XMM-Newton observations of three short period polars: V347 Pav, GG Leo and EU UMa

We present phase-resolved XMM_Newton data of three short period polars: V347 Pav, GG Leo and EU UMa. All three systems show one dominant accretion region which is seen for approximately half of the orbital cycle. GG Leo shows a strong dip feature in its X-ray and UV light curves which is due to absorption of X-rays from the accretion site by the accretion stream. The emission in the case of EU UMa is dominated by soft X-rays: its soft/hard X-ray ratio is amongst the highest seen in these objects. In contrast, GG Leo and V347 Pav shows a ratio consistent with that predicted by the standard shock model. We infer the mass of the white dwarf and explore the affect of restricting the energy range on the derived parameters.Comment: accepted MNRA

Quantum Logic Gates in Optical Lattices

We propose a new system for implementing quantum logic gates: neutral atoms trapped in a very far-off-resonance optical lattice. Pairs of atoms are made to occupy the same well by varying the polarization of the trapping lasers, and then a near-resonant electric dipole is induced by an auxiliary laser. A controlled-NOT can be implemented by conditioning the target atomic resonance on a resolvable level shift induced by the control atom. Atoms interact only during logical operations, thereby suppressing decoherence.Comment: Revised version, To appear in Phys. Rev. Lett. Three separate postscript figure

Systematic evaluation of patient-reported outcome (PRO) protocol content and reporting in UK cancer clinical trials: the EPiC study protocol.

Emerging evidence suggests that patient-reported outcome (PRO)-specific information may be omitted in trial protocols and that PRO results are poorly reported, limiting the use of PRO data to inform cancer care. This study aims to evaluate the standards of PRO-specific content in UK cancer trial protocols and their arising publications and to highlight examples of best-practice PRO protocol content and reporting where they occur. The objective of this study is to determine if these early findings are generalisable to UK cancer trials, and if so, how best we can bring about future improvements in clinical trials methodology to enhance the way PROs are assessed, managed and reported.Trials in which the primary end point is based on a PRO will have more complete PRO protocol and publication components than trials in which PROs are secondary end points.Completed National Institute for Health Research (NIHR) Portfolio Cancer clinical trials (all cancer specialities/age-groups) will be included if they contain a primary/secondary PRO end point. The NIHR portfolio includes cancer trials, supported by a range of funders, adjudged as high-quality clinical research studies. The sample will be drawn from studies completed between 31 December 2000 and 1 March 2014 (n=1141) to allow sufficient time for completion of the final trial report and publication. Two reviewers will then review the protocols and arising publications of included trials to: (1) determine the completeness of their PRO-specific protocol content; (2) determine the proportion and completeness of PRO reporting in UK Cancer trials and (3) model factors associated with PRO protocol and reporting completeness and with PRO reporting proportion.The study was approved by the ethics committee at University of Birmingham (ERN_15-0311). Trial findings will be disseminated via presentations at local, national and international conferences, peer-reviewed journals and social media including the CPROR twitter account and UOB departmental website (http://www.birmingham.ac.uk/cpro0r)

International perspectives on suboptimal patient-reported outcome trial design and reporting in cancer clinical trials: a qualitative study

Purpose: Evidence suggests that the patient-reported outcome (PRO) content of cancer trial protocols is frequently inadequate and non-reporting of PRO findings is widespread. This qualitative study examined the factors influencing suboptimal PRO protocol content, implementation, and reporting, and use of PRO data during clinical interactions. Methods: Semi-structured interviews were conducted with four stakeholder groups: (1) trialists and chief investigators; (2) people with lived experience of cancer; (3) international experts in PRO cancer trial design; (4) journal editors, funding panelists, and regulatory agencies. Data were analyzed using directed thematic analysis with an iterative coding frame. Results: Forty-four interviews were undertaken. Several factors were identified that could influenced effective integration of PROs into trials and subsequent findings. Participants described (1) late inclusion of PROs in trial design; (2) PROs being considered a lower priority outcome compared to survival; (3) trialists’ reluctance to collect or report PROs due to participant burden, missing data, and perceived reticence of journals to publish; (4) lack of staff training. Strategies to address these included training research personnel and improved communication with site staff and patients regarding the value of PROs. Examples of good practice were identified. Conclusion: Misconceptions relating to PRO methodology and its use may undermine their planning, collection, and reporting. There is a role for funding, regulatory, methodological, and journalistic institutions to address perceptions around the value of PROs, their position within the trial outcomes hierarchy, that PRO training and guidance is available, signposted, and readily accessible, with accompanying measures to ensure compliance with international best practice guidelines

MCL-CAw: A refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure

Abstract Background The reconstruction of protein complexes from the physical interactome of organisms serves as a building block towards understanding the higher level organization of the cell. Over the past few years, several independent high-throughput experiments have helped to catalogue enormous amount of physical protein interaction data from organisms such as yeast. However, these individual datasets show lack of correlation with each other and also contain substantial number of false positives (noise). Over these years, several affinity scoring schemes have also been devised to improve the qualities of these datasets. Therefore, the challenge now is to detect meaningful as well as novel complexes from protein interaction (PPI) networks derived by combining datasets from multiple sources and by making use of these affinity scoring schemes. In the attempt towards tackling this challenge, the Markov Clustering algorithm (MCL) has proved to be a popular and reasonably successful method, mainly due to its scalability, robustness, and ability to work on scored (weighted) networks. However, MCL produces many noisy clusters, which either do not match known complexes or have additional proteins that reduce the accuracies of correctly predicted complexes. Results Inspired by recent experimental observations by Gavin and colleagues on the modularity structure in yeast complexes and the distinctive properties of "core" and "attachment" proteins, we develop a core-attachment based refinement method coupled to MCL for reconstruction of yeast complexes from scored (weighted) PPI networks. We combine physical interactions from two recent "pull-down" experiments to generate an unscored PPI network. We then score this network using available affinity scoring schemes to generate multiple scored PPI networks. The evaluation of our method (called MCL-CAw) on these networks shows that: (i) MCL-CAw derives larger number of yeast complexes and with better accuracies than MCL, particularly in the presence of natural noise; (ii) Affinity scoring can effectively reduce the impact of noise on MCL-CAw and thereby improve the quality (precision and recall) of its predicted complexes; (iii) MCL-CAw responds well to most available scoring schemes. We discuss several instances where MCL-CAw was successful in deriving meaningful complexes, and where it missed a few proteins or whole complexes due to affinity scoring of the networks. We compare MCL-CAw with several recent complex detection algorithms on unscored and scored networks, and assess the relative performance of the algorithms on these networks. Further, we study the impact of augmenting physical datasets with computationally inferred interactions for complex detection. Finally, we analyse the essentiality of proteins within predicted complexes to understand a possible correlation between protein essentiality and their ability to form complexes. Conclusions We demonstrate that core-attachment based refinement in MCL-CAw improves the predictions of MCL on yeast PPI networks. We show that affinity scoring improves the performance of MCL-CAw.http://deepblue.lib.umich.edu/bitstream/2027.42/78256/1/1471-2105-11-504.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/2/1471-2105-11-504-S1.PDFhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/3/1471-2105-11-504-S2.ZIPhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/4/1471-2105-11-504.pdfPeer Reviewe

XMM-Newton observations of the eclipsing polar EP Dra

We present XMM-Newton observations of the eclipsing polar EP Dra which cover nearly 3 binary orbital cycles. The X-ray and UV data show evidence for a prominent dip before the eclipse which is due to the accretion stream obscuring the accretion region. The dip ingress is rapid in hard X-rays suggesting there is a highly collimated core of absorption. We find that a different level of absorption column density is required to match the observed count rates in different energy bands. We propose that this is due to the fact that different absorption components should be used to model the reprocessed X-rays, the shocked X-ray component and the UV emission and explore the affect that this has on the resulting fits to the spectrum. Further, there is evidence that absorption starts to obscure the softer X-rays shortly after the onset of the bright phase. This suggests that material is threaded by an unusually wide range of magnetic field lines, consistent with the suggestion of Bridge et al. We find that the period is slightly greater than that determined by Schwope & Mengel.Comment: Accepted for publication MNRAS, 6 page

GIBA: a clustering tool for detecting protein complexes

Background: During the last years, high throughput experimental methods have been developed which generate large datasets of protein - protein interactions (PPIs). However, due to the experimental methodologies these datasets contain errors mainly in terms of false positive data sets and reducing therefore the quality of any derived information. Typically these datasets can be modeled as graphs, where vertices represent proteins and edges the pairwise PPIs, making it easy to apply automated clustering methods to detect protein complexes or other biological significant functional groupings. Methods: In this paper, a clustering tool, called GIBA (named by the first characters of its developers' nicknames), is presented. GIBA implements a two step procedure to a given dataset of protein-protein interaction data. First, a clustering algorithm is applied to the interaction data, which is then followed by a filtering step to generate the final candidate list of predicted complexes. Results: The efficiency of GIBA is demonstrated through the analysis of 6 different yeast protein interaction datasets in comparison to four other available algorithms. We compared the results of the different methods by applying five different performance measurement metrices. Moreover, the parameters of the methods that constitute the filter have been checked on how they affect the final results. Conclusion: GIBA is an effective and easy to use tool for the detection of protein complexes out of experimentally measured protein - protein interaction networks. The results show that GIBA has superior prediction accuracy than previously published methods

Repeatability of the Six-Minute Walk Test and Relation to Physical Function in Survivors of a Critical Illness

Background: The Six-Minute Walk Test (6MWT) is widely used as an outcome measure in exercise rehabilitation. However, the repeatability of the 6MWT performed at home in survivors of a critical illness has not been evaluated. Objective: The purpose of this study was to evaluate, in survivors of a critical illness: (1) the repeatability of the 6MWT performed at home, (2) the effect on estimates of change in functional exercise capacity if only one 6MWT was performed at follow-up assessments, and (3) the relationship between the physical functioning (PF) score of the 36-Item Short-Form Health Survey questionnaire (SF-36) and the 6MWT. Design: Repeated measures of the 6MWT and SF-36 were obtained. Methods: Eligible participants had an intensive care unit (ICU) length of stay of ≥48 hours and were mechanically ventilated for ≥24 hours. Two 6MWTs and the SF-36 were conducted in participants' homes at weeks 1, 8, and 26 after hospital discharge. Results: One hundred seventy-three participants completed the study. The participants had a mean age of 57 years (SD=16), a mean Acute Physiology and Chronic Health Evaluation II (APACHE II) score on admission of 19 (SD=10), a mean ICU length of stay of 9 days (SD=8), and a mean mechanical ventilation time of 140 hours (SD=137). Of the 173 participants, 110 performed two 6MWTs at weeks 1, 8, and 26. There were significant mean increases in 6-minute walk distance in the second test of 15 m (P<.0001) at week 1, 13 m (P<.0001) at week 8, and 9 m (P=.04) at week 26. If only one 6MWT was performed at weeks 8 and 26, the estimate of change in 6-minute walk distance from week 1 was 19 m less (P<.001) at both weeks 8 and 26. There was a moderate to strong correlation between SF-36 PF score and 6-minute walk distance at each assessment (week 1: r=.62, P<.001; week 8: r=.55, P<.001; and week 26: r=.47, P<.001).Limitations: Some study participants were unable to perform a second 6MWT, and these participants may have differed in important aspects of function compared with those individuals who completed two 6MWTs. Conclusions: In survivors of a critical illness, the 6MWT in the home environment should be performed twice at each assessment to give an accurate reflection of change in exercise capacity over time. The SF-36 PF score was a strong indicator of 6-minute walk distance in early recovery from a critical illness