The aperiodic X-ray variability of the accreting millisecond pulsar SAX J1808.4-3658

We have studied the aperiodic variability of the 401 Hz accreting millisecond X-ray pulsar SAX J1808.4-3658 using the complete data set collected with the Rossi X-ray Timing Explorer over 14 years of observation. The source shows a number of exceptional aperiodic timing phenomena that are observed against a backdrop of timing properties that show consistent trends in all five observed outbursts and closely resemble those of other atoll sources. We performed a detailed study of the enigmatic ~410 Hz QPO, which has only been observed in SAX J1808.4-3658. We find that it appears only when the upper kHz QPO frequency is less than the 401 Hz spin frequency. The difference between the ~410 Hz QPO frequency and the spin frequency follows a similar frequency correlation as the low frequency power spectral components, suggesting that the ~410 Hz QPO is a retrograde beat against the spin frequency of a rotational phenomenon in the 9 Hz range. Comparing this 9 Hz beat feature with the Low-Frequency QPO in SAX J1808.4-3658 and other neutron star sources, we conclude that these two might be part of the same basic phenomenon. We suggest that they might be caused by retrograde precession due to a combination of relativistic, classical and magnetic torques. Additionally we present two new measurements of the lower kHz QPO, allowing us, for the first time, to measure the frequency evolution of the twin kHz QPOs in this source. The twin kHz QPOs are seen to move together over 150 Hz, maintaining a centroid frequency separation of $(0.446 \pm 0.009) \nu_{spin}$.Comment: 18 pages, 9 figures, 7 tables. Accepted for publication in Ap

Pulse amplitude depends on kHz QPO frequency in the accreting millisecond pulsar SAX J1808.4-3658

We study the relation between the 300-700 Hz upper kHz quasi-periodic oscillation (QPO) and the 401 Hz coherent pulsations across all outbursts of the accreting millisecond X-ray pulsar SAX J1808.4-3658 observed with the Rossi X-ray Timing Explorer. We find that the pulse amplitude systematically changes by a factor of ~2 when the upper kHz QPO frequency passes through 401 Hz: it halves when the QPO moves to above the spin frequency and doubles again on the way back. This establishes for the first time the existence of a direct effect of kHz QPOs on the millisecond pulsations and provides a new clue to the origin of the upper kHz QPO. We discuss several scenarios and conclude that while more complex explanations can not formally be excluded, our result strongly suggests that the QPO is produced by azimuthal motion at the inner edge of the accretion disk, most likely orbital motion. Depending on whether this azimuthal motion is faster or slower than the spin, the plasma then interacts differently with the neutron-star magnetic field. The most straightforward interpretation involves magnetospheric centrifugal inhibition of the accretion flow that sets in when the upper kHz QPO becomes slower than the spin.Comment: 5 pages, 4 figures, Accepted for publication in ApJ

The stochastic X-ray variability of the accreting millisecond pulsar MAXI J0911-655

In this work, I report on the stochastic X-ray variability of the 340 Hz accreting millisecond pulsar MAXI J0911–655. Analyzing pointed observations of the XMM-Newton and NuSTAR observatories, I find that the source shows broad band-limited stochastic variability in the 0.01-10 Hz range with a total fractional variability of ~24% rms in the 0.4-3 keV energy band that increases to ~40% rms in the 3–10 keV band. Additionally, a pair of harmonically related quasi-periodic oscillations (QPOs) are discovered. The fundamental frequency of this harmonic pair is observed between frequencies of 62 and 146 mHz. Like the band-limited noise, the amplitudes of the QPOs show a steep increase as a function of energy; this suggests that they share a similar origin, likely the inner accretion flow. Based on their energy dependence and frequency relation with respect to the noise terms, the QPOs are identified as low-frequency oscillations and discussed in terms of the Lense–Thirring precession model

Quasi-periodic pulse amplitude modulation in the accreting millisecond pulsar IGR J00291+5934

We introduce a new method for analysing the aperiodic variability of coherent pulsations in accreting millisecond X-ray pulsars. Our method involves applying a complex frequency correction to the time-domain light curve, allowing for the aperiodic modulation of the pulse amplitude to be robustly extracted in the frequency domain. We discuss the statistical properties of the resulting modulation spectrum and show how it can be correlated with the non-pulsed emission to determine if the periodic and aperiodic variability are coupled processes. Using this method, we study the 598.88 Hz coherent pulsations of the accreting millisecond X-ray pulsar IGR J00291+5934 as observed with the Rossi X-ray Timing Explorer and XMM-Newton. We demonstrate that our method easily confirms the known coupling between the pulsations and a strong 8 mHz QPO in XMM-Newton observations. Applying our method to the RXTE observations, we further show, for the first time, that the much weaker 20 mHz QPO and its harmonic are also coupled the pulsations. We discuss the implications of this coupling and indicate how it may be used to extract new information on the underlying accretion process.Comment: 12 pages, 7 figures, 1 table. Accepted for publication in Ap

The magnetic-field strengths of accreting millisecond pulsars

In this work we have estimated upper and lower limits to the strength of the magnetic dipole moment of all 14 accreting millisecond X-ray pulsars observed with the Rossi X-ray Timing Explorer (RXTE). For each source we searched the archival RXTE data for the highest and lowest flux levels with a significant detection of pulsations. We assume these flux levels to correspond to the closest and farthest location of the inner edge of the accretion disc at which channelled accretion takes place. By estimating the accretion rate from the observed luminosity at these two flux levels, we place upper and lower limits on the magnetic dipole moment of the neutron star, using assumptions from standard magnetospheric accretion theory. Finally, we discuss how our field strength estimates can be further improved as more information on these pulsars is obtained. Key words: stars: magnetic field – stars: neutron – pulsars: general – X-rays: binar

Context-aware stacked convolutional neural networks for classification of breast carcinomas in whole-slide histopathology images

Automated classification of histopathological whole-slide images (WSI) of breast tissue requires analysis at very high resolutions with a large contextual area. In this paper, we present context-aware stacked convolutional neural networks (CNN) for classification of breast WSIs into normal/benign, ductal carcinoma in situ (DCIS), and invasive ductal carcinoma (IDC). We first train a CNN using high pixel resolution patches to capture cellular level information. The feature responses generated by this model are then fed as input to a second CNN, stacked on top of the first. Training of this stacked architecture with large input patches enables learning of fine-grained (cellular) details and global interdependence of tissue structures. Our system is trained and evaluated on a dataset containing 221 WSIs of H&E stained breast tissue specimens. The system achieves an AUC of 0.962 for the binary classification of non-malignant and malignant slides and obtains a three class accuracy of 81.3% for classification of WSIs into normal/benign, DCIS, and IDC, demonstrating its potentials for routine diagnostics

The representation of protein complexes in the Protein Ontology

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/