Xinyu Zhu, Shen Sun, Lan Lin, Yutong Wu, Xiangge Ma
{"title":"Transformer-based approaches for neuroimaging: an in-depth review of their role in classification and regression tasks.","authors":"Xinyu Zhu, Shen Sun, Lan Lin, Yutong Wu, Xiangge Ma","doi":"10.1515/revneuro-2024-0088","DOIUrl":"10.1515/revneuro-2024-0088","url":null,"abstract":"<p><p>In the ever-evolving landscape of deep learning (DL), the transformer model emerges as a formidable neural network architecture, gaining significant traction in neuroimaging-based classification and regression tasks. This paper presents an extensive examination of transformer's application in neuroimaging, surveying recent literature to elucidate its current status and research advancement. Commencing with an exposition on the fundamental principles and structures of the transformer model and its variants, this review navigates through the methodologies and experimental findings pertaining to their utilization in neuroimage classification and regression tasks. We highlight the transformer model's prowess in neuroimaging, showcasing its exceptional performance in classification endeavors while also showcasing its burgeoning potential in regression tasks. Concluding with an assessment of prevailing challenges and future trajectories, this paper proffers insights into prospective research directions. By elucidating the current landscape and envisaging future trends, this review enhances comprehension of transformer's role in neuroimaging tasks, furnishing valuable guidance for further inquiry.</p>","PeriodicalId":49623,"journal":{"name":"Reviews in the Neurosciences","volume":" ","pages":"209-228"},"PeriodicalIF":3.4,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142331065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ivan Montiel, Paola C Bello-Medina, Roberto A Prado-Alcalá, Gina L Quirarte, Luis A Verdín-Ruvalcaba, Tzitzi A Marín-Juárez, Andrea C Medina
{"title":"Involvement of kinases in memory consolidation of inhibitory avoidance training.","authors":"Ivan Montiel, Paola C Bello-Medina, Roberto A Prado-Alcalá, Gina L Quirarte, Luis A Verdín-Ruvalcaba, Tzitzi A Marín-Juárez, Andrea C Medina","doi":"10.1515/revneuro-2024-0093","DOIUrl":"10.1515/revneuro-2024-0093","url":null,"abstract":"<p><p>The inhibitory avoidance (IA) task is a paradigm widely used to investigate the molecular and cellular mechanisms involved in the formation of long-term memory of aversive experiences. In this review, we discuss studies on different brain structures in rats associated with memory consolidation, such as the hippocampus, striatum, and amygdala, as well as some cortical areas, including the insular, cingulate, entorhinal, parietal and prefrontal cortex. These studies have shown that IA training triggers the release of neurotransmitters, hormones, growth factors, etc., that activate intracellular signaling pathways related to protein kinases, which induce intracellular non-genomic changes or transcriptional mechanisms in the nucleus, leading to the synthesis of proteins. We have summarized the temporal dynamics and crosstalk among protein kinase A, protein kinase C, mitogen activated protein kinase, extracellular-signal-regulated kinase, and Ca<sup>2+</sup>/calmodulin-dependent protein kinase II described in the hippocampus. Protein kinase activity has been associated with structural changes and synaptic strengthening, resulting in memory storage. However, little is known about the molecular mechanisms involved in intense IA training, which protects memory from typical amnestic treatments, such as protein synthesis inhibitors, and induces increased spinogenesis, suggesting an unexplored mechanism independent of the genomic pathway. This highly emotional experience causes an extinction-resistant memory, as has been observed in some pathological states such as post-traumatic stress disorder. We propose that the changes in spinogenesis observed after intense IA training could be generated by protein kinases via non-genomic pathways.</p>","PeriodicalId":49623,"journal":{"name":"Reviews in the Neurosciences","volume":" ","pages":"189-208"},"PeriodicalIF":3.4,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142331064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Amanda Gollo Bertollo, Maiqueli Eduarda Dama Mingoti, Zuleide Maria Ignácio
{"title":"Neurobiological mechanisms in the kynurenine pathway and major depressive disorder.","authors":"Amanda Gollo Bertollo, Maiqueli Eduarda Dama Mingoti, Zuleide Maria Ignácio","doi":"10.1515/revneuro-2024-0065","DOIUrl":"10.1515/revneuro-2024-0065","url":null,"abstract":"<p><p>Major depressive disorder (MDD) is a prevalent psychiatric disorder that has damage to people's quality of life. Tryptophan is the precursor to serotonin, a critical neurotransmitter in mood modulation. In mammals, most free tryptophan is degraded by the kynurenine pathway (KP), resulting in a range of metabolites involved in inflammation, immune response, and neurotransmission. The imbalance between quinolinic acid (QA), a toxic metabolite, and kynurenic acid (KynA), a protective metabolite, is a relevant phenomenon involved in the pathophysiology of MDD. Proinflammatory cytokines increase the activity of the enzyme indoleamine 2,3-dioxygenase (IDO), leading to the degradation of tryptophan in the KP and an increase in the release of QA. IDO activates proinflammatory genes, potentiating neuroinflammation and deregulating other physiological mechanisms related to chronic stress and MDD. This review highlights the physiological mechanisms involved with stress and MDD, which are underlying an imbalance of the KP and discuss potential therapeutic targets.</p>","PeriodicalId":49623,"journal":{"name":"Reviews in the Neurosciences","volume":" ","pages":"169-187"},"PeriodicalIF":3.4,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142156480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Milos Kostic, Nikola Zivkovic, Ana Cvetanovic, Jelena Basic, Ivana Stojanovic
{"title":"Dissecting the immune response of CD4<sup>+</sup> T cells in Alzheimer's disease.","authors":"Milos Kostic, Nikola Zivkovic, Ana Cvetanovic, Jelena Basic, Ivana Stojanovic","doi":"10.1515/revneuro-2024-0090","DOIUrl":"10.1515/revneuro-2024-0090","url":null,"abstract":"<p><p>The formation of amyloid-β (Aβ) plaques is a neuropathological hallmark of Alzheimer's disease (AD), however, these pathological aggregates can also be found in the brains of cognitively unimpaired elderly population. In that context, individual variations in the Aβ-specific immune response could be key factors that determine the level of Aβ-induced neuroinflammation and thus the propensity to develop AD. CD4<sup>+</sup> T cells are the cornerstone of the immune response that coordinate the effector functions of both adaptive and innate immunity. However, despite intensive research efforts, the precise role of these cells during AD pathogenesis is still not fully elucidated. Both pathogenic and beneficial effects have been observed in various animal models of AD, as well as in humans with AD. Although this functional duality of CD4<sup>+</sup> T cells in AD can be simply attributed to the vast phenotype heterogeneity of this cell lineage, disease stage-specific effect have also been proposed. Therefore, in this review, we summarized the current understanding of the role of CD4<sup>+</sup> T cells in the pathophysiology of AD, from the aspect of their antigen specificity, activation, and phenotype characteristics. Such knowledge is of practical importance as it paves the way for immunomodulation as a therapeutic option for AD treatment, given that currently available therapies have not yielded satisfactory results.</p>","PeriodicalId":49623,"journal":{"name":"Reviews in the Neurosciences","volume":" ","pages":"139-168"},"PeriodicalIF":3.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142141594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Comparison of data-driven thresholding methods using directed functional brain networks.","authors":"Thilaga Manickam, Vijayalakshmi Ramasamy, Nandagopal Doraisamy","doi":"10.1515/revneuro-2024-0020","DOIUrl":"10.1515/revneuro-2024-0020","url":null,"abstract":"<p><p>Over the past two centuries, intensive empirical research has been conducted on the human brain. As an electroencephalogram (EEG) records millisecond-to-millisecond changes in the electrical potentials of the brain, it has enormous potential for identifying useful information about neuronal transactions. The EEG data can be modelled as graphs by considering the electrode sites as nodes and the linear and nonlinear statistical dependencies among them as edges (with weights). The graph theoretical modelling of EEG data results in functional brain networks (FBNs), which are fully connected (complete) weighted undirected/directed networks. Since various brain regions are interconnected via sparse anatomical connections, the weak links can be filtered out from the fully connected networks using a process called thresholding. Multiple researchers in the past decades proposed many thresholding methods to gather more insights about the influential neuronal connections of FBNs. This paper reviews various thresholding methods used in the literature for FBN analysis. The analysis showed that data-driven methods are unbiased since no arbitrary user-specified threshold is required. The efficacy of four data-driven thresholding methods, namely minimum spanning tree (MST), minimum connected component (MCC), union of shortest path trees (USPT), and orthogonal minimum spanning tree (OMST), in characterizing cognitive behavior of the normal human brain is analysed using directed FBNs constructed from EEG data of different cognitive load states. The experimental results indicate that both MCC and OMST thresholding methods can detect cognitive load-induced changes in the directed functional brain networks.</p>","PeriodicalId":49623,"journal":{"name":"Reviews in the Neurosciences","volume":" ","pages":"119-138"},"PeriodicalIF":3.4,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142114112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The impact of genetic factors on the response to migraine therapy.","authors":"Daniil Tsirelis, Alexandros Tsekouras, Polyxeni Stamati, Ioannis Liampas, Elli Zoupa, Metaxia Dastamani, Zisis Tsouris, Anastasios Papadimitriou, Efthimios Dardiotis, Vasileios Siokas","doi":"10.1515/revneuro-2024-0045","DOIUrl":"10.1515/revneuro-2024-0045","url":null,"abstract":"<p><p>Migraine is a multidimensional disease affecting a large portion of the human population presenting with a variety of symptoms. In the era of personalized medicine, successful migraine treatment presents a challenge, as several studies have shown the impact of a patient's genetic profile on therapy response. However, with the emergence of contemporary treatment options, there is promise for improved outcomes. A literature search was conducted in PubMed and Scopus, in order to obtain studies investigating the impact of genetic factors on migraine therapy outcome. Overall, 23 studies were included in the current review, exhibiting diversity in the treatments used and the genetic variants investigated. Divergent genes were assessed for each category of migraine treatment. Several genetic factors were identified to contribute to the heterogeneous response to treatment. SNPs related to pharmacodynamic receptors, pharmacogenetics and migraine susceptibility loci were the most investigated variants, revealing some interesting significant results. To date, various associations have been recorded correlating the impact of genetic factors on migraine treatment responses. More extensive research needs to take place with the aim of shedding light on the labyrinthine effects of genetic variations on migraine treatment, and, consequently, these findings can promptly affect migraine treatment and improve migraine patients' life quality in the vision of precise medicine.</p>","PeriodicalId":49623,"journal":{"name":"Reviews in the Neurosciences","volume":" ","pages":"789-812"},"PeriodicalIF":3.4,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141297175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mariana Ferreira, Patrícia Carneiro, Vera Marisa Costa, Félix Carvalho, Andreas Meisel, João Paulo Capela
{"title":"Amphetamine and methylphenidate potential on the recovery from stroke and traumatic brain injury: a review.","authors":"Mariana Ferreira, Patrícia Carneiro, Vera Marisa Costa, Félix Carvalho, Andreas Meisel, João Paulo Capela","doi":"10.1515/revneuro-2024-0016","DOIUrl":"10.1515/revneuro-2024-0016","url":null,"abstract":"<p><p>The prevalence of stroke and traumatic brain injury is increasing worldwide. However, current treatments do not fully cure or stop their progression, acting mostly on symptoms. Amphetamine and methylphenidate are stimulants already approved for attention deficit hyperactivity disorder and narcolepsy treatment, with neuroprotective potential and benefits when used in appropriate doses. This review aimed to summarize pre-clinical and clinical trials testing either amphetamine or methylphenidate for the treatment of stroke and traumatic brain injury. We used PubMed as a database and included the following keywords ((methylphenidate) OR (Ritalin) OR (Concerta) OR (Biphentin) OR (amphetamine) OR (Adderall)) AND ((stroke) OR (brain injury) OR (neuroplasticity)). Overall, studies provided inconsistent results regarding cognitive and motor function. Neurite outgrowth, synaptic proteins, dendritic complexity, and synaptic plasticity increases were reported in pre-clinical studies along with function improvement. Clinical trials have demonstrated that, depending on the brain region, there is an increase in motor activity, attention, and memory due to the stimulation of the functionally depressed catecholamine system and the activation of neuronal remodeling proteins. Nevertheless, more clinical trials and pre-clinical studies are needed to understand the drugs' full potential for their use in these brain diseases namely, to ascertain the treatment time window, ideal dosage, long-term effects, and mechanisms, while avoiding their addictive potential.</p>","PeriodicalId":49623,"journal":{"name":"Reviews in the Neurosciences","volume":" ","pages":"709-746"},"PeriodicalIF":3.4,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141285108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cristina Trejo-Solís, Norma Serrano-García, Rosa Angelica Castillo-Rodríguez, Diana Xochiquetzal Robledo-Cadena, Dolores Jimenez-Farfan, Álvaro Marín-Hernández, Daniela Silva-Adaya, Citlali Ekaterina Rodríguez-Pérez, Juan Carlos Gallardo-Pérez
{"title":"Metabolic dysregulation of tricarboxylic acid cycle and oxidative phosphorylation in glioblastoma.","authors":"Cristina Trejo-Solís, Norma Serrano-García, Rosa Angelica Castillo-Rodríguez, Diana Xochiquetzal Robledo-Cadena, Dolores Jimenez-Farfan, Álvaro Marín-Hernández, Daniela Silva-Adaya, Citlali Ekaterina Rodríguez-Pérez, Juan Carlos Gallardo-Pérez","doi":"10.1515/revneuro-2024-0054","DOIUrl":"10.1515/revneuro-2024-0054","url":null,"abstract":"<p><p>Glioblastoma multiforme (GBM) exhibits genetic alterations that induce the deregulation of oncogenic pathways, thus promoting metabolic adaptation. The modulation of metabolic enzyme activities is necessary to generate nucleotides, amino acids, and fatty acids, which provide energy and metabolic intermediates essential for fulfilling the biosynthetic needs of glioma cells. Moreover, the TCA cycle produces intermediates that play important roles in the metabolism of glucose, fatty acids, or non-essential amino acids, and act as signaling molecules associated with the activation of oncogenic pathways, transcriptional changes, and epigenetic modifications. In this review, we aim to explore how dysregulated metabolic enzymes from the TCA cycle and oxidative phosphorylation, along with their metabolites, modulate both catabolic and anabolic metabolic pathways, as well as pro-oncogenic signaling pathways, transcriptional changes, and epigenetic modifications in GBM cells, contributing to the formation, survival, growth, and invasion of glioma cells. Additionally, we discuss promising therapeutic strategies targeting key players in metabolic regulation. Therefore, understanding metabolic reprogramming is necessary to fully comprehend the biology of malignant gliomas and significantly improve patient survival.</p>","PeriodicalId":49623,"journal":{"name":"Reviews in the Neurosciences","volume":" ","pages":"813-838"},"PeriodicalIF":3.4,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141263362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chris Chun Hei Lo, Peter Yat Ming Woo, Vincent C K Cheung
{"title":"Task-based EEG and fMRI paradigms in a multimodal clinical diagnostic framework for disorders of consciousness.","authors":"Chris Chun Hei Lo, Peter Yat Ming Woo, Vincent C K Cheung","doi":"10.1515/revneuro-2023-0159","DOIUrl":"10.1515/revneuro-2023-0159","url":null,"abstract":"<p><p>Disorders of consciousness (DoC) are generally diagnosed by clinical assessment, which is a predominantly motor-driven process and accounts for up to 40 % of non-communication being misdiagnosed as unresponsive wakefulness syndrome (UWS) (previously known as prolonged/persistent vegetative state). Given the consequences of misdiagnosis, a more reliable and objective multimodal protocol to diagnosing DoC is needed, but has not been produced due to concerns regarding their interpretation and reliability. Of the techniques commonly used to detect consciousness in DoC, task-based paradigms (active paradigms) produce the most unequivocal result when findings are positive. It is well-established that command following (CF) reliably reflects preserved consciousness. Task-based electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) can detect motor-independent CF and reveal preserved covert consciousness in up to 14 % of UWS patients. Accordingly, to improve the diagnostic accuracy of DoC, we propose a practical multimodal clinical decision framework centered on task-based EEG and fMRI, and complemented by measures like transcranial magnetic stimulation (TMS-EEG).</p>","PeriodicalId":49623,"journal":{"name":"Reviews in the Neurosciences","volume":" ","pages":"775-787"},"PeriodicalIF":3.4,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141158506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Anna Borne, Marcela Perrone-Bertolotti, Sarah Ferrand-Sorbets, Christine Bulteau, Monica Baciu
{"title":"Insights on cognitive reorganization after hemispherectomy in Rasmussen's encephalitis. A narrative review.","authors":"Anna Borne, Marcela Perrone-Bertolotti, Sarah Ferrand-Sorbets, Christine Bulteau, Monica Baciu","doi":"10.1515/revneuro-2024-0009","DOIUrl":"10.1515/revneuro-2024-0009","url":null,"abstract":"<p><p>Rasmussen's encephalitis is a rare neurological pathology affecting one cerebral hemisphere, therefore, posing unique challenges. Patients may undergo hemispherectomy, a surgical procedure after which cognitive development occurs in the isolated contralateral hemisphere. This rare situation provides an excellent opportunity to evaluate brain plasticity and cognitive recovery at a hemispheric level. This literature review synthesizes the existing body of research on cognitive recovery following hemispherectomy in Rasmussen patients, considering cognitive domains and modulatory factors that influence cognitive outcomes. While language function has traditionally been the focus of postoperative assessments, there is a growing acknowledgment of the need to broaden the scope of language investigation in interaction with other cognitive domains and to consider cognitive scaffolding in development and recovery. By synthesizing findings reported in the literature, we delineate how language functions may find support from the right hemisphere after left hemispherectomy, but also how, beyond language, global cognitive functioning is affected. We highlight the critical influence of several factors on postoperative cognitive outcomes, including the timing of hemispherectomy and the baseline preoperative cognitive status, pointing to early surgical intervention as predictive of better cognitive outcomes. However, further specific studies are needed to confirm this correlation. This review aims to emphasize a better understanding of mechanisms underlying hemispheric specialization and plasticity in humans, which are particularly important for both clinical and research advancements. This narrative review underscores the need for an integrative approach based on cognitive scaffolding to provide a comprehensive understanding of mechanisms underlying the reorganization in Rasmussen patients after hemispherectomy.</p>","PeriodicalId":49623,"journal":{"name":"Reviews in the Neurosciences","volume":" ","pages":"747-774"},"PeriodicalIF":3.4,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140946043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}