Investigating people’s attitudes towards participating in longitudinal health research: an intersectionality-informed perspective

BACKGROUND: Increasing evidence suggests that participation proportions in longitudinal health research vary according to sex/gender, age, social class, or migration status. Intersectionality scholarship purports that such social categories cannot be understood in isolation and makes visible the co-dependent nature of the social determinants of health and illness. This paper uses an intersectionality-informed approach in order to expand the understanding of why people participate in health research, and the impact of intersecting social structures and experiences on these attitudes. METHODS: A sample of 80 respondents who had previously either accepted or declined an invitation to participate in the German National Cohort (NAKO) participated in our interview study. Interviews were semi-structured and contained both narrative elements and more structured probes. Data analysis proceeded in two steps: first, the entire data set was analysed thematically (separately for participants and non-participants); second, key themes were compared across self-reported sex/gender, age group and migration status to identify differences and commonalities. RESULTS: Respondents' attitudes towards study participation can be categorised into four themes: wanting to make a contribution, seeking personalised health information, excitement and feeling chosen, and seeking social recognition. Besides citing logistical challenges, non-participants narrated adverse experiences with or attitudes towards science and the healthcare system that deterred them from participating. A range of social experiences and cultural value systems shaped such attitudes; in particular, this includes the cultural authority of science as an arbiter of social questions, transgressing social categories and experiences of marginalisation. Care responsibilities, predominantly borne by female respondents, also impacted upon the decision to take part in NAKO. DISCUSSION: Our findings suggest that for participants, health research constitutes a site of distinction in the sense of making a difference and being distinct or distinguishable, whereas non-participants inhabited an orientation towards science that reflected their subjective marginalisation through science. No clear relationship can thereby be presumed between social location and a particular attitude towards study participation; rather, such attitudes transgress and challenge categorical boundaries. This challenges the understanding of particular populations as more or less disadvantaged, or as more or less inclined to participate in health research

CMMSE2017: On two classes of fourth- and seventh-order vectorial methods with stable behavior

[EN] A family of fourth-order iterative methods without memory, for solving nonlinear systems, and its seventh-order extension, are analyzed. By using complex dynamics tools, their stability and reliability are studied by means of the properties of the rational function obtained when they are applied on quadratic polynomials. The stability of their fixed points, in terms of the value of the parameter, its critical points and their associated parameter planes, etc. give us important information about which members of the family have good properties of stability and whether in any of them appear chaos in the iterative process. The conclusions obtained in this dynamical analysis are used in the numerical section, where an academical problem and also the chemical problem of predicting the diffusion and reaction in a porous catalyst pellet are solved.This research was partially supported by Ministerio de Economia y Competitividad MTM2014-52016-C02-2-P and Generalitat Valenciana PROMETEO/2016/089.Cordero Barbero, A.; Guasp, L.; Torregrosa Sánchez, JR. (2018). CMMSE2017: On two classes of fourth- and seventh-order vectorial methods with stable behavior. Journal of Mathematical Chemistry. 56(7):1902-1923. https://doi.org/10.1007/s10910-017-0814-0S19021923567S. Amat, S. Busquier, Advances in Iterative Methods for Nonlinear Equations (Springer, Berlin, 2016)S. Amat, S. Busquier, S. Plaza, Review of some iterative root-finding methods from a dynamical point of view. Sci. Ser. A Math. Sci. 10, 3–35 (2004)S. Amat, S. Busquier, S. Plaza, A construction of attracting periodic orbits for some classical third-order iterative methods. Comput. Appl. Math. 189, 22–33 (2006)I.K. Argyros, Á.A. Magreñn, On the convergence of an optimal fourth-order family of methods and its dynamics. Appl. Math. Comput. 252, 336–346 (2015)D.K.R. Babajee, A. Cordero, J.R. Torregrosa, Study of multipoint iterative methods through the Cayley quadratic test. Comput. Appl. Math. 291, 358–369 (2016). doi: 10.1016/J.CAM.2014.09.020P. Blanchard, The dynamics of Newton’s method. Proc. Symp. Appl. Math. 49, 139–154 (1994)F.I. Chicharro, A. Cordero, J.R. Torregrosa, Drawing dynamical and parameters planes of iterative families and methods. Sci. World J. 2013, Article ID 780153 (2013)C. Chun, M.Y. Lee, B. Neta, J. Džunić, On optimal fourth-order iterative methods free from second derivative and their dynamics. Appl. Math. Comput. 218, 6427–6438 (2012)A. Cordero, E. Gómez, J.R. Torregrosa, Efficient high-order iterative methods for solving nonlinear systems and their application on heat conduction problems. Complexity 2017, Article ID 6457532 (2017)A. Cordero, J.R. Torregrosa, Variants of Newton’s method using fifth-order quadrature formulas. Appl. Math. Comput. 190, 686–698 (2007)R.L. Devaney, An Introduction to Chaotic Dynamical Systems (Addison-Wesley Publishing Company, Reading, 1989)P.G. Logrado, J.D.M. Vianna, Partitioning technique procedure revisited: formalism and first application to atomic problems. Math. Chem. 22, 107–116 (1997)C.G. Jesudason, I. Numerical nonlinear analysis: differential methods and optimization applied to chemical reaction rate determination. Math. Chem. 49, 1384–1415 (2011)Á.A. Magreñán, Different anomalies in a Jarratt family of iterative root-finding methods. Appl. Math. Comput. 233, 29–38 (2014)M. Mahalakshmi, G. Hariharan, K. Kannan, The wavelet methods to linear and nonlinear reaction-diffusion model arising in mathematical chemistry. Math. Chem. 51(9), 2361–2385 (2013)K. Maleknejad, M. Alizadeh, An efficient numerical scheme for solving Hammerstein integral equation arisen in chemical phenomenon. Proc. Comput. Sci. 3, 361–364 (2011)B. Neta, C. Chun, M. Scott, Basins of attraction for optimal eighth-order methods to find simple roots of nonlinear equations. Appl. Math. Comput. 227, 567–592 (2014)M.S. Petković, B. Neta, L.D. Petković, J. Džunić, Multipoint Methods for Solving Nonlinear Equations (Elsevier, Amsterdam, 2013)R.C. Rach, J.S. Duan, A.M. Wazwaz, Solving coupled Lane–Emden boundary value problems in catalytic diffusion reactions by the Adomian decomposition method. Math. Chem. 52(1), 255–267 (2014)R. Singh, G. Nelakanti, J. Kumar, A new effcient technique for solving two-point boundary value problems for integro-differential equations. Math. Chem. 52, 2030–2051 (2014

Using linear and natural cubic splines, SITAR, and latent trajectory models to characterise nonlinear longitudinal growth trajectories in cohort studies

BACKGROUND: Longitudinal data analysis can improve our understanding of the influences on health trajectories across the life-course. There are a variety of statistical models which can be used, and their fitting and interpretation can be complex, particularly where there is a nonlinear trajectory. Our aim was to provide an accessible guide along with applied examples to using four sophisticated modelling procedures for describing nonlinear growth trajectories. METHODS: This expository paper provides an illustrative guide to summarising nonlinear growth trajectories for repeatedly measured continuous outcomes using (i) linear spline and (ii) natural cubic spline linear mixed-effects (LME) models, (iii) Super Imposition by Translation and Rotation (SITAR) nonlinear mixed effects models, and (iv) latent trajectory models. The underlying model for each approach, their similarities and differences, and their advantages and disadvantages are described. Their application and correct interpretation of their results is illustrated by analysing repeated bone mass measures to characterise bone growth patterns and their sex differences in three cohort studies from the UK, USA, and Canada comprising 8500 individuals and 37,000 measurements from ages 5–40 years. Recommendations for choosing a modelling approach are provided along with a discussion and signposting on further modelling extensions for analysing trajectory exposures and outcomes, and multiple cohorts. RESULTS: Linear and natural cubic spline LME models and SITAR provided similar summary of the mean bone growth trajectory and growth velocity, and the sex differences in growth patterns. Growth velocity (in grams/year) peaked during adolescence, and peaked earlier in females than males e.g., mean age at peak bone mineral content accrual from multicohort SITAR models was 12.2 years in females and 13.9 years in males. Latent trajectory models (with trajectory shapes estimated using a natural cubic spline) identified up to four subgroups of individuals with distinct trajectories throughout adolescence. CONCLUSIONS: LME models with linear and natural cubic splines, SITAR, and latent trajectory models are useful for describing nonlinear growth trajectories, and these methods can be adapted for other complex traits. Choice of method depends on the research aims, complexity of the trajectory, and available data. Scripts and synthetic datasets are provided for readers to replicate trajectory modelling and visualisation using the R statistical computing software. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12874-022-01542-8

Sourcing and long-range transport of particulate organic matter in river bedload: Río Bermejo, Argentina

Fluvial transport of organic carbon from the terrestrial biosphere to the oceans is an important term in the global carbon cycle. Traditionally, the long-term burial flux of fluvial particulate organic carbon (POC) is estimated using river suspended sediment flux; however, organic carbon can also travel in river bedload as coarse particulate organic matter (POMBed). Estimates of fluvial POC export to the ocean are highly uncertain because few studies document POMbed sources, flux, and evolution during long-range fluvial transport from uplands to ocean basins. This knowledge gap limits our ability to determine the global terrestrial organic carbon burial flux. In this study we investigate the flux, sources, and transformations of POMBed during fluvial transport over a ∼1300 km long reach of the Río Bermejo, Argentina, which has no tributary inputs. To constrain sourcing of POMBed, we analyzed the composition and stable hydrogen and carbon isotope ratios (δ2H, δ13C) of plant wax biomarkers from POMBed at six locations along the Río Bermejo and compared this to samples of suspended sediment, soil, leaf litter, and floating organic debris (POMfloat) from both the lowland and headwater river system. Across all samples, we found no discernible differences in n-alkane average chain length or nC29 δ13C, indicting a common origin for all sampled POMBed. Leaf litter and POMfloat nC29 δ2H values decrease with elevation, making it a useful proxy for POMBed source elevation. Biomarker δ2H values suggest that POMBed is a mix of distally derived headwater and locally recruited floodplain sources at all sampling locations. These results indicate that POMBed can be preserved during transport through lowland rivers for hundreds of kilometers. However, the POMBed flux decreases with increasing transport distance, suggesting mechanical comminution of these coarse organic particles and progressive transfer into the suspended load. Our provisional estimates suggest that the carbon flux from POMBed comprises less than 1 % of the suspended load POC flux in the Río Bermejo. While this represents a small portion of the river POC flux, this coarse, high-density material likely has a higher probability of deposition and burial in sedimentary basins, potentially allowing it to be more effective in long-term CO2 drawdown relative to fine suspended particles. Because the rate and ratio of POMBed transport versus comminution likely vary across tectonic and climatic settings, additional research is needed to determine the importance of POMBed in the global carbon cycle.</p

TRANSIT Working Paper # 7

A previous version of this paper has been part of TRANSIT Deliverable 3.3 (July 2016), the second prototype of TSI theory.[Abstract] This working paper presents a set of propositions about the agency and dynamics of transformative social innovation (TSI) that have been developed as part of an EU-funded research project entitled “TRANsformative Social Innovation Theory” (TRANSIT; 2014-2017). These TSI propositions represent first steps towards the development of a new theory of TSI, taking the form of proto-explanations of the agency and dynamics of TSI, based on the bringing together of our empirical observations on TSI and the project's theoretical reviews and theoretical framings. Ideally this working paper should be read in conjunction with the working paper entitled “A framework for transformative social innovation” (Haxeltine et al 2016) which presents in skeletal terms the theoretical and conceptual framing of TSI developed in the TRANSIT project. This TSI framework builds on sustainability transition studies, social innovation research, social psychology studies of empowerment and other several other areas of social theory to deliver a bespoke theoretical and conceptual framework that is grounded in a relational ontology and which is being employed as a platform for the development of a middle-range theory of TSI. Next we provide a very brief overview of some key elements of the framework, in particular how we conceptualise social innovation, transformative change, and transformative social innovation. Propositions were developed for each of four relational dimensions implied by the TSI framework with also a brief statement of the topic addressed by each of the twelve propositions.This article is based on research carried out as part of the Transformative Social Innovation Theory (“TRANSIT”) project, which is funded by the European Union's Seventh Framework Programme (FP7) under grant agreement 61316

GC content around splice sites affects splicing through pre-mRNA secondary structures

<p>Abstract</p> <p>Background</p> <p>Alternative splicing increases protein diversity by generating multiple transcript isoforms from a single gene through different combinations of exons or through different selections of splice sites. It has been reported that RNA secondary structures are involved in alternative splicing. Here we perform a genomic study of RNA secondary structures around splice sites in humans (<it>Homo sapiens</it>), mice (<it>Mus musculus</it>), fruit flies (<it>Drosophila melanogaster</it>), and nematodes (<it>Caenorhabditis elegans</it>) to further investigate this phenomenon.</p> <p>Results</p> <p>We observe that GC content around splice sites is closely associated with the splice site usage in multiple species. RNA secondary structure is the possible explanation, because the structural stability difference among alternative splice sites, constitutive splice sites, and skipped splice sites can be explained by the GC content difference. Alternative splice sites tend to be GC-enriched and exhibit more stable RNA secondary structures in all of the considered species. In humans and mice, splice sites of first exons and long exons tend to be GC-enriched and hence form more stable structures, indicating the special role of RNA secondary structures in promoter proximal splicing events and the splicing of long exons. In addition, GC-enriched exon-intron junctions tend to be overrepresented in tissue-specific alternative splice sites, indicating the functional consequence of the GC effect. Compared with regions far from splice sites and decoy splice sites, real splice sites are GC-enriched. We also found that the GC-content effect is much stronger than the nucleotide-order effect to form stable secondary structures.</p> <p>Conclusion</p> <p>All of these results indicate that GC content is related to splice site usage and it may mediate the splicing process through RNA secondary structures.</p

Effect of Hydrogen Peroxide on Immersion Challenge of Rainbow Trout Fry with Flavobacterium psychrophilum

An experimental model for immersion challenge of rainbow trout fry (Oncorhynchus mykiss) with Flavobacterium psychrophilum, the causative agent of rainbow trout fry syndrome and bacterial cold water disease was established in the present study. Although injection-based infection models are reliable and produce high levels of mortality attempts to establish a reproducible immersion model have been less successful. Various concentrations of hydrogen peroxide (H₂O₂) were evaluated before being used as a pre-treatment stressor prior to immersion exposure to F. psychrophilum. H₂O₂ accelerated the onset of mortality and increased mortality approximately two-fold; from 9.1% to 19.2% and from 14.7% to 30.3% in two separate experiments. Clinical signs observed in the infected fish corresponded to symptoms characteristically seen during natural outbreaks. These findings indicate that pre-treatment with H₂O₂ can increase the level of mortality in rainbow trout fry after exposure to F. psychrophilum

Transcription Initiation Patterns Indicate Divergent Strategies for Gene Regulation at the Chromatin Level

The application of deep sequencing to map 5′ capped transcripts has confirmed the existence of at least two distinct promoter classes in metazoans: “focused” promoters with transcription start sites (TSSs) that occur in a narrowly defined genomic span and “dispersed” promoters with TSSs that are spread over a larger window. Previous studies have explored the presence of genomic features, such as CpG islands and sequence motifs, in these promoter classes, but virtually no studies have directly investigated the relationship with chromatin features. Here, we show that promoter classes are significantly differentiated by nucleosome organization and chromatin structure. Dispersed promoters display higher associations with well-positioned nucleosomes downstream of the TSS and a more clearly defined nucleosome free region upstream, while focused promoters have a less organized nucleosome structure, yet higher presence of RNA polymerase II. These differences extend to histone variants (H2A.Z) and marks (H3K4 methylation), as well as insulator binding (such as CTCF), independent of the expression levels of affected genes. Notably, differences are conserved across mammals and flies, and they provide for a clearer separation of promoter architectures than the presence and absence of CpG islands or the occurrence of stalled RNA polymerase. Computational models support the stronger contribution of chromatin features to the definition of dispersed promoters compared to focused start sites. Our results show that promoter classes defined from 5′ capped transcripts not only reflect differences in the initiation process at the core promoter but also are indicative of divergent transcriptional programs established within gene-proximal nucleosome organization

Oligonucleotide Frequencies of Barcoding Loci Can Discriminate Species across Kingdoms

Background: DNA barcoding refers to the use of short DNA sequences for rapid identification of species. Genetic distance or character attributes of a particular barcode locus discriminate the species. We report an efficient approach to analyze short sequence data for discrimination between species. Methodology and Principal Findings: A new approach, Oligonucleotide Frequency Range (OFR) of barcode loci for species discrimination is proposed. OFR of the loci that discriminates between species was characteristic of a species, i.e., the maxima and minima within a species did not overlap with that of other species. We compared the species resolution ability of different barcode loci using p-distance, Euclidean distance of oligonucleotide frequencies, nucleotide-character based approach and OFR method. The species resolution by OFR was either higher or comparable to the other methods. A short fragment of 126 bp of internal transcribed spacer region in ribosomal RNA gene was sufficient to discriminate a majority of the species using OFR. Conclusions/Significance: Oligonucleotide frequency range of a barcode locus can discriminate between species. Ability to discriminate species using very short DNA fragments may have wider applications in forensic and conservation studies