4,023 research outputs found
Distinct Contributions of JNK and p38 to Chromium Cytotoxicity and Inhibition of Murine Embryonic Stem Cell Differentiation
Optically Mapping Multiple Bacterial Genomes Simultaneously in a Single Run
Optical mapping of bacterial chromosomes provides an unambiguous low-resolution sequence scaffold of the entire chromosome. In comparison to some techniques, such as pulse field gel electrophoresis, cost and throughput limit the application of this technique outside of genome finishing. We have demonstrated the production of multiple bacterial maps using a single set of consumables; this significantly reduces the time and expense of map production
Holographic Duals of Near-extremal Reissner-Nordstrom Black Holes
We consider the description of
Reissner-Nordstr{\o}m black holes by studying their uplifted counterparts in
five dimensions. Assuming a natural size of the extra dimension, the near
horizon geometries for the extremal limit are exactly . We compute the scattering amplitude of a scalar field, with a
mode near threshold of frequency and extra dimensional momentum, by a near
extremal uplifted black hole. The absorption cross section agrees with the two
point function of the CFT dual to the scalar field.Comment: reference added, improper statements corrected, 17 pages, no figure
Clustering and Alignment of Polymorphic Sequences for HLA-DRB1 Genotyping
Located on Chromosome 6p21, classical human leukocyte antigen genes are highly polymorphic. HLA alleles associate with a variety of phenotypes, such as narcolepsy, autoimmunity, as well as immunologic response to infectious disease. Moreover, high resolution genotyping of these loci is critical to achieving long-term survival of allogeneic transplants. Development of methods to obtain high resolution analysis of HLA genotypes will lead to improved understanding of how select alleles contribute to human health and disease risk. Genomic DNAs were obtained from a cohort of n = 383 subjects recruited as part of an Ulcerative Colitis study and analyzed for HLA-DRB1. HLA genotypes were determined using sequence specific oligonucleotide probes and by next-generation sequencing using the Roche/454 GSFLX instrument. The Clustering and Alignment of Polymorphic Sequences (CAPSeq) software application was developed to analyze next-generation sequencing data. The application generates HLA sequence specific 6-digit genotype information from next-generation sequencing data using MUMmer to align sequences and the R package diffusionMap to classify sequences into their respective allelic groups. The incorporation of Bootstrap Aggregating, Bagging to aid in sorting of sequences into allele classes resulted in improved genotyping accuracy. Using Bagging iterations equal to 60, the genotyping results obtained using CAPSeq when compared with sequence specific oligonucleotide probe characterized 4-digit genotypes exhibited high rates of concordance, matching at 759 out of 766 (99.1%) alleles. © 2013 Ringquist et al
Ultrasonic Characterization of Porosity in Composites
The determination of levels of porosity is important in the engineering uses of graphite fiber/polymer matrix composites, since the interlaminar shear strength can be greatly reduced by excessive porosity [1]. Research in making nondestructive evaluations using ultrasonics as the probing energy has taken many directions. Hsu [2] has successfully modeled the frequency dependent attenuation to predict porosity levels in composites. Kline [3] has extended the work of Hashsin and Rosen [4] to determine the porosity and fiber volume fraction of composites by solving for the elastic coefficients of the composite structure. The propagation of leaky Lamb waves [5] has also been used to model porosity levels
Checkpoints are blind to replication restart and recombination intermediates that result in gross chromosomal rearrangements
Replication fork inactivation can be overcome by homologous recombination, but this can cause gross chromosomal rearrangements that subsequently missegregate at mitosis, driving further chromosome instability. It is unclear when the chromosome rearrangements are generated and whether individual replication problems or the resulting recombination intermediates delay the cell cycle. Here we have investigated checkpoint activation during HR-dependent replication restart using a site-specific replication fork-arrest system. Analysis during a single cell cycle shows that HR-dependent replication intermediates arise in S phase, shortly after replication arrest, and are resolved into acentric and dicentric chromosomes in G2. Despite this, cells progress into mitosis without delay. Neither the DNA damage nor the intra-S phase checkpoints are activated in the first cell cycle, demonstrating that these checkpoints are blind to replication and recombination intermediates as well as to rearranged chromosomes. The dicentrics form anaphase bridges that subsequently break, inducing checkpoint activation in the second cell cycle
Semiparametric Multivariate Accelerated Failure Time Model with Generalized Estimating Equations
The semiparametric accelerated failure time model is not as widely used as
the Cox relative risk model mainly due to computational difficulties. Recent
developments in least squares estimation and induced smoothing estimating
equations provide promising tools to make the accelerate failure time models
more attractive in practice. For semiparametric multivariate accelerated
failure time models, we propose a generalized estimating equation approach to
account for the multivariate dependence through working correlation structures.
The marginal error distributions can be either identical as in sequential event
settings or different as in parallel event settings. Some regression
coefficients can be shared across margins as needed. The initial estimator is a
rank-based estimator with Gehan's weight, but obtained from an induced
smoothing approach with computation ease. The resulting estimator is consistent
and asymptotically normal, with a variance estimated through a multiplier
resampling method. In a simulation study, our estimator was up to three times
as efficient as the initial estimator, especially with stronger multivariate
dependence and heavier censoring percentage. Two real examples demonstrate the
utility of the proposed method
The Sleeping Brain's Influence on Verbal Memory: Boosting Resistance to Interference
Memories evolve. After learning something new, the brain initiates a complex set of post-learning processing that facilitates recall (i.e., consolidation). Evidence points to sleep as one of the determinants of that change. But whenever a behavioral study of episodic memory shows a benefit of sleep, critics assert that sleep only leads to a temporary shelter from the damaging effects of interference that would otherwise accrue during wakefulness. To evaluate the potentially active role of sleep for verbal memory, we compared memory recall after sleep, with and without interference before testing. We demonstrated that recall performance for verbal memory was greater after sleep than after wakefulness. And when using interference testing, that difference was even more pronounced. By introducing interference after sleep, this study confirms an experimental paradigm that demonstrates the active role of sleep in consolidating memory, and unmasks the large magnitude of that benefit
Quantifying Inactive Lithium in Lithium Metal Batteries
Inactive lithium (Li) formation is the immediate cause of capacity loss and
catastrophic failure of Li metal batteries. However, the chemical component and
the atomic level structure of inactive Li have rarely been studied due to the
lack of effective diagnosis tools to accurately differentiate and quantify Li+
in solid electrolyte interphase (SEI) components and the electrically isolated
unreacted metallic Li0, which together comprise the inactive Li. Here, by
introducing a new analytical method, Titration Gas Chromatography (TGC), we can
accurately quantify the contribution from metallic Li0 to the total amount of
inactive Li. We uncover that the Li0, rather than the electrochemically formed
SEI, dominates the inactive Li and capacity loss. Using cryogenic electron
microscopies to further study the microstructure and nanostructure of inactive
Li, we find that the Li0 is surrounded by insulating SEI, losing the electronic
conductive pathway to the bulk electrode. Coupling the measurements of the Li0
global content to observations of its local atomic structure, we reveal the
formation mechanism of inactive Li in different types of electrolytes, and
identify the true underlying cause of low Coulombic efficiency in Li metal
deposition and stripping. We ultimately propose strategies to enable the highly
efficient Li deposition and stripping to enable Li metal anode for next
generation high energy batteries
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