Lanczos subspace filter diagonalization: Homogeneous recursive filtering and a low-storage method for the calculation of matrix elements

We develop a new iterative filter diagonalization (FD) scheme based on Lanczos subspaces and demonstrate its application to the calculation of bound-state and resonance eigenvalues. The new scheme combines the Lanczos three-term vector recursion for the generation of a tridiagonal representation of the Hamiltonian with a three-term scalar recursion to generate filtered states within the Lanczos representation. Eigenstates in the energy windows of interest can then be obtained by solving a small generalized eigenvalue problem in the subspace spanned by the filtered states. The scalar filtering recursion is based on the homogeneous eigenvalue equation of the tridiagonal representation of the Hamiltonian, and is simpler and more efficient than our previous quasi-minimum-residual filter diagonalization (QMRFD) scheme (H. G. Yu and S. C. Smith, Chem. Phys. Lett., 1998, 283, 69), which was based on solving for the action of the Green operator via an inhomogeneous equation. A low-storage method for the construction of Hamiltonian and overlap matrix elements in the filtered-basis representation is devised, in which contributions to the matrix elements are computed simultaneously as the recursion proceeds, allowing coefficients of the filtered states to be discarded once their contribution has been evaluated. Application to the HO2 system shows that the new scheme is highly efficient and can generate eigenvalues with the same numerical accuracy as the basic Lanczos algorithm.

UV-induced hyperphosphorylation of replication protein a depends on DNA replication and expression of ATM protein

Exposure to DNA-damaging agents triggers signal transduction pathways that are thought to play a role in maintenance of genomic stability. A key protein in the cellular processes of nucleotide excision repair, DNA recombination, and DNA double-strand break repair is the single-stranded DNA binding protein, RPA. We showed previously that the p34 subunit of RPA becomes hyperphosphorylated as a delayed response (4-8 h) to UV radiation (10-30 J/m(2)). Here we show that UV-induced RPA-p34 hyperphosphorylation depends on expression of ATM, the product of the gene mutated in the human genetic disorder ataxia telangiectasia (A-T). UV-induced RPA-p34 hyperphosphorylation was not observed in A-T cells, but this response was restored by ATM expression. Furthermore, purified ATM kinase phosphorylates the p34 subunit of RPA complex in vitro at many of the same sites that are phosphorylated in vivo after UV radiation. Induction of this DNA damage response was also dependent on DNA replication; inhibition of DNA replication by aphidicolin prevented induction of RPA-p34 hyperphosphorylation by UV radiation. We postulate that this pathway is triggered by the accumulation of aberrant DNA replication intermediates, resulting from DNA replication fork blockage by UV photoproducts. Further, we suggest that RPA-p34 is hyperphosphorylated as a participant in the recombinational postreplication repair of these replication products. Successful resolution of these replication intermediates reduces the accumulation of chromosomal aberrations that would otherwise occur as a consequence of UV radiation.

Integrated treatment of shrimp effluent by sedimentation, oyster filtration and macroalgal absorption: a laboratory scale study

Effluent water from shrimp ponds typically contains elevated concentrations of dissolved nutrients and suspended particulates compared to influent water. Attempts to improve effluent water quality using filter feeding bivalves and macroalgae to reduce nutrients have previously been hampered by the high concentration of clay particles typically found in untreated pond effluent. These particles inhibit feeding in bivalves and reduce photosynthesis in macroalgae by increasing effluent turbidity. In a small-scale laboratory study, the effectiveness of a three-stage effluent treatment system was investigated. In the first stage, reduction in particle concentration occurred through natural sedimentation. In the second stage, filtration by the Sydney rock oyster, Saccostrea commercialis (Iredale and Roughley), further reduced the concentration of suspended particulates, including inorganic particles, phytoplankton, bacteria, and their associated nutrients. In the final stage, the macroalga, Gracilaria edulis (Gmelin) Silva, absorbed dissolved nutrients. Pond effluent was collected from a commercial shrimp farm, taken to an indoor culture facility and was left to settle for 24 h. Subsamples of water were then transferred into laboratory tanks stocked with oysters and maintained for 24 h, and then transferred to tanks containing macroalgae for another 24 h. Total suspended solid (TSS), chlorophyll a, total nitrogen (N), total phosphorus (P), NH4+, NO3-, and PO43-, and bacterial numbers were compared before and after each treatment at: 0 h (initial); 24 h (after sedimentation); 48 h (after oyster filtration); 72 h (after macroalgal absorption). The combined effect of the sequential treatments resulted in significant reductions in the concentrations of all parameters measured. High rates of nutrient regeneration were observed in the control tanks, which did not contain oysters or macroalgae. Conversely, significant reductions in nutrients and suspended particulates after sedimentation and biological treatment were observed. Overall, improvements in water quality (final percentage of the initial concentration) were as follows: TSS (12%); total N (28%); total P (14%); NH4+ (76%); NO3- (30%); PO43-(35%); bacteria (30%); and chlorophyll a (0.7%). Despite the probability of considerable differences in sedimentation, filtration and nutrient uptake rates when scaled to farm size, these results demonstrate that integrated treatment has the potential to significantly improve water quality of shrimp farm effluent. (C) 2001 Elsevier Science B.V. All rights reserved.

The filter system for tertiary treatment of sewage effluent by land application - its performance in a subtropical environment

FILTER is an innovative, CSIRO developed system for treating effluent using high rate land application and subsequent effluent recapture via a closely spaced, subsurface drainage network. We report on the summer performance of a FILTER system established in a subtropical environment on a relatively impermeable swelling clay soil underlain by a deep regional water table. Using secondary treated sewage effluent, the FILTER system produced effluent of tertiary nutrient standards (less than or equal to5 mg/L TN; less than or equal to1 mg/L TP), with salinity levels suitable for subsequent irrigation reuse (EC less than or equal to2.5 dS/m). Removal of faecal coliforms was considerably less effective. The hydraulic loading rate achieved was about two and a half times larger than conventional irrigation demand, but this was associated with high deep percolation losses (e 3 mm/day). Comparisons are made with the original FILTER system developed and tested by Jayawardane et al. in temperate Australia. Suggestions are made for modifications to, and further testing of FILTER in a subtropical environment.

Inorganic nitrogen requirements during shoot organogenesis in tobacco leaf discs

The role of nitrate, ammonium, and culture medium pH on shoot organogenesis in Nicotiana tabacum zz100 leaf discs was examined. The nitrogen composition of a basal liquid shoot induction medium (SIM) containing 39.4 mM NO3- and 20.6 mM NH4+ was altered whilst maintaining the overall ionic balance with Na+ and Cl- ions. Omission of total nitrogen and nitrate, but not ammonium, from SIM prevented the initiation and formation of shoots. When nitrate was used as the sole source of nitrogen, a high frequency of explants initiated and produced leafy shoots. However, the numbers of shoots produced were significantly fewer than the control SIM. Buffering nitrate-only media with the organic acid 2[N-morpholinol]thanesulphonic acid (MES) could not compensate for the omission of ammonium. Ammonium used as the sole source of nitrogen appeared to have a negative effect on explant growth and morphogenesis, with a significant lowering of media pH. Buffering ammonium-only media with MES stabilized pH and allowed a low frequency of explants to initiate shoot meristems. However, no further differentiation into leafy shoots was observed. The amount of available nitrogen appears to be less important than the ratio between nitrate and ammonium. Shoot formation was achieved with a wide range of ratios, but media containing 40 mM nitrate and 20 mM ammonium (70:30) produced the greatest number of shoots per explant. Results from this study indicate a synergistic effect between ammonium and nitrate on shoot organogenesis independent of culture medium pH.

Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.

Dinoflagellate symbiosis: strategies and adaptations for the aquisition and fixation of inorganic carbon

Dinoflagellates exist in symbiosis with a number of marine invertebrates including giant clams, which are the largest of these symbiotic organisms. The dinoflagellates (Symbiodinium sp.) live intercellularly within tubules in the mantle of the host clam. The transport of inorganic carbon (Ci) from seawater to Symbiodinium (=zooxanthellae) is an essential function of hosts that derive the majority of their respiratory energy from the photosynthate exported by the zooxanthellae. Immunolocalisation studies show that the host has adapted its physiology to acquire, rather than remove CO2, from the haemolymph and clam tissues. Two carbonic anhydrase (CA) isoforms (32 and 70 kDa) play an essential part in this process. These have been localised to the mantle and gill tissues where they catalyse the interconversion of HCO3- to CO2, which then diffuses into the host tissues. The zooxanthellae exhibit a number of strategies to maximise Ci acquisition and utilisation. This is necessary as they express a form II Rubisco that has poor discrimination between CO2 and O-2. Evidence is presented for a carbon concentrating mechanism (CCM) to overcome. this disadvantage. The CCM incorporates the presence of a light-activated CA activity, a capacity to take up both HCO3- and CO2, an ability to accumulate an elevated concentration of Ci within the algal cell, and localisation of Rubisco to the pyrenoid. These algae also express both external and intracellular CAs, with the intracellular isoforms being localised to the thylakoid lumen and pyrenoid. These results have been incorporated into a model that explains the transport of Ci from seawater through the clam to the zooxanthellae.

Screening of human primary melanocytes of defined melanocortin-1 receptor genotype: Pigmentation marker, ultrastructural and UV-survival studies

Recent population studies have demonstrated an association with the red-hair and fair-skin phenotype with variant alleles of the melanocortin-1 receptor (MC1R) which result in amino acid substitutions within the coding region leading to an altered receptor activity. In particular, Arg151Cys, Arg160Trp and Asp294His were the most commonly associated variants seen in the south-east Queensland population with at least one of these alleles found in 93% of those with red hair. In order to study the individual effects of these variants on melanocyte biology and melanocytic pigmentation, we established a series of human melanocyte strains genotyped for the MC1R receptor which included wild-type consensus, variant heterozygotes, compound heterozygotes and homozygotes for Arg151Cys, Arg160Trp, Val60Leu and Val92Met alleles. These strains ranged from darkly pigmented to amelanotic, with all strains of consensus sequence having dark pigmentation. UV sensitivity was found not to be associated with either MC1R genotype or the level of pigmentation with a range of sensitivities seen across all genotypes. Ultrastructural analysis demonstrated that while consensus strains contained stage IV melanosomes in their terminal dendrites, Arg151Cys and Arg160Trp homozygote strains contained only stage II melanosomes. This was despite being able to show expression of tyrosinase and tyrosinase-related protein-1 markers, although at reduced levels and an ability to convert exogenous 3,4-dihydroxyphenyl-alanine (DOPA) to melanin in these strains.

Discrete cyanide-bridged mixed-valence Co/Fe complexes: Outer-sphere redox behaviour

The outer-sphere redox behaviour of a series of [LnCoIII-NCFeII(CN)(5)](-) (L-n = n-membered pentadentate aza-macrocycle) complexes have been studied as a function of pH and oxidising agent. All the dinuclear complexes show a double protonation process at pH approximate to 2 that produces a shift in their UV/Vis spectra. Oxidation of the different non-protonated and diprotonated complexes has been carried out with peroxodisulfate, and of the non-protonated complexes also with trisoxalatocobaltate(III). The results are in agreement with predictions from the Marcus theory. The oxidation of [Fe(phen)(3)](3+) and [IrCl6](2-) is too fast to be measured, although for the latter the transient observation of the process has been achieved at pH = 0. The study of the kinetics of the outer-sphere redox process, with the S2O82- and [Co(ox)(3)](3-) oxidants, has been carried out as a function of pH, temperature, and pressure. As a whole, the values found for the activation volumes, entropies, and enthalpies are in the following margins, for the diprotonated and non-protonated dinuclear complexes, respectively: DeltaV(not equal) from 11 to 13 and 15 to 20 cm(3) mol(-1); DeltaS(not equal) from 110 to 30 and -60 to -90 J K-1 mol(-1); DeltaH(not equal) from 115 to 80 and 50 to 65 kJ.mol(-1). The thermal activation parameters are clearly dominated by the electrostriction occurring on outer-sphere precursor formation, while the trends found for the values of the volume of activation indicate an important degree of tuning due to the charge distribution during the electron transfer process. The special arrangement on the amine ligands in the isomer trans[(L14CoNCFeII)-N-III(CN)(5)](-) accounts for important differences in solvent-assisted hydrogen bonding occurring within the outer-sphere redox process, as has been established in redox reactions of similar compounds. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003).

Síntese, aplicação e avaliação da toxicidade aguda de complexo orgânico à base de európio proposto como marcador fotoluminescente para a Identificação de resíduos de tiro

Um complexo de alta fotoluminescência é proposto como marcador óptico para a identificação de resíduos de tiro (GSR). O marcador é o complexo [Eu(PIC)3(NMK)3], de fórmula molecular Eu(C6H2N3O7)3.(C7H13NO)3, que apresenta o íon Eu3+ e os ligantes ácido pícrico (PIC) e n-metil-Ɛ-caprolactama (NMK). Foi realizada a caracterização quimicamente através de espectroscopia de emissão, espectroscopia de infravermelho com transformada de Fourier (FTIR), termogravimetria e análise térmica diferencial (TG/DTA), e espectrometria de massas com ionização por eletrospray e ressonância ciclotrônica de íons por transformada de Fourier (ESI-FT-ICR MS), e, em seguida, foram adicionadas diferentes massas do complexo a munições convencionais (de 2 a 50 mg por cartucho). Após os tiros, o GSR marcado foi visualmente e quimicamente detectado por irradiação UV (ʎ = 395 nm) e ESI-FT-ICR MS, respectivamente. Os resultados mostraram uma fotoluminescência eficiente e duradoura, sendo facilmente visível sobre a superfície do alvo, no ambiente, no cartucho deflagrado, na arma de fogo, e sobre as mãos e braços do atirador quando utilizada massa a partir de 25 mg do marcador em cartuchos .38 e 50 mg em cartuchos .40. Sua toxicidade aguda também foi avaliada empregando-se o Protocolo 423 da Organização para a Cooperação e Desenvolvimento Econômico (OECD) e apresentou DL50 de 1000 mg.kg-1, sendo classificado como de categoria 4 na escala do Sistema Globalmente Harmonizado de Classificação e Rotulagem de Produtos Químicos (GHS), considerado, portanto, de média toxicidade. O composto mostrou ser menos tóxico do que os componentes inorgânicos de munições convencionais (em especial o Pb), justificando o seu emprego como marcador de GSR.

The influence of light spectra, UV-A, and growth regulators on the in vitro seed germination of Senecio cineraria DC.

This study was carried out to investigate the effects of light spectra, additional UV-A, and different growth regulators on the in vitro germination of Senecio cineraria DC. Seeds were surface-sterilized and inoculated in MS medium to evaluate the following light spectra: white, white plus UV-A, blue, green, red or darkness. The maximum germinability was obtained using MS0 medium under white light (30%) and MS + 0.3 mg L-1 GA3 in the absence of light (30.5%). S. cineraria seeds were indifferent to light. Blue and green lights inhibited germination. Different concentrations of gibberellic acid (GA3) (0.1; 0.4; 0.6; 0.8; 1.0 and 2.0 mg L-1) and indole-3-acetic acid IAA (0.1; 0.3 and 1.0 mg L-1) were evaluated under white light and darkness. No concentration of GA3 enhanced seed germination percentage under white light. However, when the seeds were maintained in darkness, GA3 improved germination responses in all tested concentrations, except at 1.0 mg L-1. Under white light, these concentrations also increased the germination time and reduced germination rate. Germination rate, under light or darkness, was lower using IAA compared with GA3.

Adaptive deblocking filter for transform domain Wyner-Ziv video coding

Wyner-Ziv (WZ) video coding is a particular case of distributed video coding, the recent video coding paradigm based on the Slepian-Wolf and Wyner-Ziv theorems that exploits the source correlation at the decoder and not at the encoder as in predictive video coding. Although many improvements have been done over the last years, the performance of the state-of-the-art WZ video codecs still did not reach the performance of state-of-the-art predictive video codecs, especially for high and complex motion video content. This is also true in terms of subjective image quality mainly because of a considerable amount of blocking artefacts present in the decoded WZ video frames. This paper proposes an adaptive deblocking filter to improve both the subjective and objective qualities of the WZ frames in a transform domain WZ video codec. The proposed filter is an adaptation of the advanced deblocking filter defined in the H.264/AVC (advanced video coding) standard to a WZ video codec. The results obtained confirm the subjective quality improvement and objective quality gains that can go up to 0.63 dB in the overall for sequences with high motion content when large group of pictures are used.

Desenvolvimento de materiais poliméricos resistentes à radiação UV: determinação quantitativa de estabilizadores à radiação UV

A presente tese teve por objectivo principal o desenvolvimento de métodos que permitissem quantificar alguns aditivos HALS (Hindered Amine Ligth Stabilizers - Aminas Estericamente Impedidas Estabilizadoras à luz), tais como, Tinuvin 622®, Chimassorb 944® e Chimassorb 2020® presentes em amostras de corda sintética. Os métodos de quantificação compreenderam a hidrólise básica para o Tinuvin 622® e a hidrólise ácida para ambos os Chimassorbs, e a separação e identificação por HPLC-MS/MS dos produtos da mesma. Procedendo à realização do método com o respectivo padrão de cada aditivo foi possível obter-se uma curva de calibração para o Tinuvin 622® (y = 899733 X - 96173; r = 0,9979) e para o Chimassorb 944® (y = 44177 X - 18248; r = 0,9965). Relativamente ao Chimassorb 2020® foram realizados alguns ensaios preliminares fundamentais para o desenvolvimento de um método de quantificação para este aditivo. Para o Tinuvin 622® foram realizados ainda ensaios de forma a desenvolver-se um método em que a quantificação ocorresse exclusivamente pela separação do hidrolisado no HPLC com detector UV. Dado que o Tinuvin 622® não apresenta absorção no UV optou-se por realizar a derivatização fluorescente deste através da esterificação com PyCOOH (ácido pirenobutírico) em meio ácido. Nas amostras de corda foram realizados ensaios de envelhecimento e tracção, ensaios de brilho, ensaios de absorção, bem como a quantificação do Tinuvin 622® nas cordas com e sem tratamento de irradiação (envelhecimento). Comprovou-se que as amostras de corda contêm cerca de 0,2% de Tinuvin 622® e que a corda preta não contém aditivo HALS. Verificou-se que em cordas sujeitas à radiação UV, a tensão de ruptura é influenciada pela quantidade de Tinuvin 622® e que esta por sua vez depende do tempo de exposição a que a corda foi sujeita. Por outro lado, concluiu-se que a cor (pigmentos) e o brilho não apresentam influência significativa na resistência das cordas quando expostas à radiação UV.