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  • 1
    In: GigaScience, Oxford University Press (OUP), Vol. 8, No. 12 ( 2019-12-01)
    Abstract: Mass spectrometry imaging is increasingly used in biological and translational research because it has the ability to determine the spatial distribution of hundreds of analytes in a sample. Being at the interface of proteomics/metabolomics and imaging, the acquired datasets are large and complex and often analyzed with proprietary software or in-house scripts, which hinders reproducibility. Open source software solutions that enable reproducible data analysis often require programming skills and are therefore not accessible to many mass spectrometry imaging (MSI) researchers. Findings We have integrated 18 dedicated mass spectrometry imaging tools into the Galaxy framework to allow accessible, reproducible, and transparent data analysis. Our tools are based on Cardinal, MALDIquant, and scikit-image and enable all major MSI analysis steps such as quality control, visualization, preprocessing, statistical analysis, and image co-registration. Furthermore, we created hands-on training material for use cases in proteomics and metabolomics. To demonstrate the utility of our tools, we re-analyzed a publicly available N-linked glycan imaging dataset. By providing the entire analysis history online, we highlight how the Galaxy framework fosters transparent and reproducible research. Conclusion The Galaxy framework has emerged as a powerful analysis platform for the analysis of MSI data with ease of use and access, together with high levels of reproducibility and transparency.
    Type of Medium: Online Resource
    ISSN: 2047-217X
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2708999-X
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  • 2
    In: Alzheimer's & Dementia, Wiley, Vol. 18, No. S5 ( 2022-12)
    Abstract: The association between cerebral blood supply and cognition has gained increasing interest, considering the remarkable anatomical variability of the circle of Willis. Thus, qualitative classifications of the arteries contributing to the hippocampal supply has been performed in previous studies to determine whether the additional presence of vessels might translate into cognitive differences and cerebral structural changes when coexisting with vascular pathology, to the extent of constituting a cognitive reserve. Nevertheless, the promising results in these regards are not without controversy. Hence, Vessel Distance Mapping (VDM) is here introduced, in order to ascertain the correlation of VDM‐metrics with each other and with cognitive status, as well as to elucidate which metrics have the greatest impact on cognition. Method A battery of cognitive tests was used (including ADAScog and MoCA) in 51 subjects (71 ± 8.5yrs) with (n=20) and without (n=31) cerebral small vessel disease. Their hippocampal‐related vessels were manually segmented by using high‐resolution 7T Time‐of‐Flight‐MRI. Vessel distance maps were generated by computing the distances of each voxel to its nearest vessel, obtaining 3 VDM‐metrics: global‐VDM (vessel density surrogate), VS‐VDM (vessel‐specific supply), and COMD (distance to the center of mass, reflecting vessel distribution). Hippocampal masks were used to assess the whole and subregional hippocampus. Regression models were applied for evaluating the interrelation among the metrics, and their association with cognition. Result High correlations were observed for intra‐metric comparisons, as well as when comparing whole hippocampal vs. sub‐hippocampal metrics. Greater values of VDM‐metrics reflecting higher distances among vessels were associated with poorer cognitive outcomes only in subjects affected by vascular pathology (global‐VDM R²=0.7248, p=0.0054; COMD R²=0.7248, p=0.0013). Metrics revealing vascular distribution (p=0,0053) and density (p=0,0169) were the most influential on cognition, and in this context those for the whole hippocampus predominated over the subregional ones. Conclusion A mixed contribution of vessel distribution and density is proposed to confer cognitive resilience, in a way consistent with anatomical fundamentals and with previous research findings. VDM provides a new, structure‐driven approach on which to raise new questions supported by the statistical robustness of a quantitative method with potential clinical implications.
    Type of Medium: Online Resource
    ISSN: 1552-5260 , 1552-5279
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2201940-6
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  • 3
    In: Alzheimer's & Dementia, Wiley, Vol. 18, No. S6 ( 2022-12)
    Abstract: The new consensus definition of cognitive reserve (CR) provides a framework to study individual differences in cognitive functioning relative to aging and disease. CR denotes a property of the brain that allows for better than expected cognitive performance given the degree of age‐related brain changes or disease. More specifically, individual differences in patterns of brain activity during fMRI tasks might explain the differential susceptibility to pathological burden. Method According to the consensus definitions, we sought to identify and quantify CR from fMRI novelty‐contrast maps in a large multi‐centric sample (DELCODE) consisting of 215 participants with SCD, 79 with MCI, 30 with AD dementia, 56 AD relatives and 156 cognitively normal controls (CN). CSF amyloid‐42/40 ratio, CSF p‐tau and hippocampal volume (ATN) were reduced to a single number, representing a (Alzheimer’s) disease progression (DP) score. To identify a CR network, voxel‐wise linear regression models determined where functional task‐activation moderates the relationship between DP and cognition. Finally, task‐related activity within the CR network was extracted to obtain individual fMRI‐based CR scores. Result The DP score showed a strong negative quadratic association with baseline memory scores. CR voxels, in which higher or lower activation were associated with better cognition, weakening the effect of DP, were mainly located within the novelty network. They included lateral‐occipital and superior‐parietal regions, lingual and fusiform gyrus, cuneus and small parts of cingulate. While there was no association between the CR score and cognition in CNs, higher CR scores in MCI and AD patients were related to higher PACC5 scores. Conclusion We established a DP score that collapses the ATN measures into a single number, while retaining its deleterious effect on an individual’s memory score. Furthermore, a newly identified task‐dependent CR network could be used to establish a CR score, which was related to higher PACC5 scores in MCI and AD patients, suggesting a functional compensation mechanism at later stages of AD that is not yet present in CN. Thus, targeted alteration of brain activity might be a promising route to modify cognitive trajectories in MCI and AD patients. Further, detailed examination of individuals with high CR might reveal additional disease‐modifying factors.
    Type of Medium: Online Resource
    ISSN: 1552-5260 , 1552-5279
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2201940-6
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  • 4
    In: Alzheimer's & Dementia, Wiley, Vol. 16, No. S2 ( 2020-12)
    Abstract: The main contributor to hippocampal blood supply is the posterior cerebral artery. Additional contribution of the anterior choroidal artery distinguishes potential dual from single hippocampal vascular supply. In a previous study on patients with cerebral small vessel disease (CSVD) and older controls by Perosa et al. (Brain, in press), dual hippocampal vascularization was functionally associated with better cognition and structurally associated with increased anterior hippocampal volumes. The CSVD patients showed declined cognitive abilities. However, dual supply was able to alleviate performance loss in CSVD patients, indicating resilience against pathology. We examined the effect of dual vascular supply on anterior/posterior hippocampal volume and global grey matter (GM) volume, which might mediate the beneficial effect on cognition, and whether it conveys resistance against CSVD. Methods 47 subjects (71±8yrs) with/without CSVD (20/27) underwent 7T time‐of‐flight MRA for categorization of hippocampal vascularization pattern (HVP) and 3T T1‐weighted structural MRI. As measure of global cognitive function we focused on the MoCA. Automatic segmentations of the anterior and posterior hippocampus were obtained via the ASHS (Automatic Segmentation of Hippocampal Subfields) 3T T1 atlas. GM volumes were obtained by segmentation in SPM (Statistical Parametric Mapping). The effect of the HVP and CSVD on structural and cognitive measures was estimated using ANCOVAs. A mediation effect of GM volume on cognition was examined via bootstrapping. Fisher’s exact test assessed contingency of the observed pattern to both clinical groups to make inferences about resistance against CSVD. Results A region‐based approach revealed a greater bilateral anterior (but not posterior) HC volume and increased global GM volume in the dual supply group. In a mediation analysis, GM volume offset the effect of the HVP on the MoCA score, whereas bilateral anterior HC volume did not. While the HVP seems to convey some resilience against CSVD, no evidence for resistance against CSVD was found. Conclusions Previous findings of structural effects on anterior HC volume via VBM were confirmed. Besides its local effects, dual hippocampal vascular supply exerts global effects on brain structure. These effects partially account for better cognitive performance of the corresponding individuals. An int42708eraction with pathology might be restricted to resilience, but not resistance.
    Type of Medium: Online Resource
    ISSN: 1552-5260 , 1552-5279
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2201940-6
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  • 5
    In: NeuroImage, Elsevier BV, Vol. 274 ( 2023-07), p. 120094-
    Type of Medium: Online Resource
    ISSN: 1053-8119
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 1471418-8
    SSG: 5,2
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  • 6
    In: Alzheimer's & Dementia, Wiley, Vol. 18, No. S4 ( 2022-12)
    Abstract: Neuroinflammation is a hallmark of Alzheimer ́s disease (AD) and other neurodegenerative disorders and is likely to be triggered throughout different stages of the disease. Microglia and Astrocytes are the main resident glia that mediate neuroinflammation through production of cytokines, chemokines and other neuroinflammatory biomarkers. Inflammatory processes have been implicated in the pathogenesis of cerebrovascular disease and white matter (WM) injury. However, imaging studies on the contribution of inflammation on WM structure in the aging and AD are rare. Method Here, we aim to examine the relationship between inflammatory markers and WM hyperintensities (WMH) in the spectrum from normal aging towards AD. To do that, we used baseline data from the DZNE DELCODE study that is enriched in subjects at risk for development of AD and examined a panel of 16 inflammatory biomarkers from CSF of 249 subjects who also underwent FLAIR imaging. Participants included cognitively unimpaired (CU) individuals (healthy controls, AD relatives, and SCD) and cognitively impaired patients (CI) with MCI or AD dementia. WMH lesion volumes were automatically segmented from FLAIR images. Principal component analysis on the CSF markers generated one main composite factor (CP1) that included mainly TREM2, YKL40, AXL, Tyro3 and C1q (see Figure). Age, sex, vascular risk factors, Abeta ratio and ptau181 were used as covariates. Result Linear regression models showed that higher values of this inflammatory composite factor was related to lower global WMH (p 〈 0.01) and better memory performance (p 〈 0.01) in the whole sample. These effects were also significant when including whole brain GM volume as additional covariate. Mediation model showed that global WMH partially mediated the effect of neuroinflammation on memory performance. Conclusion These results suggest that some neuroinflammatory markers (e.g. sTyro3 and sAXL) might have a protective effect on WM structure, thus being beneficial for memory function as suggested by a recent study (Brosseron, Maass, Kleineidam et al, 2022), in which sTyro3 and sAXL were related to higher GM volume. Follow‐up analyses will aim to distinguish the effect of neuroinflammation in different clinical groups. Longitudinal studies are ultimately needed to determine whether the observed effect is “protective” or related to “brain reserve”.
    Type of Medium: Online Resource
    ISSN: 1552-5260 , 1552-5279
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2201940-6
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  • 7
    In: Brain Communications, Oxford University Press (OUP), Vol. 3, No. 3 ( 2021-07-01)
    Abstract: The hippocampus within the medial temporal lobe is highly vulnerable to age-related pathology such as vascular disease. We examined hippocampal vascularization patterns by harnessing the ultra-high resolution of 7 Tesla magnetic resonance angiography. Dual-supply hemispheres with a contribution of the anterior choroidal artery to hippocampal blood supply were distinguished from single-supply ones with a sole dependence on the posterior cerebral artery. A recent study indicated that a dual vascular supply is related to preserved cognition and structural hippocampal integrity in old age and vascular disease. Here, we examined the regional specificity of these structural benefits at the level of medial temporal lobe sub-regions and hemispheres. In a cross-sectional study with an older cohort of 17 patients with cerebral small vessel disease (70.7 ± 9.0 years, 35.5% female) and 27 controls (71.1 ± 8.2 years, 44.4% female), we demonstrate that differences in grey matter volumes related to the hippocampal vascularization pattern were specifically observed in the anterior hippocampus and entorhinal cortex. These regions were especially bigger in dual-supply hemispheres, but also seemed to benefit from a contralateral dual supply. We further show that total grey matter volumes were greater in people with at least one dual-supply hemisphere, indicating that the hippocampal vascularization pattern has more far-reaching structural implications beyond the medial temporal lobe. A mediation analysis identified total grey matter as a mediator of differences in global cognition. However, our analyses on multiple neuroimaging markers for cerebral small vessel disease did not reveal any evidence that an augmented hippocampal vascularization conveys resistance nor resilience against vascular pathology. We propose that an augmented hippocampal vascularization might contribute to maintaining structural integrity in the brain and preserving cognition despite age-related degeneration. As such, the binary hippocampal vascularization pattern could have major implications for brain structure and function in ageing and dementia independent of vascular pathology, while presenting a simple framework with potential applicability to the clinical setting.
    Type of Medium: Online Resource
    ISSN: 2632-1297
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 3020013-1
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