Genomes of "phiKMV-like viruses" of Pseudomonas aeruginosa contain localized single-strand interruptions

The "phiKMV-like viruses" comprise an important genus of T7 related phages infecting Pseudomonas aeruginosa. The genomes of these bacteriophages have localized single-strand interruptions (nicks), a distinguishing genomic trait previously thought to be unique for T5 related coliphages. Analysis of this feature in the newly sequenced phage fkF77 shows all four nicks to be localized on the non-coding DNA strand. They are present with high frequencies within the phage population and are introduced into the phage DNA at late stages of the lytic cycle. The general consensus sequence in the nicks (5'-CGACxxxxxCCTAoh pCTCCGG-3') was shown to be common among all phiKMV-related phages.

Genomic Analysis of Pseudomonas putida Phage tf with Localized Single-Strand DNA Interruptions

The complete sequence of the 46,267 bp genome of the lytic bacteriophage tf specific to Pseudomonas putida PpG1 has been determined. The phage genome has two sets of convergently transcribed genes and 186 bp long direct terminal repeats. The overall genomic architecture of the tf phage is similar to that of the previously described Pseudomonas aeruginosa phages PaP3, LUZ24 and phiMR299-2, and 39 out of the 72 products of predicted tf open reading frames have orthologs in these phages. Accordingly, tf was classified as belonging to the LUZ24-like bacteriophage group. However, taking into account very low homology levels between tf DNA and that of the other phages, tf should be considered as an evolutionary divergent member of the group. Two distinguishing features not reported for other members of the group were found in the tf genome. Firstly, a unique end structure - a blunt right end and a 4-nucleotide 3'-protruding left end - was observed. Secondly, 14 single-chain interruptions (nicks) were found in the top strand of the tf DNA. All nicks were mapped within a consensus sequence 5'-TACT/RTGMC-3'. Two nicks were analyzed in detail and were shown to be present in more than 90% of the phage population. Although localized nicks were previously found only in the DNA of T5-like and phiKMV-like phages, it seems increasingly likely that this enigmatic structural feature is common to various other bacteriophages.

Responses to interactive playback predict future pairing success in nightingales

Birdsong is a sexually selected trait that serves in territory defence and mate choice. Individual song traits can be affected by the body condition of the male and thus may reflect his quality. Such relations between male quality and general singing performance raise the question whether differences in male quality also affect response strategies used in dyadic interactions. To address this question, we studied the relation between pairing success of male common nightingales, Luscinia megarhynchos, and their responses to rivals posing different levels of threat. Using interactive playback, we exposed males prior to mating to either aggressively or moderately singing rivals (by song overlapping and song alternating, respectively). Males that remained unpaired throughout the season (bachelors) interrupted their singing significantly more often after being overlapped than after alternating playback, whereas subsequently mated males kept the number of singing interruptions more constant across playback treatment. This suggests that subsequently paired males are less discriminative than are bachelors when challenged by rivals varying in aggressiveness. Regardless of playback treatment, males that later became paired responded significantly more strongly than did bachelor males. Thus, an increase in singing after a vocal interaction prior to mating predicted future mating success. (c) 2006 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Near-surface temperature cycling of stone and its implications for scales of surface deterioration

Many previous studies into internal temperature gradients within stone have assumed smooth, exponential increases and decreases in sub-surface temperatures in response, for example, to diurnal patterns of heating and cooling and these have been used to explain phenomena such as large-scale contour scaling. This high-resolution experimental study, in which a porous limestone block was subjected to alternate surface heating and cooling using an infrared lamp, demonstrates that internal temperature gradients in response to short-term environmental cycles (measured in minutes) can in fact be complex and inconsistent. Results confirm the significance of very steep temperature/stress gradients within the outer 10 mm or less of exposed stone. Below this the data indicate complex patterns of temperature reversals, the amplitudes of which are attenuated with depth and which are influenced in their intensity and location by variations in the relative duration of heating and cooling phases. It is suggested that the reversals might represent ‘interference patterns’ between incoming and outgoing thermal waves, but whatever their origin they are potentially important because they occur within the zone in which many stone decay processes, especially salt weathering, operate. These processes invariably respond to temperature and moisture fluctuations, and short-term interruptions to insolation could, for example, trigger these fluctuations on numerous occasions over a day. In particular, the reversals occur at a scale that is commensurate with decay by multiple flaking and could indicate an underlying control on this previously little-researched pattern of weathering. In the context of this publication, however, the main lesson to be learned from this study is that differing scales of behaviour require different scales of enquiry.

Experimental studies of near-surface temperature cycling and surface wetting of stone and its implications for salt weathering

It has long been accepted that thermal and moisture regimes within stonework exert a major influence upon patterns of salt movement and, subsequently, the type and severity of salt-induced decay. For example, it is suggested that slow drying is more likely to bring dissolved salts to the surface, whereas rapid drying could result in the retention of some salt at or near the frequent wetting depth. In reality however, patterns of heating, cooling and surface wetting regimes that drive them – are complex and inconsistent responses to a wide range of environmental controls. As a first step to understanding the complexity of these relationships, this paper reports a series of experiments within a climatic cabinet designed to replicate the effects of short-term temperature fluctuations on the surface and sub-surface temperature regimes of a porous Jurassic limestone, and how they are influenced by surface wetting, ambient temperature and surface airflow. Preliminary results confirm the significance of very steep temperature/stress gradients within the outer centimetre or less of exposed stone under short-duration cycles of heating and cooling. This is important because this is the zone in which many stone decay processes, particularly salt weathering, operate, these processes invariably respond to temperature and moisture fluctuations, and short-term interruptions to insolation could, for example,
trigger these fluctuations on numerous occasions over a day. The data also indicate that there are complex patterns of temperature reversal with depth that are influenced in their intensity and location by surface wetting and moisture penetration, airflow across the surface and ambient air temperature. The presence of multiple temperature reversals and their variation over the course of heating and cooling phases belies previous assumtions of smooth, exponential increases and decreases in subsurface temperatures in response, for example to diurnal patterns of heating and cooling

Prevalence and Causes of Prescribing ErrorsL The PRescribing Outcomes for Trainee Doctors Engaged in Clinical Training (PROTECT) Study

Objectives: Study objectives were to investigate the prevalence and causes of prescribing errors amongst foundation doctors (i.e. junior doctors in their first (F1) or second (F2) year of post-graduate training), describe their knowledge and experience of prescribing errors, and explore their self-efficacy (i.e. confidence) in prescribing.

Method: A three-part mixed-methods design was used, comprising: prospective observational study; semi-structured interviews and cross-sectional survey. All doctors prescribing in eight purposively selected hospitals in Scotland participated. All foundation doctors throughout Scotland participated in the survey. The number of prescribing errors per patient, doctor, ward and hospital, perceived causes of errors and a measure of doctors’ self-efficacy were established.

Results: 4710 patient charts and 44,726 prescribed medicines were reviewed. There were 3364 errors, affecting 1700 (36.1%) charts (overall error rate: 7.5%; F1:7.4%; F2:8.6%; consultants:6.3%). Higher error rates were associated with : teaching hospitals (p,0.001), surgical (p = ,0.001) or mixed wards (0.008) rather thanmedical ward, higher patient turnover wards (p,0.001), a greater number of prescribed medicines (p,0.001) and the months December and June (p,0.001). One hundred errors were discussed in 40 interviews. Error causation was multi-factorial; work environment and team factors were particularly noted. Of 548 completed questionnaires (national response rate of 35.4%), 508 (92.7% of respondents) reported errors, most of which (328 (64.6%) did not reach the patient. Pressure from other staff, workload and interruptions were cited as the main causes of errors. Foundation year 2 doctors reported greater confidence than year 1 doctors in deciding the most appropriate medication regimen.

Conclusions: Prescribing errors are frequent and of complex causation. Foundation doctors made more errors than other doctors, but undertook the majority of prescribing, making them a key target for intervention. Contributing causes included work environment, team, task, individual and patient factors. Further work is needed to develop and assess interventions that address these.

'Sorry I meant the patient's left side': impact of distraction on right/left discrimination

Context Medical students can have difficulty in distinguishing left from right. Many infamous medical errors have occurred when a procedure has been performed on the wrong side, such as in the removal of the wrong kidney. Clinicians encounter many distractions during their work. There is limited information on how these affect performance. 
Objectives Using a neuropsychological paradigm, we aim to elucidate the impacts of different types of distraction on left–right (LR) discrimination ability. 
Methods Medical students were recruited to a study with four arms: (i) control arm (no distraction); (ii) auditory distraction arm (continuous ambient ward noise); (iii) cognitive distraction arm (interruptions with clinical cognitive tasks), and (iv) auditory and cognitive distraction arm. Participants’ LR discrimination ability was measured using the validated Bergen Left–Right Discrimination Test (BLRDT). Multivariate analysis of variance was used to analyse the impacts of the different forms of distraction on participants’ performance on the BLRDT. Additional analyses looked at effects of demographics on performance and correlated participants’ self-perceived LR discrimination ability and their actual performance. 
Results A total of 234 students were recruited. Cognitive distraction had a greater negative impact on BLRDT performance than auditory distraction. Combined auditory and cognitive distraction had a negative impact on performance, but only in the most difficult LR task was this negative impact found to be significantly greater than that of cognitive distraction alone. There was a significant medium-sized correlation between perceived LR discrimination ability and actual overall BLRDT performance. 
Conclusions
Distraction has a significant impact on performance and multifaceted approaches are required to reduce LR errors. Educationally, greater emphasis on the linking of theory and clinical application is required to support patient safety and human factor training in medical school curricula. Distraction has the potential to impair an individual's ability to make accurate LR decisions and students should be trained from undergraduate level to be mindful of this.

Complete nucleotide sequence of φCHU: A Luz24likevirus infecting Pseudomonas aeruginosa and displaying a unique host range

A complete nucleotide sequence of the new Pseudomonas aeruginosa Luz24likevirus phiCHU was obtained. This virus was shown to have a unique host range whereby it grew poorly on the standard laboratory strain PAO1, but infected 26 of 46 clinical isolates screened, and strains harboring IncP2 plasmid pMG53. It was demonstrated that phiCHU has single strand interruptions in its genome. Analysis of the phiCHU genome also suggested that recombination event(s) participated in the evolution of the leftmost portion of the genome, presumably encoding early genes.

‘Connected communities, “answerability” and the arts: a case study'

This co-authored essay outlines and analyses the AHRC 'Creative Interruptions' Project, 'Where do I belong?', a theatre-as-research project conducted with Afghan refugees in London under the guidance of PI Sarita Malik, Brunel University London.