A Proof of Convergence of the B-RED and P-RED Algorithms for Random Early Detection

In [8], we recently presented two computationally efficient algorithms named B-RED and P-RED for random early detection. In this letter, we present the mathematical proof of convergence of these algorithms under general conditions to local minima.

Formation of linear plasmid multimers promoted by the phage lambda Red-system in lon mutants of Escherichia coli

We report here the formation of plasmid linear multimers promoted by the Red-system of phage lambda using a multicopy plasmid comprised of lambda red alpha and red beta genes, under the control of the lambda cI857 repressor. Our observations have revealed that the multimerization of plasmid DNA is dependent on the red beta and recA genes, suggesting a concerted role for these functions in the formation of plasmid multimers. The formation of multimers occurred in a recBCD+ sbcB+ xthA+ lon genetic background at a higher frequency than in the isogenic lon+ host cells. The multimers comprised tandem repeats of monomer plasmid DNA. Treatment of purified plasmid DNA with exonuclease III revealed the presence of free double-chain ends in the molecules. Determination of the size of multimeric DNA, by pulse field gel electrophoresis, revealed that the bulk of the DNA was in the range 50-240 kb, representing approximately 5-24 unit lengths of monomeric plasmid DNA. We provide a conceptual framework for Red-system-promoted formation and enhanced accumulation of plasmid linear multimers in lon mutants of E. coli.

Anaerobic DNA cleavage activity in red light and photocytotoxicity of (pyridine-2-thiol)cobalt(III) complexes of phenanthroline bases

Cobalt(III) complexes [Co(pnt)(B)(2)](NO3)(2) (1-3) of pyridine-2-thiol (pnt) and phenanthroline bases (B), viz. 1,10-phenanthroline (phen in 1), dipyrido[3,2-d: 2',3'-f]quinoxaline (dpq in 2) and dipyrido[3,2-a:2',3'-c] phenazine (dppz in 3), have been prepared, characterized and their photo-induced anaerobic DNA cleavage activity studied. The crystal structure of 1a as mixed ClO4- and PF6- salt of 1 shows a (CoN5S)-N-III coordination geometry in which the pnt and phen showed N,S- and N,N-donor binding modes, respectively. The complexes exhibit Co(III)/Co(II) redox couple near -0.3 V (vs. SCE) in 20% DMF-Tris-HCl buffer having 0.1 M TBAP. The complexes show binding propensity to calf thymus DNA giving K-b values within 2.2 x 10(4)-7.3 x 10(5) M-1. Thermal melting and viscosity data suggest DNA surface and/or groove binding of the complexes. The complexes show significant anaerobic DNA cleavage activity in red light under argon atmosphere possibly involving sulfide anion radical or thiyl radical species. The DNA cleavage reaction under aerobic medium in red light is found to involve both singlet oxygen and hydroxyl radical pathways. The dppz complex 3 shows non-specific BSA and lysozyme protein cleavage activity in UV-A light of 365 nm via both hydroxyl and singlet oxygen pathways. The dppz complex 3 exhibits photocytotoxicity in HeLa cervical cancer cells giving IC50 values of 767 nM and 19.38 mu M in UV-A light of 365 nm and in the dark, respectively. A significant reduction of the dark toxicity of the dppz base (IC50 = 8.34 mu M in dark) is observed on binding to the cobalt(III) center.

DNA cleavage in red light promoted by copper(II) complexes of -amino acids and photoactive phenanthroline bases

Ternary copper(II) complexes [Cu(L-trp)(B)(H2O)](NO3) ( 1–3) and [Cu(L-phe)(B)(H2O)](NO3) ( 4–6) of L-tryptophan (L-trp) and L-phenylalanine (L-phe) having phenanthroline bases (B), viz. 1,10-phenanthroline (phen, 1 and 4), dipyrido[3,2-d:2,3-f]quinoxaline (dpq, 2 and 5) and dipyrido[3,2-a:2,3-c]phenazine (dppz, 3 and 6), were prepared and characterized by physico-chemical techniques. Complexes 3 and 6 were structurally characterized by X-ray crystallography and show the presence of a square pyramidal (4 + 1) CuN3O2 coordination geometry in which the N,O-donor amino acid (L-trp or L-phe) and N,N-donor phenanthroline base bind at the equatorial plane with an aqua ligand coordinated at the elongated axial site. Complex 3 shows significant distortion from the square pyramidal geometry and a strong intramolecular – stacking interaction between the pendant indole ring of L-trp and the planar dppz aromatic moiety. All the complexes display good binding propensity to the calf thymus DNA giving an order: 3, 6 (dppz) > 2, 5 (dpq) > 1, 4 (phen). The binding constant (Kb) values are in the range of 2.1 × 104–1.1 × 106 mol-1 with the binding site size (s) values of 0.17–0.63. The phen and dpq complexes are minor groove binders while the dppz analogues bind at the DNA major groove. Theoretical DNA docking studies on 2 and 3 show the close proximity of two photosensitizers, viz. the indole moiety of L-trp and the quinoxaline/phenazine of the dpq/dppz bases, to the complementary DNA strands. Complexes 2 and 3 show oxidative DNA double strand breaks (dsb) of supercoiled (SC) DNA forming a significant quantity of linear DNA along with the nicked circular (NC) form on photoexposure to UV-A light of 365 nm and red light of 647.1 nm (Ar–Kr laser). Complexes 1, 5 and 6 show only single strand breaks (ssb) forming NC DNA. The red light induced DNA cleavage involves metal-assisted photosensitization of L-trp and dpq/dppz base resulting in the formation of a reactive singlet oxygen (1O2) species.

Photochemistry of Far Red Responsive Tetrahydroquinoxaline-Based Squaraine Dyes

The photochemical and redox properties of two newly synthesized tetrahydroquinoxaline-based squaraine dyes (SQ) are investigated Using femto- and nanosecond laser flash photolysis, pulse radiolysis, and cyclic voltammetry. In acetonitrile and dichloromethane, these squaraines exist its monomers in the zwitterionic form (lambda(max) approximate to 715 nm, epsilon(max) approximate to 1.66 x 10(5) M-1 cm(-1) in acetonitrile). Their excited sin-let states ((1)SQ*) exhibit a broad absorption hand at 480 nm, with singlet lifetimes of 44 and 123 ps for the two dyes. Both squaraines exhibit poor intersystem crossing efficiency (Phi(ISC) < 0.001). Their excited triplet states ((3)SQ*), however, Ire efficiently generated by triplet-triplet energy transfer Using triplet excited 9,10-dibromoanthracene. The excited triplet states of the squaraines dyes exhibit it broad absorption hand at ca. 560 nm (epsilon(triplet) approximate to 4.2 x 10(4) M-1 cm(-1)) and undergo deactivation via triplet-triplet annihilation and ground-state quenching processes. The oxidized forms of the investigated squaraines (SQ(center dot+)) exhibit absorption maxima at 510 and 610 nm.

Infra-red spectra of crystalline chloroacetates of Cu, Ca, Sr, Ba and Pb

The infra-red spectra of Cu, Ca, Sr, Ba and Pb chloroacetates were studied in order to investigate the effect of co-ordination on the vibration spectra of the ligand. The shifts of the symmetric and antisymmetric COO− vibrational frequencies indicate a bridged structure as the most probable one for the complexes investigated. No linear relationship between the shifts of the COO− stretching frequencies and E/r (where E is the electron excitation energy and r the ionic radius) was observed. No systematic mass effect on these COO− frequencies also could be established.

Infra-red and raman spectra of BaCl2.2H2O and BaCl2.2D2O

The infra-red and Raman spectra of ordinary and deuterated barium chloride dihydrate have been studied to throw light on the intramolecular hydrogen bonds in these two crystals. The frequencies of the stretching, bending and librational modes observed in infra-red and Raman spectra exclude the possibility of at least one of the OH.... Cl hydrogen bonds, contrary to the results of NMR and neutron diffraction studies.

Raman and infra-red spectra of crystalline ammonium sulphamate

Raman spectrum of a single crystal of ammonium sulphamate has been recorded for the two different orientations using λ 2537 resonance radiation of the mercury as the exciter. Thirty-four Raman lines have been observed of which eight belong to the lattice oscillations. Weak hydrogen bonding of NH2 group in the crystal was predicted. The infra-red absorption spectrum of the substance was taken in the powder form in potassium bromide disc, using Carl Zeiss UR10 IR spectrometer. Thirty-five absorption maxima could be identified.

Raman and infra-red spectra of crystalline potassium sulphamate

Raman spectrum of a single crystal of potassium sulphamate has been recorded for the first time using λ 2536 radiation of mercury as the exciter. Thirty-three Raman lines have been observed of which nine belong to the lattice oscillations. The infra-red absorption spectrum of the substance was taken in the powder form in potassium bromide disc using Carl Zeiss UR 10 IR spectrometer. Thirty-six absorption maxima could be identified of which twenty-five have been recorded for the first time. The analysis clearly shows that the N-H bond in the crystalline potassium sulphamate is not hydrogen-bonded to any appreciable extent.

Hydrogen bonding in thiolbenzoic acid. Infra-red, ultra-violet, n.m.r. and cryoscopic studies

Dimerization of thiolbenzoic acid has been studied by infra-red, ultra-violet and n.m.r. spectroscopy and cryoscopy. The results indicate that the tendency to form S - H. O hydrogen bonds is not appreciable.

Infra-red absorption bands of co-ordinated water in titanium complexes

ORANGE red and amorphous peroxy-titanium complexes of oxalic, malonic and maleic acids1-3, when vacuum-dried, have co-ordinated water molecules firmly bonded to the central titanium atom as shown in formula (I). The peroxy-oxygen from these compounds is slowly lost even at room temperature because of the strained peroxy-group3,4. The compounds, when kept at 95°-100°C. for about three days, give deperoxygenated compounds of the type (II). However, a sample of peroxy-titanium oxalate sealed in a glass tube lost all its peroxy-oxygen in about four years and gave a white crystalline basic oxalate (II). The amorphous nature of the compounds may be due to random hydrogen bonding in the complexes. The crystallinity observed in one of the deperoxygenated titanyl oxalates may be due to the rearrangement of the molecules during ageing for more than four years. The infra-red absorption of these compounds was studied to find out the effect of co-ordination and hydrogen bonding on the infra-red bands of the free water.

Expression of lactate transporters MCT1, MCT2, MCT4 and the ancillary protein CD147 in horse muscle and red blood cells

Monocarboxylate transporters (MCTs) transport lactate and protons across cell membranes. During intense exercise, lactate and protons accumulate in the exercising muscle and are transported to the plasma. In the horse, MCTs are responsible for the majority of lactate and proton removal from exercising muscle, and are therefore also the main mechanism to hinder the decline in pH in muscle cells. Two isoforms, MCT1 and MCT4, which need an ancillary protein CD147, are expressed in equine muscle. In the horse, as in other species, MCT1 is predominantly expressed in oxidative fibres, where its likely role is to transport lactate into the fibre to be used as a fuel at rest and during light work, and to remove lactate during intensive exercise when anaerobic energy production is needed. The expression of CD147 follows the fibre type distribution of MCT1. These proteins were detected in both the cytoplasm and sarcolemma of muscle cells in the horse breeds studied: Standardbred and Coldblood trotters. In humans, training increases the expression of both MCT1 and MCT4. In this study, the proportion of oxidative fibres in the muscle of Norwegian-Swedish Coldblood trotters increased with training. Simultaneously, the expression of MCT1 and CD147, measured immunohistochemically, seemed to increase more in the cytoplasm of oxidative fibres than in the fast fibre type IIB. Horse MCT4 antibody failed to work in immunohistochemistry. In the future, a quantitative method should be introduced to examine the effect of training on muscle MCT expression in the horse. Lactate can be taken up from plasma by red blood cells (RBCs). In horses, two isoforms, MCT1 and MCT2, and the ancillary protein CD147 are expressed in RBC membranes. The horse is the only species studied in which RBCs have been found to express MCT2, and the physiological role of this protein in RBCs is unknown. The majority of horses express all three proteins, but 10-20% of horses express little or no MCT1 or CD147. This leads to large interindividual variation in the capacity to transport lactate into RBCs. Here, the expression level of MCT1 and CD147 was bimodally distributed in three studied horse breeds: Finnhorse, Standardbred and Thoroughbred. The level of MCT2 expression was distributed unimodally. The expression level of lactate transporters could not be linked to performance markers in Thoroughbred racehorses. In the future, better performance indexes should be developed to better enable the assessment of whether the level of MCT expression affects athletic performance. In human subjects, several mutations in MCT1 have been shown to cause decreased lactate transport activity in muscle and signs of myopathy. In the horse, two amino acid sequence variations, one of which was novel, were detected in MCT1 (V432I and K457Q). The mutations found in horses were in different areas compared to mutations found in humans. One mutation (M125V) was detected in CD147. The mutations found could not be linked with exercise-induced myopathy. MCT4 cDNA was sequenced for the first time in the horse, but no mutations could be detected in this protein.

A four-timescale algorithm for constrained stochastic optimization of RED

The overall performance of random early detection (RED) routers in the Internet is determined by the settings of their associated parameters. The non-availability of a functional relationship between the RED performance and its parameters makes it difficult to implement optimization techniques directly in order to optimize the RED parameters. In this paper, we formulate a generic optimization framework using a stochastically bounded delay metric to dynamically adapt the RED parameters. The constrained optimization problem thus formulated is solved using traditional nonlinear programming techniques. Here, we implement the barrier and penalty function approaches, respectively. We adopt a second-order nonlinear optimization framework and propose a novel four-timescale stochastic approximation algorithm to estimate the gradient and Hessian of the barrier and penalty objectives and update the RED parameters. A convergence analysis of the proposed algorithm is briefly sketched. We perform simulations to evaluate the performance of our algorithm with both barrier and penalty objectives and compare these with RED and a variant of it in the literature. We observe an improvement in performance using our proposed algorithm over RED, and the above variant of it.