SitesBase: a database for structure-based protein–ligand binding site comparisons

There are many components which govern the function of a protein within a cell. Here, we focus on the molecular recognition of small molecules and the prediction of common recognition by similarity between protein–ligand binding sites. SitesBase is an easily accessible database which is simple to use and holds information about structural similarities between known ligand binding sites found in the Protein Data Bank. These similarities are presented to the wider community enabling full analysis of molecular recognition and potentially protein structure–function relationships. SitesBase is accessible at

Editorial on plants as alternative hosts for human and animal pathogens

Many of the most prevalent and devastating human and animal pathogens have part of their lifecycle out-with the animal host. These pathogens have a remarkably wide capacity to adapt to a range of quite different environments: physical, chemical and biological, which is part of the key to their success. Many of the well-known pathogens that are able to jump between hosts in different biological kingdoms are transmitted through the faecal-oral and direct transmission pathways, and as such have become important food-borne pathogens. Some high-profile examples include fresh produce-associated outbreaks of Escherichia coli O157:H7 and Salmonella enterica. Other pathogens may be transmitted via direct contact or aerosols are include important zoonotic pathogens. It is possible to make a broad division between those pathogens that are passively transmitted via vectors and need the animal host for replication (e.g. virus and parasites), and those that are able to actively interact with alternative hosts, where they can proliferate (e.g. the enteric bacteria). This research topic will focus on plants as alternative hosts for human pathogens, and the role of plants in their transmission back to humans. The area is particularly exciting because it opens up new aspects to the biology of some microbes already considered to be very well characterised. One aspect of cross-kingdom host colonisation is in the comparison between the hosts and how the microbes are able to use both common and specific adaptations for each situation. The area is still in relative infancy and there are far more questions than answers at present. We aim to address important questions underlying the interactions for both the microbe and plant host in this research topic

The Impact of Antenatal Breastfeeding Education on Young Women’s Breastfeeding Self-efficacy and Breastfeeding Rates

Background: Despite the known benefits of breastfeeding to the mother, baby and society as a whole, young women’s breastfeeding rates are generally poor compared to older mothers. Effective antenatal education has been identified as one way to improve these rates. Whether or not antenatal breastfeeding education for young women can make a significant impact on their breastfeeding success is of paramount concern in this research. An important and modifiable variable, identified in the literature as influencing breastfeeding outcomes, is self-efficacy (confidence in ability to breastfeed). This breastfeeding self-efficacy in young mothers is of great interest due to this group and their infants being vulnerable in terms of breastfeeding initiation and continuation. Aim: This study aimed to identify the effects of antenatal breastfeeding education on the self-efficacy, experience and duration of breastfeeding for young women. It also aimed to replicate aspects of prior research in this area conducted overseas to see if those findings could be generalized to a New Zealand setting. Method: A repeated measure design using an existing validated tool was utilised to quantify breastfeeding self-efficacy, prior to and following, an antenatal breastfeeding education session for young pregnant women aged less than 25 years old. Findings: Breastfeeding antenatal education improved breastfeeding self-efficacy scores in urban young women less than 25 years of age. The Breastfeeding Self-efficacy Scale (short form), was found to be a reliable tool to test this. Whilst initiation rates were high in this group, there was no statistically significant link with breastfeeding self-efficacy and the duration and continuation of breastfeeding. Conclusion: Whilst breastfeeding antenatal education was shown to increase breastfeeding self-efficacy, there are many confounding factors influencing breastfeeding initiation and continuation for young women. The findings have contributed to the knowledge about breastfeeding patterns of young New Zealand women. It may be that despite international findings, an increased breastfeeding self-efficacy in this setting doesn’t impact on the rates of breastfeeding of urban New Zealand young mothers. Further research with an increased sample size and comparison groups is warranted

An effective potential for one-dimensional matter-wave solitons in an axially inhomogeneous trap

We demonstrate that a tight transverse trap with the local frequency, $\omega_{\perp}$, gradually varying in the longitudinal direction ($x$) induces an effective potential for one-dimensional solitons in a self-attractive Bose-Einstein condensate. An analytical approximation for this potential is derived by means of a variational method. In the lowest approximation, the potential is $N(S+1)\omega_{\perp}(x)$, with $N$ the soliton's norm (number of atoms), and $S$ its intrinsic vorticity (if any). The results can be used to devise nonuniform traps helping to control the longitudinal dynamics of the solitons. Numerical verification of the analytical predictions will be presented elsewhere.Comment: to be published in Physics Letters

Lorentz-Lorenz Coefficient, Critical Point Constants, and Coexistence Curve of 1,1-Difluoroethylene

We report measurements of the Lorentz-Lorenz coefficient density dependence, the critical temperature, and the critical density, of the fluid 1,1-difluoroethylene. Lorentz-Lorenz coefficient data were obtained by measuring refractive index and density of the same fluid sample independently of one another. Accurate determination of the Lorentz-Lorenz coefficient is necessary for transformation of refractive index data into density data from optics-based experiments on critical phenomena of fluid systems done with different apparatus, with which independent measurement of the refractive indes and density is not possible. Measurements were made along the coexistence curve of the fluid and span the density range 0.01 to 0.80 g/cc. The Lorentz-Lorenz coefficient results show a stronger density dependence along the coexistence curve than previously observed in other fluids, with a monotonic decrease from a density of about 0.2 g/cc onwards, and an overall variation of about 2.5% in the density range studied. No anomaly in the Lorentz-Lorenz coefficient was observed near the critical density. The critical temperature is measured at Tc=(302.964+-0.002) K (29.814 C) and the measured critical density is (0.4195+-0.0018)g/cc.Comment: 14 pages, 6 figures, MikTeX 2.4, submitted to Physical Review

“I’m getting out to nothing”: a temporal analysis of dominant discourses and practices with residents convicted of child sex offences in Probation Approved Premises

People convicted of child sex offences are viewed as a dangerous and demonised offender group, yet little research has considered their resettlement post-residency from Approved Premises. Using data from two qualitative studies carried out 15 years apart, we explore what changes there have been in the discourses and practices with residents convicted of child sex offences. We found that whilst rehabilitation and resettlement were contemporarily considered as more holistic endeavours, the primary function of the Approved Premises remains managing the risks of residents convicted of child sex offences. Most significantly, this hindered their social integration into the community

FMDV replicons encoding green fluorescent protein are replication competent

The study of replication of viruses that require high bio-secure facilities can be accomplished with less stringent containment using non-infectious 'replicon' systems. The FMDV replicon system (pT7rep) reported by Mclnerney et al. (2000) was modified by the replacement of sequences encoding chloramphenicol acetyl-transferase (CAT) with those encoding a functional L proteinase (Lpro) linked to a bi-functional fluorescent/antibiotic resistance fusion protein (green fluorescent protein/puromycin resistance, [GFP-PAC]). Cells were transfected with replicon-derived transcript RNA and GFP fluorescence quantified. Replication of transcript RNAs was readily detected by fluorescence, whilst the signal from replication-incompetent forms of the genome was >2-fold lower. Surprisingly, a form of the replicon lacking the Lpro showed a significantly stronger fluorescence signal, but appeared with slightly delayed kinetics. Replication can, therefore, be quantified simply by live-cell imaging and image analyses, providing a rapid and facile alternative to RT-qPCR or CAT assays

The relationship between chronic diseases and number of sexual partners: an exploratory analysis

Background: We investigated sex-specific associations between lifetime number of sexual partners and several health outcomes in a large sample of older adults in England. Methods: We used cross-sectional data from 2,537 men and 3,185 women aged ≥50 years participating in the English Longitudinal Study of Ageing. Participants reported the number of sexual partners they had had in their lifetime. Outcomes were self-rated health and self-reported limiting long-standing illness, cancer, coronary heart disease (CHD), and stroke. We used logistic regression to analyse associations between lifetime number of sexual partners and health outcomes, adjusted for relevant sociodemographic and health-related covariates. Results: Having had 10 or more lifetime sexual partners was associated with higher odds of reporting a diagnosis of cancer than having had 0-1 sexual partners in men (OR=1.69, 95% CI 1.01-2.83) and women (OR=1.91, 95% CI 1.04-3.51), respectively. Women who had 10 or more lifetime sexual partners also had higher odds of reporting a limiting long-standing illness (OR=1.64, 95% CI 1.15 2.35). No other statistically significant associations were observed. Conclusions: A higher lifetime number of sexual partners is associated with increased odds of reported cancer. Longitudinal research is required to establish causality. Understanding the predictive value of lifetime number of sexual partner as a behavioural risk factor may improve clinical assessment of cancer risk in older adults