On localization in holomorphic equivariant cohomology

We prove a localization formula for a "holomorphic equivariant cohomology" attached to the Atiyah algebroid of an equivariant holomorphic vector bundle. This generalizes Feng-Ma, Carrell-Liebermann, Baum-Bott and K. Liu's localization formulas.Comment: 16 pages. Completely rewritten, new title. v3: Minor changes in the exposition. v4: final version to appear in Centr. Eur. J. Mat

Evidence for the characterisation of the C-H …∏ interaction as a weak hydrogen bond: toluene and chlorobenzene solvates of 2,3,7,8-tetraphenyl-1,9,10-anthyridine

The crystal structures of the toluene and chlorobenzene solvates of 2,3,7,8-tetraphenyl-1,9,10-anthyridine are nearly identical save for differences in the mode of solvent inclusion; these differences have an important bearing on the nature of the C-H … ∏ interactions in these structures

Fibronectin molecule visualized in electron microscopy: a long, thin, flexible strand

We have determined the structure of plasma fibronectin by electron microscopy of shadowed specimens. the 440,000 molecular weight, dimeric molecule appears to be a long, thin, highly flexible strand. The contour length of the most extended molecules is 160 nm, but a distribution of lengths down to 120 nm was observed, indicating flexibility in extension as well as in bending. The average diameter of the strand is 2 nm and there are no large globular domains. the large fragments produced by limited digestion with plasmin are not globular domains but are segments of the strand, whose length corresponds to the molecular weight of the polypeptide chain. We conclude that each polypeptide chain of the dimeric molecule spans half the length of the strand, with their carboxyl termini joined at the center of the strand and their amino termini at the ends. This model is supported by images of fibronectin-fibrinogen complexes, in which the fibrinogen is always attached to an end of the fibronectin strand

Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3

Abstract Background The antizyme family is a group of small proteins that play a role in cell growth and division by regulating the biosynthesis of polyamines (putrescine, spermidine, spermine). Antizymes regulate polyamine levels primarily through binding ornithine decarboxylase (ODC), an enzyme key to polyamine production, and targeting ODC for destruction by the 26S proteosome. Ornithine decarboxylase antizyme 3 (OAZ3) is a testis-specific antizyme paralog and the only antizyme expressed in the mid to late stages of spermatogenesis. Methods To see if mutations in the OAZ3 gene are responsible for some cases of male infertility, we sequenced and evaluated the genomic DNA of 192 infertile men, 48 men of known paternity, and 34 African aborigines from the Mbuti tribe in the Democratic Republic of the Congo. The coding sequence of OAZ3 was further screened for polymorphisms by SSCP analysis in the infertile group and an additional 250 general population controls. Identified polymorphisms in the OAZ3 gene were further subjected to a haplotype analysis using PHASE 2.02 and Arlequin 2.0 software programs. Results A total of 23 polymorphisms were identified in the promoter, exons or intronic regions of OAZ3. The majority of these fell within a region of less than two kilobases. Two of the polymorphisms, -239 A/G in the promoter and 4280 C/T, a missense polymorphism in exon 5, may show evidence of association with male infertility. Haplotype analysis identified 15 different haplotypes, which can be separated into two divergent clusters. Conclusion Mutations in the OAZ3 gene are not a common cause of male infertility. However, the presence of the two divergent haplotypes at high frequencies in all three of our subsamples (infertile, control, African) suggests that they have been maintained in the genome by balancing selection, which was supported by a test of Tajima's D statistic. Evidence for natural selection in this region implies that these haplotypes may be associated with a trait other than infertility. This trait may be related to another function of OAZ3 or a region in tight linkage disequilibrium to the gene.</p

Degenerate flag varieties: moment graphs and Schr\"oder numbers

We study geometric and combinatorial properties of the degenerate flag varieties of type A. These varieties are acted upon by the automorphism group of a certain representation of a type A quiver, containing a maximal torus T. Using the group action, we describe the moment graphs, encoding the zero- and one-dimensional T-orbits. We also study the smooth and singular loci of the degenerate flag varieties. We show that the Euler characteristic of the smooth locus is equal to the large Schr\"oder number and the Poincar\'e polynomial is given by a natural statistics counting the number of diagonal steps in a Schr\"oder path. As an application we obtain a new combinatorial description of the large and small Schr\"oder numbers and their q-analogues.Comment: 25 page

The nil Hecke ring and singularity of Schubert varieties

We give a criterion for smoothness of a point in any Schubert variety in any G/B in terms of the nil Hecke ring.Comment: AMSTE

Design patterns for the development of electronic health record-driven phenotype extraction algorithms

AbstractBackgroundDesign patterns, in the context of software development and ontologies, provide generalized approaches and guidance to solving commonly occurring problems, or addressing common situations typically informed by intuition, heuristics and experience. While the biomedical literature contains broad coverage of specific phenotype algorithm implementations, no work to date has attempted to generalize common approaches into design patterns, which may then be distributed to the informatics community to efficiently develop more accurate phenotype algorithms.MethodsUsing phenotyping algorithms stored in the Phenotype KnowledgeBase (PheKB), we conducted an independent iterative review to identify recurrent elements within the algorithm definitions. We extracted and generalized recurrent elements in these algorithms into candidate patterns. The authors then assessed the candidate patterns for validity by group consensus, and annotated them with attributes.ResultsA total of 24 electronic Medical Records and Genomics (eMERGE) phenotypes available in PheKB as of 1/25/2013 were downloaded and reviewed. From these, a total of 21 phenotyping patterns were identified, which are available as an online data supplement.ConclusionsRepeatable patterns within phenotyping algorithms exist, and when codified and cataloged may help to educate both experienced and novice algorithm developers. The dissemination and application of these patterns has the potential to decrease the time to develop algorithms, while improving portability and accuracy

GALEX J201337.6+092801: The lowest gravity subdwarf B pulsator

We present the recent discovery of a new subdwarf B variable (sdBV), with an exceptionally low surface gravity. Our spectroscopy of J20136+0928 places it at Teff = 32100 +/- 500, log(g) = 5.15 +/- 0.10, and log(He/H) = -2.8 +/- 0.1. With a magnitude of B = 12.0, it is the second brightest V361 Hya star ever found. Photometry from three different observatories reveals a temporal spectrum with eleven clearly detected periods in the range 376 to 566 s, and at least five more close to our detection limit. These periods are unusually long for the V361 Hya class of short-period sdBV pulsators, but not unreasonable for p- and g-modes close to the radial fundamental, given its low surface gravity. Of the ~50 short period sdB pulsators known to date, only a single one has been found to have comparable spectroscopic parameters to J20136+0928. This is the enigmatic high-amplitude pulsator V338 Ser, and we conclude that J20136+0928 is the second example of this rare subclass of sdB pulsators located well above the canonical extreme horizontal branch in the HR diagram.Comment: 5 pages, accepted for publication in ApJ Letter

Paternal effects on early embryogenesis

Historically, less attention has been paid to paternal effects on early embryogenesis than maternal effects. However, it is now apparent that certain male factor infertility phenotypes are associated with increased DNA fragmentation and/or chromosome aneuploidies that may compromise early embryonic development. In addition, there is a growing body of evidence that the fertilizing sperm has more function than just carrying an intact, haploid genome. The paternally inherited centrosome is essential for normal fertilization, and the success of higher order chromatin packaging may impact embryogenesis. Epigenetic modifications of sperm chromatin may contribute to the reprogramming of the genome, and sperm delivered mRNA has also been hythesized to be necessary for embryogenesis. There is less information about the epigenetic factors affecting embryogenesis than genetic factors, but the epigenetics of gamete and early embryogenesis is a rapidly advancing field