7,207 research outputs found
ncIDP-assign: a SPARKY extension for the effective NMR assignment of intrinsically disordered proteins
Summary: We describe here the ncIDP-assign extension for the popular NMR assignment program SPARKY, which aids in the sequence-specific resonance assignment of intrinsically disordered proteins (IDPs). The assignment plugin greatly facilitates the effective matching of a set of connected resonances to the correct position in the sequence by making use of IDP random coil chemical shifts
Early responses to chemotherapy detected by pulse cytophotometry.
DNA/cell distributions were recorded by automated cytofluorometry (=pulse cytophotometry) in bone-marrow aspirates of leukaemia and lymphosarcoma patients subjected to chemotherapy. In most cases, early perturbations in DNA/cell histographs were observed, characteristically reflecting the known mode of action of the drugs. These changes in general preceded the clinical observation of drug response. In a series of 23 measurements in 19 patients, a positive correlation between early cytophotometric changes and clinical effects of chemotherapy was observed in 17 patients. Five patients were negative for both cytophotometric and clinical reactions and one patient was probably false-positive. The validity of the assay for early detection of drug resistance in acute leukaemia and related diseases is discussed
The Effect of the Outer Lindblad Resonance of the Galactic Bar on the Local Stellar Velocity Distribution
Hydro-dynamical modeling of the inner Galaxy suggest that the radius of the
outer Lindblad resonance (OLR) of the Galactic bar lies in the vicinity of the
Sun. How does this resonance affect the distribution function in the outer
parts of a barred disk, and can we identify any effect of the resonance in the
velocity distribution f(v) actually observed in the solar neighborhood? To
answer these questions, detailed simulations of f(v) in the outer parts of an
exponential stellar disks with nearly flat rotation curves and a rotating
central bar have been performed. For a model resembling the old stellar disk,
the OLR causes a distinct feature in f(v) over a significant fraction of the
outer disk. For positions <2kpc outside the OLR radius and at bar angles of
\~10-70 degrees, f(v) inhibits a bi-modality between the low-velocity stars
moving like the local standard of rest (LSR) and a secondary mode of stars
predominantly moving outward and rotating more slowly than the LSR.
Such a bi-modality is indeed present in f(v) inferred from the Hipparcos data
for late-type stars in the solar neighborhood. If one interpretes this observed
bi-modality as induced by the OLR -- and there are hardly any viable
alternatives -- then one is forced to deduce that the OLR radius is slightly
smaller than Ro. Moreover, by a quantitative comparison of the observed with
the simulated distributions one finds that the pattern speed of the bar is
1.85+/-0.15 times the local circular frequency, where the error is dominated by
the uncertainty in bar angle and local circular speed.
Also other, less prominent but still significant, features in the observed
f(v) resemble properties of the simulated velocity distributions, in particular
a ripple caused by orbits trapped in the outer 1:1 resonance.Comment: 14 pages, 10 figures (Fig.2 in full resolution available upon
request), accepted for publication in A
Variation at the DRD4 locus is associated with wariness and local site selection in urban black swans
BACKGROUND: Interactions between wildlife and humans are increasing. Urban animals are often less wary of humans than their non-urban counterparts, which could be explained by habituation, adaptation or local site selection. Under local site selection, individuals that are less tolerant of humans are less likely to settle in urban areas. However, there is little evidence for such temperament-based site selection, and even less is known about its underlying genetic basis. We tested whether site selection in urban and non-urban habitats by black swans (Cygnus atratus) was associated with polymorphisms in two genes linked to fear in animals, the dopamine receptor D4 (DRD4) and serotonin transporter (SERT) genes. RESULTS: Wariness in swans was highly repeatable between disturbance events (repeatability = 0.61) and non-urban swans initiated escape from humans earlier than urban swans. We found no inter-individual variation in the SERT gene, but identified five DRD4 genotypes and an association between DRD4 genotype and wariness. Individuals possessing the most common DRD4 genotype were less wary than individuals possessing rarer genotypes. As predicted by the local site selection hypothesis, genotypes associated with wary behaviour were over three times more frequent at the non-urban site. This resulted in moderate population differentiation at DRD4 (FST = 0.080), despite the sites being separated by only 30 km, a short distance for this highly-mobile species. Low population differentiation at neutrally-selected microsatellite loci and the likely occasional migration of swans between the populations reduces the likelihood of local site adaptations. CONCLUSION: Our results suggest that wariness in swans is partly genetically-determined and that wary swans settle in less-disturbed areas. More generally, our findings suggest that site-specific management strategies may be necessary that consider the temperament of local animals
Simultaneous QTL detection and genomic breeding value estimation using high density SNP chips
Background: The simulated dataset of the 13th QTL-MAS workshop was analysed to i) detect QTL and ii) predict breeding values for animals without phenotypic information. Several parameterisations considering all SNP simultaneously were applied using Gibbs sampling. Results: Fourteen QTL were detected at the different time points. Correlations between estimated breeding values were high between models, except when the model was used that assumed that all SNP effects came from one distribution. The model that used the selected 14 SNP found associated with QTL, gave close to unity correlations with the full parameterisations. Conclusions: Nine out of 18 QTL were detected, however the six QTL for inflection point were missed. Models for genomic selection were indicated to be fairly robust, e.g. with respect to accuracy of estimated breeding values. Still, it is worthwhile to investigate the number QTL underlying the quantitative traits, before choosing the model used for genomic selection
Faculty and student perceptions of the feasibility of individual studentâfaculty meetings
The extent to which students feel involved in their education positively influences academic achievement. Individual studentâfaculty meetings can foster student involvement. To be effective, faculty acknowledgement of the benefit of these meetings is a prerequisite. The aim of this study was to explore faculty perceptions of individual studentâfaculty meetings. In addition we investigated studentsâ perceptions. As part of the undergraduate programme, mandatory individual intake and follow-up meetings between first-year medical students (n = 425) and senior faculty members (n = 34) have been implemented from 2009 onwards. We administered a questionnaire on faculty perceptions of the benefit and impact of intake meetings. Subsequently, after both meetings had been held, strong and weak points of the mandatory programme were explored using open-ended questions. Studentsâ perceptions were investigated by open-ended questions as a part of the curriculum evaluation process. Faculty enjoyed the meetings (90 %), perceived the meetings to be beneficial (74 %) and expected a positive effect on student involvement (74 %). Faculty appreciated the opportunity to give advice tailored to studentsâ personal needs and levels of performance. The students appreciated the meetings and the attention given to their personal situation and study progress. Faculty and student appreciation of the meetings seems to support the assumption that the individual meetings increase studentsâ social and academic involvement. Further research should focus on the impact of individual studentâfaculty meetings on studentsâ learning behaviours
Symbiotic Ocean Modeling Using Physics-Controlled Echo State Networks
We introduce a âsymbioticâ ocean modeling strategy that leverages data-driven and machine learning methods to allow high- and low-resolution dynamical models to mutually benefit from each other. In this work we mainly focus on how a low-resolution model can be enhanced within a symbiotic model configuration. The broader aim is to enhance the representation of unresolved processes in low-resolution models, while simultaneously improving the efficiency of high-resolution models. To achieve this, we use a grid-switching approach together with hybrid modeling techniques that combine linear regression-based methods with nonlinear echo state networks. The approach is applied to both the KuramotoâSivashinsky equation and a single-layer quasi-geostrophic ocean model, and shown to simulate short-term and long-term behavior better than either purely data-based methods or low-resolution models. By maintaining key flow characteristics, the hybrid modeling techniques are also able to provide higher quality initial conditions for high-resolution models, thereby improving their efficiency.</p
Symbiotic Ocean Modeling Using Physics-Controlled Echo State Networks
We introduce a âsymbioticâ ocean modeling strategy that leverages data-driven and machine learning methods to allow high- and low-resolution dynamical models to mutually benefit from each other. In this work we mainly focus on how a low-resolution model can be enhanced within a symbiotic model configuration. The broader aim is to enhance the representation of unresolved processes in low-resolution models, while simultaneously improving the efficiency of high-resolution models. To achieve this, we use a grid-switching approach together with hybrid modeling techniques that combine linear regression-based methods with nonlinear echo state networks. The approach is applied to both the KuramotoâSivashinsky equation and a single-layer quasi-geostrophic ocean model, and shown to simulate short-term and long-term behavior better than either purely data-based methods or low-resolution models. By maintaining key flow characteristics, the hybrid modeling techniques are also able to provide higher quality initial conditions for high-resolution models, thereby improving their efficiency.</p
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