| 1. |
- Craddock, Nick, et al.
(author)
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Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
- 2010
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
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Journal article (peer-reviewed)abstract
- Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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| 2. |
- Bell, Taylor, et al.
(author)
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Nightside clouds and disequilibrium chemistry on the hot Jupiter WASP-43b
- 2024
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In: Nature Astronomy. - 2397-3366. ; 8:7, s. 879-898
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Journal article (peer-reviewed)abstract
- Hot Jupiters are among the best-studied exoplanets, but it is still poorly understood how their chemical composition and cloud properties vary with longitude. Theoretical models predict that clouds may condense on the nightside and that molecular abundances can be driven out of equilibrium by zonal winds. Here we report a phase-resolved emission spectrum of the hot Jupiter WASP-43b measured from 5 μm to 12 μm with the JWST’s Mid-Infrared Instrument. The spectra reveal a large day–night temperature contrast (with average brightness temperatures of 1,524 ± 35 K and 863 ± 23 K, respectively) and evidence for water absorption at all orbital phases. Comparisons with three-dimensional atmospheric models show that both the phase-curve shape and emission spectra strongly suggest the presence of nightside clouds that become optically thick to thermal emission at pressures greater than ~100 mbar. The dayside is consistent with a cloudless atmosphere above the mid-infrared photosphere. Contrary to expectations from equilibrium chemistry but consistent with disequilibrium kinetics models, methane is not detected on the nightside (2σ upper limit of 1–6 ppm, depending on model assumptions). Our results provide strong evidence that the atmosphere of WASP-43b is shaped by disequilibrium processes and provide new insights into the properties of the planet’s nightside clouds. However, the remaining discrepancies between our observations and our predictive atmospheric models emphasize the importance of further exploring the effects of clouds and disequilibrium chemistry in numerical models.
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| 3. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 4. |
- Hammond, Mark, et al.
(author)
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Two-dimensional Eclipse Mapping of the Hot-Jupiter WASP-43b with JWST MIRI/LRS
- 2024
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In: Astronomical Journal. - 1538-3881 .- 0004-6256. ; 168:1
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Journal article (peer-reviewed)abstract
- We present eclipse maps of the two-dimensional thermal emission from the dayside of the hot-Jupiter WASP-43b, derived from an observation of a phase curve with the JWST MIRI/LRS instrument. The observed eclipse shapes deviate significantly from those expected for a planet emitting uniformly over its surface. We fit a map to this deviation, constructed from spherical harmonics up to order ℓ max = 2 , alongside the planetary, orbital, stellar, and systematic parameters. This yields a map with a meridionally averaged eastward hot-spot shift of (7.75 ± 0.36)°, with no significant degeneracy between the map and the additional parameters. We show the latitudinal and longitudinal contributions of the dayside emission structure to the eclipse shape, finding a latitudinal signal of ∼200 ppm and a longitudinal signal of ∼250 ppm. To investigate the sensitivity of the map to the method, we fix the parameters not used for mapping and derive an “eigenmap” fitted with an optimized number of orthogonal phase curves, which yields a similar map to the ℓ max = 2 map. We also fit a map up to ℓ max = 3 , which shows a smaller hot-spot shift, with a larger uncertainty. These maps are similar to those produced by atmospheric simulations. We conclude that there is a significant mapping signal which constrains the spherical harmonic components of our model up to ℓ max = 2 . Alternative mapping models may derive different structures with smaller-scale features; we suggest that further observations of WASP-43b and other planets will drive the development of more robust methods and more accurate maps.
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| 5. |
- Holmlund, Patrik, et al.
(author)
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Effect of vibration magnitude, vibration spectrum and muscle tension on apparent mass and cross axis transfer functions during whole-body vibration exposure
- 2006
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In: Journal of Biomechanics. - : Elsevier BV. - 0021-9290 .- 1873-2380. ; 39:16, s. 3062-3070
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Journal article (peer-reviewed)abstract
- Twelve seated male subjects were exposed to 15 vibration conditions to investigate the nature and mechanisms of the non-linearity in biomechanical response. Subjects were exposed to three groups of stimuli: Group A comprised three repeats of random vertical vibration at 0.5, 1.0 and 1.5 m s-2 r.m.s. with subjects sitting in a relaxed upright posture. Group B used the same vibration stimuli as Group A, but with subjects sitting in a ‘tense' posture. Group C used vibration where the vibration spectrum was dominated by either low-frequency motion (2-7 Hz), high-frequency motion (7-20 Hz) or a 1.0 m s-2 r.m.s. sinusoid at the frequency of the second peak in apparent mass (about 10-14 Hz) added to 0.5 m s-2 r.m.s. random vibration. In the relaxed posture, frequencies of the primary peak in apparent mass decreased with increased vibration magnitude. In the tense posture, the extent of the non-linearity was reduced. For the low-frequency dominated stimulus, the primary peak frequency was lower than that for the high-frequency dominated stimulus indicating that the frequency of the primary peak in the apparent mass is dominated by the magnitude of the vibration encompassing the peak. Cross-axis transfer functions showed peaks of about 15-20% and 5% of the magnitudes of the peaks in the apparent mass for x- and y-direction transfer functions, respectively, in the relaxed posture. In the tense posture, cross-axis transfer functions reduced in magnitude with increased vibration, likely indicating a reduced fore-aft pitching of the body with increased tension, supporting the hypothesis that pitching contributes to the non-linearity in apparent mass.
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| 6. |
- Stålbrand, Henrik, et al.
(author)
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Analysis of Molecular Size Distributions of Cellulose Molecules during Hydrolysis of Cellulose by Recombinant Cellulomonas fimi -1,4-Glucanases
- 1998
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In: Applied and Environmental Microbiology. - 0099-2240. ; 64:7, s. 2374-2379
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Journal article (peer-reviewed)abstract
- Four -1,4-glucanases (cellulases) of the cellulolytic bacterium Cellulomonas fimi were purified from Escherichia coli cells transformed with recombinant plasmids. Previous analyses using soluble substrates had suggested that CenA and CenC were endoglucanases while CbhA and CbhB resembled the exo-acting cellobiohydrolases produced by cellulolytic fungi. Analysis of molecular size distributions during cellulose hydrolysis by the individual enzymes confirmed these preliminary findings and provided further evidence that endoglucanase CenC has a more processive hydrolytic activity than CenA. The significant differences between the size distributions obtained during hydrolysis of bacterial microcrystalline cellulose and acid-swollen cellulose can be explained in terms of the accessibility of -1,4-glucan chains to enzyme attack. Endoglucanases and cellobiohydrolases were much more easily distinguished when the acid-swollen substrate was used.
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| 7. |
- Sundström, Jerker, 1972-
(author)
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Difficulties to Read and Write Under Lateral Vibration Exposure : Contextual Studies Of Train Passengers Ride Comfort
- 2006
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Doctoral thesis (other academic/artistic)abstract
- Many people use the train both as a daily means of transport as well as a working place to carry out activities such as reading or writing. There are, however, several important factors in this environment that will hamper good performance of such activities. Some of the main sources of disturbance, apart form other train passengers, are noise and vibrations generated from the train itself. Although there are standards available for evaluation of ride comfort in vehicles none of them consider the effects that vibrations have on particular passengers' activities. To address these issues, three different studies were conducted to investigate how low frequency lateral vibrations influence the passengers' ability to read and write onboard trains. The first study was conducted on three types of Inter-Regional trains during normal service and included both a questionnaire survey and vibration measurements. Two proceeding laboratory studies were conducted in a train mock-up where the perceived difficulty of reading and writing was evaluated for different frequencies and amplitudes. To model and clarify how vibrations influence the processes of reading and writing the fundamentals of Human Activity Theory was used as a framework in this thesis. In the field study about 80% of the passengers were found to be reading at some point during the journey, 25% were writing by hand, and 14% worked with portable computers. The passengers applied a wide range of seated postures for their different activities. According to the standardised measurements, even the trains running on poor tracks showed acceptable levels of vibration. However, when the passengers performed a short written test, over 60 % reported to be disturbed or affected by vibrations and noise in the train. In the laboratory studies it was found that the difficulty in reading and writing is strongly influenced by both vibration frequency and acceleration amplitude. The vibration spectra of real trains were found to correspond well to the frequency characteristics of the rated difficulty. It was also observed that moderate levels of difficulty begin at fairly low vibration levels. Contextual parameters like sitting posture and type of activity also showed strong influence on how vibrations cause difficulty.
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