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

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

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

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 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. Methods: 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. Results: 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. Conclusions: 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

Placenta Previa in the Second Trimester: Sonographic and Clinical Factors Associated with Its Resolution

To identify characteristics that predict resolution of placenta previa and to develop a clinical model for likelihood of resolution

Initial Bloom Color is a Poor Predictor of Retail Color Stability in Lamb Loin Meat

The rapid browning of lamb meat on retail display reduces its appeal to consumers and thus the marketability of lamb meat. Predicting the rate of meat browning on retail display would allow retailers to effectively manage this issue. The ability of bloomed meat color at the start of retail display to predict meat browning over subsequent retail display was investigated in lamb loin meat. Mixed breed lambs (n = 4404) produced at 5 sites over 5 yr were slaughtered at ∼23kg carcass weight and measured for loin pH at 24 h, myoglobin, iron and zinc concentrations, isocitrate dehydrogenase activity and intramuscular fat. Loin meat was aged for 5 d before being re-sliced and overwrapped for color measurement over a 72 h simulated retail display. Meat redness (R630/R580) was measured after blooming and every 24 h across display using a Hunterlab spectrophotometer. Simple and partial correlation coefficients between initial and subsequent R630/R580 measures over the display were low (≤ 0.4). Accounting for key muscle traits influencing meat color such as pH24, myoglobin, iron or intramuscular fat concentration did not improve these correlations between bloomed meat color and subsequent meat color over retail display. Therefore bloomed meat color at the start of display is not a useful predictor of meat browning after 24 h of retail display. Alternatively, correlations between 24, 48, and 72 h R630/R580 were > 0.8, suggesting that meat color measured from 24 h of display can accurately predict subsequent retail meat browning

Towards a consensus around standards for smartphone apps and digital mental health

Mental disorders impact one in four people worldwide, yet access to care is challenging for those who suffer from them1. Mental health apps offer the potential to overcome access barriers for the nearly three billion people projected to own a smartphone by 2020. Although there are over 10,000 mental health apps commercially available, there are few resources available to help end users (patients, clinicians and health care organizations) to evaluate the quality and suitability of these products. Thus, there is an urgent need for an agreement about appropriate standards, principles and practices in research and evaluation of these tools.We represent leaders in mHealth research, industry and health care systems from around the globe, and we seek here to promote consensus on implementing these standards and principles for the evaluation of mental health apps. At a minimum, standards should include consideration of: a) data safety and privacy, b) effectiveness, c) user experience/adherence, d) data integration. Our consensus on the challenges and recommendations in each of these areas is presented below

A global database for metacommunity ecology, integrating species, traits, environment and space

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology

Human Immunodeficiency Virus Impairs Reverse Cholesterol Transport from Macrophages

Several steps of HIV-1 replication critically depend on cholesterol. HIV infection is associated with profound changes in lipid and lipoprotein metabolism and an increased risk of coronary artery disease. Whereas numerous studies have investigated the role of anti-HIV drugs in lipodystrophy and dyslipidemia, the effects of HIV infection on cellular cholesterol metabolism remain uncharacterized. Here, we demonstrate that HIV-1 impairs ATP-binding cassette transporter A1 (ABCA1)-dependent cholesterol efflux from human macrophages, a condition previously shown to be highly atherogenic. In HIV-1–infected cells, this effect was mediated by Nef. Transfection of murine macrophages with Nef impaired cholesterol efflux from these cells. At least two mechanisms were found to be responsible for this phenomenon: first, HIV infection and transfection with Nef induced post-transcriptional down-regulation of ABCA1; and second, Nef caused redistribution of ABCA1 to the plasma membrane and inhibited internalization of apolipoprotein A-I. Binding of Nef to ABCA1 was required for down-regulation and redistribution of ABCA1. HIV-infected and Nef-transfected macrophages accumulated substantial amounts of lipids, thus resembling foam cells. The contribution of HIV-infected macrophages to the pathogenesis of atherosclerosis was supported by the presence of HIV-positive foam cells in atherosclerotic plaques of HIV-infected patients. Stimulation of cholesterol efflux from macrophages significantly reduced infectivity of the virions produced by these cells, and this effect correlated with a decreased amount of virion-associated cholesterol, suggesting that impairment of cholesterol efflux is essential to ensure proper cholesterol content in nascent HIV particles. These results reveal a previously unrecognized dysregulation of intracellular lipid metabolism in HIV-infected macrophages and identify Nef and ABCA1 as the key players responsible for this effect. Our findings have implications for pathogenesis of both HIV disease and atherosclerosis, because they reveal the role of cholesterol efflux impairment in HIV infectivity and suggest a possible mechanism by which HIV infection of macrophages may contribute to increased risk of atherosclerosis in HIV-infected patients

A tale of two towns: A comparative study exploring the possibilities and pitfalls of social capital among people seeking recovery from substance misuse

Background: Social capital has become an influential concept in debating and understanding the modern world. Within the drug and alcohol sector, the concept of ‘recovery capital’ has gained traction with researchers suggesting that people who have access to such capital are better placed to overcome their substance use-related problems than those who do not (Cloud and Granfield, 2008), leading to requests for interventions that focus on building social capital networks (Neale & Stevenson, 2015). While accepting that the concept of social capital has enormous potential for addressing the problems associated with drug use, this paper also considers its ‘dark side’. Methods: Data were drawn from semi-structured interviews with 180 participants including 135 people who use drugs and 45 people who formerly used drugs. Results: High levels of trust, acquired through the establishment of dense social networks, are required to initiate recovery. However, these ‘strong bonds’ may also lead to the emergence of what is perceived by others as an exclusive social network that limits membership to those who qualify and abide by the ‘rules’ of the recovery community, particularly around continuous abstinence. Conclusions: Depending on the nature of the networks and the types of links participants have into them being socially connected can both inhibit and encourage recovery. Therefore, the successful application of social capital within the drugs and alcohol field requires a consideration of not only the presence or absence of social connections but their nature, the value they produce, and the social contexts within which they are developed

Role of Second-Trimester Genetic Sonography After Down Syndrome Screening

To estimate the effectiveness of second-trimester genetic sonography in modifying Down syndrome screening test results

Preconceptional Folate Supplementation and the Risk of Spontaneous Preterm Birth: A Cohort Study

In an analysis of a cohort of pregnant women, Radek Bukowski and colleagues describe an association between taking folic acid supplements and a reduction in the risk of preterm birth