The 8 and 9 September 2002 flash flood event in France: a model intercomparison

Within the framework of the European Interreg IIIb Medocc program, the HYDROPTIMET project aims at the optimization of the hydrometeorological forecasting tools in the context of intense precipitation within complex topography. Therefore, some meteorological forecast models and hydrological models were tested on four Mediterranean flash-flood events. One of them occured in France where the South-eastern ridge of the French “Massif Central”, the Gard region, experienced a devastating flood on 8 and 9 September 2002. 24 people were killed during this event and the economic damage was estimated at 1.2 billion euros. To built the next generation of the hydrometeorological forecasting chain that will be able to capture such localized and fast events and the resulting discharges, the forecasted rain fields might be improved to be relevant for hydrological purposes. In such context, this paper presents the results of the evaluation methodology proposed by Yates et al. (2005) that highlights the relevant hydrological scales of a simulated rain field. Simulated rain fields of 7 meteorological model runs concerning with the French event are therefore evaluated for different accumulation times. The dynamics of these models are either based on non-hydrostatic or hydrostatic equation systems. Moreover, these models were run under different configurations (resolution, initial conditions). The classical score analysis and the areal evaluation of the simulated rain fields are then performed in order to put forward the main simulation characteristics that improve the quantitative precipitation forecast. The conclusions draw some recommendations on the value of the quantitative precipitation forecasts and way to use it for quantitative discharge forecasts within mountainous areas

The catastrophic flash-flood event of 8–9 September 2002 in the Gard region, France: a first case study for the Cévennes–Vivarais Mediterranean Hydrometeorological Observatory

The Cévennes–Vivarais Mediterranean Hydrometeorological Observatory (OHM-CV) is a research initiative aimed at improving the understanding and modeling of the Mediterranean intense rain events that frequently result in devastating flash floods in southern France. A primary objective is to bring together the skills of meteorologists and hydrologists, modelers and instrumentalists, researchers and practitioners, to cope with these rather unpredictable events. In line with previously published flash-flood monographs, the present paper aims at documenting the 8–9 September 2002 catastrophic event, which resulted in 24 casualties and an economic damage evaluated at 1.2 billion euros (i.e., about 1 billion U.S. dollars) in the Gard region, France. A description of the synoptic meteorological situation is first given and shows that no particular precursor indicated the imminence of such an extreme event. Then, radar and rain gauge analyses are used to assess the magnitude of the rain event, which was particularly remarkable for its spatial extent with rain amounts greater than 200 mm in 24 h over 5500 km2. The maximum values of 600–700 mm observed locally are among the highest daily records in the region. The preliminary results of the postevent hydrological investigation show that the hydrologic response of the upstream watersheds of the Gard and Vidourle Rivers is consistent with the marked space–time structure of the rain event. It is noteworthy that peak specific discharges were very high over most of the affected areas (5–10 m3 s−1 km−2) and reached locally extraordinary values of more than 20 m3 s−1 km−2. A preliminary analysis indicates contrasting hydrological behaviors that seem to be related to geomorphological factors, notably the influence of karst in part of the region. An overview of the ongoing meteorological and hydrological research projects devoted to this case study within the OHM-CV is finally presented

The Nature of Notebooks: How Enlightenment Schoolchildren Transformed the Tabula Rasa

John Locke's comparison of the mind to a blank piece of paper, the tabula rasa, was one of the most recognizable metaphors of the British Enlightenment. Though scholars embrace its impact on the arts, humanities, natural sciences, and social sciences, they seldom consider why the metaphor was so successful. Concentrating on the notebooks made and used by the schoolchildren of Enlightenment Scotland, this essay contends that the answer lies in the material and visual conditions that gave rise to the metaphor's usage. By the time students had finished school, they had learned to conceptualize the pages, the script, and the figures of their notebooks as indispensable learning tools that could be manipulated by scores of adaptable folding, writing, and drawing techniques. In this article, I reveal that historicizing the epistemology and manipulability of student manuscript culture makes it possible to see that the success of Locke's metaphor was founded on its appeal to everyday note-keeping activities performed by British schoolchildren

Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes

New generation sequencing technologies have resulted in significant increases in the number of complete genomes. Functional characterization of these genomes, such as by high-throughput proteomics, is an important but challenging task due to the difficulty of scaling up existing experimental techniques. By use of comparative genomics techniques, experimental results can be transferred from one genome to another, while at the same time minimizing errors by requiring discovery in multiple genomes. In this study, protein phosphorylation, an essential component of many cellular processes, is studied using data from large-scale proteomics analyses of the phosphoproteome. Phosphorylation sites from Homo sapiens, Mus musculus and Drosophila melanogaster phosphopeptide data sets were mapped onto conserved domains in NCBI’s manually curated portion of Conserved Domain Database (CDD). In this subset, 25 phosphorylation sites are found to be evolutionarily conserved between the three species studied. Transfer of phosphorylation annotation of these conserved sites onto sequences sharing the same conserved domains yield 3253 phosphosite annotations for proteins from coelomata, the taxonomic division that spans H. sapiens, M. musculus and D. melanogaster. The method scales automatically, so as the amount of experimental phosphoproteomics data increases, more conserved phosphorylation sites may be revealed

Atypical glandular cells in conventional cervical smears: Incidence and follow-up

BACKGROUND: Atypical glandular cells on cervical smears are often associated with clinically significant uterine lesions. The frequency and accuracy of AGC-NOS (i.e. atypical glandular cells, not otherwise specified) diagnoses, regardless of the gland cell type or the degree of suspicion, and their outcome were investigated. METHODS: From January 1, 1990 to December 31, 1999 a total of 261 patients had an AGC-NOS diagnosis made by conventional cervical Papanicolaou smear interpretation representing 0.05% of all Pap-smears analyzed at the national level. 191 (73.2%) patients had a subsequent histological examination, 8 samples were not representative by origin and were excluded. RESULTS: Out of 183 AGC-NOS diagnosed, 56.3% (103/183) were associated with tissue-proven precancerous and/or cancerous lesions, 44% being of endocervical and 56% of endometrial origin. 75% of all AGC-patients were asymptomatic. 66.7% (6/9) of the patients with subsequent invasive endocervical adenocarcinoma (AC) and 56% (28/50) of those patients with invasive endometrial AC were without clinical symptoms. 3 patients out of 9 with an invasive endocervical AC were 35 years of age or less. 10.1% and 12.3% of all 'new' tissue-proven invasive endocervical or endometrial AC respectively recorded by the national Morphologic Tumour Registry (MTR) were first identified by a cytological AGC-NOS diagnosis. CONCLUSION: Our findings emphasize the importance of the cytological AGC-category even in the absence of a precise origin or cell type specification. 56% of the AGC-diagnoses being associated with significant cancerous or precancerous conditions, a complete and careful evaluation is required

Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes

<p>Abstract</p> <p>Background</p> <p>During the replication process of bacteria with circular chromosomes, an odd number of homologous recombination events results in concatenated dimer chromosomes that cannot be partitioned into daughter cells. However, many bacteria harbor a conserved dimer resolution machinery consisting of one or two tyrosine recombinases, XerC and XerD, and their 28-bp target site, <it>dif</it>.</p> <p>Results</p> <p>To study the evolution of the <it>dif/</it>XerCD system and its relationship with replication termination, we report the comprehensive prediction of <it>dif </it>sequences <it>in silico </it>using a phylogenetic prediction approach based on iterated hidden Markov modeling. Using this method, <it>dif </it>sites were identified in 641 organisms among 16 phyla, with a 97.64% identification rate for single-chromosome strains. The <it>dif </it>sequence positions were shown to be strongly correlated with the GC skew shift-point that is induced by replicational mutation/selection pressures, but the difference in the positions of the predicted <it>dif </it>sites and the GC skew shift-points did not correlate with the degree of replicational mutation/selection pressures.</p> <p>Conclusions</p> <p>The sequence of <it>dif </it>sites is widely conserved among many bacterial phyla, and they can be computationally identified using our method. The lack of correlation between <it>dif </it>position and the degree of GC skew suggests that replication termination does not occur strictly at <it>dif </it>sites.</p

Clinical effectiveness and patient perspectives of different treatment strategies for tics in children and adolescents with Tourette syndrome: a systematic review and qualitative analysis

Background: Tourette syndrome (TS) is a neurodevelopmental condition characterised by chronic motor and vocal tics affecting up to 1% of school-age children and young people and is associated with significant distress and psychosocial impairment. Objective: To conduct a systematic review of the benefits and risks of pharmacological, behavioural and physical interventions for tics in children and young people with TS (part 1) and to explore the experience of treatment and services from the perspective of young people with TS and their parents (part 2). Data Sources: For the systematic reviews (parts 1 and 2), mainstream bibliographic databases, The Cochrane Library, education, social care and grey literature databases were searched using subject headings and text words for tic* and Tourette* from database inception to January 2013. Review/research methods: For part 1, randomised controlled trials and controlled before-and-after studies of pharmacological, behavioural or physical interventions in children or young people (aged < 18 years) with TS or chronic tic disorder were included. Mixed studies and studies in adults were considered as supporting evidence. Risk of bias associated with each study was evaluated using the Cochrane tool. When there was sufficient data, random-effects meta-analysis was used to synthesize the evidence and the quality of evidence for each outcome was assessed using the Grading of Recommendations Assessment, Development and Evaluation approach. For part 2, qualitative studies and survey literature conducted in populations of children/young people with TS or their carers or in health professionals with experience of treating TS were included in the qualitative review. Results were synthesized narratively. In addition, a national parent/carer survey was conducted via the Tourettes Action website. Participants included parents of children and young people with TS aged under 18 years. Participants (young people with TS aged 10–17 years) for the in-depth interviews were recruited via a national survey and specialist Tourettes clinics in the UK. Results: For part 1, 70 studies were included in the quantitative systematic review. The evidence suggested that for treating tics in children and young people with TS, antipsychotic drugs [standardised mean difference (SMD) –0.74, 95% confidence interval (CI) –1.08 to –0.41; n = 75] and noradrenergic agents [clonidine (Dixarit®, Boehringer Ingelheim) and guanfacine: SMD –0.72, 95% CI –1.03 to –0.40; n = 164] are effective in the short term. There was little difference among antipsychotics in terms of benefits, but adverse effect profiles do differ. Habit reversal training (HRT)/comprehensive behavioural intervention for tics (CBIT) was also shown to be effective (SMD –0.64, 95% CI –0.99 to –0.29; n = 133). For part 2, 295 parents/carers of children and young people with TS contributed useable survey data. Forty young people with TS participated in in-depth interviews. Four studies were in the qualitative review. Key themes were difficulties in accessing specialist care and behavioural interventions, delay in diagnosis, importance of anxiety and emotional symptoms, lack of provision of information to schools and inadequate information regarding medication and adverse effects. Limitations: The number and quality of clinical trials is low and this downgrades the strength of the evidence and conclusions. Conclusions: Antipsychotics, noradrenergic agents and HRT/CBIT are effective in reducing tics in children and young people with TS. The balance of benefits and harms favours the most commonly used medications: risperidone (Risperdal®, Janssen), clonidine and aripiprazole (Abilify®, Otsuka). Larger and better-conducted trials addressing important clinical uncertainties are required. Further research is needed into widening access to behavioural interventions through use of technology including mobile applications (‘apps’) and video consultation. Study registration: This study is registered as PROSPERO CRD42012002059

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits

Prevalence and architecture of de novo mutations in developmental disorders.

The genomes of individuals with severe, undiagnosed developmental disorders are enriched in damaging de novo mutations (DNMs) in developmentally important genes. Here we have sequenced the exomes of 4,293 families containing individuals with developmental disorders, and meta-analysed these data with data from another 3,287 individuals with similar disorders. We show that the most important factors influencing the diagnostic yield of DNMs are the sex of the affected individual, the relatedness of their parents, whether close relatives are affected and the parental ages. We identified 94 genes enriched in damaging DNMs, including 14 that previously lacked compelling evidence of involvement in developmental disorders. We have also characterized the phenotypic diversity among these disorders. We estimate that 42% of our cohort carry pathogenic DNMs in coding sequences; approximately half of these DNMs disrupt gene function and the remainder result in altered protein function. We estimate that developmental disorders caused by DNMs have an average prevalence of 1 in 213 to 1 in 448 births, depending on parental age. Given current global demographics, this equates to almost 400,000 children born per year