Indexing strategies for rapid searches of short words in genome sequences.

Searching for matches between large collections of short (14-30 nucleotides) words and sequence databases comprising full genomes or transcriptomes is a common task in biological sequence analysis. We investigated the performance of simple indexing strategies for handling such tasks and developed two programs, fetchGWI and tagger, that index either the database or the query set. Either strategy outperforms megablast for searches with more than 10,000 probes. FetchGWI is shown to be a versatile tool for rapidly searching multiple genomes, whose performance is limited in most cases by the speed of access to the filesystem. We have made publicly available a Web interface for searching the human, mouse, and several other genomes and transcriptomes with oligonucleotide queries.

Rapid Improvement and Maintenance of the Lipid Profile After Roux-en-Y Gastric Bypass (RYGBP)

Background: Dyslipidemia, a major component of the metabolic syndrome and an important cardiovascular risk factor, is one of the commonest comorbidity associated with morbid obesity. The aim of this paper is to show that RYGBP markedly improves dyslipidemia and that this improvement maintains over time. Patients and Methods: Prospectively updated databank for bariatric patients. Patients undergoing RYGBP have yearly blood tests during follow-up. The results for lipids at one to five years were compared with preoperative values. Results: The mean excess BMI loss after one and five years was 77,9 % and 72,3%respectively. After one year, there was a significant reduction of the mean total cholesterol, LDL-cholesterol, total cholesterol/HDL ratio and triglyceride values, which maintained up to five years, and an increase of the HDL fraction, which progressed until five years. The proportion of patients with abnormal values decreased from 24,3 to 6,2% for total cholesterol, from 45,1 to 11,7 %for HDL, from 53,3 to 21,9 for LDL, and from 40,5 to 10 % for triglycerides, with no significant change between three and five years, despite some weight regain. Conclusions: RYGBP rapidly improves all components of dyslipidemia, and thereby reduces the overall cardiovascular risk in operated patients.

Iowa Fen Rapid Assessment Method for Wetlands v. 1 Quantitative Rating, 2016

Rapid assessment methods are valuable tools for collecting information about the quality and status of natural systems. However, they are not a substitute for detailed surveys of those systems. Users of this method should consider that the method may under-score or over-score the site that’s assessed, especially when the site is not a typical fen (i.e. a sedge meadow could score lower than fens, but in-fact be a relatively high quality sedge meadow). This assessment can be used throughout most of the spring, summer and fall period, however the ideal “index period” would be from late May through early October when native plant communities, as well as invasive species, are most apparent.

Rapid LC-MS/MS quantification of the major benzodiazepines and their metabolites on dried blood spots using a simple and cost-effective sample pretreatment.

BACKGROUND: Dried blood spots (DBS) sampling has gained popularity in the bioanalytical community as an alternative to conventional plasma sampling, as it provides numerous benefits in terms of sample collection and logistics. The aim of this work was to show that these advantages can be coupled with a simple and cost-effective sample pretreatment, with subsequent rapid LC-MS/MS analysis for quantitation of 15 benzodiazepines, six metabolites and three Z-drugs. For this purpose, a simplified offline procedure was developed that consisted of letting a 5-µl DBS infuse directly into 100 µl of MeOH, in a conventional LC vial. RESULTS: The parameters related to the DBS pretreatment, such as extraction time or internal standard addition, were investigated and optimized, demonstrating that passive infusion in a regular LC vial was sufficient to quantitatively extract the analytes of interest. The method was validated according to international criteria in the therapeutic concentration ranges of the selected compounds. CONCLUSION: The presented strategy proved to be efficient for the rapid analysis of the selected drugs. Indeed, the offline sample preparation was reduced to a minimum, using a small amount of organic solvent and consumables, without affecting the accuracy of the method. Thus, this approach enables simple and rapid DBS analysis, even when using a non-DBS-dedicated autosampler, while lowering the costs and environmental impact.

The Coverage of the European independence movements from a Canadian perspective: Comparisons of the francophone online press in Quebec with the English Canadian press on the independence movements in Scotland and Catalonia

This research paper provides the basis of a future doctoral thesison the construction of foreign news. We aim to highlight similarities and differences in the online news coverage of the nationalist movments in Scotland and Catalonia in the Canadian Anglophone and Francophone press. Through a qualitative and quantitative content analysis of The Montreal Gazette, The National Post, The Globe and Mail, Le Devoir and La Presse, we attempt to show the frames used in the coverage of the political developments in both “stateless regions” from January 2011 to September 2014, when a referendum on the constitutional status of Scotland has beenagreed on. In parallel to the analysis of daily online newspapers, we will use semi-structured interviews of journalists from each news organization to obtain more in-depth knowledge of the factors influencing the construction of news. Lastly, we want to find out to the extent to which the coverage on the nationalist movements in Scotland and Catalonia serve to revive the debate on the independence question of Québec

Rapid and sudden advection of warm and dry air in the Mediterranean Basin

Rapid advection of extremely warm and dry air is studied during two events in the Mediterranean Basin. On 27 August 2010 a rapid advection of extremely warm and dry air affected the northeast Iberian Peninsula during a few hours. At the Barcelona city center, the temperature reached 39.3 ° C, which is the maximum temperature value recorded during 230 yr of daily data series. On 23 March 2008 a rapid increase of temperature and drop of relative humidity were recorded for a few hours in Heraklion (Crete). During the morning on that day, the recorded temperature reached 34 °C for several hours on the northern coastline of this island.According to the World Meteorological Organization none of these events can be classified as a heat wave, which requires at least two days of abnormally high temperatures; neither are they a heat burst as defined by the American Meteorological Society, where abnormal temperatures take place during a few minutes. For this reason, we suggest naming this type of event flash heat. By using data from automatic weather stations in the Barcelona and Heraklion area and WRF mesoscale numerical simulations, these events are analyzed. Additionally, the primary risks and possible impacts on several fields are presented.

Investigation of Rapid Thermal Analysis Procedures for Prediction of the Service Life of PCCP Carbonate Coarse Aggregate: Phase I, Progress Report, HR-337, 1992

The major objective of this research project is to utilize thermal analysis techniques in conjunction with x-ray analysis methods to identify and explain chemical reactions that promote aggregate related deterioration in Portland cement concrete. The first year of this project has been spent obtaining and analyzing limestone and dolomite samples that exhibit a wide range of field service performance. Most of the samples chosen for the study also had laboratory durability test information (ASTM C 666, method B) that was readily available. Preliminary test results indicate that a strong relationship exists between the average crystallite size of the limestone (calcite) specimens and their apparent decomposition temperatures as measured by thermogravimetric analysis. Also, premature weight loss in the thermogravimetric analysis tests appeared to be related to the apparent decomposition temperature of the various calcite test specimens.

A Playful Glance at Hierarchical Questions for Two-Way Alternating Automata

Two-way alternating automata were introduced by Vardi in order to study the satisfiability problem for the modal μ-calculus extended with backwards modalities. In this paper, we present a very simple proof by way of Wadge games of the strictness of the hierarchy of Motowski indices of two-way alternating automata over trees.

Prevalence and time course of acute mountain sickness in older children and adolescents after rapid ascent to 3'450 meters

Rapport de synthèse :Grâce au développement de moyens de transport modernes, de plus en plus d'enfants et d'adolescents se rendent en haute altitude dans le cadre de leurs loisirs. Le mal aigu des montagnes est une complication fréquente des séjours en haute altitude. Ses symptômes en sont des maux de tête, une fatigue, des troubles du sommeil, des nausées et des vertiges. La vitesse d'ascension, |'attitude maximale atteinte, une susceptibilité individuelle ainsi qu'une acclimatation antérieure a l'attitude sont tous des facteurs influant sur le risque de développer un mal aigu des montagnes et sur sa sévérité. Bien que très fréquente chez l'adulte, nous ne possédions, au moment d'entreprendre |'étude faisant |'objet de cette thèse, que peu de données solides concernant la prévalence de cette affection chez l'enfant ainsi que sur son évolution au cours du temps. Cette étude a pour but de mesurer la prévalence du mal aigu des montagnes, et son évolution au cours du temps au sein d'un groupe d'enfants et d'adolescents dans des conditions contrôlées. C'est à dire en éliminant |'influence de facteurs confondants tels que l'importance de l'exercice physique fourni ou une différence dans la vitesse d'ascension. Pour ce faire nous avons évalué la présence de mal aigu des montagnes dans un groupe de 48 garçons et de filles âgés de 11 à 17 ans en bonne santé habituelle, n'ayant jamais séjourné en haute altitude au préalable. Afin d'évaluer la présence ou non de mal aigu des montagnes nous avons utilisé une version française du « Lake Louise Score >>. Les mesures furent effectuées 6,24 et 48 heures après |`arrivée à la station de recherche de la Jungfraujoch située à 3'450m. L'ascension a consisté en un trajet de train durant 2h30. Nos observations montrent que la prévalence du mal aigu des montagnes durant les 3 premiers jours ne dépasse jamais les 25%. Elle est similaire pour les deux sexes et diminue au cours du séjour. (17% après 24 heures, 8% après 48 heures) Aucun sujet n'a dû être évacué à une altitude inférieure, Cinq sujets ont eu besoin de recourir à un traitement symptomatique et y ont bien répondu Les résultats de cette étude démontrent que dans le groupe d'âge étudié, après une ascension rapide en haute altitude, la prévalence du mal aigu des montagnes est relativement faible, ses manifestations cliniques sont bénignes et, |lorsqu'' elles sont présentes, se résolvent rapidement. Ces observations suggèrent que pour la majorité des enfants et des adolescents en bonne santé et non habitués a |'attitude, un séjour en haute altitude ne présente pas de risque et une prophylaxie pharmacologique du mal aigu des montagnes n'est pas nécessaire.

Electrophysiological markers of rapid cognitive decline in mild cognitive impairment

Electroencephalography (EEG) is an easily accessible and low-cost modality that might prove to be a particularly powerful tool for the identification of subtle functional changes preceding structural or metabolic deficits in progressive mild cognitive impairment (PMCI). Most previous contributions in this field assessed quantitative EEG differences between healthy controls, MCI and Alzheimer's disease(AD) cases leading to contradictory data. In terms of MCI conversion to AD, certain longitudinal studies proposed various quantitative EEG parameters for an a priori distinction between PMCI and stable MCI. However, cross-sectional comparisons revealed a substantial overlap in these parameters between MCI patients and elderly controls. Methodological differences including variable clinical definition of MCI cases and substantial interindividual differences within the MCI group could partly explain these discrepancies. Most importantly, EEG measurements without cognitive demand in both cross-sectional and longitudinal designs have demonstrated limited sensitivity and generally do not produce significant group differences in spectral EEG parameters. Since the evolution of AD is characterized by the progressive loss of functional connectivity within neocortical association areas, event-modulated EEG dynamic analysis which makes it possible to investigate the functional activation of neocortical circuits may represent a more sensitive method to identify early alterations of neuronal networks predictive of AD development among MCI cases. The present review summarizes clinically significant results of EEG activation studies in this field and discusses future perspectives of research aiming to reach an early and individual prediction of cognitive decline in healthy elderly controls.

Rapid marine recovery after the end-Permian mass-extinction event in the absence of marine anoxia

A new Early Triassic marine fauna is described from the Central Oman Mountains. The fauna is Griesbachian in age, on the basis of abundant conodonts and ammonoids, and was deposited in an oxygenated seamount setting off the Arabian platform margin. It is the first Griesbachian assemblage from a well-oxygenated marine setting and thus provides a test for the hypothesis that widespread anoxia prevented rapid recovery. The earliest Griesbachian (parvus zone) contains a low-diversity benthic fauna dominated by the bivalves Promyalina and Claraia. A similar level of recovery characterizes the immediate postextinction interval worldwide. However, the middle upper Griesbachian sedimentary rocks (isarcica and catinata zones) contain an incredibly diverse benthic fauna of bivalves, gastropods, articulate brachiopods, a new undescribed crinoid, echinoids, and ostracods. This fauna is more diverse and ecologically complex than the typical middle to late Griesbachian faunas described from oxygen-restricted settings worldwide. The level of postextinction recovery observed in the Oman fauna is not recorded elsewhere until the Spathian. These data support the hypothesis that the apparent delay in recovery after the end-Permian extinction event was due to widespread and prolonged benthic oxygen restriction: in the absence of anoxia, marine recovery is much faster.

Ultra-rapid opiate detoxification using deep sedation and prior oral buprenorphine preparation: long-term results.

BACKGROUND: New methods of ultra-rapid opiate detoxification (URD) under intravenous sedation have been criticized because of limited data on safety and long-term follow-up. Premedication with buprenorphine has been advocated to improve safety by decreasing vomiting. Prior research has not explored URD in socially impaired patients. METHOD: Sixteen patients were detoxified with URD and prospectively evaluated over at least 30 months. Data of this procedure were compared with those of our previous study without buprenorphine preparation (Drug Alcohol Depend. 52(3) (1998) 243). The 16 patients were followed up by a general practitioner (GP) before and after URD. The GPs also supervised the 7-day course of buprenorphine treatment prescribed for the 16 patients prior to URD. RESULTS: During the procedure, only one episode of vomiting occurred instead of 13 out of 20 in our previous study. Post-procedure, only two patients experienced moderate withdrawal symptoms, such as persistent nausea, abdominal cramps and vomiting lasting from 24 to 48 h, in comparison with most patients in the previous study without buprenorphine. After a period of at least 30 months (36.0+/-6.38), the 16 patients were still alive and were regularly monitored by their GP. Only two of the 16 never relapsed after URD and reported total opiate abstinence. Fourteen patients relapsed; 12 of these were prescribed a licensed methadone substitution program and two were still using heroin. CONCLUSION: In this small sample, the data indicated that URD with buprenorphine preparation was safe and that it markedly decreased post-procedure morbidity. No patient died over a minimum 30-month follow-up period. Furthermore, the procedure was employed with socially impaired patients. In the long term, a few patients were still free of opiates, while the majority opted for a methadone maintenance program, showing that URD can serve as one possible step in a long-term treatment program.

Evaluation of a piezoelectric system as an alternative to electroencephalogram/ electromyogram recordings in mouse sleep studies.

STUDY OBJECTIVES: Traditionally, sleep studies in mammals are performed using electroencephalogram/electromyogram (EEG/EMG) recordings to determine sleep-wake state. In laboratory animals, this requires surgery and recovery time and causes discomfort to the animal. In this study, we evaluated the performance of an alternative, noninvasive approach utilizing piezoelectric films to determine sleep and wakefulness in mice by simultaneous EEG/EMG recordings. The piezoelectric films detect the animal's movements with high sensitivity and the regularity of the piezo output signal, related to the regular breathing movements characteristic of sleep, serves to automatically determine sleep. Although the system is commercially available (Signal Solutions LLC, Lexington, KY), this is the first statistical validation of various aspects of sleep. DESIGN: EEG/EMG and piezo signals were recorded simultaneously during 48 h. SETTING: Mouse sleep laboratory. PARTICIPANTS: Nine male and nine female CFW outbred mice. INTERVENTIONS: EEG/EMG surgery. MEASUREMENTS AND RESULTS: The results showed a high correspondence between EEG/EMG-determined and piezo-determined total sleep time and the distribution of sleep over a 48-h baseline recording with 18 mice. Moreover, the piezo system was capable of assessing sleep quality (i.e., sleep consolidation) and interesting observations at transitions to and from rapid eye movement sleep were made that could be exploited in the future to also distinguish the two sleep states. CONCLUSIONS: The piezo system proved to be a reliable alternative to electroencephalogram/electromyogram recording in the mouse and will be useful for first-pass, large-scale sleep screens for genetic or pharmacological studies. CITATION: Mang GM, Nicod J, Emmenegger Y, Donohue KD, O'Hara BF, Franken P. Evaluation of a piezoelectric system as an alternative to electroencephalogram/electromyogram recordings in mouse sleep studies.

Phylogenetic analysis of plastid and nuclear DNA sequences reveals a rapid late Miocene radiation of the temperate bamboo tribe Arundinarieae (Poaceae, Bambusoideae)

Background: Arundinarieae are a large tribe of temperate woody bamboos for which phylogenetics are poorly understood because of limited taxon sampling and lack of informative characters. Aims: This study assessed phylogenetic relationships, origins and classification of Arundinarieae. Methods: DNA sequences (plastid trnL-F; nuclear ITS) were used for parsimony and Bayesian inference including 41 woody bamboo taxa. Divergence dates were estimated using a relaxed Bayesian clock. Results: Arundinarieae were monophyletic but their molecular divergence was low compared to the tropical Bambuseae. Ancestors of the Arundinarieae lineage were estimated to have diverged from the other bamboos 23 (15-30) million years ago (Mya). However, the Arundinarieae radiation occurred 10 (6-16) Mya compared to 18 (11-25) Mya for the tropical Bambuseae. Some groups could be defined within Arundinarieae, but they do not correspond to recognised subtribes such as Arundinariinae or Shibataeinae. Conclusions: Arundinarieae are a relatively ancient bambusoid lineage that underwent a rapid radiation in the late Miocene. The radiation coincides with the continental collision of the Indo-Australian and Eurasian Plates. Arundinarieae are distributed primarily in East Asia and the Himalayas to northern Southeast Asia. It is unknown whether they were present in Asia long before their radiation, but we believe recent dispersal is a more likely scenario. Keywords: Arundinarieae; Bambuseae; internal transcribed spacer (ITS); molecular clock; phylogenetics; radiation; temperate bamboos; Thamnocalaminae; trnL-F