Background: The success of new sequencing technologies and informatic methods for identifying genes has made establishing gene product function a critical rate limiting step in progressing the molecular sciences. We present a method to functionally mine genomes for useful activities in vivo, using an unusual property of a member of the poxvirus family to demonstrate this screening approach.
Results: The genome of Parapoxvirus ovis (Orf virus) was sequenced, annotated, and then used to PCR-amplify its open-reading-frames. Employing a cloning-independent protocol, a viral expression-library was rapidly built and arrayed into sub-library pools. These were directly delivered into mice as expressible cassettes and assayed for an immune-modulating activity associated with parapoxvirus infection. The product of the B2L gene, a homolog of vaccinia F13L, was identified as the factor eliciting immune cell accumulation at sites of skin inoculation. Administration of purified B2 protein also elicited immune cell accumulation activity, and additionally was found to serve as an adjuvant for antigen-specific responses. Co-delivery of the B2L gene with an influenza gene-vaccine significantly improved protection in mice. Furthermore, delivery of the B2L expression construct, without antigen, non-specifically reduced tumor growth in murine models of cancer.
Conclusion: A streamlined, functional approach to genome-wide screening of a biological activity in vivo is presented. Its application to screening in mice for an immune activity elicited by the pathogen genome of Parapoxvirus ovis yielded a novel immunomodulator. In this inverted discovery method, it was possible to identify the adjuvant responsible for a function of interest prior to a mechanistic study of the adjuvant. The non-specific immune activity of this modulator, B2, is similar to that associated with administration of inactivated particles to a host or to a live viral infection. Administration of B2 may provide the opportunity to significantly impact host immunity while being itself only weakly recognized. The functional genomics method used to pinpoint B2 within an ORFeome may be more broadly applicable to screening for other biological activities in an animal.
Background: Immunosignaturing is a new peptide microarray based technology for profiling of humoral immune responses. Despite new challenges, immunosignaturing gives us the opportunity to explore new and fundamentally different research questions. In addition to classifying samples based on disease status, the complex patterns and latent factors underlying immunosignatures, which we attempt to model, may have a diverse range of applications.
Methods: We investigate the utility of a number of statistical methods to determine model performance and address challenges inherent in analyzing immunosignatures. Some of these methods include exploratory and confirmatory factor analyses, classical significance testing, structural equation and mixture modeling.
Results: We demonstrate an ability to classify samples based on disease status and show that immunosignaturing is a very promising technology for screening and presymptomatic screening of disease. In addition, we are able to model complex patterns and latent factors underlying immunosignatures. These latent factors may serve as biomarkers for disease and may play a key role in a bioinformatic method for antibody discovery.
Conclusion: Based on this research, we lay out an analytic framework illustrating how immunosignatures may be useful as a general method for screening and presymptomatic screening of disease as well as antibody discovery.
Background: High-throughput technologies such as DNA, RNA, protein, antibody and peptide microarrays are often used to examine differences across drug treatments, diseases, transgenic animals, and others. Typically one trains a classification system by gathering large amounts of probe-level data, selecting informative features, and classifies test samples using a small number of features. As new microarrays are invented, classification systems that worked well for other array types may not be ideal. Expression microarrays, arguably one of the most prevalent array types, have been used for years to help develop classification algorithms. Many biological assumptions are built into classifiers that were designed for these types of data. One of the more problematic is the assumption of independence, both at the probe level and again at the biological level. Probes for RNA transcripts are designed to bind single transcripts. At the biological level, many genes have dependencies across transcriptional pathways where co-regulation of transcriptional units may make many genes appear as being completely dependent. Thus, algorithms that perform well for gene expression data may not be suitable when other technologies with different binding characteristics exist. The immunosignaturing microarray is based on complex mixtures of antibodies binding to arrays of random sequence peptides. It relies on many-to-many binding of antibodies to the random sequence peptides. Each peptide can bind multiple antibodies and each antibody can bind multiple peptides. This technology has been shown to be highly reproducible and appears promising for diagnosing a variety of disease states. However, it is not clear what is the optimal classification algorithm for analyzing this new type of data.
Results: We characterized several classification algorithms to analyze immunosignaturing data. We selected several datasets that range from easy to difficult to classify, from simple monoclonal binding to complex binding patterns in asthma patients. We then classified the biological samples using 17 different classification algorithms. Using a wide variety of assessment criteria, we found ‘Naïve Bayes’ far more useful than other widely used methods due to its simplicity, robustness, speed and accuracy.
Conclusions: ‘Naïve Bayes’ algorithm appears to accommodate the complex patterns hidden within multilayered immunosignaturing microarray data due to its fundamental mathematical properties.
Background: A growing body of research recommends controlling alcohol availability to reduce harm. Various common approaches, however, provide dramatically different pictures of the physical availability of alcohol. This limits our understanding of the distribution of alcohol access, the causes and consequences of this distribution, and how best to reduce harm. The aim of this study is to introduce both a gravity potential measure of access to alcohol outlets, comparing its strengths and weaknesses to other popular approaches, and an empirically-derived taxonomy of neighborhoods based on the type of alcohol access they exhibit.
Methods: We obtained geospatial data on Seattle, including the location of 2402 alcohol outlets, United States Census Bureau estimates on 567 block groups, and a comprehensive street network. We used exploratory spatial data analysis and employed a measure of inter-rater agreement to capture differences in our taxonomy of alcohol availability measures.
Results: Significant statistical and spatial variability exists between measures of alcohol access, and these differences have meaningful practical implications. In particular, standard measures of outlet density (e.g., spatial, per capita, roadway miles) can lead to biased estimates of physical availability that over-emphasize the influence of the control variables. Employing a gravity potential approach provides a more balanced, geographically-sensitive measure of access to alcohol outlets.
Conclusions: Accurately measuring the physical availability of alcohol is critical for understanding the causes and consequences of its distribution and for developing effective evidence-based policy to manage the alcohol outlet licensing process. A gravity potential model provides a superior measure of alcohol access, and the alcohol access-based taxonomy a helpful evidence-based heuristic for scholars and local policymakers.
Background: Postmortem memento photography has emerged in Western hospitals as part of compassionate bereavement care for parents facing perinatal death. Many parents endorse this psychosocial intervention, yet implementation varies greatly and little research on parents’ specific needs guides health care professionals. Parents are in crisis and vulnerable after the death of their child, thus best practice is crucial. This study contributes 104 parents’ experiences and opinions toward the understanding of best practice in perinatal bereavement photography.
Methods: Parents who experienced the perinatal death of their child were recruited from U.S.-based bereavement organizations and social media sites. Volunteers completed an anonymous internet survey with open- and closed-ended questions. Direct recommendations and pertinent statements regarding the process of postmortem photography were analyzed for thematic content in keeping with conventional content analysis. Recurrent themes and sub-themes were counted to identify response patterns.
Results: Of 93 parents with pictures, 92 endorsed them. Of 11 without pictures, nine wanted them. Parents made a variety of recommendations regarding appropriate psychosocial support, the consent process, obstacles to photography, logistics of photography, and material aspects of photographs themselves. Overall, parents wanted many pictures and much variety. Some wanted professional photography while others wanted support for taking their own pictures. Parents wanted guidance from staff who respected their particular needs. Many said decisions were difficult during their crisis. Parents who were initially resistant expressed current appreciation for pictures or expressed regret that they had not participated. Parents recommended that professionals strongly encourage parents to create memento photos despite parents’ initial reservations. Persistent cultural reasons against photography emerged in one case. Quotes by parents illuminate themes and enable respondents to speak directly to health care professionals.
Conclusions: Parents overwhelmingly support postmortem bereavement photography when conducted sensitively, even if imperfectly executed. Providers significantly influence parents during their crises; mindful, patient-centered care with appropriate respect for difference is necessary. Providers must understand the importance of postmortem photographs to parents who have limited opportunity to capture memories of their child. Hospitals should provide education and support for this important psychosocial intervention.
Immunosignaturing shows promise as a general approach to diagnosis. It has been shown to detect immunological signs of infection early during the course of disease and to distinguish Alzheimer’s disease from healthy controls. Here we test whether immunosignatures correspond to clinical classifications of disease using samples from people with brain tumors. Blood samples from patients undergoing craniotomies for therapeutically naïve brain tumors with diagnoses of astrocytoma (23 samples), Glioblastoma multiforme (22 samples), mixed oligodendroglioma/astrocytoma (16 samples), oligodendroglioma (18 samples), and 34 otherwise healthy controls were tested by immunosignature. Because samples were taken prior to adjuvant therapy, they are unlikely to be perturbed by non-cancer related affects. The immunosignaturing platform distinguished not only brain cancer from controls, but also pathologically important features about the tumor including type, grade, and the presence or absence of O6-methyl-guanine-DNA methyltransferase methylation promoter (MGMT), an important biomarker that predicts response to temozolomide in Glioblastoma multiformae patients.
Background: There is much concern regarding undisclosed corporate authorship (“ghostwriting”) in the peer-reviewed medical literature. However, there are no studies of how disclosure of ghostwriting alone impacts the perceived credibility of research results.
Findings: We conducted a randomized vignette study with experienced nurses (n = 67), using a fictional study of antidepressant medication. The vignette described a randomized controlled trial and gave efficacy and adverse effect rates. Participants were randomly assigned to one of two authorship conditions, either (a) traditional authorship (n = 35) or (b) ghostwritten paper (n = 32), and then completed a perceived credibility scale. Our primary hypothesis was that the median perceived credibility score total would be lower in the group assigned to the ghostwritten paper. Our secondary hypotheses were that participants randomized to the ghostwritten condition would be less likely to (a) recommend the medication, and (b) want the psychiatrist in the vignette as their own clinician. We also asked respondents to estimate efficacy and adverse effect rates for the medication.
There was a statistically significant difference in perceived credibility among those assigned to the ghostwriting condition. This amounted to a difference of 9.0 points on the 35-point perceived credibility scale as tested through the Mann–Whitney U test. There was no statistically significant difference between groups in terms of recommending the medication, wanting the featured clinician as their own, or in estimates of efficacy or adverse effects (p > .05 for all such comparisons).
Conclusion: In this study, disclosure of ghostwriting resulted in lower perceived credibility ratings.
Background: Despite improvements in maternity healthcare services over the last few decades, more than 2.7 million babies worldwide are stillborn each year. The global health agenda is silent about stillbirth, perhaps, in part, because its wider impact has not been systematically analysed or understood before now across the world. Our study aimed to systematically review, evaluate and summarise the current evidence regarding the psychosocial impact of stillbirth to parents and their families, with the aim of improving guidance in bereavement care worldwide.
Methods: Systematic review and meta-summary (quantitative aggregation of qualitative findings) of quantitative, qualitative, and mixed-methods studies. All languages and countries were included.
Results: Two thousand, six hundred and nineteen abstracts were identified; 144 studies were included. Frequency effect sizes (FES %) were calculated for each theme, as a measure of their prevalence in the literature. Themes ranged from negative psychological symptoms post bereavement (77 · 1) and in subsequent pregnancies (27 · 1), to disenfranchised grief (31 · 2), and incongruent grief (28 · 5), There was also impact on siblings (23 · 6) and on the wider family (2 · 8). They included mixed-feelings about decisions made when the baby died (12 · 5), avoidance of memories (13 · 2), anxiety over other children (7 · 6), chronic pain and fatigue (6 · 9), and a different approach to the use of healthcare services (6 · 9). Some themes were particularly prominent in studies of fathers; grief suppression (avoidance)(18 · 1), employment difficulties, financial debt (5 · 6), and increased substance use (4 · 2). Others found in studies specific to mothers included altered body image (3 · 5) and impact on quality of life (2 · 1). Counter-intuitively, Some themes had mixed connotations. These included parental pride in the baby (5 · 6), motivation for engagement in healthcare improvement (4 · 2) and changed approaches to life and death, self-esteem, and own identity (25 · 7). In studies from low/middle income countries, stigmatisation (13 · 2) and pressure to prioritise or delay conception (9) were especially prevalent.
Conclusion: Experiencing the birth of a stillborn child is a life-changing event. The focus of the consequences may vary with parent gender and country. Stillbirth can have devastating psychological, physical and social costs, with ongoing effects on interpersonal relationships and subsequently born children. However, parents who experience the tragedy of stillbirth can develop resilience and new life-skills and capacities. Future research should focus on developing interventions that may reduce the psychosocial cost of stillbirth.
The Arctic, even more so than other parts of the world, has warmed substantially over the past few decades. Temperature and humidity influence the rate of development, survival and reproduction of pathogens and thus the incidence and prevalence of many infectious diseases. Higher temperatures may also allow infected host species to survive winters in larger numbers, increase the population size and expand their habitat range. The impact of these changes on human disease in the Arctic has not been fully evaluated. There is concern that climate change may shift the geographic and temporal distribution of a range of infectious diseases. Many infectious diseases are climate sensitive, where their emergence in a region is dependent on climate-related ecological changes. Most are zoonotic diseases, and can be spread between humans and animals by arthropod vectors, water, soil, wild or domestic animals. Potentially climate-sensitive zoonotic pathogens of circumpolar concern include Brucella spp., Toxoplasma gondii, Trichinella spp., Clostridium botulinum, Francisella tularensis, Borrelia burgdorferi, Bacillus anthracis, Echinococcus spp., Leptospira spp., Giardia spp., Cryptosporida spp., Coxiella burnetti, rabies virus, West Nile virus, Hantaviruses, and tick-borne encephalitis viruses.
There is an increasing awareness that health care must move from post-symptomatic treatment to presymptomatic intervention. An ideal system would allow regular inexpensive monitoring of health status using circulating antibodies to report on health fluctuations. Recently, we demonstrated that peptide microarrays can do this through antibody signatures (immunosignatures). Unfortunately, printed microarrays are not scalable. Here we demonstrate a platform based on fabricating microarrays (~10 M peptides per slide, 330,000 peptides per assay) on silicon wafers using equipment common to semiconductor manufacturing. The potential of these microarrays for comprehensive health monitoring is verified through the simultaneous detection and classification of six different infectious diseases and six different cancers. Besides diagnostics, these high-density peptide chips have numerous other applications both in health care and elsewhere.