David N Kennedy

David N Kennedy
University of Massachusetts Medical School | UMMS · Department of Psychiatry

Ph.D.

About

408
Publications
49,458
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
50,863
Citations
Additional affiliations
October 1988 - October 2008
Massachusetts General Hospital
Position
  • Researcher

Publications

Publications (408)
Article
Full-text available
Digital services such as repositories and science gateways have become key resources for the neuroscience community, but users often have a hard time orienting themselves in the service landscape to find the best fit for their particular needs. INCF has developed a set of recommendations and associated criteria for choosing or setting up and runnin...
Article
Full-text available
In this perspective article, we consider the critical issue of data and other research object standardisation and, specifically, how international collaboration, and organizations such as the International Neuroinformatics Coordinating Facility (INCF) can encourage that emerging neuroscience data be Findable, Accessible, Interoperable, and Reusable...
Preprint
Full-text available
Digital services such as repositories and science gateways have become key resources for the neuroscience community, but users often have a hard time orienting themselves in the service landscape to find the best fit for their particular needs. INCF (International Neuroinformatics Coordinating Facility) has developed a set of recommendations and as...
Article
Full-text available
DataLad is a Python-based tool for the joint management of code, data, and their relationship,built on top of a versatile system for data logistics (git-annex) and the most popular distributed version control system (Git). It adapts principles of open-source software development and distribution to address the technical challenges of data managemen...
Article
Full-text available
The Adolescent Brain Cognitive Development (ABCD) Study is the largest single-cohort prospective longitudinal study of neurodevelopment and children's health in the United States. A cohort of n= 11,880 children aged 9-10 years (and their parents/guardians) were recruited across 22 sites and are being followed with in-person visits on an annual basi...
Article
Full-text available
A Correction to this paper has been published: https://doi.org/10.1007/s12021-021-09522-x
Article
Full-text available
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 f...
Article
Background: 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 a...
Article
Full-text available
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 is...
Article
Full-text available
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 segmentati...
Article
Full-text available
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 he...
Article
Background: 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 a...
Preprint
Full-text available
The choice of preprocessing pipeline introduces variability in neuroimaging analyses that affects the reproducibility of the scientific findings. The features derived from structural and functional MR imaging data are sensitive to the algorithmic or parametric differences of the preprocessing tasks, such as image normalization, registration, and se...
Article
Full-text available
The last decade has seen increasing attention to the problem of scientific reproducibility, across a broad range of scientific fields (Camerer et al., 2016;Morrison, 2014;Open Science Collaboration, 2015). Within the field of neuroimaging, there has been a particular focus on issues of analytic variability (Bowring et al., 2019;Carp, 2012) statisti...
Article
This document provides a simple, generic checklist that authors of academic work (papers, books, conference abstracts, blog posts, etc.) can use to ensure they are following good practice when referencing and citing software they have used, both created by themselves for their research as well as obtained from other sources. It may also be used and...
Article
This document provides a minimal, generic checklist that developers of software (either open or closed source) used in research can use to ensure they are following good practice around software citation. This will help developers get credit for the software they create, and improve transparency, reproducibility, and reuse.
Article
Full-text available
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 brai...
Preprint
Full-text available
The main output of the FORCE11 Software Citation working group (https://www.force11.org/group/software-citation-working-group) was a paper on software citation principles (https://doi.org/10.7717/peerj-cs.86) published in September 2016. This paper laid out a set of six high-level principles for software citation (importance, credit and attribution...
Article
The main output of the FORCE11 Software Citation working group (https://www.force11.org/group/software-citation-working-group) was a paper on software citation principles (https://doi.org/10.7717/peerj-cs.86) published in September 2016. This paper laid out a set of six high-level principles for software citation (importance, credit and attribution...
Article
Full-text available
This article presents a practical roadmap for scholarly data repositories to implement data citation in accordance with the Joint Declaration of Data Citation Principles (Data Citation Synthesis Group, 2014), a synopsis and harmonization of the recommendations of major science policy bodies. The roadmap was developed by the Repositories Early Adopt...
Article
Previous research has reported changes in mu rhythm, the central rhythm of the alpha frequency band, in both intentional and spontaneous interpersonal coordination. The current study was designed to extend existing findings on social synchrony to the pendulum swinging task and simultaneously measured time unfolding behavioral synchrony and EEG esti...
Article
Full-text available
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 generali...
Article
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 generali...
Article
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 s...
Preprint
Full-text available
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 is...
Preprint
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 generali...
Preprint
Full-text available
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 ABCD Study is a collaborative effort, including a Coordinating Center, 21 data acquisition sites across the United States, and a Data Analysis and Informatics Cent...
Article
Full-text available
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...
Article
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...
Conference Paper
Full-text available
Text simplification (TS) aims to reduce the lexical and structural complexity of a text, while still retaining the semantic meaning. Current automatic TS techniques are limited to either lexical-level applications or manually defining a large amount of rules. In this paper, we propose to simplify text from both level of lexicons and sentences. We c...
Article
Full-text available
Text simplification (TS) aims to reduce the lexical and structural complexity of a text, while still retaining the semantic meaning. Current automatic TS techniques are limited to either lexical-level applications or manually defining a large amount of rules. In this paper, we propose to simplify text from both level of lexicons and sentences. We c...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
Background This study was to examine the insular cortical functional connectivity in drug naïve patients with first episode schizophrenia and to explore the relationship between the connectivity and the severity of clinical symptoms. Methods Thirty-seven drug naïve patients with schizophrenia and 25 healthy controls were enrolled in this study. A...
Data
The complete results of group comparison in connectivity values among the insular cortex with ipsilateral cortical ROIs. (DOC)
Article
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...
Conference Paper
Full-text available
Table of contents I1 Introduction to the 2015 Brainhack Proceedings R. Cameron Craddock, Pierre Bellec, Daniel S. Margules, B. Nolan Nichols, Jörg P. Pfannmöller A1 Distributed collaboration: the case for the enhancement of Brainspell’s interface AmanPreet Badhwar, David Kennedy, Jean-Baptiste Poline, Roberto Toro A2 Advancing open science through...
Article
Full-text available
In our original article, we stated, “Annual DOI creation costs range from $500 (for non-degree granting departments) to $25,000 (for entire degree-granting institutions) per 1 million DOIs minted.” This is incorrect. The University of California EZID service offers annual DOI creation at $835 (for non-degree granting departments) to $2500 (for enti...
Article
Full-text available
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 fo...
Article
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% boy...
Article
Full-text available
Data analysis requires new approaches in many domains for evaluating tools and techniques , particularly when the data sets grow large and more complex. Evaluation–as–a– service (EaaS) was coined as a term to represent evaluation approaches based on APIs, virtual machines or source code submission, different from the common paradigm of evaluating t...
Article
Full-text available
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...
Article
So, besides this amusing parallel between data and children, what have we learned? We are reminded to get identifiers for our data, encourage our data to socialize with other data, and plan in advance for the long-term archival of our data. If we can do this in a well-controlled environment, the benefits, individually and as a community, in terms c...
Article
Dyslexia and language impairment (LI) are complex traits with substantial genetic components. We recently completed an association scan of the DYX2 locus, where we observed associations of markers in DCDC2, KIAA0319, ACOT13, and FAM65B with reading-, language-, and IQ-related traits. Additionally, the effects of reading-associated DYX3 markers were...
Data
Table S1. The goal of this doc is to keep track of publications that have reported RRIDs and cross check the RRID, to ensure the authors are using the correct ID.
Article
Full-text available
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...
Article
Full-text available
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 ans...
Article
Full-text available
Article
Full-text available
Background and Aims—Growing evidence suggests abnormalities in brain morphology including hippocampal structure in patients with methamphetamine (MA) dependence. Yet little is known about the possible gender difference. This study was performed to examine hippocampal volume in abstinent male and female MA users, and to further explore its relations...
Article
Full-text available
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 m...
Article
After participating in this activity, learners should be better able to:Assess the resting state and diffusion tensor imaging connectivity literature regarding subjects with autism spectrum disorder. 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 umbr...
Article
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...
Article
Full-text available
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 ans...
Article
Full-text available
Dyslexia and language impairment (LI) are complex traits with substantial genetic components. We recently completed an association scan of the DYX2 locus, where we observed associations of markers in DCDC2, KIAA0319, ACOT13, and FAM65B with reading-, language-, and IQ-related traits. Additionally, the effects of reading-associated DYX3 markers were...
Article
Socioeconomic disparities are associated with differences in cognitive development. The extent to which this translates to disparities in brain structure is unclear. We investigated relationships between socioeconomic factors and brain morphometry, independently of genetic ancestry, among a cohort of 1,099 typically developing individuals between 3...