rudyvdbrink/CitationDatabase huggingface dataset:
[Bayesian brain: Can we model emotion?].
L'Encephale, 2021

Computational modeling builds mathematical models of cognitive phenomena to simulate patterns of perception, decision-making, and belief updating. These models mathematically represent the information processing by combining an anterior probability distribution, a likelihood function and a set of parameters and hyperparameters. Their use popularized the conception of a nervous system functioning as a predictive machine, or "bayesian brain". Applied to psychiatry, these models seek to explain how psychiatric dysfunction may emerge mechanistically. Despite the significance of emotions for cognitive phenomena and for psychiatric disorders, few computational models offer mathematical representations of emotion or incorporate emotional factors into their modeling parameters. We present here some computational hypotheses for the modeling of affective parameters, and we suggest that computational psychiatry would benefit from these modeling parameters.
Multi-subject Stochastic Blockmodels for adaptive analysis of individual differences in human brain network cluster structure.
NeuroImage, 2020

There is considerable interest in elucidating the cluster structure of brain networks in terms of modules, blocks or clusters of similar nodes. However, it is currently challenging to handle data on multiple subjects since most of the existing methods are applicable only on a subject-by-subject basis or for analysis of an average group network. The main limitation of per-subject models is that there is no obvious way to combine the results for group comparisons, and of group-averaged models that they do not reflect the variability between subjects. Here, we propose two new extensions of the classical Stochastic Blockmodel (SBM) that use a mixture model to estimate blocks or clusters of connected nodes, combined with a regression model to capture the effects of subject-level covariates on individual differences in cluster structure. The proposed Multi-Subject Stochastic Blockmodels (MS-SBMs) can flexibly account for between-subject variability in terms of homogeneous or heterogeneous covariate effects on connectivity using subject demographics such as age or diagnostic status. Using synthetic data, representing a range of block sizes and cluster structures, we investigate the accuracy of the estimated MS-SBM parameters as well as the validity of inference procedures based on the Wald, likelihood ratio and permutation tests. We show that the proposed multi-subject SBMs recover the true cluster structure of synthetic networks more accurately and adaptively than standard methods for modular decomposition (i.e. the Fast Louvain and Newman Spectral algorithms). Permutation tests of MS-SBM parameters were more robustly valid for statistical inference and Type I error control than tests based on standard asymptotic assumptions. Applied to analysis of multi-subject resting-state fMRI networks (13 healthy volunteers; 12 people with schizophrenia; n=268 brain regions), we show that Heterogeneous Stochastic Blockmodel (Het-SBM) identifies a range of network topologies simultaneously, including modular and core structures.
Trends in the proportionate mortalities attributed to noncommunicable diseases in sub-Saharan Africa for the period 2000 to 2016.
The International journal of health planning and management, 2020

Noncommunicable diseases (NCDs) remain a growing global health issue and sub-Saharan Africa (SSA) is no exception. Using secondary data obtained from the World Bank on 48 SSA countries, we describe the trends in the proportionate mortalities attributed to NCDs in SSA between 2000 and 2016. The baseline proportionate mortalities attributed to NCDs in SSA increased from 22.49% in 2000 to 33.69% in 2016, representing about 11% increase. The trend was replicated across the low-, middle-, and high-income countries in SSA. The highest change in the NCD mortalities in low-income SSA countries was seen in Eritrea where NCD mortalities increased from 19.3% in the year 2000 to 45.2% in 2016. In Rwanda, it rose from 24.8% to 44% during the same period. Ghana, a lower-middle-income country, also witnessed an increase from 27.3% in 2000 to 42.7% in 2016. The general increasing trend in the burden of NCD mortalities in SSA implies the need for higher prioritization of NCD prevention and control initiatives. There is a need for a greater contribution of nontraditional stakeholders in health through a multi-sectoral approach. We also recommend integrating NCD prevention and control strategies into existing public health structures being used for communicable disease control.
Blood NAD levels are reduced in very old patients hospitalized for heart failure.
Experimental gerontology, 2020

Age-associated decline in nicotinamide adenine dinucleotide (NAD) tissue levels has emerged as potential driving mechanism in the establishment of energy metabolism perturbations in the context of chronic diseases, notably heart failure.
Western Diet Causes Obesity-Induced Nonalcoholic Fatty Liver Disease Development by Differentially Compromising the Autophagic Response.
Antioxidants (Basel, Switzerland), 2020

Nonalcoholic fatty liver disease (NAFLD) is characterized by the development of steatosis, which can ultimately compromise liver function. Mitochondria are key players in obesity-induced metabolic disorders; however, the distinct role of hypercaloric diet constituents in hepatic cellular oxidative stress and metabolism is unknown. Male mice were fed either a high-fat (HF) diet, a high-sucrose (HS) diet or a combined HF plus HS (HFHS) diet for 16 weeks. This study shows that hypercaloric diets caused steatosis; however, the HFHS diet induced severe fibrotic phenotype. At the mitochondrial level, lipidomic analysis showed an increased cardiolipin content for all tested diets. Despite this, no alterations were found in the coupling efficiency of oxidative phosphorylation and neither in mitochondrial fatty acid oxidation (FAO). Consistent with unchanged mitochondrial function, no alterations in mitochondrial-induced reactive oxygen species (ROS) and antioxidant capacity were found. In contrast, the HF and HS diets caused lipid peroxidation and provoked altered antioxidant enzyme levels/activities in liver tissue. Our work provides evidence that hepatic oxidative damage may be caused by augmented levels of peroxisomes and consequently higher peroxisomal FAO-induced ROS in the early NAFLD stage. Hepatic damage is also associated with autophagic flux impairment, which was demonstrated to be diet-type dependent. The HS diet induced a reduction in autophagosomal formation, while the HF diet reduced levels of cathepsins. The accumulation of damaged organelles could instigate hepatocyte injuries and NAFLD progression.
Odor discrimination in terrestrial and aquatic environments in California sea lions (Zalophus californianus) living in captivity.
Physiology & behavior, 2021

Pinnipeds, as any mammal species, use multimodal signals, including olfactory ones, to ensure vital functions. Thus, some pinniped species seem able to use olfaction in both social and foraging contexts and to discriminate between different odors in air including both natural and artificial odors, but studies on that topic remain scarce. Here, we studied the olfactory capabilities of California sea lions living in captivity at La Flèche Zoo (France) in both terrestrial and aquatic environments. We used two categories of odors: social odors (from familiar individuals of the same group, unfamiliar individuals from another Zoo, animal zookeepers and a terrestrial carnivore) and non-social odors (food and odors identified as repellents in certain vertebrates). Several behavioral parameters were measured and analyzed as the number and duration of contact with the odor, mouth openings, vocalizations (air only) and air bubble production (water only). Our results, although limited by the low number of animals monitored (n = 5), suggest that California sea lions are able to discriminate between different odors both in the air and under water. In the aquatic environment, the process allowing the perception of odors remains to be characterized. Applications to this work could be considered in captive conditions as well as in the wild.
Voluntary Actions Modulate Perception and Neural Representation of Action-Consequences in a Hand-Dependent Manner.
Cerebral cortex (New York, N.Y. : 1991), 2020

Evoked neural activity in sensory regions and perception of sensory stimuli are modulated when the stimuli are the consequence of voluntary movement, as opposed to an external source. It has been suggested that such modulations are due to motor commands that are sent to relevant sensory regions during voluntary movement. However, given the anatomical-functional laterality bias of the motor system, it is plausible that the pattern of such behavioral and neural modulations will also exhibit a similar bias, depending on the effector triggering the stimulus (e.g., right/left hand). Here, we examined this issue in the visual domain using behavioral and neural measures (fMRI). Healthy participants judged the relative brightness of identical visual stimuli that were either self-triggered (using right/left hand button presses), or triggered by the computer. Stimuli were presented either in the right or left visual field. Despite identical physical properties of the visual consequences, we found stronger perceptual modulations when the triggering hand was ipsi- (rather than contra-) lateral to the stimulated visual field. Additionally, fMRI responses in visual cortices differentiated between stimuli triggered by right/left hand. Our findings support a model in which voluntary actions induce sensory modulations that follow the anatomical-functional bias of the motor system.
Functional connectome fingerprinting accuracy in youths and adults is similar when examined on the same day and 1.5-years apart.
Human brain mapping, 2020

Pioneering studies have shown that individual correlation measures from resting-state functional magnetic resonance imaging studies can identify another scan from that same individual. This method is known as "connectotyping" or functional connectome "fingerprinting." We analyzed a unique dataset of 12-30 years old (N = 140) individuals who had two distinct resting state scans on the same day and again 12-18 months later to assess the sensitivity and specificity of fingerprinting accuracy across different time scales (same day, ~1.5 years apart) and developmental periods (youths, adults). Sensitivity and specificity to identify one's own scan was high (average AUC = 0.94), although it was significantly higher in the same day (average AUC = 0.97) than 1.5-years later (average AUC = 0.91). Accuracy in youths (average AUC = 0.93) was not significantly different from adults (average AUC = 0.96). Multiple statistical methods revealed select connections from the Frontoparietal, Default, and Dorsal Attention networks enhanced the ability to identify an individual. Identification of these features generalized across datasets and improved fingerprinting accuracy in a longitudinal replication data set (N = 208). These results provide a framework for understanding the sensitivity and specificity of fingerprinting accuracy in adolescents and adults at multiple time scales. Importantly, distinct features of one's "fingerprint" contribute to one's uniqueness, suggesting that cognitive and default networks play a primary role in the individualization of one's connectome.
Recapitulating the Bayesian framework for neurosurgical outpatient care and a cost-benefit analysis of telemedicine for socioeconomically disadvantaged patients in the Philippines during the pandemic.
Neurosurgical focus, 2020

In the Philippines during recent months, a neurosurgical center that caters primarily to socioeconomically disadvantaged patients has encountered unprecedented changes in practice patterns brought about by the COVID-19 pandemic. In particular, the usual task of outpatient care has shifted to the telemedicine format, bringing along all of its attendant advantages and gargantuan challenges. The authors sought to determine the responsiveness of this telemedicine setup to the needs of their disadvantaged patients and explored the application of Bayesian inference to enhance the use of teleconsultation in daily clinical decision-making.
Breaking Tradition to Bridge Bench and Bedside: Accelerating the MD-PhD-Residency Pathway.
Academic medicine : journal of the Association of American Medical Colleges, 2021

Physician-scientists are individuals trained in both clinical practice and scientific research. Often, the goal of physician-scientist training is to address pressing questions in biomedical research. The established pathways to formally train such individuals are mainly MD-PhD programs and physician-scientist track residencies. Although graduates of these pathways are well equipped to be physician-scientists, numerous factors, including funding and length of training, discourage application to such programs and impede success rates.
Establishment of an in vitro model for analyzing mitochondrial ultrastructure in PRKN-mutated patient iPSC-derived dopaminergic neurons.
Molecular brain, 2021

Mitochondrial structural changes are associated with the regulation of mitochondrial function, apoptosis, and neurodegenerative diseases. PRKN is known to be involved with various mechanisms of mitochondrial quality control including mitochondrial structural changes. Parkinson's disease (PD) with PRKN mutations is characterized by the preferential degeneration of dopaminergic neurons in the substantia nigra pars compacta, which has been suggested to result from the accumulation of damaged mitochondria. However, ultrastructural changes of mitochondria specifically in dopaminergic neurons derived from iPSC have rarely been analyzed. The main reason for this would be that the dopaminergic neurons cannot be distinguished directly among a mixture of iPSC-derived differentiated cells under electron microscopy. To selectively label dopaminergic neurons and analyze mitochondrial morphology at the ultrastructural level, we generated control and PRKN-mutated patient tyrosine hydroxylase reporter (TH-GFP) induced pluripotent stem cell (iPSC) lines. Correlative light-electron microscopy analysis and live cell imaging of GFP-expressing dopaminergic neurons indicated that iPSC-derived dopaminergic neurons had smaller and less functional mitochondria than those in non-dopaminergic neurons. Furthermore, the formation of spheroid-shaped mitochondria, which was induced in control dopaminergic neurons by a mitochondrial uncoupler, was inhibited in the PRKN-mutated dopaminergic neurons. These results indicate that our established TH-GFP iPSC lines are useful for characterizing mitochondrial morphology, such as spheroid-shaped mitochondria, in dopaminergic neurons among a mixture of various cell types. Our in vitro model would provide insights into the vulnerability of dopaminergic neurons and the processes leading to the preferential loss of dopaminergic neurons in patients with PRKN mutations.
A feedback loop governs the relationship between lipid metabolism and longevity.
eLife, 2020

The relationship between lipid metabolism and longevity remains unclear. Although fat oxidation is essential for weight loss, whether it remains beneficial when sustained for long periods, and the extent to which it may attenuate or augment lifespan remain important unanswered questions. Here, we develop an experimental handle in the
Glycosphingolipids and neuroinflammation in Parkinson's disease.
Molecular neurodegeneration, 2020

Parkinson's disease is a progressive neurodegenerative disease characterized by the loss of dopaminergic neurons of the nigrostriatal pathway and the formation of neuronal inclusions known as Lewy bodies. Chronic neuroinflammation, another hallmark of the disease, is thought to play an important role in the neurodegenerative process. Glycosphingolipids are a well-defined subclass of lipids that regulate crucial aspects of the brain function and recently emerged as potent regulators of the inflammatory process. Deregulation in glycosphingolipid metabolism has been reported in Parkinson's disease. However, the interrelationship between glycosphingolipids and neuroinflammation in Parkinson's disease is not well known. This review provides a thorough overview of the links between glycosphingolipid metabolism and immune-mediated mechanisms involved in neuroinflammation in Parkinson's disease. After a brief presentation of the metabolism and function of glycosphingolipids in the brain, it summarizes the evidences supporting that glycosphingolipids (i.e. glucosylceramides or specific gangliosides) are deregulated in Parkinson's disease. Then, the implications of these deregulations for neuroinflammation, based on data from human inherited lysosomal glycosphingolipid storage disorders and gene-engineered animal studies are outlined. Finally, the key molecular mechanisms by which glycosphingolipids could control neuroinflammation in Parkinson's disease are highlighted. These include inflammasome activation and secretion of pro-inflammatory cytokines, altered calcium homeostasis, changes in the blood-brain barrier permeability, recruitment of peripheral immune cells or production of autoantibodies.
Which Factors in Spinocerebellar Ataxia Type 3 Patients Are Associated with Restless Legs Syndrome/Willis-Ekbom Disease?
Cerebellum (London, England), 2021

There is evidence of a higher prevalence of restless legs syndrome/Willis-Ekbom disease (RLS/WED) in individuals with spinocerebellar ataxia type 3 (SCA3), although the factors underlying this association remain unknown. The present study aimed to determine the prevalence of RLS/WED in SCA3 patients and to investigate which factors of SCA3 patients are associated with presence of RLS/WED. From February to August of 2006, we carried out clinical interviews in 40 controls and 40 SCA3 patients, diagnosed and followed up at Faculty of Medicine of Ribeirão Preto, University of São Paulo. Twenty-seven SCA3 patients were submitted to a detailed clinical protocol, electroneuromyography, blood work up, polysomnography (PSG), suggested immobilization test (SIT), and magnetic resonance image (MRI). RLS/WED was found in 27.5% of SCA3 patients and 2.5% of normal controls (p = 0.003). The factors related to RLS/WED in SCA3 patients were female gender, age at start of the symptoms of ataxia after 30 years, presence of peripheral neuropathy, and documented iron deficiency. Among SCA3 patients, those with RLS showed higher values of maximal discomfort level and discomfort level sum compared to non-RLS individuals on SIT. There is a relation between RLS/WED and SCA3, which seems to be resultant of different factors whose identification could improve the quality of assistance to those patients as well as to promote a better comprehension of the pathophysiology of both RLS/WED and SCA3.
ChaRTr: An R toolbox for modeling choices and response times in decision-making tasks.
Journal of neuroscience methods, 2019

Decision-making is the process of choosing and performing actions in response to sensory cues to achieve behavioral goals. Many mathematical models have been developed to describe the choice behavior and response time (RT) distributions of observers performing decision-making tasks. However, relatively few researchers use these models because it demands expertise in various numerical, statistical, and software techniques.
An Intersubjective View of Empathy and Hypnotic Trance: Response to Wickramasekera II.
The American journal of clinical hypnosis, 2016

In response to Wickramasekera II's description of his empathic involvement theory of hypnosis in "Mysteries of hypnosis and the self are revealed by the psychology and neuroscience of empathy" (Wickramasekera II, 2015), Henning offers further reflections on what empathy might be and what it allows therapists to do, particularly in conditions of hypnotic trance. She defines her intersubjective view of hypnotic trance as an experience in which client and therapist mutually engage in a shared state of consciousness, and a mutual bidirectional or multidirectional exchange of verbal and nonverbal, as well as conscious and unconscious, material occurs, and which may include shared taking on of roles and expectations in each party, as suggested by the other, particularly when both client and therapist are highly hypnotizable. Research on the concept of "mutual hypnosis," or co-trance, is reviewed, and barriers to scholarly discussions about intersubjectivity in therapy relationships are described. Concepts from other disciplines and traditions, including quantum physics, transpersonal psychology, contemplative Christianity, and shamanistic practices and trance in other cultures are then offered to clarify the processes of intersubjectivity, and perspectives about empathy and hypnotic co-trance are offered from the context of the author's own clinical work as a trauma therapist. Finally, suggestions are provided for future research approaches and methods to further explore and understand these phenomena.
Investigating an in silico approach for prioritizing antidepressant drug prescription based on drug-induced expression profiles and predicted gene expression.
The pharmacogenomics journal, 2021

In clinical practice, an antidepressant prescription is a trial and error approach, which is time consuming and discomforting for patients. This study investigated an in silico approach for ranking antidepressants based on their hypothetical likelihood of efficacy. We predicted the transcriptomic profile of citalopram remitters by performing an in silico transcriptomic-wide association study on STAR*D GWAS data (N = 1163). The transcriptional profile of remitters was compared with 21 antidepressant-induced gene expression profiles in five human cell lines available in the connectivity-map database. Spearman correlation, Pearson correlation, and the Kolmogorov-Smirnov test were used to determine the similarity between antidepressant-induced profiles and remitter profiles, subsequently calculating the average rank of antidepressants across the three methods and a p value for each rank by using a permutation procedure. The drugs with the top ranks were those having a high positive correlation with the expression profiles of remitters and that may have higher chances of efficacy in the tested patients. In MCF7 (breast cancer cell line), escitalopram had the highest average rank, with an average rank higher than expected by chance (p = 0.0014). In A375 (human melanoma) and PC3 (prostate cancer) cell lines, escitalopram and citalopram emerged as the second-highest ranked antidepressants, respectively (p = 0.0310 and 0.0276, respectively). In HA1E (kidney) and HT29 (colon cancer) cell types, citalopram and escitalopram did not fall among top antidepressants. The correlation between citalopram remitters' and (es)citalopram-induced expression profiles in three cell lines suggests that our approach may be useful and with future improvements, it can be applicable at the individual level to tailor treatment prescription.