Mathematical modeling of the radial profile of basilar membrane vibrations in the inner ear

Motivated by recent experimental results we seek an explanation of asymmetry in the radial profile of basilar membrane vibrations in the inner ear. We study a sequence of one-dimensional beam models which take into account variations in the bending stiffness of the basilar membrane as well as the potential presence of structural hinges. Our results suggest that the main cause of asymmetry is likely to be differences between the boundary conditions at the two extremes of the basilar membrane's width. This has fundamental implications for more detailed numerical simulations of the entire cochle

Two-parameter nonsmooth grazing bifurcations of limit cycles: classification and open problems

This paper proposes a strategy for the classification of codimension-two grazing bifurcations of limit cycles in piecewise smooth systems of ordinary differential equations. Such nonsmooth transitions (C-bifurcations) occur when the cycle interacts with a discontinuity boundary of phase space in a non-generic way. Several such codimension-one events have recently been identified, causing for example period-adding or sudden onset of chaos. Here, the focus is on codimension-two grazings that are local in the sense that the dynamics can be fully described by an appropriate Poincaré map from a neighbourhood of the grazing point (or points) of the critical cycle to itself. It is proposed that codimension-two grazing bifurcations can be divided into three distinct types: either the grazing point is degenerate, or the the grazing cycle is itself degenerate (e.g. non-hyperbolic) or we have the simultaneous occurrence of two grazing events. A careful distinction is drawn between their occurrence in systems with discontinuous states, discontinuous vector fields, or that have discontinuity in some derivative of the vector field. Examples of each kind of bifurcation are presented, mostly derived from mechanical applications. For each example, where possible, principal bifurcation curves characteristic to the codimension-two scenario are presented and general features of the dynamics discussed. Many avenues for future research are opened.

Single event upset studies for the ATLAS SCT and pixel optical links

Optical data transmission has been chosen for the ATLAS Pixel and SemiConductor Tracker to deliver both timing and control information to the detector modules and transmit tracking data to the remote computer room. Radiation hardness of individuals optical components and their ASICs drivers have been reported in previous papers. We will report here the Single Event Upset studies carried out on a customised optopackage using a high-energy pion beam. It will be shown that the system is sufficiently robust to SEU at the ATLAS SCT level

Nonlinear models of development, amplification and compression in the mammalian cochlea

This paper reviews current understanding and presents new results on some of the nonlinear processes that underlie the function of the mammalian cochlea. These processes occur within mechano-sensory hair cells that form part of the organ of Corti. After a general overview of cochlear physiology, mathematical modelling results are presented in three parts. First, the dynamic interplay between ion channels within the sensory inner hair cells is used to explain some new electrophysiological recordings from early development. Next, the state of the art is reviewed in modelling the electro-motility present within the outer hair cells (OHCs), including the current debate concerning the role of cell body motility versus active hair bundle dynamics. A simplified model is introduced that combines both effects in order to explain observed amplification and compression in experiments. Finally, new modelling evidence is presented that structural longitudinal coupling between OHCs may be necessary in order to capture all features of the observed mechanical responses.</jats:p

Adverse pregnancy and neonatal outcomes associated with <i>Neisseria gonorrhoeae:</i> systematic review and meta-analysis.

ObjectiveTo examine associations between Neisseria gonorrhoeae (NG) infection during pregnancy and the risk of preterm birth, spontaneous abortion, premature rupture of membranes, perinatal mortality, low birth weight and ophthalmia neonatorum.Data sourcesWe searched Medline, EMBASE, the Cochrane Library and Cumulative Index to Nursing and Allied Health Literature for studies published between 1948 and 14 January 2020.MethodsStudies were included if they reported testing for NG during pregnancy and compared pregnancy, perinatal and/or neonatal outcomes between women with and without NG. Two reviewers independently assessed papers for inclusion and extracted data. Risk of bias was assessed using established checklists for each study design. Summary ORs with 95% CIs were generated using random effects models for both crude and, where available, adjusted associations.ResultsWe identified 2593 records and included 30 in meta-analyses. Women with NG were more likely to experience preterm birth (OR 1.55, 95% CI 1.21 to 1.99, n=18 studies); premature rupture of membranes (OR 1.41, 95% CI 1.02 to 1.92, n=9); perinatal mortality (OR 2.16, 95% CI 1.35 to 3.46, n=9); low birth weight (OR 1.66, 95% CI 1.12 to 2.48, n=8) and ophthalmia neonatorum (OR 4.21, 95% CI 1.36 to 13.04, n=6). Summary adjusted ORs were, for preterm birth 1.90 (95% CI 1.14 to 3.19, n=5) and for low birth weight 1.48 (95% CI 0.79 to 2.77, n=4). In studies with a multivariable analysis, age was the variable most commonly adjusted for. NG was more strongly associated with preterm birth in low-income and middle-income countries (OR 2.21, 95% CI 1.40 to 3.48, n=7) than in high-income countries (OR 1.38, 95% CI 1.04 to 1.83, n=11).ConclusionsNG is associated with a number of adverse pregnancy and newborn outcomes. Further research should be done to determine the role of NG in different perinatal mortality outcomes because interventions that reduce mortality will have the greatest impact on reducing the burden of disease in low-income and middle-income countries.Prospero registration numberCRD42016050962

Accreting Millisecond X-Ray Pulsars

Accreting Millisecond X-Ray Pulsars (AMXPs) are astrophysical laboratories without parallel in the study of extreme physics. In this chapter we review the past fifteen years of discoveries in the field. We summarize the observations of the fifteen known AMXPs, with a particular emphasis on the multi-wavelength observations that have been carried out since the discovery of the first AMXP in 1998. We review accretion torque theory, the pulse formation process, and how AMXP observations have changed our view on the interaction of plasma and magnetic fields in strong gravity. We also explain how the AMXPs have deepened our understanding of the thermonuclear burst process, in particular the phenomenon of burst oscillations. We conclude with a discussion of the open problems that remain to be addressed in the future.Comment: Review to appear in "Timing neutron stars: pulsations, oscillations and explosions", T. Belloni, M. Mendez, C.M. Zhang Eds., ASSL, Springer; [revision with literature updated, several typos removed, 1 new AMXP added

Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions

The rapid development of next generation sequencing (NGS) technology provides a new chance to extend the scale and resolution of genomic research. How to efficiently map millions of short reads to the reference genome and how to make accurate SNP calls are two major challenges in taking full advantage of NGS. In this article, we reviewed the current software tools for mapping and SNP calling, and evaluated their performance on samples from The Cancer Genome Atlas (TCGA) project. We found that BWA and Bowtie are better than the other alignment tools in comprehensive performance for Illumina platform, while NovoalignCS showed the best overall performance for SOLiD. Furthermore, we showed that next-generation sequencing platform has significantly lower coverage and poorer SNP-calling performance in the CpG islands, promoter and 5′-UTR regions of the genome. NGS experiments targeting for these regions should have higher sequencing depth than the normal genomic region