Randomized scheduling algorithms for high-aggregate bandwidth switches

The aggregate bandwidth of a switch is its port count multiplied by its operating line rate. We consider switches with high-aggregate bandwidths; for example, a 30-port switch operating at 40 Gb/s or a 1000-port switch operating at 1 Gb/s. Designing high-performance schedulers for such switches with input queues is a challenging problem for the following reasons: (1) high performance requires finding good matchings; (2) good matchings take time to find; and (3) in high-aggregate bandwidth switches there is either too little time (due to high line rates) or there is too much work to do (due to a high port count). We exploit the following features of the switching problem to devise simple-to-implement, high-performance schedulers for high-aggregate bandwidth switches: (1) the state of the switch (carried in the lengths of its queues) changes slowly with time, implying that heavy matchings will likely stay heavy over a period of time and (2) observing arriving packets will convey useful information about the state of the switch. The above features are exploited using hardware parallelism and randomization to yield three scheduling algorithms - APSARA, LAURA, and SERENA. These algorithms are shown to achieve 100% throughput and simulations show that their delay performance is quite close to that of the maximum weight matching, even when the traffic is correlated. We also consider the stability property of these algorithms under generic admissible traffic using the fluid-model technique. The main contribution of this paper is a suite of simple to implement, high-performance scheduling algorithms for input-queued switches. We exploit a novel operation, called MERGE, which combines the edges of two matchings to produce a heavier match, and study of the properties of this operation via simulations and theory. The stability proof of the randomized algorithms we present involves a derandomization procedure and uses methods which may have wider applicability.     

Preferential exclusion of sucrose from recombinant interleukin-1 receptor antagonist: role in restricted conformational mobility and compaction of native state

Understanding the mechanism for sucrose-induced protein stabilization is important in many diverse fields, ranging from biochemistry and environmental physiology to pharmaceutical science. Timasheff and Lee [Lee, J. C. & Timasheff, S. N. (1981) J. Biol. Chem. 256, 7193-7201] have established that thermodynamic stabilization of proteins by sucrose is due to preferential exclusion of the sugar from the protein's surface, which increases protein chemical potential. The current study measures the preferential exclusion of 1 M sucrose from a protein drug, recombinant interleukin 1 receptor antagonist (rhIL-1ra). It is proposed that the degree of preferential exclusion and increase in chemical potential are directly proportional to the protein surface area and that, hence, the system will favor the protein state with the smallest surface area. This mechanism explains the observed sucrose-induced restriction of rhIL-1ra conformational fluctuations, which were studied by hydrogen-deuterium exchange and cysteine reactivity measurements. Furthermore, infrared spectroscopy of rhlL-1ra suggested that a more ordered native conformation is induced by sucrose. Electron paramagnetic resonance spectroscopy demonstrated that in the presence of sucrose, spin-labeled cysteine 116 becomes more buried in the protein's interior and that the hydrodynamic diameter of the protein is reduced. The preferential exclusion of sucrose from the protein and the resulting shift in the equilibrium between protein states toward the most compact conformation account for sucrose-induced effects on rhIL-1ra.     

Electrical characterization of carbon nanotube Y-junctions: a foundation for new nanoelectronics

A review on the syntheses and electrical characterization of Y-shaped multi-walled carbon nanotube morphologies is presented. Modified thermal CVD processes, using Ti precursors, are used to grow Y-junctions of different geometries and distribution of catalyst particles. It has been established that novel electrical switching behavior is feasible, where any one of the three branches of the Y-junction can be used for modulating the electrical current flow through the other two branches. Current blocking behavior, leading to perfect rectification, is seen which could be related to the interplay of the carrier lifetime and the transit time. The overall goal is to investigate the possibility of obtaining novel functionality at the nanoscale, which can lead to new device paradigms.     

Vasopressin receptor subtypes differentially modulate calcium-activated potassium currents in the horizontal limb of the diagonal band of Broca

Because many testicular toxicants cause damage to specific stages of spermatogenesis, the present study has investigated the utility of a model in which the testis is synchronized to contain only a few closely related spermatogenic stages. The susceptibility of different stages to 1,3-dinitrobenzene (1,3-DNB) toxicity was investigated in rats, the testes of which had been stage synchronized by a vitamin A depletion/repletion (VADR) procedure. 1,3-DNB (25 mg/kg, IP) or vehicle was injected 58, 61, or 78 d after vitamin A readministration, and testicular histopathology was evaluated 48 h later. At the time of sacrifice, testes in the three groups were synchronized to stages I-VI, VII-IX, or X-XIV+I. The data indicated that tubules in all stages of spermatogenesis, in both synchronized and unsynchronized animals, demonstrated histopathologic changes in response to 1,3-DNB. However, the lesion seen in synchronized animals was more severe and less stage specific than that seen in weight-matched, unsynchronized animals. This increase in degree of susceptibility could be partially explained by differences in toxicokinetics. Stage-synchronized testes could provide unique insights into stage-specific cellular and molecular events, especially for in vitro studies where the stage enrichment could be maximally exploited. However, results obtained from in vivo toxicity studies using animals subjected to VADR should be interpreted carefully in light of the confounding physiologic/metabolic perturbations potentially induced by the VADR procedure.     

Presentation and treatment of spontaneous aortocaval fistula

BACKGROUND: Spontaneous rupture of abdominal aortic aneurysm into the inferior vena cava is rare. The clinical presentation is highly variable, and the diagnosis can be difficult, often being made only at operation. The aortocaval fistula results in a large left-to-right shunt, which can cause cardiac failure. Once the diagnosis is made, treatment is by surgical closure of the fistula and repair of the aneurysm with a graft. METHODS: This is a retrospective review of a single surgeon's experience with aortocaval fistula complicating abdominal aortic aneurysms. RESULTS: Over a 15-year period, we had five patients with spontaneous aortocaval fistula who were treated operatively. Preoperative diagnosis was made in two, suspected in one, and not made in two, one of whom died (the only perioperative death in the series). CONCLUSIONS: Spontaneous aortocaval fistulas are uncommon, and their preoperative recognition is difficult. Hematuria in association with an abdominal aortic aneurysm should raise the suspicion of an aortocaval fistula. Surgical correction is possible, with survival rates comparable to those associated with rupture of aneurysms into the retroperitoneum. Early operative control of the fistula is important to optimize the preload to the heart.     

The catalytic core of RNase P

A deletion mutant of the catalytic RNA component of Escherichia coli RNase P missing residues 87-241 retains the ability to interact with the protein component to form a functional catalyst. The deletion of this phylogenetically conserved region significantly increases the Km, indicating that the deleted structures may be important for binding to the precursor tRNA substrate but not for the cleavage reaction. Under some reaction conditions, this RNase P deletion mutant can become a relatively non-specific nuclease, indicating that this RNA's catalytic center may be more exposed. The catalytic core of the RNase P is formed by less than one third of the 377 residues of the RNase P RNA.     

Effects of Na+ and Mg2+ on the structures of supercoiled DNAs: comparison of simulations with experiments

Recent cryo-electron microscopy (cryo-EM) results suggest that sufficient NaCl concentration (> or approximately 0.1 M) and superhelix density (> or approximately-0.05) cause circular DNAs to adopt highly extended, tightly interwound configurations, in which the strands are laterally contiguous along almost their entire length. Millimolar levels of MgCl2 reportedly act synergistically with NaCl to produce similar conformations. However, Monte Carlo simulations with purely repulsive interduplex forces failed to reproduce such structures. In the present work, solution measurements of particular physical properties were performed both to characterize the effects of Na+ and Mg2+ on DNA structure and to provide quantitative tests of Monte Carlo simulations of circular DNAs. Supercoiled p30 delta DNAs in 10 mM Tris plus 0, 0.122, and 0.1 M NaCl, and 0.1 M NaCl plus 4 mM Mg2+ were examined by static and dynamic light scattering (LS and DLS), time-resolved fluorescence polarization anisotropy (FPA) of intercalated ethidium, and circular dichroism (CD) spectroscopy. Upon addition of 0.122 M NaCl, the radius of gyration (Rg) decreased substantially, which indicates that p30 delta adopts a more compact structure. This contradicts the cryo-EM studies, where molecular extension and Rg both increase upon adding 0.1 M NaCl. In 0.1 M NaCl, the torsion constant measured by FPA is practically invariant to superhelix density, and the plateau diffusion coefficient at large scattering vector (Dplat) is likewise nearly the same at both relaxed and native superhelix densities. Such invariance is difficult to reconcile with any transition from relaxed circles to tightly interwound structures with laterally contiguous strands. Metropolis Monte Carlo simulations were performed to generate canonically distributed sets of structures, from which average Do values and scattered intensity ratios, [symbol: see text]I (zero) [symbol: see text]/[symbol: see text] l(k) [symbol: see text], were calculated. Agreement between simulations and experiments in regard to [symbol: see text] I(O) [symbol: see text] /[symbol: see text] I(k) [symbol: see text], D(zero) and the supercoiling free energy, delta Gsc (delta l), is remarkably good for the most extensively studied p30 delta samples. The simulated structures exhibit no sign of very tight interwinding with extensive lateral contacts, but instead exhibit most probable superhelix diameters of 85 to 90 A. When 4 mM Mg2+ was added to native supercoiled p30 delta in 0.1 M NaCl, Rg decreased, D(zero) increased, and the longest internal relaxation rate (1/tau 2(zero)) increased, all of which indicate a further overall contraction of the molecular envelope. The torsion constant exhibited a slight increase that is hardly statistically significant. In this case, agreement between the simulations and experiments was only semi-quantitative for most samples investigated, although the predicted contraction was exhibited by all five samples of p30 delta and one of pBR322 DNA. The simulated structures in 0.1 M NaCl plus 4 mM Mg2+ again showed no sign of extensive lateral contacts. A plausible explanation is proposed for the highly extended, tightly interwound structures seen in cryo-EM, and explicitly tested by Monte Carlo simulations of a 1000 bp circular DNA at +25 and -50 degrees C. Structures identical to those seen in cryo-EM are in fact the equilibrium structures in the simulations at -50 degrees C, and the estimated time for equilibration (2.3 x 10(-6) second) is much smaller than the estimated time for vitrification (1 x 10(-4) second).