bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal filtering strategies for task-specific functional PET imaging
Authors: Reed Murray Bruce , León Magdalena Ponce de , Klug Sebastian , Milz Christian , Silberbauer Leo Robert , Falb Pia , Godbersen Godber Mathis , Jamadar Sharna , Chen Zhaolin , Nics Lukas , Hacker Marcus , Lanzenberger Rupert , Hahn Andreas 
Published: April 2024

AbstractFunctional Positron Emission Tomography (fPET) has advanced as an effective tool for investigating dynamic processes in glucose metabolism and neurotransmitter action, offering potential insights into brain function, disease progression, and treatment development. Despite significant methodological advances, extracting stimulation-specific information presents additional challenges in optimizing signal processing across both spatial and temporal domains, which are essential for obtaining clinically relevant insights. This study aims to provide a systematic evaluation of state-of-the-art filtering techniques for fPET imaging.Forty healthy participants underwent a single [18F]FDG PET/MR scan, engaging in the cognitive task Tetris®. Twenty thereof also underwent a second PET/MR session. Eight filtering techniques, including 3D and 4D Gaussian smoothing, highly constrained backprojection (hypr), iterative hypr (Ihypr4D), two MRI-Markov Random Field (MRI-MRF) filters (L=10 and 14 mm neighborhood) as well as static and dynamic Non-Local Means (sNLM and dNLM respectively) approaches, were applied to fPET data. Test-retest reliability (intraclass correlation coefficient), the identifiability of the task signal (temporal signal-to-noise ratio (tSNR)), spatial task-based activation (group level t-values), and sample size calculations were assessed.Results indicate distinct performance between filtering techniques. Compared to standard 3D Gaussian smoothing, dNLM, sNLM, MRI-MRF L=10 and Ihypr4D filters exhibited superior tSNR, while only dNLM and hypr showed improved test-retest reliability. Spatial task-based activation was enhanced by both NLM filters and MRI-MRF approaches. The dNLM enabled a minimum reduction of 15.4% in required sample size.The study systematically evaluated filtering techniques in fPET data processing, highlighting their strengths and limitations. The dNLM filter emerges as a promising choice, with improved performance across all metrics. However, filter selection should align with specific study objectives, considering factors like processing time and resource constraints.
ALTERATIONS IN PEROXISOMAL-MITOCHONDRIAL INTERPLAY IN SKELETAL MUSCLE ACCELERATES MUSCLE DYSFUNCTION
Authors: Scalabrin Marco , Turco Eloisa , Nogara Leonardo , Gherardi Gaia , Trani Giulia , Negro Samuele , Romero Anais Franco , Jaspers Yorrick , Baschiera Elisa , De Cegli Rossella , Del Prete Eugenio , Cali Tito , Blaauw Bert , Salviati Leonardo , Rigoni Michela , Mammucari Cristina , Caspar-Bauguil Sylvie , Moro Cedric , Sandri Marco , Kemp Stephan , Romanello Vanina 
Published: April 2024

ABSTRACTWhole-body energy expenditure, as well as glucose and lipid metabolism, are regulated by skeletal muscles, which account for 40-50% of human body mass. Peroxisomes are dynamic organelles that play a crucial role in lipid metabolism and clearance of reactive oxygen species, however their role in muscles remains poorly understood.To clarify this issue, we generated a muscle-specific transgenic mouse line with peroxisome import deficiency resulting from deletion of peroxisomal biogenesis factor 5 (Pex5). Pex5 inhibition disrupted the tethering between peroxisomes and mitochondria, impaired lipid metabolism and reduced muscle force and exercise performance. Moreover, mitochondrial content and function were also altered, accelerating age-related structural defects, neuromuscular junction degeneration, and muscle atrophy. Altogether, our findings show the importance of preserving peroxisomal function and their contact sites with mitochondria to maintain muscle health during aging.
Plaque-associated endogenous IgG and its impact on immunohistochemical detection of mouse monoclonal IgG antibodies in mouse models of Alzheimer’s disease
Authors: Ito Shogo , Yamauchi Kenta , Hama Hiroshi , Koike Masato , Miyawaki Atsushi , Hioki Hiroyuki 
Published: April 2024

AbstractExperimental studies for Alzheimer’s disease (AD) have largely depended on transgenic mice with β-amyloidosis. Here, we report plaque-associated endogenous immunoglobulin G (PA-IgG) and its impact on indirect immunohistochemical detection of mouse monoclonal IgG antibodies (Ms monoclonal IgG Abs) in the brain of AD mouse models. Immunostaining for Ms IgG in AD mouse models demonstrated endogenous IgG in the brain parenchyma accumulated on microglia associated with amyloid β (Aβ) plaques and/or Aβ plaques themselves. This PA-IgG caused robust off-target binding of secondary Abs against Ms IgG (H+L) in indirect immunohistochemistry using Ms monoclonal IgG Abs. Blocking with Fab fragments of anti-Ms IgG (H+L) Ab was not effective against off-target binding. Unexpectedly, we found that secondary Abs that specifically recognize Ms IgG1, 2a, 2b, and 3 did not cause off-target binding on frozen brain sections ofAppNL-G-F/NL-G-Fmice, and enabled specific labeling of Ms monoclonal IgG Abs in the AD mouse model brains. We further demonstrated that indirect detection with a conventional secondary Ab against Ms IgG (H+L) Ab could lead to erroneous conclusions regarding Aβ plaque burden and phosphorylated tau accumulation inAppNL-G-F/NL-G-Fmice, and the use of Ms IgG subclass specific secondary Abs allowed to avoid the inevitable impediment caused by the endogenous IgG accumulation. Specific indirect detection of Ms monoclonal IgG Abs in AD mouse models by the use of secondary Abs against Ms IgG subclass would accelerate AD research by expanding the choice of Abs available for histochemical analysis in AD studies.
Human adipose stromal cells differentiate towards a tendon phenotype with adapted visco-elastic properties in a 3D-culture system
Authors: Hordé Maxime , Fouchard Jonathan , Laffray Xavier , Blavet Cédrine , Béréziat Véronique , Lagathu Claire , Gaut Ludovic , Duprez Delphine , Havis Emmanuelle 
Published: April 2024

AbstractTendon cell differentiation relies on molecular and mechanical parameters that control the expression of tendon-associated transcription factors and extracellular matrix proteins. However, the minimal cues able to initiate tendon differentiation from progenitor cells remains unknown. We analysed the tendon differentiation program in human adipose stromal cells (hASCs) cultured in a minimal 3D-system. We generated 3D-hASC constructs by embedding hASCs in a type-I collagen gel under a static uniaxial geometrical constraint with no additional molecular and mechanical cues, and assessed tendon-associated gene expression and mechanical properties for up to three weeks in culture. Analysis of tendon-associated genes revealed a molecular progression consistent with the acquisition of a tendon phenotype. The analysis of viscoelastic properties of 3D-hASC constructs by nano-indentation indicated a progressive increase in tissue stiffness up to 10 kPa, concomitant with a reduced stress relaxation indicative of solid-like mechanical properties. These changes in mechanical properties parallel the molecular change of matrix genes during the time of cultures. In summary, we have established that hASCs cultured in a minimal 3D-system progress into the tendon differentiation program associated with variations of mechanical properties.
CN-model: A dynamic model for the coupled carbon and nitrogen cycles in terrestrial ecosystems
Authors: Stocker Benjamin D. , Prentice I. Colin 
Published: April 2024

AbstractReducing uncertainty in carbon cycle projections relies on reliable representations of interactions between the carbon and nutrient cycles. Here, we build on a set of principles and hypotheses, funded in established theoretical understanding and supported by empirical evidence, to formulate and implement a dynamic model of carbon-nitrogen cycle (C-N) interactions in terrestrial ecosystems. The model combines a representation of photosynthetic acclimation to the atmospheric environment with implications for canopy and leaf N, a representation of functional balance for modelling C allocation and growth different tissues, and a representation of plant N uptake based on a first principles-informed, simplified description of solute transport in the soil. Here, we provide a comprehensive description of the model and its implementation and demonstrate the stability and functionality of the model for simulating seasonal variations of ecosystem C and N fluxes and pools. This may provide a way forward for representing key ecosystem processes related to C and N cycling based on established theoretical concepts with strong empirical support.
SLAMF7 and SLAMF8 receptors shape human plasmacytoid dendritic cell responses to intracellular bacteria
Authors: Pellegrini Joaquín Miguel , Keriel Anne , Gorvel Laurent , Hanniffy Sean , Arce-Gorvel Vilma , Bosilkovski Mile , Solera Javier , Méresse Stéphane , Mémet Sylvie , Gorvel Jean-Pierre 
Published: April 2024

AbstractPlasmacytoid dendritic cells (pDC), professional type I interferon (IFN) producing cells, have been implicated in host responses against bacterial infections. However, their role in host defense is debated and the operating molecular mechanisms are unknown. Certain Signaling Lymphocyte Activation Molecule Family (SLAMF) members act as microbial sensors and modulate immune functions in response to infection. Here by analyzing multiple human blood transcriptomic datasets, we report the involvement of SLAMF7 and SLAMF8 in many infectious diseases, with elevated levels associated with type I IFN responses in salmonellosis and brucellosis patients. We further identify SLAMF7 and SLAMF8 as key regulators of human pDC function. Silencing of these receptors hinders pDC maturation and abrogates cytokine production during infection with acute (Salmonella) or chronic (Brucella) inflammation-inducing bacteria. Mechanistically, we show that SLAMF7 and SLAMF8 signal through NF-κB, IRF7 and STAT-1, and limit mitochondrial ROS accumulation uponSalmonellainfection. This SLAMF7/8-dependent control of mitochondrial ROS levels favors bacterial persistence and NF-κB activation. Overall, our results unravel essential shared roles of SLAMF7 and SLAMF8 in finely tuning human pDC responses to intracellular bacterial infections with high diagnosis and therapeutic perspectives.
Socialization causes long-lasting behavioral changes
Authors: Gil-Martí Beatriz , Isidro-Mézcua Julia , Poza-Rodriguez Adriana , Asti Tello Gerson S. , Treves Gaia , Turiégano Enrique , Beckwith Esteban J. , Martin Francisco A 
Published: April 2024

SUMMARYIn modern human societies, social isolation acts as a negative factor for health and life quality. On the other hand, social interaction also has profound effects on animal and human behaviors, reducing aggressiveness, feeding and loss of sleep. Here, we observe that in the flyDrosophila melanogasterthese behavioral changes long-last even after social interaction has ceased, suggesting that the socialization experience triggers behavioral plasticity. We find that impairing long-term memory mechanisms either genetically or by anesthesia abolishes the expected behavioral changes in response to social interaction. Furthermore, we show that socialization increases CREB-dependent neuronal activity and synaptic plasticity in the mushroom body, the main insect memory center analogous to mammalian hippocampus. We propose that social interaction triggers socialization awareness, understood as long-lasting changes in behavior caused by experience with mechanistic similarities to long-term memory formation.
Common neural mechanisms supporting time judgements in humans and monkeys
Authors: Rodriguez-Larios Julio , Rassi Elie , Mendoza Germán , Merchant Hugo , Haegens Saskia 
Published: April 2024

AbstractThere has been an increasing interest in identifying the biological underpinnings of human time perception, for which purpose research in non-human primates (NHP) is common. Although previous work, based on behaviour, suggests that similar mechanisms support time perception across species, the neural correlates of time estimation in humans and NHP have not been directly compared. In this study, we assess whether brain evoked responses during a time categorization task are similar across species. Specifically, we assess putative differences in post-interval evoked potentials as a function of perceived duration in human EEG (N = 24) and local field potential (LFP) and spike recordings in pre-supplementary motor area (pre-SMA) of one monkey. Event-related potentials (ERPs) differed significantly after the presentation of the temporal interval between “short” and “long” perceived durations in both species, even when the objective duration of the stimuli was the same. Interestingly, the polarity of the reported ERPs was reversed for incorrect trials (i.e., the ERP of a “long” stimulus looked like the ERP of a “short” stimulus when a time categorization error was made). Hence, our results show that post-interval potentials reflect the perceived (rather than the objective) duration of the presented time interval in both NHP and humans. In addition, firing rates in monkey’s pre-SMA also differed significantly between short and long perceived durations and were reversed in incorrect trials. Together, our results show that common neural mechanisms support time categorization in NHP and humans, thereby suggesting that NHP are a good model for investigating human time perception.
Amblyopic deficits in monocular processing and binocular interactions revealed by submillimeter 7T fMRI and EEG frequency tagging
Authors: Wang Yue , Qian Chencan , Gao Yige , Zhou Yulian , Zhang Xiaotong , Wen Wen , Zhang Peng 
Published: April 2024

AbstractDisruption of retinal input early in life can lead to amblyopia, a condition characterized by reduced visual acuity despite corrected optics. Although extensive losses of neural activity have been found in the early visual cortex, it remains unclear whether they reflect deficits in feedforward or feedback processing, or abnormal binocular interactions. Combining submillimeter 7T fMRI and EEG frequency tagging, our study revealed the precise neural deficits in monocular processing and binocular interactions in human adults with unilateral amblyopia. Cortical depth-dependent fMRI revealed monocular response deficits in cortical layers of the primary visual cortex (V1) receiving thalamic input, which carried over to the downstream areas (V2-V4) in feedforward processing. Binocular stimulation produced a greater signal loss in the superficial layers of V1, consistent with suppression from the fellow eye by lateral inhibition. EEG data further demonstrate reduced suppression from the amblyopic eye, weakened binocular integration, and delayed monocular and binocular processing. Our results support attenuated and delayed monocular processing in V1 layers receiving thalamic input in human amblyopia, followed by imbalanced binocular suppression and weakened binocular integration in the superficial layers, which further reduced signal strength and processing speed. These precise neural deficits can help developing more targeted and effective treatments for the vision disorder.SignificanceCortical depth-dependent 7T fMRI and EEG frequency tagging revealed attenuated and delayed neural activity in monocular processing and binocular interactions in human amblyopia. Neural deficits in monocular processing arise from the input layers of V1, followed by imbalanced binocular suppression and weakened binocular integration in the superficial layers. The precise neural deficits at high spatiotemporal resolution can help developing more targeted and effective treatment for amblyopia.Graphical abstractThis figure illustrates the precise neural deficits of amblyopia in monocular processing and binocular interactions based on the main findings of the current study. Attenuated and delayed neural activity arises from V1 cortical layers receiving thalamic input in monocular processing, followed by imbalanced binocular suppression and weakened binocular integration in the superficial layers, further reducing visual signal strength and processing speed.
Embodiment of an artificial limb in the mouse model
Authors: Hayatou Zineb , Wang Hongkai , Chaillet Antoine , Shulz Daniel E. , Ego-Stengel Valérie , Estebanez Luc 
Published: April 2024

SummaryBody ownership disorders can be triggered by disease or body damage. Methods to probe limb embodiment are required to address those disorders. This includes the development of neuroprostheses that better integrate into the body scheme of the user. To this end, the “rubber hand illusion” protocol is a key behavioural method to probe the powerful embodiment that can be triggered by congruent somatosensory and visual inputs from the limb.So far, the neurophysiology of limb embodiment remains poorly known, in part because translating the rubber hand illusion to animal models such as the mouse remains challenging. Yet, mapping out the brain circuits of embodiment thanks to the use of genetic and optogenetic research tools would allow to propose novel embodiment restoration strategies.Here we show that the rubber hand illusion described in humans can be translated to the mouse forelimb model using an automated, videography-based procedure. We exposed head-fixed mice to a visible, static 3D-printed replica of the right forelimb, while their own forelimb was hidden from their sight. We synchronously brushed their hidden forelimb and the replica. Following these visuo-tactile associations, the replica was visually threatened, and we probed the reaction of the mice using automated tracking of pupils and facial expression. The mice focused significantly more their gaze towards the threatened forelimb replica after receiving synchronous tactile and visual information compared to asynchronous. More generally, across test and control conditions, the mouse pupillary response was consistent with the human overt response to the rubber hand illusion. Thus, our results show that mice exhibit quantifiable behavioural markers of the embodiment of an artificial forelimb.
Exposure to light supresses the activity of the medial and superior amygdala during emotional processing
Authors: Campbell Islay , Aizpurua Jose Fermin Balda , Sharifpour Roya , Paparella Ilenia , Beckers Elise , Berger Alexandre , Koshmanova Ekaterina , Mortazavi Nasrin , Read John , Phillips Christophe , Collette Fabienne , Sherif Siya , Talwar Puneet , Zubkov Mikhail , Lamalle Laurent , Vandewalle Gilles 
Published: April 2024

AbstractBackgroundLight 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.MethodsWe 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.ResultsWe 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.ConclusionWe 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.
Unveiling the complete invasion history ofD. melanogaster: three horizontal transfers of transposable elements in the last 30 years
Authors: Pianezza Riccardo , Scarpa Almorò , Haider Anna , Signor Sarah , Kofler Robert 
Published: April 2024

AbstractTransposable elements (TEs) are repetitive sequences capable of mobilizing within genomes, exerting significant influence on evolution throughout the tree of life. Using a novel approach that does not require prior knowledge about the sequence of repeats, we identified three novel TE invasions inD. melanogaster:MLEspread between 1990-2000,Souslikbetween 2009-2012, andTransib1between 2013-2016. We recapitulate prior findings, revealing that a total of 11 TEs invadedD. melanogasterover the past two centuries. Leveraging data from over 1400 arthropod genomes, we provide evidence that the TE invasions were triggered by horizontal transfers, withD. simulansand species of theD. willistonigroup acting as putative donors. Through analysis of∼600 short-read datasets spanning diverse geographic regions, we reveal the rapidity of TE invasions:Transib1swiftly multiplied from three isolated epicenters in 2014 to all investigated populations within just two years. Our findings suggest that anthropogenic activities, facilitating habitat and population expansions ofD. melanogaster, might have accelerated the rate of horizontal transposon transfer as well the spread of the TEs into the worldwide population. Given the significant impact of TEs in genomes and the potential involvement of humans in their dispersal, our research has crucial implications for both evolution and ecology.
Glophyt: a user-friendly, general-purpose program for nonlinear and multidimensional curve fitting via a hybrid stochastic and deterministic approach
Authors: Czaplicki Georges , Mazeres Serge 
Published: April 2024

AbstractBackgroundModel validation depends on the agreement between the predicted and experimental data. However, finding solutions to problems, described by equations with many parameters, for which virtually nothing is known, is a difficult task. For example, the extraction of kinetic parameters from complex schemes representing the conversion of a substrate into a product by an enzyme in the presence of an inhibitor is extremely difficult, as even the orders of magnitude of the parameters are not known. This makes curve fitting very difficult in case of multidimensional and nonlinear data. This article presents a graphical user interface-based program employing a hybrid stochastic and deterministic approach, which allows for easy and reliable determination of model parameters.ResultsThe program has been extensively used in several laboratories at our institute and has proven to be efficient in determining model parameters in many different fields. Although its origins are related to kinetic studies in enzymology, it has been successfully tested on data from various sources, such as pharmacological studies of ligand−receptor binding, entomological studies of populations, bacterial growth, photosynthesis, toxicology, differential scanning calorimetry, isothermal titration calorimetry and nuclear magnetic resonance spectroscopy.ConclusionsThis program presents an effective solution for researchers facing the problem of extracting model parameters from multidimensional and nonlinear data where even the orders of magnitude of parameters are not known. Its graphical user interface makes it easy to use, does not require any programming skills, and it is cost-free. It is available for Windows and Linux platforms.