilised for this dataset. Each animal was scanned twice on a 9.4T Bruker Magnetic Resonance Imaging (MRI) scanner using a cryogenically cooled coil with 0.1 mg/kg body weight/h (low) or 0.3 mg/kg body weight/h (high) medetomidine doses; 0.5% isoflurane was used in conjunction with both doses. The scans were one week apart, and the first session's dose was decided randomly. In each session, the animal had a pre-stimulation resting-state functional Magnetic Resonance Imaging (rs-fMRI) scan followed by 10 min where mild, constant electrical stimulation to the forepaw was applied, and a post-stimulation rs-fMRI scan. Each fMRI scan lasted 10 min, and there was 5 min break between fMRI scans. The dataset included, for each animal, a pair of forward-phase and reverse-phase gradient echo Echo-Planar-Imaging (EPI) images for EPI distortion correction purpose and three (unprocessed) functional MRI images acquired using the same EPI sequence: prior, during, and post-stimulation. The MRI data was saved in compressed NIFTI format converted from Bruker DICOMs. The dataset also included the pre-processed functional MRI images, with the following pre-processing steps: slice-timing correction, temporal despiking, motion correction, distortion correction, band-pass filtration at 0.01-0.2 Hz, and spatial normalisation. This dataset adds to the publicly available collection of resting-state functional MRI in the mice and facilitates reproducibility and validation of functional imaging and its analysis.

Instant tissue field and magnetic susceptibility mapping from MRI raw phase using Laplacian enhanced deep neural networks.

Quantitative susceptibility mapping (QSM) is an MRI post-processing technique that produces spatially resolved magnetic susceptibility maps from phase data. However, the traditional QSM reconstruction pipeline involves multiple non-trivial steps, including phase unwrapping, background field removal, and dipole inversion. These intermediate steps not only increase the reconstruction time but accumulates errors. This study aims to overcome existing limitations by developing a Laplacian-of-Trigonometric-functions (LoT) enhanced deep neural network for near-instant quantitative field and susceptibility mapping (i.e., iQFM and iQSM) from raw MRI phase data. The proposed iQFM and iQSM methods were compared with established reconstruction pipelines on simulated and in vivo datasets. In addition, experiments on patients with intracranial hemorrhage and multiple sclerosis were also performed to test the generalization of the proposed neural networks. The proposed iQFM and iQSM methods in healthy subjects yielded comparable results to those involving the intermediate steps while dramatically improving reconstruction accuracies on intracranial hemorrhages with large susceptibilities. High susceptibility contrast between multiple sclerosis lesions and healthy tissue was also achieved using the proposed methods. Comparative studies indicated that the most significant contributor to iQFM and iQSM over conventional multi-step methods was the elimination of traditional Laplacian unwrapping. The reconstruction time on the order of minutes for traditional approaches was shortened to around 0.1 s using the trained iQFM and iQSM neural networks.

Traumatic brain injury alterations in the functional connectome are associated with neuroinflammation but not tau in a P30IL tauopathy mouse model.

INTRODUCTION: Traumatic Brain Injury (TBI) is often associated with long-term cognitive deficits and altered brain networks which have been linked with accumulation of neurofibrillary tau tangles and neuroinflammation. In this work, we investigated the changes in the brain post-TBI in an Alzheimer's disease pR5 tauopathy model and evaluated the contribution of tauopathy and neuroinflammation to connectivity alterations using resting-state functional Magnetic Resonance Imaging (rs-fMRI). METHOD: 26 P301L tau transgenic mice of 8-9 months of age (21-35 g) expressing the human tau isoform carrying the pathogenic P301L mutation were used for the study. Animals were assessed at day 1 and 7 post-injury/craniotomy and were randomly divided into four groups. All animals underwent an MRI scan on a 9.4T Bruker system where rsfMRI was acquired. Following imaging, brains were stained with pSer (396 + 404), glial fibrillary acidic protein (GFAP), and ionised calcium-binding adaptor molecule-1 (Iba-1). Group-information-guided Independent Component Analysis (GIG-ICA) and region-of-interest (ROI)-based network connectivity approaches were applied. Principal Component Regression was applied to predict connectivity network strength from the corresponding ROIs. RESULTS: TBI mice showed decreased functional connectivity in the dentate gyrus, thalamus, and other areas compared to sham animals at day 1 post-injury with the majority of changes resolving at day 7. Principal Component Regression showed only the contralateral CA1 network strength was correlated with the CA1's astrocyte and microglia cell density and the ipsilateral thalamus network strength was correlated with the ipsilateral thalamus' astrocyte and microglia cell density. CONCLUSION: We present the first report on the temporal alterations in functional connectivity in a P30IL mouse model following TBI. Connectivity between key regions known to be affected in Alzheimer's disease were short-term and reversible following injury. Connectivity strength in CA1 and thalamus showed significant correlation with astrocyte and microglial cell density but not tau density.