Publications by authors named "David N Kennedy"

118 Publications

An assessment of the autism neuroimaging literature for the prospects of re-executability.

F1000Res 2020 24;9:1031. Epub 2020 Aug 24.

Eunice Kennedy Shriver Center, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, 01655, USA.

The degree of reproducibility of the neuroimaging literature in psychiatric application areas has been called into question and the issues that relate to this reproducibility are extremely complex. Some of these complexities have to do with the underlying biology of the disorders that we study and others arise due to the technology we apply to the analysis of the data we collect. Ultimately, the observations we make get communicated to the rest of the community through publications in the scientific literature. We sought to perform a 're-executability survey' to evaluate the recent neuroimaging literature with an eye toward seeing if the technical aspects of our publication practices are helping or hindering the overall quest for a more reproducible understanding of brain development and aging. The topic areas examined include availability of the data, the precision of the imaging method description and the reporting of the statistical analytic approach, and the availability of the complete results. We applied the survey to 50 publications in the autism neuroimaging literature that were published between September 16, 2017 to October 1, 2018. The results of the survey indicate that for the literature examined, data that is not already part of a public repository is rarely available, software tools are usually named but versions and operating system are not, it is expected that reasonably skilled analysts could approximately perform the analyses described, and the complete results of the studies are rarely available.  We have identified that there is ample room for improvement in research publication practices. We hope exposing these issues in the retrospective literature can provide guidance and motivation for improving this aspect of our reporting practices in the future.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.12688/f1000research.25306.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7968525.2PMC
April 2021

Biomarkers Based on Comprehensive Hierarchical EEG Coherence Analysis: Example Application to Social Competence in Autism (Preliminary Results).

Neuroinformatics 2021 Mar 30. Epub 2021 Mar 30.

The Eunice Kennedy Shriver Center Department of Psychiatry, University of Massachusetts Medical School, 55 Lake Avenue North, Room S3-312, Worcester, MA, 01655, USA.

Electroencephalography (EEG) coherence analysis, based on measurement of synchronous oscillations of neuronal clusters, has been used extensively to evaluate functional connectivity in brain networks. EEG coherence studies have used a variety of analysis variables (e.g., time and frequency resolutions corresponding to the analysis time period and frequency bandwidth), regions of the brain (e.g., connectivity within and between various cortical lobes and hemispheres) and experimental paradigms (e.g., resting state with eyes open or closed; performance of cognitive tasks). This variability in study designs has resulted in difficulties in comparing the findings from different studies and assimilating a comprehensive understanding of the underlying brain activity and regions with abnormal functional connectivity in a particular disorder. In order to address the variability in methods across studies and to facilitate the comparison of research findings between studies, this paper presents the structure and utilization of a comprehensive hierarchical electroencephalography (EEG) coherence analysis that allows for formal inclusion of analysis duration, EEG frequency band, cortical region, and experimental test condition in the computation of the EEG coherences. It further describes the method by which this EEG coherence analysis can be utilized to derive biomarkers related to brain (dys)function and abnormalities. In order to document the utility of this approach, the paper describes the results of the application of this method to EEG and behavioral data from a social synchrony paradigm in a small cohort of adolescents with and without Autism Spectral Disorder.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12021-021-09517-8DOI Listing
March 2021

A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility.

Neuroinformatics 2021 Jan 27. Epub 2021 Jan 27.

Department of Neuroscience, School of Medicine, University of California, San Diego, La Jolla, CA, USA.

There is great need for coordination around standards and best practices in neuroscience to support efforts to make neuroscience a data-centric discipline. Major brain initiatives launched around the world are poised to generate huge stores of neuroscience data. At the same time, neuroscience, like many domains in biomedicine, is confronting the issues of transparency, rigor, and reproducibility. Widely used, validated standards and best practices are key to addressing the challenges in both big and small data science, as they are essential for integrating diverse data and for developing a robust, effective, and sustainable infrastructure to support open and reproducible neuroscience. However, developing community standards and gaining their adoption is difficult. The current landscape is characterized both by a lack of robust, validated standards and a plethora of overlapping, underdeveloped, untested and underutilized standards and best practices. The International Neuroinformatics Coordinating Facility (INCF), an independent organization dedicated to promoting data sharing through the coordination of infrastructure and standards, has recently implemented a formal procedure for evaluating and endorsing community standards and best practices in support of the FAIR principles. By formally serving as a standards organization dedicated to open and FAIR neuroscience, INCF helps evaluate, promulgate, and coordinate standards and best practices across neuroscience. Here, we provide an overview of the process and discuss how neuroscience can benefit from having a dedicated standards body.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12021-020-09509-0DOI Listing
January 2021

Understanding the impact of preprocessing pipelines on neuroimaging cortical surface analyses.

Gigascience 2021 Jan;10(1)

Montreal Neurological Institute & Hospital, McGill University, Neurology and Neurosurgery, 3801 University Street, Montreal, H3A 2B4H3A 2B4, Montreal, QC, Canada.

Background: The choice of preprocessing pipeline introduces variability in neuroimaging analyses that affects the reproducibility of scientific findings. Features derived from structural and functional MRI data are sensitive to the algorithmic or parametric differences of preprocessing tasks, such as image normalization, registration, and segmentation to name a few. Therefore it is critical to understand and potentially mitigate the cumulative biases of pipelines in order to distinguish biological effects from methodological variance.

Methods: Here we use an open structural MRI dataset (ABIDE), supplemented with the Human Connectome Project, to highlight the impact of pipeline selection on cortical thickness measures. Specifically, we investigate the effect of (i) software tool (e.g., ANTS, CIVET, FreeSurfer), (ii) cortical parcellation (Desikan-Killiany-Tourville, Destrieux, Glasser), and (iii) quality control procedure (manual, automatic). We divide our statistical analyses by (i) method type, i.e., task-free (unsupervised) versus task-driven (supervised); and (ii) inference objective, i.e., neurobiological group differences versus individual prediction.

Results: Results show that software, parcellation, and quality control significantly affect task-driven neurobiological inference. Additionally, software selection strongly affects neurobiological (i.e. group) and individual task-free analyses, and quality control alters the performance for the individual-centric prediction tasks.

Conclusions: This comparative performance evaluation partially explains the source of inconsistencies in neuroimaging findings. Furthermore, it underscores the need for more rigorous scientific workflows and accessible informatics resources to replicate and compare preprocessing pipelines to address the compounding problem of reproducibility in the age of large-scale, data-driven computational neuroscience.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/gigascience/giaa155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7821710PMC
January 2021

Psychiatric Symptomatology, Mood Regulation, and Resting State Functional Connectivity of the Amygdala: Preliminary Findings in Youth With Mood Disorders and Childhood Trauma.

Front Psychiatry 2020 18;11:525064. Epub 2020 Sep 18.

Eunice Kennedy Shriver Center, University of Massachusetts Medical School, Worcester, MA, United States.

Background: As mood dysregulation and hyperarousal are overlapping and prominent features of posttraumatic stress disorder (PTSD), and mood disorders (MD) including bipolar disorder (BD), we aimed to clarify the role of trauma and MD on the resting state functional connectivity (RSFC) of amygdala in MD youth with or without trauma exposure, and healthy controls (HC).

Methods: Of 23 subjects, 21 completed the magnetic resonance imaging (MRI) protocol, 5 were excluded for subject motion, leaving final sample size of 16: nine subjects with MD (5/9 with trauma), and 7 HC. Youth were assessed with Schedule for Affective Disorders and Schizophrenia for School Aged Children-Present and Lifetime Version (K-SADS-PL), and other behavioral measures including Young Mania Rating Scale (YMRS). Imaging data were acquired using functional MRI in 3-T scanner. Imaging included T1-weighted structural MRI and 6-min resting state acquisition.

Results: In between group analysis, the average correlation coefficients between left anterior cingulate cortex (Acc) and left insula cortex with left amygdala regions were significantly larger in HC compared to the patient population. Connectivity between left amygdala and left cingulate cortex shows a significant negative correlation with YMRS severity.

Conclusions: In this preliminary study, MD with trauma youth had more manic symptoms and difficulties regulating anger. While MD youth showed reduced RSFC of left amygdala with left acc and left insula, no significant difference between the subgroups of children with MD was observed. However, when looking at both clinical groups together, we observed a significant correlation of RSFC of left amygdala to left acc, and YMRS scores.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpsyt.2020.525064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7531261PMC
September 2020

Image processing and analysis methods for the Adolescent Brain Cognitive Development Study.

Neuroimage 2019 11 12;202:116091. Epub 2019 Aug 12.

National Institute on Drug Abuse, United States.

The Adolescent Brain Cognitive Development (ABCD) Study is an ongoing, nationwide study of the effects of environmental influences on behavioral and brain development in adolescents. The main objective of the study is to recruit and assess over eleven thousand 9-10-year-olds and follow them over the course of 10 years to characterize normative brain and cognitive development, the many factors that influence brain development, and the effects of those factors on mental health and other outcomes. The study employs state-of-the-art multimodal brain imaging, cognitive and clinical assessments, bioassays, and careful assessment of substance use, environment, psychopathological symptoms, and social functioning. The data is a resource of unprecedented scale and depth for studying typical and atypical development. The aim of this manuscript is to describe the baseline neuroimaging processing and subject-level analysis methods used by ABCD. Processing and analyses include modality-specific corrections for distortions and motion, brain segmentation and cortical surface reconstruction derived from structural magnetic resonance imaging (sMRI), analysis of brain microstructure using diffusion MRI (dMRI), task-related analysis of functional MRI (fMRI), and functional connectivity analysis of resting-state fMRI. This manuscript serves as a methodological reference for users of publicly shared neuroimaging data from the ABCD Study.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.neuroimage.2019.116091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981278PMC
November 2019

Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging.

Front Neuroinform 2019 7;13. Epub 2019 Feb 7.

TCG, Inc., Washington, DC, United States.

There has been a recent major upsurge in the concerns about reproducibility in many areas of science. Within the neuroimaging domain, one approach is to promote reproducibility is to target the re-executability of the publication. The information supporting such re-executability can enable the detailed examination of how an initial finding generalizes across changes in the processing approach, and sampled population, in a controlled scientific fashion. ReproNim: A Center for Reproducible Neuroimaging Computation is a recently funded initiative that seeks to facilitate the "last mile" implementations of core re-executability tools in order to reduce the accessibility barrier and increase adoption of standards and best practices at the neuroimaging research laboratory level. In this report, we summarize the overall approach and tools we have developed in this domain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fninf.2019.00001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6374302PMC
February 2019

Functional asymmetry of thalamocortical networks in subjects at ultra-high risk for psychosis and first-episode schizophrenia.

Eur Neuropsychopharmacol 2019 04 13;29(4):519-528. Epub 2019 Feb 13.

Department of Psychiatry, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China. Electronic address:

Disrupted functional asymmetry has been implicated in schizophrenia. However, it remains unknown whether disrupted functional asymmetry originates from intra-hemispheric and/or inter-hemispheric functional connectivity (FC) in the patients, and whether it starts at very early stage of psychosis. Seventy-six patients with first-episode, drug-naive schizophrenia, 74 subjects at ultra-high risk for psychosis (UHR), and 71 healthy controls underwent resting-state functional magnetic resonance imaging. The 'Parameter of asymmetry' (PAS) metric was calculated and support vector machine (SVM) classification analysis was applied to analyze the data. Compared with healthy controls, patients exhibited decreased PAS in the left thalamus/pallidum, right hippocampus/parahippocampus, right inferior frontal gyrus/insula, right thalamus, and left inferior parietal lobule, and increased PAS in the left calcarine, right superior occipital gyrus/middle occipital gyrus, and right precentral gyrus/postcentral gyrus. By contrast, UHR subjects showed decreased PAS in the left thalamus relative to healthy controls. A negative correlation was observed between decreased PAS in the right hippocampus/parahippocampus and Brief Visuospatial Memory Test-Revised (BVMT-R) scores in the patients (r = -0.364, p = 0.002). Moreover, the PAS values in the left thalamus could discriminate the patients/UHR subjects from the controls with acceptable sensitivities (68.42%/81.08%). First-episode patients and UHR subjects shared decreased PAS in the left thalamus. This observed pattern of functional asymmetry highlights the involvement of the thalamus in the pathophysiology of psychosis and may also be applied as a very early marker for psychosis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.euroneuro.2019.02.006DOI Listing
April 2019

Neuroimaging Neuroinformatics: Sample Size and Other Evolutionary Topics.

Authors:
David N Kennedy

Neuroinformatics 2018 04;16(2):149-150

University of Massachusetts Medical School, Worcester, MA, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12021-018-9379-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5985218PMC
April 2018

Making replication prestigious.

Behav Brain Sci 2018 01;41:e131

Department of Psychology,Stanford University,Stanford, CA

Making replication studies widely conducted and published requires new incentives. Academic awards can provide such incentives by highlighting the best and most important replications. The Organization for Human Brain Mapping (OHBM) has led such efforts by recently introducing the OHBM Replication Award. Other communities can adopt this approach to promote replications and reduce career cost for researchers performing them.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1017/S0140525X18000663DOI Listing
January 2018

Coordination Impairments Are Associated With Falling Among Older Adults.

Exp Aging Res 2017 Oct-Dec;43(5):430-439. Epub 2017 Oct 26.

m Department of Physical Medicine and Rehabilitation , Harvard Medical School , Boston , Massachusetts , USA.

Background/Study Context: Approximately one third of older adults over the age of 65, and over 40% of those over 80 years, fall each year, leading to fractures, morbidity, and mortality. Annual direct medical costs due to falls in the United States are approximately $19.2 billion. The identification of new treatable risk factors for falls has the potential to advance their prevention and rehabilitation.

Methods: A cross-sectional study of 127 community-dwelling adults aged 67-99 years was conducted. An electronic gait walkway was used to assess gait coordination, measured as the Phase Coordination Index during normal speed walking. A motion capture system was used to assess rhythmic interlimb antiphase ankle coordination, measured as the standard deviation of ankle relative phase. Having fallen in the previous year was self-reported retrospectively. Odds ratios for falling as a function of coordination quartiles were determined using multivariable logistic regression.

Results: Adjusting for age, sex, body mass index, number of chronic conditions, Mini-Mental State Examination score, gait speed, and the variability of step length, time, and width, the odds ratios for falling based upon being in the 4th (the poorest) quartiles of gait or ankle coordination were 5.5 (95% confidence interval [CI]: 1.2-24.7) and 8.2 (95% CI: 2.2-31.3), respectively, and 3.7 (95% CI: 1.0-13.8) for the 3rd quartile of gait coordination, compared with the best (the 1st) coordination quartiles. Similar results were found in regression without adjustment for gait characteristics.

Conclusion: The results support the hypothesis that impaired gait and rhythmic interlimb ankle coordination are associated with a history of falls in the past year. Prospective longitudinal research is needed to determine the possible direction of causality between falls and impaired coordination.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/0361073X.2017.1369634DOI Listing
June 2018

A very simple, re-executable neuroimaging publication.

F1000Res 2017 10;6:124. Epub 2017 Feb 10.

Eunice K. Shriver Center and Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA.

Reproducible research is a key element of the scientific process. Re-executability of neuroimaging workflows that lead to the conclusions arrived at in the literature has not yet been sufficiently addressed and adopted by the neuroimaging community. In this paper, we document a set of procedures, which include supplemental additions to a manuscript, that unambiguously define the data, workflow, execution environment and results of a neuroimaging analysis, in order to generate a verifiable re-executable publication. Re-executability provides a starting point for examination of the generalizability and reproducibility of a given finding.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.12688/f1000research.10783.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516225PMC
February 2017

Mobile Monitoring of Traumatic Brain Injury in Older Adults: Challenges and Opportunities.

Neuroinformatics 2017 07;15(3):227-230

Eunice Kennedy Shriver Center & Department of Psychiatry, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01605, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12021-017-9335-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5564208PMC
July 2017

Rhythmic Interlimb Coordination Impairments Are Associated With Mobility Limitations Among Older Adults.

Exp Aging Res 2017 Jul-Sep;43(4):337-345

k Department of Physical Medicine Rehabilitation , Harvard Medical School , Boston , Massachusetts , USA.

Background/Study Context: Mobility limitations affect more than 25% of adults aged 70 years or older. This study tested the hypothesis that impairments in ankle and shoulder coordination are associated with mobility limitations among older adults.

Methods: his study consisted of conducted a cross-sectional analysis from a sample of community-dwelling older adults (N = 130) aged ≥67 years. Motion capture equipment was used to collect kinematic data during rhythmic antiphase coordination of the right and left: (a) ankles moving in dorsi-plantarflexion; and (b) glenohumeral ("shoulder") moving in flexion-extension while paced by an auditory metronome. Coordination variability was measured as the standard deviation of the relative phase between right and left body segments. Mobility limitations were defined as a score of ≤9 on the Short Physical Performance Battery (SPPB). Odds ratios for mobility limitations as a function of coordination variability quartiles were determined using multivariable logistic regression.

Results: Adjusting for age, gender, body mass index, number of chronic conditions and Mini-Mental State Examination score, the odds ratios for mobility limitation (SPPB score ≤9) were 7.38 (95% confidence interval [CI]: 2.20-24.78) and 15.40 (95% CI: 4.31-55.07) for the 3rd and 4th (the poorest) ankle coordination quartiles, respectively, and 6.73 (95% CI: 2.11-21.51) for the 4th shoulder coordination quartile, compared with the best (the 1st) coordination quartiles.

Conclusion: The results supported the hypothesis that impaired interlimb ankle and shoulder coordination are associated with the manifestation of mobility limitations. These findings indicate the need for further study of the role of coordination impairments as potential contributors to poor mobility among older adults.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/0361073X.2017.1333819DOI Listing
June 2018

The Information Sharing Statement Grows Some Teeth.

Authors:
David N Kennedy

Neuroinformatics 2017 04;15(2):113-114

University of Massachusetts Medical School, Worcester, MA, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12021-017-9331-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502776PMC
April 2017

Rhythmic Interlimb Coordination Impairments and the Risk for Developing Mobility Limitations.

J Gerontol A Biol Sci Med Sci 2017 Aug;72(8):1143-1148

New England GRECC, VA Boston Healthcare System, Massachusetts.

Background: The identification of novel rehabilitative impairments that are risk factors for mobility limitations may improve their prevention and treatment among older adults. We tested the hypothesis that impaired rhythmic interlimb ankle and shoulder coordination are risk factors for subsequent mobility limitations among older adults.

Methods: We conducted a 1-year prospective cohort study of community-dwelling older adults (N = 99) aged 67 years and older who did not have mobility limitations (Short Physical Performance Battery score > 9) at baseline. Participants performed antiphase coordination of the right and left ankles or shoulders while paced by an auditory metronome. Using multivariable logistic regression, we determined odds ratios (ORs) for mobility limitations at 1-year follow-up as a function of coordination variability and asymmetry.

Results: After adjusting for age, sex, body mass index, Mini-Mental State Examination score, number of chronic conditions, and baseline Short Physical Performance Battery score, ORs were significant for developing mobility limitations based on a 1 SD difference in the variability of ankle (OR = 1.88; 95% confidence interval [CI]: 1.16-3.05) and shoulder (OR = 1.96; 95% CI: 1.17-3.29) coordination. ORs were significant for asymmetry of shoulder (OR = 2.11; 95% CI: 1.25-3.57), but not ankle (OR = 0.95; 95% CI: 0.59-1.55) coordination. Similar results were found in unadjusted analyses.

Conclusions: The results support our hypothesis that impaired interlimb ankle and shoulder coordination are risk factors for the development of mobility limitations. Future work is needed to further examine the peripheral and central mechanisms underlying this relationship and to test whether enhancing coordination alters mobility limitations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/gerona/glw236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861956PMC
August 2017

Corrigendum: Data Citation in Neuroimaging: Proposed Best Practices for Data Identification and Attribution.

Front Neuroinform 2016 5;10:43. Epub 2016 Oct 5.

Eunice Kennedy Shriver Center, University of Massachusetts Medical SchoolWorcester, MA, USA; Child and Adolescent NeuroDevelopment Initiative, Department of Psychiatry, University of Massachusetts Medical SchoolWorcester, MA, USA.

[This corrects the article on p. 34 in vol. 10, PMID: 27570508.].
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fninf.2016.00043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5050202PMC
October 2016

Data Citation in Neuroimaging: Proposed Best Practices for Data Identification and Attribution.

Front Neuroinform 2016 12;10:34. Epub 2016 Aug 12.

Eunice Kennedy Shriver Center, University of Massachusetts Medical SchoolWorcester MA, USA; Child and Adolescent NeuroDevelopment Initiative, Department of Psychiatry, University of Massachusetts Medical SchoolWorcester MA, USA.

Data sharing and reuse, while widely accepted as good ideas, have been slow to catch on in any concrete and consistent way. One major hurdle within the scientific community has been the lack of widely accepted standards for citing that data, making it difficult to track usage and measure impact. Within the neuroimaging community, there is a need for a way to not only clearly identify and cite datasets, but also to derive new aggregate sets from multiple sources while clearly maintaining lines of attribution. This work presents a functional prototype of a system to integrate Digital Object Identifiers (DOI) and a standardized metadata schema into a XNAT-based repository workflow, allowing for identification of data at both the project and image level. These item and source level identifiers allow any newly defined combination of images, from any number of projects, to be tagged with a new group-level DOI that automatically inherits the individual attributes and provenance information of its constituent parts. This system enables the tracking of data reuse down to the level of individual images. The implementation of this type of data identification system would impact researchers and data creators, data hosting facilities, and data publishers, but the benefit of having widely accepted standards for data identification and attribution would go far toward making data citation practical and advantageous.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fninf.2016.00034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981598PMC
August 2016

Gray matter maturation and cognition in children with different APOE ε genotypes.

Neurology 2016 Aug 13;87(6):585-94. Epub 2016 Jul 13.

From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA.

Objective: The aims of the current study were to determine whether children with the 6 different APOE ε genotypes show differences in gray matter maturation, particularly for those with ε4 and ε2 alleles, which are associated with poorer outcomes in many neurologic disorders.

Methods: A total of 1,187 healthy children (aged 3-20 years, 52.1% boys, 47.9% girls) with acceptable data from the cross-sectional Pediatric Imaging Neurocognition and Genetics Study were evaluated for the effects of 6 APOE ε genotypes on macroscopic and microscopic cortical and subcortical gray matter structures (measured with 3-tesla MRI and FreeSurfer for automated morphometry) and on cognition (NIH Toolbox).

Results: Among APOE ε4 carriers, age-related changes in brain structures and cognition varied depending on genotype, with the smallest hippocampi in ε2ε4 children, the lowest hippocampal fractional anisotropy in younger ε4ε4 children, the largest medial orbitofrontal cortical areas in ε3ε4 children, and age-dependent thinning of the entorhinal cortex in ε4ε4 children. Younger ε4ε4 children had the lowest scores on executive function and working memory, while younger ε2ε4 children performed worse on attention tasks. Larger parietal gyri in the younger ε2ε4 children, and thinner temporal and cingulate isthmus cortices or smaller hippocampi in the younger ε4ε4 children, predicted poorer performance on attention or working memory.

Conclusions: Our findings validated and extended prior smaller studies that showed altered brain development in APOE ε4-carrier children. The ε4ε4 and ε2ε4 genotypes may negatively influence brain development and brain aging at the extremes of age. Studying APOE ε polymorphisms in young children may provide the earliest indicators for individuals who might benefit from early interventions or preventive measures for future brain injuries and dementia.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1212/WNL.0000000000002939DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4977368PMC
August 2016

The Resource Identification Initiative: a cultural shift in publishing.

Brain Behav 2016 01 8;6(1):e00417. Epub 2015 Dec 8.

Department of Medical Informatics & Clinical Epidemiology OHSU Library Oregon Health and Science University 3181 SW Sam Jackson Park Road Portland, Oregon 97239 USA.

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, that is, reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as "How did other studies use resource X?" To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and scientific reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (i.e., software and databases). RRIDs are assigned by an authoritative database, for example, a model organism database for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( http://scicrunch.org/resources). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40 with RRIDs appearing in 62 different journals to date. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/brb3.417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834942PMC
January 2016

The Social Life of Data.

Authors:
David N Kennedy

Neuroinformatics 2016 Apr;14(2):129-30

Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12021-016-9298-5DOI Listing
April 2016

The Resource Identification Initiative: A Cultural Shift in Publishing.

J Comp Neurol 2016 Jan;524(1):8-22

Oregon Health & Science University (OHSU) Library, Department of Medical Informatics & Clinical Epidemiology, Portland, Oregon, USA.

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as "How did other studies use resource X?" To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the Methods sections of articles and thereby improve identifiability and scientific reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their articles prior to publication for three resource types: antibodies, model organisms, and tools (i.e., software and databases). RRIDs are assigned by an authoritative database, for example, a model organism database for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central Web portal (http://scicrunch.org/resources). RRIDs meet three key criteria: they are machine-readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 articles have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40, with RRIDs appearing in 62 different journals to date. Here we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/cne.23913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684178PMC
January 2016

The Resource Identification Initiative: A cultural shift in publishing.

F1000Res 2015 29;4:134. Epub 2015 May 29.

Department of Medical Informatics & Clinical Epidemiology, OHSU, Portland, Oregon, 97239, USA.

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to allow humans and algorithms to identify the exact resources that are reported or answer basic questions such as "What other studies used resource X?" To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (including software and databases). RRIDs represent accession numbers assigned by an authoritative database, e.g., the model organism databases, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( www.scicrunch.org/resources). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are generally accurate in performing the task of identifying resources and supportive of the goals of the project. We also show that identifiability of the resources pre- and post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on reproducibility relating to research resources.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4648211PMC
http://dx.doi.org/10.12688/f1000research.6555.2DOI Listing
December 2015

The Resource Identification Initiative: A Cultural Shift in Publishing.

Neuroinformatics 2016 Apr;14(2):169-82

OHSU Library, Department of Medical Informatics & Clinical Epidemiology, 9500 Gillman Dr.#0446, la Jolla, CA, 92093-0446, USA.

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as "How did other studies use resource X?" To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and scientific reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (i.e., software and databases). RRIDs are assigned by an authoritative database, for example a model organism database, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( http://scicrunch.org/resources ). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40 with RRIDs appearing in 62 different journals to date. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5072392PMC
http://dx.doi.org/10.1007/s12021-015-9284-3DOI Listing
April 2016

Anxiety is related to indices of cortical maturation in typically developing children and adolescents.

Brain Struct Funct 2016 07 17;221(6):3013-25. Epub 2015 Jul 17.

Center for Human Development, University of California, San Diego, 9500 Gilman Drive, MC 0115, La Jolla, CA, 92093, USA.

Anxiety is a risk factor for many adverse neuropsychiatric and socioeconomic outcomes, and has been linked to functional and structural changes in the ventromedial prefrontal cortex (VMPFC). However, the nature of these differences, as well as how they develop in children and adolescents, remains poorly understood. More effective interventions to minimize the negative consequences of anxiety require better understanding of its neurobiology in children. Recent research suggests that structural imaging studies may benefit from clearly delineating between cortical surface area and thickness when examining these associations, as these distinct cortical phenotypes are influenced by different cellular mechanisms and genetic factors. The present study examined relationships between cortical surface area and thickness of the VMPFC and a self-report measure of anxiety (SCARED-R) in 287 youths aged 7-20 years from the Pediatric Imaging, Neurocognition, and Genetics (PING) study. Age and gender interactions were examined for significant associations in order to test for developmental differences. Cortical surface area and thickness were also examined simultaneously to determine whether they contribute independently to the prediction of anxiety. Anxiety was negatively associated with relative cortical surface area of the VMPFC as well as with global cortical thickness, but these associations diminished with age. The two cortical phenotypes contributed additively to the prediction of anxiety. These findings suggest that higher anxiety in children may be characterized by both delayed expansion of the VMPFC and an altered trajectory of global cortical thinning. Further longitudinal studies will be needed to confirm these findings.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5064818PMC
http://dx.doi.org/10.1007/s00429-015-1085-9DOI Listing
July 2016

Connectivity in Autism: A Review of MRI Connectivity Studies.

Harv Rev Psychiatry 2015 Jul-Aug;23(4):223-44

From the Child and Adolescent NeuroDevelopment Initiative, Department of Psychiatry, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655.

Autism spectrum disorder (ASD) affects 1 in 50 children between the ages of 6 and 17 years. The etiology of ASD is not precisely known. ASD is an umbrella term, which includes both low- (IQ < 70) and high-functioning (IQ > 70) individuals. A better understanding of the disorder and how it manifests in individual subjects can lead to more effective intervention plans to fulfill the individual's treatment needs.Magnetic resonance imaging (MRI) is a non-invasive investigational tool that can be used to study the ways in which the brain develops or deviates from the typical developmental trajectory. MRI offers insights into the structure, function, and metabolism of the brain. In this article, we review published studies on brain connectivity changes in ASD using either resting state functional MRI or diffusion tensor imaging.The general findings of decreases in white matter integrity and in long-range neural coherence are well known in the ASD literature. Nevertheless, the detailed localization of these findings remains uncertain, and few studies link these changes in connectivity with the behavioral phenotype of the disorder. With the help of data sharing and large-scale analytic efforts, however, the field is advancing toward several convergent themes, including the reduced functional coherence of long-range intra-hemispheric cortico-cortical default mode circuitry, impaired inter-hemispheric regulation, and an associated, perhaps compensatory, increase in local and short-range cortico-subcortical coherence.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5083037PMC
http://dx.doi.org/10.1097/HRP.0000000000000072DOI Listing
March 2016

The NITRC image repository.

Neuroimage 2016 Jan 2;124(Pt B):1069-1073. Epub 2015 Jun 2.

TCG, Inc., Washington, DC, USA.

The Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC - www.nitrc.org) suite of services include a resources registry, image repository and a cloud computational environment to meet the needs of the neuroimaging researcher. NITRC provides image-sharing functionality through both the NITRC Resource Registry (NITRC-R), where bulk data files can be released through the file release system (FRS), and the NITRC Image Repository (NITRC-IR), a XNAT-based image data management system. Currently hosting 14 projects, 6845 subjects, and 8285 MRI imaging sessions, NITRC-IR provides a large array of structural, diffusion and resting state MRI data. Designed to be flexible about management of data access policy, NITRC provides a simple, free, NIH-funded service to support resource sharing in general, and image sharing in particular.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.neuroimage.2015.05.074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651733PMC
January 2016

The Pediatric Imaging, Neurocognition, and Genetics (PING) Data Repository.

Neuroimage 2016 Jan 1;124(Pt B):1149-1154. Epub 2015 May 1.

Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA; Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, USA; Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Department of Radiology, University of California, San Diego, La Jolla, CA, USA.

The main objective of the multi-site Pediatric Imaging, Neurocognition, and Genetics (PING) study was to create a large repository of standardized measurements of behavioral and imaging phenotypes accompanied by whole genome genotyping acquired from typically-developing children varying widely in age (3 to 20 years). This cross-sectional study produced sharable data from 1493 children, and these data have been described in several publications focusing on brain and cognitive development. Researchers may gain access to these data by applying for an account on the PING portal and filing a data use agreement. Here we describe the recruiting and screening of the children and give a brief overview of the assessments performed, the imaging methods applied, the genetic data produced, and the numbers of cases for whom different data types are available. We also cite sources of more detailed information about the methods and data. Finally we describe the procedures for accessing the data and for using the PING data exploration portal.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.neuroimage.2015.04.057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4628902PMC
January 2016