Real-time disk scheduling in a mixed-media file system

This paper presents our real-time disk scheduler called the Delta L scheduler, which optimizes unscheduled best-effort disk requests by giving priority to best-effort disk requests while meeting real-time request deadlines. Our scheduler tries to execute real-time disk requests as much as possible in the background. Only when real-time request deadlines are endangered, our scheduler gives priority to real-time disk requests. The Delta L disk scheduler is part of our mixed-media file system called Clockwise. An essential part of our work is extensive and detailed raw disk performance measurements. The Delta L disk scheduler for its real-time schedulability analysis and to decide whether scheduling a best-effort request before a real-time request violates real-time constraints uses these raw performance measurements. Further, a Clockwise off-line simulator uses the raw performance measurements where a number of different disk schedulers are compared. We compare the Delta L scheduler with a prioritizing Latest Start Time (LST) scheduler and non-prioritizing EDF scheduler. The Delta L scheduler is comparable to LST in achieving low latencies for best-effort requests under light to moderate real-time loads and better in achieving low latencies for best-effort requests for extreme real-time loads. The simulator is calibrated to an actual Clockwise. Clockwise runs on a 200MHz Pentium-Pro based PC with PCI bus, multiple SCSI controllers and disks on Linux 2.2.x and the Nemesis kernel. Clockwise performance is dictated by the hardware: all available bandwidth can be committed to real-time streams, provided hardware overloads do not occur

Clockwise: a mixed-media file system

This paper presents Clockwise, a mixed-media file system. The primary goal of Clockwise is to provide a storage architecture that supports the storage and retrieval of best-effort and real-time file system data. Clockwise provides an abstraction called a dynamic partition that groups lists of related (large) blocks on one or more disks. Dynamic partitions can grow and shrink in size and reading or writing of dynamic partitions can be scheduled explicitly. With respect to scheduling, Clockwise uses a novel strategy to pre-calculate schedule slack time and it schedules best-effort requests before queued real-time requests in this slack tim

Cut-and-paste file-systems: integrating simulators and file-systems

We have implemented an integrated and configurable file system called the PFS and a trace-driven file-system simulator called Patsy. Patsy is used for off-line analysis of file-system algorithms, PFS is used for on-line file-system data storage. Algorithms are first analyzed in Patsy and when we are satisfied\ud with the performance results, migrated into PFS for on-line usage. Since Patsy and PFS are derived from a common cut-and-paste file-system framework, this migration proceeds smoothly.\ud We have found this integration quite useful: algorithm bottlenecks have been found through Patsy that could have led to performance degradations in PFS. Off-line simulators are simpler to analyze compared to on-line file-systems because a work load can repeatedly be replayed on the same off-line simulator. This is almost impossible in on-line file-systems since it is hard to provide similar conditions for each experiment run. Since simulator and file-system are integrated (hence, use the same code), experiment results from the simulator have relevance in the real system. \ud This paper describes the cut-and-paste framework, the instantiation of the framework to PFS and Patsy and finally, some of the experiments we conducted in Patsy

Sensitivity Analysis for the Assessment of Causal Vaccine Effects on Viral Load in HIV Vaccine Trials

Vaccines with limited ability to prevent HIV infection may positively impact the HIV/AIDS pandemic by preventing secondary transmission and disease in vaccine recipients who become infected. To evaluate the impact of vaccination on secondary transmission and disease, efficacy trials assess vaccine effects on HIV viral load and other surrogate endpoints measured after infection. A standard test that compares the distribution of viral load between the infected subgroups of vaccine and placebo recipients does not assess a causal effect of vaccine, because the comparison groups are selected after randomization. To address this problem, we formulate clinically relevant causal estimands using the principal stratification framework developed by Frangakis and Rubin (2002), and propose a class of logistic selection bias models whose members identify the estimands. Given a selection model in the class, procedures are developed for testing and estimation of the causal effect of vaccination on viral load in the principal stratum of subjects who would be infected regardless of randomization assignment. We show how the procedures can be used for a sensitivity analysis that quantifies how the causal effect of vaccination varies with the presumed magnitude of selection bias

The VIRUS-P Exploration of Nearby Galaxies (VENGA): Survey Design and First Results

VENGA is a large-scale extragalactic IFU survey, which maps the bulges, bars and large parts of the outer disks of 32 nearby normal spiral galaxies. The targets are chosen to span a wide range in Hubble types, star formation activities, morphologies, and inclinations, at the same time of having vast available multi-wavelength coverage from the far-UV to the mid-IR, and available CO and 21cm mapping. The VENGA dataset will provide 2D maps of the SFR, stellar and gas kinematics, chemical abundances, ISM density and ionization states, dust extinction and stellar populations for these 32 galaxies. The uniqueness of the VIRUS-P large field of view permits these large-scale mappings to be performed. VENGA will allow us to correlate all these important quantities throughout the different environments present in galactic disks, allowing the conduction of a large number of studies in star formation, structure assembly, galactic feedback and ISM in galaxies.Comment: 7 pages, 3 figures, proceedings of the "Third Biennial Frank N. Bash Symposium, New Horizons in Astronomy" held in Austin, TX, Oct. 2009. To be published in the Astronomical Society of the Pacific Conference Series, eds. L. Stanford, L. Hao, Y. Mao, J. Gree

Central ions and lateral asparagine/glutamine zippers stabilize the post-fusion hairpin conformation of the SARS coronavirus spike glycoprotein

AbstractThe coronavirus spike glycoprotein is a class I membrane fusion protein with two characteristic heptad repeat regions (HR1 and HR2) in its ectodomain. Here, we report the X-ray structure of a previously characterized HR1/HR2 complex of the severe acute respiratory syndrome coronavirus spike protein. As expected, the HR1 and HR2 segments are organized in antiparallel orientations within a rod-like molecule. The HR1 helices form an exceptionally long (120 Å) internal coiled coil stabilized by hydrophobic and polar interactions. A striking arrangement of conserved asparagine and glutamine residues of HR1 propagates from two central chloride ions, providing hydrogen-bonding “zippers” that strongly constrain the path of the HR2 main chain, forcing it to adopt an extended conformation at either end of a short HR2 α-helix

Modeling the impact and costs of semiannual mass drug administration for accelerated elimination of lymphatic filariasis

textabstractThe Global Program to Eliminate Lymphatic Filariasis (LF) has a target date of 2020. This program is progressing well in many countries. However, progress has been slow in some countries, and others have not yet started their mass drug administration (MDA) programs. Acceleration is needed. We studied how increasing MDA frequency from once to twice per year would affect program duration and costs by using computer simulation modeling and cost projections. We used the LYMFASIM simulation model to estimate how many annual or semiannual MDA rounds would be required to eliminate LF for Indian and West African scenarios with varied pre-control endemicity and coverage levels. Results were used to estimate total program costs assuming a target population of 100,000 eligibles, a 3% discount rate, and not counting the costs of donated drugs. A sensitivity analysis was done to investigate the robustness of these results with varied assumptions for key parameters. Model predictions suggested that semiannual MDA will require the same number of MDA rounds to achieve LF elimination as annual MDA in most scenarios. Thus semiannual MDA programs should achieve this goal in half of the time required for annual programs. Due to efficiency gains, total program costs for semiannual MDA programs are projected to be lower than those for annual MDA programs in most scenarios. A sensitivity analysis showed that this conclusion is robust. Semiannual MDA is likely to shorten the time and lower the cost required for LF elimination in countries where it can be implemented. This strategy may improve prospects for global elimination of LF by the target year 2020