Oscillatory eigenmodes and stability of one and two arbitrary fractional vortices in long Josephson 0-kappa-junctions

We investigate theoretically the eigenmodes and the stability of one and two arbitrary fractional vortices pinned at one and two $\kappa$-phase discontinuities in a long Josephson junction. In the particular case of a single $\kappa$-discontinuity, a vortex is spontaneously created and pinned at the boundary between the 0 and $\kappa$-regions. In this work we show that only two of four possible vortices are stable. A single vortex has an oscillatory eigenmode with a frequency within the plasma gap. We calculate this eigenfrequency as a function of the fractional flux carried by a vortex. For the case of two vortices, pinned at two $\kappa$-discontinuities situated at some distance $a$ from each other, splitting of the eigenfrequencies occur. We calculate this splitting numerically as a function of $a$ for different possible ground states. We also discuss the presence of a critical distance below which two antiferromagnetically ordered vortices form a strongly coupled ``vortex molecule'' that behaves as a single object and has only one eigenmode.Comment: submitted to Phys. Rev. B (

Exploring the drivers of variation in trophic mismatches:A systematic review of long-term avian studies

Many organisms reproduce in seasonal environments, where selection on timing of reproduction is particularly strong as consumers need to synchronize reproduction with the peaked occurrence of their food. When a consumer species changes its phenology at a slower rate than its resources, this may induce a trophic mismatch, that is, offspring growing up after the peak in food availability, potentially leading to reductions in growth and survival. However, there is large variation in the degree of trophic mismatches as well as in its effects on reproductive output. Here, we explore the potential causes for variation in the strength of trophic mismatches in published studies of birds. Specifically, we ask whether the changes in the degree of mismatch that have occurred over time can be explained by a bird's (a) breeding latitude, (b) migration distance, and/or (c) life-history traits. We found that none of these three factors explain changes in the degree of mismatch over time. Nevertheless, food phenology did advance faster at more northerly latitudes, while shifts in bird phenology did not show a trend with latitude. We argue that the lack of support in our results is attributable to the large variation in the metrics used to describe timing of food availability. We propose a pathway to improve the quantification of trophic mismatches, guided by a more rigorous understanding of links between consumers and their resources

The effect of volumetric breast density on the risk of screen-detected and interval breast cancers: a cohort study.

BACKGROUND: In the light of the breast density legislation in the USA, it is important to know a woman's breast cancer risk, but particularly her risk of a tumor that is not detected through mammographic screening (interval cancer). Therefore, we examined the associations of automatically measured volumetric breast density with screen-detected and interval cancer risk, separately. METHODS: Volumetric breast measures were assessed automatically using Volpara version 1.5.0 (Matakina, New Zealand) for the first available digital mammography (DM) examination of 52,814 women (age 50 - 75 years) participating in the Dutch biennial breast cancer screening program between 2003 and 2011. Breast cancer information was obtained from the screening registration system and through linkage with the Netherlands Cancer Registry. We excluded all screen-detected breast cancers diagnosed as a result of the first digital screening examination. During a median follow-up period of 4.2 (IQR 2.0-6.2) years, 523 women were diagnosed with breast cancer of which 299 were screen-detected and 224 were interval breast cancers. The associations between volumetric breast measures and breast cancer risk were determined using Cox proportional hazards analyses. RESULTS: Percentage dense volume was found to be positively associated with both interval and screen-detected breast cancers (hazard ratio (HR) 8.37 (95% CI 4.34-16.17) and HR 1.39 (95% CI 0.82-2.36), respectively, for Volpara density grade category (VDG) 4 compared to VDG1 (p for heterogeneity < 0.001)). Dense volume (DV) was also found to be positively associated with both interval and screen-detected breast cancers (HR 4.92 (95% CI 2.98-8.12) and HR 2.30 (95% CI 1.39-3.80), respectively, for VDG-like category (C)4 compared to C1 (p for heterogeneity = 0.041)). The association between percentage dense volume categories and interval breast cancer risk (HR 8.37) was not significantly stronger than the association between absolute dense volume categories and interval breast cancer risk (HR 4.92). CONCLUSIONS: Our results suggest that both absolute dense volume and percentage dense volume are strong markers of breast cancer risk, but that they are even stronger markers for predicting the occurrence of tumors that are not detected during mammography breast cancer screening

Assessing the reliability and validity of a health-related quality of life instrument, CPADULT, in a Dutch sample of adults with severe disabilities who are non-ambulatory

Background: A measure to provide insight regarding health-related quality of life of adults with severe motor and intellectual disabilities was lacking. For this reason, the CPADULT was developed. This measure includes domains relating to an individual's physical, mental, and social functioning. The purpose of this study was to assess the psychometric characteristics of the CPADULT.Method: Caregivers (n = 47; 77% female, 23% male) of individuals with severe disabilities who are non-ambulatory completed the questionnaire. Internal consistency, test–retest reliability and construct validity were analysed.Results: Internal consistency was adequate with Cronbach's alpha values from 0.75 to 0.95. Test–retest reliability was good, as intraclass correlation coefficient of the total score was 0.84 (domains: 0.61–0.89). Construct validity was confirmed with significant differences between subgroups of motor or intellectual abilities.Conclusion: The CPADULT has sufficient reliability and validity as a proxy measure of health-related quality of life for adults with severe disabilities who are non-ambulatory.</p

Assessing the reliability and validity of a health-related quality of life instrument, CPADULT, in a Dutch sample of adults with severe disabilities who are non-ambulatory

Background: A measure to provide insight regarding health-related quality of life of adults with severe motor and intellectual disabilities was lacking. For this reason, the CPADULT was developed. This measure includes domains relating to an individual's physical, mental, and social functioning. The purpose of this study was to assess the psychometric characteristics of the CPADULT.Method: Caregivers (n = 47; 77% female, 23% male) of individuals with severe disabilities who are non-ambulatory completed the questionnaire. Internal consistency, test–retest reliability and construct validity were analysed.Results: Internal consistency was adequate with Cronbach's alpha values from 0.75 to 0.95. Test–retest reliability was good, as intraclass correlation coefficient of the total score was 0.84 (domains: 0.61–0.89). Construct validity was confirmed with significant differences between subgroups of motor or intellectual abilities.Conclusion: The CPADULT has sufficient reliability and validity as a proxy measure of health-related quality of life for adults with severe disabilities who are non-ambulatory.</p

Thermodynamics of Protein Folding

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which is where the previous topics meet to explore three dimensional protein structures through computational analysis. We provide an overview of existing computational techniques, to validate, simulate, predict and analyse protein structures. More importantly, it will aim to provide practical knowledge about how and when to use such techniques. We will consider proteins from three major vantage points: Protein structure quantification, Protein structure prediction, and Protein simulation & dynamics. In the previous chapter, "Introduction to Protein Folding", we introduced the concept of free energy and the protein folding landscape. Here, we provide a deeper, more formal underpinning of free energy in terms of the entropy and enthalpy; to this end, we will first need to better define the meaning of equilibrium, entropy and enthalpy. When we understand these concepts, we will come back for a more quantitative explanation of protein folding and dynamics. We will discuss the influence of temperature on the free energy landscape, and the difference between microstates and macrostates.Comment: editorial responsability: Juami H. M. van Gils, K. Anton Feenstra, Sanne Abeln. This chapter is part of the book "Introduction to Protein Structural Bioinformatics". The Preface arXiv:1801.09442 contains links to all the (published) chapters. The update adds available arxiv hyperlinks for the chapter

Thermodynamics of Protein Folding

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which is where the previous topics meet to explore three dimensional protein structures through computational analysis. We provide an overview of existing computational techniques, to validate, simulate, predict and analyse protein structures. More importantly, it will aim to provide practical knowledge about how and when to use such techniques. We will consider proteins from three major vantage points: Protein structure quantification, Protein structure prediction, and Protein simulation &amp; dynamics. In the previous chapter, "Introduction to Protein Folding", we introduced the concept of free energy and the protein folding landscape. Here, we provide a deeper, more formal underpinning of free energy in terms of the entropy and enthalpy; to this end, we will first need to better define the meaning of equilibrium, entropy and enthalpy. When we understand these concepts, we will come back for a more quantitative explanation of protein folding and dynamics. We will discuss the influence of temperature on the free energy landscape, and the difference between microstates and macrostates

Development and sensibility assessment of a health-related quality of life instrument for adults with severe disabilities who are non-ambulatory

Background Insight in health-related quality of life (HRQoL) of adults with severe disabilities who are non-ambulatory is important, but a measure is lacking. The aim was to develop a HRQoL measure for this group. Method The developmental process consisted of the adaptation process of a proxy HRQoL measure for children with severe disabilities who are non-ambulatory and the assessment of the sensibility of the developed instrument. A three-step process was used: focus groups, e-survey and interviews. Results In total, 72% of the items remained unchanged. Three new items and one element to an existing item were added. In ten items, the formulation of the items was adapted to the target group. Concerning the sensibility, respondents suggested minor changes to the instruction and the output scales. Conclusions This study has yielded a proxy HRQoL measure for adults with severe disabilities who are non-ambulatory, the CPADULT, with good sensibility