A difference boosting neural network for automated star-galaxy classification

In this paper we describe the use of a new artificial neural network, called the difference boosting neural network (DBNN), for automated classification problems in astronomical data analysis. We illustrate the capabilities of the network by applying it to star galaxy classification using recently released, deep imaging data. We have compared our results with classification made by the widely used Source Extractor (SExtractor) package. We show that while the performance of the DBNN in star-galaxy classification is comparable to that of SExtractor, it has the advantage of significantly higher speed and flexibility during training as well as classification.Comment: 9 pages, 1figure, 7 tables, accepted for publication in Astronomy and Astrophysic

Connections Between Local and Global Turbulence in Accretion Disks

We analyze a suite of global magnetohydrodynamic (MHD) accretion disk simulations in order to determine whether scaling laws for turbulence driven by the magnetorotational instability, discovered via local shearing box studies, are globally robust. The simulations model geometrically-thin disks with zero net magnetic flux and no explicit resistivity or viscosity. We show that the local Maxwell stress is correlated with the self-generated local vertical magnetic field in a manner that is similar to that found in local simulations. Moreover, local patches of vertical field are strong enough to stimulate and control the strength of angular momentum transport across much of the disk. We demonstrate the importance of magnetic linkages (through the low-density corona) between different regions of the disk in determining the local field, and suggest a new convergence requirement for global simulations -- the vertical extent of the corona must be fully captured and resolved. Finally, we examine the temporal convergence of the average stress, and show that an initial long-term secular drift in the local flux-stress relation dies away on a time scale that is consistent with turbulent mixing of the initial magnetic field.Comment: 8 Pages, 7 Figures ApJ, In Pres

On the interaction of Jupiter's Great Red Spot and zonal jet streams

In this paper, Jupiter's Great Red Spot (GRS) is used to determine properties of the Jovian atmosphere that cannot otherwise be found. These properties include the potential vorticity of the GRS and its neighboring jet streams, the shear imposed on the GRS by the jet streams, and the vertical entropy gradient (i.e., Rossby deformation radius). The cloud cover of the GRS, which is often used to define the GRS's area and aspect ratio, is found to differ significantly from the region of the GRS's potential vorticity anomaly. The westward-going jet stream to the north of the GRS and the eastward-going jet stream to its south are each found to have a large potential vorticity ``jump''. The jumps have opposite sign and as a consequence of their interaction with the GRS, the shear imposed on the GRS is reduced. The east-west to north-south aspect ratio of the GRS's potential vorticity anomaly depends on the ratio of the imposed shear to the strength of the anomaly. The aspect ratio is found to be $\approx$2:1, but without the opposing jumps it would be much greater. The GRS's high-speed collar and quiescent interior require that the potential vorticity in the interior be approximately half that in the collar. No other persistent geophysical vortex has a significant minimum of potential vorticity in its interior and laboratory vortices with such a minimum are unstable.Comment: Manuscript accepted to Journal of the Atmospheric Sciences, March 2007. v2: minor stylistic changes (after journal proof reading

Treatment Patterns and Health Resource Utilization Among Patients Diagnosed With Early Stage Resected Non–Small Cell Lung Cancer at US Community Oncology Practices

AbstractBackgroundPlatin-based adjuvant chemotherapy has extended survival in clinical trials in patients with completely resected non–small cell lung cancer (NSCLC). There are few data on the use of adjuvant therapy in community-based clinical practice in the United States.Materials and MethodsThis was a retrospective observational study using electronic medical record and billing data collected during routine care at US community oncology sites in the Vector Oncology Data Warehouse between January 2007 and January 2014. Patients aged ≥ 18 years with a primary diagnosis of stage IB to IIIA NSCLC were eligible if they had undergone surgical resection. Treatment patterns, health care resource use, and cost were recorded, stratified by stage at diagnosis.ResultsThe study included 609 patients (mean age, 64.8 years, 52.9% male), of whom 215 had stage IB disease, 130 stage IIA/II, 110 stage IIB, and 154 stage IIIA. Adjuvant systemic therapy after resection was provided to 345 (56.7%) of 609 patients, with lower use in patients with stage IB disease (39.1%) than stage II to IIIA disease (64.9-68.2%) (P < .0001). The most common adjuvant regimen at all stages was the combination of carboplatin and paclitaxel. There were no statistically significant differences in office visits or incidence of hospitalization by disease stage. During adjuvant treatment, the total monthly median cost per patient was $17,389.75 (interquartile range,$8,815.61 to $23,360.85).ConclusionAdjuvant systemic therapy was used in some patients with stage IB NSCLC and in the majority of patients with stage IIA to IIIA disease. There were few differences in regimen or health care resource use by disease stage

Fold Designability, Distribution, and Disease

Fold designability has been estimated by the number of families contained in that fold. Here, we show that among orthologous proteins, sequence divergence is higher for folds with greater numbers of families. Folds with greater numbers of families also tend to have families that appear more often in the proteome and greater promiscuity (the number of unique “partner” folds that the fold is found with within the same protein). We also find that many disease-related proteins have folds with relatively few families. In particular, a number of these proteins are associated with diseases occurring at high frequency. These results suggest that family counts reflect how certain structures are distributed in nature and is an important characteristic associated with many human diseases

Non-peptidic antagonists of the CGRP receptor, BIBN4096BS and MK-0974, interact with the calcitonin receptor-like receptor via methionine-42 and RAMP1 via tryptophan-74

The receptor for calcitonin gene-related peptide (CGRP) has been the target for the development of novel small molecule antagonists for the treatment of migraine. Two such antagonists, BIBN4096BS and MK-0974, have shown great promise in clinical trials and hence a deeper understanding of the mechanism of their interaction with the receptor is now required. The structure of the CGRP receptor is unusual since it is comprised of a hetero-oligomeric complex between the calcitonin receptor-like receptor (CRL) and an accessory protein (RAMP1). Both the CLR and RAMP1 components have extracellular domains which interact with each other and together form part of the peptide-binding site. It seems likely that the antagonist binding site will also be located on the extracellular domains and indeed Trp-74 of RAMP1 has been shown to form part of the binding site for BIBN4096BS. However, despite a chimeric study demonstrating the role of the N-terminal domain of CLR in antagonist binding, no specific residues have been identified. Here we carry out a mutagenic screen of the extreme N-terminal domain of CLR (residues 23-63) and identify a mutant, Met-42-Ala, which displays 48-fold lower affinity for BIBN4096BS and almost 900-fold lower affinity for MK-0974. In addition, we confirm that the Trp-74-Lys mutation at human RAMP1 reduces BIBN4096BS affinity by over 300-fold and show for the first time a similar effect for MK-0974 affinity. The data suggest that the non-peptide antagonists occupy a binding site close to the interface of the N-terminal domains of CLR and RAMP1