16p11.2 and 22q11.2 Copy Number Variants (CNVs) confer high risk for Autism Spectrum Disorder (ASD), schizophrenia (SZ), and Attention-Deficit-Hyperactivity-Disorder (ADHD), but their impact on ...functional connectivity (FC) remains unclear. Here we report an analysis of resting-state FC using magnetic resonance imaging data from 101 CNV carriers, 755 individuals with idiopathic ASD, SZ, or ADHD and 1,072 controls. We characterize CNV FC-signatures and use them to identify dimensions contributing to complex idiopathic conditions. CNVs have large mirror effects on FC at the global and regional level. Thalamus, somatomotor, and posterior insula regions play a critical role in dysconnectivity shared across deletions, duplications, idiopathic ASD, SZ but not ADHD. Individuals with higher similarity to deletion FC-signatures exhibit worse cognitive and behavioral symptoms. Deletion similarities identified at the connectivity level could be related to the redundant associations observed genome-wide between gene expression spatial patterns and FC-signatures. Results may explain why many CNVs affect a similar range of neuropsychiatric symptoms.
Abstract
Background
With the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient ...large-scale data processing is growing.
Findings
Here we present GenPipes, a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for high-performance computing clusters and the cloud. GenPipes already implements 12 validated and scalable pipelines for various genomics applications, including RNA sequencing, chromatin immunoprecipitation sequencing, DNA sequencing, methylation sequencing, Hi-C, capture Hi-C, metagenomics, and Pacific Biosciences long-read assembly. The software is available under a GPLv3 open source license and is continuously updated to follow recent advances in genomics and bioinformatics. The framework has already been configured on several servers, and a Docker image is also available to facilitate additional installations.
Conclusions
GenPipes offers genomics researchers a simple method to analyze different types of data, customizable to their needs and resources, as well as the flexibility to create their own workflows.
Purpose
Neuroimaging provides great utility in complex spinal surgeries, particularly when anatomical geometry is distorted by pathology (tumour, degeneration, etc.). Spinal cord MRI diffusion ...tractography can be used to generate streamlines; however, it is unclear how well they correspond with white matter tract locations along the cord microstructure. The goal of this work was to evaluate the spatial correspondence of DTI tractography with anatomical MRI in healthy anatomy (where anatomical locations can be well defined in T1-weighted images).
Methods
Ten healthy volunteers were scanned on a 3T system. T1-weighted (1 × 1 × 1 mm) and diffusion-weighted images (EPI readout, 2 × 2 × 2 mm, 30 gradient directions) were acquired and subsequently registered (Spinal Cord Toolbox (SCT)). Atlas-based (SCT) anatomic label maps of the left and right lateral corticospinal tracts were identified for each vertebral region (C2–C6) from T1 images. Tractography streamlines were generated with a customized approach, enabling seeding of specific spinal tract regions corresponding to individual vertebral levels. Spatial correspondence of generated fibre streamlines with anatomic tract segmentations was compared in unseeded regions of interest (ROIs).
Results
Spatial correspondence of the lateral corticospinal tract streamlines was good over a single vertebral ROI (Dice’s similarity coefficient (DSC) = 0.75 ± 0.08, Hausdorff distance = 1.08 ± 0.17 mm). Over larger ROI, fair agreement between tractography and anatomical labels was achieved (two levels: DSC = 0.67 ± 0.13, three levels: DSC = 0.52 ± 0.19).
Conclusion
DTI tractography produced good spatial correspondence with anatomic white matter tracts, superior to the agreement between multiple manual tract segmentations (DSC ~ 0.5). This supports further development of spinal cord tractography for computer-assisted neurosurgery.
ABSTRACT
Space-based projects are providing a wealth of high-quality asteroseismic data, including frequencies for a large number of stars showing solar-like oscillations. These data open the ...prospect for precise determinations of key stellar parameters, of particular value to the study of extra-solar planetary systems. Given the quantity of the available and expected data, it is important to develop efficient and reliable techniques for analyzing them, including the determination of stellar parameters from the observed frequencies. Here we present the SEEK package developed for the analysis of asteroseismic data from the
Kepler
mission. A central goal of the package is to obtain a fast and automatic determination of the stellar radius and other parameters in a form that is statistically well defined. The algorithms are tested by comparing the results of the analysis with independent measurements of stellar radius and mass for a sample of well-observed stars. We conclude that the SEEK package fixes stellar parameters with accuracy and precision.
Background Québec was the Canadian province most impacted by COVID-19, with 401,462 cases as of September 24th, 2021, and 11,347 deaths due mostly to a very severe first pandemic wave. In April 2020, ...we assembled the Coronavirus Sequencing in Québec (CoVSeQ) consortium to sequence SARS-CoV-2 genomes in Québec to track viral introduction events and transmission within the province. Methods Using genomic epidemiology, we investigated the arrival of SARS-CoV-2 to Québec. We report 2921 high-quality SARS-CoV-2 genomes in the context of > 12,000 publicly available genomes sampled globally over the first pandemic wave (up to June 1st, 2020). By combining phylogenetic and phylodynamic analyses with epidemiological data, we quantify the number of introduction events into Québec, identify their origins, and characterize the spatiotemporal spread of the virus. Results Conservatively, we estimated approximately 600 independent introduction events, the majority of which happened from spring break until 2 weeks after the Canadian border closed for non-essential travel. Subsequent mass repatriations did not generate large transmission lineages (> 50 sequenced cases), likely due to mandatory quarantine measures in place at the time. Consistent with common spring break and "snowbird" destinations, most of the introductions were inferred to have originated from Europe via the Americas. Once introduced into Québec, viral lineage sizes were overdispersed, with a few lineages giving rise to most infections. Consistent with founder effects, the earliest lineages to arrive tended to spread most successfully. Fewer than 100 viral introductions arrived during spring break, of which 7-12 led to the largest transmission lineages of the first wave (accounting for 52-75% of all sequenced infections). These successful transmission lineages dispersed widely across the province. Transmission lineage size was greatly reduced after March 11th, when a quarantine order for returning travellers was enacted. While this suggests the effectiveness of early public health measures, the biggest transmission lineages had already been ignited prior to this order. Conclusions Combined, our results reinforce how, in the absence of tight travel restrictions or quarantine measures, fewer than 100 viral introductions in a week can ensure the establishment of extended transmission chains.
We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software ...containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science.
Science gateways often rely on workflow engines to execute applications on distributed infrastructures. We investigate six software architectures commonly used to integrate workflow engines into ...science gateways. In tight integration, the workflow engine shares software components with the science gateway. In service invocation, the engine is isolated and invoked through a specific software interface. In task encapsulation, the engine is wrapped as a computing task executed on the infrastructure. In the pool model, the engine is bundled in an agent that connects to a central pool to fetch and execute workflows. In nested workflows, the engine is integrated as a child process of another engine. In workflow conversion, the engine is integrated through workflow language conversion. We describe and evaluate these architectures with metrics for assessment of integration complexity, robustness, extensibility, scalability and functionality. Tight integration and task encapsulation are the easiest to integrate and the most robust. Extensibility is equivalent in most architectures. The pool model is the most scalable one and meta-workflows are only available in nested workflows and workflow conversion. These results provide insights for science gateway architects and developers.
•We study 6 software architectures to integrate workflow engines in science gateways.•We describe these architectures in a consistent framework.•We assess their complexity, robustness, extensibility, scalability and functionality.•Results provide insights for science gateway architects and developers.
We combine results from interferometry, asteroseismology and spectroscopy to determine accurate fundamental parameters of 23 bright solar-type stars, from spectral type F5 to K2 and luminosity ...classes III–V. For some stars we can use direct techniques to determine the mass, radius, luminosity and effective temperature, and we compare with indirect methods that rely on photometric calibrations or spectroscopic analyses. We use the asteroseismic information available in the literature to infer an indirect mass with an accuracy of 4–15 per cent. From indirect methods we determine luminosity and radius to 3 per cent. We find evidence that the luminosity from the indirect method is slightly overestimated (≈ 5 per cent) for the coolest stars, indicating that their bolometric corrections (BCs) are too negative. For Teff we find a slight offset of −40 ± 20 K between the spectroscopic method and the direct method, meaning the spectroscopic temperatures are too high. From the spectroscopic analysis we determine the detailed chemical composition for 13 elements, including Li, C and O. The metallicity ranges from Fe/H=−1.7 to +0.4, and there is clear evidence for α-element enhancement in the metal-poor stars. We find no significant offset between the spectroscopic surface gravity and the value from combining asteroseismology with radius estimates. From the spectroscopy we also determine v sin i and we present a new calibration of macroturbulence and microturbulence. From the comparison between the results from the direct and spectroscopic methods we claim that we can determine Teff, log g and Fe/H with absolute accuracies of 80 K, 0.08 and 0.07 dex. Photometric calibrations of Strömgren indices provide accurate results for Teff and Fe/H but will be more uncertain for distant stars when interstellar reddening becomes important. The indirect methods are important to obtain reliable estimates of the fundamental parameters of relatively faint stars when interferometry cannot be used. This paper is the first to compare direct and indirect methods for a large sample of stars, and we conclude that indirect methods are valid, although slight corrections may be needed.
Context. Helioseismology has enabled us to better understand the solar interior, while also allowing us to better constrain solar models. But now is a tremendous epoch for asteroseismology as space ...missions dedicated to studying stellar oscillations have been launched within the last years (MOST and CoRoT). CoRoT has already proved valuable results for many types of stars, while Kepler, which was launched in March 2009, will provide us with a huge number of seismic data very soon. This is an opportunity to better constrain stellar models and to finally understand stellar structure and evolution. Aims. The goal of this research work is to estimate the global parameters of any solar-like oscillating target in an automatic manner. We want to determine the global parameters of the acoustic modes (large separation, range of excited pressure modes, maximum amplitude, and its corresponding frequency), retrieve the surface rotation period of the star and use these results to estimate the global parameters of the star (radius and mass). Methods. To prepare for the arrival and the analysis of hundreds of solar-like oscillating stars, we have developed a robust and automatic pipeline, which was partially adapted from helioseismic methods. The pipeline consists of data analysis techniques, such as Fast Fourier Transform, wavelets, autocorrelation, as well as the application of minimisation algorithms for stellar-modelling. Results. We apply our pipeline to some simulated lightcurves from the asteroFLAG team and the Aarhus-asteroFLAG simulator, and obtain results that are consistent with the input data to the simulations. Our strategy gives correct results for stars with magnitudes below 11 with only a few 10% of bad determinations among the reliable results. We then apply the pipeline to the Sun and three CoRoT targets. In particular we determine the large separation and radius of the Sun, HD49933, HD181906, and HD181420.
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