NS-Forest: A machine learning method for the objective identification of minimum marker gene combinations for cell type determination from single cell RNA sequencing DOI Creative Commons
Brian D. Aevermann,

Yun Zhang,

Mark Novotny

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2020, Volume and Issue: unknown

Published: Sept. 24, 2020

Abstract Single cell genomics is rapidly advancing our knowledge of phenotypic types and states. Driven by single cell/nucleus RNA sequencing (scRNA-seq) data, comprehensive atlas projects covering a wide range organisms tissues are currently underway. As result, it critical that the transcriptional phenotypes discovered defined disseminated in consistent concise manner. Molecular biomarkers have historically played an important role biological research, from defining immune cell-types surface protein expression to diseases molecular drivers. Here we describe machine learning-based marker gene selection algorithm, NS-Forest version 2.0, which leverages non-linear attributes random forest feature binary scoring approach discover minimal combinations precisely captures type identity represented complete scRNA-seq profiles. The genes selected provide barcode necessary sufficient characteristics for semantic definition serve as useful tools downstream investigation. use identify human brain middle temporal gyrus reveals importance signaling non-coding RNAs neuronal identity.

Language: Английский

Challenges in Scaling Down of Free-Floating Implantable Neural Interfaces to Millimeter Scale DOI Creative Commons
Kai-Wen Yang, Keonghwan Oh, Sohmyung Ha

et al.

IEEE Access, Journal Year: 2020, Volume and Issue: 8, P. 133295 - 133320

Published: Jan. 1, 2020

Implantable neural interface devices are an emerging technology for continuous brain monitoring and brain-computer (BCI). Recording of electrical signals from neurons interest has led to more efficient personalized diagnosis, treatment, prognosis neurological disorders. It facilitates the dynamic mapping whole brain, improving our understanding links between functions behaviors. Stimulation targeted nerves been utilized as effective therapy Parkinson's disease, essential tremor, dystonia, etc. also developed motor neuroprosthetic devices, quality life many. Although initial designs were bulky, recent advances in semiconductor nano-, micro-technology enabled miniaturization such millimeter scale. Free-floating implants miniature size highly scalable be distributed around region extensively. They clinically viable they cause less disturbance body induce tissue immune response. However, these research efforts scaling down have faced challenges resulted decreasing implants, including issues pertaining wireless powering, data communication, signal recording, stimulation. Through extensive literature simulations, limits trade-offs regarding implant investigated analyzed each aspect challenges. State-of-the-art development future trends advanced interfaces explored.

Language: Английский

Citations

27

Dual GRIN lens two-photon endoscopy for high-speed volumetric and deep brain imaging DOI Creative Commons

Yu-Feng Chien,

Jyun-Yi Lin,

Po‐Ting Yeh

et al.

Biomedical Optics Express, Journal Year: 2020, Volume and Issue: 12(1), P. 162 - 162

Published: Nov. 19, 2020

Studying neural connections and activities in vivo is fundamental to understanding brain functions. Given the cm-size three-dimensional circuit dynamics, deep-tissue, high-speed volumetric imaging highly desirable for study. With sub-micrometer spatial resolution, intrinsic optical sectioning, deep-tissue penetration capability, two-photon microscopy (2PM) has found a niche neuroscience. However, current 2PM typically relies on slow axial scan imaging, maximal depth only about 1 mm. Here, we demonstrate that by integrating gradient-index (GRIN) lens tunable acoustic GRIN (TAG) into 2PM, both volume-imaging rate can be significantly improved. Specifically, an ∼ 1-cm long allows relay from any target region of mouse brain, while TAG provides sub-second volume via 100 kHz MHz scan. This technique enables study calcium dynamics cm-deep regions with sub-cellular spatiotemporal paving way interrogating deep-brain functional connectome.

Language: Английский

Citations

27

Temporal information in the anterior cingulate cortex relates to accumulated experiences DOI

Ryan A. Wirt,

Talha K. Soluoku,

Ryan M. Ricci

et al.

Current Biology, Journal Year: 2024, Volume and Issue: 34(13), P. 2921 - 2931.e3

Published: June 21, 2024

Language: Английский

Citations

3

Overcoming biological barriers: Precision engineered extracellular vesicles for personalized neuromedicine DOI Creative Commons
V. Ravichandiran, Anuradha Kesharwani,

Anupriya

et al.

Precision medicine and engineering., Journal Year: 2024, Volume and Issue: 1(2), P. 100010 - 100010

Published: Oct. 19, 2024

Language: Английский

Citations

3

A comparative study between state‐of‐the‐art MRI deidentification and AnonyMI, a new method combining re‐identification risk reduction and geometrical preservation DOI Creative Commons
Ezequiel Mikulan,

S. Russo,

Flavia Maria Zauli

et al.

Human Brain Mapping, Journal Year: 2021, Volume and Issue: 42(17), P. 5523 - 5534

Published: Sept. 14, 2021

Abstract Deidentifying MRIs constitutes an imperative challenge, as it aims at precluding the possibility of re‐identification a research subject or patient, but same time should preserve much geometrical information possible, in order to maximize data reusability and facilitate interoperability. Although several deidentification methods exist, no comprehensive comparative evaluation performance has been carried out across them. Moreover, possible ways these can compromise subsequent analysis not exhaustively tested. To tackle issues, we developed AnonyMI, novel MRI method, implemented user‐friendly 3D Slicer plugin‐in, which providing balance between identity protection preservation. test features, performed two series analyses on compared AnonyMI other state‐of‐the‐art methods, evaluate, time, how efficient they are deidentifying affect analyses, with particular emphasis source localization procedures. Our results show that all three significantly reduce risk provides best conservation. Notably, also offers technical advantages such interface, multiple input–output capabilities, being tailored specific needs, batch processing visualization for quality assurance.

Language: Английский

Citations

18

BrainBase: a curated knowledgebase for brain diseases DOI Creative Commons
Lin Liu, Yang Zhang, Guangyi Niu

et al.

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 50(D1), P. D1131 - D1138

Published: Oct. 8, 2021

Brain is the central organ of nervous system and any brain disease can seriously affect human health. Here we present BrainBase (https://ngdc.cncb.ac.cn/brainbase), a curated knowledgebase for diseases that aims to provide whole picture associated genes. Specifically, based on manual curation 2768 published articles along with information retrieval from several public databases, features comprehensive collection 7175 disease-gene associations spanning total 123 linking 5662 genes, 16 591 drug-target interactions covering 2118 drugs/chemicals 623 five types specific genes in light expression specificity tissue/regions/cerebrospinal fluid/cells. In addition, considering severity glioma among tumors, current version incorporates 21 multi-omics datasets, presents molecular profiles across various samples/conditions identifies four groups featured potential clinical significance. Collectively, integrates not only valuable but also through data analysis, accordingly bearing great promise serve as diseases.

Language: Английский

Citations

18

Optically Selective Neuron Stimulation with a Wavefront Shaping‐Empowered Multimode Fiber DOI Creative Commons
Tianting Zhong, Zhihai Qiu, Yong Wu

et al.

Advanced Photonics Research, Journal Year: 2021, Volume and Issue: 3(3)

Published: Dec. 22, 2021

Optogenetics is proved to be a powerful tool for exploring the connection between behavior and neural circuits. The progress greatly benefits from advances of optical techniques that enable high spatiotemporal resolution selective single‐neuron stimulation through modulating light. Efficient propagation modulated light, however, handicapped by strong scattering in biological tissues, which results inherent tradeoff penetration depth resolution. Schemes like graded index (GRIN) lens‐based microendoscopes are developed yield more confined delivery but tissue damage caused insertion bulky components cannot ignored. Herein, an optically precise neuron using ultrathin multimode fiber (MMF) demonstrated, empowered wavefront shaping achieve light focusing rapid raster scanning without mechanical movement at distal end MMF even mouse skull. With this method, primary neurons expressing Chr2 can regulated spatiotemporally experiment. Although lot shall further improved, work may open up new venues noninvasive or minimally invasive all‐optical investigation circuits used‐to‐be inaccessible brain regions.

Language: Английский

Citations

17

A Proposed Brain-, Spine-, and Mental- Health Screening Methodology (NEUROSCREEN) for Healthcare Systems: Position of the Society for Brain Mapping and Therapeutics DOI
Mohammad Nami, Robert W. Thatcher, Nasser H. Kashou

et al.

Journal of Alzheimer s Disease, Journal Year: 2022, Volume and Issue: 86(1), P. 21 - 42

Published: Jan. 11, 2022

The COVID-19 pandemic has accelerated neurological, mental health disorders, and neurocognitive issues. However, there is a lack of inexpensive efficient brain evaluation screening systems. As result, considerable fraction patients with or psychobehavioral predicaments either do not get timely diagnosed fail to receive personalized treatment plans. This especially true in the elderly populations, wherein only 16% seniors say they regular cognitive evaluations. Therefore, great need for development an optimized clinical workflow methodology like what already existence prostate breast exams. Such should be designed facilitate objective early detection cost-effective such disorders. In this paper we have reviewed existing protocols, recent technological advances suggested reliable workflows screening. protocols range from questionnaires smartphone apps multi-modality mapping advanced imaging where applicable. To that end, Society Brain Mapping Therapeutics (SBMT) proposes Brain, Spine Mental Health Screening (NEUROSCREEN) as multi-faceted approach. Beside other assessment tools, NEUROSCREEN employs guided assessments quantitative electroencephalography (qEEG) well potential genetic testing decline risk effective tools diagnosis, monitor disease progression, guide interventions. Operationalizing expected result reduced healthcare costs improving quality life at national later, global scales.

Language: Английский

Citations

11

Neurobiological reduction: From cellular explanations of behavior to interventions DOI Creative Commons
David Parker

Frontiers in Psychology, Journal Year: 2022, Volume and Issue: 13

Published: Dec. 22, 2022

Scientific reductionism, the view that higher level functions can be explained by properties at some lower-level or levels, has been an assumption of nervous system analyses since acceptance neuron doctrine in late 19th century, and became a dominant experimental approach with development intracellular recording techniques mid-20th century. Subsequent refinements electrophysiological approaches continual molecular genetic have promoted focus on cellular mechanisms explanations sensory, motor, cognitive functions. Reductionist assumptions also influenced our views etiology treatment psychopathologies, more recently led to claims we can, even should, pharmacologically enhance normal brain. Reductionism remains area active debate philosophy science. In neuroscience psychology, typically focuses mind-brain question cognition, how if they neurobiological terms. However, these debates are affected complexity phenomena being considered difficulty obtaining necessary detail. We instead ask whether features identified simpler aspects systems support current explaining behaviors. While my is do not, this does not invite opposing prevalent dichotomous thinking detail irrelevant should computations representations. need consider address long-standing dilemma ostensibly through discrete cell communication generate population effects across multiple spatial temporal scales behavior.

Language: Английский

Citations

11

Monitoring of Stimulus Evoked Murine Somatosensory Cortex Hemodynamic Activity With Volumetric Multi-Spectral Optoacoustic Tomography DOI Creative Commons
Benedict Mc Larney,

Magdalena Anastasia Hutter,

Oleksiy Degtyaruk

et al.

Frontiers in Neuroscience, Journal Year: 2020, Volume and Issue: 14

Published: June 3, 2020

Sensory stimulation is an attractive paradigm for studying brain activity using various optical-, ultrasound- and MRI-based functional neuroimaging methods. Optoacoustics has been recently suggested as a powerful new tool scalable mapping of multiple hemodynamic parameters with rich contrast previously unachievable spatio-temporal resolution. Yet, its utility the processing peripheral inputs at whole level so far not quantified. We employed volumetric multi-spectral optoacoustic tomography (vMSOT) to non-invasively monitor HbO, HbR HbT dynamics across mouse somatosensory cortex evoked by electrical paw stimuli. show that elevated contralateral activation preserved in HbO map (invisible MRI) under isoflurane anesthesia. Brain shown be predominantly confined cortex, strongest hindpaw region sensorimotor cortex. Furthermore, vMSOT detected presence initial dip delta channel. Sensorimotor cortical was identified over all other regions but HbR. Pearson's correlation enabled localizing response further highlighting ability bridge imaging performance deficiencies modalities.

Language: Английский

Citations

16