| 1. |
- Clark, Andrew G., et al.
(author)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Journal article (peer-reviewed)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 2. |
- Lambert, A., et al.
(author)
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Validation of the Aura Microwave Limb Sounder middle atmosphere water vapor and nitrous oxide measurements
- 2007
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In: Journal of Geophysical Research. - 0148-0227 .- 2156-2202. ; 112:D24
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Journal article (peer-reviewed)abstract
- The quality of the version 2.2 (v2.2) middle atmosphere water vapor and nitrous oxide measurements from the Microwave Limb Sounder (MLS) on the Earth Observing System (EOS) Aura satellite is assessed. The impacts of the various sources of systematic error are estimated by a comprehensive set of retrieval simulations. Comparisons with correlative data sets from ground-based, balloon and satellite platforms operating in the UV/ visible, infrared and microwave regions of the spectrum are performed. Precision estimates are also validated, and recommendations are given on the data usage. The v2.2 H 2 O data have been improved over v1.5 by providing higher vertical resolution in the lower stratosphere and better precision above the stratopause. The single-profile precision is ∼0.2-0.3 ppmv (4-9%), and the vertical resolution is ∼3-4 km in the stratosphere. The precision and vertical resolution become worse with increasing height above the stratopause. Over the pressure range 0.1-0.01 hPa the precision degrades from 0.4 to 1.1 ppmv (6-34%), and the vertical resolution degrades to ∼12-16 km. The accuracy is estimated to be 0.2-0.5 ppmv (4-11%) for the pressure range 68-0.01 hPa. The scientifically useful range of the H 2 O data is from 316 to 0.002 hPa, although only the 82-0.002 hPa pressure range is validated here. Substantial improvement has been achieved in the v2.2 N 2 O data over v1.5 by reducing a significant low bias in the stratosphere and eliminating unrealistically high biased mixing ratios in the polar regions. The single-profile precision is ∼13-25 ppbv (7-38%), the vertical resolution is ∼4-6 km and the accuracy is estimated to be 3-70 ppbv (9-25%) for the pressure range 100-4.6 hPa. The scientifically useful range of the N 2 O data is from 100 to 1 hPa. Copyright 2007 by the American Geophysical Union.
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| 3. |
- Margulies, Elliott H, et al.
(author)
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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- 2007
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In: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 17:6, s. 760-774
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Journal article (peer-reviewed)abstract
- A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.
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| 4. |
- Simons, F. E., et al.
(author)
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Risk assessment in anaphylaxis: current and future approaches
- 2007
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In: J Allergy Clin Immunol. - : Elsevier BV. - 0091-6749. ; 120:1 Suppl
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Journal article (peer-reviewed)abstract
- Risk assessment of individuals with anaphylaxis is currently hampered by lack of (1) an optimal and readily available laboratory test to confirm the clinical diagnosis of an anaphylaxis episode and (2) an optimal method of distinguishing allergen-sensitized individuals who are clinically tolerant from those at risk for anaphylaxis episodes after exposure to the relevant allergen. Our objectives were to review the effector mechanisms involved in the pathophysiology of anaphylaxis; to explore the possibility of developing an optimal laboratory test to confirm the diagnosis of an anaphylaxis episode, and the possibility of improving methods to distinguish allergen sensitization from clinical reactivity; and to develop a research agenda for risk assessment in anaphylaxis. Researchers from the American Academy of Allergy, Asthma & Immunology and the European Academy of Allergology and Clinical Immunology held a PRACTALL (Practical Allergy) meeting to discuss these objectives. New approaches being investigated to support the clinical diagnosis of anaphylaxis include serial measurements of total tryptase in serum during an anaphylaxis episode, and measurement of baseline total tryptase levels after the episode. Greater availability of the test for mature beta-tryptase, a more specific mast cell activation marker for anaphylaxis than total tryptase, is needed. Measurement of chymase, mast cell carboxypeptidase A3, platelet-activating factor, and other mast cell products may prove to be useful. Consideration should be given to measuring a panel of mediators from mast cells and basophils. New approaches being investigated to help distinguish sensitized individuals at minimum or no risk from those at increased risk of developing anaphylaxis include measurement of the ratio of allergen-specific IgE to total IgE, determination of IgE directed at specific allergenic epitopes, measurement of basophil activation markers by using flow cytometry, and assessment of allergen-specific cytokine responses. Algorithms have been developed for risk assessment of individuals with anaphylaxis, along with a research agenda for studies that could lead to an improved ability to confirm the clinical diagnosis of anaphylaxis and to identify allergen-sensitized individuals who are at increased risk of anaphylaxis.
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| 5. |
- Kennergren, Charles, 1948, et al.
(author)
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Laser-assisted lead extraction: the European experience.
- 2007
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In: Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology. - : Oxford University Press (OUP). - 1099-5129. ; 9:8, s. 651-6
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Journal article (peer-reviewed)abstract
- AIMS: The aim of this study is to investigate the safety and effectiveness of Excimer laser-assisted lead extraction in Europe. The final European multi-centre study experience is presented. METHOD AND RESULTS: The Excimer is a cool cutting laser (50 degrees C) with a wavelength of 308 nm. The energy is emitted from the tip of a flexible sheath and is absorbed by proteins and lipids, 64% of the energy is absorbed at a tissue depth of 0.06 mm. The sheath is positioned over the lead, and the fibrosis surrounding the lead is vaporized while advancing the sheath without damaging other leads. From August 1996 to March 2001, 383 leads (170 atrial, 213 ventricular) in 292 patients (mean age 61.6 years, range 13-96) were extracted at 14 European centres. Mean implantation time was 74 months (3-358). Most frequent indications were pocket infection (26%), non-functional leads (21%), patient morbidity (21%), septicaemia or endocarditis (14%), erosion (5%), and lead interference (8%). Median extraction time was 15 min (1-300). Complete extraction was achieved in 90.9% of the leads and partial extraction in 3.4%. Extraction failed in 5.7% of the leads. Major complications = perforations caused 10/22 (3.4/5.7%) of the failures. Most partially extracted patients were considered clinically successful, as only minor lead parts without clinical significance were left. Femoral non-laser technique was used to remove 8/12 of the non-complication failures. The total complication rate, including five minor complications (1.7%), was 5.1%. No in-hospital mortality occurred. CONCLUSION: Pacing and implantable cardioverter-defibrillator leads can safely, effectively, and predictably be extracted. Open-heart extractions can be limited to special cases. The results indicate that the traditional policy of abandoning redundant leads, instead of removing them, may be obsolete in many patients.
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| 6. |
- Sperling, L., et al.
(author)
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Detection of chromosomal abnormalities, congenital abnormalities and transfusion syndrome in twins
- 2007
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In: Ultrasound in Obstetrics & Gynecology. - : Wiley. - 1469-0705 .- 0960-7692. ; 29:5, s. 517-526
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Journal article (peer-reviewed)abstract
- Objective To evaluate the outcome of screening for structural malformations in twins and the outcome of screening for twin-twin transfusion syndrome (TTTS) among monochorionic twins through a number of ultrasound scans from 12 weeks' gestation. Methods Enrolled into this prospective multicenter observational study were women with twin pregnancies diagnosed before 14 + 6 gestational weeks. The monochorionic pregnancies were scanned every second week until 23 weeks in order to rule out early TTTS. All pregnancies had an anomaly scan in week 19 and fetal echocardiography in week 21 that was performed by specialists in fetal echocardiography. Zygosity was determined by DNA analysis in all twin pairs with the same sex. Results Among the 495 pregnancies the prenatal detection rate for severe structural abnormalities including chromosomal aneuploidies was 83% by the combination of a first-trimester nuchal translucency scan and the anomaly scan in week 19. The incidence of severe structural abnormalities was 2.6% and two-thirds of these anomalies were cardiac. There was no significant difference between the incidence in monozygotic and dizygotic twins, nor between twins conceived naturally or those conceived by assisted reproduction. The incidence of TTTS was 23% from 12 weeks until delivery, and all those monochorionic twin pregnancies that miscarried had signs of TTTS. Conclusion Twin pregnancies have an increased risk of congenital malformations and one out of four monochorionic pregnancies develops TTTS. Ultrasound screening to assess chorionicity and follow-up of monochorionic pregnancies to detect signs of TTTS, as well as malformation screening, are therefore essential in the antenatal care of twin pregnancies. Copyright (c) 2007 IS UOG. Published by John Wiley & Sons, Ltd.
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