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Neuroinformatics

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https://read.qxmd.com/read/30739281/inter-network-high-order-functional-connectivity-in-hofc-and-its-alteration-in-patients-with-mild-cognitive-impairment
#1
Han Zhang, Panteleimon Giannakopoulos, Sven Haller, Dinggang Shen, Seong-Whan Lee, Shijun Qiu
Little is known about the high-order interactions among brain regions measured by the similarity of higher-order features (other than the raw blood-oxygen-level-dependent signals) which can characterize higher-level brain functional connectivity (FC). Previously, we proposed FC topographical profile-based high-order FC (HOFC) and found that this metric could provide supplementary information to traditional FC for early Alzheimer's disease (AD) detection. However, whether such findings apply to network-level brain functional integration is unknown...
February 9, 2019: Neuroinformatics
https://read.qxmd.com/read/30649677/handling-multiplicity-in-neuroimaging-through-bayesian-lenses-with-multilevel-modeling
#2
Gang Chen, Yaqiong Xiao, Paul A Taylor, Justin K Rajendra, Tracy Riggins, Fengji Geng, Elizabeth Redcay, Robert W Cox
Here we address the current issues of inefficiency and over-penalization in the massively univariate approach followed by the correction for multiple testing, and propose a more efficient model that pools and shares information among brain regions. Using Bayesian multilevel (BML) modeling, we control two types of error that are more relevant than the conventional false positive rate (FPR): incorrect sign (type S) and incorrect magnitude (type M). BML also aims to achieve two goals: 1) improving modeling efficiency by having one integrative model and thereby dissolving the multiple testing issue, and 2) turning the focus of conventional null hypothesis significant testing (NHST) on FPR into quality control by calibrating type S errors while maintaining a reasonable level of inference efficiency...
January 16, 2019: Neuroinformatics
https://read.qxmd.com/read/30635864/identifying-weak-signals-in-inhomogeneous-neuronal-images-for-large-scale-tracing-of-sparsely-distributed-neurites
#3
Shiwei Li, Tingwei Quan, Hang Zhou, FangFang Yin, Anan Li, Ling Fu, Qingming Luo, Hui Gong, Shaoqun Zeng
Tracing neurites constitutes the core of neuronal morphology reconstruction, a key step toward neuronal circuit mapping. Modern optical-imaging techniques allow observation of nearly complete mouse neuron morphologies across brain regions or even the whole brain. However, high-level automation reconstruction of neurons, i.e., the reconstruction with a few of manual edits requires discrimination of weak foreground points from the inhomogeneous background. We constructed an identification model, where empirical observations made from neuronal images were summarized into rules for designing feature vectors that to classify foreground and background, and a support vector machine (SVM) was used to learn these feature vectors...
January 11, 2019: Neuroinformatics
https://read.qxmd.com/read/30617757/what-is-old-is-new-again-investigating-and-analyzing-the-mysteries-of-the-claustrum
#4
EDITORIAL
John Darrell Van Horn
No abstract text is available yet for this article.
January 7, 2019: Neuroinformatics
https://read.qxmd.com/read/30604083/stochastic-rank-aggregation-for-the-identification-of-functional-neuromarkers
#5
Paola Galdi, Michele Fratello, Francesca Trojsi, Antonio Russo, Gioacchino Tedeschi, Roberto Tagliaferri, Fabrizio Esposito
The main challenge in analysing functional magnetic resonance imaging (fMRI) data from extended samples of subject (N > 100) is to extract as much relevant information as possible from big amounts of noisy data. When studying neurodegenerative diseases with resting-state fMRI, one of the objectives is to determine regions with abnormal background activity with respect to a healthy brain and this is often attained with comparative statistical models applied to single voxels or brain parcels within one or several functional networks...
January 2, 2019: Neuroinformatics
https://read.qxmd.com/read/30565026/small-animal-multivariate-brain-analysis-samba-a-high-throughput-pipeline-with-a-validation-framework
#6
Robert J Anderson, James J Cook, Natalie Delpratt, John C Nouls, Bin Gu, James O McNamara, Brian B Avants, G Allan Johnson, Alexandra Badea
While many neuroscience questions aim to understand the human brain, much current knowledge has been gained using animal models, which replicate genetic, structural, and connectivity aspects of the human brain. While voxel-based analysis (VBA) of preclinical magnetic resonance images is widely-used, a thorough examination of the statistical robustness, stability, and error rates is hindered by high computational demands of processing large arrays, and the many parameters involved therein. Thus, workflows are often based on intuition or experience, while preclinical validation studies remain scarce...
December 19, 2018: Neuroinformatics
https://read.qxmd.com/read/30552549/automatic-thalamus-segmentation-on-unenhanced-3d-t1-weighted-images-comparison-of-publicly-available-segmentation-methods-in-a-pediatric-population
#7
Salem Hannoun, Rayyan Tutunji, Maria El Homsi, Stephanie Saaybi, Roula Hourani
The anatomical structure of the thalamus renders its segmentation on 3DT1 images harder due to its low tissue contrast, and not well-defined boundaries. We aimed to investigate the differences in the precision of publicly available segmentation techniques on 3DT1 images acquired at 1.5 T and 3 T machines compared to the thalamic manual segmentation in a pediatric population. Sixty-eight subjects were recruited between the ages of one and 18 years. Manual segmentation of the thalamus was done by three junior raters, and then corrected by an experienced rater...
December 14, 2018: Neuroinformatics
https://read.qxmd.com/read/30542954/automated-neuron-reconstruction-from-3d-fluorescence-microscopy-images-using-sequential-monte-carlo-estimation
#8
Miroslav Radojević, Erik Meijering
Microscopic images of neuronal cells provide essential structural information about the key constituents of the brain and form the basis of many neuroscientific studies. Computational analyses of the morphological properties of the captured neurons require first converting the structural information into digital tree-like reconstructions. Many dedicated computational methods and corresponding software tools have been and are continuously being developed with the aim to automate this step while achieving human-comparable reconstruction accuracy...
December 12, 2018: Neuroinformatics
https://read.qxmd.com/read/30460455/model-based-and-model-free-techniques-for-amyotrophic-lateral-sclerosis-diagnostic-prediction-and-patient-clustering
#9
Ming Tang, Chao Gao, Stephen A Goutman, Alexandr Kalinin, Bhramar Mukherjee, Yuanfang Guan, Ivo D Dinov
Amyotrophic lateral sclerosis (ALS) is a complex progressive neurodegenerative disorder with an estimated prevalence of about 5 per 100,000 people in the United States. In this study, the ALS disease progression is measured by the change of Amyotrophic Lateral Sclerosis Functional Rating Scale (ALSFRS) score over time. The study aims to provide clinical decision support for timely forecasting of the ALS trajectory as well as accurate and reproducible computable phenotypic clustering of participants. Patient data are extracted from DREAM-Phil Bowen ALS Prediction Prize4Life Challenge data, most of which are from the Pooled Resource Open-Access ALS Clinical Trials Database (PRO-ACT) archive...
November 20, 2018: Neuroinformatics
https://read.qxmd.com/read/30443819/a-text-mining-pipeline-using-active-and-deep-learning-aimed-at-curating-information-in-computational-neuroscience
#10
Matthew Shardlow, Meizhi Ju, Maolin Li, Christian O'Reilly, Elisabetta Iavarone, John McNaught, Sophia Ananiadou
The curation of neuroscience entities is crucial to ongoing efforts in neuroinformatics and computational neuroscience, such as those being deployed in the context of continuing large-scale brain modelling projects. However, manually sifting through thousands of articles for new information about modelled entities is a painstaking and low-reward task. Text mining can be used to help a curator extract relevant information from this literature in a systematic way. We propose the application of text mining methods for the neuroscience literature...
November 15, 2018: Neuroinformatics
https://read.qxmd.com/read/30406865/an-end-to-end-system-for-automatic-characterization-of-iba1-immunopositive-microglia-in-whole-slide-imaging
#11
Alexander D Kyriazis, Shahriar Noroozizadeh, Amir Refaee, Woongcheol Choi, Lap-Tak Chu, Asma Bashir, Wai Hang Cheng, Rachel Zhao, Dhananjay R Namjoshi, Septimiu E Salcudean, Cheryl L Wellington, Guy Nir
Traumatic brain injury (TBI) is one of the leading causes of death and disability worldwide. Detailed studies of the microglial response after TBI require high throughput quantification of changes in microglial count and morphology in histological sections throughout the brain. In this paper, we present a fully automated end-to-end system that is capable of assessing microglial activation in white matter regions on whole slide images of Iba1 stained sections. Our approach involves the division of the full brain slides into smaller image patches that are subsequently automatically classified into white and grey matter sections...
November 8, 2018: Neuroinformatics
https://read.qxmd.com/read/30382537/automated-metadata-suggestion-during-repository-submission
#12
Robert A McDougal, Isha Dalal, Thomas M Morse, Gordon M Shepherd
Knowledge discovery via an informatics resource is constrained by the completeness of the resource, both in terms of the amount of data it contains and in terms of the metadata that exists to describe the data. Increasing completeness in one of these categories risks reducing completeness in the other because manually curating metadata is time consuming and is restricted by familiarity with both the data and the metadata annotation scheme. The diverse interests of a research community may drive a resource to have hundreds of metadata tags with few examples for each making it challenging for humans or machine learning algorithms to learn how to assign metadata tags properly...
October 31, 2018: Neuroinformatics
https://read.qxmd.com/read/30368637/eeg-eog-based-virtual-keyboard-toward-hybrid-brain-computer-interface
#13
REVIEW
Sarah M Hosni, Howida A Shedeed, Mai S Mabrouk, Mohamed F Tolba
The past twenty years have ignited a new spark in the research of Electroencephalogram (EEG), which was pursued to develop innovative Brain Computer Interfaces (BCIs) in order to help severely disabled people live a better life with a high degree of independence. Current BCIs are more theoretical than practical and are suffering from numerous challenges. New trends of research propose combining EEG to other simple and efficient bioelectric inputs such as Electro-oculography (EOG) resulting from eye movements, to produce more practical and robust Hybrid Brain Computer Interface systems (hBCI) or Brain/Neuronal Computer Interface (BNCI)...
October 27, 2018: Neuroinformatics
https://read.qxmd.com/read/30357708/cocaine-induced-preference-conditioning-a-machine-vision-perspective
#14
V Javier Traver, Filiberto Pla, Marta Miquel, Maria Carbo-Gas, Isis Gil-Miravet, Julian Guarque-Chabrera
Existing work on drug-induced synaptic changes has shown that the expression of perineuronal nets (PNNs) at the cerebellar cortex can be regulated by cocaine-related memory. However, these studies on animals have mostly relied on limited manually-driven procedures, and lack some more rigorous statistical approaches and more automated techniques. In this work, established methods from computer vision and machine learning are considered to build stronger evidence of those previous findings. To that end, an image descriptor is designed to characterize PNNs images; unsupervised learning (clustering) is used to automatically find distinctive patterns of PNNs; and supervised learning (classification) is adopted for predicting the experiment group of the mice from their PNN images...
October 24, 2018: Neuroinformatics
https://read.qxmd.com/read/30328551/the-residual-center-of-mass-an-image-descriptor-for-the-diagnosis-of-alzheimer-disease
#15
Alexandre Yukio Yamashita, Alexandre Xavier Falcão, Neucimar Jerônimo Leite
A crucial quest in neuroimaging is the discovery of image features (biomarkers) associated with neurodegenerative disorders. Recent works show that such biomarkers can be obtained by image analysis techniques. However, these techniques cannot be directly compared since they use different databases and validation protocols. In this paper, we present an extensive study of image descriptors for the diagnosis of Alzheimer Disease (AD) and introduce a new one, named Residual Center of Mass (RCM). The RCM descriptor explores image moments and other techniques to enhance brain regions and select discriminative features for the diagnosis of AD...
October 17, 2018: Neuroinformatics
https://read.qxmd.com/read/30291569/rhesus-macaque-brain-atlas-regions-aligned-to-an-mri-template
#16
Jeffrey M Moirano, Gleb Y Bezgin, Elizabeth O Ahlers, Rolf Kötter, Alexander K Converse
To aid in the analysis of rhesus macaque brain images, we aligned digitized anatomical regions from the widely used atlas of Paxinos et al. to a published magnetic resonance imaging (MRI) template based on a large number of subjects. Digitally labelled atlas images were aligned to the template in 2D and then in 3D. The resulting grey matter regions appear qualitatively to be well registered to the template. To quantitatively validate the procedure, MR brain images of 20 rhesus macaques were aligned to the template along with regions drawn by hand in striatal and cortical areas in each subject's MRI...
October 5, 2018: Neuroinformatics
https://read.qxmd.com/read/30284672/fused-group-lasso-regularized-multi-task-feature-learning-and-its-application-to-the-cognitive-performance-prediction-of-alzheimer-s-disease
#17
Xiaoli Liu, Peng Cao, Jianzhong Wang, Jun Kong, Dazhe Zhao
Alzheimer's disease (AD) is characterized by gradual neurodegeneration and loss of brain function, especially for memory during early stages. Regression analysis has been widely applied to AD research to relate clinical and biomarker data such as predicting cognitive outcomes from MRI measures. Recently, multi-task based feature learning (MTFL) methods with sparsity-inducing [Formula: see text]-norm have been widely studied to select a discriminative feature subset from MRI features by incorporating inherent correlations among multiple clinical cognitive measures...
October 4, 2018: Neuroinformatics
https://read.qxmd.com/read/30022314/special-issue-on-high-performance-computing-in-bio-medical-informatics
#18
EDITORIAL
Luping Zhou, Islem Rekik, Chenggang Yan, Guorong Wu
No abstract text is available yet for this article.
October 2018: Neuroinformatics
https://read.qxmd.com/read/29948843/predict-mirna-disease-association-with-collaborative-filtering
#19
Yatong Jiang, Bingtao Liu, Linghui Yu, Chenggang Yan, Hujun Bian
The era of human brain science research is dawning. Researchers utilize the various multi-disciplinary knowledge to explore the human brain,such as physiology and bioinformatics. The emerging disease association prediction technology can speed up the study of diseases, so as to better understanding the structure and function of human body. There are increasing evidences that miRNA plays a significant role in nervous system development, adult function, plasticity, and vulnerability to neurological disease states...
October 2018: Neuroinformatics
https://read.qxmd.com/read/29907892/a-robust-reduced-rank-graph-regression-method-for-neuroimaging-genetic-analysis
#20
Xiaofeng Zhu, Weihong Zhang, Yong Fan
To characterize associations between genetic and neuroimaging data, a variety of analytic methods have been proposed in neuroimaging genetic studies. These methods have achieved promising performance by taking into account inherent correlation in either the neuroimaging data or the genetic data alone. In this study, we propose a novel robust reduced rank graph regression based method in a linear regression framework by considering correlations inherent in neuroimaging data and genetic data jointly. Particularly, we model the association analysis problem in a reduced rank regression framework with the genetic data as a feature matrix and the neuroimaging data as a response matrix by jointly considering correlations among the neuroimaging data as well as correlations between the genetic data and the neuroimaging data...
October 2018: Neuroinformatics
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