Uncovering hidden duplicated content in public transcriptomics data.

As part of the development of the database Bgee (a dataBase for Gene Expression Evolution), we annotate and analyse expression data from different types and different sources, notably Affymetrix data from GEO and ArrayExpress, and RNA-Seq data from SRA. During our quality control procedure, we have identified duplicated content in GEO and ArrayExpress, affecting ∼14% of our data: fully or partially duplicated experiments from independent data submissions, Affymetrix chips reused in several experiments, or reused within an experiment. We present here the procedure that we have established to filter such duplicates from Affymetrix data, and our procedure to identify future potential duplicates in RNA-Seq data. Database URL: http://bgee.unil.ch/

Abortion in public reason

What abortion laws a liberal political community ought to have? Much has been said about the moral problem of abortion, but there has not been yet (to my knowledge) a fully articulate account of the bearing of the competing answers to this ethical problem on liberal public reason. The first part of my project consists in a critical review of the different attempts to solve the various philosophical puzzles, both metaphysical and moral, posed by the abortion problem. Why is it wrong to kill beings like you and me? By answering this question we shall gain a better insight into those properties we have that give us such strong reasons against killing beings like us. Here we face a tremendous philosophical diffuculty, for it is not possible to determine what the robustest account of the wrongness of killing is without dealing with deeper metaethical and metaphysical problems. Indeed, consequentialist and nonconsequentialist moral theories differ in what it is that makes an action morally wrong -is it just the outcome of the action as compared with the outcomes of its alternatives? Or is it something else? Also, what are we essentially? Is the foetus merely our precursor? Then killing a foetus is relevantly similar to contraception. Or is the foetus one of us? If so, when we kill it, are we depriving it of a future as valuable as ours? Perhaps the relation of identity (the fact that it is its future as opposed to someone else's) doesn't matter. That may be because the foetus is an aggregate of biological and psychological facts and perhaps aggregates are not substances. Or maybe it is a substance but only psychological realtions matter, not personal identity. The second part of my project has to do with the different status these metaphisical and ethical positions ought to have in liberal public reason. Though this is the part in which most research is still needed, my own intuition is that, given the depth of the philosphical views in competition, restrictive abortion laws ought to be considered unrespectful to citizens' autonomy.

Quelle place pour la psychothérapie dans la psychiatrie publique [What place for psychotherapy in public psychiatry?].

The question of the place of psychotherapy in psychiatric public care is posed in this article. We will address this question first by presenting two clinical and research programmes which were implemented in a clinical psychiatric unit, section Karl Jaspers (Service of General Psychiatry) of the Department of Psychiatry CHUV, in Lausanne with the collaboration of the University Institute of Psychotherapy. The first one puts forward psychodynamic psychotherapy of depressed inpatients; the clinical programme and the research questions on efficacy of this treatment are discussed. The second focuses on the early treatment of patients with Borderline Personality Disorder, in particular in its research question on the effect of the motive-oriented therapeutic relationship in this process. We conclude by underlining the convergences of the two programmes.

Gender differences in HIV progression to AIDS and death in industrialized countries: slower disease progression following HIV seroconversion in women.

To evaluate sex differences in human immunodeficiency virus (HIV) disease progression before (pre-1997) and after (1997-2006) introduction of highly active antiretroviral therapy, the authors used data from a collaboration of 23 HIV seroconverter cohort studies from Europe, Australia, and Canada restricted to the 6,923 seroconverters infected through injecting drug use and sex between men and women. Within a competing risk framework, they used Cox proportional hazards models allowing for late entry to evaluate sex differences in time from HIV seroconversion to death, to acquired immunodeficiency syndrome (AIDS), and to each first AIDS-defining disease and death without AIDS. While no significant sex differences were found before 1997, from 1997 onward, women had a lower risk of AIDS (adjusted cumulative relative risk (aCRR) = 0.76, 95% confidence interval (CI): 0.63, 0.90) and death (adjusted hazard ratio = 0.68, 95% CI: 0.56, 0.82) than men did. Compared with men, women also had lower risks of AIDS dementia complex (aCRR = 0.23, 95% CI: 0.07, 0.74), tuberculosis (aCRR = 0.60, 95% CI: 0.39, 0.92), Kaposi's sarcoma (aCRR = 0.27, 95% CI: 0.07, 0.99), lymphomas (aCRR = 0.47, 95% CI: 0.23, 0.96), and death without AIDS (aCRR = 0.74, 95% CI: 0.56, 0.98). Sex differences in HIV disease progression have become larger and statistically significant in the era of highly active antiretroviral therapy, supporting a stronger impact of health interventions among women.

Value for Money and Policy Review of the Economic Cost and Charges Associated with Private and Semi-Private Treatment Services in Public Hospitals - Final Report

This Value for Money and Policy Review (VFM&PR) of the Economic Cost and Charges Associated with Private and Semi-Private Treatment Services in Public Hospitals was initiated by the Department of Health and Children in June 2009 and was conducted under the auspices of the Governmentâ?Ts Value for Money & Policy Review Initiative 2009-2011. The Review was overseen by an independently chaired National Steering Group comprised of senior representatives from the Department of Health and Children, the Department of Finance, and the Health Service Executive (HSE). Download document here Download Explanatory Note  

Value for Money and Policy Review of the Economic Cost and Charges Associated with Private and Semi-Private Treatment Services in Public Hospitals - Interim Report

This report sets out a revised costing methodology and an estimate of the gap which currently exists between private and semi-private bed charges and the average economic cost. While the Steering Group considers the costing methodology proposed as an improvement on the approach taken in previous years and a good overall approximation of the difference on average between economic costs and current charges, it recognises that the current charging regime does not take sufficient account of the variation between different categories of patient. Download document here Note to Readers

The category 'natural' in the discourse of couples who used medically assisted procreation

As a constantly evolving set of complex biotechnologies, medically assisted procreation (MAP) jeopardises a category that seems to be taken for granted: that of 'natural'. What is 'natural' or not when MAP is used to procreate? What are the boundaries between a 'natural' and a 'non-natural' fertilisation? Drawing upon a dialogical approach to language and cognition, our study examined the semantic field of the category 'natural' as expressed in interviews between a psychiatrist and seven couples who resorted to MAP and had to decide whether to keep their frozen pre-embryonic cells (zygotes) for further procreation or to allow them be destroyed. We examined how these couples evoked the category 'natural' and showed that in their argumentation, the category 'natural' encompassed a wide variety of phenomena, which shifted the boundaries between the 'natural' and 'non-natural'. In so doing, the couples 'renaturalised' MAP, normalized it, moved the boundaries between what is legitimate or not, and showed their accountability. Hence, reference to the category 'natural' seemed to act both as an argumentative and a psychological resource in the elaboration of the person's experience in resorting to MAP.

Programmed cell death in Trypanosoma cruzi induced by Bothrops jararaca venom

Cells die through a programmed process or accidental death, know as apoptosis or necrosis, respectively. Bothrops jararaca is a snake whose venom inhibits the growth of Trypanosoma cruzi epimastigote forms causing mitochondrion swelling and cell death. The aim of the present work was to determine the type of death induced in epimastigotes of T. cruzi by this venom. Parasite growth was inhibited after venom treatment, and 50% growth inhibition was obtained with 10 µg/ml. Ultrastructural observations confirmed mitochondrion swelling and kinetoplast disorganization. Furthermore, cytoplasmic condensation, loss of mitochondrion membrane potential, time-dependent increase in phosphatidylserine exposure at the outer leaflet plasma membrane followed by permeabilization, activation of caspase like protein and DNA fragmentation were observed in epimastigotes throughout a 24 h period of venom treatment. Taken together, these results indicate that the stress induced in epimastigote by this venom, triggers a programmed cell death process, similar to metazoan apoptosis, which leads to parasite death.

General and Abdominal Adiposity and Risk of Death in Europe

Previous studies have relied predominantly on the body-mass index (BMI, the weight in kilograms divided by the square of the height in meters) to assess the association of adiposity with the risk of death, but few have examined whether the distribution of body fat contributes to the prediction of death. This study examined the association of BMI, waist circumference, and waist-to-hip ratio with the risk of death among 359,387 participants from nine countries in the European Prospective Investigation into Cancer and Nutrition (EPIC). A Cox regression analysis was used, with age as the time variable, and stratified the models according to study center and age at recruitment, with further adjustment for educational level, smoking status, alcohol consumption, physical activity, and height.

Impact of a smoking ban in public places: a rapid assessment in the Seychelles.

Background We assessed the impact of a smoking ban in hospitality venues in the Seychelles 9 months after legislation was implemented. Methods Survey officers observed compliance with the smoking ban in 38 most popular hospitality venues and administered a structured questionnaire to two customers, two workers and one manager in each venue. Results Virtually no customers or workers were seen smoking in the indoor premises. Patrons, workers and managers largely supported the ban. The personnel of the hospitality venues reported that most smokers had no difficulty refraining from smoking. However, a third of workers did not systematically request customers to stop smoking and half of them did not report adequate training. Workers reported improved health. No substantial change in the number of customers was noted. Conclusion A ban on public smoking was generally well implemented in hospitality venues but some less than optimal findings suggest the need for adequate training of workers and strengthened enforcement measures. The simple and inexpensive methodology used in this rapid survey may be a useful approach to evaluate the implementation and impact of clean air policy in low and middle-income countries.

Recognising diversity in Public Health NI

The fifth Director of Public Health Annual Report for Northern Ireland, launched on 16 June 2014, celebrates diversity in the population.��The report recognises the opportunities and challenges posed by population diversity and highlights some of the key programmes introduced to meet these needs.The presentation slides from key speakers from the launch event on 16 June 2014 and all parallel sessions will be��appended below.��Please note:��The PHA cannot be held responsible for any breach of copyright that may exist within individual presentations.Read more here>>

Director of Public Health annual report 2013 and additional core tables Recognising diversity in Public Health

The fifth Director of Public Health Annual Report for Northern Ireland, launched on 16 June 2014, celebrates diversity in our population.Diversity is about people and how we value and appreciate those who are not like us. People differ in all sorts of ways which may not always be obvious or visible. These differences might include race and ethnicity, culture and belief, gender and sexuality, age and social status, ability, and use of health and social care services