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  • Springer Science and Business Media LLC  (244)
  • 1
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    Online Resource
    Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
    Springer Science and Business Media LLC ; 2023
    In:  Nature Biotechnology
    Details
    In: Nature Biotechnology, Springer Science and Business Media LLC
    Abstract: Characterization and integration of the genome, epigenome, transcriptome, proteome and metabolome of different datasets is difficult owing to a lack of ground truth. Here we develop and characterize suites of publicly available multi-omics reference materials of matched DNA, RNA, protein and metabolites derived from immortalized cell lines from a family quartet of parents and monozygotic twin daughters. These references provide built-in truth defined by relationships among the family members and the information flow from DNA to RNA to protein. We demonstrate how using a ratio-based profiling approach that scales the absolute feature values of a study sample relative to those of a concurrently measured common reference sample produces reproducible and comparable data suitable for integration across batches, labs, platforms and omics types. Our study identifies reference-free ‘absolute’ feature quantification as the root cause of irreproducibility in multi-omics measurement and data integration and establishes the advantages of ratio-based multi-omics profiling with common reference materials.
    Type of Medium: Online Resource
    ISSN: 1087-0156 , 1546-1696
    URL: Article
    DOI: 10.1038/s41587-023-01934-1
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 1494943-X
    detail.hit.zdb_id: 1311932-1
    SSG: 12
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  • 2
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    Mapping the aberrant brain functional connectivity in new daily persistent headache: a resting-state functional magnetic resonance imaging study
    Springer Science and Business Media LLC ; 2023
    In:  The Journal of Headache and Pain Vol. 24, No. 1 ( 2023-04-26)
    Details
    In: The Journal of Headache and Pain, Springer Science and Business Media LLC, Vol. 24, No. 1 ( 2023-04-26)
    Abstract: The pathogenesis of new daily persistent headache (NDPH) is not fully understood. We aim to map aberrant functional connectivity (FC) in patients with NDPH using resting-state functional magnetic resonance imaging (MRI). Methods Brain structural and functional MRI data were acquired from 29 patients with NDPH and 37 well-matched healthy controls (HCs) in this cross-sectional study. Region of interest (ROI) based analysis was used to compare FC between patients and HCs, with 116 brain regions in the automated anatomical labeling (AAL) atlas were defined as seeds. The correlations between aberrant FC and patients’ clinical characteristics, and neuropsychological evaluation were also investigated. Results Compared with HCs, patients with NDPH showed increased FC in the left inferior occipital gyrus, right thalamus and decreased FC in right lingual gyrus, left superior occipital gyrus, right middle occipital gyrus, left inferior occipital gyrus, right inferior occipital gyrus, right fusiform gyrus, left postcentral gyrus, right postcentral gyrus, right thalamus and right superior temporal gyrus. There were no correlation between FC of these brain regions and clinical characteristics, neuropsychological evaluation after Bonferroni correction ( p   〉  0.05/266). Conclusions Patients with NDPH showed aberrant FC in multiple brain regions involved in perception and regulation of emotion and pain. Trial registration ClinicalTrials.gov Identifier: NCT05334927.
    Type of Medium: Online Resource
    ISSN: 1129-2377
    URL: Article
    DOI: 10.1186/s10194-023-01577-2
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2020168-0
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  • 3
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    Cerebral perfusion variance in new daily persistent headache and chronic migraine: an arterial spin-labeled MR imaging study
    Springer Science and Business Media LLC ; 2022
    In:  The Journal of Headache and Pain Vol. 23, No. 1 ( 2022-12)
    Details
    In: The Journal of Headache and Pain, Springer Science and Business Media LLC, Vol. 23, No. 1 ( 2022-12)
    Abstract: New daily persistent headache (NDPH) and chronic migraine (CM) are two different types of headaches that might involve vascular dysregulation. There is still a lack of clarity about altered brain perfusion in NDPH and CM. This study aimed to investigate the cerebral perfusion variances of NDPH and CM using multi-delay pseudo-continuous arterial spin-labeled magnetic resonance imaging (pCASL-MRI). Methods Fifteen patients with NDPH, 18 patients with CM, and 15 age- and sex-matched healthy controls (HCs) were included. All participants underwent 3D multi-delay pCASL-MRI to obtain cerebral perfusion data, including arrival-time-corrected cerebral blood flow (CBF) and arterial cerebral blood volume (aCBV). The automated anatomical labeling atlas 3 (AAL3) was used to parcellate 170 brain regions. The CBF and aCBV values in each brain region were compared among the three groups. Correlation analyses between cerebral perfusion parameters and clinical variables were performed. Results Compared with HC participants, patients with NDPH were found to have decreased CBF and aCBV values in multiple regions in the right hemisphere, including the right posterior orbital gyrus (OFCpost.R), right middle occipital gyrus (MOG.R), and ventral anterior nucleus of right thalamus (tVA.R), while patients with CM showed increased CBF and aCBV values presenting in the ventral lateral nucleus of left thalamus (tVL.L) and right thalamus (tVL.R) compared with HCs (all p   〈  0.05). In patients with NDPH, after age and sex adjustment, the increased aCBV values of IFGorb. R were positively correlated with GAD-7 scores; and the increased CBF and aCBV values of tVA.R were positively correlated with disease duration. Conclusion The multi-delay pCASL technique can detect cerebral perfusion variation in patients with NDPH and CM. The cerebral perfusion changes may suggest different variations between NDPH and CM, which might provide hemodynamic evidence of these two types of primary headaches.
    Type of Medium: Online Resource
    ISSN: 1129-2369 , 1129-2377
    URL: Article
    DOI: 10.1186/s10194-022-01532-7
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2020168-0
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  • 4
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    Altered functional connectivity of the right caudate nucleus in chronic migraine: a resting-state fMRI study
    Springer Science and Business Media LLC ; 2022
    In:  The Journal of Headache and Pain Vol. 23, No. 1 ( 2022-12)
    Details
    In: The Journal of Headache and Pain, Springer Science and Business Media LLC, Vol. 23, No. 1 ( 2022-12)
    Abstract: The definitive pathogenic mechanisms underlying chronic migraine (CM) remain unclear. Mounting evidence from functional and structural magnetic resonance imaging (MRI) studies suggests that the caudate nucleus (CN) plays a role in the cognitive, sensory, and emotional integration of pain information in patients with migraine. However, evidence concerning the role played by CN in CM patients is limited. Here, we used the CN as the seed to explore patterns of functional connectivity (FC) among healthy controls (HCs), patients with episodic migraine (EM), and patients with CM. Methods We included 25 HCs, 23 EM patients, and 46 CM patients in this study. All participants underwent resting-state functional MRI scans on a GE 3.0T MRI system. We performed seed-based FC analyses among the three groups using the bilateral CNs as seeds. We also compared the subgroups of CM (with and without medication overuse headache, males and females) and performed Pearson’s correlation analyses between FC values and the clinical features of CM patients. Results FC values between the right CN and five clusters (mainly involved in emotion, cognition, and sensory-related brain regions) were higher in CM patients than in HCs. Compared to EM patients, enhanced FC values between the bilateral precuneus, left anterior cingulate gyrus, right middle cingulate cortex, right lingual gyrus, and right CN were shown in the CM patients. There were no significant differences between CM patients with and without MOH, males and females. FC values between the bilateral calcarine cortex, lingual gyrus, and right CN were positively correlated with body mass index. Moreover, right CN-related FC values in the left calcarine cortex and right lingual gyrus were inversely correlated with visual analogue scale scores for headaches. Conclusion Our results revealed abnormal right CN-based FC values in CM patients, suggesting dysfunction of brain networks associated with pain perception and multi-regulation (emotion, cognition, and sensory). Aberrant FC of the CN can provide potential neuroimaging markers for the diagnosis and treatment of CM.
    Type of Medium: Online Resource
    ISSN: 1129-2369 , 1129-2377
    URL: Article
    DOI: 10.1186/s10194-022-01506-9
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2020168-0
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  • 5
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    Author Correction: Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling
    Springer Science and Business Media LLC ; 2023
    In:  Nature Biotechnology
    Details
    In: Nature Biotechnology, Springer Science and Business Media LLC
    Type of Medium: Online Resource
    ISSN: 1087-0156 , 1546-1696
    URL: Article
    DOI: 10.1038/s41587-023-02008-y
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 1494943-X
    detail.hit.zdb_id: 1311932-1
    SSG: 12
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  • 6
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    Alterations in regional homogeneity and multiple frequency amplitudes of low-frequency fluctuation in patients with new daily persistent headache: a resting-state functional magnetic resonance imaging study
    Springer Science and Business Media LLC ; 2023
    In:  The Journal of Headache and Pain Vol. 24, No. 1 ( 2023-02-23)
    Details
    In: The Journal of Headache and Pain, Springer Science and Business Media LLC, Vol. 24, No. 1 ( 2023-02-23)
    Abstract: New daily persistent headache (NPDH) is a rare primary headache that is highly disabling. The pathophysiology of NDPH is still unclear, and we aimed to reveal the underlying mechanism of NDPH through functional magnetic resonance imaging (fMRI) analysis. Methods In this cross-sectional study, thirty patients with NDPH and 30 healthy controls (HCs) were recruited. The blood oxygen level-dependent (BOLD) sequences of all participants were obtained using the GE 3.0 T system. We performed ReHo, ALFF (conventional band: 0.01–0.08 Hz, slow-5: 0.01–0.027 Hz, slow-4: 0.027–0.073 Hz) and seed-based to the whole brain functional connectivity (FC) analysis in the NDPH and HC groups. The sex difference analysis of ReHo, ALFF, and FC values was conducted in the NDPH group. We also conducted Pearson’s correlation analysis between ReHo, ALFF, FC values and clinical characteristics (pain intensity, disease duration, HIT-6, GAD-7, PHQ-9, and PSQI scores). Results Both increased ReHo (P FWE-corr  = 0.012) and ALFF values (0.01–0.08 Hz, P FWE-corr  = 0.009; 0.027–0.073 Hz, P FWE-corr =0.044) of the left middle occipital gyrus (MOG_L) were found in the NDPH group compared to the HC group. There was no significant difference in FC maps between the two groups. Compared to the HC group, no difference was found in ReHo ( p  = 0.284), ALFF ( p  = 0.246), and FC ( p  = 0.118) z scores of the MOG_L in the NDPH group. There was also no sex difference in ReHo ( p  = 0.288), ALFF ( p  = 0.859), or FC z score ( p  = 0.118) of the MOG_L in patients with NDPH. There was no correlation between ReHo, ALFF, FC z scores and clinical characteristics after Bonferroni correction ( p   〈  0.05/18). Conclusions Patients with NDPH may have abnormal activation of the visual system. Abnormal visual activation may occur mainly in higher frequency band of the classical band. No sex differences in brain activity were found in patients with NDPH.
    Type of Medium: Online Resource
    ISSN: 1129-2377
    URL: Article
    DOI: 10.1186/s10194-023-01543-y
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2020168-0
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  • 7
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    Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling
    Springer Science and Business Media LLC ; 2023
    In:  Nature Biotechnology
    Details
    In: Nature Biotechnology, Springer Science and Business Media LLC
    Abstract: Certified RNA reference materials are indispensable for assessing the reliability of RNA sequencing to detect intrinsically small biological differences in clinical settings, such as molecular subtyping of diseases. As part of the Quartet Project for quality control and data integration of multi-omics profiling, we established four RNA reference materials derived from immortalized B-lymphoblastoid cell lines from four members of a monozygotic twin family. Additionally, we constructed ratio-based transcriptome-wide reference datasets between two samples, providing cross-platform and cross-laboratory ‘ground truth’. Investigation of the intrinsically subtle biological differences among the Quartet samples enables sensitive assessment of cross-batch integration of transcriptomic measurements at the ratio level. The Quartet RNA reference materials, combined with the ratio-based reference datasets, can serve as unique resources for assessing and improving the quality of transcriptomic data in clinical and biological settings.
    Type of Medium: Online Resource
    ISSN: 1087-0156 , 1546-1696
    URL: Article
    DOI: 10.1038/s41587-023-01867-9
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 1494943-X
    detail.hit.zdb_id: 1311932-1
    SSG: 12
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  • 8
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    ARRDC4 regulates enterovirus 71-induced innate immune response by promoting K63 polyubiquitination of MDA5 through TRIM65
    Springer Science and Business Media LLC ; 2017
    In:  Cell Death & Disease Vol. 8, No. 6 ( 2017-06-08), p. e2866-e2866
    Details
    In: Cell Death & Disease, Springer Science and Business Media LLC, Vol. 8, No. 6 ( 2017-06-08), p. e2866-e2866
    Abstract: Enterovirus 71 (EV71) is the main causative agent of hand, foot and mouth disease (HFMD), which induces significantly elevated levels of cytokines and chemokines, leading to local or system inflammation and severe complications, whereas the underlying regulatory mechanisms and the inflammatory pathogenesis remain elusive. ARRDC4 is one member of arrestins family, having important roles in glucose metabolism and G-protein-coupled receptors (GPCRs) related physiological and pathological processes, however, the function of ARRDC4 in innate immune system is largely unknown. Here we identified that ARRDC4 expression was increased after EV71 infection in THP-1-derived macrophages and verified in EV71-infected HFMD patients and the healthy candidates. The expression level of ARRDC4 was positively correlated with the serum concentration of IL-6, TNF- α and CCL3 in clinical specimens. ARRDC4 interacted with MDA5 via the arrestin-like N domain, and further recruited TRIM65 to enhance the K63 ubiquitination of MDA5, resulting in activation of the downstream innate signaling pathway and transcription of proinflammatory cytokines during EV71 infection. Our data highlight new function of ARRDC4 in innate immunity, contributing to the better understanding about regulation of MDA5 activation after EV71 infection, and also suggest ARRDC4 may serve as a potential target for intervention of EV71-induced inflammatory response.
    Type of Medium: Online Resource
    ISSN: 2041-4889
    URL: Article
    DOI: 10.1038/cddis.2017.257
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 2541626-1
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  • 9
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    Gamma-aminobutyric acid and glutamate/glutamine levels in the dentate nucleus and periaqueductal gray with episodic and chronic migraine: a proton magnetic resonance spectroscopy study
    Springer Science and Business Media LLC ; 2022
    In:  The Journal of Headache and Pain Vol. 23, No. 1 ( 2022-12)
    Details
    In: The Journal of Headache and Pain, Springer Science and Business Media LLC, Vol. 23, No. 1 ( 2022-12)
    Abstract: The pathogenesis of migraine chronification remains unclear. Functional and structural magnetic resonance imaging studies have shown impaired functional and structural alterations in the brains of patients with chronic migraine. The cerebellum and periaqueductal gray (PAG) play pivotal roles in the neural circuits of pain conduction and analgesia in migraine. However, few neurotransmitter metabolism studies of these migraine-associated regions have been performed. To explore the pathogenesis of migraine chronification, we measured gamma-aminobutyric acid (GABA) and glutamate/glutamine (Glx) levels in the dentate nucleus (DN) and PAG of patients with episodic and chronic migraine and healthy subjects. Methods Using the MEGA-PRESS sequence and a 3-Tesla magnetic resonance scanner (Signa Premier; GE Healthcare, Chicago, IL, USA), we obtained DN and PAG metabolite concentrations from patients with episodic migraine ( n  = 25), those with chronic migraine ( n  = 24), and age-matched and sex-matched healthy subjects ( n  = 16). Patients with chronic migraine were further divided into those with ( n  = 12) and without ( n  = 12) medication overuse headache. All scans were performed at the Beijing Tiantan Hospital, Capital Medical University. Results We found that patients with chronic migraine had significantly lower levels of GABA/water (p = 0.011) and GABA/creatine (Cr) (p = 0.026) in the DN and higher levels of Glx/water (p = 0.049) in the PAG than healthy controls. In all patients with migraine, higher GABA levels in the PAG were significantly associated with poorer sleep quality (GABA/water: r  = 0.515, p  = 0.017, n  = 21; GABA/Cr: r  = 0.522, p  = 0.015, n  = 21). Additionally, a lower Glx/Cr ratio in the DN may be associated with more severe migraine disability ( r  = -0.425, p  = 0.055, n  = 20), and lower GABA/water ( r  = -0.424, p  = 0.062, n  = 20) and Glx/Water ( r  = -0.452, p  = 0.045, n  = 20) may be associated with poorer sleep quality. Conclusions Neurochemical levels in the DN and PAG may provide evidence of the pathological mechanisms of migraine chronification. Correlations between migraine characteristics and neurochemical levels revealed the pathological mechanisms of the relevant characteristics.
    Type of Medium: Online Resource
    ISSN: 1129-2369 , 1129-2377
    URL: Article
    DOI: 10.1186/s10194-022-01452-6
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2020168-0
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  • 10
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    MYB-CC transcription factor, TaMYBsm3, cloned from wheat is involved in drought tolerance
    Springer Science and Business Media LLC ; 2019
    In:  BMC Plant Biology Vol. 19, No. 1 ( 2019-12)
    Details
    In: BMC Plant Biology, Springer Science and Business Media LLC, Vol. 19, No. 1 ( 2019-12)
    Type of Medium: Online Resource
    ISSN: 1471-2229
    URL: Article
    DOI: 10.1186/s12870-019-1751-9
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
    detail.hit.zdb_id: 2059868-3
    SSG: 12
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