Forest fires cluster detection with space-time scan statistics

Forest fires are defined as uncontrolled fires often occurring in wildland areas, but that can also affect houses or agricultural resources. Causes are both natural (e.g.,lightning phenomena) and anthropogenic (human negligence or arsons).Major environmental factors influencing the fire ignition and propagation are climate and vegetation. Wildfires are most common and severe during drought period and on windy days. Moreover, under water-stress conditions, which occur after a long hot and dry period, the vegetation is more vulnerable to fire. These conditions are common in the United State and Canada, where forest fires represent a big problem. We focused our analysis on the state of Florida, for which a big dataset on forest fires detection is readily available. USDA Forest Service Remote Sensing Application Center, in collaboration with NASA-Goddard Space Flight Center and the University of Maryland, has compiled daily MODIS Thermal Anomalies (fires and biomass burning images) produced by NASA using a contextual algorithm that exploits the strong emission of mid-infrared radiation from fires. Fire classes were converted in GIS format: daily MODIS fire detections are provided as the centroids of the 1 kilometer pixels and compiled into daily Arc/INFO point coverage.

Mindfulness in informal caregivers of palliative patients.

OBJECTIVES: Mindfulness is a concept of growing impact on psychotherapy and has been shown to be effective for stress reduction and to improve psychological well-being. Existential Behavioural Therapy (EBT) was developed to support relatives of palliative care (PC) patients to cope with their situation during caregiving and bereavement. Mindfulness training was a core element of the intervention. We investigated the relationship between mindfulness, mental distress, and psychological well-being in informal caregivers, and evaluated if the effects of the intervention were mediated by mindfulness. METHODS: Relatives of PC inpatients took part in a randomized-controlled EBT trial and completed the Cognitive and Affective Mindfulness Scale-Revised, items from the Five Facets of Mindfulness as well as the Brief Symptom Inventory, the Satisfaction with Life Scale, the WHOQOL-BREF, a numerical rating scale on quality of life (range 0-10), and the Schedule for Meaning in Life Evaluation at pre- and post-intervention, and a 3- and 12-months follow-up. RESULTS: One-hundred-and-thirty carers were included, most of them (71.6%) recently being bereaved at the beginning of the intervention. High correlations between mindfulness and mental distress (r = -0.51, p < 0.001) as well as life satisfaction (r = 0.52, p < 0.001) were found. Mindfulness was a significant predictor of improvement in psychological distress, meaning in life and quality of life three months after the intervention. The EBT effects were partly mediated by mindfulness. SIGNIFICANCE OF RESULTS: Mindfulness seems to be a promising concept in supporting informal caregivers of PC patients. Further research is needed to identify the required format and intensity of mindfulness practice necessary for improvement.

ESCMID postgraduate technical workshop on intracellular bacteria: from biology to clinic.

Infection by intracellular bacteria can lead to several diseases in both veterinary and human medicine. Unfortunately, the biology of these intracellular bacteria is highly complex due to their interactions with their host cells. Thus, it is very important to develop several tools in order to better understand the complex intracellular life of these pathogens, so allowing to improve the diagnosis options and the treatments of infectious diseases that they are causing. The workshop organised in Villars-sur-Ollon (Switzerland) by the ESCMID Study group on intracellular bacteria was a good opportunity to enhance our knowledge on these fastidious pathogens. During 5 days, 15 speakers gave 41 talks, covering all fields, from biology to clinic of different intracellular bacteria such as Bartonella, Chlamydia, Coxiella, Ehrlichia, Listeria, Parachlamydia, Rickettsia, and Waddlia. The format of this postgraduate course, which took place in the Swiss mountains, allowed interactive sessions and living discussions between the participants coming from all around the world. One of the major strength was to gather epidemiologists, clinical microbiologists, infectious diseases specialists, entomologists, veterinarians as well as bioinformaticians, biochemists and biologists to deliver a unique "one-health science" on intracellular bacteria. Here, we summarise the main take-home messages delivered during this meeting.

Identification of potential rockfall source areas at a regional scale using a DEM-based geomorphometric analysis

The availability of high resolution Digital Elevation Models (DEM) at a regional scale enables the analysis of topography with high levels of detail. Hence, a DEM-based geomorphometric approach becomes more accurate for detecting potential rockfall sources. Potential rockfall source areas are identified according to the slope angle distribution deduced from high resolution DEM crossed with other information extracted from geological and topographic maps in GIS format. The slope angle distribution can be decomposed in several Gaussian distributions that can be considered as characteristic of morphological units: rock cliffs, steep slopes, footslopes and plains. A terrain is considered as potential rockfall sources when their slope angles lie over an angle threshold, which is defined where the Gaussian distribution of the morphological unit "Rock cliffs" become dominant over the one of "Steep slopes". In addition to this analysis, the cliff outcrops indicated by the topographic maps were added. They contain however "flat areas", so that only the slope angles values above the mode of the Gaussian distribution of the morphological unit "Steep slopes" were considered. An application of this method is presented over the entire Canton of Vaud (3200 km2), Switzerland. The results were compared with rockfall sources observed on the field and orthophotos analysis in order to validate the method. Finally, the influence of the cell size of the DEM is inspected by applying the methodology over six different DEM resolutions.

Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'.

Background: The variety of DNA microarray formats and datasets presently available offers an unprecedented opportunity to perform insightful comparisons of heterogeneous data. Cross-species studies, in particular, have the power of identifying conserved, functionally important molecular processes. Validation of discoveries can now often be performed in readily available public data which frequently requires cross-platform studies.Cross-platform and cross-species analyses require matching probes on different microarray formats. This can be achieved using the information in microarray annotations and additional molecular biology databases, such as orthology databases. Although annotations and other biological information are stored using modern database models ( e. g. relational), they are very often distributed and shared as tables in text files, i.e. flat file databases. This common flat database format thus provides a simple and robust solution to flexibly integrate various sources of information and a basis for the combined analysis of heterogeneous gene expression profiles.Results: We provide annotationTools, a Bioconductor-compliant R package to annotate microarray experiments and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file databases. First, annotationTools contains a specialized set of functions for mining this widely used database format in a systematic manner. It thus offers a straightforward solution for annotating microarray experiments. Second, building on these basic functions and relying on the combination of information from several databases, it provides tools to easily perform cross-species analyses of gene expression data.Here, we present two example applications of annotationTools that are of direct relevance for the analysis of heterogeneous gene expression profiles, namely a cross-platform mapping of probes and a cross-species mapping of orthologous probes using different orthology databases. We also show how to perform an explorative comparison of disease-related transcriptional changes in human patients and in a genetic mouse model.Conclusion: The R package annotationTools provides a simple solution to handle microarray annotation and orthology tables, as well as other flat molecular biology databases. Thereby, it allows easy integration and analysis of heterogeneous microarray experiments across different technological platforms or species.

Information provision and information needs in adult survivors of childhood cancer.

BACKGROUND: Knowledge about their past medical history is central for childhood cancer survivors to ensure informed decisions in their health management. Knowledge about information provision and information needs in this population is still scarce. We thus aimed to assess: (1) the information survivors reported to have received on disease, treatment, follow-up, and late effects; (2) their information needs in these four domains and the format in which they would like it provided; (3) the association with psychological distress and quality of life (QoL). PROCEDURE: As part of the Follow-up survey of the Swiss Childhood Cancer Survivor Study, we sent a questionnaire to all survivors (≥18 years) who previously participated to the baseline survey, were diagnosed with cancer after 1990 at an age of <16 years. RESULTS: Most survivors had received oral information only (on illness: oral: 82%, written: 38%, treatment: oral: 79%, written: 36%; follow-up: oral: 77%, written: 23%; late effects: oral: 68%, written: 14%). Most survivors who had not previously received any information rated it as important, especially information on late effects (71%). A large proportion of survivors reported current information needs and would like to receive personalized information especially on late effects (44%). Survivors with higher information needs reported higher psychological distress and lower QoL. CONCLUSIONS: Survivors want to be more informed especially on possible late effects, and want to receive personalized information. Improving information provision, both qualitatively and quantitatively, will allow survivors to have better control of their health and to become better decision makers.

Psychose, cannabis et groupes motivationnels

En s'appuyant sur les acquis démontrés de l'entretien motivationnel individuel chez les patients psychotiques consommateurs de cannabis, une équipe suisse a complété leur prise en charge individuelle par des groupes motivationnels. Le format de ces groupes mobilise davantage ces patients et favorise notamment une mise en scène de la balance décisionnelle.

Introducing a first AIDS vaccine in Switzerland: a Policy Delphi analysis.

This preliminary exploration was limited by a number of factors. The format of the study has necessarily induced some form of selection bias of the panelists, because of the complexity of some questions, and the time required to complete the questionnaires. Several issues have not been addressed. One example could be the response to HIV infection occurring in a vaccinee. The study also did not address the difficulties related to the licensing of the vaccine. Indeed, the proposed scenario assumed that the vaccine had been registered as a starting point for the analysis. Finally, it has not been possible to conduct a sensitivity analysis, in order to evaluate how the responses would have been modified if some important characteristics of the vaccine had been modified.Very diverse evaluations were given in response to questions related with attitudes and perception of AIDS and AIDS vaccine. The possibility that vaccine availability or usage can be associated with an increased frequency in risky behaviors was spontaneously mentioned by half of the panelists. The estimation of the proportion of persons at highest risk who would choose to use this vaccine also indicated a high degree of uncertainty. This study offers important lessons. According to a broad and diverse panel of individuals, an incompletely effective AIDS vaccine would result in an additional level of complexity for the AIDS prevention strategy, rather than a simplification. The use of such a vaccine would have to be coupled with counselling. This implies a sustained emphasis on the recommendations which have been central to the STOP AIDS campaigns until now. In addition, consensual issues, as well as other issues more likely to be controversial have been identified. This should greatly help focusing the work of any committee designated to develop and implement a vaccination policy if an AIDS vaccine became available. Finally, our experience with the Policy Delphi indicates that this mode of structured communication could be usefully applied to other public health issues presenting a high visibility as well as a complex relationship with public perception.

L'examen clinique du sein : vidéos d'enseignement des compétences cliniques en gynécologie destinés à un module en ligne

Cette thèse présente un travail audiovisuel « L'examen clinique du sein ». Avec l'unité « L'examen génital » elle forme le module « Gynécologie » du projet Virtual Skills Lab (VSL). Le but du projet VSL est d'établir un portail d'enseignement en ligne pour l'enseignement des compétences cliniques (ce terme étant utilisé ici comme équivalent de l'anglais « clinical skills »). Les compétences traitées sont celles exigées par le Catalogue suisse des objectifs d'apprentissage. L'unité « L'examen clinique du sein » est constituée d'une multitude de courtes séquences vidéo qui peuvent être regardées à la suite ou de manière individuelle. Elle est divisée en étapes logiques telles que l'inspection ou la palpation. Chacune de ces étapes appelées « skill » est présentée de deux façons : comme vue d'ensemble et par une approche pas à pas. La séquence « vue d'ensemble » présente le skill en temps réel et représente donc une visualisation du but à atteindre par l'apprenant. Le skill est décomposé en petites étapes (step), les procédures sont montrées au ralenti, munies d'une explication par une voix off. Le format de ces séquences est présenté en double largeur, la partie de gauche montre l'action, la partie de droite est utilisée pour des tableaux ou des graphiques explicatifs. Les différents gestes des compétences cliniques sont rarement standardisés. Pour VSL, un processus de validation sur la base d'un consensus suisse a été mis en place. Ceci ne veut néanmoins pas dire que les modules VSL validés ont été intégrés dans le curriculum de toutes les universités suisses. Vu la complexité des curriculums et la multitude de facteurs entrant enjeu, notamment sur l'intégration des moyens d'enseignement audiovisuels, leur implémentation est une phase critique de tout projet de ce genre. En Suisse, le multilinguisme y ajoute un degré de complexité. A Lausanne, « L'examen clinique du sein » a été introduit aussi bien dans la formation pré- que postgraduée.

Quantification of glucuronidated and sulfated steroids in human urine by ultra-high pressure liquid chromatography quadrupole time-of-flight mass spectrometry.

The urinary steroid profile is constituted by anabolic androgenic steroids, including testosterone and its relatives, that are extensively metabolized into phase II sulfated or glucuronidated steroids. The use of liquid chromatography coupled to mass spectrometry (LC-MS) is an issue for the direct analysis of conjugated steroids, which can be used as urinary markers of exogenous steroid administration in doping analysis, without hydrolysis of the conjugated moiety. In this study, a sensitive and selective ultra high-pressure liquid chromatography coupled to quadrupole time-of-flight mass spectrometer (UHPLC-QTOF-MS) method was developed to quantify major urinary metabolites simultaneously after testosterone intake. The sample preparation of the urine (1 mL) was performed by solid-phase extraction on Oasis HLB sorbent using a 96-well plate format. The conjugated steroids were analyzed by UHPLC-QTOF-MS(E) with a single-gradient elution of 36 min (including re-equilibration time) in the negative electrospray ionization mode. MS(E) analysis involved parallel alternating acquisitions of both low- and high-collision energy functions. The method was validated and applied to samples collected from a clinical study performed with a group of healthy human volunteers who had taken testosterone, which were compared with samples from a placebo group. Quantitative results were also compared to GC-MS and LC-MS/MS measurements, and the correlations between data were found appropriate. The acquisition of full mass spectra over the entire mass range with QTOF mass analyzers gives promise of the opportunity to extend the steroid profile to a higher number of conjugated steroids.

5-Azacytidine to Treat Acute Myeloid Leukemia In Elderly or Frail Patients: A Phase II Study (SAKK 30/07).

Background: Acute Myeloid Leukemia (AML) in the elderly is notoriously difficult to treat and has a low remission rate with very few long term survivors when using standard treatment approaches. Azacytidine, a hypomethylating agent, has been shown to induce remission and prolong survival in patients with myelodysplastic syndromes; studying this approach to patients with AML is therefore warranted. We present results of an ongoing phase II trial treating elderly or frail AML patients with Azacytidine. Methods: AML elderly or frail patients, and therefore unfit for an intensive chemotherapy regimens, with a WHO performance status 3 were considered for this trial. Trial therapy consisted of 100mg/m2 of Azacytidine injected subcutaneously on 5 consecutive days every 28 days up to 6 cycles, stopping at 6 months if no hematological improvement achieved, or earlier in the case of progression or complications. Treatment was continued beyond 6 months in responding patients. Trial therapy was considered uninteresting if the response rate (CR + PR) within 6 months of therapy initiation was 15% or less and promising if 34% or more. Using the exact single-stage phase II design by A'Hern with a 5% significance level and 90% power, 43 patients were required: If 10 or fewer achieved a response within 6 months the trial therapy should not be considered for further investigation in its current format for this indication and patient population. Results: Between September 2008 and January 2010, 45 evaluable patients across 10 Swiss centers were accrued with a median follow-up of 7 months (range: 0 - 13). 27 (60%) were male, median age was 74 (range: 55 - 86) years and 35 (78.8%) had performance status 0-1. Patients had been excluded from more intensive chemotherapy regimens because of age (n = 37) or due to comorbidities or patient refusal (n=8). Five patients had therapy related AML. Patients received a median of 3 (range: 1 - 10) cycles. Treatment was stopped for not achieving a response by the 6th cycle in 2 patients and earlier in 26 patients (for disease progression in 5, toxicity in 3, patient refusal in 2, recurrent infections in 1, and death in 8). Seventeen patients remain on therapy. The median time spent in the hospital was 12 days (1 - 30) in 24/38 patients hospitalized during the first treatment cycle and 13 days (2 - 28) in 15/31 patients hospitalized during subsequent cycles. Adverse events of grade III or higher most frequently reported were constitutional or hematologic, i.e. fatigue in 5, febrile neutropenia in 8, infections in 6, dyspnea in 6, anemia in 3, neutropenia in 12 and thrombocytopenia in 10, hemorrhage in 2 and retinal detachment in 5. Based on available data on 38 patients, CR/CRi or hematologic improvement or stable disease within 6 months of trial registration was observed in a proportion of patients. Final and mature data, determining whether the predefined proportion of responding patients has been reached or not, will be presented at the conference. Up to now there were a total of 26 deaths. Median overall survival time was 5.7 months (95% CI: 3.1, 8.7). Conclusions: The current results of this slightly modified Azacytidine schedule demonstrate a feasible new therapy option for elderly or frail AML patients in an outpatient setting with moderate, mainly hematologic toxicity.

AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context.

SUMMARY: We present a tool designed for visualization of large-scale genetic and genomic data exemplified by results from genome-wide association studies. This software provides an integrated framework to facilitate the interpretation of SNP association studies in genomic context. Gene annotations can be retrieved from Ensembl, linkage disequilibrium data downloaded from HapMap and custom data imported in BED or WIG format. AssociationViewer integrates functionalities that enable the aggregation or intersection of data tracks. It implements an efficient cache system and allows the display of several, very large-scale genomic datasets. AVAILABILITY: The Java code for AssociationViewer is distributed under the GNU General Public Licence and has been tested on Microsoft Windows XP, MacOSX and GNU/Linux operating systems. It is available from the SourceForge repository. This also includes Java webstart, documentation and example datafiles.

The UniProt-GO Annotation database in 2011.

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360,000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set.

The role of alliance in the relationship between therapist competence and outcome in brief psychodynamic psychotherapy.

Therapist competence is a key variable for psychotherapy research. Empirically, the relationship between competence and therapeutic outcome has shown contradictory results and needs to be clarified, especially with regard to possible variables influencing this relationship. A total of 78 outpatients were treated by 15 therapists in a very brief 4-session format, based on psychoanalytic theory. Data were analyzed by means of a nested design using hierarchical linear modeling. No direct link between therapist competence and outcome has been found, however, results corroborated the importance of alliance patterns as moderator in the relationship between therapist competence and outcome. Only in dyads with alliance change over the course of treatment was it clear that competence is positively related to outcome. These findings are discussed with regard to the importance for outcome of therapist competence and alliance construction processes.

E-learning initiatives in forensic interpretation: report on experiences from current projects and outlook

This paper reports on the purpose, design, methodology and target audience of E-learning courses in forensic interpretation offered by the authors since 2010, including practical experiences made throughout the implementation period of this project. This initiative was motivated by the fact that reporting results of forensic examinations in a logically correct and scientifically rigorous way is a daily challenge for any forensic practitioner. Indeed, interpretation of raw data and communication of findings in both written and oral statements are topics where knowledge and applied skills are needed. Although most forensic scientists hold educational records in traditional sciences, only few actually followed full courses that focussed on interpretation issues. Such courses should include foundational principles and methodology - including elements of forensic statistics - for the evaluation of forensic data in a way that is tailored to meet the needs of the criminal justice system. In order to help bridge this gap, the authors' initiative seeks to offer educational opportunities that allow practitioners to acquire knowledge and competence in the current approaches to the evaluation and interpretation of forensic findings. These cover, among other aspects, probabilistic reasoning (including Bayesian networks and other methods of forensic statistics, tools and software), case pre-assessment, skills in the oral and written communication of uncertainty, and the development of independence and self-confidence to solve practical inference problems. E-learning was chosen as a general format because it helps to form a trans-institutional online-community of practitioners from varying forensic disciplines and workfield experience such as reporting officers, (chief) scientists, forensic coordinators, but also lawyers who all can interact directly from their personal workplaces without consideration of distances, travel expenses or time schedules. In the authors' experience, the proposed learning initiative supports participants in developing their expertise and skills in forensic interpretation, but also offers an opportunity for the associated institutions and the forensic community to reinforce the development of a harmonized view with regard to interpretation across forensic disciplines, laboratories and judicial systems.