scholarly journals Dense reconstruction of brain-wide neuronal population close to the ground truth

2017 ◽  
Author(s):  
Zhou Hang ◽  
Li Shiwei ◽  
Li Anan ◽  
Xiong Feng ◽  
Li Ning ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Ground Truth ◽  
Neuronal Population ◽  
Projection Neurons ◽  
Neuronal Populations ◽  
Digital Reconstruction ◽  
Single Axon ◽  
Starting Point ◽  
Human Labor ◽  
High Level

AbstractRecent progresses allow imaging specific neuronal populations at single-axon level across mouse brain. However, digital reconstruction of neurons in large dataset requires months of human labor. Here, we developed a tool to solve this problem. Our tool offers a special error-screening system for fast localization of submicron errors in densely packed neurites and along long projection across the whole brain, thus achieving reconstruction close to the ground-truth. Moreover, our tool equips algorithms that significantly reduce intensive manual interferences and achieve high-level automation, with speed 5 times faster compared to semi-automatic tools. We also demonstrated reconstruction of 35 long projection neurons around one injection site of a mouse brain at an affordable time cost. Our tool is applicable with datasets of 10 TB or higher from various light microscopy, and provides a starting point for the reconstruction of neuronal population for neuroscience studies at a single-cell level.

scholarly journals Decoding grasp and speech signals from the cortical grasp circuit in a tetraplegic human

2021 ◽  
Author(s):  
Sarah Kim Wandelt ◽  
Spencer Kellis ◽  
David Bjanes ◽  
Kelsie Pejsa ◽  
Brian Lee ◽  
...  
Keyword(s):  
Premotor Cortex ◽  
Neuronal Population ◽  
Brain Areas ◽  
Robotic Arms ◽  
Additional Information ◽  
Neuronal Populations ◽  
Brain Signals ◽  
Cord Injury ◽  
Population Sizes ◽  
High Level

Tetraplegia from spinal cord injury leaves many patients paralyzed below the neck, leaving them unable to perform most activities of daily living. Brain-machine interfaces (BMIs) could give tetraplegic patients more independence by directly utilizing brain signals to control external devices such as robotic arms or hands. The cortical grasp network has been of particular interest because of its potential to facilitate the restoration of dexterous object manipulation. However, a network that involves such high-level cortical areas may also provide additional information, such as the encoding of speech. Towards understanding the role of different brain areas in the human cortical grasp network, neural activity related to motor intentions for grasping and performing speech was recorded in a tetraplegic patient in the supramarginal gyrus (SMG), the ventral premotor cortex (PMv), and the somatosensory cortex (S1). We found that in high-level brain areas SMG and PMv, grasps were well represented by firing rates of neuronal populations already at visual cue presentation. During motor imagery, grasps could be significantly decoded from all brain areas. At identical neuronal population sizes, SMG and PMv achieved similar highly-significant decoding abilities, demonstrating their potential for grasp BMIs. During speech, SMG encoded both spoken grasps and colors, in contrast to PMv and S1, which were not able to significantly decode speech.These findings suggest that grasp signals can robustly be decoded at a single unit level from the cortical grasping circuit in human. Data from PMv suggests a specialized role in grasping, while SMG's role is broader and extends to speech. Together, these results indicate that brain signals from high-level areas of the human cortex can be exploited for a variety of different BMI applications.

scholarly journals Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yi Chen ◽  
Fons. J. Verbeek ◽  
Katherine Wolstencroft
Keyword(s):  
Gene Ontology ◽  
Enrichment Analysis ◽  
Biological Data ◽  
Hallmarks Of Cancer ◽  
High Throughput Analysis ◽  
Knowledge Resources ◽  
Gene Set ◽  
Cancer Hallmarks ◽  
Starting Point ◽  
High Level

Abstract Background The hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell development and tumourigenesis. However, methods for translating these high-level concepts into data-level associations between hallmarks and genes (for high throughput analysis), vary widely between studies. The examination of different strategies to associate and map cancer hallmarks reveals significant differences, but also consensus. Results Here we present the results of a comparative analysis of cancer hallmark mapping strategies, based on Gene Ontology and biological pathway annotation, from different studies. By analysing the semantic similarity between annotations, and the resulting gene set overlap, we identify emerging consensus knowledge. In addition, we analyse the differences between hallmark and gene set associations using Weighted Gene Co-expression Network Analysis and enrichment analysis. Conclusions Reaching a community-wide consensus on how to identify cancer hallmark activity from research data would enable more systematic data integration and comparison between studies. These results highlight the current state of the consensus and offer a starting point for further convergence. In addition, we show how a lack of consensus can lead to large differences in the biological interpretation of downstream analyses and discuss the challenges of annotating changing and accumulating biological data, using intermediate knowledge resources that are also changing over time.

scholarly journals How does the robot feel? Perception of valence and arousal in emotional body language

2018 ◽  
Vol 9 (1) ◽  
pp. 168-182 ◽  
Author(s):  
Mina Marmpena ◽  
Angelica Lim ◽  
Torbjørn S. Dahl
Keyword(s):  
Human Perception ◽  
Ground Truth ◽  
Body Language ◽  
Human Robot Interaction ◽  
Behavioral Experiments ◽  
Robot Interaction ◽  
Expression Of Emotion ◽  
Exploratory Approach ◽  
Starting Point ◽  
Valence And Arousal

Abstract Human-robot interaction in social robotics applications could be greatly enhanced by robotic behaviors that incorporate emotional body language. Using as our starting point a set of pre-designed, emotion conveying animations that have been created by professional animators for the Pepper robot, we seek to explore how humans perceive their affect content, and to increase their usability by annotating them with reliable labels of valence and arousal, in a continuous interval space. We conducted an experiment with 20 participants who were presented with the animations and rated them in the two-dimensional affect space. An inter-rater reliability analysis was applied to support the aggregation of the ratings for deriving the final labels. The set of emotional body language animations with the labels of valence and arousal is available and can potentially be useful to other researchers as a ground truth for behavioral experiments on robotic expression of emotion, or for the automatic selection of robotic emotional behaviors with respect to valence and arousal. To further utilize the data we collected, we analyzed it with an exploratory approach and we present some interesting trends with regard to the human perception of Pepper’s emotional body language, that might be worth further investigation.

scholarly journals Robust α-synuclein pathology in select brainstem neuronal populations is a potential instigator of multiple system atrophy

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Ethan W. Hass ◽  
Zachary A. Sorrentino ◽  
Grace M. Lloyd ◽  
Nikolaus R. McFarland ◽  
Stefan Prokop ◽  
...  
Keyword(s):  
Multiple System Atrophy ◽  
Lewy Bodies ◽  
Biochemical Properties ◽  
Detection Methods ◽  
Inferior Olivary Nucleus ◽  
Cytoplasmic Inclusions ◽  
Neuronal Populations ◽  
Carboxy Terminal Region ◽  
High Level ◽  
Carboxy Terminal

AbstractMultiple system atrophy (MSA) is an insidious middle age-onset neurodegenerative disease that clinically presents with variable degrees of parkinsonism and cerebellar ataxia. The pathological hallmark of MSA is the progressive accumulation of glial cytoplasmic inclusions (GCIs) in oligodendrocytes that are comprised of α-synuclein (αSyn) aberrantly polymerized into fibrils. Experimentally, MSA brain samples display a high level of seeding activity to induce further αSyn aggregation by a prion-like conformational mechanism. Paradoxically, αSyn is predominantly a neuronal brain protein, with only marginal levels expressed in normal or diseased oligodendrocytes, and αSyn inclusions in other neurodegenerative diseases, including Parkinson’s disease and Dementia with Lewy bodies, are primarily found in neurons. Although GCIs are the hallmark of MSA, using a series of new monoclonal antibodies targeting the carboxy-terminal region of αSyn, we demonstrate that neuronal αSyn pathology in MSA patient brains is remarkably abundant in the pontine nuclei and medullary inferior olivary nucleus. This neuronal αSyn pathology has distinct histological properties compared to GCIs, which allows it to remain concealed to many routine detection methods associated with altered biochemical properties of the carboxy-terminal domain of αSyn. We propose that these previously underappreciated sources of aberrant αSyn could serve as a pool of αSyn prion seeds that can initiate and continue to drive the pathogenesis of MSA.

scholarly journals Evidence for Inhibition of Topoisomerase 1A by Gold(III) Macrocycles and Chelates TargetingMycobacterium tuberculosisandMycobacterium abscessus

2018 ◽  
Vol 62 (5) ◽  
Author(s):  
Rashmi Gupta ◽  
Carolina Rodrigues Felix ◽  
Matthew P. Akerman ◽  
Kate J. Akerman ◽  
Cathryn A. Slabber ◽  
...  
Keyword(s):  
Mycobacterium Abscessus ◽  
Cross Resistance ◽  
Human Pathogens ◽  
Intrinsic Resistance ◽  
Content Type ◽  
Starting Point ◽  
Scalable Synthesis ◽  
High Level ◽  
Novel Drug

ABSTRACTMycobacterium tuberculosisand the fast-growing speciesMycobacterium abscessusare two important human pathogens causing persistent pulmonary infections that are difficult to cure and require long treatment times. The emergence of drug-resistantM. tuberculosisstrains and the high level of intrinsic resistance ofM. abscessuscall for novel drug scaffolds that effectively target both pathogens. In this study, we evaluated the activity of bis(pyrrolide-imine) gold(III) macrocycles and chelates, originally designed as DNA intercalators capable of targeting human topoisomerase types I and II (Topo1 and Topo2), againstM. abscessusandM. tuberculosis. We identified a total of 5 noncytotoxic compounds active against both mycobacterial pathogens under replicatingin vitroconditions. We chose one of these hits, compound 14, for detailed analysis due to its potent bactericidal mode of inhibition and scalable synthesis. The clinical relevance of this compound was demonstrated by its ability to inhibit a panel of diverseM. tuberculosisandM. abscessusclinical isolates. Prompted by previous data suggesting that compound 14 may target topoisomerase/gyrase enzymes, we demonstrated that it lacked cross-resistance with fluoroquinolones, which target theM. tuberculosisgyrase.In vitroenzyme assays confirmed the potent activity of compound 14 against bacterial topoisomerase 1A (Topo1) enzymes but not gyrase. Novel scaffolds like compound 14 with potent, selective bactericidal activity againstM. tuberculosisandM. abscessusthat act on validated but underexploited targets like Topo1 represent a promising starting point for the development of novel therapeutics for infections by pathogenic mycobacteria.

scholarly journals JEWELRY IN CELUK: ITS TRENDS, DEVELOPMENT, AND IMPLICATIONS FOR THE VILLAGE ARTISANS

2018 ◽  
Vol 2 (1) ◽  
pp. 70
Author(s):  
I Ketut Sida Arsa ◽  
Ni Made Ary Widiastini
Keyword(s):  
Production Management ◽  
Casting Machine ◽  
Ethnographic Study ◽  
Positive Contribution ◽  
Low Level ◽  
The People ◽  
Human Labor ◽  
Method Of Production ◽  
High Level ◽  
The Village

This study was aimed at explaining jewelry production, its development and implications of the developing trends. This study was conducted in Celuk Village, Gianyar Regency, a place or arena of production, distribution and at the same time sale of jewelry in Bali, Indonesia, in which Celuk is regarded as the basis for jewelry. This paper explains the development of jewelry at the beginning of the emergence of tourism and the implications, and the introduction of casting machine as the method of production which had an implication in the change of human labor, in which the artisans became machine power regarded as more professional in jewelry production. The data of this ethnographic study were collected through observation, in-depth interview, library research, and internet search. The finding showed that the presence of jewelry that is developing in Celuk Village does not give an optimal positive contribution to the community of the village as artisans, but in stead, it gives profits to the people outside the village who are involved in the development of the jewelry trends. The entrance of tourism with the implication on the high level of jewelry production and sale in Celuk Village started from 1980s gave profits to tour guides who were regarded as the ones who deserve to get fee in a large amount by the artisans. When there was a trend in jewelry in 2010-2014, in which the demand for jewelry like accessories for kebaya cloth for going to the temple and a ring with gemstone drove away the artisans whose position had been replaced by casting machines and workers who came from outside of Celuk Village who were regarded more professional by jewelry business people in producing standard jewelry in a large quantity. In this paper it is understood that artisans in Celuk Village are not able to obtain an optimal use from jewelry trends that develop in their location due to various factors such as the low level of education of the artisans, low level of profesionalism in working, and the low level of ability of the artisans in production management

scholarly journals Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain

2022 ◽  
Vol 15 ◽  
Author(s):  
Kyra T. Newmaster ◽  
Fae A. Kronman ◽  
Yuan-ting Wu ◽  
Yongsoo Kim
Keyword(s):  
Data Analysis ◽  
Mouse Brain ◽  
Neuronal Cell ◽  
Cell Types ◽  
Developmental Time ◽  
Cell Type ◽  
Level Data ◽  
Primary Model ◽  
Resolution Mapping ◽  
High Level

The brain is composed of diverse neuronal and non-neuronal cell types with complex regional connectivity patterns that create the anatomical infrastructure underlying cognition. Remarkable advances in neuroscience techniques enable labeling and imaging of these individual cell types and their interactions throughout intact mammalian brains at a cellular resolution allowing neuroscientists to examine microscopic details in macroscopic brain circuits. Nevertheless, implementing these tools is fraught with many technical and analytical challenges with a need for high-level data analysis. Here we review key technical considerations for implementing a brain mapping pipeline using the mouse brain as a primary model system. Specifically, we provide practical details for choosing methods including cell type specific labeling, sample preparation (e.g., tissue clearing), microscopy modalities, image processing, and data analysis (e.g., image registration to standard atlases). We also highlight the need to develop better 3D atlases with standardized anatomical labels and nomenclature across species and developmental time points to extend the mapping to other species including humans and to facilitate data sharing, confederation, and integrative analysis. In summary, this review provides key elements and currently available resources to consider while developing and implementing high-resolution mapping methods.

scholarly journals Den glatte musikken og muligheten for en erfaring

2020 ◽  
pp. 79-94
Author(s):  
Bendik Fredriksen
Keyword(s):  
Work Of Art ◽  
Negative Term ◽  
Starting Point ◽  
Physical Objects ◽  
High Level

A word often used to describe music is “smooth”. It is mostly meant as a negative term, used to label music as commercial, light, superficial and easily forgotten. However, smooth music is also well-made, with a high level of professionality. In this chapter I take as a starting point the criticism of beauty as smoothness found in Byung-Chul Han’s book Die Errettung des Schönen [Saving beauty], and investigate how this criticism applies to music. Furthermore, I try to define what makes music smooth. While smoothness can easily be defined when speaking about physical objects, music is evasive. Hence, smoothness is defined metaphorically, and according to what it is not, e.g. a work of art, or something that can lead to an experience, a concept I discuss in light of Gadamer, Heidegger, Adorno and Vetlesen. I claim that due to the elusive character of music almost any music can lead to an experience, but it is not a product of the subject’s efforts alone. Moreover, smoothness as a characteristic of music seems to have a liminal quality to it, as it cannot be defined in light of its opposite, but is trapped in its own perfection.

scholarly journals DENSE 3D OBJECT RECONSTRUCTION USING STRUCTURED-LIGHT SCANNER AND DEEP LEARNING

2020 ◽  
Vol XLIII-B2-2020 ◽  
pp. 777-783
Author(s):  
V. V. Kniaz ◽  
V. A. Mizginov ◽  
L. V. Grodzitkiy ◽  
N. A. Fomin ◽  
V. A. Knyaz
Keyword(s):  
Optical Flow ◽  
3D Model ◽  
Stereo Matching ◽  
Structured Light ◽  
Primary Source ◽  
Ground Truth ◽  
Complex Surface ◽  
Systems Model ◽  
Structured Light Scanner ◽  
Starting Point

Abstract. Structured light scanners are intensively exploited in various applications such as non-destructive quality control at an assembly line, optical metrology, and cultural heritage documentation. While more than 20 companies develop commercially available structured light scanners, structured light technology accuracy has limitations for fast systems. Model surface discrepancies often present if the texture of the object has severe changes in brightness or reflective properties of its texture. The primary source of such discrepancies is errors in the stereo matching caused by complex surface texture. These errors result in ridge-like structures on the surface of the reconstructed 3D model. This paper is focused on the development of a deep neural network LineMatchGAN for error reduction in 3D models produced by a structured light scanner. We use the pix2pix model as a starting point for our research. The aim of our LineMatchGAN is a refinement of the rough optical flow A and generation of an error-free optical flow B̂. We collected a dataset (which we term ZebraScan) consisting of 500 samples to train our LineMatchGAN model. Each sample includes image sequences (Sl, Sr), ground-truth optical flow B and a ground-truth 3D model. We evaluate our LineMatchGAN on a test split of our ZebraScan dataset that includes 50 samples. The evaluation proves that our LineMatchGAN improves the stereo matching accuracy (optical flow end point error, EPE) from 0.05 pixels to 0.01 pixels.

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