Survey sequencing and radiation hybrid mapping to construct comparative maps.

In MURPHY WJ (ed.) Phylogenomics, Humana Press. (Methods in Molecular Biology, 422)International audienceRadiation hybrid (RH) mapping has become one of the most well-established techniques for economically and efficiently navigating genomes of interest. The success of the technique relies on random chromosome breakage of a target genome, which is then captured by recipient cells missing a preselected marker. Selection for hybrid cells that have DNA fragments bearing the marker of choice, plus a random set of DNA fragments from the initial irradiation, generates a set of cell lines that recapitulates the genome of the target organism several-fold. Markers or genes of interest are analyzed by PCR using DNA isolated from each cell line. Statistical tools are applied to determine both the linear order of markers on each chromosome, and the confidence of each placement. The resolution of the resulting map relies on many factors, most notably the degree of breakage from the initial radiation as well as the number of hybrid clones and mean retention value.A high-resolution RH map of a genome derived from low pass or survey sequencing (coverage from 1 to 2 times) can provide essentially the same comparative data on gene order that is derived from high-coverage (greater than x7) genome sequencing. When combined with fluorescence in situ hybridization, RH maps are complete and ordered blueprints for each chromosome. They give information about the relative order and spacing of genes and markers, and allow investigators to move between target and reference genomes, such as those of mouse or human, with ease although the approach is not limited to mammal genomes

Design, analysis and test verification of advanced encapsulation systems, phase 2 program results

Optical, electrical isolation, thermal structural, structural deflection, and thermal tests are reported. The utility of the optical, series capacitance, and structural deflection models was verified

Repeat-length variation in a wheat cellulose synthase-like gene is associated with altered tiller number and stem cell wall composition

The tiller inhibition gene (tin) that reduces tillering in wheat (Triticum aestivum) is also associated with large spikes, increased grain weight, and thick leaves and stems. In this study, comparison of near-isogenic lines (NILs) revealed changes in stem morphology, cell wall composition, and stem strength. Microscopic analysis of stem cross-sections and chemical analysis of stem tissue indicated that cell walls in tin lines were thicker and more lignified than in free-tillering NILs. Increased lignification was associated with stronger stems in tin plants. A candidate gene for tin was identified through map-based cloning and was predicted to encode a cellulose synthase-like (Csl) protein with homology to members of the CslA clade. Dinucleotide repeat-length polymorphism in the 5′UTR region of the Csl gene was associated with tiller number in diverse wheat germplasm and linked to expression differences of Csl transcripts between NILs. We propose that regulation of Csl transcript and/or protein levels affects carbon partitioning throughout the plant, which plays a key role in the tin phenotype.J. Hyles, S. Vautrin, F. Pettolino, C. MacMillan, Z. Stachurski, J. Breen, H. Berges, T. Wicker, and W. Spielmeye

Physical activity interventions and therapeutic exercise in adults with rare neurological disorders: development of a core outcome measure set

måsjekke

Intra-subject repeatability of in vivo intervertebral motion parameters using quantitative fluoroscopy.

Purpose: In vivo quantification of intervertebral motion through imaging has progressed to a point where biomarkers for low back pain are emerging. This makes possible deeper study of the condition’s biometrics. However, the measurement of change over time involves error. The purpose of this prospective investigation is to determine the intra-subject repeatability of six in vivo intervertebral motion parameters using quantitative fluoroscopy. Methods: Intra-subject reliability (ICC) and minimal detectable change (MDC) of baseline to 6-week follow-up measurements were calculated for 6 lumbar spine intervertebral motion parameters in 109 healthy volunteers. A standardised quantitative fluoroscopy (QF) protocol was used to provide measurements in the coronal and sagittal planes using both passive recumbent and active weight bearing motion. Parameters were: intervertebral range of motion (IV-RoM), laxity, motion sharing inequality (MSI), motion sharing variability (MSV), flexion translation, and anterior disc height change during flexion. Results: The best overall intra subject reliability (ICC) and agreement (MDT) were for disc height (ICC 0.89, MDC 43%) and IV-RoM (ICC 0.96, MDC 60%) and the worst for MSV (ICC 0.04, MCD 408%). Laxity, MSI and translation had acceptable reliability (most ICCs >0.60), but not agreement (MDC >85%). Conclusion: Disc height and IV-RoM measurement using QF could be considered for randomised trials while laxity, MSI and translation could be considered for moderators, correlates or mediators of patient reported outcomes. MSV had both poor reliability and agreement over 6 weeks

Star formation triggered by HII regions in our Galaxy: First results for N49 from the Herschel infrared survey of the Galactic plane

It has been shown that by means of different physical mechanisms the expansion of HII regions can trigger the formation of new stars of all masses. This process may be important to the formation of massive stars but has never been quantified in the Galaxy. We use Herschel-PACS and -SPIRE images from the Herschel Infrared survey of the Galactic plane, Hi-GAL, to perform this study. We combine the Spitzer-GLIMPSE and -MIPSGAL, radio-continuum and sub-millimeter surveys such as ATLASGAL with Hi-GAL to study Young Stellar Objects (YSOs) observed towards Galactic HII regions. We select a representative HII region, N49, located in the field centered on l=30 degr observed as part of the Hi-GAL Science Demonstration Phase, to demonstrate the importance Hi-GAL will have to this field of research. Hi-GAL PACS and SPIRE images reveal a new population of embedded young stars, coincident with bright ATLASGAL condensations. The Hi-GAL images also allow us, for the first time, to constrain the physical properties of the newly formed stars by means of fits to their spectral energy distribution. Massive young stellar objects are observed at the borders of the N49 region and represent second generation massive stars whose formation has been triggered by the expansion of the ionized region. Hi-GAL enables us to detect a population of young stars at different evolutionary stages, cold condensations only being detected in the SPIRE wavelength range. The far IR coverage of Hi-GAL strongly constrains the physical properties of the YSOs. The large and unbiased spatial coverage of this survey offers us a unique opportunity to lead, for the first time, a global study of star formation triggered by HII regions in our Galaxy.Comment: 4 pages, 2 figures, accepted by A&A (Special issue on Herschel first results

Moving frames applied to shell elasticity

Exterior calculus and moving frames are used to describe curved elastic shells. The kinematics follow from the Lie-derivative on forms whereas the dynamics via stress-forms.Comment: 20 pages, 1 figur

An Invitation to Higher Gauge Theory

In this easy introduction to higher gauge theory, we describe parallel transport for particles and strings in terms of 2-connections on 2-bundles. Just as ordinary gauge theory involves a gauge group, this generalization involves a gauge '2-group'. We focus on 6 examples. First, every abelian Lie group gives a Lie 2-group; the case of U(1) yields the theory of U(1) gerbes, which play an important role in string theory and multisymplectic geometry. Second, every group representation gives a Lie 2-group; the representation of the Lorentz group on 4d Minkowski spacetime gives the Poincar\'e 2-group, which leads to a spin foam model for Minkowski spacetime. Third, taking the adjoint representation of any Lie group on its own Lie algebra gives a 'tangent 2-group', which serves as a gauge 2-group in 4d BF theory, which has topological gravity as a special case. Fourth, every Lie group has an 'inner automorphism 2-group', which serves as the gauge group in 4d BF theory with cosmological constant term. Fifth, every Lie group has an 'automorphism 2-group', which plays an important role in the theory of nonabelian gerbes. And sixth, every compact simple Lie group gives a 'string 2-group'. We also touch upon higher structures such as the 'gravity 3-group' and the Lie 3-superalgebra that governs 11-dimensional supergravity.Comment: 60 pages, based on lectures at the 2nd School and Workshop on Quantum Gravity and Quantum Geometry at the 2009 Corfu Summer Institut

L-infinity algebra connections and applications to String- and Chern-Simons n-transport

We give a generalization of the notion of a Cartan-Ehresmann connection from Lie algebras to L-infinity algebras and use it to study the obstruction theory of lifts through higher String-like extensions of Lie algebras. We find (generalized) Chern-Simons and BF-theory functionals this way and describe aspects of their parallel transport and quantization. It is known that over a D-brane the Kalb-Ramond background field of the string restricts to a 2-bundle with connection (a gerbe) which can be seen as the obstruction to lifting the PU(H)-bundle on the D-brane to a U(H)-bundle. We discuss how this phenomenon generalizes from the ordinary central extension U(1) -> U(H) -> PU(H) to higher categorical central extensions, like the String-extension BU(1) -> String(G) -> G. Here the obstruction to the lift is a 3-bundle with connection (a 2-gerbe): the Chern-Simons 3-bundle classified by the first Pontrjagin class. For G = Spin(n) this obstructs the existence of a String-structure. We discuss how to describe this obstruction problem in terms of Lie n-algebras and their corresponding categorified Cartan-Ehresmann connections. Generalizations even beyond String-extensions are then straightforward. For G = Spin(n) the next step is "Fivebrane structures" whose existence is obstructed by certain generalized Chern-Simons 7-bundles classified by the second Pontrjagin class.Comment: 100 pages, references and clarifications added; correction to section 5.1 and further example to 9.3.1 adde