scholarly journals Differences in subcortico-cortical interactions identified from connectome and microcircuit models in autism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Bo-yong Park ◽  
Seok-Jun Hong ◽  
Sofie L. Valk ◽  
Casey Paquola ◽  
Oualid Benkarim ◽  
...  
Keyword(s):  
Data Exchange ◽  
Computational Models ◽  
Simulation Models ◽  
Autism Diagnostic Observation Schedule ◽  
Supervised Machine Learning ◽  
Global Network ◽  
Imaging Data ◽  
Phenotypic Data ◽  
Severity Scores ◽  
High Level

AbstractThe pathophysiology of autism has been suggested to involve a combination of both macroscale connectome miswiring and microcircuit anomalies. Here, we combine connectome-wide manifold learning with biophysical simulation models to understand associations between global network perturbations and microcircuit dysfunctions in autism. We studied neuroimaging and phenotypic data in 47 individuals with autism and 37 typically developing controls obtained from the Autism Brain Imaging Data Exchange initiative. Our analysis establishes significant differences in structural connectome organization in individuals with autism relative to controls, with strong between-group effects in low-level somatosensory regions and moderate effects in high-level association cortices. Computational models reveal that the degree of macroscale anomalies is related to atypical increases of recurrent excitation/inhibition, as well as subcortical inputs into cortical microcircuits, especially in sensory and motor areas. Transcriptomic association analysis based on postmortem datasets identifies genes expressed in cortical and thalamic areas from childhood to young adulthood. Finally, supervised machine learning finds that the macroscale perturbations are associated with symptom severity scores on the Autism Diagnostic Observation Schedule. Together, our analyses suggest that atypical subcortico-cortical interactions are associated with both microcircuit and macroscale connectome differences in autism.

scholarly journals Connectome and microcircuit models implicate atypical subcortico-cortical interactions in autism pathophysiology

2020 ◽  
Author(s):  
Bo-yong Park ◽  
Seok-Jun Hong ◽  
Sofie Valk ◽  
Casey Paquola ◽  
Oualid Benkarim ◽  
...  
Keyword(s):  
Computational Models ◽  
Simulation Models ◽  
Repetitive Behaviors ◽  
Supervised Machine Learning ◽  
Global Network ◽  
Childhood And Adolescence ◽  
Developmental Gene ◽  
Gene Enrichment ◽  
High Level ◽  
Biological Context

AbstractBoth macroscale connectome miswiring and microcircuit anomalies have been suggested to play a role in the pathophysiology of autism. However, an overarching framework that consolidates these macro and microscale perspectives of the condition is lacking. Here, we combined connectome-wide manifold learning and biophysical simulation models to understand associations between global network perturbations and microcircuit dysfunctions in autism. Our analysis established that autism showed significant differences in structural connectome organization relative to neurotypical controls, with strong effects in low-level somatosensory regions and moderate effects in high-level association cortices. Computational models revealed that the degree of macroscale anomalies was related to atypical increases of subcortical inputs into cortical microcircuits, especially in sensory and motor areas. Transcriptomic decoding and developmental gene enrichment analyses provided biological context and pointed to genes expressed in cortical and thalamic areas during childhood and adolescence. Supervised machine learning showed the macroscale perturbations predicted socio-cognitive symptoms and repetitive behaviors. Our analyses provide convergent support that atypical subcortico-cortical interactions may contribute to both microcircuit and macroscale connectome anomalies in autism.

scholarly journals Examination of Local Functional Homogeneity in Autism

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Lili Jiang ◽  
Xiao-Hui Hou ◽  
Ning Yang ◽  
Zhi Yang ◽  
Xi-Nian Zuo
Keyword(s):  
Data Exchange ◽  
Insular Cortex ◽  
Autism Diagnostic Observation Schedule ◽  
Superior Temporal Sulcus ◽  
Imaging Data ◽  
Local Connectivity ◽  
Restricted Interests ◽  
Developed Surface ◽  
Brain Structure And Function ◽  
The Right

Increasing neuroimaging evidence suggests that autism patients exhibit abnormal brain structure and function. We used the Autism Brain Imaging Data Exchange (ABIDE) sample to analyze locally focal (~8 mm) functional connectivity of 223 autism patients and 285 normal controls from 15 international sites using a recently developed surface-based approach. We observed enhanced local connectivity in the middle frontal cortex, left precuneus, and right superior temporal sulcus, and reduced local connectivity in the right insular cortex. The local connectivity in the right middle frontal gyrus was positively correlated with the total score of the autism diagnostic observation schedule whereas the local connectivity within the right superior temporal sulcus was positively correlated with total subscores of both the communication and the stereotyped behaviors and restricted interests of the schedule. Finally, significant interactions between age and clinical diagnosis were detected in the left precuneus. These findings replicated previous observations that used a volume-based approach and suggested possible neuropathological impairments of local information processing in the frontal, temporal, parietal, and insular cortices. Novel site-variability analysis demonstrated high reproducibility of our findings across the 15 international sites. The age-disease interaction provides a potential target region for future studies to further elucidate the neurodevelopmental mechanisms of autism.

scholarly journals The Cost of Untracked Diversity in Brain-Imaging Prediction

2021 ◽  
Author(s):  
Oualid Benkarim ◽  
Casey Paquola ◽  
Bo-yong Park ◽  
Valeria Kebets ◽  
Seok-Jun Hong ◽  
...  
Keyword(s):  
Brain Imaging ◽  
Data Exchange ◽  
Predictive Accuracy ◽  
Population Diversity ◽  
Population Heterogeneity ◽  
Disease Classification ◽  
Supervised Machine Learning ◽  
Single Subject ◽  
Imaging Data ◽  
The Impact

Brain-imaging research enjoys increasing adoption of supervised machine learning for single-subject disease classification. Yet, the success of these algorithms likely depends on population diversity, including demographic differences and other factors that may be outside of primary scientific interest. Here, we capitalize on propensity scores as a composite confound index to quantify diversity due to major sources of population stratification. We delineate the impact of population heterogeneity on the predictive accuracy and pattern stability in two separate clinical cohorts: the Autism Brain Imaging Data Exchange (ABIDE, n=297) and the Healthy Brain Network (HBN, n=551). Across various analysis scenarios, our results uncover the extent to which cross-validated prediction performances are interlocked with diversity. The instability of extracted brain patterns attributable to diversity is located preferentially to the default mode network. Our collective findings highlight the limitations of prevailing deconfounding practices in mitigating the full consequences of population diversity.

Correlation of Pore Structure and Permeability by SEM-Image Analysis

1990 ◽  
Vol 48 (1) ◽  
pp. 428-429
Author(s):  
C. A. Callender ◽  
Wm. C. Dawson ◽  
J. J. Funk
Keyword(s):  
Image Analysis ◽  
Pore Structure ◽  
Imaging System ◽  
Pore Space ◽  
Simulation Models ◽  
Image Analyzer ◽  
Imaging Data ◽  
Sem Images ◽  
Thin Sections ◽  
Rock Types

The geometric structure of pore space in some carbonate rocks can be correlated with petrophysical measurements by quantitatively analyzing binaries generated from SEM images. Reservoirs with similar porosities can have markedly different permeabilities. Image analysis identifies which characteristics of a rock are responsible for the permeability differences. Imaging data can explain unusual fluid flow patterns which, in turn, can improve production simulation models.Analytical SchemeOur sample suite consists of 30 Middle East carbonates having porosities ranging from 21 to 28% and permeabilities from 92 to 2153 md. Engineering tests reveal the lack of a consistent (predictable) relationship between porosity and permeability (Fig. 1). Finely polished thin sections were studied petrographically to determine rock texture. The studied thin sections represent four petrographically distinct carbonate rock types ranging from compacted, poorly-sorted, dolomitized, intraclastic grainstones to well-sorted, foraminiferal,ooid, peloidal grainstones. The samples were analyzed for pore structure by a Tracor Northern 5500 IPP 5B/80 image analyzer and a 80386 microprocessor-based imaging system. Between 30 and 50 SEM-generated backscattered electron images (frames) were collected per thin section. Binaries were created from the gray level that represents the pore space. Calculated values were averaged and the data analyzed to determine which geological pore structure characteristics actually affect permeability.

scholarly journals Distributed Simulation Platforms and Data Passing Tools for Natural Hazards Engineering: Reviews, Limitations, and Recommendations

2021 ◽  
Author(s):  
Lichao Xu ◽  
Szu-Yun Lin ◽  
Andrew W. Hlynka ◽  
Hao Lu ◽  
Vineet R. Kamat ◽  
...  
Keyword(s):  
Natural Hazards ◽  
Data Exchange ◽  
Distributed Simulation ◽  
Distributed Data ◽  
Interactive Simulation ◽  
Integrated Simulation ◽  
Domain Specific ◽  
Advantages And Disadvantages ◽  
High Level ◽  
Data Passing

AbstractThere has been a strong need for simulation environments that are capable of modeling deep interdependencies between complex systems encountered during natural hazards, such as the interactions and coupled effects between civil infrastructure systems response, human behavior, and social policies, for improved community resilience. Coupling such complex components with an integrated simulation requires continuous data exchange between different simulators simulating separate models during the entire simulation process. This can be implemented by means of distributed simulation platforms or data passing tools. In order to provide a systematic reference for simulation tool choice and facilitating the development of compatible distributed simulators for deep interdependent study in the context of natural hazards, this article focuses on generic tools suitable for integration of simulators from different fields but not the platforms that are mainly used in some specific fields. With this aim, the article provides a comprehensive review of the most commonly used generic distributed simulation platforms (Distributed Interactive Simulation (DIS), High Level Architecture (HLA), Test and Training Enabling Architecture (TENA), and Distributed Data Services (DDS)) and data passing tools (Robot Operation System (ROS) and Lightweight Communication and Marshalling (LCM)) and compares their advantages and disadvantages. Three specific limitations in existing platforms are identified from the perspective of natural hazard simulation. For mitigating the identified limitations, two platform design recommendations are provided, namely message exchange wrappers and hybrid communication, to help improve data passing capabilities in existing solutions and provide some guidance for the design of a new domain-specific distributed simulation framework.

scholarly journals Predicting severe pneumonia in the emergency department: a global study of the Pediatric Emergency Research Networks (PERN)—study protocol

BMJ Open ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. e041093
Author(s):  
Todd Adam Florin ◽  
Daniel Joseph Tancredi ◽  
Lilliam Ambroggio ◽  
Franz E Babl ◽  
Stuart R Dalziel ◽  
...  
Keyword(s):  
Emergency Department ◽  
Prediction Model ◽  
Severe Disease ◽  
Pediatric Emergency ◽  
Global Network ◽  
Clinical Prediction ◽  
Emergency Research ◽  
Research Networks ◽  
Clinical Prediction Model ◽  
Severity Scores

IntroductionPneumonia is a frequent and costly cause of emergency department (ED) visits and hospitalisations in children. There are no evidence-based, validated tools to assist physicians in management and disposition decisions for children presenting to the ED with community-acquired pneumonia (CAP). The objective of this study is to develop a clinical prediction model to accurately stratify children with CAP who are at risk for low, moderate and severe disease across a global network of EDs.Methods and analysisThis study is a prospective cohort study enrolling up to 4700 children with CAP at EDs at ~80 member sites of the Pediatric Emergency Research Networks (PERN; https://pern-global.com/). We will include children aged 3 months to <14 years with a clinical diagnosis of CAP. We will exclude children with hospital admissions within 7 days prior to the study visit, hospital-acquired pneumonias or chronic complex conditions. Clinical, laboratory and imaging data from the ED visit and hospitalisations within 7 days will be collected. A follow-up telephone or text survey will be completed 7–14 days after the visit. The primary outcome is a three-tier composite of disease severity. Ordinal logistic regression, assuming a partial proportional odds specification, and recursive partitioning will be used to develop the risk stratification models.Ethics and disseminationThis study will result in a clinical prediction model to accurately identify risk of severe disease on presentation to the ED. Ethics approval was obtained for all sites included in the study. Cincinnati Children’s Hospital Institutional Review Board (IRB) serves as the central IRB for most US sites. Informed consent will be obtained from all participants. Results will be disseminated through international conferences and peer-reviewed publications. This study overcomes limitations of prior pneumonia severity scores by allowing for broad generalisability of findings, which can be actively implemented after model development and validation.

An efficient approach to converting three-dimensional image data into highly accurate computational models

2008 ◽  
Vol 366 (1878) ◽  
pp. 3155-3173 ◽  
Author(s):  
P.G Young ◽  
T.B.H Beresford-West ◽  
S.R.L Coward ◽  
B Notarberardino ◽  
B Walker ◽  
...  
Keyword(s):  
Mesh Generation ◽  
Computational Models ◽  
Three Dimensional ◽  
Image Data ◽  
Model Material ◽  
Imaging Data ◽  
Material Inhomogeneity ◽  
Dimensional Image ◽  
Wide Range ◽  
Impact Modelling

Image-based meshing is opening up exciting new possibilities for the application of computational continuum mechanics methods (finite-element and computational fluid dynamics) to a wide range of biomechanical and biomedical problems that were previously intractable owing to the difficulty in obtaining suitably realistic models. Innovative surface and volume mesh generation techniques have recently been developed, which convert three-dimensional imaging data, as obtained from magnetic resonance imaging, computed tomography, micro-CT and ultrasound, for example, directly into meshes suitable for use in physics-based simulations. These techniques have several key advantages, including the ability to robustly generate meshes for topologies of arbitrary complexity (such as bioscaffolds or composite micro-architectures) and with any number of constituent materials (multi-part modelling), providing meshes in which the geometric accuracy of mesh domains is only dependent on the image accuracy (image-based accuracy) and the ability for certain problems to model material inhomogeneity by assigning the properties based on image signal strength. Commonly used mesh generation techniques will be compared with the proposed enhanced volumetric marching cubes (EVoMaCs) approach and some issues specific to simulations based on three-dimensional image data will be discussed. A number of case studies will be presented to illustrate how these techniques can be used effectively across a wide range of problems from characterization of micro-scaffolds through to head impact modelling.

German Seismic and Infrasound Networks Contributing to the European Integrated Data Archive (EIDA)

2021 ◽  
Vol 92 (3) ◽  
pp. 1854-1875 ◽  
Author(s):  
Klaus Stammler ◽  
Monika Bischoff ◽  
Andrea Brüstle ◽  
Lars Ceranna ◽  
Stefanie Donner ◽  
...  
Keyword(s):  
Information Transfer ◽  
Data Exchange ◽  
Seismic Hazard Assessment ◽  
Data Archive ◽  
Waveform Data ◽  
Level Data ◽  
Data Products ◽  
Global Seismicity ◽  
High Level ◽  
Test Ban

Abstract Germany has a long history in seismic instrumentation. The installation of the first station sites was initiated in those regions with seismic activity. Later on, with an increasing need for seismic hazard assessment, seismological state services were established over the course of several decades, using heterogeneous technology. In parallel, scientific research and international cooperation projects triggered the establishment of institutional and nationwide networks and arrays also focusing on topics other than monitoring local or regional areas, such as recording global seismicity or verification of the compliance with the Comprehensive Nuclear-Test-Ban Treaty. At each of the observatories and data centers, an extensive analysis of the recordings is performed providing high-level data products, for example, earthquake catalogs, as a base for supporting state or federal authorities, to inform the public on topics related to seismology, and for information transfer to international institutions. These data products are usually also accessible at websites of the responsible organizations. The establishment of the European Integrated Data Archive (EIDA) led to a consolidation of existing waveform data exchange mechanisms and their definition as standards in Europe, along with a harmonization of the applied data quality assurance procedures. In Germany, the German Regional Seismic Network as national backbone network and the state networks of Saxony, Saxony-Anhalt, Thuringia, and Bavaria spearheaded the national contributions to EIDA. The benefits of EIDA are attracting additional state and university networks, which are about to join the EIDA community now.

scholarly journals Entity Type Recognition for Heterogeneous Semantic Graphs

AI Magazine ◽  
2015 ◽  
Vol 36 (1) ◽  
pp. 75-86 ◽  
Author(s):  
Jennifer Sleeman ◽  
Tim Finin ◽  
Anupam Joshi
Keyword(s):  
Machine Learning ◽  
Background Knowledge ◽  
Knowledge Bases ◽  
Heterogeneous Data ◽  
Unstructured Data ◽  
Supervised Machine Learning ◽  
Coreference Resolution ◽  
Multiple Sources ◽  
Fine Grained ◽  
High Level

We describe an approach for identifying fine-grained entity types in heterogeneous data graphs that is effective for unstructured data or when the underlying ontologies or semantic schemas are unknown. Identifying fine-grained entity types, rather than a few high-level types, supports coreference resolution in heterogeneous graphs by reducing the number of possible coreference relations that must be considered. Big data problems that involve integrating data from multiple sources can benefit from our approach when the datas ontologies are unknown, inaccessible or semantically trivial. For such cases, we use supervised machine learning to map entity attributes and relations to a known set of attributes and relations from appropriate background knowledge bases to predict instance entity types. We evaluated this approach in experiments on data from DBpedia, Freebase, and Arnetminer using DBpedia as the background knowledge base.

JCAMP-DX for NMR

1993 ◽  
Vol 47 (8) ◽  
pp. 1093-1099 ◽  
Author(s):  
Antony N. Davies ◽  
Peter Lampen
Keyword(s):  
Spectral Data ◽  
Data Exchange ◽  
Data Transfer ◽  
Nmr Imaging ◽  
Successful Implementation ◽  
Independent Data ◽  
Imaging Data ◽  
Loss Of Information ◽  
Storage Media ◽  
Different Origin

Following the development and publication of the JCAMP-DX protocol 4.24 and its successful implementation in the field of infrared spectroscopy, data exchange without loss of information, between systems of different origin and internal format, has become a reality. The benefits of this system-independent data transfer standard have been recognized by workers in other areas who have expressed a wish for an equivalent, compatible standard in their own fields. This publication details a protocol for the exchange of Nuclear Magnetic Resonance (NMR) spectral data without any loss of information and in a format that is compatible with all storage media and computer systems. The protocol detailed below is designed for spectral data transfer, and its use for NMR imaging data transfer has not as yet been investigated.

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