Experimental evidence of a {\phi} Josephson junction

We demonstrate experimentally the existence of Josephson junctions having a doubly degenerate ground state with an average Josephson phase \psi=\pm{\phi}. The value of {\phi} can be chosen by design in the interval 0<{\phi}<\pi. The junctions used in our experiments are fabricated as 0-{\pi} Josephson junctions of moderate normalized length with asymmetric 0 and {\pi} regions. We show that (a) these {\phi} Josephson junctions have two critical currents, corresponding to the escape of the phase {\psi} from -{\phi} and +{\phi} states; (b) the phase {\psi} can be set to a particular state by tuning an external magnetic field or (c) by using a proper bias current sweep sequence. The experimental observations are in agreement with previous theoretical predictions

The Invisible Thin Red Line

The aim of this paper is to argue that the adoption of an unrestricted principle of bivalence is compatible with a metaphysics that (i) denies that the future is real, (ii) adopts nomological indeterminism, and (iii) exploits a branching structure to provide a semantics for future contingent claims. To this end, we elaborate what we call Flow Fragmentalism, a view inspired by Kit Fine (2005)’s non-standard tense realism, according to which reality is divided up into maximally coherent collections of tensed facts. In this way, we show how to reconcile a genuinely A-theoretic branching-time model with the idea that there is a branch corresponding to the thin red line, that is, the branch that will turn out to be the actual future history of the world

Asymptotic Behavior of Ext functors for modules of finite complete intersection dimension

Let $R$ be a local ring, and let $M$ and $N$ be finitely generated $R$-modules such that $M$ has finite complete intersection dimension. In this paper we define and study, under certain conditions, a pairing using the modules \Ext_R^i(M,N) which generalizes Buchweitz's notion of the Herbrand diference. We exploit this pairing to examine the number of consecutive vanishing of \Ext_R^i(M,N) needed to ensure that \Ext_R^i(M,N)=0 for all $i\gg 0$. Our results recover and improve on most of the known bounds in the literature, especially when $R$ has dimension at most two

Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha-helices.Comment: 4 pages, 2 figure

Mental Disorder in Children with Physical Conditions: a Pilot Study

OBJECTIVES: Methodologically, to assess the feasibility of participant recruitment and retention, as well as missing data in studying mental disorder among children newly diagnosed with chronic physical conditions (ie, multimorbidity). Substantively, to examine the prevalence of multimorbidity, identify sociodemographic correlates and model the influence of multimorbidity on changes in child quality of life and parental psychosocial outcomes over a 6-month follow-up. DESIGN: Prospective pilot study. SETTING: Two children\u27s tertiary-care hospitals. PARTICIPANTS: Children aged 6-16 years diagnosed in the past 6 months with one of the following: asthma, diabetes, epilepsy, food allergy or juvenile arthritis, and their parents. OUTCOME MEASURES: Response, participation and retention rates. Child mental disorder using the Mini International Neuropsychiatric Interview at baseline and 6 months. Child quality of life, parental symptoms of stress, anxiety and depression, and family functioning. All outcomes were parent reported. RESULTS: Response, participation and retention rates were 90%, 83% and 88%, respectively. Of the 50 children enrolled in the study, the prevalence of multimorbidity was 58% at baseline and 42% at 6 months. No sociodemographic characteristics were associated with multimorbidity. Multimorbidity at baseline was associated with declines over 6 months in the following quality of life domains: physical well-being, β=-4.82 (-8.47, -1.17); psychological well-being, β=-4.10 (-7.62, -0.58) and school environment, β=-4.17 (-8.18, -0.16). There was no association with parental psychosocial outcomes over time. CONCLUSIONS: Preliminary evidence suggests that mental disorder in children with a physical condition is very common and has a negative impact on quality of life over time. Based on the strong response rate and minimal attrition, our approach to study child multimorbidity appears feasible and suggests that multimorbidity is an important concern for families. Methodological and substantive findings from this pilot study have been used to implement a larger, more definitive study of child multimorbidity, which should lead to important clinical implications

IMPACT study on intervening with a manualised package to achieve treatment adherence in people with tuberculosis: protocol paper for a mixed-methods study, including a pilot randomised controlled trial

Kielmann, Karina - ORCID 0000-0001-5519-1658 https://orcid.org/0000-0001-5519-1658Introduction Compared with the rest of the UK and Western Europe, England has high rates of the infectious disease tuberculosis (TB). TB is curable, although treatment is for at least 6 months and longer when disease is drug resistant. If patients miss too many doses (non-adherence), they may transmit infection for longer and the infecting bacteria may develop resistance to the standard drugs used for treatment. Non-adherence may therefore risk both their health and that of others. Within England, certain population groups are thought to be at higher risk of non-adherence, but the factors contributing to this have been insufficiently determined, as have the best interventions to promote adherence. The objective of this study was to develop a manualised package of interventions for use as part of routine care within National Health Services to address the social and cultural factors that lead to poor adherence to treatment for TB disease.Methods and analysis This study uses a mixed-methods approach, with six study components. These are (1) scoping reviews of the literature; (2) qualitative research with patients, carers and healthcare professionals; (3) development of the intervention; (4) a pilot randomised controlled trial of the manualised intervention; (5) a process evaluation to examine clinical utility; and (6) a cost analysis.Ethics and dissemination This study received ethics approval on 24 December 2018 from Camberwell St. Giles Ethics Committee, UK (REC reference 18/LO/1818). Findings will be published and disseminated through peer-reviewed publications and conference presentations, published in an end of study report to our funder (the National Institute for Health Research, UK) and presented to key stakeholders.Trial registration number ISRCTN95243114Secondary identifying numbers University College London/University College London Hospitals Joint Research Office 17/0726. National Institute for Health Research, UK 16/88/06.https://doi.org/10.1136/bmjopen-2019-032760http://bmjopen.bmj.com/cgi/content/full/bmjopen-2019-0327609pubpub1

Ultrametric spaces of branches on arborescent singularities

Let $S$ be a normal complex analytic surface singularity. We say that $S$ is arborescent if the dual graph of any resolution of it is a tree. Whenever $A,B$ are distinct branches on $S$, we denote by $A \cdot B$ their intersection number in the sense of Mumford. If $L$ is a fixed branch, we define $U_L(A,B)= (L \cdot A)(L \cdot B)(A \cdot B)^{-1}$ when $A \neq B$ and $U_L(A,A) =0$ otherwise. We generalize a theorem of P{\l}oski concerning smooth germs of surfaces, by proving that whenever $S$ is arborescent, then $U_L$ is an ultrametric on the set of branches of $S$ different from $L$. We compute the maximum of $U_L$, which gives an analog of a theorem of Teissier. We show that $U_L$ encodes topological information about the structure of the embedded resolutions of any finite set of branches. This generalizes a theorem of Favre and Jonsson concerning the case when both $S$ and $L$ are smooth. We generalize also from smooth germs to arbitrary arborescent ones their valuative interpretation of the dual trees of the resolutions of $S$. Our proofs are based in an essential way on a determinantal identity of Eisenbud and Neumann.Comment: 37 pages, 16 figures. Compared to the first version on Arxiv, il has a new section 4.3, accompanied by 2 new figures. Several passages were clarified and the typos discovered in the meantime were correcte

Local alignment of generalized k-base encoded DNA sequence

<p>Abstract</p> <p>Background</p> <p>DNA sequence comparison is a well-studied problem, in which two DNA sequences are compared using a weighted edit distance. Recent DNA sequencing technologies however observe an encoded form of the sequence, rather than each DNA base individually. The encoded DNA sequence may contain technical errors, and therefore encoded sequencing errors must be incorporated when comparing an encoded DNA sequence to a reference DNA sequence.</p> <p>Results</p> <p>Although two-base encoding is currently used in practice, many other encoding schemes are possible, whereby two ore more bases are encoded at a time. A generalized <it>k</it>-base encoding scheme is presented, whereby feasible higher order encodings are better able to differentiate errors in the encoded sequence from true DNA sequence variants. A generalized version of the previous two-base encoding DNA sequence comparison algorithm is used to compare a <it>k</it>-base encoded sequence to a DNA reference sequence. Finally, simulations are performed to evaluate the power, the false positive and false negative SNP discovery rates, and the performance time of <it>k</it>-base encoding compared to previous methods as well as to the standard DNA sequence comparison algorithm.</p> <p>Conclusions</p> <p>The novel generalized <it>k</it>-base encoding scheme and resulting local alignment algorithm permits the development of higher fidelity ligation-based next generation sequencing technology. This bioinformatic solution affords greater robustness to errors, as well as lower false SNP discovery rates, only at the cost of computational time.</p

Young children's research: children aged 4-8 years finding solutions at home and at school

Children's research capacities have become increasingly recognised by adults, yet children remain excluded from the academy, with reports of their research participation generally located in adults' agenda. Such practice restricts children's freedom to make choices in matters affecting them, underestimates children’s capabilities and denies children particular rights. The present paper reports on one aspect of a small-scale critical ethnographic study adopting a constructivist grounded approach to conceptualise ways in which children's naturalistic behaviours may be perceived as research. The study builds on multi-disciplinary theoretical perspectives, embracing 'new' sociology, psychology, economics, philosophy and early childhood education and care (ECEC). Research questions include: 'What is the nature of ECEC research?' and 'Do children’s enquiries count as research?' Initially, data were collected from the academy: professional researchers (n=14) confirmed 'finding solutions' as a research behaviour and indicated children aged 4-8 years, their practitioners and primary carers as 'theoretical sampling'. Consequently, multi-modal case studies were constructed with children (n=138) and their practitioners (n=17) in three ‘good’ schools, with selected children and their primary carers also participating at home. This paper reports on data emerging from children aged 4-8 years at school (n=17) and at home (n=5). Outcomes indicate that participating children found diverse solutions to diverse problems, some of which they set themselves. Some solutions engaged children in high order thinking, whilst others did not; selecting resources and trialing activities engaged children in 'finding solutions'. Conversely, when children's time, provocations and activities were directed by adults, the quality of their solutions was limited, they focused on pleasing adults and their motivation to propose solutions decreased. In this study, professional researchers recognised 'finding solutions' as research behaviour and children aged 4-8 years naturalistically presented with capacities for finding solutions; however, the children's encounters with adults affected the solutions they found

Validation of Differentially Expressed Immune Biomarkers in Latent and Active Tuberculosis by Real-Time PCR

Tuberculosis (TB) remains a major global threat and diagnosis of active TB ((ATB) both extra-pulmonary (EPTB), pulmonary (PTB)) and latent TB (LTBI) infection remains challenging, particularly in high-burden countries which still rely heavily on conventional methods. Although molecular diagnostic methods are available, e.g., Cepheid GeneXpert, they are not universally available in all high TB burden countries. There is intense focus on immune biomarkers for use in TB diagnosis, which could provide alternative low-cost, rapid diagnostic solutions. In our previous gene expression studies, we identified peripheral blood leukocyte (PBL) mRNA biomarkers in a non-human primate TB aerosol-challenge model. Here, we describe a study to further validate select mRNA biomarkers from this prior study in new cohorts of patients and controls, as a prerequisite for further development. Whole blood mRNA was purified from ATB patients recruited in the UK and India, LTBI and two groups of controls from the UK (i) a low TB incidence region (CNTRLA) and (ii) individuals variably-domiciled in the UK and Asia ((CNTRLB), the latter TB high incidence regions). Seventy-two mRNA biomarker gene targets were analyzed by qPCR using the Roche Lightcycler 480 qPCR platform and data analyzed using GeneSpring™ 14.9 bioinformatics software. Differential expression of fifty-three biomarkers was confirmed between MTB infected, LTBI groups and controls, seventeen of which were significant using analysis of variance (ANOVA): CALCOCO2, CD52, GBP1, GBP2, GBP5, HLA-B, IFIT3, IFITM3, IRF1, LOC400759 (GBP1P1), NCF1C, PF4V1, SAMD9L, S100A11, TAF10, TAPBP, and TRIM25. These were analyzed using receiver operating characteristic (ROC) curve analysis. Single biomarkers and biomarker combinations were further assessed using simple arithmetic algorithms. Minimal combination biomarker panels were delineated for primary diagnosis of ATB (both PTB and EPTB), LTBI and identifying LTBI individuals at high risk of progression which showed good performance characteristics. These were assessed for suitability for progression against the standards for new TB diagnostic tests delineated in the published World Health Organization (WHO) technology product profiles (TPPs)