Generalized Linear Mixed Models (GLMMs) are widely used in biomedical, psychological, ecological, and social science research to analyze clustered, longitudinal, and repeated-measures data. Although numerous software implementations exist, researchers often face challenges selecting appropriate modeling frameworks, specifying model structures, handling missing data, comparing estimation methods, and reproducing analyses across statistical software platforms. FlexibleGLMM is an open-source R Shiny application that provides a graphical user interface (GUI) for fitting, evaluating, and reporting generalized linear mixed models without requiring programming expertise. The application integrates multiple established R packages for mixed-effects modeling and provides functionality for model diagnostics, effect estimation, visualization, and automated reporting. In addition, FlexibleGLMM facilitates replication of analyses performed in other commonly available statistical tools, allowing researchers to compare results across software ecosystems. The application is intended for researchers, clinicians, students, and statisticians seeking a unified and reproducible framework for GLMM analysis through an interactive web-based environment.

Nigrosomes are formed by clusters of pigmented dopaminergic cells in the substantia nigra that critically contribute to dopaminergic function. The ever-increasing resolution of ultra-high-field MRI brings clinical imaging of these clusters into reach, promising unprecedented insight into the functional role of the nigrosomes and their early degeneration in Parkinson’s disease. However, due to the nigrosomes’ small extents and intricate shapes, they are not included in current MRI brain atlases, preventing nigrosome-specific MRI data analysis. We provide a comprehensive 3D histological atlas of the five nigrosomes co-aligned to the widely-used MNI152 2009b space. This atlas is based on 3D-reconstructed, ultra-high-resolution block-face images and gold-standard nigrosome delineations in calbindin-D28K immunohistochemistry. We validated the atlas’s accuracy using the multimodal ultra-high-resolution post mortem BigBrain dataset and demonstrated its consistency with qualitative nigrosome atlases based on classical 2D histology. We provide detailed usage instructions for applying our atlas to ultra-high-resolution and -field MRI data. The openly available atlas enables neuroimaging studies of the nigrosomes, opening a new avenue toward understanding the differential involvement of the nigrosomes in the healthy and diseased brain and the development of neuroimaging biomarkers of dopaminergic neurodegeneration.

Dysfunction of the Locus coeruleus (LC), a small brainstem nucleus which consists of the brain's primary source of norepinephrine, is linked to various neurological and psychiatric disorders. Light exposure influences many non-image-forming (NIF) biological functions including those modulated by LC activity. Yet direct evidence of light-driven modulation of the LC has remained elusive due to the structure's small size and deep location. Using ultra-high-field (7 Tesla) functional MRI during an emotional task under varying illuminances, we demonstrate that light modulates LC activity in an emotion-dependent manner. We show that increased illuminance dampens LC responses to negative emotional stimuli while enhancing responses to neutral stimuli. Furthermore, we provide tentative evidence that within an emotional context, light may affect LC activity through the basomedial nucleus of the amygdala as well as through a region of the hypothalamus encompassing the lateral hypothalamus. These findings open avenues for the development of targeted, non-pharmacological treatments leveraging light to modulate norepinephrine tone and/or LC activity in several neuropsychiatric disorders. Significance Statement:Dysfunction of the Locus Coeruleus (LC), a small nucleus of brain and the main source of norepinephrine, is linked to various brain disorders. Here we provide in vivo evidence that exposure to light can alter the activity of the LC with higher illuminance leading to dampened LC responses to negative emotional stimuli. These findings identify the LC as a key target for the therapeutic effects of light on emotion, offering a biological framework for using light to treat neuropsychiatric disorders.

Background: Light plays a significant role in regulating various non-visual biological processes, such as stimulating alertness and cognition. However, the precise subcortical neural pathways are not fully established, including within the hypothalamus. In particular, how the hypothalamus processes are modulated by time-of-day and developmental stages, remains poorly understood. Methods: In this study, we used 7 Tesla functional magnetic resonance imaging to examine in vivo the impact of different light illuminance (0.16, 37, 92, and 190 melanopic equivalent daylight illuminance: mel-EDI lux) on the activity of the hypothalamus of healthy young adults (N=33; 20 women; 24.3 +/- 3.2y) and adolescents (N=16; 5 women; 16.8 +/- 1.1y) while they completed an auditory executive task, in the morning or in the evening. Results: Performance to the task improved with increasing illuminance irrespective of time of day and age group. When focusing on time-of-day differences in young adults, we found that the regional impact of light illuminance on the activity of the hypothalamus was consistent between the morning and the evening, with the posterior and anterior hypothalamus, respectively, showing increased and decreased activity with increasing illuminance. When focusing on developmental stages differences, during the evening session only, we found similar regional patterns in adolescents and young adult. The magnitude of the response at the highest illuminance was, however, larger in adolescents, with a larger deactivation of the superior-anterior and inferior-tubular hypothalamus. Conclusions: These findings reveal a complex and non-uniform impact of light on hypothalamus activity and provide novel insights into how light influences vary with developmental stages. ### Competing Interest Statement The authors have declared no competing interest. Fonds National de la Recherche Scientifique European Union’s Horizon 2020, 860613 Fondation Léon Frédéricq University of Liège, https://ror.org/00afp2z80 European Regional Development Fund Foundation Recherche Alzheimer, SAO-FRA 2022/0014 EU Joint Programme Neurodegenerative Disease Research, IRONSLEEP, SCAIFIELD

Quantitative MRI (qMRI) measures relaxation rates, exchange rates, and proton densities that reflect biophysical properties of tissue and are ideally free from protocol- and scanner-dependence. In practice, qMRI has not yet achieved this level of independence from sequence and hardware choice, and quantitative estimates often differ across sites and acquisition schemes. At the same time, pooling data across different sources can be beneficial to statistical power of longitudinal, cross-sectional, or case-control studies. Here, we investigate how protocol and hardware differences can affect pooling data from different sources in large ultra high field (UHF) qMRI studies in the context of healthy aging. We combine the openly available aging UHF qMRI MP2RAGEME-based dataset with two different multiparameter mapping (MPM)-based sets of qMRI data. We evaluate how pooling affects age dependence of qMRI parameters and investigate protocol-related biases, with a particular focus on subcortical structures. We focus the analysis, first, on replication and expansion of the previously published qMRI dataset on normative aging, second, the examination of the protocol influence on the estimated qMRI values, and third, on detecting the protocol effect on the age dependence inferred from the data. We find that the age-related changes in the pooled dataset for R1 measure around 4-17% of the lifespan mean in different structures. Similarly, age-related R2* variation in different structures constitutes around 6-30% of the lifespan mean in the pooled dataset. Subcortical structure volume change is on the order of 5-26%. We further observe larger relative difference between protocols for R1 and volume, while R2* remains more consistent for most regions. We show how pooling the UHF qMRI data from different sites and collected with different quantitative protocols can be both detrimental and beneficial for the analysis outcomes.

Abstract Purpose Brain ageing involves interrelated changes in molecular processes, neuroinflammatory mechanisms, brain macro- and microstructure, sleep physiology, and cognition. The 50 to 70 years age range represents a critical transition period, in which these subtle alterations may precede measurable cognitive decline and the onset of clinical neurodegenerative disease. To allow systematic investigation of these early alterations and the subsequent progression in brain aging, we provide an open-access data resource from a multidisciplinary longitudinal study integrating neuroimaging, genetics, sleep, and neuropsychological phenotyping with assessments at baseline and at 2-year follow-up. Acquisition and Validation Methods The baseline cohort comprises 101 community-dwelling participants (50-69 years old) who underwent magnetic resonance imaging (MRI) using a 3T protocol that included high-resolution structural imaging (T1- and T2-weighted), quantitative multi-parametric acquisitions with B1 mapping, and multi-shell diffusion-weighted imaging. Moreover, positron emission tomography (PET) imaging was performed using [18F]Flutemetamol or [18F]Florbetapir (amyloid- β tracers) in all participants, with a subset also undergoing [18F]THK-5351 PET (tau-related/neuroinflammation). The dataset was complemented by extensive phenotypic data, including sleep and neuropsychological assessments, and by genotype data through genome-wide analysis. 66 participants underwent a 2-year cognitive follow-up, enabling longitudinal analyses of cognitive trajectories. Data acquisition and curation were performed using standardized procedures, with systematic quality control to support reliable cross-sectional and longitudinal analyses. Data Format and Usage Notes All data are distributed in a BIDS-compliant format, and released in open-access (EBRAINS). Potential Applications This dataset supports multimodal analyses, allowing the identification of interpretable patterns characterizing brain ageing from multiple perspectives. It enables the comparison of different models to derive (semi)quantitative MRI parameters, the discovery of imaging biomarkers associated with early cognitive decline, and the monitoring or prediction of brain ageing progression. In addition, it offers focused coverage of adults aged 50–70 years, which is often underrepresented in existing healthy subjects public datasets. Key Points COFITAGE is a deeply phenotyped, longitudinal, multimodal dataset of 101 healthy late middle-aged adults (50-70 years). The COFITAGE dataset combines PET, MRI, sleep phenotyping, genotyping, and extensive neuropsychological assessment. The dataset supports diverse applications, from preclinical AD biomarker studies to investigations of hippocampal vulnerability, amyloid-tau-metabolism interactions, sleep-dependent modulation of molecular pathology, and multimodal predictive modeling of cognitive trajectories.

STUDY OBJECTIVES:Sleep disturbances are increasingly recognized as early features of Alzheimer's disease (AD) neuropathology. Specifically, spontaneous arousals during sleep have been associated with the burden of Amyloid beta in the brain of healthy late middle-aged individuals. However, it remains unclear whether heterogeneity of arousals relates to genetic risk for AD in younger adults or to cognitive change later in life. Here, we evaluated the association between arousals, polygenic risk scores (PRS) for AD, and cognitive performance and change in healthy young and late-middle-aged individuals. METHODS:We classified spontaneous arousals using in-lab EEG sleep recordings in 453 younger individuals (22±2.7y; 49 women) and 87 late middle-aged individuals (59.3±5.3y; 59 women) based on their association with sleep stage transitions and changes in muscle tone. We examined the associations between arousal types, AD-PRS, baseline cognitive performance and, in late middle-aged individuals, cognitive change over 2 and 7 years. RESULTS:The prevalence of arousals associated with sleep stage transition was higher in late middle-aged vs. younger individuals. In late middle-aged but not younger individuals, transition arousals with muscle tone increases correlated with lower AD-PRS, better attentional performance and lower memory change over follow-ups, whereas transition arousals without muscle tone increases were linked to higher AD-PRS, poorer baseline attention, and greater memory change across follow-up periods. CONCLUSIONS:The heterogeneity in spontaneous arousals during sleep may reflect their physiological intensity or underlying neural activation, and may indicate vulnerability to AD in late middle-aged individuals. The findings may help identify early markers of neurodegenerative risk.

OBJECTIVE:Parkinson's disease (PD) is one of the rare diseases in which sleep alteration is a true marker of disease outcome. Yet, how the association between sleep and PD emerges over the healthy lifetime is not established. We examined the association between the polygenic risk score (PRS) for PD and the variability in the electrophysiology of rapid eye movement (REM) sleep in 433 younger (18-31 years) healthy individuals and 85 late-midlife (50-69 years) healthy individuals. METHODS:In this prospective cross-sectional study, in-lab electroencephalography recordings of sleep were recorded to extract REM sleep metrics. PRS was computed using SBayesR approach. RESULTS:Generalized additive model for location, scale, and shape analysis showed significant association of REM duration (pcorrected = 0.03) and theta energy in REM (pcorrected = 0.004) with PRS for PD in interaction with the age group. In the younger subsample, REM duration and theta energy were positively associated with PD PRS. In contrast, in the late-midlife subsample, the same associations were negative (although only qualitatively for REM theta energy) and may differ between men and women. INTERPRETATION:REM sleep is associated with the PRS for PD in early adulthood, 2 to 5 decades before typical symptoms onset. The association changes from positive in younger individuals, presumably free of alpha-synuclein, to negative in late-midlife individuals, possibly because of the progressive presence of alpha-synuclein aggregates or of the repeated increased oxidative metabolism imposed by REM sleep. Our findings may unravel core associations between PD and sleep and may contribute to novel intervention targets to prevent or delay PD. ANN NEUROL 2026;99:922-934.

Animal studies show that sleep regulation depends on subcortical networks, but whether the connectivity between subcortical areas contributes to human sleep variability remains unclear. We investigated whether the effective connectivity between the LC and hypothalamic subparts during wakefulness relates to sleep electrophysiology. Thirty-three younger (~22 y, 27 women) and 18 late middle-aged (~61 y, 14 women) healthy individuals underwent 7-Tesla functional MRI during wakefulness to assess LC–hypothalamus effective connectivity. Additionally, sleep EEG was recorded at night in the lab to examine the relationships between effective connectivity measures and REM sleep theta energy as well as sigma power prior to REM. Connectivity analyses revealed strong mutual positive influences between the LC and both the anterior–superior and posterior hypothalamus, consistent with animal studies. Aging was negatively associated with the connectivity from the anterior–superior hypothalamus (including the preoptic area) to the LC. In late middle-aged adults, but not younger adults, stronger effective connectivity from the anterior–superior hypothalamus to the LC was associated with lower REM theta energy. This association extended to other low-frequency bands during REM and NREM sleep. These findings highlight the age-dependent modulation of LC–hypothalamus interactions and their potential roles in sleep regulation, providing new insights into neural mechanisms underlying age-related sleep changes.

Animal studies established that the locus coeruleus (LC) plays important roles in sleep and wakefulness regulation. Whether it contributes to sleep variability in humans is not yet established. Here, we investigated if the in vivo activity of the LC is related to the variability in the quality of Rapid Eye Movement (REM) sleep. We assessed the LC activity of 34 healthy younger ( 22y) and 18 older ( 61y) individuals engaged in bottom-up and top-down cognitive tasks using 7-Tesla functional Magnetic Resonance Imaging (fMRI). We further recorded their sleep electroencephalogram (EEG) to evaluate associations between LC fMRI measures and REM sleep EEG metrics. Theta oscillation energy during REM sleep was positively associated with LC response in the top-down task. In contrast, REM sleep theta energy was negatively associated with LC activity in older individuals during the bottom-up task. Importantly, sigma oscillations power immediately preceding a REM sleep episode was positively associated with LC activity in the top-down task. LC activity during wakefulness was related to REM sleep intensity and to a transient EEG change preceding REM sleep, a feature causally related to LC activity in animal studies. The associations depend on the cognitive task, suggesting that a balanced level of LC tonic activity during wakefulness is required for optimal expression of REM sleep. The findings may have implications for the high prevalence of sleep complaints reported in aging and for disorders such as insomnia, Alzheimer’s, and Parkinson’s disease, for which the LC may play pivotal roles through sleep.

Cognitive Reserve(CR) a concept based on the brain plasticity, is a mechanism that delays or minimizes clinical manifestations of brain changes due to aging. Prospective epidemiologic studies non-demented individuals have shown that education, occupational duration and complexity, and greater lifetime engagement in cognitively stimulating activities are associated with a reduced risk of dementia. We study the cognitive reserve and its neuroimaging correlate. Prospective cross-sectional study. 500 subjects were screened, Recruitment of subjects with inclusion criteria of age 40-80 yr without neurodegenerative or psychiatric disorder. Clinical History and presence of CVD risk factors were investigated. MMSE, MOCA, Selected neuropsychology tests were done to evaluate cognitive status, CR assessed by CRIq scale. Biochemical and MRI(volumetry) and DTI(FA, Diffusivity. 252 pts were recruited, Mean age -53 yrs. 33% female. Diabetes(17%) and hypertension(24%). Mean MOCA score 24.CRIq was high in 10 subjects and majority had medium score. Significant association was found between Verbal and Category fluency with low CRIq and Serum ferritin with brain volume. Fractional isotropy(FA) values were reduced in central part of corpous callosum corelated with verbal fluency. Cognitive reserve can play a significant modifiable risk factor for cognitive decline. Neuroimaging can play an important biomarker to diagnose and in prognosis of cognitive impairment.

The brain mechanisms through which changes in season and light exposure modulate mood may involve different nuclei of the amygdala. We aimed to test this hypothesis using 7 Tesla functional magnetic resonance imaging in 29 healthy young adults. We first considered time-of-year changes in activity that are related to the slow change in photoperiod. We find that the response to emotional stimuli of selected medial and superior nuclei of the amygdala peaked around the start of winter or increased with worse mood status. We further assessed how alternating short exposures to light of different illuminance acutely affected the regional activity of the amygdala. We show that the same areas showed a linear reduction of activity when exposed to increasing light illuminance, specifically when processing emotional stimuli. Importantly, the impact of light on part of these nuclei peaked around the start of summer or decreased with worse mood. These findings provide additional evidence that humans show seasonality and that, for mood, it involves parts of the amygdala. The results bring insights into the mechanisms that underlie the long-term and acute impact of light on mood and that may contribute to the benefits of light therapy in the treatment of mood disorders.

Study Objectives Animal research has demonstrated that sleep regulation heavily depends on a network of subcortical nuclei. In particular, whether the crosstalk between the Locus Coeruleus (LC) and hypothalamic nuclei influences sleep variability and age-related changes in humans remains unexplored. This study investigated whether the effective connectivity between the LC and subparts of the hypothalamus is associated with the electrophysiology of rapid eye movement sleep (REMS). Methods Thirty-three healthy younger (∼22y, 27 women) and 18 older (∼61y, 14 women) individuals underwent 7-Tesla functional magnetic resonance imaging during wakefulness to investigate the effective connectivity between LC and distinct hypothalamus subparts encompassing several nuclei. Additionally, we recorded their sleep electroencephalogram (EEG) to explore relationships between effective connectivity measures and REMS theta energy and sigma power prior to REMS episodes. Results The effective connectivity analysis revealed robust evidence of a mutual positive influence between the LC and the anterior-superior and posterior hypothalamus, supporting the idea that the connectivity patterns observed in animal models are also present in humans. Furthermore, our results suggest that in older adults, stronger effective connectivity from the anterior-superior hypothalamus, including the preoptic area, to the LC is associated with reduced REM theta energy. Specificity analysis showed that this association was not limited to REM theta energy but also extended to specific lower-frequency bands during REMS and NREMS. Conclusions These findings highlight the complex age-dependent modulation of the LC circuitry and its role in sleep regulation. Understanding these neural interactions offers valuable insight into the mechanisms driving age-related sleep changes. ### Competing Interest Statement The authors have declared no competing interest. The processed data and analysis scripts supporting the results included in this manuscript are publicly available via the following open repository: (to be defined upon acceptance of the paper). The raw data could be identified and linked to a single subject and represent a large amount of data and cannot be openly shared. Researchers willing to access to the raw data should send a request to the corresponding author (GV). Data sharing will require evaluation of the request by the local Research Ethics Board and the signature of a data transfer agreement (DTA).

Light affects not only vision but also attention, alertness, and cognition, primarily through intrinsically photosensitive retinal ganglion cells sensitive to blue-wavelength light. While previous research has shown that light influences brain regional activity, its impact on brain connectivity remains unclear. Using 7-Tesla fMRI, this study examined how light modulates thalamo-cortical connectivity during an auditory executive task involving the thalamus, the prefrontal cortex (in supramarginal gyrus : SMG), and parietal cortex (in the inferior frontal junction : IFJ). Fifty-five participants, including young adults (19-30y: scanned in the morning or evening) and adolescents (15-16y: scanned in the evening), were studied. Across all groups, moderate blue-enriched light strengthened SMG-to-IFJ connectivity, while low-illuminance orange light enhanced thalamus-to-SMG connectivity. High-illuminance blue-enriched light strengthened thalamus-to-IFJ connectivity only in the morning for young adults, while moderate blue-enriched light enhanced thalamus-to-SMG connectivity in adolescents in the evening. These findings suggest that the thalamus plays a key role in mediating light’s cognitive effects and timing and age influence non-image-forming responses. ### Competing Interest Statement The authors have declared no competing interest.

Background Light can influence several non-image-forming biological effects including the modulation of mood and emotional processing through neural circuitry that remains to be fully established. Rodent data showed that nuclei the amygdala, known to be important to mood regulation and emotional processing, receive direct inputs from the retina and mediate part of the affective impact of light. Here, we wanted to assess whether these animal findings translate to human beings. We determine the dynamics of the impact of light exposure on the activity of the amygdala, and whether the dynamics varied across its volume, during the processing of emotional stimulation. Methods We used 7 Tesla functional magnetic resonance imaging to assess the impact of variations in light illuminance on the regional activity of the amygdala in healthy young adults (N = 29; 18 women; 24 ± 3.1y) during an auditory emotional task. Results We find that several subregions of the amygdala, including the medial nucleus that receives direct retinal projection, showed a marked and linear reduction of activity with increasing illuminance when processing emotionally charged stimuli. Conclusion We speculate that it is through the medial nucleus that light affects the emotional state of healthy individuals. These findings shed more light on the mechanisms that underlie the biological impact of light on the brain and may contribute to the benefits of light therapy in the treatment of mood disorders. ### Competing Interest Statement The authors have declared no competing interest.

The regional integrity of brain subcortical structures has been implicated in sleep-wake regulation, however, their associations with sleep parameters remain largely unexplored. Here, we assessed association between quantitative Magnetic Resonance Imaging (qMRI)-derived marker of the myelin content of the brainstem and the variability in the sleep electrophysiology in a large sample of 18-to-31 years healthy young men (N = 321; similar to 22 years). Separate Generalized Additive Model for Location, Scale and Shape (GAMLSS) revealed that sleep onset latency and slow wave energy were significantly associated with MTsat estimates in the brainstem (p(corrected) <= 0.03), with overall higher MTsat value associated with values reflecting better sleep quality. The association changed with age, however (MTsat-by-age interaction-p(corrected) <= 0.03), with higher MTsat value linked to better values in the two sleep metrics in the younger individuals of our sample aged similar to 18 to 20 years. Similar associations were detected across different parts of the brainstem (p(corrected) <= 0.03), suggesting that the overall maturation and integrity of the brainstem was associated with both sleep metrics. Our results suggest that myelination of the brainstem nuclei essential to regulation of sleep is associated with inter-individual differences in sleep characteristics during early adulthood. They may have implications for sleep disorders or neurological diseases related to myelin.

Objective: Parkinson's disease (PD) is one of the rare diseases for which sleep alteration is a true marker of disease outcome. Yet, how the association between sleep and PD emerges over the healthy lifetime is not established. We examined association between polygenic risk score (PRS) for PD and the variability in the electrophysiology of Rapid Eye Movement (REM) sleep in 345 younger (18-31y) and 85 older (50-69y) healthy individuals. Methods: In this prospective cross-sectional study, in-lab EEG recordings of sleep were recorded to extract REM sleep metrics. PRS was computed using SBayesR approach. Results: Generalized Additive Model for Location, Scale and Shape (GAMLSS) analysis showed significant association of REM duration (pcorr=0.002) and theta energy in REM (pcorr=0.0002) with PRS for PD in interaction with age group. In the younger sub-sample, REM duration and theta energy were positively associated with PD PRS. In contrast, in the older sub-sample, the same associations were negative (though only qualitatively for REM theta energy) and may differ between men and women. Interpretation: REM sleep is associated with the PRS for PD in early adulthood, 2 to 5 decades prior to typical symptoms onset. The association switches from positive in younger individuals, presumably free of alpha-synuclein, to negative in older individuals, possibly because of the progressive presence of alpha-synuclein aggregates or of the repeated increased oxidative metabolism imposed by REM sleep. Our findings may unravel core associations between PD and sleep and may contribute to novel intervention targets to prevent or delay PD. ### Competing Interest Statement Christian Berthomier is an owner of Physip, the company that analyzed the EEG data. This ownership and the collaboration had no impact on the design, data acquisition, results and interpretations of the findings. The other authors declare that no competing interests exist.

Light exerts multiple non-image-forming biological effects on physiology including the stimulation of alertness and cognition. However, the subcortical circuitry underlying the stimulating impact of light is not established in humans. We used 7 Tesla functional magnetic resonance imaging to assess the impact of variations in light illuminance on the regional activity of the hypothalamus while healthy young adults (N=26; 16 women; 24.3±2.9 y) were completing two auditory cognitive tasks. We find that, during both the executive and emotional tasks, higher illuminance triggered an activity increase over the posterior part of the hypothalamus, which includes part of the tuberomamillary nucleus and the posterior part of the lateral hypothalamus. In contrast, increasing illuminance evoked a decrease in activity over the anterior and ventral parts of the hypothalamus, encompassing notably the suprachiasmatic nucleus and another part of the tuberomammillary nucleus. Critically, the performance of the executive task was improved under higher illuminance and was negatively correlated with the activity of the posterior hypothalamus area. These findings reveal the distinct local dynamics of different hypothalamus regions that underlie the impact of light on cognition.