Heap Reference Analysis Using Access Graphs

Despite significant progress in the theory and practice of program analysis, analysing properties of heap data has not reached the same level of maturity as the analysis of static and stack data. The spatial and temporal structure of stack and static data is well understood while that of heap data seems arbitrary and is unbounded. We devise bounded representations which summarize properties of the heap data. This summarization is based on the structure of the program which manipulates the heap. The resulting summary representations are certain kinds of graphs called access graphs. The boundedness of these representations and the monotonicity of the operations to manipulate them make it possible to compute them through data flow analysis. An important application which benefits from heap reference analysis is garbage collection, where currently liveness is conservatively approximated by reachability from program variables. As a consequence, current garbage collectors leave a lot of garbage uncollected, a fact which has been confirmed by several empirical studies. We propose the first ever end-to-end static analysis to distinguish live objects from reachable objects. We use this information to make dead objects unreachable by modifying the program. This application is interesting because it requires discovering data flow information representing complex semantics. In particular, we discover four properties of heap data: liveness, aliasing, availability, and anticipability. Together, they cover all combinations of directions of analysis (i.e. forward and backward) and confluence of information (i.e. union and intersection). Our analysis can also be used for plugging memory leaks in C/C++ languages.Comment: Accepted for printing by ACM TOPLAS. This version incorporates referees' comment

Long-Term Stability of an Area-Reversible Atom-Interferometer Sagnac Gyroscope

We report on a study of the long-term stability and absolute accuracy of an atom interferometer gyroscope. This study included the implementation of an electro-optical technique to reverse the vector area of the interferometer for reduced systematics and a careful study of systematic phase shifts. Our data strongly suggests that drifts less than 96 $\mu$deg/hr are possible after empirically removing shifts due to measured changes in temperature, laser intensity, and several other experimental parameters.Comment: 4 pages, 4 figures, submitted to PR

Indirect Detection of Kaluza-Klein Dark Matter from Latticized Universal Dimensions

We consider Kaluza-Klein dark matter from latticized universal dimensions. We motivate and investigate two different lattice models, where the models differ in the choice of boundary conditions. The models reproduce relevant features of the continuum model for Kaluza-Klein dark matter. For the model with simple boundary conditions, this is the case even for a model with only a few lattice sites. We study the effects of the latticization on the differential flux of positrons from Kaluza-Klein dark matter annihilation in the galactic halo. We find that for different choices of the compactification radius, the differential positron flux rapidly converges to the continuum model results as a function of the number of lattice sites. In addition, we consider the prospects for upcoming space-based experiments such as PAMELA and AMS-02 to probe the latticization effect.Comment: 25 pages, 9 figures, LaTeX. Final version published in JCA

Involvement of Noradrenergic Neurotransmission in the Stress- but not Cocaine-Induced Reinstatement of Extinguished Cocaine-Induced Conditioned Place Preference in Mice: Role for β-2 Adrenergic Receptors

The responsiveness of central noradrenergic systems to stressors and cocaine poses norepinephrine as a potential common mechanism through which drug re-exposure and stressful stimuli promote relapse. This study investigated the role of noradrenergic systems in the reinstatement of extinguished cocaine-induced conditioned place preference by cocaine and stress in male C57BL/6 mice. Cocaine- (15 mg/kg, i.p.) induced conditioned place preference was extinguished by repeated exposure to the apparatus in the absence of drug and reestablished by a cocaine challenge (15 mg/kg), exposure to a stressor (6-min forced swim (FS); 20–25°C water), or administration of the α-2 adrenergic receptor (AR) antagonists yohimbine (2 mg/kg, i.p.) or BRL44408 (5, 10 mg/kg, i.p.). To investigate the role of ARs, mice were administered the nonselective β-AR antagonist, propranolol (5, 10 mg/kg, i.p.), the α-1 AR antagonist, prazosin (1, 2 mg/kg, i.p.), or the α-2 AR agonist, clonidine (0.03, 0.3 mg/kg, i.p.) before reinstatement testing. Clonidine, prazosin, and propranolol failed to block cocaine-induced reinstatement. The low (0.03 mg/kg) but not high (0.3 mg/kg) clonidine dose fully blocked FS-induced reinstatement but not reinstatement by yohimbine. Propranolol, but not prazosin, blocked reinstatement by both yohimbine and FS, suggesting the involvement of β-ARs. The β-2 AR antagonist ICI-118551 (1 mg/kg, i.p.), but not the β-1 AR antagonist betaxolol (10 mg/kg, i.p.), also blocked FS-induced reinstatement. These findings suggest that stress-induced reinstatement requires noradrenergic signaling through β-2 ARs and that cocaine-induced reinstatement does not require AR activation, even though stimulation of central noradrenergic neurotransmission is sufficient to reinstate

Continuous monitoring of pulse period variations in Her X-1 using Swift/BAT

Context: Monitoring of pulse period variations in accreting binary pulsars is an important tool to study the interaction between the magnetosphere of the neutron star and the accretion disk. While the X-ray flux of the brightest X-ray pulsars have been successfully monitored over many years (e.g. with RXTE/ASM, CGRO/BATSE, Swift/BAT), the possibility to monitor their pulse timing properties continuously has so far been very limited. Aims: In our work we show that the Swift/BAT observations can be used to monitor coherent pulsations of bright X-ray sources and use the Swift archival data to study one of the most enigmatic X-ray pulsars, Hercules X-1. A quasi-continuous monitoring of the pulse period and the pulse period derivative of an X-ray pulsar, here Her X-1, is achieved over a long time (<~ 4 yrs). We compare our observational results with predictions of accretion theory and use them to test different aspects of the physical model of the system. Methods: In our analysis we use the data accumulated with Swift/BAT starting from the beginning of 2005 (shortly after launch) until the present time. To search for pulsations and for their subsequent analysis we used the count rate measured by the BAT detector in the entire field of view. Results: The slope of the correlation between the locally determined spin-up rate and the X-ray luminosity is measured for Her X-1 and found to be in agreement with predictions of basic accretion torque theory. The observed behaviour of the pulse period together with the previously measured secular decrease of the system's orbital period is discussed in the frame of a model assuming ejection of matter close to the inner boundary of the accretion disk.Comment: 7 pages, 5 figures, accepted for publication in Astronomy & Astrophysic

Magnetic and superconducting properties of Cd2Re2O7: Cd NMR and Re NQR

We report Cd NMR and Re NQR studies on Cd2Re2O7, the first superconductor among pyrochlore oxides Tc=1 K. Re NQR spectrum at zero magnetic field below 100 K rules out any magnetic or charge order. The spin-lattice relaxation rate below Tc exhibits a pronounced coherence peak and behaves within the weak-coupling BCS theory with nearly isotropic energy gap. Cd NMR results point to moderate ferromagnetic enhancement at high temperatures followed by rapid decrease of the density of states below the structural transition temperature of 200 K.Comment: 4 pages, 4 figure

Two ~35 day clocks in Her X-1: evidence for neutron star free precession

We present evidence for the existence of two ~35 day clocks in the Her X-1/HZ Her binary system. ~35 day modulations are observed 1) in the Turn-On cycles with two on- and two off-states, and 2) in the changing shape of the pulse profiles which re-appears regularly. The two ways of counting the 35 day cycles are generally in synchronization. This synchronization did apparently break down temporarily during the long Anomalous Low (AL3) which Her X-1 experienced in 1999/2000, in the sense that there must have been one extra Turn-On cycle. Our working hypothesis is that there are two clocks in the system, both with a period of about ~35 days: precession of the accretion disk (the less stable "Turn-On clock") and free precession of the neutron star (the more stable "Pulse profile clock"). We suggest that free precession of the neutron star is the master clock, and that the precession of the accretion disk is basically synchronized to that of the neutron star through a feed-back mechanism in the binary system. However, the Turn-On clock can slip against its master when the accretion disk has a very low inclination, as is observed to be the case during AL3. We take the apparent correlation between the histories of the Turn-Ons, of the Anomalous Lows and of the pulse period evolution, with a 5 yr quasi-periodicity, as evidence for strong physical interaction and feed-back between the major components in the system. We speculate that the 5 yr (10 yr) period is either due to a corresponding activity cycle of HZ Her or a natural ringing period of the physical system of coupled components. The question whether free precession really exists in neutron stars is of great importance for the understanding of matter with supra-nuclear density.Comment: 6 pages, 5 figures, accepted for publication by A&

Searching for periodic sources with LIGO

We investigate the computational requirements for all-sky, all-frequency searches for gravitational waves from spinning neutron stars, using archived data from interferometric gravitational wave detectors such as LIGO. These sources are expected to be weak, so the optimal strategy involves coherent accumulaton of signal-to-noise using Fourier transforms of long stretches of data (months to years). Earth-motion-induced Doppler shifts, and intrinsic pulsar spindown, will reduce the narrow-band signal-to-noise by spreading power across many frequency bins; therefore, it is necessary to correct for these effects before performing the Fourier transform. The corrections can be implemented by a parametrized model, in which one does a search over a discrete set of parameter values. We define a metric on this parameter space, which can be used to determine the optimal spacing between points in a search; the metric is used to compute the number of independent parameter-space points Np that must be searched, as a function of observation time T. The number Np(T) depends on the maximum gravitational wave frequency and the minimum spindown age tau=f/(df/dt) that the search can detect. The signal-to-noise ratio required, in order to have 99% confidence of a detection, also depends on Np(T). We find that for an all-sky, all-frequency search lasting T=10^7 s, this detection threshhold is at a level of 4 to 5 times h(3/yr), where h(3/yr) is the corresponding 99% confidence threshhold if one knows in advance the pulsar position and spin period.Comment: 18 pages, LaTeX, 12 PostScript figures included using psfig. Submitted to Phys. Rev.

Fos-expressing neuronal ensemble in rat ventromedial prefrontal cortex encodes cocaine seeking but not food seeking in rats

Neuronal ensembles in ventromedial prefrontal cortex (vmPFC) play a role in both cocaine and palatable food seeking. However, it is unknown whether similar or different vmPFC neuronal ensembles mediate food and cocaine seeking. Here, we used the Daun02 inactivation procedure to assess whether the neuronal ensembles mediating food and cocaine seeking can be functionally distinguished. We trained male and female Fos-LacZ rats to self-administer palatable food pellets and cocaine on alternating days for 18 days. We then exposed the rats to a brief nonreinforced food- or cocaine-seeking test to induce Fos and β-gal in neuronal ensembles associated with food or cocaine seeking, respectively and infused Daun02 into vmPFC to ablate the β-gal-expressing ensembles. Two days later, we tested the rats for food or cocaine seeking under extinction conditions. Although inactivation of the food-seeking ensemble did not influence food or cocaine seeking, inactivation of the cocaine-seeking ensemble reduced cocaine seeking but not food seeking. Results indicate that the neuronal ensemble activated by cocaine seeking in vmPFC is functionally separate from the ensemble activated by food seeking

Deep generative modeling for single-cell transcriptomics.

Single-cell transcriptome measurements can reveal unexplored biological diversity, but they suffer from technical noise and bias that must be modeled to account for the resulting uncertainty in downstream analyses. Here we introduce single-cell variational inference (scVI), a ready-to-use scalable framework for the probabilistic representation and analysis of gene expression in single cells ( https://github.com/YosefLab/scVI ). scVI uses stochastic optimization and deep neural networks to aggregate information across similar cells and genes and to approximate the distributions that underlie observed expression values, while accounting for batch effects and limited sensitivity. We used scVI for a range of fundamental analysis tasks including batch correction, visualization, clustering, and differential expression, and achieved high accuracy for each task