There have been three episodes of lava dome growth at Shiveluch volcano, Kamchatka since the Plinian explosive eruption in 1964. The episodes in 1980–1981, 1993–1995 and 2001–2004 have discharged at ...least 0.27
km
3 of silicic andesite magma. A time-averaged mean extrusion rate of 0.2
m
3/s is thus estimated for the last 40
years. Here the 2001–2004 activity is described and compared with the earlier episodes. The recent activity involved three pulses in extrusion rate and a transition to ongoing lava extrusion. Estimated magma temperatures are in the range 830 to 900
°C, with 850
°C as the best estimate, using the plagioclase−amphibole phenocryst assemblage and Fe−Ti oxides. Melt inclusions in amphibole and plagioclase have maximum water contents of 5.1
wt.%, implying a minimum pressure of ∼
155
MPa for water-saturated conditions. The magma chamber depth is estimated to be about 5–6
km or more, a result consistent with geophysical data. The thicknesses of opx–mt–amph reaction rims on olivine xenocrysts are used to estimate the residence time of olivine crystals in the shallow chamber in the range 2 months to 4 years, suggesting replenishment of deeper magma into the shallow chamber contemporaneous with eruption. The absence of decompression-driven breakdown rims around amphiboles indicates ascent times of less than 7
days. Volcanological observations of the start of the 2001–2004 episode suggest approximately 16 days for the ascent time and a conduit equivalent to a cylinder of diameter approximately 53–71
m. Application of a conduit flow model indicates that the magma chamber was replenished during the 2001–2004 eruption, consistent with the results of olivine reaction rims, and that the chamber has an estimated volume of order 7
km
3.
Many current gene prediction methods use only one model to represent protein-coding regions in a genome, and so are less likely to predict the location of genes that have an atypical sequence ...composition. It is likely that future improvements in gene finding will involve the development of methods that can adequately deal with intra-genomic compositional variation.
This work explores a new approach to gene-prediction, based on the Self-Organizing Map, which has the ability to automatically identify multiple gene models within a genome. The current implementation, named RescueNet, uses relative synonymous codon usage as the indicator of protein-coding potential.
While its raw accuracy rate can be less than other methods, RescueNet consistently identifies some genes that other methods do not, and should therefore be of interest to gene-prediction software developers and genome annotation teams alike. RescueNet is recommended for use in conjunction with, or as a complement to, other gene prediction methods.
ORegAnno is an open-source, open-access database and literature curation system for community-based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites ...and regulatory variants. The current release comprises 30 145 records curated from 922 publications and describing regulatory sequences for over 3853 genes and 465 transcription factors from 19 species. A new feature called the 'publication queue' allows users to input relevant papers from scientific literature as targets for annotation. The queue contains 4438 gene regulation papers entered by experts and another 54 351 identified by text-mining methods. Users can enter or 'check out' papers from the queue for manual curation using a series of user-friendly annotation pages. A typical record entry consists of species, sequence type, sequence, target gene, binding factor, experimental outcome and one or more lines of experimental evidence. An evidence ontology was developed to describe and categorize these experiments. Records are cross-referenced to Ensembl or Entrez gene identifiers, PubMed and dbSNP and can be visualized in the Ensembl or UCSC genome browsers. All data are freely available through search pages, XML data dumps or web services at: http://www.oreganno.org.
Diagnosis of Helicobacter pylori Cirak, Meltem Yalinay; Akyön, Yakut; Mégraud, Francis
Helicobacter (Cambridge, Mass.),
October 2007, Letnik:
12, Številka:
s1
Journal Article
Recenzirano
Odprti dostop
Although there are attempts to perform Helicobacter pylori diagnosis directly in vivo using magnification endoscopy, most articles on diagnosis this year concerned non‐invasive tests and molecular ...methods. For urea breath tests, there are attempts to have a quicker and cheaper test and to evaluate its role in cases of premalignant lesions. For stool antigens tests, evaluation of kits using monoclonal antibodies was carried out. Molecular tests have been applied for typing and detection of resistant mutants.
This study aims to determine the in vitro susceptibility of Helicobacter pylori to clarithromycin, metronidazole, amoxycillin and tetracycline, the four antibiotics commonly used in eradication ...therapies. These data are used to evaluate the efficacy of current empiric treatment of H. pylori infection in the Southern Region of Ireland. Culture is performed on gastric biopsy samples obtained from 147 consecutive patients undergoing gastroscopy for investigation of dyspepsia. Susceptibility testing to metronidazole, clarithromycin, amoxycillin and tetracycline is performed on the isolates by Etest. Isolates demonstrating clarithromycin resistance are subjected to polymerase chain reaction (PCR) amplification and nucleotide sequence analysis to identify the presence of point mutations in the peptidyltransferase region of the 23S rRNA gene previously associated with resistance to clarithromycin. Prevalence of H. pylori in the population studied was 31% (45 isolates). Antimicrobial resistance to metronidazole and clarithromycin was detected in nine (20%) and four (8.9%) of the isolates, respectively. A single isolate demonstrated co-resistance to metronidazole and clarithromycin (2.2%). No resistance was detected to either amoxycillin or tetracycline. The low level of resistance demonstrated among this group of isolates indicates that the empiric treatment currently in place in the Southern Region of Ireland is likely to be successful.
Because congenital anomalies of the fetal neck may alter the normal anatomy of the upper airway, a prospective evaluation of the fetal trachea, hypopharynx, and esophagus was undertaken in 50 ...consecutive fetuses of 18 to 38 menstrual weeks. The cervical trachea was visualized in 47 of 50 fetuses (94 per cent) and had an average internal diameter of 2.6 mm with a range of 2 to 4 mm. The average diameter of the hypopharynx was 5.5 mm on parasagittal section (range 4-8 mm) and 7.1 mm when imaged in the coronal plane (range 4-10 mm). The configuration of the fetal hypopharynx and larynx varied with fetal respiration and swallowing in a characteristic manner. In no case was a persistent fluid collection observed in the region of the cervical esophagus, suggesting that the fetal esophagus is collapsed in the resting state.
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