774 research outputs found
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
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
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
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
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
The regulatory subunit of PKA-I remains partially structured and undergoes β-aggregation upon thermal denaturation
Background: The regulatory subunit (R) of cAMP-dependent protein kinase (PKA) is a modular flexible protein that responds with large conformational changes to the binding of the effector cAMP. Considering its highly dynamic nature, the protein is rather stable. We studied the thermal denaturation of full-length RIα and a truncated RIα(92-381) that contains the tandem cyclic nucleotide binding (CNB) domains A and B. Methodology/Principal Findings: As revealed by circular dichroism (CD) and differential scanning calorimetry, both RIα proteins contain significant residual structure in the heat-denatured state. As evidenced by CD, the predominantly α-helical spectrum at 25°C with double negative peaks at 209 and 222 nm changes to a spectrum with a single negative peak at 212-216 nm, characteristic of β-structure. A similar α→β transition occurs at higher temperature in the presence of cAMP. Thioflavin T fluorescence and atomic force microscopy studies support the notion that the structural transition is associated with cross-β-intermolecular aggregation and formation of non-fibrillar oligomers. Conclusions/Significance: Thermal denaturation of RIα leads to partial loss of native packing with exposure of aggregation-prone motifs, such as the B' helices in the phosphate-binding cassettes of both CNB domains. The topology of the β-sandwiches in these domains favors inter-molecular β-aggregation, which is suppressed in the ligand-bound states of RIα under physiological conditions. Moreover, our results reveal that the CNB domains persist as structural cores through heat-denaturation. © 2011 Dao et al
Academic Performance and Behavioral Patterns
Identifying the factors that influence academic performance is an essential
part of educational research. Previous studies have documented the importance
of personality traits, class attendance, and social network structure. Because
most of these analyses were based on a single behavioral aspect and/or small
sample sizes, there is currently no quantification of the interplay of these
factors. Here, we study the academic performance among a cohort of 538
undergraduate students forming a single, densely connected social network. Our
work is based on data collected using smartphones, which the students used as
their primary phones for two years. The availability of multi-channel data from
a single population allows us to directly compare the explanatory power of
individual and social characteristics. We find that the most informative
indicators of performance are based on social ties and that network indicators
result in better model performance than individual characteristics (including
both personality and class attendance). We confirm earlier findings that class
attendance is the most important predictor among individual characteristics.
Finally, our results suggest the presence of strong homophily and/or peer
effects among university students
Self-Organization and Regulation of Intrinsically Disordered Proteins with Folded N-Termini
How do mostly disordered proteins coordinate the specific assembly of very large signal transduction protein complexes? A newly emerging hypothesis may provide some clues towards a molecular mechanism
Human spermatogenic failure purges deleterious mutation load from the autosomes and both sex chromosomes, including the gene DMRT1
Gonadal failure, along with early pregnancy loss and perinatal death, may be an important filter that limits the propagation
of harmful mutations in the human population. We hypothesized that men with spermatogenic impairment, a disease with
unknown genetic architecture and a common cause of male infertility, are enriched for rare deleterious mutations
compared to men with normal spermatogenesis. After assaying genomewide SNPs and CNVs in 323 Caucasian men with
idiopathic spermatogenic impairment and more than 1,100 controls, we estimate that each rare autosomal deletion
detected in our study multiplicatively changes a man’s risk of disease by 10% (OR 1.10 [1.04–1.16], p,261023), rare X-linked
CNVs by 29%, (OR 1.29 [1.11–1.50], p,161023), and rare Y-linked duplications by 88% (OR 1.88 [1.13–3.13], p,0.03). By
contrasting the properties of our case-specific CNVs with those of CNV callsets from cases of autism, schizophrenia, bipolar
disorder, and intellectual disability, we propose that the CNV burden in spermatogenic impairment is distinct from the
burden of large, dominant mutations described for neurodevelopmental disorders. We identified two patients with
deletions of DMRT1, a gene on chromosome 9p24.3 orthologous to the putative sex determination locus of the avian ZW
chromosome system. In an independent sample of Han Chinese men, we identified 3 more DMRT1 deletions in 979 cases of
idiopathic azoospermia and none in 1,734 controls, and found none in an additional 4,519 controls from public databases.
The combined results indicate that DMRT1 loss-of-function mutations are a risk factor and potential genetic cause of human
spermatogenic failure (frequency of 0.38% in 1306 cases and 0% in 7,754 controls, p = 6.261025). Our study identifies other
recurrent CNVs as potential causes of idiopathic azoospermia and generates hypotheses for directing future studies on the
genetic basis of male infertility and IVF outcomes.This work was partially funded by the Portuguese Foundation for Science and Technology FCT/MCTES (PIDDAC) and co-financed by European funds (FEDER) through the COMPETE program, research grant PTDC/SAU-GMG/101229/2008. IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology, and Higher Education and is partially supported by FCT. AML is the recipient of a postdoctoral fellowship from FCT (SFRH/BPD/73366/2010). CO is supported by a grant from the United States National Institutes of Health (R01 HD21244), JDS is supported by Damon Runyon Clinical Investigator Award, Alex's Lemonade Stand Foundation Epidemiology Award, and the Eunice Kennedy Shriver Children's Health Research Career Development Award NICHD 5K12HD001410. Support for humans studies and specimens were provided by the NIH/NIDDK George M. O'Brien Center for Kidney Disease Kidney Translational Research Core (P30DK079333) grant to Washington University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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