{\phi}^4 Solitary Waves in a Parabolic Potential: Existence, Stability, and Collisional Dynamics

We explore a {\phi}^4 model with an added external parabolic potential term. This term dramatically alters the spectral properties of the system. We identify single and multiple kink solutions and examine their stability features; importantly, all of the stationary structures turn out to be unstable. We complement these with a dynamical study of the evolution of a single kink in the trap, as well as of the scattering of kink and anti-kink solutions of the model. We see that some of the key characteristics of kink-antikink collisions, such as the critical velocity and the multi-bounce windows, are sensitively dependent on the trap strength parameter, as well as the initial displacement of the kink and antikink

Understanding discrepancies in parent-child reporting of emotional and behavioural problems: Effects of relational and socio-demographic factors

<p>Abstract</p> <p>Background</p> <p>Discrepancies between parents and children in their assessment of children's mental health affect the evaluation of need for services and must be taken seriously. This article presents the differences between parents' and children's reports of the children's symptoms and social impairment, based on the results of the Strengths and Difficulties Questionnaire (SDQ). The interrelationship between relational aspects and socio-demographic factors with patterns of disagreement are explored.</p> <p>Methods</p> <p>Differences in the prevalence and means of SDQ symptom and impact scores were obtained from 8,154 primary school children, aged between 10 and 13 years, and their parents. Agreement between matched pairs was measured using Pearson's and Spearman's rho correlations. Socio-demographic variables, communication patterns and parental engagement were analysed as possible correlates of informant discrepancies using bivariate and multivariate logistic regression models.</p> <p>Results</p> <p>In general, although children reported more symptoms, they reported less impact of perceived difficulties than parents. The parents were more consistent in their evaluation of symptoms and impact than were the children. Exploration of highly discrepant subgroups showed that, when children reported the most symptoms and impact, qualitative aspects of the parent-child relationship and family structure seemed to be more powerful predictors of disagreement than were gender of the child and socio-demographic variables. When parents reported the most symptoms and impact, low parental educational level, low income and male gender of the child played an additional role.</p> <p>Conclusions</p> <p>Our findings underline the importance of paying attention to child reports of emotional-behavioural difficulties, particularly when parents do not identify these problems. Considerations on what meaning parent-child discrepancy might have in the context of the parent-child relationship or the family's psychosocial status should be integrated in the overall understanding of the child's situation and subsequent recommendations.</p

Mercury DPM: fast, flexible particle simulations in complex geometries part II: applications

MercuryDPM is a particle-simulation software developed open-source by a global network of researchers. It was designed ​ab initio to simulate realistic geometries and materials, thus it contains several unique features not found in any other particle simulation software. These features have been discussed in a companion paper published in the DEM7 conference proceedings; here we present several challenging setups implemented in MercuryDPM ​ . Via these setups, we demonstrate the unique capability of the code to simulate and analyse highly complex geotechnical and industrial applications.These tups implemented include complex geometries such as (i) a screw conveyor, (ii) steady-state inflow conditions for chute flows, (iii) a confined conveyor belt to simulate a steady-state breaking wave, and(iii)aquasi-2D cylindrical slice to efficiently study shear flows.​MercuryDPM is also parallel, which we showcase via a multi-million particle simulations of a rotating drum. We further demonstrate how to simulate complex particle interactions, including: (i)deformable, charged clay particles; and (ii) liquid bridges and liquid migration in wet particulates, (iii) non-spherical particles implemented via superquadrics. Finally, we show how to analyse and complex systems using the unique micro-macro mapping (coarse-graining) tool MercuryCG

Complex trait subtypes identification using transcriptome profiling reveals an interaction between two QTL affecting adiposity in chicken

<p>Abstract</p> <p>Background</p> <p>Integrative genomics approaches that combine genotyping and transcriptome profiling in segregating populations have been developed to dissect complex traits. The most common approach is to identify genes whose eQTL colocalize with QTL of interest, providing new functional hypothesis about the causative mutation. Another approach includes defining subtypes for a complex trait using transcriptome profiles and then performing QTL mapping using some of these subtypes. This approach can refine some QTL and reveal new ones.</p> <p>In this paper we introduce Factor Analysis for Multiple Testing (FAMT) to define subtypes more accurately and reveal interaction between QTL affecting the same trait. The data used concern hepatic transcriptome profiles for 45 half sib male chicken of a sire known to be heterozygous for a QTL affecting abdominal fatness (AF) on chromosome 5 distal region around 168 cM.</p> <p>Results</p> <p>Using this methodology which accounts for hidden dependence structure among phenotypes, we identified 688 genes that are significantly correlated to the AF trait and we distinguished 5 subtypes for AF trait, which are not observed with gene lists obtained by classical approaches. After exclusion of one of the two lean bird subtypes, linkage analysis revealed a previously undetected QTL on chromosome 5 around 100 cM. Interestingly, the animals of this subtype presented the same q paternal haplotype at the 168 cM QTL. This result strongly suggests that the two QTL are in interaction. In other words, the "q configuration" at the 168 cM QTL could hide the QTL existence in the proximal region at 100 cM. We further show that the proximal QTL interacts with the previous one detected on the chromosome 5 distal region.</p> <p>Conclusion</p> <p>Our results demonstrate that stratifying genetic population by molecular phenotypes followed by QTL analysis on various subtypes can lead to identification of novel and interacting QTL.</p

Pyoderma gangrenosum – a review

Pyoderma gangrenosum (PG) is a rare noninfectious neutrophilic dermatosis. Clinically it starts with sterile pustules that rapidly progress and turn into painful ulcers of variable depth and size with undermined violaceous borders. The legs are most commonly affected but other parts of the skin and mucous membranes may also be involved. Course can be mild or malignant, chronic or relapsing with remarkable morbidity. In many cases PG is associated with an underlying disease, most commonly inflammatory bowel disease, rheumatic or haematological disease and malignancy. Diagnosis of PG is based on history of an underlying disease, typical clinical presentation, histopathology, and exclusion of other diseases that would lead to a similar appearance. The peak of incidence occurs between the ages of 20 to 50 years with women being more often affected than men. Aetiology has not been clearly determined yet. The treatment of PG is a challenge. Randomized, double-blinded prospective multicenter trials for PG are not available. The best documented treatments are systemic corticosteroids and ciclosporin A. Combinations of steroids with cytotoxic drugs are used in resistant cases. The combination of steroids with sulfa drugs or immunosuppressants has been used as steroid-sparing modalities. Anti-tumor necrosis alpha therapy in Crohn's disease showed a rapid response of PG. Skin transplants and the application of bioengineered skin is useful in selected cases as a complement to the immunosuppressive treatment. Topical therapy with modern wound dressings is useful to minimize pain and the risk of secondary infections. Despite recent advances in therapy, the prognosis of PG remains unpredictable

Ubiquitin transfer by a RING E3 ligase occurs from a closed E2~ubiquitin conformation

Funding: Investigator Award from the Wellcome Trust (098391/Z/12/Z) and (217196/Z/19/Z) and a Programme grant from Cancer Research UK (C434/A21747) to R.T.H.; J.C.P. thanks the University of St Andrews for financial support.Based on extensive structural analysis it was proposed that RING E3 ligases prime the E2~ubiquitin conjugate (E2~Ub) for catalysis by locking it into a closed conformation, where ubiquitin is folded back onto the E2 exposing the restrained thioester bond to attack by substrate nucleophile. However the proposal that the RING dependent closed conformation of E2~Ub represents the active form that mediates ubiquitin transfer has yet to be experimentally tested. To test this hypothesis we use single molecule Förster Resonance Energy Transfer (smFRET) to measure the conformation of a FRET labelled E2~Ub conjugate, which distinguishes between closed and alternative conformations. We describe a real-time FRET assay with a thioester linked E2~Ub conjugate to monitor single ubiquitination events and demonstrate that ubiquitin is transferred to substrate from the closed conformation. These findings are likely to be relevant to all RING E3 catalysed reactions ligating ubiquitin and other ubiquitin-like proteins (Ubls) to substrates.Publisher PDFPeer reviewe

Growth rate, health and welfare in a dairy herd with natural suckling until 6–8 weeks of age: a case report

Over a period of two years, growth rate and health were measured for dairy calves allowed to suckle their mothers up to 6–8 weeks of age. Thirty-one calves were weighted weekly, and the mean daily growth rate was 1.2 ± 0.03 kg from birth up to 13 weeks of age. Illness in calves and young stock was not observed. In the cows, the mean incidences of ketosis, displaced abomasum, puerperal paresis, mastitis, teat injury and retained placenta were 0, 0, 8, 22, 1 and 1%, respectively, during a 6-year period. The mean daily gain of 56 growing bulls was 1.4 kg when slaughtered at 15 months of age, which is higher than the mean daily gain of 0.95 kg in the population. Probiotics, hormones and vaccines were not used, and antibiotics were only used for treating illness. The present study indicates many advantages and few problems when dairy calves are penned together with the cows and allowed natural feeding up to 6–8 weeks of age. This production system was easy to manage, preferred by the farmer, and may satisfy the public concern regarding the practice of immediate separation of cow and calf in commercial milk production

Directed Evaluation of Enterotoxigenic Escherichia coli Autotransporter Proteins as Putative Vaccine Candidates

Diarrheal diseases are responsible for more than 1.5 million deaths annually in developing countries. Enterotoxigenic E. coli (ETEC) are among the most common bacterial causes of diarrhea, accounting for an estimated 300,000–500,000 deaths each year, mostly in young children. There unfortunately is not yet a vaccine that can offer sustained, broad-based protection against ETEC. While most vaccine development effort has focused on plasmid-encoded finger-like ETEC adhesin structures known as colonization factors, additional effort is needed to identify conserved target antigens. Epidemiologic studies suggest that immune responses to uncharacterized, chromosomally encoded antigens could contribute to protection resulting from repeated infections. Earlier studies of immune responses to ETEC infection had identified a class of surface-expressed molecules known as autotransporters (AT). Therefore, available ETEC genome sequences were examined to identify conserved ETEC autotransporters not shared by the commensal E. coli HS strain, followed by studies of the immune response to these antigens, and tests of their utility as vaccine components. Two chromosomally encoded ATs, identified in ETEC, but not in HS, were found to be immunogenic and protective in an animal model, suggesting that conserved AT molecules contribute to protective immune responses that follow natural ETEC infection and offering new potential targets for vaccines

A model of impairment and functional limitation in rheumatoid arthritis

BACKGROUND: We have previously proposed a theoretical model for studying physical disability and other outcomes in rheumatoid arthritis (RA). The purpose of this paper is to test a model of impairment and functional limitation in (RA), using empirical data from a sample of RA patients. We based the model on the disablement process framework. METHODS: We posited two distinct types of impairment in RA: 1) Joint inflammation, measured by the tender, painful and swollen joint counts; and 2) Joint deformity, measured by the deformed joint count. We hypothesized direct paths from the two impairments to functional limitation, measured by the shirt-button speed, grip strength and walking velocity. We used structural equation modeling to test the hypothetical relationships, using empirical data from a sample of RA patients recruited from six rheumatology clinics. RESULTS: The RA sample was comprised of 779 RA patients. In the structural equation model, the joint inflammation impairment displayed a strong significant path toward the measured variables of joint pain, tenderness and swelling (standardized regression coefficients 0.758, 0.872 and 0.512, P ≤ 0.001 for each). The joint deformity impairment likewise displayed significant paths toward the measured upper limb, lower limb, and other deformed joint counts (standardized regression coefficients 0.849, 0.785, 0.308, P ≤ 0.001 for each). Both the joint inflammation and joint deformity impairments displayed strong direct paths toward functional limitation (standardized regression coefficients of -0.576 and -0.564, respectively, P ≤ 0.001 for each), and explained 65% of its variance. Model fit to data was fair to good, as evidenced by a comparative fit index of 0.975, and the root mean square error of approximation = 0.058. CONCLUSION: This evidence supports the occurrence of two distinct impairments in RA, joint inflammation and joint deformity, that together, contribute strongly to functional limitations in this disease. These findings may have implications for investigators aiming to measure outcome in RA