| 1. |
- Bradnam, K. R., et al.
(författare)
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Assemblathon 2 : Evaluating de novo methods of genome assembly in three vertebrate species
- 2013
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Ingår i: GigaScience. - : BioMed Central (BMC). - 2047-217X. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
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| 2. |
- Connolly, L. J., et al.
(författare)
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Effects of small-volume soccer and vibration training on body composition, aerobic fitness, and muscular PCr kinetics for inactive women aged 20-45
- 2014
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Ingår i: Journal of Sport and Health Science. - : Elsevier BV. - 2095-2546. ; 3:4, s. 284-292
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: The present study investigated the effects of 16 weeks of small-volume, small-sided soccer training soccer group (SG, n = 13) and oscillating whole-body vibration training vibration group (VG, n = 17) on body composition, aerobic fitness, and muscle PCr kinetics in healthy inactive premenopausal women in comparison with an inactive control group (CO, n = 14). Methods: Training for SG and VG consisted of twice-weekly 15-min sessions with average heart rates (HRs) of similar to 155 and 90 bpm respectively. Pre- and post-measurements of body composition (DXA), phosphocreatine (PCr) on-and off-kinetics, and HR measurements during standardised submaximal exercise were performed. Results: After 16 weeks of training in SG, fat percentage was lowered (p = 0.03) by 1.7% +/- 2.4% from 37.5% +/- 6.9% to 35.8% +/- 6.2% and the PCr decrease in the quadriceps during knee-extension ramp exercise was attenuated (4% +/- 8%, p = 0.04), with no changes in VG or CO (time-group effect: p = 0.03 and p = 0.03). Submaximal exercise HR was also reduced in SG after 16 weeks of training (6% +/- 5% of HRmax, p = 0.01). Conclusion: Short duration soccer training for 16 weeks appears to be sufficient to induce favourable changes in body composition and indicators of aerobic fitness and muscle oxidative capacity in untrained premenopausal women. Copyright (C) 2014, Shanghai University of Sport. Production and hosting by Elsevier B.V. All rights reserved.
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| 3. |
- Andersson, Martin, 1974, et al.
(författare)
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Vesicle and bilayer formation of diphytanoylphosphatidylcholine (DPhPC) and diphytanoylphosphatidylethanolamine (DPhPE) mixtures and their bilayers' electrical stability
- 2011
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Ingår i: Colloids and Surfaces B: Biointerfaces. - : Elsevier BV. - 0927-7765 .- 1873-4367. ; 82:2, s. 550-561
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Tidskriftsartikel (refereegranskat)abstract
- Lipid bilayers are of interest in applications where a cell membrane mimicking environment is desired. The performance of the lipid bilayer is largely dependent on the physical and chemical properties of the component lipids. Lipid bilayers consisting of phytanoyl lipids have proven to be appropriate choices since they exhibit high mechanical and chemical stability. In addition, such bilayers have high electrical resistances. Two different phytanoyl lipids, 1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhPC) and 1,2-diphytanoyl-sn-glycero-3-phosphoethanolamine(DPhPE), and various combinations of the two have been investigated with respect to their behavior in aqueous solutions, their interactions with solid surfaces, and their electrical stability. Dynamic light scattering, nuclear magnetic resonance diffusion, and cryogenic transmission electron microscopy measurements showed that pure DPhPC as well as mixtures of DPhPC and DPhPE consisting of greater than 50% (mol%) DPhPC formed unilamellar vesicles. If the total lipid concentration was greater than 0.15 g/l, then the vesicles formed solid-supported bilayers on plasma-treated gold and silica surfaces by the process of spontaneous vesicle adsorption and rupture, as determined by quartz crystal microbalance with dissipation monitoring and atomic force microscopy. The solid-supported bilayers exhibited a high degree of viscoelasticity, probably an effect of relatively high amounts of imbibed water or incomplete vesicle fusion. Lipid compositions consisting of greater than 50% DPhPE formed small flower-like vesicular structures along with discrete liquid crystalline structures, as evidenced by cryogenic transmission electron microscopy. Furthermore, electrophysiology measurements were performed on bilayers using the tip-dip methodology and the bilayers' capacity to retain its electrical resistance towards an applied potential across the bilayer was evaluated as a function of lipid composition. It was shown that the lipid ratio significantly affected the bilayer's electrical stability, with pure DPhPE having the highest stability followed by 3DPhPC:7DPhPE and 7DPhPC:3DPhPE in decreasing order. The bilayer consisting of 5DPhPC:5DPhPE had the lowest stability towards the applied electrical potential.
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| 4. |
- Thomas, Andrew G., et al.
(författare)
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Adsorption Studies of p-Aminobenzoic Acid on the Anatase TiO2(101) Surface
- 2014
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 30:41, s. 12306-12314
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Tidskriftsartikel (refereegranskat)abstract
- The adsorption of p-aminobenzoic acid (pABA) on the anatase TiO2(101) surface has been investigated using synchrotron radiation photoelectron spectroscopy, near edge X-ray absorption fine structure (NEXAFS) spectroscopy, and density functional theory (DFT). Photoelectron spectroscopy indicates that the molecule is adsorbed in a bidentate mode through the carboxyl group following deprotonation. NEXAFS spectroscopy and DFT calculations of the adsorption structures indicate the ordering of a monolayer of the amino acid on the surface with the plane of the ring in an almost upright orientation. The adsorption of pABA on nanoparticulate TiO2 leads to a red shift of the optical absorption relative to bare TiO2 nanoparticles. DFT and valence band photoelectron spectroscopy suggest that the shift is attributed to the presence of the highest occupied molecular orbitals in the TiO2 band gap region and the presence of new molecularly derived states near the foot of the TiO2 conduction band.
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