A unified metric of human immune health.

Immunological health has been challenging to characterize but could be defined as the absence of immune pathology. While shared features of some immune diseases and the concept of immunologic resilience based on age-independent adaptation to antigenic stimulation have been developed, general metrics of immune health and its utility for assessing clinically healthy individuals remain ill defined. Here we integrated transcriptomics, serum protein, peripheral immune cell frequency and clinical data from 228 patients with 22 monogenic conditions impacting key immunological pathways together with 42 age- and sex-matched healthy controls.

Assessing informative tract segmentation and nTMS for pre-operative planning.

Background: Deep learning-based (DL) methods are the best-performing methods for white matter tract segmentation in anatomically healthy subjects. However, tract annotations are variable or absent in clinical data and manual annotations are especially difficult in patients with tumors where normal anatomy may be distorted. Direct cortical and subcortical stimulation is the gold standard ground truth to determine the cortical and sub-cortical lo- cation of motor-eloquent areas intra-operatively.

Multiomics integration of 22 immune-mediated monogenic diseases reveals an emergent axis of human immune health.

Monogenic diseases are often studied in isolation due to their rarity. Here we utilize multiomics to assess 22 monogenic immune-mediated conditions with age- and sex-matched healthy controls. Despite clearly detectable disease-specific and "pan-disease" signatures, individuals possess stable personal immune states over time.

Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19.

Acute viral infections can have durable functional impacts on the immune system long after recovery, but how they affect homeostatic immune states and responses to future perturbations remain poorly understood. Here we use systems immunology approaches, including longitudinal multimodal single-cell analysis (surface proteins, transcriptome and V(D)J sequences) to comparatively assess baseline immune statuses and responses to influenza vaccination in 33 healthy individuals after recovery from mild, non-hospitalized COVID-19 (mean, 151 days after diagnosis) and 40 age- and sex-matched control individuals who had never had COVID-19. At the baseline and independent of time after COVID-19, recoverees had elevated T cell activation signatures and lower expression of innate immune genes including Toll-like receptors in monocytes.

Software tool for visualization of a probabilistic map of the epileptogenic zone from seizure semiologies.

Around one third of epilepsies are drug-resistant. For these patients, seizures may be reduced or cured by surgically removing the epileptogenic zone (EZ), which is the portion of the brain giving rise to seizures. If noninvasive data are not sufficiently lateralizing or localizing, the EZ may need to be localized by precise implantation of intracranial electroencephalography (iEEG) electrodes.

Brain Lesion Synthesis via Progressive Adversarial Variational Auto-Encoder.

Laser interstitial thermal therapy (LITT) is a novel minimally invasive treatment that is used to ablate intracranial structures to treat mesial temporal lobe epilepsy (MTLE). Region of interest (ROI) segmentation before and after LITT would enable automated lesion quantification to objectively assess treatment efficacy. Deep learning techniques, such as convolutional neural networks (CNNs) are state-of-the-art solutions for ROI segmentation, but require large amounts of annotated data during the training.

OMiCC: An expanded and enhanced platform for meta-analysis of public gene expression data.

OMiCC (OMics Compendia Commons) is a biologist-friendly web platform that facilitates data reuse and integration. Users can search over 40,000 publicly available gene expression studies, annotate and curate samples, and perform meta-analysis. Since the initial publication, we have incorporated RNA-seq datasets, compendia sharing, RESTful API support, and an additional meta-analysis method based on random effects.

Probabilistic landscape of seizure semiology localizing values.

Semiology describes the evolution of symptoms and signs during epileptic seizures and contributes to the evaluation of individuals with focal drug-resistant epilepsy for curative resection. Semiology varies in complexity from elementary sensorimotor seizures arising from primary cortex to complex behaviours and automatisms emerging from distributed cerebral networks. Detailed semiology interpreted by expert epileptologists may point towards the likely site of seizure onset, but this process is subjective.

Informative and Reliable Tract Segmentation for Preoperative Planning.

Identifying white matter (WM) tracts to locate eloquent areas for preoperative surgical planning is a challenging task. Manual WM tract annotations are often used but they are time-consuming, suffer from inter- and intra-rater variability, and noise intrinsic to diffusion MRI may make manual interpretation difficult. As a result, in clinical practice direct electrical stimulation is necessary to precisely locate WM tracts during surgery.

A Framework for Augmented Intelligence in Allergy and Immunology Practice and Research-A Work Group Report of the AAAAI Health Informatics, Technology, and Education Committee.

Artificial and augmented intelligence (AI) and machine learning (ML) methods are expanding into the health care space. Big data are increasingly used in patient care applications, diagnostics, and treatment decisions in allergy and immunology. How these technologies will be evaluated, approved, and assessed for their impact is an important consideration for researchers and practitioners alike.

Influenza vaccination and single cell multiomics reveal sex dimorphic immune imprints of prior mild COVID-19.

Viral infections can have profound and durable functional impacts on the immune system. There is an urgent need to characterize the long-term immune effects of SARS-CoV-2 infection given the persistence of symptoms in some individuals and the continued threat of novel variants. Here we use systems immunology, including longitudinal multimodal single cell analysis (surface proteins, transcriptome, and V(D)J sequences) from 33 previously healthy individuals after recovery from mild, non-hospitalized COVID-19 and 40 age- and sex-matched healthy controls with no history of COVID-19 to comparatively assess the post-infection immune status (mean: 151 days after diagnosis) and subsequent innate and adaptive responses to seasonal influenza vaccination.

Machine Learning for Localizing Epileptogenic-Zone in the Temporal Lobe: Quantifying the Value of Multimodal Clinical-Semiology and Imaging Concordance.

Epilepsy affects 50 million people worldwide and a third are refractory to medication. If a discrete cerebral focus or network can be identified, neurosurgical resection can be curative. Most excisions are in the temporal-lobe, and are more likely to result in seizure-freedom than extra-temporal resections.

Comparison of robotic and manual implantation of intracerebral electrodes: a single-centre, single-blinded, randomised controlled trial.

There has been a significant rise in robotic trajectory guidance devices that have been utilised for stereotactic neurosurgical procedures. These devices have significant costs and associated learning curves. Previous studies reporting devices usage have not undertaken prospective parallel-group comparisons before their introduction, so the comparative differences are unknown.

Resection of the piriform cortex for temporal lobe epilepsy: a Novel approach on imaging segmentation and surgical application.

Background: The piriform cortex (PC) occupies both banks of the endorhinal sulcus and has an important role in the pathophysiology of temporal lobe epilepsy (TLE). A recent study showed that resection of more than 50% of PC increased the odds of becoming seizure free by a factor of 16.

Objective: We report the feasibility of manual segmentation of PC and application of the Geodesic Information Flows (GIF) algorithm to automated segmentation, to guide resection.

Intraoperative overlay of optic radiation tractography during anteromesial temporal resection: a prospective validation study.

Objective: Anteromesial temporal lobe resection (ATLR) results in long-term seizure freedom in patients with drug-resistant focal mesial temporal lobe epilepsy (MTLE). There is significant anatomical variation in the anterior projection of the optic radiation (OR), known as Meyer's loop, between individuals and between hemispheres in the same individual. Damage to the OR results in contralateral superior temporal quadrantanopia that may preclude driving in 33%-66% of patients who achieve seizure freedom.

TorchIO: A Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning.

Background And Objective: Processing of medical images such as MRI or CT presents different challenges compared to RGB images typically used in computer vision. These include a lack of labels for large datasets, high computational costs, and the need of metadata to describe the physical properties of voxels. Data augmentation is used to artificially increase the size of the training datasets.

Enhancing the estimation of fiber orientation distributions using convolutional neural networks.

Local fiber orientation distributions (FODs) can be computed from diffusion magnetic resonance imaging (dMRI). The accuracy and ability of FODs to resolve complex fiber configurations benefits from acquisition protocols that sample a high number of gradient directions, a high maximum b-value, and multiple b-values. However, acquisition time and scanners that follow these standards are limited in clinical settings, often resulting in dMRI acquired at a single shell (single b-value).

Occipitocervical instrumented fixation utilising patient-specific C2 3D-printed spinal screw trajectory guides in complex paediatric skeletal dysplasia.

Purpose: Instability of the craniocervical junction in paediatric patients with skeletal dysplasia poses a unique set of challenges including anatomical abnormalities, poor bone quality, skeletal immaturity and associated general anaesthetic risks. Instrumented fixation provides optimal stabilisation and fusion rates. The small vertebrae make the placement of C2 pedicle screws technically demanding with low margins of error between the spinal canal and the vertebral artery.

Patient-specific prediction of SEEG electrode bending for stereotactic neurosurgical planning.

PURPOSE : Electrode bending observed after stereotactic interventions is typically not accounted for in either computer-assisted planning algorithms, where straight trajectories are assumed, or in quality assessment, where only metrics related to entry and target points are reported. Our aim is to provide a fully automated and validated pipeline for the prediction of stereo-electroencephalography (SEEG) electrode bending. METHODS : We transform electrodes of 86 cases into a common space and compare features-based and image-based neural networks on their ability to regress local displacement ([Formula: see text]) or electrode bending ([Formula: see text]).

Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19.

COVID-19 exhibits extensive patient-to-patient heterogeneity. To link immune response variation to disease severity and outcome over time, we longitudinally assessed circulating proteins as well as 188 surface protein markers, transcriptome, and T cell receptor sequence simultaneously in single peripheral immune cells from COVID-19 patients. Conditional-independence network analysis revealed primary correlates of disease severity, including gene expression signatures of apoptosis in plasmacytoid dendritic cells and attenuated inflammation but increased fatty acid metabolism in CD56CD16 NK cells linked positively to circulating interleukin (IL)-15.