scholarly journals Can fMRI functional connectivity index dynamic neural communication?

2021 ◽  
Author(s):  
Sonsoles Alonso Martinez ◽  
Alberto Llera Arenas ◽  
Gert T Ter Horst ◽  
Diego Vidaurre
Keyword(s):  
Functional Connectivity ◽  
Large Scale ◽  
Necessary Conditions ◽  
Principal Component ◽  
Temporal Complexity ◽  
Neural Communication ◽  
Connectivity Model ◽  
Neural Populations ◽  
Changing Patterns ◽  
Brain Fmri

In order to continuously respond to a changing environment and support self-generating cognition and behaviour, neural communication must be highly flexible and dynamic at the same time than hierarchically organized. While whole-brain fMRI measures have revealed robust yet changing patterns of statistical dependencies between regions, it is not clear whether these statistical patterns (referred to as functional connectivity) can reflect dynamic large-scale communication in a way that is relevant to cognition. For functional connectivity to reflect actual communication, we propose three necessary conditions: it must span sufficient temporal complexity to support the needs of cognition while still being highly organized so that the system behaves reliably; it must be able to adapt to the current behavioural context; and it must exhibit fluctuations at sufficiently short timescales. In this paper, we introduce principal components of connectivity analysis (PCCA), an approach based on running principal component analysis on multiple runs of a time-varying functional connectivity model to show that functional connectivity follows low- yet multi-dimensional trajectories that can be reliably measured, and that these trajectories meet the aforementioned criteria to index flexible communication between neural populations and support moment-to-moment cognition.

scholarly journals Identifying optimal working points of individual Virtual Brains: A large-scale brain network modelling study

2020 ◽  
Author(s):  
Paul Triebkorn ◽  
Joelle Zimmermann ◽  
Leon Stefanovski ◽  
Dipanjan Roy ◽  
Ana Solodkin ◽  
...  
Keyword(s):  
Functional Connectivity ◽  
Brain Function ◽  
Large Scale ◽  
Brain Activity ◽  
Brain Network ◽  
Model Parameters ◽  
Network Modelling ◽  
Neural Populations ◽  
Global Coupling ◽  
The Brain

AbstractUsing The Virtual Brain (TVB, thevirtualbrian.org) simulation platform, we explored for 50 individual adult human brains (ages 18-80), how personalized connectome based brain network modelling captures various empirical observations as measured by functional magnetic resonance imaging (fMRI) and electroencephalography (EEG). We compare simulated activity based on individual structural connectomes (SC) inferred from diffusion weighted imaging with fMRI and EEG in the resting state. We systematically explore the role of the following model parameters: conduction velocity, global coupling and graph theoretical features of individual SC. First, a subspace of the parameter space is identified for each subject that results in realistic brain activity, i.e. reproducing the following prominent features of empirical EEG-fMRI activity: topology of resting-state fMRI functional connectivity (FC), functional connectivity dynamics (FCD), electrophysiological oscillations in the delta (3-4 Hz) and alpha (8-12 Hz) frequency range and their bimodality, i.e. low and high energy modes. Interestingly, FCD fit, bimodality and static FC fit are highly correlated. They all show their optimum in the same range of global coupling. In other words, only when our local model is in a bistable regime we are able to generate switching of modes in our global network. Second, our simulations reveal the explicit network mechanisms that lead to electrophysiological oscillations, their bimodal behaviour and inter-regional differences. Third, we discuss biological interpretability of the Stefanescu-Jirsa-Hindmarsh-Rose-3D model when embedded inside the large-scale brain network and mechanisms underlying the emergence of bimodality of the neural signal.With the present study, we set the cornerstone for a systematic catalogue of spatiotemporal brain activity regimes generated with the connectome-based brain simulation platform The Virtual Brain.Author SummaryIn order to understand brain dynamics we use numerical simulations of brain network models. Combining the structural backbone of the brain, that is the white matter fibres connecting distinct regions in the grey matter, with dynamical systems describing the activity of neural populations we are able to simulate brain function on a large scale. In order to make accurate prediction with this network, it is crucial to determine optimal model parameters. We here use an explorative approach to adjust model parameters to individual brain activity, showing that subjects have their own optimal point in the parameter space, depending on their brain structure and function. At the same time, we investigate the relation between bistable phenomena on the scale of neural populations and the changed in functional connectivity on the brain network scale. Our results are important for future modelling approaches trying to make accurate predictions of brain function.

scholarly journals Dynamic changes in large-scale functional connectivity predict performance in a multisensory task

2019 ◽  
Author(s):  
Karl J. Hollensteiner ◽  
Edgar Galindo-Leon ◽  
Florian Pieper ◽  
Gerhard Engler ◽  
Guido Nolte ◽  
...  
Keyword(s):  
Functional Connectivity ◽  
Long Range ◽  
Large Scale ◽  
Principal Component ◽  
Stimulus Onset ◽  
Functional Coupling ◽  
Phase Coupling ◽  
Network State ◽  
Task Period ◽  
Response Onset

AbstractComplex and variable behavior requires fast changes of functional connectivity in large-scale cortical networks. Here, we report on the cortical dynamics of functional coupling across visual, auditory and parietal areas during a lateralized detection task in the ferret. We hypothesized that fluctuations in coupling, indicative of dynamic variations in the network state, might predict the animals’ performance. While power for hit and miss trials showed significant differences only around stimulus and response onset, phase coupling already differed before stimulus onset. Principal component analysis of directed coupling at the single-trial level during this period revealed subnetworks that most strongly related to behavior. While higher global phase coupling of visual and auditory regions to parietal cortex was predictive of task performance, a second component showed that a reduction in coupling between subnetworks of sensory modalities was also necessary, probably to allow a better detection of the unimodal signals. Furthermore, we observed that long-range coupling became more predominant during the task period compared to the pre-stimulus baseline. Taken together, these results suggest that fluctuations in the network state, particular with respect to long-range connectivity, are key determinants of the animals’ behavior.

scholarly journals Content-Based Estimation of Brain MRI Tilt in Three Orthogonal Directions

2021 ◽  
Author(s):  
Pooja Prabhu ◽  
A. K. Karunakar ◽  
Sanjib Sinha ◽  
N. Mariyappa ◽  
G. K. Bhargava ◽  
...  
Keyword(s):  
Large Scale ◽  
Brain Mri ◽  
Similarity Measures ◽  
Principal Component ◽  
Brain Anatomy ◽  
Morphological Operations ◽  
Mr Images ◽  
Tilt Correction ◽  
Brain Mr Images ◽  
The Brain

AbstractIn a general scenario, the brain images acquired from magnetic resonance imaging (MRI) may experience tilt, distorting brain MR images. The tilt experienced by the brain MR images may result in misalignment during image registration for medical applications. Manually correcting (or estimating) the tilt on a large scale is time-consuming, expensive, and needs brain anatomy expertise. Thus, there is a need for an automatic way of performing tilt correction in three orthogonal directions (X, Y, Z). The proposed work aims to correct the tilt automatically by measuring the pitch angle, yaw angle, and roll angle in X-axis, Z-axis, and Y-axis, respectively. For correction of the tilt around the Z-axis (pointing to the superior direction), image processing techniques, principal component analysis, and similarity measures are used. Also, for correction of the tilt around the X-axis (pointing to the right direction), morphological operations, and tilt correction around the Y-axis (pointing to the anterior direction), orthogonal regression is used. The proposed approach was applied to adjust the tilt observed in the T1- and T2-weighted MR images. The simulation study with the proposed algorithm yielded an error of 0.40 ± 0.09°, and it outperformed the other existing studies. The tilt angle (in degrees) obtained is ranged from 6.2 ± 3.94, 2.35 ± 2.61, and 5 ± 4.36 in X-, Z-, and Y-directions, respectively, by using the proposed algorithm. The proposed work corrects the tilt more accurately and robustly when compared with existing studies.

scholarly journals Principal component analysis tomography in near-infrared integral field spectroscopy of young stellar objects – I. Revisiting the high-mass protostar W33A

2021 ◽  
Vol 503 (1) ◽  
pp. 270-291
Author(s):  
F Navarete ◽  
A Damineli ◽  
J E Steiner ◽  
R D Blum
Keyword(s):  
Large Scale ◽  
Near Infrared ◽  
Rotation Axis ◽  
Principal Component ◽  
Young Stellar Objects ◽  
High Mass ◽  
Continuum Emission ◽  
Rotating Disc ◽  
Stellar Objects ◽  
K Band

ABSTRACT W33A is a well-known example of a high-mass young stellar object showing evidence of a circumstellar disc. We revisited the K-band NIFS/Gemini North observations of the W33A protostar using principal components analysis tomography and additional post-processing routines. Our results indicate the presence of a compact rotating disc based on the kinematics of the CO absorption features. The position–velocity diagram shows that the disc exhibits a rotation curve with velocities that rapidly decrease for radii larger than 0.1 arcsec (∼250 au) from the central source, suggesting a structure about four times more compact than previously reported. We derived a dynamical mass of 10.0$^{+4.1}_{-2.2}$ $\rm {M}_\odot$ for the ‘disc + protostar’ system, about ∼33 per cent smaller than previously reported, but still compatible with high-mass protostar status. A relatively compact H2 wind was identified at the base of the large-scale outflow of W33A, with a mean visual extinction of ∼63 mag. By taking advantage of supplementary near-infrared maps, we identified at least two other point-like objects driving extended structures in the vicinity of W33A, suggesting that multiple active protostars are located within the cloud. The closest object (Source B) was also identified in the NIFS field of view as a faint point-like object at a projected distance of ∼7000 au from W33A, powering extended K-band continuum emission detected in the same field. Another source (Source C) is driving a bipolar $\rm {H}_2$ jet aligned perpendicular to the rotation axis of W33A.

scholarly journals Farmers’ Perceptions of Commercial Insect-Based Feed for Sustainable Livestock Production in Kenya

2021 ◽  
Vol 13 (10) ◽  
pp. 5359
Author(s):  
Afrika Onguko Okello ◽  
Jonathan Makau Nzuma ◽  
David Jakinda Otieno ◽  
Michael Kidoido ◽  
Chrysantus Mbi Tanga
Keyword(s):  
Food Systems ◽  
Large Scale ◽  
Principal Component ◽  
Farm Income ◽  
Purchase Decisions ◽  
Wealth Status ◽  
Feed Formulation ◽  
Alternative Protein ◽  
Livestock Products ◽  
The Impact

The utilization of insect-based feeds (IBF) as an alternative protein source is increasingly gaining momentum worldwide owing to recent concerns over the impact of food systems on the environment. However, its large-scale adoption will depend on farmers’ acceptance of its key qualities. This study evaluates farmer’s perceptions of commercial IBF products and assesses the factors that would influence its adoption. It employs principal component analysis (PCA) to develop perception indices that are subsequently used in multiple regression analysis of survey data collected from a sample of 310 farmers. Over 90% of the farmers were ready and willing to use IBF. The PCA identified feed performance, social acceptability of the use of insects in feed formulation, feed versatility and marketability of livestock products reared on IBF as the key attributes that would inform farmers’ purchase decisions. Awareness of IBF attributes, group membership, off-farm income, wealth status and education significantly influenced farmers’ perceptions of IBF. Interventions such as experimental demonstrations that increase farmers’ technical knowledge on the productivity of livestock fed on IBF are crucial to reducing farmers’ uncertainties towards acceptability of IBF. Public partnerships with resource-endowed farmers and farmer groups are recommended to improve knowledge sharing on IBF.

scholarly journals Large-Scale Precipitation Variability over Northwest China Inferred from Tree Rings

2011 ◽  
Vol 24 (13) ◽  
pp. 3457-3468 ◽  
Author(s):  
Keyan Fang ◽  
Xiaohua Gou ◽  
Fahu Chen ◽  
Edward Cook ◽  
Jinbao Li ◽  
...  
Keyword(s):  
Tree Ring ◽  
Large Scale ◽  
Principal Component ◽  
Northwest China ◽  
Poor Quality ◽  
Contour Method ◽  
Precipitation Reconstruction ◽  
Nw China ◽  
Climate Station ◽  
Instrumental Records

Abstract A preliminary study of a point-by-point spatial precipitation reconstruction for northwestern (NW) China is explored, based on a tree-ring network of 132 chronologies. Precipitation variations during the past ~200–400 yr (the common reconstruction period is from 1802 to 1990) are reconstructed for 26 stations in NW China from a nationwide 160-station dataset. The authors introduce a “search spatial correlation contour” method to locate candidate tree-ring predictors for the reconstruction data of a given climate station. Calibration and verification results indicate that most precipitation reconstruction models are acceptable, except for a few reconstructions (stations Hetian, Hami, Jiuquan, and Wuwei) with degraded quality. Additionally, the authors compare four spatial precipitation factors in the instrumental records and reconstructions derived from a rotated principal component analysis (RPCA). The northern and southern Xinjiang factors from the instrumental and reconstructed data agree well with each other. However, differences in spatial patterns between the instrumentation and reconstruction data are also found for the other two factors, which probably result from the relatively poor quality of a few stations. Major drought events documented in previous studies—for example, from the 1920s through the 1930s for the eastern part of NW China—are reconstructed in this study.

scholarly journals Codon usage bias and environmental adaptation in microbial organisms

2021 ◽  
Author(s):  
Davide Arella ◽  
Maddalena Dilucca ◽  
Andrea Giansanti
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Pathogenic Bacteria ◽  
Large Scale ◽  
Synonymous Codon ◽  
Principal Component ◽  
Gene Copy ◽  
Phenotypic Traits ◽  
Translational Efficiency ◽  
Microbial Organisms

AbstractIn each genome, synonymous codons are used with different frequencies; this general phenomenon is known as codon usage bias. It has been previously recognised that codon usage bias could affect the cellular fitness and might be associated with the ecology of microbial organisms. In this exploratory study, we investigated the relationship between codon usage bias, lifestyles (thermophiles vs. mesophiles; pathogenic vs. non-pathogenic; halophilic vs. non-halophilic; aerobic vs. anaerobic and facultative) and habitats (aquatic, terrestrial, host-associated, specialised, multiple) of 615 microbial organisms (544 bacteria and 71 archaea). Principal component analysis revealed that species with given phenotypic traits and living in similar environmental conditions have similar codon preferences, as represented by the relative synonymous codon usage (RSCU) index, and similar spectra of tRNA availability, as gauged by the tRNA gene copy number (tGCN). Moreover, by measuring the average tRNA adaptation index (tAI) for each genome, an index that can be associated with translational efficiency, we observed that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, are characterised by a reduced translational efficiency, consistently with their need to adapt to different environments. Our results show that synonymous codon choices might be under strong translational selection, which modulates the choice of the codons to differently match tRNA availability, depending on the organism’s lifestyle needs. To our knowledge, this is the first large-scale study that examines the role of codon bias and translational efficiency in the adaptation of microbial organisms to the environment in which they live.

scholarly journals Characterization of Pharmaceutical Tablets Using UV Hyperspectral Imaging as a Rapid Line to Line Analysis Tool

Sensors ◽  
2021 ◽  
Vol 21 (13) ◽  
pp. 4436
Author(s):  
Mohammad Al Ktash ◽  
Mona Stefanakis ◽  
Barbara Boldrini ◽  
Edwin Ostertag ◽  
Marc Brecht
Keyword(s):  
Hyperspectral Imaging ◽  
Large Scale ◽  
Solid Phase ◽  
Ultra Violet ◽  
Principal Component ◽  
Ccd Camera ◽  
Conveyor Belt ◽  
Hyperspectral Data ◽  
Analysis Tool ◽  
Sample Set

A laboratory prototype for hyperspectral imaging in ultra-violet (UV) region from 225 to 400 nm was developed and used to rapidly characterize active pharmaceutical ingredients (API) in tablets. The APIs are ibuprofen (IBU), acetylsalicylic acid (ASA) and paracetamol (PAR). Two sample sets were used for a comparison purpose. Sample set one comprises tablets of 100% API and sample set two consists of commercially available painkiller tablets. Reference measurements were performed on the pure APIs in liquid solutions (transmission) and in solid phase (reflection) using a commercial UV spectrometer. The spectroscopic part of the prototype is based on a pushbroom imager that contains a spectrograph and charge-coupled device (CCD) camera. The tablets were scanned on a conveyor belt that is positioned inside a tunnel made of polytetrafluoroethylene (PTFE) in order to increase the homogeneity of illumination at the sample position. Principal component analysis (PCA) was used to differentiate the hyperspectral data of the drug samples. The first two PCs are sufficient to completely separate all samples. The rugged design of the prototype opens new possibilities for further development of this technique towards real large-scale application.

scholarly journals Relationships between Southeast Australian Temperature Anomalies and Large-Scale Climate Drivers

2014 ◽  
Vol 27 (4) ◽  
pp. 1395-1412 ◽  
Author(s):  
Alexandre O. Fierro ◽  
Lance M. Leslie
Keyword(s):  
Large Scale ◽  
Southern Oscillation ◽  
Power Spectra ◽  
Warm Season ◽  
Principal Component ◽  
Temperature Variability ◽  
Maximum Temperature ◽  
Past Century ◽  
Tasman Sea ◽  
Australian Continent

Abstract Over the past century, particularly after the 1960s, observations of mean maximum temperatures reveal an increasing trend over the southeastern quadrant of the Australian continent. Correlation analysis of seasonally averaged mean maximum temperature anomaly data for the period 1958–2012 is carried out for a representative group of 10 stations in southeast Australia (SEAUS). For the warm season (November–April) there is a positive relationship with the El Niño–Southern Oscillation (ENSO) and the Pacific decadal oscillation (PDO) and an inverse relationship with the Antarctic Oscillation (AAO) for most stations. For the cool season (May–October), most stations exhibit similar relationships with the AAO, positive correlations with the dipole mode index (DMI), and marginal inverse relationships with the Southern Oscillation index (SOI) and the PDO. However, for both seasons, the blocking index (BI, as defined by M. Pook and T. Gibson) in the Tasman Sea (160°E) clearly is the dominant climate mode affecting maximum temperature variability in SEAUS with negative correlations in the range from r = −0.30 to −0.65. These strong negative correlations arise from the usual definition of BI, which is positive when blocking high pressure systems occur over the Tasman Sea (near 45°S, 160°E), favoring the advection of modified cooler, higher-latitude maritime air over SEAUS. A point-by-point correlation with global sea surface temperatures (SSTs), principal component analysis, and wavelet power spectra support the relationships with ENSO and DMI. Notably, the analysis reveals that the maximum temperature variability of one group of stations is explained primarily by local factors (warmer near-coastal SSTs), rather than teleconnections with large-scale drivers.

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