nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework.

Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets.

IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data.

In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is a crucial step. This process is highly impacted by allele annotations. Aligning sequences, assigning them to specific germline alleles, and inferring individual genotypes are challenging when the repertoire is highly mutated, or sequence reads do not cover the whole V region. Here, we propose an alternative naming scheme for the V alleles, as well as a novel method to infer individual genotypes. We demonstrate the strengths of the two by comparing their outcomes to other genotype inference methods. We validate the genotype approach with independent genomic long-read data. The naming scheme is compatible with current annotation tools and pipelines. Analysis results can be converted from the proposed naming scheme to the nomenclature determined by the International Union of Immunological Societies (IUIS). Both the naming scheme and the genotype procedure are implemented in a freely available R package (PIgLET https://bitbucket.org/yaarilab/piglet). To allow researchers to further explore the approach on real data and to adapt it for their uses, we also created an interactive website (https://yaarilab.github.io/IGHV_reference_book).

Mindboggling morphometry of human brains.

Mindboggle (http://mindboggle.info) is an open source brain morphometry platform that takes in preprocessed T1-weighted MRI data and outputs volume, surface, and tabular data containing label, feature, and shape information for further analysis. In this article, we document the software and demonstrate its use in studies of shape variation in healthy and diseased humans. The number of different shape measures and the size of the populations make this the largest and most detailed shape analysis of human brains ever conducted. Brain image morphometry shows great potential for providing much-needed biological markers for diagnosing, tracking, and predicting progression of mental health disorders. Very few software algorithms provide more than measures of volume and cortical thickness, while more subtle shape measures may provide more sensitive and specific biomarkers. Mindboggle computes a variety of (primarily surface-based) shapes: area, volume, thickness, curvature, depth, Laplace-Beltrami spectra, Zernike moments, etc. We evaluate Mindboggle's algorithms using the largest set of manually labeled, publicly available brain images in the world and compare them against state-of-the-art algorithms where they exist. All data, code, and results of these evaluations are publicly available.

nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework.

Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets. nf-core/airrflow is available free of charge, under the MIT license on GitHub (https://github.com/nf-core/airrflow). Detailed documentation and example results are available on the nf-core website at (https://nf-co.re/airrflow).

Brain white matter pathways of resilience to chronic back pain: a multisite validation.

Chronic back pain (CBP) is a global health concern with significant societal and economic burden. While various predictors of back pain chronicity have been proposed, including demographic and psychosocial factors, neuroimaging studies have pointed to brain characteristics as predictors of CBP. However, large-scale, multisite validation of these predictors is currently lacking. In two independent longitudinal studies, we examined white matter diffusion imaging data and pain characteristics in patients with subacute back pain (SBP) over six- and 12-month periods. Diffusion data from individuals with CBP and healthy controls (HC) were analyzed for comparison. Whole-brain tract-based spatial statistics analyses revealed that a cluster in the right superior longitudinal fasciculus (SLF) tract had larger fractional anisotropy (FA) values in patients who recovered (SBPr) compared to those with persistent pain (SBPp), and predicted changes in pain severity. The SLF FA values accurately classified patients at baseline and follow-up in a third publicly available dataset (Area under the Receiver Operating Curve ~ 0.70). Notably, patients who recovered had FA values larger than those of HC suggesting a potential role of SLF integrity in resilience to CBP. Structural connectivity-based models also classified SBPp and SBPr patients from the three data sets (validation accuracy 67%). Our results validate the right SLF as a robust predictor of CBP development, with potential for clinical translation. Cognitive and behavioral processes dependent on the right SLF, such as proprioception and visuospatial attention, should be analyzed in subacute stages as they could prove important for back pain chronicity.

A ubiquitous spectrolaminar motif of local field potential power across the primate cortex.

The mammalian cerebral cortex is anatomically organized into a six-layer motif. It is currently unknown whether a corresponding laminar motif of neuronal activity patterns exists across the cortex. Here we report such a motif in the power of local field potentials (LFPs). Using laminar probes, we recorded LFPs from 14 cortical areas across the cortical hierarchy in five macaque monkeys. The laminar locations of recordings were histologically identified by electrolytic lesions. Across all areas, we found a ubiquitous spectrolaminar pattern characterized by an increasing deep-to-superficial layer gradient of high-frequency power peaking in layers 2/3 and an increasing superficial-to-deep gradient of alpha-beta power peaking in layers 5/6. Laminar recordings from additional species showed that the spectrolaminar pattern is highly preserved among primates-macaque, marmoset and human-but more dissimilar in mouse. Our results suggest the existence of a canonical layer-based and frequency-based mechanism for cortical computation.

A Retrospective Study: Multimodal Analgesia Quality Measure Implementation and Patient Outcome Assessment.

Current research has demonstrated that nonopioid multimodal analgesia decreases perioperative opioid consumption, postoperative nausea and vomiting (PONV), and pain scores. However, no research has been conducted to examine the patient outcomes of Merit-based Incentive Payment System (MIPS) 477. This study evaluates those outcomes following implementation of MIPS 477. The medical records of 400 adult patients who underwent elective and urgent laparoscopic gynecological procedures at a facility in the Mid-Atlantic region were reviewed. Data collection included patient characteristics, analgesics administered, pain scores at postanesthesia care unit (PACU) arrival and discharge, and antiemetic administration in PACU. This study's primary outcomes were postoperative pain scores, total intraoperative and postoperative opioid consumption, and PONV. Twenty-nine patients (7.8%) met the criteria as a control group, and 341 patients (92.2%) met the criteria as a treatment group. Pain scores were higher upon PACU arrival among the control group (P = .001). The total intraoperative morphine milligram equivalents (MMEs) administered was less among the treatment group (P = .04). The treatment group had reduced total intraoperative MMEs and pain scores at PACU arrival. However, there was no statistical significance in PACU discharge pain score, total PACU MMEs, and PONV in both groups.

SARS-CoV-2 Saliva Mass Screening in Primary Schools: A 10-Week Sentinel Surveillance Study in Munich, Germany.

Representative, actively collected surveillance data on asymptomatic SARS-CoV-2 infections in primary schoolchildren remain scarce. We evaluated the feasibility of a saliva mass screening concept and assessed infectious activity in primary schools. During a 10-week period from 3 March to 21 May 2021, schoolchildren and staff from 17 primary schools in Munich participated in the sentinel surveillance, cohort study. Participants were tested using the Salivette® system, testing was supervised by trained school staff, and samples were processed via reverse transcription quantitative polymerase chain reaction (RT-qPCR). We included 4433 participants: 3752 children (median age, 8 [range, 6-13] years; 1926 girls [51%]) and 681 staff members (median age, 41 [range, 14-71] years; 592 women [87%]). In total, 23,905 samples were processed (4640 from staff), with participants representing 8.3% of all primary schoolchildren in Munich. Only eight cases were detected: Five out of 3752 participating children (0.13%) and three out of 681 staff members (0.44%). There were no secondary cases. In conclusion, supervised Salivette® self-sampling was feasible, reliable, and safe and thus constituted an ideal method for SARS-CoV-2 mass screenings in primary schoolchildren. Our findings suggest that infectious activity among asymptomatic primary schoolchildren and staff was low. Primary schools appear to continue to play a minor role in the spread of SARS-CoV-2 despite high community incidence rates.

A framework for mining signatures from event sequences and its applications in healthcare data.

This paper proposes a novel temporal knowledge representation and learning framework to perform large-scale temporal signature mining of longitudinal heterogeneous event data. The framework enables the representation, extraction, and mining of high-order latent event structure and relationships within single and multiple event sequences. The proposed knowledge representation maps the heterogeneous event sequences to a geometric image by encoding events as a structured spatial-temporal shape process. We present a doubly constrained convolutional sparse coding framework that learns interpretable and shift-invariant latent temporal event signatures. We show how to cope with the sparsity in the data as well as in the latent factor model by inducing a double sparsity constraint on the ß-divergence to learn an overcomplete sparse latent factor model. A novel stochastic optimization scheme performs large-scale incremental learning of group-specific temporal event signatures. We validate the framework on synthetic data and on an electronic health record dataset.

Recovery of macular pigment spectrum in vivo using hyperspectral image analysis.

We investigated the feasibility of a novel method for hyperspectral mapping of macular pigment (MP) in vivo. Six healthy subjects were recruited for noninvasive imaging using a snapshot hyperspectral system. The three-dimensional full spatial-spectral data cube was analyzed using non-negative matrix factorization (NMF), wherein the data was decomposed to give spectral signatures and spatial distribution, in search for the MP absorbance spectrum. The NMF was initialized with the in vitro MP spectrum and rank 4 spectral signature decomposition was used to recover the MP spectrum and optical density in vivo. The recovered MP spectra showed two peaks in the blue spectrum, characteristic of MP, giving a detailed in vivo demonstration of these absorbance peaks. The peak MP optical densities ranged from 0.08 to 0.22 (mean 0.15+∕-0.05) and became spatially negligible at diameters 1100 to 1760 µm (4 to 6 deg) in the normal subjects. This objective method was able to exploit prior knowledge (the in vitro MP spectrum) in order to extract an accurate in vivo spectral analysis and full MP spatial profile, while separating the MP spectra from other ocular absorbers. Snapshot hyperspectral imaging in combination with advanced mathematical analysis provides a simple cost-effective approach for MP mapping in vivo.

Dynamic soft drusen remodelling in age-related macular degeneration.

AIMS: To demonstrate and quantify the dynamic remodelling process of soft drusen resorption and new drusen formation in age-related macular degeneration (AMD) with novel interactive methods. METHODS: Twenty patients with large soft drusen bilaterally and without advanced AMD were imaged at baseline and again at a mean interval of 2 years (40 eyes, 80 images). Each of the 40 serial pairs of images was precisely registered by an automated technique. The drusen were segmented by a user-interactive method based on a background levelling algorithm and classified into three groups: new drusen (only in the final image), resorbed drusen (present initially but not in the final image) and stable drusen (present in both images). We measured each of these classes as well as the absolute change in drusen |D1-D0| and the dynamic drusen activity (creation and resorption) D(new)+D(resorbed). RESULTS: Mean dynamic activity for the right eye (OD) was 7.33±5.50%, significantly greater than mean absolute change (2.71±2.89%, p=0.0002, t test), with similar results for the left eye (OS). However, dynamic activity OD compared with OS (mean 7.33±5.50 vs 7.91±4.16%, NS) and absolute net change OD versus OS (2.71±2.89 vs 3.46±3.97%, NS) tended to be symmetrical between fellow eyes. CONCLUSIONS: Dynamic remodelling processes of drusen resorption and new drusen formation are distinct disease activities that can occur simultaneously and are not captured by change in total drusen load. Dynamic changes occur at rates more than twice that of net changes, and may be a useful marker of disease activity.

A partial intensity invariant feature descriptor for multimodal retinal image registration.

Detection of vascular bifurcations is a challenging task in multimodal retinal image registration. Existing algorithms based on bifurcations usually fail in correctly aligning poor quality retinal image pairs. To solve this problem, we propose a novel highly distinctive local feature descriptor named partial intensity invariant feature descriptor (PIIFD) and describe a robust automatic retinal image registration framework named Harris-PIIFD. PIIFD is invariant to image rotation, partially invariant to image intensity, affine transformation, and viewpoint/perspective change. Our Harris-PIIFD framework consists of four steps. First, corner points are used as control point candidates instead of bifurcations since corner points are sufficient and uniformly distributed across the image domain. Second, PIIFDs are extracted for all corner points, and a bilateral matching technique is applied to identify corresponding PIIFDs matches between image pairs. Third, incorrect matches are removed and inaccurate matches are refined. Finally, an adaptive transformation is used to register the image pairs. PIIFD is so distinctive that it can be correctly identified even in nonvascular areas. When tested on 168 pairs of multimodal retinal images, the Harris-PIIFD far outperforms existing algorithms in terms of robustness, accuracy, and computational efficiency.

Lipofuscin and autofluorescence metrics in progressive STGD.

PURPOSE: To evaluate Stargardt disease (STGD) progression and relative lipofuscin levels via autofluorescence image analysis. METHODS: The relationship between focally increased autofluorescence (FIAF), geographic atrophy (GA) and focally decreased autofluorescence (FDAF) was analyzed in serial, registered autofluorescence (AF) scans of 10 patients with STGD (20 eyes, 40 scans; mean follow-up, 2.0 years) using automated techniques. RESULTS: GA progressed uniformly in a transition zone with minimal FIAF. Only 4.3% of FIAF progressed to GA or FDAF, despite significant progression of GA (median 30%/year) and FDAF (mean, 29%/year). As a spatial predictor, the mean chance of FIAF for progression to FDAF was 4.3% +/- 4.4%, significantly less than that of random areas (6.7% +/- 4.0%, P = 0.029, Mann-Whitney test). In the seven eyes with GA, the mean chance of FIAF in the transition zone for transition to GA was 12% +/- 8.9%, significantly less than that of random areas (33% +/- 3.6%, P = 0.026, Mann-Whitney test). CONCLUSIONS: Autofluorescent flecks and FIAF deposits with AF levels elevated above the initial macular background were less likely in the short term (2 years) to transform to GA and FDAF (AF levels below the final background) than random areas, suggesting additional mechanisms beyond direct lipofuscin toxicity. FIAF/FDAF levels were observed to fluctuate, with focal remodeling of FIAF and FDAF, or rarely, even transition of FDAF to FIAF. FDAF tended to develop, not coincident with, but adjacent to initial FIAF. Because AF identifies these characteristic biological markers so specifically, autofluorescence metrics merit consideration in the study of STGD.

Potential of computer-aided diagnosis to improve CT lung cancer screening.

The development of low-dose spiral computed tomography (CT) has rekindled hope that effective lung cancer screening might yet be found. Screening is justified when there is evidence that it will extend lives at reasonable cost and acceptable levels of risk. A screening test should detect all extant cancers while avoiding unnecessary workups. Thus optimal screening modalities have both high sensitivity and specificity. Due to the present state of technology, radiologists must opt to increase sensitivity and rely on follow-up diagnostic procedures to rule out the incurred false positives. There is evidence in published reports that computer-aided diagnosis technology may help radiologists alter the benefit-cost calculus of CT sensitivity and specificity in lung cancer screening protocols. This review will provide insight into the current discussion of the effectiveness of lung cancer screening and assesses the potential of state-of-the-art computer-aided design developments.

Coarse to fine segmentation of Stargardt rings using an expert guided dual ellipse model.

Computer aided diagnosis in the medical image domain requires adaptive knowledge-based models to handle uncertainty, ambiguity, and noise. We propose an expert guided coupled dual ellipse model in a coarse to fine energy minimization framework. In our approach we enforce subspace model constraints by fusing domain knowledge and model information to guide the segmentation process on the fly. We apply our method to the task of retinal Stargardt segmentation a disease that manifests itself in a ring like structure around the macula. Quantitative evaluations on synthetic and real data sets show the performance of our framework. Experimental results demonstrate that our framework performance well with an area under the ROC curve of 0.93.

Interactive segmentation for geographic atrophy in retinal fundus images.

Fundus auto-fluorescence (FAF) imaging is a non-invasive technique for in vivo ophthalmoscopic inspection of age-related macular degeneration (AMD), the most common cause of blindness in developed countries. Geographic atrophy (GA) is an advanced form of AMD and accounts for 12-21% of severe visual loss in this disorder [3]. Automatic quantification of GA is important for determining disease progression and facilitating clinical diagnosis of AMD. The problem of automatic segmentation of pathological images still remains an unsolved problem. In this paper we leverage the watershed transform and generalized non-linear gradient operators for interactive segmentation and present an intuitive and simple approach for geographic atrophy segmentation. We compare our approach with the state of the art random walker [5] algorithm for interactive segmentation using ROC statistics. Quantitative evaluation experiments on 100 FAF images show a mean sensitivity/specificity of 98.3/97.7% for our approach and a mean sensitivity/specificity of 88.2/96.6% for the random walker algorithm.

Interactive Image Analysis in Age-related Macular Degeneration (AMD) and Stargardt Disease (STGD).

The literature of the last three decades is replete with automatic methods for retinal image analysis. Acceptance has been limited due to post-processing or tuning requirements that may be just as time consuming as the original manual methods. The point of view herein is that by taking advantage of the human visual system and expert knowledge from the outset, the promised efficiencies of digital methods can be achieved in practice as well as in theory. Thus, simple labeling of regions of interest that is accepted and easily performed in a few moments by the human can provide enormous advantage to an already well-developed algorithm. Three examples are provided: drusen segmentation, image registration, and geographic atrophy segmentation, with applications to disease understanding.

A hybrid segmentation approach for geographic atrophy in fundus auto-fluorescence images for diagnosis of age-related macular degeneration.

Fundus auto-fluorescence (FAF) images with hypo-fluorescence indicate geographic atrophy (GA) of the retinal pigment epithelium (RPE) in age-related macular degeneration (AMD). Manual quantification of GA is time consuming and prone to inter- and intra-observer variability. Automatic quantification is important for determining disease progression and facilitating clinical diagnosis of AMD. In this paper we describe a hybrid segmentation method for GA quantification by identifying hypo-fluorescent GA regions from other interfering retinal vessel structures. First, we employ background illumination correction exploiting a non-linear adaptive smoothing operator. Then, we use the level set framework to perform segmentation of hypo-fluorescent areas. Finally, we present an energy function combining morphological scale-space analysis with a geometric model-based approach to perform segmentation refinement of false positive hypo- fluorescent areas due to interfering retinal structures. The clinically apparent areas of hypo-fluorescence were drawn by an expert grader and compared on a pixel by pixel basis to our segmentation results. The mean sensitivity and specificity of the ROC analysis were 0.89 and 0.98%.

Tangential curved planar reformation for topological and orientation invariant visualization of vascular trees.

Recently, extensions to curved planar reformation (CPR) were proposed to improve vascular visualization of medical images. While these projective transformations provide enhanced visualization of vascular trees, non-planar alignment and arbitrary topology can cause visualization artifacts. Vascular trees in medical images are not aligned to planar cross-sections of volumetric image slices and thus aggravate simultaneous visualization of diagnostic features. Complex tree topology and non-planar alignment requires the need for an adaptive projection scheme to prevent visualization artifacts while preserving correctness of anatomical information. In this paper, we present algorithmic details for topological and orientation invariant visualization of vascular trees. Vascular high-level description of the medial axis guides the reformation process by flattening the vascular tree interior to successive image planes for respective radial sampling angles. Tree orientations are estimated from intrinsic shape properties of the vascular tree for rotation invariant projection. Radial sampling planes perpendicular to the medial axis tangents are the basis for topological invariant visualization of complete vascular interiors. We present experimental results on two different vascular tree topologies and demonstrate that our method is able to produce artifact free visualization of vascular interiors.