Binets: fundamental building blocks for phylogenetic networks

Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph having a unique root in which the leaves are labelled by a given set of species. Recently, some approaches have been developed to construct phylogenetic networks from collections of networks on 2- and 3-leaved networks, which are known as binets and trinets, respectively. Here we study in more depth properties of collections of binets, one of the simplest possible types of networks into which a phylogenetic network can be decomposed. More speci_cally, we show that if a collection of level-1 binets is compatible with some binary network, then it is also compatible with a binary level-1 network. Our proofs are based on useful structural results concerning lowest stable ancestors in networks. In addition, we show that, although the binets do not determine the topology of the network, they do determine the number of reticulations in the network, which is one of its most important parameters. We also consider algorithmic questions concerning binets. We show that deciding whether an arbitrary set of binets is compatible with some network is at least as hard as the well-known Graph Isomorphism problem. However, if we restrict to level-1 binets, it is possible to decide in polynomial time whether there exists a binary network that displays all the binets. We also show that to _nd a network that displays a maximum number of the binets is NP-hard, but that there exists a simple polynomial-time 1/3-approximation algorithm for this problem. It is hoped that these results will eventually assist in the development of new methods for constructing phylogenetic networks from collections of smaller networks

Thinking about Later Life: Insights from the Capability Approach

A major criticism of mainstream gerontological frameworks is the inability of such frameworks to appreciate and incorporate issues of diversity and difference in engaging with experiences of aging. Given the prevailing socially structured nature of inequalities, such differences matter greatly in shaping experiences, as well as social constructions, of aging. I argue that Amartya Sen’s capability approach (2009) potentially offers gerontological scholars a broad conceptual framework that places at its core consideration of human beings (their values) and centrality of human diversity. As well as identifying these key features of the capability approach, I discuss and demonstrate their relevance to thinking about old age and aging. I maintain that in the context of complex and emerging identities in later life that shape and are shaped by shifting people-place and people-people relationships, Sen’s capability approach offers significant possibilities for gerontological research

The stigmatisation of source isolation: a literature review

Background: Isolation precautions in patients with multi-drug-resistant bacteria and other communicable infectious agents can be associated with adverse effects. Patients’ perspectives of isolation suggest that the imposed environment and procedures create barriers to their physical, social and emotional needs.Aims: The purpose of this paper is to review the literature to uncover any reliable evidence supporting the assertion that stigma is a significant characteristic of the experience of source isolation in healthcare settings.Methods: The methodological framework of Arksey and O’Malley was applied to this review. A total of 14 papers identified from 189 abstracts screened were included in the review.Results: The research reviewed suggests a clear association between stigmatisation and isolation in which stigma does have a direct negative effect on patients placed in hospital isolation. None of the studies found evidence to the contrary.Conclusions: The implications of this literature review for policy-makers and healthcare professionals suggest that when isolation or other forms of constraint are implemented and in use, patients must be provided with strengthened forms of support, including social and emotional support, and given access to healthcare of optimal quality to prevent the associated adverse effects of isolation as much as possibl

Indirect comparison of interventions using published randomised trials: systematic review of PDE-5 inhibitors for erectile dysfunction

BACKGROUND: There are no randomised and properly blinded trials directly comparing one PDE-5 inhibitor with another in a normal home setting. Valid indirect comparisons with a common comparator must examine equivalent doses, similar duration, similar populations, with the same outcomes reported in the same way. METHODS: Published randomised, double-blind trials of oral PDE-5 inhibitors for erectile dysfunction were sought from reference lists in previous reviews and electronic searching. Analyses of efficacy and harm were carried out for each treatment, and results compared where there was a common comparator and consistency of outcome reporting, using equivalent doses. RESULTS: Analysis was limited by differential reporting of outcomes. Sildenafil trials were clinically and geographically more diverse. Tadalafil and vardenafil trials tended to use enriched enrolment. Using all trials, the three interventions were similar for consistently reported efficacy outcomes. Rates of successful intercourse for sildenafil, tadalafil and vardenafil were 65%, 62%, and 59%, with placebo rates of 23–28%. The rates of improved erections were 76%, 75% and 71%, respectively, with placebo rates of 22–24%, and NNTs of 1.9 or 2.0. Reporting of withdrawals was less consistent, but all-cause withdrawals for sildenafil, tadalafil and vardenafil were 8% 13% and 20%. All three drugs were well tolerated, with headache being the most commonly reported event at 13–17%. There were few serious adverse events. CONCLUSION: There were differences between trials in outcomes reported, limiting comparisons, and the most useful outcomes were not reported. For common outcomes there was similar efficacy between PDE-5 inhibitors

Placebo and other psychological interactions in headache treatment

We present a theory according which a headache treatment acts through a specific biological effect (when it exists), a placebo effect linked to both expectancy and repetition of its administration (conditioning), and a non-specific psychological effect. The respective part of these components varies with the treatments and the clinical situations. During antiquity, suggestions and beliefs were the mainstays of headache treatment. The word placebo appeared at the beginning of the eighteenth century. Controversies about its effect came from an excessive interpretation due to methodological bias, inadequate consideration of the variation of the measure (regression to the mean) and of the natural course of the disease. Several powerful studies on placebo effect showed that the nature of the treatment, the associated announce, the patients’ expectancy, and the repetition of the procedures are of paramount importance. The placebo expectancy is associated with an activation of pre-frontal, anterior cingular, accumbens, and periacqueducal grey opioidergic neurons possibly triggered by the dopaminergic meso-limbic system. In randomized control trials, several arms design could theoretically give information concerning the respective part of the different component of the outcome and control the natural course of the disease. However, for migraine and tension type headache attacks treatment, no three arm (verum, placebo, and natural course) trial is available in the literature. Indirect evidence of a placebo effect in migraine attack treatment, comes from the high amplitude of the improvement observed in the placebo arms (28% of the patients). This figure is lower (6%) when using the harder criterium of pain free at 2 h. But these data disregard the effect of the natural course. For prophylactic treatment with oral medication, the trials performed in the last decades report an improvement in 21% of the patients in the placebo arms. However, in these studies the duration of administration was limited, the control of attacks uncertain as well as the evolution of the co-morbid psycho-pathology. Considering the reviews and meta-analysis of complex prophylactic procedures, it must be concluded that their effect is mostly linked to a placebo and non-specific psychological effects. Acupuncture may have a slight specific effect on tension type headache, but not on migraine. Manual therapy studies do not exhibit difference between manipulation, mobilization, and controls; touch has no proven specific effect. A comprehensive efficacy review of biofeedback studies concludes to a small specific effect on tension type headache but not on migraine. A review of behavioral treatment conclude to an interesting mean improvement but did not demonstrated a specific effect with the exception of a four arm study including a pseudo meditation control group. Expectation-linked placebo, conditioning, and non-specific psychological effects vary according clinical situations and psychological context; likely low in RCT, high after anempathic medical contact, and at its maximum with a desired charismatic healer. The announcements of doctors strongly influence the beliefs of patients, and in consequence their pain and anxiety sensibilities; this modulates the amplitude of the placebo and the non-specific psychological effects and is therefore a major determinant of the therapeutic success. Furthermore, any repetitive contact, even through a placebo, may interfere positively with the psychopathological co-morbidity. One has to keep in mind that the non-specific psychological interactions play a major role in the improvement of the majority of the headache sufferers

iDAH Research Software Engineering (RSE) Steering Group working paper

This is the final version. Available from the iDAH Research Software Engineering (RSE) Steering Group via the DOI in this record. Our purpose was to convene a broad and representative group from the UK Research Software Engineering (RSE) community to discuss opportunities for and barriers to the development of Arts & Humanities (AH) RSE capability, with a specific focus on contributing to the AHRC Infrastructure for Digital Innovation and Curation in Arts and Humanities (iDAH) project and a wider remit to consider longer term strategic priorities and opportunities for alignment with UKRI and EU initiatives. The discussion was intended to be foundational, inclusive, and broad-ranging, involving a wide stakeholder group encouraged to engage in ‘blue-sky’ thinking over short, medium, and long-term time horizons. The analysis contained in this working paper should be read in that context, as a reflection of early stage discussions intended to provide a platform for future more focused activity. Additional discussion and analysis is needed to produce substantive actionable conclusions

Oxidative methane activation over yttrium stabilised zirconia

Mechanism of C–H bond cleavage, involving electron transfer to adsorbed oxygen on YSZ by electronic structure calculations.</p

REINTERPRETATION OF I2I_{2} VISIBLE CONTINUUM

$^{1}$G. E. Busch, J. F. Cornelius, R. T. Mahoney, R. I. Morse, D. W. Schlosser and K. R. Wilson, Rev. Sci, Instr 41, 1066 (1970). $^{2}$J. I. Steinfeld, J. D. Campbell and N. A. Weiss, J. Mol. Spectry, 29, 204 (1969); A. Chutjian, J. Chem. Phys. 51. 5414 (1969), J. Tellinghuisen, University of California, Radiation Laboratory Report UCRL-19112 (1969), unpublished. $^{3}$R. T. Mahoney, R. J. Oldman, R. K. Sander and K. R. Wilson, Bull. Am. Phys. Soc. 14, 850 (1969).""Author Institution: University of California(This is a last minute paper, not in the preliminary program, and replaces the original N4.) We have demonstrated by photofragment spectroscopy that the long accepted assignment of the main iodine visible continuum as being almost entirely due to the $B^{3}\Pi_{o^{+}_{u}}\leftarrow {x^{1}}\Sigma_{o_{g}^{+}}$ parallel transition, which gives one excited and one ground state atom, is incorrect. In reality, a perpendicular transition to a $I_{u}$ state (most probably $^{1}\Pi_{1u}$) dissociating to ground state atoms is of comparable importance. By crossing a molecular beam of $I_{2}$ with pulses of polarized light from a laser-pumped tunable dye laser and measuring the time of flight to a mass-spectrometer detector as a function of angle of the recoiling I $atoms,^{1}$ we have separated at several wavelengths the $B^{3}\Pi_{o}+_{o}$ and $I_{u}$ components of the continuum absorption. The results, which clearly distinguish between the two components both by angular and translational energy distributions, allow us to determine directly the ratios of absorption probability to the two states. Our conclusions are consistent with recent $studies^{2}$ of the $I_{2}$ visible banded region by Steinfeld. Campbell and Weiss, by Chutjian, and by Brewer and Tellinghuisen which also indicate the importance of another state in addition to $B^{3}{\Pi_{o}}^{+}_{g}$. The additional state is again probably $^{1}\Pi_{1u}$, bringing the new interpretation of the $I_{2}$ visible spectrum into close parallel with the accepted interpretations of the $Cl_{2}$ and $Br_{2}^{3}$ visible spectra. We thank NSF for support of these experiments and NIH for support of the on-line computer system we used