@article{2128, abstract = {We introduce a technique for handling Whitney decompositions in Gaussian harmonic analysis and apply it to the study of Gaussian analogues of the classical tent spaces T 1,q of Coifman–Meyer–Stein.}, author = {Jan Maas and van Neerven, Jan M and Portal, Pierre}, journal = {Arkiv för Matematik}, number = {2}, pages = {379 -- 395}, publisher = {Springer}, title = {{Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure}}, doi = {10.1007/s11512-010-0143-z}, volume = {50}, year = {2012}, } @article{2203, abstract = {We show that the electric dipole-dipole interaction between a pair of polar molecules undergoes an all-out transformation when superimposed by a far-off-resonant optical field. The combined interaction potential becomes tunable by variation of wavelength, polarisation and intensity of the optical field and its dependence on the intermolecular separation exhibits a crossover from an inverse-power to an oscillating behaviour. The ability thereby offered to control molecular interactions opens up avenues toward the creation and manipulation of novel phases of ultracold polar gases among whose characteristics is a long-range entanglement of the dipoles' mutual orientation. We devised an accurate analytic model of such optical-field-dressed dipole-dipole interaction potentials, which enables a straightforward access to the optical-field parameters required for the design of intermolecular interactions in the laboratory.}, author = {Mikhail Lemeshko and Friedrich, Břetislav}, journal = {Molecular Physics}, number = {15-16}, pages = {1873 -- 1881}, publisher = {Taylor & Francis}, title = {{Interaction between polar molecules subject to a far-off-resonant optical field: Entangled dipoles up- or down-holding each other}}, doi = {10.1080/00268976.2012.689868}, volume = {110}, year = {2012}, } @article{2201, abstract = {We study the growth dynamics of ordered structures of strongly interacting polar molecules in optical lattices. Using a dipole blockade of microwave excitations, we map the system onto an interacting spin-1/2 model possessing ground states with crystalline order, and describe a way to prepare these states by nonadiabatically driving the transitions between molecular rotational levels. The proposed technique bypasses the need to cross a phase transition and allows for the creation of ordered domains of considerably larger size compared to approaches relying on adiabatic preparation.}, author = {Lemeshko, Mikhail and Krems, Roman and Weimer, Hendrik}, journal = {Physical Review Letters}, number = {3}, publisher = {American Physical Society}, title = {{Nonadiabatic preparation of spin crystals with ultracold polar molecules}}, doi = {10.1103/PhysRevLett.109.035301}, volume = {109}, year = {2012}, } @article{2202, abstract = {We propose a method for sensitive parallel detection of low-frequency electromagnetic fields based on the fine structure interactions in paramagnetic polar molecules. Compared to the recently implemented scheme employing ultracold 87Rb atoms by Böhi, the technique based on molecules offers a 100-fold higher sensitivity, the possibility to measure both the electric and magnetic field components, and a probe of a wide range of frequencies from the dc limit to the THz regime.}, author = {Alyabyshev, Sergey V and Mikhail Lemeshko and Krems, Roman V}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {1}, publisher = {American Physical Society}, title = {{Sensitive imaging of electromagnetic fields with paramagnetic polar molecules}}, doi = {10.1103/PhysRevA.86.013409}, volume = {86}, year = {2012}, } @article{2263, abstract = {Nestin-cre transgenic mice have been widely used to direct recombination to neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs). Here we report that a readily utilized, and the only commercially available, Nestin-cre line is insufficient for directing recombination in early embryonic NSCs and NPCs. Analysis of recombination efficiency in multiple cre-dependent reporters and a genetic mosaic line revealed consistent temporal and spatial patterns of recombination in NSCs and NPCs. For comparison we utilized a knock-in Emx1cre line and found robust recombination in NSCs and NPCs in ventricular and subventricular zones of the cerebral cortices as early as embryonic day 12.5. In addition we found that the rate of Nestin-cre driven recombination only reaches sufficiently high levels in NSCs and NPCs during late embryonic and early postnatal periods. These findings are important when commercially available cre lines are considered for directing recombination to embryonic NSCs and NPCs.}, author = {Liang, Huixuan and Hippenmeyer, Simon and Ghashghaei, H.}, journal = {Biology open}, number = {12}, pages = {1200 -- 1203}, publisher = {The Company of Biologists}, title = {{A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors}}, doi = {10.1242/bio.20122287}, volume = {1}, year = {2012}, } @inproceedings{2267, abstract = {Capturing real-world objects with laser-scanning technology has become an everyday task. Recently, the acquisition of dynamic scenes at interactive frame rates has become feasible. A high-quality visualization of the resulting point cloud stream would require a per-frame reconstruction of object surfaces. Unfortunately, reconstruction computations are still too time-consuming to be applied interactively. In this paper we present a local surface reconstruction and visualization technique that provides interactive feedback for reasonably sized point clouds, while achieving high image quality. Our method is performed entirely on the GPU and in screen pace, exploiting the efficiency of the common rasterization pipeline. The approach is very general, as no assumption is made about point connectivity or sampling density. This naturally allows combining the outputs of multiple scanners in a single visualization, which is useful for many virtual and augmented reality applications. }, author = {Preiner, Reinhold and Jeschke, Stefan and Wimmer, Michael}, location = {Calgari, Italy}, pages = {139 -- 148}, publisher = {Eurographics Association}, title = {{Auto splats: Dynamic point cloud visualization on the GPU}}, doi = {10.2312/EGPGV/EGPGV12/139-148}, year = {2012}, } @article{2262, abstract = {Mosaic Analysis with Double Markers (MADM) is a method for generating genetically mosaic mice, in which sibling mutant and wild-type cells are labeled with different fluorescent markers. It is a powerful tool that enables analysis of gene function at the single cell level in vivo. It requires transgenic cassettes to be located between the centromere and the mutation in the gene of interest on the same chromosome. Here we compare procedures for introduction of MADM cassettes into new loci in the mouse genome, and describe new approaches for expanding the utility of MADM. We show that: 1) Targeted homologous recombination outperforms random transgenesis in generation of reliably expressed MADM cassettes, 2) MADM cassettes in new genomic loci need to be validated for biallelic and ubiquitous expression, 3) Recombination between MADM cassettes on different chromosomes can be used to study reciprocal chromosomal deletions/duplications, and 4) MADM can be modified to permit transgene expression by combining it with a binary expression system. The advances described in this study expand current, and enable new and more versatile applications of MADM.}, author = {Tasic, Bosiljka and Miyamichi, Kazunari and Simon Hippenmeyer and Dani, Vardhan S. and Zeng, H. and Joo, William and Zong, Hui and Chen-Tsai, Yanru and Luo, Liqun}, journal = {PLoS One}, number = {3}, publisher = {Public Library of Science}, title = {{Extensions of MADM (Mosaic Analysis with Double Markers) in Mice }}, doi = {10.1371/journal.pone.0033332}, volume = {7}, year = {2012}, } @inproceedings{2268, abstract = {This paper presents an analytic formulation for anti-aliased sampling of 2D polygons and 3D polyhedra. Our framework allows the exact evaluation of the convolution integral with a linear function defined on the polytopes. The filter is a spherically symmetric polynomial of any order, supporting approximations to refined variants such as the Mitchell-Netravali filter family. This enables high-quality rasterization of triangles and tetrahedra with linearly interpolated vertex values to regular and non-regular grids. A closed form solution of the convolution is presented and an efficient implementation on the GPU using DirectX and CUDA C is described. }, author = {Thomas Auzinger and Guthe, Michael and Stefan Jeschke}, number = {121}, pages = {335 -- 344}, publisher = {Wiley-Blackwell}, title = {{Analytic anti-aliasing of linear functions on polytopes}}, doi = {http://dx.doi.org/10.1111/j.1467-8659.2012.03012.x}, volume = {31}, year = {2012}, } @article{2302, abstract = {We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its (next) operator propagates mass values through this set of nodes. We propose an approximate implementation of the (next) operator, based on threshold abstraction, which propagates only "significant" mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model's variables.}, author = {Henzinger, Thomas A and Mateescu, Maria}, journal = {IEEE ACM Transactions on Computational Biology and Bioinformatics}, number = {2}, pages = {310 -- 322}, publisher = {IEEE}, title = {{The propagation approach for computing biochemical reaction networks}}, doi = {10.1109/TCBB.2012.91}, volume = {10}, year = {2012}, } @article{2313, abstract = {The translation of "next-generation" sequencing directly to the clinic is still being assessed but has the potential for genetic diseases to reduce costs, advance accuracy, and point to unsuspected yet treatable conditions. To study its capability in the clinic, we performed whole-exome sequencing in 118 probands with a diagnosis of a pediatric-onset neurodevelopmental disease in which most known causes had been excluded. Twenty-two genes not previously identified as disease-causing were identified in this study (19% of cohort), further establishing exome sequencing as a useful tool for gene discovery. New genes identified included EXOC8 in Joubert syndrome and GFM2 in a patient with microcephaly, simplified gyral pattern, and insulin-dependent diabetes. Exome sequencing uncovered 10 probands (8% of cohort) with mutations in genes known to cause a disease different from the initial diagnosis. Upon further medical evaluation, these mutations were found to account for each proband's disease, leading to a change in diagnosis, some of which led to changes in patient management. Our data provide proof of principle that genomic strategies are useful in clarifying diagnosis in a proportion of patients with neurodevelopmental disorders.}, author = {Dixon-Salazar, Tracy J and Silhavy, Jennifer L and Udpa, Nitin and Schroth, Jana and Bielas, Stephanie L and Schaffer, Ashleigh E and Olvera, Jesus and Bafna, Vineet K and Zaki, Maha S and Abdel-Salam, Ghada M and Mansour, Lobna A and Selim, Laila A and Abdel-Hadi, Sawsan S and Marzouki, Naima and Ben-Omran, Tawfeg I and Al-Saana, Nouriya A and Sönmez, Fatma M and Celep, Figen and Azam, Matloob and Hill, Kiley J and Collazo, Adrienne and Fenstermaker, Ali G and Gaia Novarino and Akizu, Naiara and Garimella, Kiran V and Sougnez, Carrie L and Russ, Carsten and Gabriel, Stacey B and Gleeson, Joseph G}, journal = {Science Translational Medicine}, number = {138}, publisher = {American Association for the Advancement of Science}, title = {{Exome sequencing can improve diagnosis and alter patient management}}, doi = {10.1126/scitranslmed.3003544}, volume = {4}, year = {2012}, }