Perturbation theory vs. simulation for tadpole improvement factors in pure gauge theories

We calculate the mean link in Landau gauge for Wilson and improved SU(3) anisotropic gauge actions, using two loop perturbation theory and Monte Carlo simulation employing an accelerated Langevin algorithm. Twisted boundary conditions are employed, with a twist in all four lattice directions considerably improving the (Fourier accelerated) convergence to an improved lattice Landau gauge. Two loop perturbation theory is seen to predict the mean link extremely well even into the region of commonly simulated gauge couplings and so can be used remove the need for numerical tuning of self-consistent tadpole improvement factors. A three loop perturbative coefficient is inferred from the simulations and is found to be small. We show that finite size effects are small and argue likewise for (lattice) Gribov copies and double Dirac sheets.Comment: 13 pages of revtex

Hybrid configuration content of heavy S-wave mesons

We use the non-relativistic expansion of QCD (NRQCD) on the lattice to study the lowest hybrid configuration contribution to the ground state of heavy S-wave mesons. Using lowest-order lattice NRQCD to create the heavy-quark propagators, we form a basis of ``unperturbed'' S-wave and hybrid states. We then apply the lowest-order coupling of the quark spin and chromomagnetic field at an intermediate time slice to create ``mixed'' correlators between the S-wave and hybrid states. From the resulting amplitudes, we extract the off-diagonal element of our two-state Hamiltonian. Diagonalizing this Hamiltonian gives us the admixture of hybrid configuration within the meson ground state. The present effort represents a continuation of previous work: the analysis has been extended to include lattices of varying spacings, source operators having better overlap with the ground states, and the pseudoscalar (along with the vector) channel. Results are presented for bottomonium ($\Upsilon$, $\eta_b^{}$) using three different sets of quenched lattices. We also show results for charmonium ($J/\psi$, $\eta_c^{}$) from one lattice set, although we note that the non-relativistic approximation is not expected to be very good in this case.Comment: 9 pages, 7 figures, version to appear in Phys Rev

Photon blockade and quantum dynamics in intracavity coherent photoassociation of Bose-Einstein condensates

We demonstrate that a photon blockade effect exists in the intracavity coherent photoassociation of an atomic Bose-Einstein condensate and that the dynamics of the coupled atomic and molecular condensates can only be successfully described by a quantum treatment of all the interacting fields. We show that the usual mean-field calculational approaches give answers that are qualitatively wrong, even for the mean fields. The quantization of the fields gives a degree of freedom that is not present in analogous nonlinear optical processes. The difference between the semiclassical and quantum predictions can actually increase as the three fields increase in size so that there is no obvious classical limit for this process

Multidimensional quantum solitons with nondegenerate parametric interactions: Photonic and Bose-Einstein condensate environments

We consider the quantum theory of three fields interacting via parametric and repulsive quartic couplings. This can be applied to treat photonic chi((2)) and chi((3)) interactions, and interactions in atomic Bose-Einstein condensates or quantum Fermi gases, describing coherent molecule formation together with a-wave scattering. The simplest two-particle quantum solitons or bound-state solutions of the idealized Hamiltonian, without a momentum cutoff, are obtained exactly. They have a pointlike structure in two and three dimensions-even though the corresponding classical theory is nonsingular. We show that the solutions can be regularized with a momentum cutoff. The parametric quantum solitons have much more realistic length scales and binding energies than chi((3)) quantum solitons, and the resulting effects could potentially be experimentally tested in highly nonlinear optical parametric media or interacting matter-wave systems. N-particle quantum solitons and the ground state energy are analyzed using a variational approach. Applications to atomic/molecular Bose-Einstein condensates (BEC's) are given, where we predict the possibility of forming coupled BEC solitons in three space dimensions, and analyze superchemistry dynamics

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Effects of sleep deprivation on neural functioning: an integrative review

Sleep deprivation has a broad variety of effects on human performance and neural functioning that manifest themselves at different levels of description. On a macroscopic level, sleep deprivation mainly affects executive functions, especially in novel tasks. Macroscopic and mesoscopic effects of sleep deprivation on brain activity include reduced cortical responsiveness to incoming stimuli, reflecting reduced attention. On a microscopic level, sleep deprivation is associated with increased levels of adenosine, a neuromodulator that has a general inhibitory effect on neural activity. The inhibition of cholinergic nuclei appears particularly relevant, as the associated decrease in cortical acetylcholine seems to cause effects of sleep deprivation on macroscopic brain activity. In general, however, the relationships between the neural effects of sleep deprivation across observation scales are poorly understood and uncovering these relationships should be a primary target in future research

Genetic drivers of kidney defects in the digeorge syndrome

BACKGROUND The DiGeorge syndrome, the most common of the microdeletion syndromes, affects multiple organs, including the heart, the nervous system, and the kidney. It is caused by deletions on chromosome 22q11.2; the genetic driver of the kidney defects is unknown. METHODS We conducted a genomewide search for structural variants in two cohorts: 2080 patients with congenital kidney and urinary tract anomalies and 22,094 controls. We performed exome and targeted resequencing in samples obtained from 586 additional patients with congenital kidney anomalies. We also carried out functional studies using zebrafish and mice. RESULTS We identified heterozygous deletions of 22q11.2 in 1.1% of the patients with congenital kidney anomalies and in 0.01% of population controls (odds ratio, 81.5; P = 4.5×1014). We localized the main drivers of renal disease in the DiGeorge syndrome to a 370-kb region containing nine genes. In zebrafish embryos, an induced loss of function in snap29, aifm3, and crkl resulted in renal defects; the loss of crkl alone was sufficient to induce defects. Five of 586 patients with congenital urinary anomalies had newly identified, heterozygous protein-Altering variants, including a premature termination codon, in CRKL. The inactivation of Crkl in the mouse model induced developmental defects similar to those observed in patients with congenital urinary anomalies. CONCLUSIONS We identified a recurrent 370-kb deletion at the 22q11.2 locus as a driver of kidney defects in the DiGeorge syndrome and in sporadic congenital kidney and urinary tract anomalies. Of the nine genes at this locus, SNAP29, AIFM3, and CRKL appear to be critical to the phenotype, with haploinsufficiency of CRKL emerging as the main genetic driver

Pteridófitas da Serra Negra, Minas Gerais, Brasil

Este trabalho apresenta uma lista de espécies de pteridófitas que ocorrem na Serra Negra, Minas Gerais. A serra está inserida no complexo da Serra da Mantiqueira situada entre Rio Preto, Lima Duarte, Santa Bárbara do Monte Verde e Olaria, tendo seus limites nos pontos 21º58'11"S 43º53'21" W, 22º01'46,4" S 43º52'31,5" W, 21º58'21,4" S 43º50'06,5" W e 21º58'53" S 43º56'08" W. A vegetação da serra é formada por um mosaico de fitofisionomias, sendo encontradas formações florestais (florestas ombrófilas e semidecíduas) e campestres (campos rupestres). O inventário florístico foi realizado entre os anos de 2003 e 2008, em excursões mensais para coleta de amostras e registro de dados. Na serra foram registradas 209 táxons infragenéricos distribuídas em 24 famílias e 75 gêneros. As famílias com maior número de espécies foram Polypodiaceae (40), Dryopteridaceae (33) e Pteridaceae (25). A maioria das espécies (109) foi encontrada ocorrendo exclusivamente no interior de floresta. Em relação ao hábito, 69 espécies foram encontradas exclusivamente como terrestres, 37 como rupícolas ou terrestres e 32 exclusivamente epífitas. Este trabalho revela uma elevada riqueza de pteridófitas na região e indica a importância de estudos desta natureza na conservação e manejo das pteridófitas em Minas Gerais.This work presents an inventory of pteridophyte species that occur in the Serra Negra, of Minas Gerais. The area is part of the Mantiqueira Range, and is situated between the coordinates 21º58'11"S 43º53'21" W, 22º01'4.4" S, 43º52'31.5" W, 21º58'21.4" S, 43º50'06.5" W and 21º58'53" S, 43º56'08" W. The vegetation in the Serra Negra is characterized by a mosaic of different phytophysiognomies, divided into forests (evergreen and seasonal semideciduous forests) and open formations (rocky grasslands). The inventory was carried out from 2003 to 2008, during monthly excursions to collect botanical material and data in the study area. A total of 209 species, distributed in 24 families and 75 genera, were recorded. The families with the highest number of species were Polypodiaceae (40), Dryopteridaceae (33) and Pteridaceae (25). More than the half (110) of the inventoried species were recorded exclusively in the forests formations. Sixty-nine species were terrestrial, 37 were saxicolous or terrestrial and 32 were epiphytes. This work shows that this region is rich in ferns and reveals the importance of this kind of study for conservation and management of pteridophytes in the state of Minas Gerais

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy