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Abstract Background Attention deficits belong to the main cognitive symptoms of schizophrenia and come along with altered neural activity in previously described cerebral networks. Given the high heritability of schizophrenia the question arises if impaired function of these networks is modulated by susceptibility genes and detectable in healthy risk allele carriers. Methods The present event-related fMRI study investigated the effect of the single nucleotide polymorphism (SNP) rs1018381 of the DTNBP1 (dystrobrevin-binding protein 1) gene on brain activity in 80 subjects while performing the attention network test (ANT). In this reaction time task three domains of attention are probed simultaneously: alerting, orienting and executive control of attention. Results Risk allele carriers showed impaired performance in the executive control condition associated with reduced neural activity in the left superior frontal gyrus [Brodmann area (BA) 9]. Risk allele carriers did not show alterations in the alerting and orienting networks. Conclusions BA 9 is a key region of schizophrenia pathology and belongs to a network that has been shown previously to be involved in impaired executive control mechanisms in schizophrenia. Our results identified the impact of DTNBP1 on the development of a specific attention deficit via modulation of a left prefrontal network.

Purpose: Brain segmentation and multi-parameter mapping (MPM) are important steps in neurodegenerative disease characterization. However, acquiring both a high-resolution T1w sequence like MPRAGE (standard input to brain segmentation) and an MPM in the same neuroimaging protocol increases scan time and patient discomfort, making it difficult to combine both in clinical examinations., Methods: A novel approach to synthesize T1w images from MPM images, named MPRAGE like , is proposed and compared to the standard technique used to produce synthetic MPRAGE images (synMPRAGE). Twenty-three healthy subjects were scanned with the same imaging protocol at three different 7T sites using universal parallel transmit RF pulses. SNR, CNR, and automatic brain segmentation results from both MPRAGE like and synMPRAGE were compared against an acquired MPRAGE., Results: The proposed MPRAGE like technique produced higher SNR values than synMPRAGE for all regions evaluated while also having higher CNR values for subcortical structures. MPRAGE was still the image with the highest SNR values overall. For automatic brain segmentation, MPRAGE like outperformed synMPRAGE when compared to MPRAGE (median Dice Similarity Coefficient of 0.90 versus 0.29 and Average Asymmetric Surface Distance of 0.33 versus 2.93 mm, respectively), in addition to being simple, flexible, and considerably more robust to low image quality than synMPRAGE., Conclusion: The MPRAGE like technique can provide a better and more reliable alternative to synMPRAGE as a substitute for MPRAGE, especially when automatic brain segmentation is of interest and scan time is limited., (© 2025 The Author(s). Magnetic Resonance in Medicine published by Wiley Periodicals LLC on behalf of International Society for Magnetic Resonance in Medicine.)

Purpose: MR-based FID navigators (FIDnavs) do not require gradient pulses and are attractive for prospective motion correction (PMC) due to short acquisition times and high sampling rates. However, accuracy and precision are limited and depend on a separate calibration measurement. Besides FIDnavs, stationary NMR field probes are also capable of measuring local, motion-induced field changes. In this work, a linear model is calibrated between field probe data and motion parameters analog to FIDnav calibration and both tracking methods are compared and combined for PMC., Methods: FIDnavs and field probe navigators were implemented in a fast 3D-EPI sequence and calibrated by a linear model to realignment motion parameters of the 3D-EPI time series. A workflow was established to correct head motion prospectively by FIDnavs, field probe navigators or a combination of both. Large motions were instructed to test the accuracy and the impact on image quality in 1 mm 3 $$ 1\kern0.1667em {\mathrm{mm}}^3 $$ EPI data., Results: In a group of five subjects, FIDnavs demonstrated approximately doubled accuracy and precision in comparison with field probe navigators for large motions, especially nodding motions were tracked less accurately by field probes. A combination of both methods could not improve the accuracy consistently. Motion artifacts in high-resolution data were reduced similarly by both PMC methods, although artifacts remained due to susceptibility-induced B0 changes., Conclusion: Stationary field probe navigators can be calibrated equivalently as FIDnavs and enable rapid PMC of large and fast motions. Although they reveal decreased accuracy, their contrast-independence facilitates the potential insertion into many sequences., (© 2025 The Author(s). Magnetic Resonance in Medicine published by Wiley Periodicals LLC on behalf of International Society for Magnetic Resonance in Medicine.)

Neuroimaging has an essential role in studies of brain health and of cerebrovascular and neurodegenerative diseases, requiring the availability of versatile magnetic resonance imaging (MRI) acquisition and processing protocols. We designed and developed a multipurpose high-resolution MRI protocol for large-scale and long-term population neuroimaging studies that includes structural, diffusion-weighted and functional MRI modalities. This modular protocol takes almost 1 h of scan time and is, apart from a concluding abdominal scan, entirely dedicated to the brain. The protocol links the acquisition of an extensive set of MRI contrasts directly to the corresponding fully automated data processing pipelines and to the required quality assurance of the MRI data and of the image-derived phenotypes. Since its successful implementation in the population-based Rhineland Study (ongoing, currently more than 11,000 participants, target participant number of 20,000), the proposed MRI protocol has proved suitable for epidemiological and clinical cross-sectional and longitudinal studies, including multisite studies. The approach requires expertise in magnetic resonance image acquisition, in computer science for the data management and the execution of processing pipelines, and in brain anatomy for the quality assessment of the MRI data. The protocol takes ~1 h of MRI acquisition and ~20 h of data processing to complete for a single dataset, but parallelization over multiple datasets using high-performance computing resources reduces the processing time. By making the protocol, MRI sequences and pipelines available, we aim to contribute to better comparability, interoperability and reusability of large-scale neuroimaging data., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. Springer Nature Limited.)

Objective: To assess whether arterial spin labeling perfusion images of healthy controls can enhance ictal single-photon emission computed tomography analysis and whether the acquisition of the interictal image can be omitted., Methods: We developed 2 pipelines: The first uses ictal and interictal images and compares these to single-photon emission computed tomography and arterial spin labeling of healthy controls. The second pipeline uses only the ictal image and the analogous healthy controls. Both pipelines were compared to the gold standard analysis and evaluated on data of individuals with epilepsy who underwent ictal single-photon emission computed tomography imaging during presurgical evaluation between 2010 and 2022. Fifty healthy controls prospectively underwent arterial spin labeling imaging. The correspondence between the detected hyperperfusion and the postoperative resection cavity or the presumably affected lobe was assessed using Dice score and mean Euclidean distance. Additionally, the outcomes of the pipelines were automatically assigned to 1 of 5 concordance categories., Results: Inclusion criteria were met by 43 individuals who underwent epilepsy surgery and by 73 non-surgical individuals with epilepsy. Compared to the gold standard analysis, both pipelines resulted in significantly higher Dice scores and lower mean distances (p < 0.05). The combination of both provided localizing results in 85/116 cases, compared to 54/116 generated by the current gold standard analysis and the ictal image alone produced localizing results in 60/116 (52%) cases., Interpretation: We propose a new ictal single-photon emission computed tomography protocol; it finds relevantly more ictal hyperperfusion, and halves the radiation dose in about half of the individuals. ANN NEUROL 2024;96:1160-1173., (© 2024 The Author(s). Annals of Neurology published by Wiley Periodicals LLC on behalf of American Neurological Association.)

The BonnMu resource is a transposon tagged mutant collection designed for functional genomics studies in maize. To expand this resource, we crossed an active Mutator (Mu) stock with dent (B73, Co125) and flint (DK105, EP1, and F7) germplasm, resulting in the generation of 8064 mutagenized BonnMu F 2 -families. Sequencing of these Mu-tagged families revealed 425 924 presumptive heritable Mu insertions affecting 36 612 (83%) of the 44 303 high-confidence gene models of maize (B73v5). On average, we observed 12 Mu insertions per gene (425 924 total insertions/36 612 affected genes) and 53 insertions per BonnMu F 2 -family (425 924 total insertions/8064 families). Mu insertions and photos of seedling phenotypes from segregating BonnMu F 2 -families can be accessed through the Maize Genetics and Genomics Database (MaizeGDB). Downstream examination via the automated Mutant-seq Workflow Utility (MuWU) identified 94% of the presumptive germinal insertion sites in genic regions and only a small fraction of 6% inserting in non-coding intergenic sequences of the genome. Consistently, Mu insertions aligned with gene-dense chromosomal arms. In total, 42% of all BonnMu insertions were located in the 5' untranslated region of genes, corresponding to accessible chromatin. Furthermore, for 38% of the insertions (163 843 of 425 924 total insertions) Mu1, Mu8 and MuDR were confirmed to be the causal Mu elements. Our publicly accessible European BonnMu resource has archived insertions covering two major germplasm groups, thus facilitating both forward and reverse genetics studies., (© 2024 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Cold stress during early development limits maize (Zea mays L.) production in temperate zones. Low temperatures restrict root growth and reprogram gene expression. Here, we provide a systematic transcriptomic landscape of maize primary roots, their tissues, and cell types in response to cold stress. The epidermis exhibited a unique transcriptomic cold response, and genes involved in root hair formation were dynamically regulated in this cell type by cold. Consequently, activation of genes involved in root hair tip growth contributed to root hair recovery under moderate cold conditions. The maize root hair defective mutants roothair defective 5 (rth5) and roothair defective 6 (rth6) displayed enhanced cold tolerance with respect to primary root elongation. Furthermore, DEHYDRATION RESPONSE ELEMENT-BINDING PROTEIN 2.1 (DREB2.1) was the only member of the dreb subfamily of AP2/EREB transcription factor genes upregulated in primary root tissues and cell types but exclusively downregulated in root hairs upon cold stress. Plants overexpressing dreb2.1 significantly suppressed root hair elongation after moderate cold stress. Finally, the expression of rth3 was regulated by dreb2.1 under cold conditions, while rth6 transcription was regulated by DREB2.1 irrespective of the temperature regime. We demonstrated that dreb2.1 negatively regulates root hair plasticity at low temperatures by coordinating the expression of root hair defective genes in maize., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

We present the results of the human genomic small variant calling benchmarking initiative of the German Research Foundation (DFG) funded Next Generation Sequencing Competence Network (NGS-CN) and the German Human Genome-Phenome Archive (GHGA). In this effort, we developed NCBench, a continuous benchmarking platform for the evaluation of small genomic variant callsets in terms of recall, precision, and false positive/negative error patterns. NCBench is implemented as a continuously re-evaluated open-source repository. We show that it is possible to entirely rely on public free infrastructure (Github, Github Actions, Zenodo) in combination with established open-source tools. NCBench is agnostic of the used dataset and can evaluate an arbitrary number of given callsets, while reporting the results in a visual and interactive way. We used NCBench to evaluate over 40 callsets generated by various variant calling pipelines available in the participating groups that were run on three exome datasets from different enrichment kits and at different coverages. While all pipelines achieve high overall quality, subtle systematic differences between callers and datasets exist and are made apparent by NCBench.These insights are useful to improve existing pipelines and develop new workflows. NCBench is meant to be open for the contribution of any given callset. Most importantly, for authors, it will enable the omission of repeated re-implementation of paper-specific variant calling benchmarks for the publication of new tools or pipelines, while readers will benefit from being able to (continuously) observe the performance of tools and pipelines at the time of reading instead of at the time of writing., Competing Interests: No competing interests were disclosed., (Copyright: © 2024 Hanssen F et al.)

The BonnMu resource represents a tagged collection of maize ( Zea mays L.) Mutator ( Mu ) transposon-induced mutants, designed for functional genomics studies. Here, we describe the use of the BonnMu collection for identifying and characterizing mutations. Specifically, we describe workflows for use in both reverse and forward genetics strategies in maize. For reverse genetics, users first acquire a BonnMu F 2 stock of interest based on data accessible at the Maize Genetics and Genomics Database (MaizeGDB). We provide details here for their subsequent propagation and for the confirmation of Mu insertions by genotyping via PCR, with the ultimate goal of establishing genotype-phenotype relationships of interest. For forward genetics studies, we describe a workflow that involves a combined approach of Mutant-Seq (Mu-Seq) and bulked segregant RNA-seq (BSR-Seq), to identify the causal gene underlying a mutant phenotype of interest., (© 2024 Cold Spring Harbor Laboratory Press.)

Mutator ( Mu ) transposons facilitate untargeted insertional mutagenesis in maize by moving within the genome and disrupting genes. Such an approach has been used to generate collections such as the BonnMu resource, a Mu- tagged maize population for functional genomics studies. Mutant-Seq (Mu-Seq) is a sequencing-based method for the high-throughput identification and mapping of Mu insertion sites. The approach involves the construction of multiplexed sequencing libraries (known as Mu-Seq libraries) from Mu -tagged populations, followed by high-throughput sequencing and data processing using the Mu-Seq Workflow Utility (MuWU) tool, to determine the location of Mu insertions. Here, we provide a detailed protocol for Mu-Seq, from the generation of the maize Mu -tagged mutant population to data analysis. Researchers can use this approach to develop mutant collections customized to specific genetic backgrounds of interest, which can aid in characterizing genotype-specific mutations and identifying candidate genes linked to visible mutant phenotypes., (© 2024 Cold Spring Harbor Laboratory Press.)

Purpose: High resolution fMRI is a rapidly growing research field focused on capturing functional signal changes across cortical layers. However, the data acquisition is limited by low spatial frequency EPI artifacts; termed here as Fuzzy Ripples. These artifacts limit the practical applicability of acquisition protocols with higher spatial resolution, faster acquisition speed, and they challenge imaging in lower brain areas., Methods: We characterize Fuzzy Ripple artifacts across commonly used sequences and distinguish them from conventional EPI Nyquist ghosts, off-resonance effects, and GRAPPA artifacts. To investigate their origin, we employ dual polarity readouts., Results: Our findings indicate that Fuzzy Ripples are primarily caused by readout-specific imperfections in k-space trajectories, which can be exacerbated by inductive coupling between third-order shims and readout gradients. We also find that these artifacts can be mitigated through complex-valued averaging of dual polarity EPI or by disconnecting the third-order shim coils., Conclusion: The proposed mitigation strategies allow overcoming current limitations in layer-fMRI protocols: (1)Achieving resolutions beyond 0.8mm is feasible, and even at 3T, we achieved 0.53mm voxel functional connectivity mapping.(2)Sub-millimeter sampling acceleration can be increased to allow sub-second TRs and laminar whole brain protocols with up to GRAPPA 8.(3)Sub-millimeter fMRI is achievable in lower brain areas, including the cerebellum., Competing Interests: Conflict of interest: Omer Faruk Gulban is an employee of Brain Innovation (Maastricht, NL). The work presented here may be partly specific to industrial design choices of SIEMENS Healthineers’ UHF scanners. This vendor is used in 83% of all human layer-fMRI papers (source: www.layerfmri.com/papers).