Turbulence transition and the edge of chaos in pipe flow

The linear stability of pipe flow implies that only perturbations of sufficient strength will trigger the transition to turbulence. In order to determine this threshold in perturbation amplitude we study the \emph{edge of chaos} which separates perturbations that decay towards the laminar profile and perturbations that trigger turbulence. Using the lifetime as an indicator and methods developed in (Skufca et al, Phys. Rev. Lett. {\bf 96}, 174101 (2006)) we show that superimposed on an overall $1/\Re$-scaling predicted and studied previously there are small, non-monotonic variations reflecting folds in the edge of chaos. By tracing the motion in the edge we find that it is formed by the stable manifold of a unique flow field that is dominated by a pair of downstream vortices, asymmetrically placed towards the wall. The flow field that generates the edge of chaos shows intrinsic chaotic dynamics.Comment: 4 pages, 5 figure

An efficient algorithm for learning to rank from preference graphs

In this paper, we introduce a framework for regularized least-squares (RLS) type of ranking cost functions and we propose three such cost functions. Further, we propose a kernel-based preference learning algorithm, which we call RankRLS, for minimizing these functions. It is shown that RankRLS has many computational advantages compared to the ranking algorithms that are based on minimizing other types of costs, such as the hinge cost. In particular, we present efficient algorithms for training, parameter selection, multiple output learning, cross-validation, and large-scale learning. Circumstances under which these computational benefits make RankRLS preferable to RankSVM are considered. We evaluate RankRLS on four different types of ranking tasks using RankSVM and the standard RLS regression as the baselines. RankRLS outperforms the standard RLS regression and its performance is very similar to that of RankSVM, while RankRLS has several computational benefits over RankSVM

Association of the tumour necrosis factor alpha -308 but not the interleukin 10 -627 promoter polymorphism with genetic susceptibility to primary sclerosing cholangitis

BACKGROUND AND AIMS Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease of unknown aetiology. Abnormalities in immune regulation and genetic associations suggest that PSC is an immune mediated disease. Several polymorphisms within the tumour necrosis factor α (TNF-α) and interleukin 10 (IL-10) promoter genes have been described which influence expression of these cytokines. This study examines the possible association between polymorphisms at the −308 and −627 positions in the TNF-α and IL-10 promoter genes, respectively, and susceptibility to PSC. METHODS TNF-α −308 genotypes were studied by polymerase chain reaction (PCR) in 160 PSC patients from Norway and the UK compared with 145 ethnically matched controls. IL-10 −627 genotypes were studied by PCR in 90 PSC patients compared with 84 ethnically matched controls. RESULTS A total of 16% of Norwegian PSC patients and 12% of British PSC patients were homozygous for the TNF2 allele compared with 3% and 6% of respective controls. The TNF2 allele was present in 60% of PSC patients versus 30% of controls (ORcombined data=3.2 (95% confidence intervals (CI) 1.8–4.5); pcorr=10−5). The association between the TNF2 allele and susceptibility to PSC was independent of the presence of concurrent inflammatory bowel disease (IBD) in the PSC patients; 61% of PSC patients without IBD had TNF2 compared with 30% of controls (ORcombined data=3.2 (95% CI 1.2–9.0); pcorr=0.006 ). There was no difference in the −627 IL-10 polymorphism distributions between patients and controls in either population. The increase in TNF2 allele in PSC patients only occurs in the presence of DRB1*0301 (DR3) and B8. In the combined population data, DRB1*0301 showed a stronger association with susceptibility to PSC than both the TNF2 and B8 alleles (ORcombined data=3.8, pcorr=10−6 v ORcombined data=3.2, pcorr=10−5 vORcombined data =3.41, pcorr=10−4, respectively). CONCLUSIONS This study identified a significant association between possession of the TNF2 allele, a G→A substitution at position −308 in the TNF-α promoter, and susceptibility to PSC. This association was secondary to the association of PSC with the A1-B8-DRB1*0301-DQA1*0501-DQB1*0201 haplotype. No association was found between the IL-10 −627 promoter polymorphism and PSC

Competition between transients in the rate of approach to a fixed point

Dynamical systems studies of differential equations often focus on the behavior of solutions near critical points and on invariant manifolds, to elucidate the organization of the associated flow. In addition, effective methods, such as the use of Poincare maps and phase resetting curves, have been developed for the study of periodic orbits. However, the analysis of transient dynamics associated with solutions on their way to an attracting fixed point has not received much rigorous attention. This paper introduces methods for the study of such transient dynamics. In particular, we focus on the analysis of whether one component of a solution to a system of differential equations can overtake the corresponding component of a reference solution, given that both solutions approach the same stable node. We call this phenomenon tolerance, which derives from a certain biological effect. Here, we establish certain general conditions, based on the initial conditions associated with the two solutions and the properties of the vector field, that guarantee that tolerance does or does not occur in two-dimensional systems. We illustrate these conditions in particular examples, and we derive and demonstrate additional techniques that can be used on a case by case basis to check for tolerance. Finally, we give a full rigorous analysis of tolerance in two-dimensional linear systems.Comment: Resolution on the figures of the paper has been reduced to conserve file space. Animation files are viewable at: http://people.mbi.ohio-state.edu/jday/Tol_Animations.htm

Molecular forms of butyrylcholinesterase and obesity

This study compared obese (N = 134) and unobese (N = 92) male blood donors, regarding the relative intensity (RI) and activity of different molecular forms (G1, G2, G4 and G1-ALB) of butyrylcholinesterase (BChE, EC 3.1.1.8) found in plasma, thereby searching for an association between these variables with obesity and SNPs of exons 1 and 4 of the BCHE gene. It was shown that obese and unobese individuals do not differ in the RI of each BChE band, even when classifying the sample into three genotypes of exons 1 and 4 of the BCHE gene (-116GG/539AA, -116GG/539AT, -116GA/539AT). Although the mean BChE activity of each band was significantly higher in obese than in unobese blood donors, the proportions of BChE bands were maintained, even under the metabolic stress associated to obesity, thereby leading to infer that this proportion is somehow regulated, and may therefore be important for BChE functions

Host genotype interacts with aerial spore communities and influences the needle mycobiome of Norway spruce

The factors shaping the composition of the tree mycobiome are still under investigation. We tested the effects of host genotype, site, host phenotypic traits, and air fungal spore communities on the assembly of the fungi inhabiting Norway spruce needles. We used Norway spruce clones and spore traps within the collection sites and characterized both needle and air mycobiome communities by high-throughput sequencing of the ITS2 region. The composition of the needle mycobiome differed between Norway spruce clones, and clones with high genetic similarity had a more similar mycobiome. The needle mycobiome also varied across sites and was associated with the composition of the local air mycobiome and climate. Phenotypic traits such as diameter at breast height or crown health influenced the needle mycobiome to a lesser extent than host genotype and air mycobiome. Altogether, our results suggest that the needle mycobiome is mainly driven by the host genotype in combination with the composition of the local air spore communities. Our work highlights the role of host intraspecific variation in shaping the mycobiome of trees and provides new insights on the ecological processes structuring fungal communities inhabiting woody plants.This research was supported by the Swedish research council for Environment, Agricultural Sciences and Spatial Planning, FORMAS, project 2016-00798. M.E. and H.D.C were also supported by Formas project 2017-00402. J.O. was partially supported by the 'Ramon y Cajal' fellowship RYC-2015-17459. The authors would like to thank the owners of the seed orchards, Svenska skogsplantor AB and Sodra skogsagarna AB, for allowing us to sample the trees and assisting with the air mycobiome sampling. The authors also thank Antonio Rizzi, Rena Gadjieva, Maria Jonsson, and Katarina Ihrmark for their assistance with the laboratory and field work. The authors would like to acknowledge the support of the National Genomics Infrastructure (NGI)/Uppsala, Genome Center and UPPMAX for assisting us in massive parallel sequencing and computational infrastructure. Work performed at NGI/Uppsala Genome Center was funded by RFI/VR and Science for Life Laboratory, Sweden

Calretinin is a novel candidate marker for adverse ovarian effects of early life exposure to mixtures of endocrine disruptors in the rat

Open Access via Springer Compact Acknowledgements This work was funded by the Ministry of Environment and Food of Denmark, and by a grant from the European Commission 7th Framework Program CONTAMED (Contaminant mixtures and human reproductive health-novel strategies for health impact and risk assessment of endocrine disrupters, grant agreement no.: 215202), as well as the Medical Research Council (UK) (MR/L010011/1 to PAF) and the EU Horizon 2020 project FREIA (Grant Number 825100). We would like to thank Heidi Letting, the Animal facilities at DTU food, and the University of Aberdeen Proteomics Core Facility for their support and assistance in this work.Peer reviewedPublisher PD

Immunization with HIV protease peptides linked to syngeneic erythrocytes

New potent vaccine adjuvants are desirable for increasing the efficacy of novel vaccine modalities such as DNA and peptides. We therefore tested if syngeneic erythrocytes could serve as delivery vectors for selected HIV peptides and compared the potency of these constructs to immunization with peptides in phosphate buffered saline or in incomplete Freunds adjuvant. Immunization of mice with peptides in a low dose (5 ng) coupled to erythrocytes induced a weak immune response in mice. These peptides alone (5 μg) gave no immune responses, while formulating the peptides (50 μg) in IFA induced strong homologous immunity as well as prominent cross reactivity to a related mutant epitope. Thus, vaccine delivery using syngeneic erythrocytes, although attractive for clinical use, might be of limited value due to the low amount of antigen that can be loaded per erythrocyte