Education & Certifications

  • PhD, Stony Brook University, Integrative Neuroscience (2013)
  • MA, Stony Brook University, Psychology (2010)
  • BA, Clark University, Psychology (2008)
  • Certified Instructor, Software Carpentry

All Publications

  • Evaluation of Data Sharing After Implementation of the International Committee of Medical Journal Editors Data Sharing Statement Requirement. JAMA network open Danchev, V. n., Min, Y. n., Borghi, J. n., Baiocchi, M. n., Ioannidis, J. P. 2021; 4 (1): e2033972


    The benefits of responsible sharing of individual-participant data (IPD) from clinical studies are well recognized, but stakeholders often disagree on how to align those benefits with privacy risks, costs, and incentives for clinical trialists and sponsors. The International Committee of Medical Journal Editors (ICMJE) required a data sharing statement (DSS) from submissions reporting clinical trials effective July 1, 2018. The required DSSs provide a window into current data sharing rates, practices, and norms among trialists and sponsors.To evaluate the implementation of the ICMJE DSS requirement in 3 leading medical journals: JAMA, Lancet, and New England Journal of Medicine (NEJM).This is a cross-sectional study of clinical trial reports published as articles in JAMA, Lancet, and NEJM between July 1, 2018, and April 4, 2020. Articles not eligible for DSS, including observational studies and letters or correspondence, were excluded. A MEDLINE/PubMed search identified 487 eligible clinical trials in JAMA (112 trials), Lancet (147 trials), and NEJM (228 trials). Two reviewers evaluated each of the 487 articles independently.Publication of clinical trial reports in an ICMJE medical journal requiring a DSS.The primary outcomes of the study were declared data availability and actual data availability in repositories. Other captured outcomes were data type, access, and conditions and reasons for data availability or unavailability. Associations with funding sources were examined.A total of 334 of 487 articles (68.6%; 95% CI, 64%-73%) declared data sharing, with nonindustry NIH-funded trials exhibiting the highest rates of declared data sharing (89%; 95% CI, 80%-98%) and industry-funded trials the lowest (61%; 95% CI, 54%-68%). However, only 2 IPD sets (0.6%; 95% CI, 0.0%-1.5%) were actually deidentified and publicly available as of April 10, 2020. The remaining were supposedly accessible via request to authors (143 of 334 articles [42.8%]), repository (89 of 334 articles [26.6%]), and company (78 of 334 articles [23.4%]). Among the 89 articles declaring that IPD would be stored in repositories, only 17 (19.1%) deposited data, mostly because of embargo and regulatory approval. Embargo was set in 47.3% of data-sharing articles (158 of 334), and in half of them the period exceeded 1 year or was unspecified.Most trials published in JAMA, Lancet, and NEJM after the implementation of the ICMJE policy declared their intent to make clinical data available. However, a wide gap between declared and actual data sharing exists. To improve transparency and data reuse, journals should promote the use of unique pointers to data set location and standardized choices for embargo periods and access requirements.

    View details for DOI 10.1001/jamanetworkopen.2020.33972

    View details for PubMedID 33507256

  • Data management and sharing: Practices and perceptions of psychology researchers. PloS one Borghi, J. A., Van Gulick, A. E. 2021; 16 (5): e0252047


    Research data is increasingly viewed as an important scholarly output. While a growing body of studies have investigated researcher practices and perceptions related to data sharing, information about data-related practices throughout the research process (including data collection and analysis) remains largely anecdotal. Building on our previous study of data practices in neuroimaging research, we conducted a survey of data management practices in the field of psychology. Our survey included questions about the type(s) of data collected, the tools used for data analysis, practices related to data organization, maintaining documentation, backup procedures, and long-term archiving of research materials. Our results demonstrate the complexity of managing and sharing data in psychology. Data is collected in multifarious forms from human participants, analyzed using a range of software tools, and archived in formats that may become obsolete. As individuals, our participants demonstrated relatively good data management practices, however they also indicated that there was little standardization within their research group. Participants generally indicated that they were willing to change their current practices in light of new technologies, opportunities, or requirements.

    View details for DOI 10.1371/journal.pone.0252047

    View details for PubMedID 34019600

  • Surgical Stabilization of Rib Fracture to Mitigate Pulmonary Complication and Mortality: A Systematic Review and Bayesian Meta-Analysis. Journal of the American College of Surgeons Choi, J. n., Gomez, G. I., Kaghazchi, A. n., Borghi, J. A., Spain, D. A., Forrester, J. D. 2020

    View details for DOI 10.1016/j.jamcollsurg.2020.10.022

    View details for PubMedID 33212228

  • Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers. PloS one Borghi, J. A., Van Gulick, A. E. 2018; 13 (7): e0200562


    Neuroimaging methods such as magnetic resonance imaging (MRI) involve complex data collection and analysis protocols, which necessitate the establishment of good research data management (RDM). Despite efforts within the field to address issues related to rigor and reproducibility, information about the RDM-related practices and perceptions of neuroimaging researchers remains largely anecdotal. To inform such efforts, we conducted an online survey of active MRI researchers that covered a range of RDM-related topics. Survey questions addressed the type(s) of data collected, tools used for data storage, organization, and analysis, and the degree to which practices are defined and standardized within a research group. Our results demonstrate that neuroimaging data is acquired in multifarious forms, transformed and analyzed using a wide variety of software tools, and that RDM practices and perceptions vary considerably both within and between research groups, with trainees reporting less consistency than faculty. Ratings of the maturity of RDM practices from ad-hoc to refined were relatively high during the data collection and analysis phases of a project and significantly lower during the data sharing phase. Perceptions of emerging practices including open access publishing and preregistration were largely positive, but demonstrated little adoption into current practice.

    View details for DOI 10.1371/journal.pone.0200562

    View details for PubMedID 30011302

  • Support Your Data: A Research Data Management Guide for Researchers Research Ideas and Outcomes Borghi, J. A., Abrams, S., Lowenberg, D., Simms, S., Chodacki, J. 2018; 4

    View details for DOI 10.3897/rio.4.e26439

  • Alterations in visual cortical activation and connectivity with prefrontal cortex during working memory updating in major depressive disorder NEUROIMAGE-CLINICAL Le, T. M., Borghi, J. A., Kujawa, A. J., Klein, D. N., Leung, H. 2017; 14: 43–53


    The present study examined the impacts of major depressive disorder (MDD) on visual and prefrontal cortical activity as well as their connectivity during visual working memory updating and related them to the core clinical features of the disorder. Impairment in working memory updating is typically associated with the retention of irrelevant negative information which can lead to persistent depressive mood and abnormal affect. However, performance deficits have been observed in MDD on tasks involving little or no demand on emotion processing, suggesting dysfunctions may also occur at the more basic level of information processing. Yet, it is unclear how various regions in the visual working memory circuit contribute to behavioral changes in MDD. We acquired functional magnetic resonance imaging data from 18 unmedicated participants with MDD and 21 age-matched healthy controls (CTL) while they performed a visual delayed recognition task with neutral faces and scenes as task stimuli. Selective working memory updating was manipulated by inserting a cue in the delay period to indicate which one or both of the two memorized stimuli (a face and a scene) would remain relevant for the recognition test. Our results revealed several key findings. Relative to the CTL group, the MDD group showed weaker postcue activations in visual association areas during selective maintenance of face and scene working memory. Across the MDD subjects, greater rumination and depressive symptoms were associated with more persistent activation and connectivity related to no-longer-relevant task information. Classification of postcue spatial activation patterns of the scene-related areas was also less consistent in the MDD subjects compared to the healthy controls. Such abnormalities appeared to result from a lack of updating effects in postcue functional connectivity between prefrontal and scene-related areas in the MDD group. In sum, disrupted working memory updating in MDD was revealed by alterations in activity patterns of the visual association areas, their connectivity with the prefrontal cortex, and their relationship with core clinical characteristics. These results highlight the role of information updating deficits in the cognitive control and symptomatology of depression.

    View details for DOI 10.1016/j.nicl.2017.01.004

    View details for Web of Science ID 000405984300005

    View details for PubMedID 28138426

    View details for PubMedCentralID PMC5257188