Annals Impact Factor 1.67. Welcome to the IF club: achievement and challenges

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Strong Correlation Between Noise Features at Low Frequency and the Kilohertz QPOs in the X-Ray Binary 4U 1728-34

We study the timing properties of the low mass X-ray binary 4U 1728-34 using recently released data from the Rossi X-Ray Timing Explorer. This binary, like many others with accreting neutron stars, is known to exhibit strong quasi-periodic oscillations (QPOs) of its X-ray flux near 1 kHz. In addition to the kilohertz QPOs, the Fourier power spectra show a broken power law noise component, with a break frequency between 1 and 50 Hz, and a Lorentzian between 10 and 50 Hz. We find that the frequencies of the break and the low-frequency Lorentzian are well correlated with the frequencies of the kilohertz QPOs. The slope of the correlation is similar to that expected if the oscillations are due to relativistic frame dragging (Lense-Thirring precession) in the inner accretion disk (Stella & Vietri 1998). The correlation is also nearly identical to the one found in Z-sources between the the well known QPOs on the horizontal branch and the kilohertz QPOs, suggesting that the low frequency oscillations are a similar phenomenon in these sources. The frequency of the break in the power spectra is also correlated with the frequencies of the kilohertz QPOs. As previously noted for the similar binaries 4U 1608-50 and 4U 1705-44, this broken power law component closely resembles that of black hole candidates in the low state, where the break frequency is taken as an indicator of mass accretion rate. The relation between break frequency and kilohertz QPO frequency thus provides additional proof that the frequency of the kilohertz QPOs increases with mass accretion rate.Comment: ApJL in press, see the 'QPO page' at http://www.astro.uva.nl/ecford/qpos.htm

A support vector machine based test for incongruence between sets of trees in tree space

BACKGROUND: The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene trees may have been influenced by other evolutionary processes such as selection, gene duplication, or horizontal gene transfer. RESULTS: Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributions of gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approach maps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) to measure the separation between two sets of pre-defined trees. We use a permutation test to assess the significance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to the comparison of gene trees simulated within different species trees across a range of species tree depths. Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect very small differences between two set of gene trees generated under different species trees. Our statistical test can also include tree reconstruction into its test framework through a variety of phylogenetic optimality criteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the form of receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detection of differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, it controlled false positive and false negative rates very well, indicating a high degree of accuracy. CONCLUSIONS: The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it an applicable test for any scenario where evolutionary or other factors can lead to trees with different multi-dimensional distributions. The software GeneOut is freely available under the GNU public license

A rare case of isolated duodenal metastases from hepatocellular carcinoma associated with p53 and ki-67 expression: a case report

Hepatocellular carcinoma (HCC) is the most common primary tumor of the liver worldwide. The incidence of HCC is increasing in North America secondary to rises in chronic liver disease from alcohol abuse and viral hepatitis. HCC most commonly metastasizes hematogenously or through lymphatics to the lungs and regional lymph nodes. Involvement of small bowel is rare and typically results from direct invasion and extension. We examined the molecular features related to this extremely rare case of isolated duodenal metastasis of HCC and noted p53 and Ki-67 positive staining. Here, we review the possible molecular and immunohistochemical studies that may aid definitive diagnosis and the evidence for the management of metastatic hepatocellular carcinoma

Recent Shifts in the Occurrence, Cause, and Magnitude of Animal Mass Mortality Events

Mass mortality events (MMEs) are rapidly occurring catastrophic demographic events that punctuate background mortality levels. Individual MMEs are staggering in their observed magnitude: re- moving more than 90% of a population, resulting in the death of more than a billion individuals, or producing 700 million tons of dead biomass in a single event. Despite extensive documentation of individual MMEs, we have no understanding of the major features characterizing the occurrence and magnitude of MMEs, their causes, or trends through time. Thus, no framework exists for contextualizing MMEs in the wake of ongoing global and regional perturbations to natural systems. Here we present an analysis of 727 published MMEs from across the globe, affecting 2,407 animal populations. We show that the magnitude of MMEs has been intensifying for birds, fishes, and marine invertebrates; invariant for mammals; and decreasing for reptiles and amphibians. These shifts in magnitude proved robust when we accounted for an increase in the occurrence of MMEs since 1940. However, it remains unclear whether the increase in the occurrence of MMEs represents a true pattern or simply a perceived increase. Regardless, the increase in MMEs appears to be associated with a rise in disease emergence, biotoxicity, and events produced by multiple interacting stressors, yet temporal trends in MME causes varied among taxa and may be associated with increased de- tectability. In addition, MMEs with the largest magnitudes were those that resulted from multiple stressors, starvation, and disease. These results advance our understanding of rare demographic processes and their relationship to global and regional perturba- tions to natural systems

Gravitational Waves from Core Collapse Supernovae

We present the gravitational wave signatures for a suite of axisymmetric core collapse supernova models with progenitors masses between 12 and 25 solar masses. These models are distinguished by the fact they explode and contain essential physics (in particular, multi-frequency neutrino transport and general relativity) needed for a more realistic description. Thus, we are able to compute complete waveforms (i.e., through explosion) based on non-parameterized, first-principles models. This is essential if the waveform amplitudes and time scales are to be computed more precisely. Fourier decomposition shows that the gravitational wave signals we predict should be observable by AdvLIGO across the range of progenitors considered here. The fundamental limitation of these models is in their imposition of axisymmetry. Further progress will require counterpart three-dimensional models.Comment: 10 pages, 5 figure

A novel method to allow noninvasive, longitudinal imaging of the murine immune system in vivo

In vivo imaging has revolutionized understanding of the spatiotemporal complexity that subserves the generation of successful effector and regulatory immune responses. Until now, invasive surgery has been required for microscopic access to lymph nodes (LNs), making repeated imaging of the same animal impractical and potentially affecting lymphocyte behavior. To allow longitudinal in vivo imaging, we conceived the novel approach of transplanting LNs into the mouse ear pinna. Transplanted LNs maintain the structural and cellular organization of conventional secondary lymphoid organs. They participate in lymphocyte recirculation and exhibit the capacity to receive and respond to local antigenic challenge. The same LN could be repeatedly imaged through time without the requirement for surgical exposure, and the dynamic behavior of the cells within the transplanted LN could be characterized. Crucially, the use of blood vessels as fiducial markers also allowed precise re-registration of the same regions for longitudinal imaging. Thus, we provide the first demonstration of a method for repeated, noninvasive, in vivo imaging of lymphocyte behavior