Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1.

MOTIVATION: Analysis of millions of pyro-sequences is currently playing a crucial role in the advance of environmental microbiology. Taxonomy-independent, i.e. unsupervised, clustering of these sequences is essential for the definition of Operational Taxonomic Units. For this application, reproducibility and robustness should be the most sought after qualities, but have thus far largely been overlooked. RESULTS: More than 1 million hyper-variable internal transcribed spacer 1 (ITS1) sequences of fungal origin have been analyzed. The ITS1 sequences were first properly extracted from 454 reads using generalized profiles. Then, otupipe, cd-hit-454, ESPRIT-Tree and DBC454, a new algorithm presented here, were used to analyze the sequences. A numerical assay was developed to measure the reproducibility and robustness of these algorithms. DBC454 was the most robust, closely followed by ESPRIT-Tree. DBC454 features density-based hierarchical clustering, which complements the other methods by providing insights into the structure of the data. AVAILABILITY: An executable is freely available for non-commercial users at ftp://ftp.vital-it.ch/tools/dbc454. It is designed to run under MPI on a cluster of 64-bit Linux machines running Red Hat 4.x, or on a multi-core OSX system. CONTACT: dbc454@vital-it.ch or nicolas.guex@isb-sib.ch.

Recommendations on percutaneous coronary intervention for the reperfusion of acute ST elevation myocardial infarction

Little information is currently available from the various societies of cardiology on primary percutaneous coronary intervention (PCI) for acute myocardial infarction (AMI). Since primary PCI is the main method of reperfusion in AMI in many centres, and since of all cardiac emergencies AMI represents the most urgent situation for PCI, recommendations based on scientific evidence and expert experience would be useful for centres practising primary PCI, or those looking to establish a primary PCI programme. To this aim, a task force for primary PCI in AMI was formed to develop a set of recommendations to complement and assist clinical judgment. This paper represents the product of their recommendations.

Effectiveness of a brief integrative multiple substance use intervention among young men with and without booster sessions.

Brief interventions (BI) commonly employ screening and target a single substance. Multi-substance interventions are a more adequate reflection of risk behaviors in adolescents and young adults. Systematic screening complicates BI in many settings. The effectiveness of a voluntary multi-substance intervention among 19-year-old men and the incremental impact of booster sessions were analyzed. Participants were enrolled during mandatory army conscription in Switzerland. Compared with 461 controls, 392 BI subjects showed reduced substance use on 10 of 12 measures (4 tobacco, 4 cannabis, and 2 alcohol measures). Between-group effects were small and non-significant (except for cannabis use prevalence). Three-month booster sessions were not effective and even contraindicated. The usefulness of targeting multi-substances during BIs without prior screening depends on the value of small effects. The addition of booster sessions was not effective and therefore is not recommended.

Early antifungal intervention strategies in ICU patients.

PURPOSE OF REVIEW: Despite progress in the understanding of the pathophysiology of invasive candidiasis, and the development of new classes of well tolerated antifungals, invasive candidiasis remains a disease difficult to diagnose, and associated with significant morbidity and mortality. Early antifungal treatment may be useful in selected groups of patients who remain difficult to identify prospectively. The purpose of this review is to summarize the recent development of risk-identification strategies targeting early identification of ICU patients susceptible to benefit from preemptive or empirical antifungal treatment. RECENT FINDINGS: Combinations of different risk factors are useful in identifying high-risk patients. Among the many risk factors predisposing to invasive candidiasis, colonization has been identified as one of the most important. In contrast to prospective surveillance of the dynamics of colonization (colonization index), integration of clinical colonization status in risk scores models significantly improve their accuracy in identifying patients at risk of invasive candidiasis. SUMMARY: To date, despite limited prospective validation, clinical models targeted at early identification of patients at risk to develop invasive candidiasis represent a major advance in the management of patients at risk of invasive candidiasis. Moreover, large clinical studies using such risk scores or predictive rules are underway.

Effect of a lifestyle intervention on adiposity and fitness in socially disadvantaged subgroups of preschoolers: a cluster-randomized trial (Ballabeina).

OBJECTIVE: A multidimensional lifestyle intervention performed in 652 preschoolers (72% of migrant, 38% of low educational level (EL) parents) reduced body fat, but not BMI and improved fitness. The objective of this study is to examine whether the intervention was equally effective in children of migrant and/or low EL parents.¦METHODS: Cluster-randomized controlled single blinded trial, conducted in 2008/09 in 40 randomly selected preschools in Switzerland. The culturally tailored intervention consisted of a physical activity program and lessons on nutrition, media use and sleep. Primary outcomes included BMI and aerobic fitness. Secondary outcomes included %body fat, waist circumference and motor agility.¦RESULTS: Children of migrant parents benefitted similarly from the intervention compared to their counterparts (p for interaction≥ 0.09). However, children of low EL parents benefitted less, although these differences did not reach statistical significance (p for interaction≥ 0.06). Average intervention effect sizes for BMI were -0.10, -0.05, -0.11 and 0.04 kg/m(2) and for aerobic fitness were 0.55, 0.20, 0.37 and -0.05 stages for children of non-migrant, migrant, middle/high EL and low EL parents, respectively.¦CONCLUSIONS: This intervention was similarly effective among preschoolers of migrant parents compared to their counterparts, while children of low EL parents benefitted less.

Native Grassland Conversion: the Roles of Risk Intervention and Switching Costs

We develop a real option model of the irreversible native grassland conversion decision. Upon plowing, native grassland can be followed by either a permanent cropping system or a system in which land is put under cropping (respectively, grazing) whenever crop prices are high (respectively, low). Switching costs are incurred upon alternating between cropping and grazing. The effects of risk intervention in the form of crop insurance subsidies are studied, as are the effects of cropping innovations that reduce switching costs. We calibrate the model by using cropping return data for South Central North Dakota from 1989 to 2012. Simulations show that a risk intervention that offsets 20% of a cropping return shortfall increases the sod-busting cost threshold, below which native sod will be busted, by 41% (or $43.7/acre). Omitting cropping return risk across time underestimates this sod-busting cost threshold by 23% (or $24.35/acre), and hence underestimates the native sod conversion caused by crop production.

Circadian Variations of Ischemic Burden Among Patients with Myocardial Infarction Undergoing Primary Percutaneous Coronary Intervention

Introduction Le rythmes circadiens influencent différents paramètres de la physiologie et de la physiopathologie cardiovasculaire. Récemment, une relation entre la taille d'un infarctus et l'heure du jour à laquelle il se produit a été suggérée dans des modèles expérimentaux d'infarctus du myocarde. Le but de cette étude a été de déterminer si les rythmes circadiens pouvaient influencer la gravité d'un infarctus en terme de taille et de mortalité chez les patients hospitalisés pour un infarctus du myocarde avec sus-décalage du segment ST (STEMI) ayant bénéficié d'une intervention coronarienne percutanée primaire (ICPP). Méthode Chez 353 patients consécutifs admis avec un STEMI et traités par ICPP, l'heure à la survenue des symptômes, le pic de créatine kinase (reflet de la taille d'un infarctus) et le suivi à 30 jours ont été collectés. Les patients ont été répartis en 4 groupes en fonction de l'heure de survenue de leurs symptômes (00 :00 - 05h59, 06:00 - 11 59 12 00-17h59 et 18h00-23h59). Résultats Aucune différence statistiquement significative n'a été retrouvée entre les différents groupes en ce qui concerne les caractéristiques des patients ou de leur prise en charge. Après analyse multivariée, nous avons mis en évidence une différence statistiquement significative entre les pics de créatine kinase chez les patients avec survenue des symptômes entre 00 :00 et 05:59, qui étaient plus élevés que les pics de créatine kinase chez les patients avec survenue des symptômes à tout autre moment de la journée (augmentation moyenne de 38,4%, ρ <0.05). A 30 jours, la mortalité des patients avec survenue des symptômes entre 00 :00 et 05:59 était également significativement plus élevé que celle des patients avec survenue à tout autre moment de la journée (p <0.05). Conclusion Notre étude démontre une corrélation indépendante entre la taille d'un infarctus STEMI traité par ICPP et le moment de la journée où les symptômes apparaissent. Ces résultats suggèrent que ce moment devrait être un paramètre important à prendre en compte pour évaluer le pronostic des patients.

Public health significance of bipolar disorder: implications for early intervention and prevention.

OBJECTIVES: Early intervention and preventive strategies have become major targets of research and service development in psychiatry over the last few years. Compared to schizophrenia, bipolar disorder (BD) has received limited attention in this regard. In this paper, we review the available literature in order to explore the public health significance of BD and the extent to which this may justify the development of early intervention strategies for this disorder. METHODS: The main computerized psychiatric literature databases were accessed. This included Medline and PsychInfo, using the following keywords: bipolar, early intervention, staging model, burden, caregiver, public health, and manic depression. RESULTS: BD is often recurrent and has an impact that goes well beyond symptomatic pathology. The burden it incurs is linked not only to its cardinal clinical features, but also to cognitive dysfunction, poor functional outcome, poor physical health, high rate of comorbidities, and suicide. At a societal level, BD induces enormous direct and indirect costs and has a major impact on caregivers. The available literature reveals a usually long delay between illness onset and the start of treatment, and the absence of specific guidelines for the treatment of the early phase of BD. CONCLUSIONS: Considering the major impact of BD on patients and society, there is an urgent need for the development of early intervention strategies aimed at earlier detection and more specific treatment of the early phase of the disorder.

Influence of socioeconomic factors on delays, management and outcome amongst patients with acute myocardial infarction undergoing primary percutaneous coronary intervention.

The outcome after primary percutaneous coronary intervention (pPCI) for ST-elevation myocardial infarction (STEMI) is strongly affected by time delays. In this study, we sought to identify the impact of specific socioeconomic factors on time delays, subsequent STEMI management and outcomes in STEMI patients undergoing pPCI, who came from a well-defined region of the French part of Switzerland. A total of 402 consecutive patients undergoing pPCI for STEMI in a large tertiary hospital were retrospectively studied. Symptom-to-first-medical-contact time was analysed for the following socioeconomic factors: level of education, origin and marital status. Main exclusion criteria were: time delay beyond 12 hours, previous treatment with fibrinolytic agents or patients immediately referred for coronary artery bypass graft surgery. Therefore, 222 patients were finally included. At 1 year, there was no difference in mortality between the different socioeconomic groups. Furthermore, there was no difference in management characteristics between them. Symptom-to-first-medical-contact time was significantly longer for patients with a low level of education, Swiss citizens and unmarried patients, with median differences of 23 minutes, 18 minutes and 13 minutes, respectively (p <0.05). Nevertheless, no difference was found regarding in-hospital management and clinical outcome. This study demonstrates that symptom-to-first-medical-contact time is longer amongst people with a lower educational level, Swiss citizens and unmarried people. Because of the low mortality rate in general, these differences in delays did not affect clinical outcomes. Still, tertiary prevention measures should particularly focus on these vulnerable populations.

Early ACCESS (EA) – Early Hearing Detection and Intervention (EHDI) Questions and Answers Summary

This is a six page document of Qusetions and Answer for Early Hearing Detecting and Inventation.

Intervention of carbonate components in petrogenesis of the pyroxene nephelinites from the Jbel Saghro (Anti-Atlas, Morocco)

The Jbel Saghro alkaline complex was emplaced close to the eastern edge of the Moroccan Anti-Atlas. Within the northern part, two types of nephelinite were recognized [Ibhi and Nachit, 1999 and lbhi, 2000]. The first type (olivine-rich nephelinite) constitutes the main volcanic mass south of the Bou Gafer granit (fig. 1), where the volcanism had been active at least during 2 Ma, between 9.6 and 7.5 +/- 0.1 Ma [Berrahma et al., 1993]. The second group outcrops in the north (Foum El Kouss). It consists of pyroxene nephelinites which are younger (2.9 +/- 0.1 Ma) [Berrahma et al., 1993], and bears carbonatitic xenoliths, melteigitic pyroxenites and metasomatised peridotite xenoliths. Geochemically, the pyroxene nephelinite is highly enriched in LILE compared with the first one. The mineralogical and geochemical characteristics may be explained by the incorporation of carbonatitic and melteigitic pyroxenite segregates of carbonatitic affinity.

Age vs. Experience: Evaluation of a Video Feedback Intervention for Newly Licensed Teen Drivers, TPF-5(207), 2013

This project examines the effects of age, experience, and video-based feedback on the rate and type of safety-relevant events captured on video event recorders in the vehicles of three groups of newly licensed young drivers: 1. 14.5- to 15.5-year-old drivers who hold a minor school license (see Appendix A for the provisions of the Iowa code governing minor school licenses); 2. 16-year-old drivers with an intermediate license who are driving unsupervised for the first time; 3. 16-year-old drivers with an intermediate license who previously drove unsupervised for at least four months with a school license. METHODS: The young drivers’ vehicles were equipped with an event-triggered video recording device for 24 weeks. Half of the participants received feedback regarding their driving, and the other half received no feedback at all and served as a control group. The number of safety-relevant events per 1,000 miles (i.e., “event rate”) was analyzed for 90 participants who completed the study. RESULTS: On average, the young drivers who received the video-based intervention had significantly lower event rates than those in the control group. This finding was true for all three groups. An effect of experience was seen for drivers in the control group; the 16-year-olds with driving experience had significantly lower event rates than the 16-year-olds without experience. When the intervention concluded, an increase in event rate was seen for the school license holders, but not for either group of 16-year-old drivers. There is strong evidence that giving young drivers video-based feedback, regardless of their age or level of driving experience, is effective in reducing the rate of safety-relevant events relative to a control group who do not receive feedback. Specific comparisons with regard to age and experience indicated that the age of the driver did not have an effect on the rate of safety-events, while experience did. Young drivers with six months or more of additional experience behind the wheel had nearly half as many safety-relevant events as those without that experience.