Representation of the transfer functions of given structures by their eigen-vibrations, taking into consideration any arbitrary excitation

Eigen-vibration representation of transfer functions for structures by considering arbitrary excitation

A new metric for probability distributions

We introduce a metric for probability distributions, which is bounded, information-theoretically motivated, and has a natural Bayesian interpretation. The square root of the well-known chi(2) distance is an asymptotic approximation to it. Moreover, it is a close relative of the capacitory discrimination and Jensen-Shannon divergence.Publisher PDFPeer reviewe

OpenSPIM - an open access platform for light sheet microscopy

Light sheet microscopy promises to revolutionize developmental biology by enabling live in toto imaging of entire embryos with minimal phototoxicity. We present detailed instructions for building a compact and customizable Selective Plane Illumination Microscopy (SPIM) system. The integrated OpenSPIM hardware and software platform is shared with the scientific community through a public website, thereby making light sheet microscopy accessible for widespread use and optimization to various applications.Comment: 7 pages, 3 figures, 6 supplementary videos, submitted to Nature Methods, associated public website http://openspim.or

On space vehicle attitude stabilization by passive control moment gyros

Equations of motion for passive control moment gyro stabilization of space vehicle attitud

Theory of short-range magnetic order for the t-J model

We present a self-consistent theory of magnetic short-range order based on a spin-rotation-invariant slave-boson representation of the 2D t-J model. In the functional-integral scheme, at the nearest-neighbour pair-approximation level, the bosonized t-J Lagrangian is transformed to a classical Heisenberg model with an effective (doping-dependent) exchange interaction which takes into account the interrelation of ``itinerant'' and ``localized'' magnetic behaviour. Evaluating the theory in the saddle-point approximation, we find a suppression of antiferromagnetic and incommensurate spiral long-range-ordered phases in the favour of a paramagnetic phase with pronounced antiferromagnetic short-range correlations.Comment: 2 pages, 1 Postscript figure, LTpaper.sty, Proc. XXI Int. Conf. on Low Temp. Phys. Prague 9

Green's-function theory of the Heisenberg ferromagnet in a magnetic field

We present a second-order Green's-function theory of the one- and two-dimensional S=1/2 ferromagnet in a magnetic field based on a decoupling of three-spin operator products, where vertex parameters are introduced and determined by exact relations. The transverse and longitudinal spin correlation functions and thermodynamic properties (magnetization, isothermal magnetic susceptibility, specific heat) are calculated self-consistently at arbitrary temperatures and fields. In addition, exact diagonalizations on finite lattices and, in the one-dimensional case, exact calculations by the Bethe-ansatz method for the quantum transfer matrix are performed. A good agreement of the Green's-function theory with the exact data, with recent quantum Monte Carlo results, and with the spin polarization of a $\nu=1$ quantum Hall ferromagnet is obtained. The field dependences of the position and height of the maximum in the temperature dependence of the susceptibility are found to fit well to power laws, which are critically analyzed in relation to the recently discussed behavior in Landau's theory. As revealed by the spin correlation functions and the specific heat at low fields, our theory provides an improved description of magnetic short-range order as compared with the random phase approximation. In one dimension and at very low fields, two maxima in the temperature dependence of the specific heat are found. The Bethe-ansatz data for the field dependences of the position and height of the low-temperature maximum are described by power laws. At higher fields in one and two dimensions, the temperature of the specific heat maximum linearly increases with the field.Comment: 9 pages, 9 figure

Structure of the Oligosaccharyl Transferase Complex at 12 Å Resolution

SummaryOligosaccharyl transferase (OT) catalyzes the transfer of a lipid-linked oligosaccharide to the nascent polypeptide emerging from the translocon. Currently, there is no structural information on the membrane-embedded OT complex, which consists of eight different polypeptide chains. We report a 12 Å resolution cryo-electron microscopy structure of OT from yeast. We mapped the locations of four essential OT subunits through a maltose-binding protein fusion strategy. OT was found to have a large domain in the lumenal side of endoplasmic reticulum where the catalysis occurs. The lumenal domain mainly comprises the catalytic Stt3p, the donor substrate-recognizing Wbp1p, and the acceptor substrate-recognizing Ost1p. A prominent groove was observed between these subunits, and we propose that the nascent polypeptide from the translocon threads through this groove while being scanned by the Ost1p subunit for the presence of the glycosylation sequon

Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks

Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states

New Perspectives in Sinographic Language Processing Through the Use of Character Structure

Chinese characters have a complex and hierarchical graphical structure carrying both semantic and phonetic information. We use this structure to enhance the text model and obtain better results in standard NLP operations. First of all, to tackle the problem of graphical variation we define allographic classes of characters. Next, the relation of inclusion of a subcharacter in a characters, provides us with a directed graph of allographic classes. We provide this graph with two weights: semanticity (semantic relation between subcharacter and character) and phoneticity (phonetic relation) and calculate "most semantic subcharacter paths" for each character. Finally, adding the information contained in these paths to unigrams we claim to increase the efficiency of text mining methods. We evaluate our method on a text classification task on two corpora (Chinese and Japanese) of a total of 18 million characters and get an improvement of 3% on an already high baseline of 89.6% precision, obtained by a linear SVM classifier. Other possible applications and perspectives of the system are discussed.Comment: 17 pages, 5 figures, presented at CICLing 201

Gephyrin, the enigmatic organizer at GABAergic synapses

GABAA receptors are clustered at synaptic sites to achieve a high density of postsynaptic receptors opposite the input axonal terminals. This allows for an efficient propagation of GABA mediated signals, which mostly result in neuronal inhibition. A key organizer for inhibitory synaptic receptors is the 93 kDa protein gephyrin that forms oligomeric superstructures beneath the synaptic area. Gephyrin has long been known to be directly associated with glycine receptor β subunits that mediate synaptic inhibition in the spinal cord. Recently, synaptic GABAA receptors have also been shown to directly interact with gephyrin and interaction sites have been identified and mapped within the intracellular loops of the GABAA receptor α1, α2, and α3 subunits. Gephyrin-binding to GABAA receptors seems to be at least one order of magnitude weaker than to glycine receptors (GlyRs) and most probably is regulated by phosphorylation. Gephyrin not only has a structural function at synaptic sites, but also plays a crucial role in synaptic dynamics and is a platform for multiple protein-protein interactions, bringing receptors, cytoskeletal proteins and downstream signaling proteins into close spatial proximity