Gene Function Classification Using Bayesian Models with Hierarchy-Based Priors

We investigate the application of hierarchical classification schemes to the annotation of gene function based on several characteristics of protein sequences including phylogenic descriptors, sequence based attributes, and predicted secondary structure. We discuss three Bayesian models and compare their performance in terms of predictive accuracy. These models are the ordinary multinomial logit (MNL) model, a hierarchical model based on a set of nested MNL models, and a MNL model with a prior that introduces correlations between the parameters for classes that are nearby in the hierarchy. We also provide a new scheme for combining different sources of information. We use these models to predict the functional class of Open Reading Frames (ORFs) from the E. coli genome. The results from all three models show substantial improvement over previous methods, which were based on the C5 algorithm. The MNL model using a prior based on the hierarchy outperforms both the non-hierarchical MNL model and the nested MNL model. In contrast to previous attempts at combining these sources of information, our approach results in a higher accuracy rate when compared to models that use each data source alone. Together, these results show that gene function can be predicted with higher accuracy than previously achieved, using Bayesian models that incorporate suitable prior information

D6.7 Report on the experience of conducting the case studies

One of the main aims of the case studies was to publish improved market reports. The data collected as part of the six case studies have been, or will shortly be, published in the five improved national organic market reports and one first regional market report (MOAN case study). This will make a contribution towards filling the many gaps that continue to exist in organic market data collection in Europe

A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context.

An important step in understanding the regulation of a prokaryotic genome is the generation of its transcription unit map. The current strongest operon predictor depends on the distributions of intergenic distances (IGD) separating adjacent genes within and between operons. Unfortunately, experimental data on these distance distributions are limited to Escherichia coli and Bacillus subtilis. We suggest a new graph algorithmic approach based on comparative genomics to identify clusters of conserved genes independent of IGD and conservation of gene order. As a consequence, distance distributions of operon pairs for any arbitrary prokaryotic genome can be inferred. For E.coli, the algorithm predicts 854 conserved adjacent pairs with a precision of 85%. The IGD distribution for these pairs is virtually identical to the E.coli operon pair distribution. Statistical analysis of the predicted pair IGD distribution allows estimation of a genome-specific operon IGD cut-off, obviating the requirement for a training set in IGD-based operon prediction. We apply the method to a representative set of eight genomes, and show that these genome-specific IGD distributions differ considerably from each other and from the distribution in E.coli

HyMeX: A 10-Year Multidisciplinary Program on the Mediterranean Water Cycle

Drobinski, P. ... et. al.-- 20 pages, 10 figures, 1 table, supplement material http://journals.ametsoc.org/doi/suppl/10.1175/BAMS-D-12-00244.1HyMeX strives to improve our understanding of the Mediterranean water cycle, its variability from the weather-scale events to the seasonal and interannual scales, and its characteristics over one decade (2010–20), with a special focus on hydrometeorological extremes and the associated social and economic vulnerability of the Mediterranean territoriesHyMeX was developed by an international group of scientists and is currently funded by a large number of agencies. It has been the beneficiary of financial contributions from CNRS; Météo-France; CNES; IRSTEA; INRA; ANR; Collectivité Territoriale de Corse; KIT; CNR; Université de Toulouse; Grenoble Universités; EUMETSAT; EUMETNET; AEMet; Université Blaise Pascal, Clermont Ferrand; Université de la Méditerranée (Aix-Marseille II); Université Montpellier 2; CETEMPS; Italian Civil Protection Department; Université Paris- Sud 11; IGN; EPFL; NASA; New Mexico Tech; IFSTTAR; Mercator Ocean; NOAA; ENEA; TU Delft; CEA; ONERA; IMEDEA; SOCIB; ETH; MeteoCat; Consorzio LAMMA; IRD; National Observatory of Athens; Ministerio de Ciencia e Innovación; CIMA; BRGM; Wageningen University and Research Center; Department of Geophysics, University of Zagreb; Institute of Oceanography and Fisheries, Split, Croatia; INGV; OGS; Maroc Météo; DHMZ; ARPA Piemonte; ARPA-SIMC Emilia-Romagna; ARPA Calabria; ARPA Friuli Venezia Giulia; ARPA Liguria; ISPRA; University of Connecticut; Università degli Studi dell'Aquila; Università di Bologna; Università degli Studi di Torino; Università degli Studi della Basilicata; Università La Sapienza di Roma; Università degli Studi di Padova; Università del Salento; Universitat de Barcelona; Universitat de les Illes Balears; Universidad de Castilla-La Mancha; Universidad Complutense de Madrid; MeteoSwiss; and DLR. It also received support from the European Community's Seventh Framework Programme (e.g., PERSEUS, CLIM-RUN)Peer reviewe

Fluctuating Hemiparesis Secondary to Moyamoya Phenomenon in a Child with Down Syndrome: a case report

Moyamoya phenomenon is a term used to describe extensive collateralization of the circle of Willis arteries associated with severe unilateral or bilateral internal carotid artery stenosis or occlusion in the presence of certain conditions. Down syndrome is among these conditions. A case is reported of a young girl with Down syndrome who presented with fluctuating right-sided weakness and facial droop found to have cerebral ischemia. Subsequent investigations disclosed characteristic "puff of smoke" patterns on angiographic studies consistent with moyamoya phenomenon. The patient was initially treated with aspirin and eventually underwent an encephalomyosynangiosis. This young patient with Down syndrome and moyamoya phenomenon serves as a reminder of the association between these two conditions

Branch facial nerve trauma after superficial temporal artery biopsy: a case report

<p>Abstract</p> <p>Introduction</p> <p>Giant cell arteritis is an emergency requiring prompt diagnosis and treatment. Superficial temporal artery biopsy is the gold diagnostic standard. Complications are few and infrequent; however, facial nerve injury has been reported, leaving an untoward cosmetic outcome. This case report is to the best of our knowledge only the fourth one presented in the available literature so far regarding facial nerve injury from superficial temporal artery biopsy.</p> <p>Case presentation</p> <p>A 73-year-old Caucasian woman presented for neurological evaluation regarding eyebrow and facial asymmetry after a superficial temporal artery biopsy for presumptive giant cell arteritis-induced cephalalgia.</p> <p>Conclusion</p> <p>Damage to branches of the facial nerve may occur after superficial temporal artery biopsy, resulting in eyebrow droop. Although an uncommon and sparsely reported complication, all clinicians of various specialties involved in the care of these patients should be aware of this given the gravity of giant cell arteritis and the widespread use of temporal artery biopsy.</p

Timing Calibration and Windowing Technique Comparison for Lightning Mapping Arrays

Since their introduction 22 years ago, lightning mapping arrays (LMA) have played a central role in the investigation of lightning physics. Even in recent years with the proliferation of digital interferometers and the introduction of the LOw Frequency ARray (LOFAR) radio telescope, LMAs still play an important role in lightning science. LMA networks use a simple windowing technique that records the highest pulse in either 80 μs or 10 μs fixed windows in order to apply a time-of-arrival location technique. In this work, we develop an LMA-emulator that uses lightning data recorded by LOFAR to simulate an LMA, and we use it to test three new styles of pulse windowing. We show that they produce very similar results as the more traditional LMA windowing, implying that LMA lightning mapping results are relatively independent of windowing technique. In addition, each LMA station has its GPS-conditioned clock. While the timing accuracy of GPS receivers has improved significantly over the years, they still significantly limit the timing measurements of the LMA. Recently, new time-of-arrival techniques have been introduced that can be used to self-calibrate systematic offsets between different receiving stations. Applying this calibration technique to a set of data with 32 ns uncertainty, observed by the Colorado LMA, improves the timing uncertainty to 19 ns. This technique is not limited to LMAs and could be used to help calibrate future multi-station lightning interferometers