An automated pipeline for constructing personalized virtual brains from multimodal neuroimaging data

AbstractLarge amounts of multimodal neuroimaging data are acquired every year worldwide. In order to extract high-dimensional information for computational neuroscience applications standardized data fusion and efficient reduction into integrative data structures are required. Such self-consistent multimodal data sets can be used for computational brain modeling to constrain models with individual measurable features of the brain, such as done with The Virtual Brain (TVB). TVB is a simulation platform that uses empirical structural and functional data to build full brain models of individual humans. For convenient model construction, we developed a processing pipeline for structural, functional and diffusion-weighted magnetic resonance imaging (MRI) and optionally electroencephalography (EEG) data. The pipeline combines several state-of-the-art neuroinformatics tools to generate subject-specific cortical and subcortical parcellations, surface-tessellations, structural and functional connectomes, lead field matrices, electrical source activity estimates and region-wise aggregated blood oxygen level dependent (BOLD) functional MRI (fMRI) time-series. The output files of the pipeline can be directly uploaded to TVB to create and simulate individualized large-scale network models that incorporate intra- and intercortical interaction on the basis of cortical surface triangulations and white matter tractograpy. We detail the pitfalls of the individual processing streams and discuss ways of validation. With the pipeline we also introduce novel ways of estimating the transmission strengths of fiber tracts in whole-brain structural connectivity (SC) networks and compare the outcomes of different tractography or parcellation approaches. We tested the functionality of the pipeline on 50 multimodal data sets. In order to quantify the robustness of the connectome extraction part of the pipeline we computed several metrics that quantify its rescan reliability and compared them to other tractography approaches. Together with the pipeline we present several principles to guide future efforts to standardize brain model construction. The code of the pipeline and the fully processed data sets are made available to the public via The Virtual Brain website (thevirtualbrain.org) and via github (https://github.com/BrainModes/TVB-empirical-data-pipeline). Furthermore, the pipeline can be directly used with High Performance Computing (HPC) resources on the Neuroscience Gateway Portal (http://www.nsgportal.org) through a convenient web-interface

1-methylnicotinamide and its structural analog 1,4-dimethylpyridine for the prevention of cancer metastasis

Background: 1-methylnicotinamide (1-MNA), an endogenous metabolite of nicotinamide, has recently gained interest due to its anti-inflammatory and anti-thrombotic activities linked to the COX-2/PGI2 pathway. Given the previously reported anti-metastatic activity of prostacyclin (PGI2), we aimed to assess the effects of 1-MNA and its structurally related analog, 1,4-dimethylpyridine (1,4-DMP), in the prevention of cancer metastasis. Methods: All the studies on the anti-tumor and anti-metastatic activity of 1-MNA and 1,4-DMP were conducted using the model of murine mammary gland cancer (4T1) transplanted either orthotopically or intravenously into female BALB/c mouse. Additionally, the effect of the investigated molecules on cancer cell-induced angiogenesis was estimated using the matrigel plug assay utilizing 4T1 cells as a source of pro-angiogenic factors. Results: Neither 1-MNA nor 1,4-DMP, when given in a monotherapy of metastatic cancer, influenced the growth of 4T1 primary tumors transplanted orthotopically; however, both compounds tended to inhibit 4T1 metastases formation in lungs of mice that were orthotopically or intravenously inoculated with 4T1 or 4T1-luc2-tdTomato cells, respectively. Additionally, while 1-MNA enhanced tumor vasculature formation and markedly increased PGI2 generation, 1,4-DMP did not have such an effect. The anti-metastatic activity of 1-MNA and 1,4-DMP was further confirmed when both agents were applied with a cytostatic drug in a combined treatment of 4T1 murine mammary gland cancer what resulted in up to 80 % diminution of lung metastases formation. Conclusions: The results of the studies presented below indicate that 1-MNA and its structural analog 1,4-DMP prevent metastasis and might be beneficially implemented into the treatment of metastatic breast cancer to ensure a comprehensive strategy of metastasis control

c-di-AMP Is a New Second Messenger in Staphylococcus aureus with a Role in Controlling Cell Size and Envelope Stress.

Published versio

Insight into the Assembly Properties and Functional Organisation of the Magnetotactic Bacterial Actin-like Homolog, MamK

Magnetotactic bacteria (MTB) synthesize magnetosomes, which are intracellular vesicles comprising a magnetic particle. A series of magnetosomes arrange themselves in chains to form a magnetic dipole that enables the cell to orient itself along the Earth’s magnetic field. MamK, an actin-like homolog of MreB has been identified as a central component in this organisation. Gene deletion, fluorescence microscopy and in vitro studies have yielded mechanistic differences in the filament assembly of MamK with other bacterial cytoskeletal proteins within the cell. With little or no information on the structural and behavioural characteristics of MamK outside the cell, the mamK gene from Magnetospirillium gryphiswaldense was cloned and expressed to better understand the differences in the cytoskeletal properties with its bacterial homologues MreB and acitin. Despite the low sequence identity shared between MamK and MreB (22%) and actin (18%), the behaviour of MamK monitored by light scattering broadly mirrored that of its bacterial cousin MreB primarily in terms of its pH, salt, divalent metal-ion and temperature dependency. The broad size variability of MamK filaments revealed by light scattering studies was supported by transmission electron microscopy (TEM) imaging. Filament morphology however, indicated that MamK conformed to linearly orientated filaments that appeared to be distinctly dissimilar compared to MreB suggesting functional differences between these homologues. The presence of a nucleotide binding domain common to actin-like proteins was demonstrated by its ability to function both as an ATPase and GTPase. Circular dichroism and structural homology modelling showed that MamK adopts a protein fold that is consistent with the ‘classical’ actin family architecture but with notable structural differences within the smaller domains, the active site region and the overall surface electrostatic potential

The past, present, and future of the Brain Imaging Data Structure (BIDS)

The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS

Chemotaxis Arrays in Vibrio Species and Their Intracellular Positioning by the ParC/ParP System

Microbial Biotechnolog

Aligned fractures on asteroid Ryugu as an indicator of thermal fracturing

Context. Asteroid and comet surfaces are exposed to a complex environment that includes low gravity, high temperature gradients, and a bombardment of micrometeorites and cosmic rays. Surface material exposed to this environment evolves in a specific way depending on various factors such as the bodiesa-size, heliocentric distance, and composition. Fractures in boulders, as seen on asteroid Ryugu, can help to determine and constrain the dominant processes eroding small-body surface materials. It is also possible to estimate fracture growth timescales based on the abundance and length of fractures in boulders. Aims. We analyse the number, orientation, and length of fractures on asteroid Ryugu to establish the relation between the fractures and the processes that may have formed them. We also compare our results to similar investigations conducted on other small bodies and estimate the timescale of fracture growth. Methods. 198 high-resolution Hayabusa2 images of asteroid Ryugu suitable for our fracture analysis were selected and map-projected. Within these images, fractures in boulders were manually mapped using the QGIS software. The fracture coordinates were extracted and the fracturesa-orientation and length were computed for 1521 identified fractures. Results. Fractures in boulders on asteroid Ryugu are found to be preferentially north-south aligned, suggesting a formation through thermal erosion. Modeling the fracture length indicates a fracture growth timescale of 30 000 to 40 000 yr, slightly younger than ages found previously for asteroid Bennu. The errors in these ages, due to uncertainties about the thermophysical parameters used in this model, are substantial (âà  à  33 000 yr +250 000 yr). However, even with these large errors, the model suggests that thermal fracturing is a geologically fast process. These times are not too dissimilar to those quoted in the literature for Ryugu and Bennu, since similar thermophysical material parameters for Ryugu and Bennu seem likely.Validerad;2024;Nivå 2;2024-04-08 (marisr);Full text license: CC BY</p