Dissipation production in a closed two-level quantum system as a test of the irreversibility of the dynamics

Irreversible behavior in open stochastic dynamical systems is quantified by stochastic entropy production, a property that measures the difference in likelihoods of forward and subsequent backward system evolution. But for a closed system, governed by deterministic dynamics, such an approach is not appropriate. Instead, we can consider the difference in likelihoods of forward and "obverse"behavior: the latter being a backward trajectory initiated at the same time as the forward trajectory. Such a comparison allows us to define "dissipation production,"an analog of stochastic entropy production. It quantifies the breakage of a property of the evolution termed "obversibility"just as stochastic entropy production quantifies a breakage of reversibility. Both are manifestations of irreversibility. In this study we discuss dissipation production in a quantum system. We consider a simple, deterministic, two-level quantum system characterized by a statistical ensemble of state vectors, and we provide numerical results to illustrate the ideas. We consider cases that both do and do not satisfy an Evans-Searles Fluctuation Theorem for the dissipation production, and hence identify conditions under which the system displays time-asymmetric average behavior: an arrow of time

Binding Sites Analyser (BiSA): Software for genomic binding sites archiving and overlap analysis

Genome-wide mapping of transcription factor binding and histone modification reveals complex patterns of interactions. Identifying overlaps in binding patterns by different factors is a major objective of genomic studies, but existing methods to archive large numbers of datasets in a personalised database lack sophistication and utility. Therefore we have developed transcription factor DNA binding site analyser software (BiSA), for archiving of binding regions and easy identification of overlap with or proximity to other regions of interest. Analysis results can be restricted by chromosome or base pair overlap between regions or maximum distance between binding peaks. BiSA is capable of reporting overlapping regions that share common base pairs; regions that are nearby; regions that are not overlapping; and average region sizes. BiSA can identify genes located near binding regions of interest, genomic features near a gene or locus of interest and statistical significance of overlapping regions can also be reported. Overlapping results can be visualized as Venn diagrams. A major strength of BiSA is that it is supported by a comprehensive database of publicly available transcription factor binding sites and histone modifications, which can be directly compared to user data. The documentation and source code are available on http://bisa.sourceforge.net © 2014 Khushi et al

Complete bilayer adsorption of C16TAB on the surface of mica using neutron reflection.

We present neutron reflection data from an alkylammonium surfactant (C16TAB) at the mica/water interface. The system is studied in situ in a noninvasive manner and indicates the formation of a complete adsorbed bilayer with little evidence of defects. A detailed analysis suggests that the data are not consistent with some other previously reported adsorbed structures, such as micelles or cylinders.BPThis is the accepted manuscript. The final version is available at http://pubs.acs.org/doi/full/10.1021/acs.jpcb.5b00397

Bioinformatic analysis of cis-regulatory interactions between progesterone and estrogen receptors in breast cancer

Supplemental Information: Enrichment analysis of ERα-PR common regions using GREAT, doi: 10.7717/peerj.654/supp-1.Copyright © 2014 Khushi et al. Chromatin factors interact with each other in a cell and sequence-specific manner in order to regulate transcription and a wealth of publically available datasets exists describing the genomic locations of these interactions. Our recently published BiSA (Binding Sites Analyser) database contains transcription factor binding locations and epigenetic modifications collected from published studies and provides tools to analyse stored and imported data. Using BiSA we investigated the overlapping cis-regulatory role of estrogen receptor alpha (ERα) and progesterone receptor (PR) in the T-47D breast cancer cell line. We found that ERα binding sites overlap with a subset of PR binding sites. To investigate further, we re-analysed raw data to remove any biases introduced by the use of distinct tools in the original publications. We identified 22,152 PR and 18,560 ERα binding sites (<5% false discovery rate) with 4,358 overlapping regions among the two datasets. BiSA statistical analysis revealed a non-significant overall overlap correlation between the two factors, suggesting that ERα and PR are not partner factors and do not require each other for binding to occur. However, Monte Carlo simulation by Binary Interval Search (BITS), Relevant Distance, Absolute Distance, Jaccard and Projection tests by Genometricorr revealed a statistically significant spatial correlation of binding regions on chromosome between the two factors. Motif analysis revealed that the shared binding regions were enriched with binding motifs for ERα, PR and a number of other transcription and pioneer factors. Some of these factors are known to co-locate with ERα and PR binding. Therefore spatially close proximity of ERα binding sites with PR binding sites suggests that ERα and PR, in general function independently at the molecular level, but that their activities converge on a specific subset of transcriptional targets.Australian Postgraduate Award (APA); Westmead Medical Research Foundation (WMRF) Top-Up scholarship

Pathological and phylogenetic characterization of Amphibiothecum sp. infection in an isolated amphibian (Lissotriton helveticus) population on the island of Rum (Scotland)

Outbreaks of cutaneous infectious disease in amphibians are increasingly being attributed to an overlooked group of fungal-like pathogens, the Dermocystids. During the last 10 years on the Isle of Rum, Scotland, palmate newts (Lissotriton helveticus) have been reportedly afflicted by unusual skin lesions. Here we present pathological and molecular findings confirming that the pathogen associated with these lesions is a novel organism of the order Dermocystida, and represents the first formally reported, and potentially lethal, case of amphibian Dermocystid infection in the UK. Whilst the gross pathology and the parasite cyst morphology were synonymous to those described in a study from infected L. helveticus in France, we observed a more extreme clinical outcome on Rum involving severe subcutaneous oedema. Phylogenetic topologies supported synonymy between Dermocystid sequences from Rum and France and as well as their distinction from Amphibiocystidium spp. Phylogenetic analysis also suggested that the amphibian-infecting Dermocystids are not monophyletic. We conclude that the L. helveticusinfecting pathogen represents a single, novel species; Amphibiothecum meredithae

Dilemmas in doing insider research in professional education

This article explores the dilemmas I encountered when researching social work education in England as an insider researcher who was simultaneously employed as an educator in the host institution. This was an ethnographic project deploying multiple methods and generating rich case study material which informed the student textbook Becoming a Social Worker the four-year period of the project. First, ethical dilemmas emerged around informed consent and confidentiality when conducting surveys of students and reading their portfolios. Second, professional dilemmas stemmed from the ways in which my roles as a researcher, academic tutor, social worker and former practice educator converged and collided. Third, political dilemmas pertained to the potential for the project to crystallize and convey conflicts among stakeholders in the university and community. Since the majority of research in social work education is conducted by insiders, we have a vital interest in making sense of such complexity

Subdivision of the bacterioferritin comigratory protein family of bacterial peroxiredoxins based on catalytic activity.

© American Chemical Society,2010. Post-print version of article deposited in accordance with SHERPA RoMEO guidelinesPeroxiredoxins are ubiquitous proteins that catalyze the reduction of hydroperoxides, thus conferring resistance to oxidative stress. Using high-resolution mass spectrometry, we recently reclassified one such peroxiredoxin, bacterioferritin comigratory protein (BCP) of Escherichia coli, as an atypical 2-Cys peroxiredoxin that functions through the formation of an intramolecular disulfide bond between the active and resolving cysteine. An engineered E. coli BCP, which lacked the resolving cysteine, retained enzyme activity through a novel catalytic pathway. Unlike the active cysteine, the resolving cysteine of BCP peroxiredoxins is not conserved across all members of the family. To clarify the catalytic mechanism of native BCP enzymes that lack the resolving cysteine, we have investigated the BCP homologue of Burkholderia cenocepacia. We demonstrate that the B. cenocepacia BCP (BcBCP) homologue functions through a 1-Cys catalytic pathway. During catalysis, BcBCP can utilize thioredoxin as a reductant for the sulfenic acid intermediate. However, significantly higher peroxidase activity is observed utilizing glutathione as a resolving cysteine and glutaredoxin as a redox partner. Introduction of a resolving cysteine into BcBCP changes the activity from a 1-Cys pathway to an atypical 2-Cys pathway, analogous to the E. coli enzyme. In contrast to the native B. cenocepacia enzyme, thioredoxin is the preferred redox partner for this atypical 2-Cys variant. BCP-deficient B. cenocepacia exhibit a growth-phase-dependent hypersensitivity to oxidative killing. On the basis of sequence alignments, we believe that BcBCP described herein is representative of the major class of bacterial BCP peroxiredoxins. To our knowledge, this is the first detailed characterization of their catalytic activity. These studies support the subdivision of the BCP family of peroxiredoxins into two classes based on their catalytic activity

Timing of surgical intervention for developmental dysplasia of the hip: a randomised controlled trial (Hip 'Op)

Background: Developmental dysplasia of the hip (DDH) is a very common congenital disorder, and late-presenting cases often require surgical treatment. Surgical reduction of the hip may be complicated by avascular necrosis (AVN), which occurs as a result of interruption to the femoral head blood supply during treatment and can result in long-term problems. Some surgeons delay surgical treatment until the ossific nucleus (ON) has developed, whereas others believe that the earlier the reduction is performed, the better the result. Currently there is no definitive evidence to support either strategy. Objectives: To determine, in children aged 12 weeks to 13 months, whether or not delayed surgical treatment of a congenitally dislocated hip reduces the incidence of AVN at 5 years of age. The main clinical outcome measures were incidence of AVN and the need for a secondary surgical procedure during 5 years’ follow-up. In addition, to perform (1) a qualitative evaluation of the adopted strategy and (2) a health economic analysis based on NHS and societal costs. Design: Phase III, unmasked, randomised controlled trial with qualitative and health economics analyses. Participants were randomised 1 : 1 to undergo either early or delayed surgery. Setting: Paediatric orthopaedic surgical centres in the UK. Participants: Children aged 12 weeks to 13 months with DDH, either newly diagnosed or following failed splintage, and who required surgery. We had a target recruitment of 636 children. Interventions: Surgical reduction of the hip performed as per the timing allocated at randomisation. Main outcome measures: Primary outcome – incidence of AVN at 5 years of age (according to the Kalamchi and MacEwen classification). Secondary outcomes – need for secondary surgery, presence or absence of the ON at the time of primary treatment, quality of life for the main carer and child, and a health economics and qualitative analysis. Results: The trial closed early after reaching < 5% of the recruitment target. Fourteen patients were randomised to early treatment and 15 to delayed treatment. Implementation of rescue strategies did not improve recruitment. No primary outcome data were collected, and no meaningful conclusions could be made from the small number of non-qualitative secondary outcome data. The qualitative work generated rich data around three key themes: (1) access to, and experiences of, primary and secondary care; (2) the impact of surgery on family life; and (3) participants’ experiences of being in the trial. Limitations: Overoptimistic estimates of numbers of eligible patients seen at recruiting centres during the planning of the trial, as well as an overestimation of the recruitment rate, may have also contributed to unrealistic expectations on achievable patient numbers. Future work: There may be scope for investigation using routinely available data. Conclusions: Hip ’Op has highlighted the importance of accurate advance information on numbers of available eligible patients, as well as support from all participating investigators when conducting surgical research. Despite substantial consultation with parents of children in the planning stage, the level of non-participation experienced during recruitment was much higher than anticipated. The qualitative work has emphasised the need for appropriate advice and robust support for parents regarding the ‘real-life’ aspects of managing children with DDH. Trial registration: Current Controlled Trials ISRCTN76958754. Funding: This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 21, No. 63. See the NIHR Journals Library website for further project information