Liveness-Based Garbage Collection for Lazy Languages

We consider the problem of reducing the memory required to run lazy first-order functional programs. Our approach is to analyze programs for liveness of heap-allocated data. The result of the analysis is used to preserve only live data---a subset of reachable data---during garbage collection. The result is an increase in the garbage reclaimed and a reduction in the peak memory requirement of programs. While this technique has already been shown to yield benefits for eager first-order languages, the lack of a statically determinable execution order and the presence of closures pose new challenges for lazy languages. These require changes both in the liveness analysis itself and in the design of the garbage collector. To show the effectiveness of our method, we implemented a copying collector that uses the results of the liveness analysis to preserve live objects, both evaluated (i.e., in WHNF) and closures. Our experiments confirm that for programs running with a liveness-based garbage collector, there is a significant decrease in peak memory requirements. In addition, a sizable reduction in the number of collections ensures that in spite of using a more complex garbage collector, the execution times of programs running with liveness and reachability-based collectors remain comparable

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

Medial prefrontal cortex neuronal activation and synaptic alterations after stress-induced reinstatement of palatable food seeking: a study using c-fos-GFP transgenic female rats

Relapse to maladaptive eating habits during dieting is often provoked by stress and there is evidence for a role of ovarian hormones in stress responses and feeding. We studied the role of these hormones in stress-induced reinstatement of food seeking and medial prefrontal cortex (mPFC) neuronal activation in c-fos-GFP transgenic female rats, which express GFP in strongly activated neurons. Food-restricted ovariectomized or sham-operated c-fos-GFP rats were trained to lever-press for palatable food pellets. Subsequently, lever-pressing was extinguished and reinstatement of food seeking and mPFC neuronal activation was assessed after injections of the pharmacological stressor yohimbine (0.5-2 mg/kg) or pellet priming (1-4 noncontingent pellets). Estrous cycle effects on reinstatement were also assessed in wild-type rats. Yohimbine- and pellet-priming-induced reinstatement was associated with Fos and GFP induction in mPFC; both reinstatement and neuronal activation were minimally affected by ovarian hormones in both c-fos-GFP and wild-type rats. c-fos-GFP transgenic rats were then used to assess glutamatergic synaptic alterations within activated GFP-positive and nonactivated GFP-negative mPFC neurons following yohimbine-induced reinstatement of food seeking. This reinstatement was associated with reduced AMPA receptor/NMDA receptor current ratios and increased paired-pulse facilitation in activated GFP-positive but not GFP-negative neurons. While ovarian hormones do not appear to play a role in stress-induced relapse of food seeking in our rat model, this reinstatement was associated with unique synaptic alterations in strongly activated mPFC neurons. Our paper introduces the c-fos-GFP transgenic rat as a new tool to study unique synaptic changes in activated neurons during behavio

Distinct fos-expressing neuronal ensembles in the ventromedial prefrontal cortex mediate food reward and extinction memories

In operant learning, initial reward-associated memories are thought to be distinct from subsequent extinction-associated memories. Memories formed during operant learning are thought to be stored in “neuronal ensembles.” Thus, we hypothesize that different neuronal ensembles encode reward- and extinction-associated memories. Here, we examined prefrontal cortex neuronal ensembles involved in the recall of reward and extinction memories of food self-administration.Wefirst trained rats to lever press for palatable food pellets for 7 d (1 h/d) and then exposed them to 0, 2, or 7 daily extinction sessions in which lever presses were not reinforced. Twenty-four hours after the last training or extinction session, we exposed the rats to either a short 15 min extinction test session or left them in their homecage (a control condition). We found maximal Fos (a neuronal activity marker) immunoreactivity in the ventral medial prefrontal cortex of rats that previously received 2 extinction sessions, suggesting that neuronal ensembles in this area encode extinction memories. We then used the Daun02 inactivation procedure to selectively disrupt ventral medial prefrontal cortex neuronal ensembles that were activated during the 15 min extinction session following 0 (no extinction) or 2 prior extinction sessions to determine the effects of inactivating the putative food reward and extinction ensembles, respectively, on subsequent nonreinforced food seeking 2 d later. Inactivation of the food reward ensembles decreased food seeking, whereas inactivation of the extinction ensembles increased food seeking. Our results indicate that distinct neuronal ensembles encoding operant reward and extinction memories intermingle within the same cortical area

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

galign: A Tool for Rapid Genome Polymorphism Discovery

BACKGROUND: Highly parallel sequencing technologies have become important tools in the analysis of sequence polymorphisms on a genomic scale. However, the development of customized software to analyze data produced by these methods has lagged behind. METHODS/PRINCIPAL FINDINGS: Here I describe a tool, 'galign', designed to identify polymorphisms between sequence reads obtained using Illumina/Solexa technology and a reference genome. The 'galign' alignment tool does not use Smith-Waterman matrices for sequence comparisons. Instead, a simple algorithm comparing parsed sequence reads to parsed reference genome sequences is used. 'galign' output is geared towards immediate user application, displaying polymorphism locations, nucleotide changes, and relevant predicted amino-acid changes for ease of information processing. To do so, 'galign' requires several accessory files easily derived from an annotated reference genome. Direct sequencing as well as in silico studies demonstrate that 'galign' provides lesion predictions comparable in accuracy to available prediction programs, accompanied by greater processing speed and more user-friendly output. We demonstrate the use of 'galign' to identify mutations leading to phenotypic consequences in C. elegans. CONCLUSION/SIGNIFICANCE: Our studies suggest that 'galign' is a useful tool for polymorphism discovery, and is of immediate utility for sequence mining in C. elegans

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

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&

An accretion disk model for periodic timing variations of pulsars

The long-term, highly periodic and correlated variations in both the pulse shape and the rate of slow-down of two isolated pulsars (PSRs) PSR B1828-11 and PSR B1642-03 were discovered recently. This phenomenon may provide evidence for "free precession" as suggested in the literature. Some authors presented various kinds of models to explain this phenomenon within the framework of free precession. Here we present an accretion disk model for this precession phenomenon instead. Under reasonable parameters, the observed phenomenon can be explained by an isolated pulsar with a fossil disk. This may link radio pulsars and anomalous X-ray pulsars (AXPs) and present an indirect evidence for the existence of the fossil disk in nature.Comment: 4 pages, 2 figures, to appear in A&A Lette

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.