Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion.

Chlamydia trachomatis is the world's most prevalent bacterial sexually transmitted infection and leading infectious cause of blindness, yet it is one of the least understood human pathogens, in part due to the difficulties of in vitro culturing and the lack of available tools for genetic manipulation. Genome sequencing has reinvigorated this field, shedding light on the contemporary history of this pathogen. Here, we analyze 563 full genomes, 455 of which are novel, to show that the history of the species comprises two phases, and conclude that the currently circulating lineages are the result of evolution in different genomic ecotypes. Temporal analysis indicates these lineages have recently expanded in the space of thousands of years, rather than the millions of years as previously thought, a finding that dramatically changes our understanding of this pathogen's history. Finally, at a time when almost every pathogen is becoming increasingly resistant to antimicrobials, we show that there is no evidence of circulating genomic resistance in C. trachomatis

Recurrent respiratory papillomatosis: an overview of current thinking and treatment

Human papillomaviruses (HPV) infection in benign laryngeal papillomas is well established. The vast majority of recurrent respiratory papillomatosis lesions are due to HPV types 6 and 11. Human papillomaviruses are small non-enveloped viruses (>8 kb), that replicate within the nuclei of infected host cells. Infected host basal cell keratinocytes and papillomas arise from the disordered proliferation of these differentiating keratinocytes. Surgical debulking of papillomas is currently the treatment of choice; newer surgical approaches utilizing microdebriders are replacing laser ablation. Surgery aims to secure an adequate airway and improve and maintain an acceptable quality of voice. Adjuvant treatments currently used include cidofovir, indole-3-carbinol, ribavirin, mumps vaccine, and photodynamic therapy. The recent licensing of prophylactic HPV vaccines is a most interesting development. The low incidence of RRP does pose significant problems in recruitment of sufficient numbers to show statistical significance. Large multi-centre collaborative clinical trials are therefore required. Even so, sufficient clinical follow-up data would take several years

Two meta-analyses of distant healing studies

Reviews of empirical work on the efficacy of distant healing have found that interceding on behalf of patients through prayer or by adopting various practices that incorporate an intention to heal can have some positive effect upon their wellbeing (e.g., Benor, 1990; Dossey, 1993), but reviewers have also raised concerns about study quality and the diversity of healing approaches adopted — ranging from techniques that usually involve close physical proximity between practitioner and patient, such as therapeutic touch and Reiki healing, through to techniques that work at a distance, such as psychic healing or intercessionary prayer to a higher being — and this makes the findings difficult to interpret since in some cases the beneficial effects could be attributable to placebo effects or to the consequences of general lifestyle changes that are involved in holistic approaches to medicine. Some of these concerns can be addressed by conducting double-blind randomised controlled clinical trials. These entail the random allocation of participants (or patients) to either a treatment or control condition so as to control for selection bias (or alternatively participants are matched on the basis of other variables that are thought to affect the prognosis of their health condition, such as age, gender, co-morbidity, and so on), with patients and attending physicians remaining blind to the allocation so as to control for placebo improvements. Some of the research that meet these criteria has been summarised by Astin, Harkness and Ernst (2000), who identified 23 studies, collectively involving 2774 participants, that produced the predicted improvement in condition with a combined effect size of .40 (p < .001). Despite remaining concerns about the heterogeneity of the database and methodological limitations with some studies, the authors were able to conclude that the evidence was sufficiently strong to warrant further study. However, Astin et al.‘s review is still susceptible to counter explanations in terms of their inability to create an appropriate control condition, since there can be no guarantee that control patients are not beneficiaries of healing intentions from friends, family or their own religious groups, or that relationships between healing intention and wellbeing are not obscured by reliance on relatively crude health outcomes. We planned to address this by focusing on healing studies that involved biological systems other than ‗whole‘ humans (i.e. to include animal andplant work but also work involving human biological matter such as blood samples or cell cultures), which allow for more circumscribed outcome measures and are less susceptible to placebo and expectancy effects. Secondly, since Astin‘s reviews have been published, doubts have been cast concerning the legitimacy of work conducted by Daniel P. Wirth such that it would be unsafe to base conclusions on data that he has provided. There have also been a number of replication attempts since Astin et al.‘s review. We therefore planned to conduct an updated review that included more recent studies and excluded Wirth‘s work. For phase 1, 65 non-whole human studies from 50 papers were eligible for review. The combined effect size weighted by sample size yielded a highly significant r of .381. The fail-safe N gave the value 8332, which is much larger than the critical number (calculated as 335), suggesting that publication bias is unlikely to be responsible for significance. However the effect sizes in the database are significantly heterogeneous, and 25 outliers need to be cropped in order to reduce to non-significance at p > .01, giving a weighted mean effect size for the cropped studies of r = .283, which is still significant. Study outcomes were not correlated with blind ratings of methodological quality, but the average quality rating for these studies is very low (mean quality rating [MQR] = 4.4/10). Studies were blocked by target system type: the 31 in vitro studies had the highest average quality rating (5.35) and a weighted mean effect size, r = .311; 18 studies of non-human animals (e.g., rats, mice, bush babies) had an MQR of 4.07 and a significant r = .218; 16 studies of plants or seeds (MQR = 3.22), gave a significant weighted mean effect size, r = .413. For phase 2, 61 whole human studies across 59 papers that were eligible for review. When combined, these studies yielded a small effect size of r = .145 that was significant. The fail-safe N was 3560 against a critical number of 315. This database is also significantly heterogeneous (χ2 = 512.01), but the mean weighted effect sized for the cropped sample actually increases to r = .202. Holistic judgements of study quality were negatively correlated with study outcome, suggesting that the observed effect might – at least in part – be attributable to methodological shortcomings. Whole human studies were blocked by target system: 9 Reiki or Johrei studies (MQR = 5.50), which gave a weighted mean effect size, r = .285; 11 studies incorporated intercessionary prayer (MQR = 5.33), giving the smallest weighted mean effect size, r = .078; therapeutic touch was implemented in 19 studies (MQR = 5.25), giving a weighted mean effect size, r = .346; and 22 unspecified /other studies (MQR = 5.94) gave a weighted mean effect size, r = .167. Findings with the non-whole human database suggest that subjects in the active condition were observed to have a significant improvement in wellbeing relative to control subjects under circumstances that do not seem to be susceptible to placebo and expectancy effects. Findings with the whole human database gave a smaller mean effect size but this was still significant and suggests that the effect is not dependent upon the inclusion of Wirth‘s suspect studies and is robust enough to accommodate some high profile failures to replicate. Both databases show problems with heterogeneity and with study quality and recommendations are made for necessary standards for future replication attempt

Meta-analysis of distant healing studies using non-whole human samples

As part of a larger project investigating spiritual healing, we are conducting a meta-analysis of existing literature on healing and complementary therapies. The supposed linkage between spirituality and health has long been of interest to parapsychologists since it provides one source of evidence for a connection between ‘mind’ (intentionality) and ‘matter’ (tangible effects in the world, particularly with respect to the claims of psychic healers), with two of the earliest substantive reviews of empirical work on the efficacy of healing having been conducted by prominent parapsychologists (Schouten, 1993; Solfvin, 1984). As with other reviews of healing research (e.g.,Astin, Harkness & Ernst, 2000;Benor, 1990; Dossey, 1993), these authors found that interceding on behalf of patients through prayer or by adopting various practices that incorporate an intention to heal can have some positive effect upon their wellbeing. However, these reviewers also raised concerns about certain aspects of the methodologies of the studies reviewed, such as the difficulty in finding pure control groups (participants in sick samples are likely to be prayed for by relatives and friends), a need for more detailed measures of psychological factors, the need for much larger sample sizes and effects of scepticism.In particular, these findings aredifficult to interpret becausein some cases the beneficial effects could be attributable to placebo effects or to the consequences of general lifestyle changes that are involved in holistic approaches to medicine. It is therefore our aim to conduct a mathematical review of previous studies to try and identify methodological features which affect findings and to try and assess the status of the evidence that suggests a distant healing effect. This initial meta analysis will take into account studies using non-whole human target subjects, including work with human red blood cells (Braud, 2003), mice (Bengston & Moga, 2007), seeds (Creath & Schwartz, 2004) and other target samples, as these studies would be unlikely to be affected by placebo effects due to the nature of the target subjects. The inclusion criteria for studies are as follows: Distinguishing features: All studies must look at the effects of spiritual healing (using psychological intent to manipulate the health or well being of the samples). Studies looking at direct mental influence without healing intention will not be included unless the effects ofthe intention on the system have an obvious link to health and well being. For instance, studies investigatingthe effects of human intention upon DNA would be included but studies looking at the effects of mental influence on GSR would not. Search Strategy: Possible studies will be identified by searching the Swetswise, ASSIA, PsychNET, Web of Science, Cochrane Library, British nursing Index, Cinahl Full Text and Informaworld databases as well as Google Scholar. Search terms to be used are “Spiritual healing”, “Distance Healing” “Noetic Healing” “Intercessory Prayer” “Laying on of hands” “Therapeutic Touch” and “Reiki” plus “Animals” “Plants” “Yeast” “Bacteria” and “Cells”. The papers resulting from these searches will then be read and any relevant references located. Linguistic range: Only studies published in English will be used. Research methods: The healing conducted must not involve direct touching. Data collection is ongoing and it is anticipated that the meta analysis will be completed by July 2011. In this presentation we will describe that data collection process and report on the results of our analysi