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(1) Background: Coronavirus disease 2019 (COVID-19) is a dominant, rapidly spreading respiratory disease. However, the factors influencing COVID-19 mortality still have not been confirmed. The pathogenesis of COVID-19 is unknown, and relevant mortality predictors are lacking. This study aimed to investigate COVID-19 mortality in patients with pre-existing health conditions and to examine the association between COVID-19 mortality and other morbidities. (2) Methods: De-identified data from 113,882, including 14,877 COVID-19 patients, were collected from the UK Biobank. Different types of data, such as disease history and lifestyle factors, from the COVID-19 patients, were input into the following three machine learning models: Deep Neural Networks (DNN), Random Forest Classifier (RF), eXtreme Gradient Boosting classifier (XGB) and Support Vector Machine (SVM). The Area under the Curve (AUC) was used to measure the experiment result as a performance metric. (3) Results: Data from 14,876 COVID-19 patients were input into the machine learning model for risk-level mortality prediction, with the predicted risk level ranging from 0 to 1. Of the three models used in the experiment, the RF model achieved the best result, with an AUC value of 0.86 (95% CI 0.84–0.88). (4) Conclusions: A risk-level prediction model for COVID-19 mortality was developed. Age, lifestyle, illness, income, and family disease history were identified as important predictors of COVID-19 mortality. The identified factors were related to COVID-19 mortality.

In resting-state functional magnetic resonance imaging (fMRI), functional connectivity measures can be influenced by the presence of a strong global component. A widely used pre-processing method for reducing the contribution of this component is global signal regression, in which a global mean time series signal is projected out of the fMRI time series data prior to the computation of connectivity measures. However, the use of global signal regression is controversial because the method can bias the correlation values to have an approximately zero mean and may in some instances create artifactual negative correlations. In addition, while many studies treat the global signal as a non-neural confound that needs to be removed, evidence from electrophysiological and fMRI measures in primates suggests that the global signal may contain significant neural correlates. In this study, we used simultaneously acquired fMRI and electroencephalographic (EEG) measures of resting-state activity to assess the relation between the fMRI global signal and EEG measures of vigilance in humans. We found that the amplitude of the global signal (defined as the standard deviation of the global signal) exhibited a significant negative correlation with EEG vigilance across subjects studied in the eyes-closed condition. In addition, increases in EEG vigilance due to the ingestion of caffeine were significantly associated with both a decrease in global signal amplitude and an increase in the average level of anti-correlation between the default mode network and the task-positive network. •Global signal amplitude (GSamp) is negatively correlated with EEG vigilance.•Caffeine-induced decreases in GSamp are related to increases in EEG vigilance.•Increases in EEG vigilance are related to increases in DMN-TPN anti-correlation.

Changes in vigilance or alertness during a typical resting state fMRI scan are inevitable and have been found to affect measures of functional brain connectivity. Since it is not often feasible to monitor vigilance with EEG during fMRI scans, it would be of great value to have methods for estimating vigilance levels from fMRI data alone. A recent study, conducted in macaque monkeys, proposed a template-based approach for fMRI-based estimation of vigilance fluctuations. Here, we use simultaneously acquired EEG/fMRI data to investigate whether the same template-based approach can be employed to estimate vigilance fluctuations of awake humans across different resting-state conditions. We first demonstrate that the spatial pattern of correlations between EEG-defined vigilance and fMRI in our data is consistent with the previous literature. Notably, however, we observed a significant difference between the eyes-closed (EC) and eyes-open (EO) conditions, finding stronger negative correlations with vigilance in regions forming the default mode network and higher positive correlations in thalamus and insula in the EC condition when compared to the EO condition. Taking these correlation maps as “templates” for vigilance estimation, we found that the template-based approach produced fMRI-based vigilance estimates that were significantly correlated with EEG-based vigilance measures, indicating its generalizability from macaques to humans. We also demonstrate that the performance of this method was related to the overall amount of variability in a subject's vigilance state, and that the template-based approach outperformed the use of the global signal as a vigilance estimator. In addition, we show that the template-based approach can be used to estimate the variability across scans in the amplitude of the vigilance fluctuations. We discuss the benefits and tradeoffs of using the template-based approach in future fMRI studies. •Template-based approach can be used to estimate vigilance fluctuations of awake humans at rest.•The approach can be used when external vigilance monitoring (such as with EEG) is not feasible.•Performance of this method is related to the amount of variability in a subject's vigilance state.•It can be used to estimate the variability across runs in the amplitude of the vigilance fluctuations.•Template-based approach outperforms the use of the global signal as a vigilance estimator.

Resting-state functional connectivity magnetic resonance imaging is proving to be an essential tool for the characterization of functional networks in the brain. Two of the major networks that have been identified are the default mode network (DMN) and the task positive network (TPN). Although prior work indicates that these two networks are anti-correlated, the findings are controversial because the anti-correlations are often found only after the application of a pre-processing step, known as global signal regression, that can produce artifactual anti-correlations. In this paper, we show that, for subjects studied in an eyes-closed rest state, caffeine can significantly enhance the detection of anti-correlations between the DMN and TPN without the need for global signal regression. In line with these findings, we find that caffeine also leads to widespread decreases in connectivity and global signal amplitude. Using a recently introduced geometric model of global signal effects, we demonstrate that these decreases are consistent with the removal of an additive global signal confound. In contrast to the effects observed in the eyes-closed rest state, caffeine did not lead to significant changes in global functional connectivity in the eyes-open rest state. ► Caffeine causes widespread decreases in functional connectivity. ► Caffeine reduces the global signal amplitude. ► Caffeine enhances the detection of the anti-correlations between the DMN and TPN.

Abstract Background Radiogenomics is an emerging tool with applications in screening for molecular biomarkers in diagnostic and prognostic assessment through the extraction of quantitative data from medical images (Shui et al., Front Oncol 2021). In this study, we aim to develop machine learning (ML) models to predict the most common genomic alterations present in our subset of renal cell carcinoma patients (pts). Methods Retrospectively, pts with tissue genomic testing from CT-guided biopsy samples were identified. Genomic testing was done via GEM ExTra assay, a CAP-accredited, CLIA-certified test encompassing tumor whole exome sequencing and whole transcriptome sequencing (TGen; Phoenix, AZ). Biopsy sample collection sites were identified from pre-biopsy contrast CT images, and the lesions were segmented with ITK-SNAP software, from which 510 radiomic features were extracted with Pyradiomics. The Least Absolute Shrinkage and Selection Operator (LASSO) regression was used to select the most relevant features. Logistic regression (LR) and support vector machine (SVM) classifiers were built for the prediction of PBRM1, VHL, and SETD2 gene alterations. Multiple metrics were used to evaluate the predictive performance via leave-one-out cross-validation, including the area under the receiver operating characteristic (AUROC) and the area under the precision-recall curve (AUPRC). Feature importance was evaluated with Shapley additive explanations (SHAP) method. Results A total of 14 RCC pts (10:4 M:F) with genomic testing from CT-guided biopsies were identified. The majority of pts were White (85.7%) and had clear cell histology (71.4%). The most common locations for the CT-guided biopsy were lung (18.2%), soft tissue (13.6%), kidney (9.1%), and bone (9.1%). The most common alterations were seen in PBRM1 (50%), VHL (43.9%), and SETD2 (35.7%) genes. The PBRM1 gene was predicted with the highest AUROC (0.84) and AUPRC (0.88) with the SVM classifier, followed by the SETD2 gene (AUROC=0.78 and AUPRC=0.66) with LR classifier and VHL gene (AUROC=0.56 and AUPRC=0.65) with SVM classifier. Notably, all three models showed good sensitivity in classifying gene mutation status (PBRM1: 0.86; VHL: 0.88; SETD2: 0.89). Among all radiomic features, first-order features, Gray Level Size Zone Matrix features, and Gray Level Dependence Matrix features were found to be the most important features for predictions. Conclusions Using a CT-based radiomics analysis of the biopsy area, we showed that SVM and LR prediction models could predict PBRM1, VHL, and SETD2 mutations with high accuracy. These models may assist in identifying potentially actionable alterations and yield ease in treatment selection for RCC. Further extensive studies are warranted to validate our findings and improve our model. CDMRP DOD Funding: no

To assess the microstructural properties of cerebral white matter in children with congenital sensorineural hearing loss (CSNHL). Children (>4 years of age) with profound CSNHL and healthy controls with normal hearing (the control group) were enrolled and underwent brain magnetic resonance imaging (MRI) scans with diffusion tensor imaging (DTI). DTI parameters including fractional anisotropy, mean diffusivity, axial diffusivity, and radial diffusivity were obtained from a whole-brain tract-based spatial statistics analysis and were compared between the two groups. In addition, a region of interest (ROI) approach focusing on auditory cortex, i.e., Heschl's gyrus, using visual cortex, i.e., forceps major as an internal control, was performed. Correlations between mean DTI values and age were obtained with the ROI method. The study cohort consisted of 23 children with CSHNL (11 boys and 12 girls; mean age ± SD: 7.21 ± 2.67 years; range: 4.1-13.5 years) and 18 children in the control group (11 boys and 7 girls; mean age ± SD: 10.86 ± 3.56 years; range: 4.5-15.3 years). We found the axial diffusivity values being significantly greater in the left anterior thalamic radiation, right corticospinal tract, and corpus callosum in the CSHNL group than in the control group ( < 0.05). Significantly higher radial diffusivity values in the white matter tracts were noted in the CSHNL group as compared to the control group ( < 0.05). The fractional anisotropy values in the Heschl's gyrus in the CSNHL group were lower compared to the control group ( = 0.0015). There was significant negative correlation between the mean fractional anisotropy values in Heschl's gyrus and age in the CSNHL group < 7 years of age ( = -0.59, = 0.004). Our study showed higher axial and radial diffusivities in the children affected by CNHNL as compared to the hearing children. We also found lower fractional anisotropy values in the Heschl's gyrus in the CSNHL group. Furthermore, we identified negative correlation between the fractional anisotropy values and age up to 7 years in the children born deaf. Our study findings suggest that myelination and axonal structure may be affected due to acoustic deprivation. This information may help to monitor hearing rehabilitation in the deaf children.

In the real world, learning often proceeds in an unsupervised manner without explicit instructions or feedback. In this study, we employed an experimental paradigm in which subjects explored an immersive virtual reality environment on each of two days. On day 1, subjects implicitly learned the location of 39 objects in an unsupervised fashion. On day 2, the locations of some of the objects were changed, and object location recall performance was assessed and found to vary across subjects. As prior work had shown that functional magnetic resonance imaging (fMRI) measures of resting-state brain activity can predict various measures of brain performance across individuals, we examined whether resting-state fMRI measures could be used to predict object location recall performance. We found a significant correlation between performance and the variability of the resting-state fMRI signal in the basal ganglia, hippocampus, amygdala, thalamus, insula, and regions in the frontal and temporal lobes, regions important for spatial exploration, learning, memory, and decision making. In addition, performance was significantly correlated with resting-state fMRI connectivity between the left caudate and the right fusiform gyrus, lateral occipital complex, and superior temporal gyrus. Given the basal ganglia's role in exploration, these findings suggest that tighter integration of the brain systems responsible for exploration and visuospatial processing may be critical for learning in a complex environment.

In resting-state functional magnetic resonance imaging (fMRI), the temporal correlation between spontaneous fluctuations of the blood oxygenation level dependent (BOLD) signal from different brain regions is used to assess functional connectivity. However, because the BOLD signal is an indirect measure of neuronal activity, its complex hemodynamic nature can complicate the interpretation of differences in connectivity that are observed across conditions or subjects. For example, prior studies have shown that caffeine leads to widespread reductions in BOLD connectivity but were not able to determine if neural or vascular factors were primarily responsible for the observed decrease. In this study, we used source-localized magnetoencephalography (MEG) in conjunction with fMRI to further examine the origins of the caffeine-induced changes in BOLD connectivity. We observed widespread and significant (p < 0.01) reductions in both MEG and fMRI connectivity measures, suggesting that decreases in the connectivity of resting-state neuro-electric power fluctuations were primarily responsible for the observed BOLD connectivity changes. The MEG connectivity decreases were most pronounced in the beta band. By demonstrating the similarity in MEG and fMRI based connectivity changes, these results provide evidence for the neural basis of resting-state fMRI networks and further support the potential of MEG as a tool to characterize resting-state connectivity.

In resting-state functional connectivity magnetic resonance imaging (fcMRI) studies, measures of functional connectivity are often calculated after the removal of a global mean signal component. While the application of the global signal regression approach has been shown to reduce the influence of physiological artifacts and enhance the detection of functional networks, there is considerable controversy regarding its use as the method can lead to significant bias in the resultant connectivity measures. In addition, evidence from recent studies suggests that the global signal is linked to neural activity and may carry clinically relevant information. For instance, in a prior study we found that the amplitude of the global signal was negatively correlated with EEG measures of vigilance across subjects and experimental runs. Furthermore, caffeine-related decreases in global signal amplitude were associated with increases in EEG vigilance. In this study, we extend the prior work by examining measures of global signal amplitude and EEG vigilance under eyes-closed (EC) and eyes-open (EO) resting-state conditions. We show that changes (EO minus EC) in the global signal amplitude are negatively correlated with the associated changes in EEG vigilance. The slope of this EO–EC relation is comparable with the slope of the previously reported relation between caffeine-related changes in the global signal amplitude and EEG vigilance. Our findings provide further support for a basic relationship between global signal amplitude and EEG vigilance. •Abbreviations: global signal amplitude (GSamp); eyes open (EO); eyes closed (EC)•Changes (EO–EC) in GSamp are inversely correlated with changes in EEG vigilance.•EO–EC relation between GSamp and vigilance is comparable to caffeine-related relation.

Abstract Background Metastatic renal cell carcinoma (mRCC) is a molecularly heterogeneous disease commonly driven by somatic mutations in genes such as VHL, PBRM1, and BAP1. Although next-generation sequencing (NGS) is the gold standard for identifying such mutations, it remains costly and logistically challenging. Given that genetic alterations often lead to morphological changes, we hypothesized that an artificial intelligence (AI) model applied to hematoxylin and eosin (H&E)-stained whole-slide images (WSIs) could predict underlying somatic mutations. Methods We identified consecutive patients with mRCC who had undergone clinical NGS and had available H&E-stained histopathology slides. Patients with somatic alterations in at least one target gene were annotated. WSIs were tiled into non-overlapping 256 × 256-pixel patches. Background tiles were excluded based on brightness. Across 160 total WSIs, 3 slides had no valid tissue tiles and were excluded. The final dataset included 157 slides with usable content. From 69 672 tile attempts, 28 924 tiles (41.5%) passed quality filters and were used for model development. Two modeling pipelines were implemented: (1) slide-level, aggregating global features from WSIs, and (2) tile-level, embedding and classifying each tile with prediction aggregation at the slide level. Embeddings were generated using DINOv2 and the GigaPath foundation model. To evaluate model performance, we used receiver operating characteristic (ROC) curves and computed the area under the curve (AUC) for both slide-level and tile-level pipelines. ROC analysis was applied at both the tile level and the patient-aggregated level. Principal component analysis (PCA) was used for embedding visualization. Violin plots summarized patient-level AUCs across genes. Results A total of 157 WSIs (one per patient) were analyzed. The cohort included 83 VHL with pathogenic variants (PV) (52.9%) and 74 VHL-wild type (47.1%), along with PVs in: PBRM1 (48/157, 30.6%), BAP1 (9/157, 5.7%), PTEN (8/157, 5.1%), TSC1 (7/157, 4.5%), KDM5C (14/157, 8.9%), SETD2 (27/157, 17.2%), MTOR (8/157, 5.1%), TERT (19/157, 12.1%), and NF2 (2/157, 1.3%). Slide-level modeling demonstrated limited performance in mutation prediction. However, tile-level modeling substantially improved performance. The ROC curve for tile-level VHL prediction achieved AUC = 0.7206. Other tile-based AUCs included PBRM1 (0.76), PTEN (0.80), BAP1 (0.69), TSC1 (0.70), and NF2 (0.62), while lower performance persisted for MTOR (0.25), TERT (0.46), and KDM5C (0.47). PCA of tile embeddings revealed partial clustering by mutation status, and heatmaps localized high-probability regions consistent with expected histologic features. Conclusions Tile-level AI modeling enables accurate, interpretable prediction of somatic mutations in mRCC using H&E-stained WSIs. This approach may offer a scalable and accessible tool for expanding molecular profiling in settings without widespread access to NGS.