Description: Consistent behavioral differences among individuals, that is, personality, are described in numerous species. Nevertheless, the development of behavioral consistency over ontogeny remains unclear, including whether the personality of individuals is consistent throughout life, and if adult personality can be predicted already at young age. We investigated the ontogeny of personality in the red junglefowl ( Gallus gallus ) by scoring personality of hatchlings at 5 time points through adulthood, including before and after the major developmental stages of becoming independent and sexual mature. We use the conceptual framework laid out by Stamps and Groothuis (2010a) to holistically investigate the observed changes in behavioral response over ontogeny. We demonstrate that mean values of behavioral responses changed across ontogeny and stabilized after independence. Rank-order consistencies of behavioral responses were overall low across independence and sexual maturation. Only in 1 case could low rank-order consistencies potentially be explained by different phenotypes displaying different amounts of change in behavior; more explorative individuals decreased in exploration after independence, while less explorative individuals remained so. Correlations among behavior varied across ontogeny and weakened after sexual maturation. Our results demonstrate that both absolute values and consistency of behavioral traits may change across ontogeny and that individual developmental trajectories and adult personality only to some extent can be predicted early in life. These results have implications for future studies on personality, highlighting that the life stage at which individuals are scored affects the observed consistency of behavioral responses.

Description: Background Transformation of indolent lymphomas (IL) to an aggressive histology (TIL) often results in a rapid clinical course, treatment refractoriness and shortened survival. Although rituximab-containing regimens (R-chemo) have become standard of care in CD20-positive TIL, the role of autologous stem-cell transplantation (ASCT) is still debated. The purpose of this study was to determine whether the outcome of TIL patients improved if they, at transformation, also received ASCT. Furthermore, we investigated the outcome of cases with histologically low- and high-grade components diagnosed either simultaneously or after a period of overt indolent disease. We also analyzed, whether prior rituximab treatment during the indolent course of the disease affected outcome after transformation. Patients and methods Eighty-five patients (≤68 years) with histologically confirmed TIL were included. Five-year overall (OS) and progression-free survival (PFS) were calculated. Selected parameters were tested in a multivariate analysis. All analyses were conducted on three cohorts: (i) whole cohort (all TIL), (ii) patients with co-existing evidence of both indolent and aggressive histology at diagnosis (Composite/discordant TIL) and (iii) patients transformed after prolonged prior indolent disease (sequential TIL). Results Fifty-four patients (64%) received ASCT consolidation and 31 (36%) did not. Within the ‘all TIL’ cohort, the 5-year OS and PFS for R-chemo + ASCT versus R-chemo alone, were 67% versus 48% ( P = 0.11) and 60% versus 30% ( P = 0.02), respectively. Furthermore, in ‘Composite/discordant TIL’ R-chemo + ASCT showed no impact on OS (76% versus 67%; P = 0.66) or PFS (71% versus 62%; P = 0.54). Conversely, R-chemo + ASCT improved the outcome of ‘sequential TIL’ (OS 62% versus 36%; P = 0.07; PFS 53% versus 6%; P = 0.002), regardless of prior rituximab therapy. The beneficial effect of ASCT was significantly higher in patients who had not received rituximab at IL stage. Conclusions ASCT improved the outcome in sequential, but not composite/discordant TIL. The beneficial impact of ASCT was greater in patients, who were rituximab-naïve at transformation.

Description: Background: High accessibility of unhealthy food stores may contribute to a poor dietary quality. Research on the link between neighbourhood food environment and consumption is limited, especially in a European context. The objective of this study was to examine the relationship between convenience stores (CS) and dietary quality within the Capital Region of Denmark.  Method: Cross-sectional study of the geographic food environment in the Capital Region of Denmark based on 47 623 subjects (age 16+ years) with complete information on retail food environment and dietary quality. A categorization procedure to identify CS from a government list of inspected food stores (the Smiley register) was developed. Using GIS network analyses, density of CS within 0.25 km and 0.5 km network buffers from residency was calculated for participants in metropolitan and non-metropolitan areas, respectively. Information on dietary intake and confounders is derived from a questionnaire survey. Multi-level analyses were performed, adjusting for age, sex, individual socio-economic factors and area socio-economic status.  Results: In the non-metropolitan population, the odds of having an unhealthy diet increased significantly ( P 〈 0.0001) with increased density of CS. Compared to individuals who did not have a CS within 0.5 km from their home, the odds ratios were 1.20 (95% CI: 1.09–1.33) and 1.37 (95% CI: 1.19–1.57) for individuals having 1 or ≥2 CS, respectively. In the fully adjusted model, the overall association remained significant ( P = 0.015) and odds ratios diminished to 1.14 (1.02–1.27) and 1.18 (1.01–1.38).  Conclusion: High accessibility of CS in neighbourhoods is associated with less healthy dietary habits among residents.

Description: Background Human noroviruses are the leading cause of acute gastroenteritis. Strains of the GII.4 genotype cause pandemic waves associated with viral evolution and subsequent antigenic drift and ligand-binding modulation. In November 2015, a novel GII.4 Sydney recombinant variant (GII.P16-GII.4 Sydney) emerged and replaced GII.Pe-GII.4 Sydney as the predominant cause of acute gastroenteritis in the 2016–2017 season in the United States. Methods Virus-like particles of GII.4 2012 and GII.4 2015 were compared for ligand binding and antibody reactivity, using a surrogate neutralization assay. Results Residue changes in the capsid between GII.4 2012 and GII.4 2015 decreased the potency of human polyclonal sera and monoclonal antibodies. A change in epitope A resulted in the complete loss of reactivity of a class of blockade antibodies and reduced levels of a second antibody class. Epitope D changes modulated monoclonal antibody potency and ligand-binding patterns. Conclusions Substitutions in blockade antibody epitopes between GII.4 2012 and GII.4 2015 influenced antigenicity and ligand-binding properties. Although the impact of polymerases on fitness remains uncertain, antigenic variation resulting in decreased potency of antibodies to epitope A, coupled with altered ligand binding, likely contributed significantly to the spread of GII.4 2015 and its replacement of GII.4 2012 as the predominant norovirus outbreak strain.

Description: Motivation: Metabolic reaction maps allow visualization of genome-scale models and high-throughput data in a format familiar to many biologists. However, creating a map of a large metabolic model is a difficult and time-consuming process. MetDraw fully automates the map-drawing process for metabolic models containing hundreds to thousands of reactions. MetDraw can also overlay high-throughput ‘omics’ data directly on the generated maps. Availability and implementation: Web interface and source code are freely available at http://www.metdraw.com . Contact: papin@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Elementary flux mode (EFM) is a useful tool in constraint-based modeling of metabolic networks. The property that every flux distribution can be decomposed as a weighted sum of EFMs allows certain applications of EFMs to studying flux distributions. The existence of biologically infeasible EFMs and the non-uniqueness of the decomposition, however, undermine the applicability of such methods. Efforts have been made to find biologically feasible EFMs by incorporating information from transcriptional regulation and thermodynamics. Yet, no attempt has been made to distinguish biologically feasible EFMs by considering their graphical properties. A previous study on the transcriptional regulation of metabolic genes found that distinct branches at a branch point metabolite usually belong to distinct metabolic pathways. This suggests an intuitive property of biologically feasible EFMs, i.e. minimal branching. Results: We developed the concept of minimal branching EFM and derived the minimal branching decomposition (MBD) to decompose flux distributions. Testing in the core Escherichia coli metabolic network indicated that MBD can distinguish branches at branch points and greatly reduced the solution space in which the decomposition is often unique. An experimental flux distribution from a previous study on mouse cardiomyocyte was decomposed using MBD. Comparison with decomposition by a minimum number of EFMs showed that MBD found EFMs more consistent with established biological knowledge, which facilitates interpretation. Comparison of the methods applied to a complex flux distribution in Lactococcus lactis similarly showed the advantages of MBD. The minimal branching EFM concept underlying MBD should be useful in other applications. Contact: sinhu@bio.dtu.dk or p.ji@polyu.edu.hk Supplementary information: Supplementary data are available at Bioinformatics online.