CLAW-MRM: omprehensive ipidomics utomation orkflow for ultiple eaction onitoring Using Large Language Models.

Lipidomic profiling generates vast datasets, making manual annotation and trend interpretation complex and time-intensive. The structural and chemical diversity of the lipidome further complicates the analysis. While existing tools support targeted lipid identification, they often lack automated workflows and seamless integration with statistical and bioinformatics tools.

Multimodal Nano-DESI Mass Spectrometry Imaging Reveals Phospholipids Accumulation in and around Amyloid Plaques in Alzheimer's Disease.

Alzheimer's disease (AD), characterized by β-amyloid plaques, is increasingly recognized by lipid dysregulation as a key factor in its pathology. Mass spectrometry imaging (MSI), a powerful tool for mapping the spatial distribution of biomolecules in tissue sections, is ideally suited for investigating region-specific molecular alterations in diseased animal tissues. Recent MSI advancements have revealed plaque-associated molecular features in the AD brain, highlighting the role of metabolic dysfunction in disease progression.

Glial Biologist's Guide to Mass Spectrometry-Based Lipidomics: A Tutorial From Sample Preparation to Data Analysis.

Neurological diseases are associated with disruptions in the brain lipidome that are becoming central to disease pathogenesis. Traditionally perceived as static structural support in membranes, lipids are now known to be actively involved in cellular signaling, energy metabolism, and other cellular activities involving membrane curvature, fluidity, fusion or fission. Glia are critical in the development, health, and function of the brain, and glial regulation plays a major role in disease.

Beyond awareness: the binding of reflexive mechanisms with the conscious mind: a perspective from default space theory.

How do reflexes operate so quickly with so much multimodal information on the environment? How might unconscious processes help reveal the nature of consciousness? The Default Space Theory of Consciousness (DST) offers a novel way to interpret these questions by describing how sensory inputs, cognitive functions, emotional states, and unconscious processes are integrated by a single unified internal representation. Recent developments in neuroimaging and electrophysiology, such as fMRI, EEG, and MEG, have improved our knowledge of the brain mechanisms that underpin the conscious mind and have highlighted the importance of neural oscillations and sensory integration in its formation. In this article, we put forth a perspective on an underresearched relationship of reflexes with the dynamic character of consciousness and suggest that future research should focus on the interplay of the unconscious processes of reflexes and correlates of the contents of consciousness to better understand its nature.

Recent Developments in Machine Learning for Mass Spectrometry.

Statistical analysis and modeling of mass spectrometry (MS) data have a long and rich history with several modern MS-based applications using statistical and chemometric methods. Recently, machine learning (ML) has experienced a renaissance due to advents in computational hardware and the development of new algorithms for artificial neural networks (ANN) and deep learning architectures. Moreover, recent successes of new ANN and deep learning architectures in several areas of science, engineering, and society have further strengthened the ML field.

Senescent glia link mitochondrial dysfunction and lipid accumulation.

Senescence is a cellular state linked to ageing and age-onset disease across many mammalian species. Acutely, senescent cells promote wound healing and prevent tumour formation; but they are also pro-inflammatory, thus chronically exacerbate tissue decline. Whereas senescent cells are active targets for anti-ageing therapy, why these cells form in vivo, how they affect tissue ageing and the effect of their elimination remain unclear.

Comprehensive Lipidomic Automation Workflow using Large Language Models.

Lipidomics generates large data that makes manual annotation and interpretation challenging. Lipid chemical and structural diversity with structural isomers further complicates annotation. Although, several commercial and open-source software for targeted lipid identification exists, it lacks automated method generation workflows and integration with statistical and bioinformatics tools.

Lesion-remote astrocytes govern microglia-mediated white matter repair.

Spared regions of the damaged central nervous system undergo dynamic remodeling and exhibit a remarkable potential for therapeutic exploitation. Here, lesion-remote astrocytes (LRAs), which interact with viable neurons, glia and neural circuitry, undergo reactive transformations whose molecular and functional properties are poorly understood. Using multiple transcriptional profiling methods, we interrogated LRAs from spared regions of mouse spinal cord following traumatic spinal cord injury (SCI).

Mass Spectrometry-based Single-Cell Lipidomics: Advancements, Challenges, and the Path Forward.

In the past decade, lipidomics, now recognized as standalone subdiscipline of metabolomics, has gained considerable attention. Due to its sensitivity and unparalleled versatility, mass spectrometry (MS) has emerged as the tool of choice for lipid identification and detection. Traditional MS-based lipidomics are performed on bulk cell samples.

Identification of Monomethyl Branched-Chain Lipids by a Combination of Liquid Chromatography Tandem Mass Spectrometry and Charge-Switching Chemistries.

While various mass spectrometric approaches have been applied to lipid analysis, unraveling the extensive structural diversity of lipids remains a significant challenge. Notably, these approaches often fail to differentiate between isomeric lipids─a challenge that is particularly acute for branched-chain fatty acids (FAs) that often share similar (or identical) mass spectra to their straight-chain isomers. Here, we utilize charge-switching strategies that combine ligated magnesium dications with deprotonated fatty acid anions.

Harnessing the Spatial Foundation of Mind in Breaking Vicious Cycles in Anxiety, Insomnia, and Depression: The Future of Virtual Reality Therapy Applications.

Mental Illnesses, particularly anxiety, insomnia, and depression often involve vicious cycles which are self-perpetuating and can trap one into a more chronic state. For example in the case of insomnia, sympathetic overactivity, intrusive thoughts, and emotional instability due to sleep loss can perpetuate further sleep loss the next night and so on. In this article, we put forward a perspective on breaking these vicious cycles based on preeminent theories in global and spatial cognition, that the foundation of the conscious mind is a spatial coordinate system.

Respiratory Rhythm, Autonomic Modulation, and the Spectrum of Emotions: The Future of Emotion Recognition and Modulation.

Pulmonary ventilation and respiration are considered to be primarily involved in oxygenation of blood for oxygen delivery to cells throughout the body for metabolic purposes. Other pulmonary physiological observations, such as respiratory sinus arrhythmia, Hering Brewer reflex, cardiorespiratory synchronization, and the heart rate variability (HRV) relationship with breathing rhythm, lack complete explanations of physiological/functional significance. The spectrum of waveforms of breathing activity correlate to anxiety, depression, anger, stress, and other positive and negative emotions.

On the Hierarchical Organization of Oscillatory Assemblies: Layered Superimposition and a Global Bioelectric Framework.

Bioelectric oscillations occur throughout the nervous system of nearly all animals, revealed to play an important role in various aspects of cognitive activity such as information processing and feature binding. Modern research into this dynamic and intrinsic bioelectric activity of neural cells continues to raise questions regarding their role in consciousness and cognition. In this theoretical article, we assert a novel interpretation of the hierarchical nature of "brain waves" by identifying that the superposition of multiple oscillations varying in frequency corresponds to the superimposing of the contents of consciousness and cognition.

Multimodal Integration and Phenomenal Spatiotemporal Binding: A Perspective From the Default Space Theory.

How does the integrated and unified conscious experience arise from the vastly distributed activities of the nervous system? How is the information from the many cones of the retina bound with information coming from the cochlea to create the association of sounds with objects in visual space? In this perspective article, we assert a novel viewpoint on the "binding problem" in which we explain a metastable operation of the brain and body that may provide insight into this problem. In our view which is a component of the Default Space Theory (DST), consciousness arises from a metastable synchronization of local computations into a global coherence by a framework of widespread slow and ultraslow oscillations coordinated by the thalamus. We reinforce a notion shared by some consciousness researchers such as Revonsuo and the Fingelkurts that a spatiotemporal matrix is the foundation of phenomenological experience and that this phenomenology is directly tied to bioelectric operations of the nervous system.

Self-Regulation of Breathing as an Adjunctive Treatment of Insomnia.

Sleep is a quiescent behavioral state during which complex homeostatic functions essential to health and well-being occur. Insomnia is a very common psychiatric disorder leading to a myriad of detrimental effects including loss of concentration, memory, and performance as well as disease. Current pharmaceutical treatments can be expensive, impairing, unhealthy, and habit-forming.

Unraveling the role of genetics in the pathogenesis of diabetic retinopathy.

Diabetic retinopathy (DR) is a microvascular disease of the retina and the leading cause of visual disability in diabetic patients. Genetic factors have shown to play a pivotal role in DR onset, and several candidate genes have been associated with its progression. A literature search was performed to identify the genes known to be associated with DR through linkage analysis, candidate gene association, and genome-wide association studies (GWAS).

Top Mysteries of the Mind: Insights From the Default Space Model of Consciousness.

Aside from the nature of consciousness itself, there are still many unsolved problems in the neurosciences. Despite the vast and quickly growing body of work in this field, we still find ourselves perplexed at seemingly simple qualities of our mental being such as why we need to sleep. The neurosciences are at least beginning to take a hold on these mysteries and are working toward solving them.