Survey of 800+ data sets from human tissue and body fluid reveals xenomiRs are likely artifacts

miRNAs are small 22-nucleotide RNAs that can post-transcriptionally regulate gene expression. It has been proposed that dietary plant miRNAs can enter the human bloodstream and regulate host transcripts; however, these findings have been widely disputed. We here conduct the first comprehensive meta-study in the field, surveying the presence and abundances of cross-species miRNAs (xenomiRs) in 824 sequencing data sets from various human tissues and body fluids. We find that xenomiRs are commonly present in tissues (17%) and body fluids (69%); however, the abundances are low, comprising 0.001% of host human miRNA counts. Further, we do not detect a significant enrichment of xenomiRs in sequencing data originating from tissues and body fluids that are exposed to dietary intake (such as liver). Likewise, there is no significant depletion of xenomiRs in tissues and body fluids that are relatively separated from the main bloodstream (such as brain and cerebro-spinal fluids). Interestingly, the majority (81%) of body fluid xenomiRs stem from rodents, which are a rare human dietary contribution but common laboratory animals. Body fluid samples from the same studies tend to group together when clustered by xenomiR compositions, suggesting technical batch effects. Last, we performed carefully designed and controlled animal feeding studies, in which we detected no transfer of plant miRNAs into rat blood, or bovine milk sequences into piglet blood. In summary, our comprehensive computational and experimental results indicate that xenomiRs originate from technical artifacts rather than dietary intake.

Parental experiences of providing skin-to-skin care to their newborn infant--part 2: a qualitative meta-synthesis

AIM

To synthesize and interpret qualitative research findings focusing on parental experiences of skin-to-skin care (SSC) for newborn infants.

BACKGROUND

SSC induces many benefits for newborn infants and their parents. Three meta-analyses have been conducted on physiological outcomes, but no previous qualitative meta-synthesis on parental experiences of SSC has been identified.

DESIGN

The present meta-synthesis was guided by the methodology described by Paterson and co-workers.

DATA SOURCES

Four databases were searched, without year or language limitations, up until December 2013. Manual searches were also performed. The searches and subsequent quality appraisal resulted in the inclusion of 29 original qualitative papers from 9 countries, reporting experiences from 401 mothers and 94 fathers.

REVIEW METHODS

The meta-synthesis entails a meta-data analysis, analysis of meta-method, and meta-theory in the included primary studies. Based on the three analyses, the meta-synthesis represents a new interpretation of a phenomenon. The results of the meta-data analysis have been presented as a qualitative systematic review in a separate paper.

RESULTS

When synthesizing and interpreting the findings from the included analyses, a theoretical model of Becoming a parent under unfamiliar circumstances emerged. Providing SSC seems to be a restorative as well as an energy-draining experience. A supportive environment has been described as facilitating the restorative experience, whereas obstacles in the environment seem to make the provision of SSC energy-draining for parents. When the process is experienced as positive, it facilitates the growth of parental self-esteem and makes the parents ready to assume full responsibility for their child.

CONCLUSION

The results show that SSC can be interpreted not only as a family-including and important health care intervention but also in terms of actually becoming a parent. The process of becoming a parent in this specific situation is influenced by external factors in three different levels; family and friends, community, and society at large. The descriptions of providing SSC are similar to what has previously been described as the natural process of becoming a mother or a father.

Parental experiences of providing skin-to-skin care to their newborn infant--part 1: a qualitative systematic review

AIM

To describe parental experiences of providing skin-to-skin care (SSC) to their newborn infants.

BACKGROUND

SSC care for newborn infants has been reported to have positive physiological and psychological benefits to the infants and their parents. No systematic review regarding parental experiences has been identified.

DESIGN

In this first part of a meta-study, the findings of a systematic literature review on parental experience of SSC care are presented.

DATA SOURCES

Four databases were searched, without year or language limitations, up until December 2013. Manual searches were performed in reference lists and in a bibliography of the topic.

REVIEW METHODS

After a quality-appraisal process, data from the original articles were extracted and analysed using qualitative content analysis.

RESULTS

The systematic and manual searches led to the inclusion of 29 original qualitative papers from nine countries, reporting experiences from 401 mothers and 94 fathers. Two themes that characterized the provision of SSC emerged: a restoring experience and an energy-draining experience.

CONCLUSION

This review has added scientific and systematic knowledge about parental experiences of providing SSC. Further research about fathers' experiences is recommended.

Parents' experiences of neonatal transfer. A meta-study of qualitative research 2000-2017

Transfers of critically ill neonates are frequent phenomena. Even though parents' participation is regarded as crucial in neonatal care, a transfer often means that parents and neonates are separated. A systematic review of the parents' experiences of neonatal transfer is lacking. This paper describes a meta-study addressing qualitative research about parents' experiences of neonatal transfer. Through deconstruction and reflections of theories, methods, and empirical data, the aim was to achieve a deeper understanding of theoretical, empirical, contextual, historical, and methodological issues of qualitative studies concerning parents' experiences of neonatal transfer over the course of this meta-study (2000-2017). Meta-theory and meta-method analyses showed that caring, transition, and family-centered care were main theoretical frames applied and that interviewing with a small number of participants was the preferred data collection method. The meta-data-analysis showed that transfer was a scary, unfamiliar, and threatening experience for the parents; they were losing familiar context, were separated from their neonate, and could feel their parenthood disrupted. We identified 'wavering and wandering' as a metaphoric representation of the parents' experiences. The findings add knowledge about meta-study as an approach for comprehensive qualitative research and point at the value of meta-theory and meta-method analyses.

Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis

BACKGROUND

Different methods have been developed to infer regulatory networks from heterogeneous omics datasets and to construct co-expression networks. Each algorithm produces different networks and efforts have been devoted to automatically integrate them into consensus sets. However each separate set has an intrinsic value that is diluted and partly lost when building a consensus network. Here we present a methodology to generate co-expression networks and, instead of a consensus network, we propose an integration framework where the different networks are kept and analysed with additional tools to efficiently combine the information extracted from each network.

RESULTS

We developed a workflow to efficiently analyse information generated by different inference and prediction methods. Our methodology relies on providing the user the means to simultaneously visualise and analyse the coexisting networks generated by different algorithms, heterogeneous datasets, and a suite of analysis tools. As a show case, we have analysed the gene co-expression networks of Mycobacterium tuberculosis generated using over 600 expression experiments. Regarding DNA damage repair, we identified SigC as a key control element, 12 new targets for LexA, an updated LexA binding motif, and a potential mismatch repair system. We expanded the DevR regulon with 27 genes while identifying 9 targets wrongly assigned to this regulon. We discovered 10 new genes linked to zinc uptake and a new regulatory mechanism for ZuR. The use of co-expression networks to perform system level analysis allows the development of custom made methodologies. As show cases we implemented a pipeline to integrate ChIP-seq data and another method to uncover multiple regulatory layers.

CONCLUSIONS

Our workflow is based on representing the multiple types of information as network representations and presenting these networks in a synchronous framework that allows their simultaneous visualization while keeping specific associations from the different networks. By simultaneously exploring these networks and metadata, we gained insights into regulatory mechanisms in M. tuberculosis that could not be obtained through the separate analysis of each data type.

Meta-Study as Diagnostic: Toward Content Over Form in Qualitative Synthesis

Having previously conducted qualitative syntheses of the diabetes literature, we wanted to explore the changes in theoretical approaches, methodological practices, and the construction of substantive knowledge which have recently been presented in the qualitative diabetes literature. The aim of this research was to explore the feasibility of synthesizing existing qualitative syntheses of patient perspectives of diabetes using meta-study methodology. A systematic review of qualitative literature, published between 2000 and 2013, was conducted. Six articles were identified as qualitative syntheses. The meta-study methodology was used to compare the theoretical, methodological, analytic, and synthetic processes across the six studies, exploring the potential for an overarching synthesis. We identified that while research questions have increasingly concentrated on specific aspects of diabetes, the focus on systematic review processes has led to the neglect of qualitative theory and methods. This can inhibit the production of compelling results with meaningful clinical applications. Although unable to produce a synthesis of syntheses, we recommend that researchers who conduct qualitative syntheses pay equal attention to qualitative traditions and systematic review processes, to produce research products that are both credible and applicable.

Sporting Activities for Individuals Who Experienced Trauma During Their Youth: A Meta-Study

The purpose of this study was to critically examine the qualitative research on childhood trauma survivors' experiences of sporting activities. A comprehensive search of health and social science databases, manual journal searches, and contact with experts yielded 7,395 records. Full-text screening resulted in a final sample of 16 studies. Meta-study methodology was used as a diagnostic tool to rigorously analyze the theory, methods, and findings of the included studies. Studies with explicit connections between philosophy, theory, and methodology resulted in a more robust and critical contribution to the literature. There was much diversity in terms of methodological approaches and qualitative methods which was important in revealing the multifaceted nature of experiences in sporting activities following trauma. Findings from the reviewed studies indicated that a sense of belonging, psychological escape, embodied experience, and the physical and social environmental are important considerations in the study of sporting activities for trauma survivors.

A Meta-Study of Qualitative Research Examining Sport and Recreation Experiences of Indigenous Youth

Participation in sport and recreation may contribute to various holistic benefits among Indigenous youth in Canada. However, there is a need for a consolidated evidence base to support the development of sport and recreation opportunities that could facilitate such holistic benefits. The purpose of this research was to produce a meta-study of qualitative research examining sport and recreation experiences of Indigenous youth in Canada. Following record identification and screening, 20 articles were retained for analysis and synthesis. Strengths and weaknesses of included studies were identified through the meta-method and meta-theory analysis. The meta-data analysis revealed five themes that represent the sport and recreation experiences of Indigenous youth. Working collaboratively with community members, our final meta-synthesis situated these five themes within the integrated Indigenous ecological model. This review consolidates the qualitative evidence base, and provides direction for future research and practice.

Research using hashtags: A meta-synthesis

In the last 20 years, research using hashtags has grown considerably. The changes that occurred in the digital environment have influenced their diffusion and development. Today, there is considerable research on hashtags, their use, and on hashtag activism. Likewise, there is a growing interest in their descriptive measures and their metrics. This article aimed to provide a review of this area of research and studies to outline the traits of hashtag research, which are yet nascent. To achieve this, we used a meta-study to produce a meta-synthesis capable of bringing out similarities and differences in research using hashtags and identifying spaces for the generation of new knowledge.