bluuebunny/crossref_metadata_2025 huggingface dataset:
Survey ofPseudomonas aeruginosagenotypes in colonised cystic fibrosis patients
Authors: Van daele S. , Vaneechoutte M. , De Boeck K. , Knoop C. , Malfroot A. , Lebecque P. , Leclercq-Foucart J. , Van Schil L. , Desager K. , De Baets F.
Published: June 2006

The current authors aimed to examine whether cystic fibrosis (CF) patients in Belgium sharedPseudomonas aeruginosagenotypes and to compare the genotypes of isolates from the same patients during two consecutive years. A Belgian databank of theP. aeruginosagenotypes of all colonised CF patients was created.

Sputum samples from a total of 276P. aeruginosacolonised patients during 2003, and from a subgroup of 95 patients in 2004, were analysed. Patients were asked about any social contact between each other by questionnaire. AllP. aeruginosaisolates exhibiting different colonial morphology on McConkey agar were first genotyped using arbitrarily primed PCR, whereafter single representatives of each randomly amplified polymorphic DNA-type were further genotyped by fluorescent amplified fragment length polymorphism analysis.

In the 213 patients from whomP. aeruginosacould be cultured (resulting in 910 isolates), a total of 163 genotypes were found. The majority (75%) of patients harboured only one genotype. In most of the limited number of clusters, previous contacts between patients could be suspected. In 80% of the patients studied during both years,P. aeruginosagenotype remained unchanged.

In conclusion, most colonised cystic fibrosis patients harbour only onePseudomonas aeruginosagenotype, despite showing different colonial morphotypes. The number of clusters is limited, and most patients seem to retain the same genotypic strain during both years.
Improving the accuracy of protein secondary structure prediction using structural alignment
Authors: Montgomerie Scott , Sundararaj Shan , Gallin Warren J , Wishart David S
Published: June 2006

Background

The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3) of about 75%. We believe this accuracy could be further improved by including structure (as opposed to sequence) database comparisons as part of the prediction process. Indeed, given the large size of the Protein Data Bank (>35,000 sequences), the probability of a newly identified sequence having a structural homologue is actually quite high.

Results

We have developed a method that performs structure-based sequence alignments as part of the secondary structure prediction process. By mapping the structure of a known homologue (sequence ID >25%) onto the query protein's sequence, it is possible to predict at least a portion of that query protein's secondary structure. By integrating this structural alignment approach with conventional (sequence-based) secondary structure methods and then combining it with a "jury-of-experts" system to generate a consensus result, it is possible to attain very high prediction accuracy. Using a sequence-unique test set of 1644 proteins from EVA, this new method achieves an average Q3 score of 81.3%. Extensive testing indicates this is approximately 4–5% better than any other method currently available. Assessments using non sequence-unique test sets (typical of those used in proteome annotation or structural genomics) indicate that this new method can achieve a Q3 score approaching 88%.

Conclusion

By using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called PROTEUS, that performs these secondary structure predictions is accessible athttp://wishart.biology.ualberta.ca/proteus. For high throughput or batch sequence analyses, the PROTEUS programs, databases (and server) can be downloaded and run locally.
In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India
Authors: Thangaraj Kumarasamy , Chaubey Gyaneshwer , Singh Vijay Kumar , Vanniarajan Ayyasamy , Thanseem Ismail , Reddy Alla G , Singh Lalji
Published: June 2006

Background

Macrohaplogroups 'M' and 'N' have evolved almost in parallel from a founder haplogroup L3. Macrohaplogroup N in India has already been defined in previous studies and recently the macrohaplogroup M among the Indian populations has been characterized. In this study, we attempted to reconstruct and re-evaluate the phylogeny of Macrohaplogroup M, which harbors more than 60% of the Indian mtDNA lineage, and to shed light on the origin of its deep rooting haplogroups.

Results

Using 11 whole mtDNA and 2231 partial coding sequence of Indian M lineage selected from 8670 HVS1 sequences across India, we have reconstructed the tree including Andamanese-specific lineage M31 and calculated the time depth of all the nodes. We defined one novel haplogroup M41, and revised the classification of haplogroups M3, M18, and M31.

Conclusion

Our result indicates that the Indian mtDNA pool consists of several deep rooting lineages of macrohaplogroup 'M' suggesting in-situ origin of these haplogroups in South Asia, most likely in the India. These deep rooting lineages are not language specific and spread over all the language groups in India. Moreover, our reanalysis of the Andamanese-specific lineage M31 suggests population specific two clear-cut subclades (M31a1 and M31a2). Onge and Jarwa share M31a1 branch while M31a2 clade is present in only Great Andamanese individuals. Overall our study supported the one wave, rapid dispersal theory of modern humans along the Asian coast.
Community-based surveillance of malaria vector larval habitats: a baseline study in urban Dar es Salaam, Tanzania
Authors: Vanek Michael J , Shoo Bryson , Mtasiwa Deo , Kiama Michael , Lindsay Steven W , Fillinger Ulrike , Kannady Khadija , Tanner Marcel , Killeen Gerry F
Published: June 2006

Background

As the population of Africa rapidly urbanizes it may be possible to protect large populations from malaria by controlling aquatic stages of mosquitoes. Here we present a baseline evaluation of the ability of community members to detect mosquito larval habitats with minimal training and supervision in the first weeks of an operational urban malaria control program.

Methods

The Urban Malaria Control Programme of Dar es Salaam recruited and provided preliminary training to teams of Community-Owned Resource Persons (CORPs) who performed weekly surveys of mosquito breeding sites. Two trained mosquito biologists accompanied each of these teams for one week and evaluated the sensitivity of this system for detecting potential Anopheles habitats.

Results

Overall, 42.4% of 986 habitats surveyed by an inspection team had previously been identified by CORPs. Agricultural habitats were detected less often than other habitats (30.8% detected, Odds Ratio [95%CI] = 0.46 [0.29–0.73], P = 0.001). Non-agricultural artificial habitats were less suitable than other habitats (29.3% occupancy, OR = 0.69 [0.46–1.03], P = 0.066) but still constituted 45% (169/289) of occupied habitats because of their abundance (51 % of all habitats).

Conclusion

The levels of coverage achieved by modestly trained and supported CORPs at the start of the Dar es Salaam UMCP were insufficient to enable effective suppression of malaria transmission through larval control. Further operational research is required to develop surveillance systems that are practical, affordable, effective and acceptable so that community-based integrated vector management can be implemented in cities across Africa.
Quantum dots – a versatile tool in plant science?
Authors: Müller Frank , Houben Andreas , Barker Peter E , Xiao Yan , Käs Josef A , Melzer Michael
Published: June 2006

An optically stable, novel class of fluorophores (quantum dots) for in situ hybridisation analysis was tested to investigate their signal stability and intensity in plant chromosome analyses. Detection of hybridisation sites in situ was based on fluorescence from streptavidin-linked inorganic crystals of cadmium selenide. Comparison of quantum dots (QDs) with conventional detection systems (Alexa 488) in immunolabeling experiments demonstrated greater sensitivity than the conventional system. In contrast, detection of QDs in in situ hybridisation of several plant chromosomes, using several high-copy sequences, was less sensitve than Alexa 488. Thus, semiconductor nanocrystal fluorophores are more suitable for immunostaining but not for in situ hybridisation of plant chromosomes.
Modulation of granulocyte-endothelium interactions by antileukoproteinase: inhibition of anti-type II collagen antibody-induced leukocyte attachment to the synovial endothelium
Authors: Sehnert Bettina , Gierer Philip , Ibrahim Saleh , Kühl Anja , Voll Reinhard , Nandakumar Kutty Selva , Holmdahl Rikard , Hallmann Rupert , Vollmar Brigitte , Burkhardt Harald
Published: June 2006

Antileukoproteinase (ALP) is a physiological inhibitor of granulocytic serine proteases that has been shown to have anti-inflammatory properties in addition to its antiproteolytic activity. On the basis of its potential to block anti-collagen type II (CII) antibody-induced arthritis (CAIA) and to suppress the conformational activation of β2-integrins in leukocytes, the present study was undertaken to investigate its interference with leukocyte adherence to cytokine-activated endothelium. The potential of recombinant ALP to block the interactions of leukocytes with the endothelial lining was concomitantly investigated in vitro and in vivo. Thus, intravital fluorescence microscopic imaging of leukocyte rolling and firm adhesion to postcapillary venules were performed in the knee joints of DBA1/J mice after intravenous injection of anti-CII mAbs. An IL-1β-activated endothelial layer formed by a murine glomerular cell line (glEND.2) was used to assay the interaction with human leukocytes in vitro. Electromobility shift and luciferase reporter gene assays permitted the analysis of cytokine-induced activation of the NF-κB pathway. Fluorescence-activated cell sorting was applied to determine endothelial E-selectin expression. Leukocyte rolling and firm adhesion to the synovial endothelium in an early response to the anti-CII antibody transfer were significantly decreased in ALP-pretreated mice. Concomitantly, ALP suppressed the IL-1β-induced NF-κB activation and the upregulation of E-selectin expression in glEND.2 cells in vitro. These findings support the notion that the newly uncovered properties of ALP to interfere with cytokine signalling and upregulation of adhesion molecules in endothelial cells are likely to contribute to the therapeutic potential of ALP in immune-complex-induced tissue injury.
The MHC2TA-168A>G gene polymorphism is not associated with rheumatoid arthritis in Austrian patients
Authors: Yazdani-Biuki Babak , Brickmann Kerstin , Wohlfahrt Klaus , Mueller Thomas , März Winfried , Renner Wilfried , Gutjahr Manuela , Langsenlehner Uwe , Krippl Peter , Wascher Thomas C , Paulweber Bernhard , Graninger Winfried , Brezinschek Hans-Peter
Published: June 2006

An association between susceptibility to rheumatoid arthritis (RA) and a common -168A>G polymorphism in the MHC2TA gene with differential major histocompatibility complex (MHC) II molecule expression was recently reported in a Swedish population. The objective of the present study was to replicate this finding by examining the -168A>G polymorphism in an Austrian case–control study. Three hundred and sixty-two unrelated RA cases and 351 sex-matched and age-matched controls as well as 1,709 Austrian healthy individuals were genotyped. All participants were from the same ethnic background. Genotyping was performed using 5' allelic discrimination assays. The association between susceptibility to RA and the -168A>G single nucleotide polymorphism was examined by chi-square test. Comparison was made assuming a dominant effect (AG + GG genotypes versus AA genotype). In contrast to the primary report, the frequency of MHC2TA -168G allele carriers was not significantly different between patients and controls in the Austrian cohort. The homozygous MHC2TA -168 GG genotype was more frequent in matched controls than in Austrian RA patients. There was no association between the presence of RA-specific autoantibodies and the MHC2TA -168 GG genotype. In this cohort of Austrian patients, no association between the MHC2TA polymorphism and RA was found.
ESR Studies on Poly(methyl acrylate) Radicals in the Frozen State
Authors: Sugiyama Yoshio
Published: June 2006

Poly(methyl acrylate) radical and poly(methyl acrylate-α-d) radical, generated from the polymerization of methyl acrylate (MA) and methyl acrylate-α-d (MA-d) in the frozen (solid) state, have been investigated by Electron Spin Resonance (ESR). The α-position selective deuteration of poly(MA) radical made the shoulders of poly(MA) radical emerge as more clearly isolated peaks. Both ESR spectra of poly(MA) radicals and those of poly(MA-d) radicals were simulated for the conformational ratio 2.2 between a stable conformation and eclipsed conformations. The energy difference between the stable conformation and two eclipsed conformations was estimated to be 0.27 kcal mol−1 for poly(MA) radical in the thermal equilibrium solid state.
Preparation and Some Properties of One Structural Isomer of Tetra-Substituted Phthalocyanine; 1,8,15,22-Tetrakis(pentan-3′-yloxy)phthalocyanine and Its Metal(II) Complexes
Authors: Kasuga Kuninobu , Asano Kenichiro , Lin Liang , Sugimori Tamotsu , Handa Makoto , Abe Koji , Kikkawa Takahiro , Fujiwara Takaji
Published: June 2006

The title phthalocyanine (1) was prepared from 3-(pentan-3′-yloxy)phthalonitrile, of which a bulky substituent on the 3-position caused an exclusive formation of 1 out of the possible structural isomers.

Complexes of magnesium(II), cobalt(II), nickel(II), copper(II), and zinc(II) were prepared by refluxing a DMF solution of 1 and corresponding metal(II) chlorides, and were characterized by the absorption and 1H NMR spectra as well as elemental analyses.

Magnesium(II) and zinc(II) complexes showed a new band at the longer wavelength side of the Q band in chloroform, probably due to the formation of a face-to-face slipped dimer.

Compound 1 and its magnesium(II), nickel(II), or copper(II) complex showed three ring-oxidative and reductive processes, and the zinc(II) complex showed four in dichloromethane in their cyclic voltammograms. The cobalt(II) complex showed five processes, two of which arose from a central cobalt(II) ion. The oxidation of the cobalt(II) ion occurred at a more negative potential in DMF.

The crystal structure of the nickel(II) complex was determined by an X-ray analysis; substitution on the 1,8,15, and 22 positions of the ring by pentan-3-yloxy groups was confirmed. The molecules are stacked with a distance of 3.32 Å between the phthalocyanine rings.
Convenient Preparation of Pheophytin b from Plant Extract through the C7-Reduced Intermediate
Authors: Oba Toru , Masada Yukiko , Tamiaki Hitoshi
Published: June 2006

A new method for the large scale preparation of Pheophytin (=Pheo) b is presented. The difficulty in chromatographic isolation of Pheo a and b, tetrapyrrole pigments, from the large amount of plant extract was overcome by an increase in polarity of the pigment given by a selective modification of Pheo b. Treatment of plant extract containing both Pheo a and b, carotenoids, lipids, etc. with a mild reductant t-BuNH2BH3 induced selective reduction of the C7-formyl group of Pheo b, but left unaffected other carbonyl moieties of the molecules. The resulting compound 7-hydroxymethyl-Pheo b was readily separated from intact Pheo a by silica gel column chromatography. Pure Pheo b was obtained by oxidation of the 7-hydroxymethyl-Pheo b with pyridinium chlorochromate. One of the reasons why the present method is superior to the previous ones is that Pheo a was obtained simultaneously as an intact form. Another is the utility of the intermediate compound, 7-hydroxymethyl-Pheo b: as the starting material for syntheses of various compounds as well as a model of ingredients in the photosynthetic systems, such as a light-harvesting apparatus of green photosynthetic bacteria.
Radical Cyclization of Allyl 2-Iodophenyl Ether, N,N-Diallyl-2-iodoaniline, and 2-Iodoethanal Acetal by Means of Trialkylmanganate(II)
Authors: Inoue Rie , Nakao Junko , Shinokubo Hiroshi , Oshima Koichiro
Published: June 2006

Treatment of allyl 2-halophenyl ethers with tributylmanganate (n-Bu3MnLi or n-Bu3MnMgBr) provided dihydrobenzofuran derivatives in good yield. Indoline derivatives are also produced effectively starting from 2-iodoaniline compounds. The reaction could proceed by the following sequences: (1) formation of a radical by treatment of iodophenol or iodoaniline derivatives with tributylmanganate(II), (2) radical cyclization, and (3) recombination of radical and manganese species giving alkylmanganese(II) compound. The reaction proved to proceed in the presence of a catalytic amount of manganese(II) chloride under atmospheric oxygen. The manganese catalyzed radical cyclization could also be applied to 2-iodoethanal acetal, in which case the presence of oxygen was not necessary.
Anomalous Electronic Absorption in Lapacholi–Alcohol Solutions
Authors: Portugal Samira da Guia Mello , Herrera Juan Omar Machuca , Brinn Ira Mark
Published: June 2006

An anomalous band at the red end of the absorption spectrum of lapachol (an anti-cancer compound) appears when the solvent used is a lighter molecular-weight alcohol, but not in purely aqueous solution. This band does not follow Beer’s law, and is attributed to a weak transition of the structurally modified monomeric ortho naphthoquinone tautomer in these solvents. The “normal” para tautomer is considered to exist predominantly in the dimeric form at all concentrations above approximately 10−4 M. This interpretation is supported by spectroscopic data on structurally related compounds, as well as molecular-orbital calculations.
Molecular Conformation of Butanenitrile in Gas, Liquid, Glass, and Crystalline States: In Relation to the Stability of the Glass State
Authors: Ishii Kikujiro , Nakayama Hideyuki , Koyama Kei , Yokoyama Yoshihiro , Ohashi Yuji
Published: June 2006

Molecular conformation of butanenitrile in gas, liquid, glass, and crystalline states was studied to clarify the cause of the stability of its glass state against crystallization. The crystal comprises gauche molecules. However, the trans and gauche conformations have energies very close to each other, with an in-between energy barrier that cannot be surmounted at low temperatures. The multiple conformation that exists in gas and liquid is frozen in the glass, keeping the glass of butanenitrile in the disordered state even at temperatures as high as 100 K.
Photoreduction of Hydrogencarbonate or Ethylene Catalyzed by Trisodium Trisulfonatophthalocyaninatozincate(II)
Authors: Kasuga Kuninobu , Terauchi Masumi , Hara Mayu , Nishie Kenji , Sugimori Tamotsu , Handa Makoto
Published: June 2006

In an aqueous dimethyl sulfoxide (DMSO) solution of triethanolamine (TEOA), the photosensitizer of the title complex (1), and 1,1′-dimethyl-4,4′-bipyridinium dichloride (MVCl2), MV•+ radicals were formed upon irradiation with visible light; the photoreduction proceeded with light from both the B- (340 nm) and Q- (674 nm) band wavelengths of 1.

The photoreduction of hydrogencarbonate to methane was performed in an aqueous DMSO solution of an electron donor, 1, MVCl2, and ruthenium colloid upon irradiation with visible light. Ethylene was also photoreduced to ethane upon the irradiation of an aqueous solution of an electron donor, 1, MVCl2, and palladium colloid.
Synthesis and Properties of s-Alkyl-Substituted Silanediyl-Bridged and Silanetriyl-Bridged Diiron Complexes, Cp2(CO)2Fe2(μ-CO)[μ-Si(X)CHR2] and Cp2(CO)2Fe2(μ-CO)[μ-Si(DMAP)CHR2]+I− (X = H, I; R = Et, Ph; DMAP = 4-(Dimethylamino)pyridine)
Authors: Luh Lung-Shiang , Wen Yuh-Sheng , Tobita Hiromi , Ogino Hiroshi
Published: June 2006

Photolysis of 2 molar amounts of CpFe(CO)2SiMe3 (= FpSiMe3, 1) with s-alkylsilanes R2CHSiH3 (2a: R = Et; 2b: R = Ph) produces the silylene (or silanediyl)-bridged diiron complexes Cp2(CO)2Fe2(μ-CO)[μ-Si(H)CHR2] (3a: R = Et; 3b: R = Ph) which exist mainly in cis-form. The treatment of cis-3 with an excess amount of CH2I2 stereoselectively affords the iodosilylene-bridged diiron complexes Cp2(CO)2Fe2(μ-CO)[μ-Si(I)CHR2] (4a: R = Et; 4b: R = Ph) in cis-form. The reaction of complexes 4 with 4-(dimethylamino)pyridine (= DMAP) gives the base-stabilized silylyne (or silanetriyl)-bridged diiron complexes Cp2(CO)2Fe2(μ-CO)[μ-Si(DMAP)CHR2]+I− (5a: R = Et; 5b: R = Ph) in 35 and 43% yields, respectively. The cis–trans isomerization of complexes 3 was studied under thermal and photochemical reaction conditions. The molar ratios of the cis and trans isomers of complexes 3 in the thermal equilibrium at 50 °C were 95 : 5 (3a) and 78 : 22 (3b), respectively, and in the photostationary state at 10 °C were 80 : 20 and 30 : 70, respectively. The structures of complexes 3b and 4b have been characterized by X-ray diffraction.
Photoinduced Electron Transfer from Tetraphenyl-Substituted 1,2-Digermacyclohexa-3,5-dienes and Related Compounds to C60
Authors: Mochida Kunio , Akazawa Miyuki , Fijitsuka Mamoru , Watanabe Akira , Ito Osamu
Published: June 2006

The irradiation of benzene–benzonitrile solutions of 3,4,5,6-tetraphenyl-substituted 1,2-digermacyclohexa-3,5-dienes and related compounds in the presence of C60 afforded the corresponding ring-contracted products, namely 1-germacyclopenta-2,4-dienes, with the extrusion of germylene and ring-expanded oxadigerma compounds, namely 1-oxa-2,7-digermacyclohepta-3,5-dienes. The laser flash photolysis of a benzene–benzonitrile solution of 1,2-digermacyclohexa-3,5-dienes in the presence of C60 showed that the transient absorption band of the C60 triplet state (TC60*) appeared immediately at 730 nm. With the decay of TC60*, the absorption bands of the radical anion of C60•− appeared at 1060 nm, showing that an electron transfer takes place from 1,2-digermacyclohexa-3,5-dienes to TC60*. The formation of cyclic oxadigerma compounds was explained by processes of both the photooxidation of 1,2-digermacyclohexa-3,5-dienes in the absence of C60 with singlet oxygen and oxidation of the cation radical of 1,2-digermacyclohexa-3,5-dienes with triplet oxygen.
Crystal Structure of Cesium Salt of β-Isomer of A-Type Vanadium-Trisubstituted Dodecatungstophosphate Anion, A-β-Cs5.4H0.6[PV3W9O40]·12H2O
Authors: Kawafune Isao , Tamura Hatsue , Matsubayashi Gen-estu
Published: June 2006

The crystal structure of the title compound as the cesium salt of the vanadium-trisubstituted dodecatungstophosphate anion was determined by a single X-ray analysis. The anion is a geometrical β-isomer and an A-type positional isomer; three V atoms are not in disorder with W atoms, being linked to one another through the corner-sharing oxygen atom. The V–V distances are substantially shortened in comparison with the corresponding W–W ones of the β-tungstosilicate analogs, which is attributable to a difference in ion radii of V5+ (0.68 Å) and W6+ (0.74 Å). A non-bonded contact between a Cs atom and one of the bridging oxygen atoms in the V–O–V bonds is apparently short compared with the other contacts between the Cs atoms and oxygen atoms of the polyanion. Taking into consideration that this Cs atom is in disorder with a proton, this bridging oxygen atom is considered to be protonated. A bond-valence calculation for the bridging oxygen atoms in the polyanion also suggests protonation of this bridging oxygen atom.
Steric-Hindrance Effect of a Substituent in the Self-Assembly Process of Copper(II) Complexes with Quadridentate Schiff-Base Ligands Involving a 2-Substituted-Imidazole Moiety
Authors: Matsumoto Naohide , Mimura Masaaki , Sunatsuki Yukinari , Eguchi Shingo , Mizuguchi Yukiko , Miyasaka Hitoshi , Nakashima Toshio
Published: June 2006

Four copper(II) complexes with unsymmetrical quadridentate ligands involving an imidazole moiety, [CuHLn]ClO4 (1—4; n = 1—4), have been prepared and characterized, where HL1 = N-salicylidene-N′-(2-methylimidazol-4-ylmethylidene)-1,3-propanediamine, HL2 = N-salicylidene-N′-(2-phenylimidazol-4-ylmethylidene)-1,3-propanediamine, HL3 = N-acetylacetonylidene-N′-(2-methylimidazol-4-ylmethylidene)ethylenediamine, HL4 = N-acetylacetonylidene-N′-(2-phenylimidazol-4-ylmethylidene)ethylenediamine, respectively. The corresponding deprotonated complexes 1′—4′ were obtained when 1—4 were treated under an alkaline condition. Deprotonation of the imidazole moiety of the copper(II) complex motivates a self-assembly process which is formed by an axial coordination of the imidazolate nitrogen atom of a molecular unit to the copper(II) ion of another unit. 1′—3′ assumes a self-assembled imidazolate-bridged infinite-chain structure {Cu(II)–Im}n in the solid state, while the polymeric species dissociates to monomeric species in the solution state. 4′ consists of a discrete deprotonated monomeric species, even in the solid state. The physical measurements, including reflectance and absorption spectra, cryomagnetic measurements, and single-crystal X-ray analyses, revealed that the self-assembly behavior for the series of copper(II) complexes depends both on the steric effect of the substituent of 2-substituted-4-formylimidazole moiety and the ligand field strength of the equatorial quadridentate ligand.
Studies on Dichalcogena Dications of 2-Center-2-electron and 3-Center-4-electron Bonds: Isolation and Intermediary Formation
Authors: Furukawa Naomichi
Published: June 2006

1,5-(Dithia and diselena)cyclooctanes gave the dithia and diselena dications. Their structures were determined by X-ray crystallographic analyses. Similarly, dithia and diselena dications were produced on oxidation with 2 equiv of NOBF4 or NOPF6 or on treatment of the corresponding monooxides with Tf2O or concd H2SO4 from the sterically congested bis-sulfides or bis-selenides, such as 1,9-bis(thio- or seleno-substituted)dibenzochalcogenophene, 1,8-bis(thio- or seleno-substituted)naphthalenes and 2,2′-(thio- or seleno-substituted) 1,1′-biphenyls. These dications, however, were found to be unstable and to release the substituents attached at the chalcogen atoms. These either generated reactive species, i.e., quinodimethane and alkyl cations or demonstrated new reactions such as thio-Claisen rearrangement or photochemical conversion of naphtho[1,8-de]-1,3-dithiin derivatives.

Diphenyl chalcogenides bearing 2,6-bis(methylthiomethyl), 2,6-bis(methylselenomethyl) and 2,6-bis[(dimethylamino)methyl] substituents produced the hypervalent chalcogenuranes(λ4). Their structures were determined by X-ray crystallographic analyses and their charge distributions were estimated by the ab initio MO-calculation and 77Se- or 125Te-NMR spectroscopy. Methyl 2,6-bis[(dimethylamino)methyl]phenyl selenide and telluride gave stable monoselenenium and monotellurenium cations on oxidative demethylation by the reaction with t-BuOCl. These are the first monovalent selenenium and tellurenium cation species.
Optically Active Cobalt(III) Complexes Containing Partial Cubane Co3O4 Core: Syntheses and Structures of the Isomers of [Co3(L)3(μ-OH)3(μ3-O)]Cl (L = Ethylenediamine-N-acetate)
Authors: Ama Tomoharu , Shiro Motoo , Takeuchi Akiyoshi , Yonemura Toshiaki , Kawaguchi Hiroshi , Yasui Takaji
Published: June 2006

Four isomers (T0, T1, T2, and T3) of [Co3(edma)3(μ-OH)3(μ3-O)]Cl (edma: ethylenediamine-N-acetate) containing a partial cubane Co3O4 core were isolated and optically resolved. The geometrical structures and absolute configurations of optically active -T2 chloride–water (1/7) and -T3 chloride–water (1/7) were determined by the X-ray diffraction method. The absolute configurations of optically active T0 and T1 were assigned on the basis of the NMR, UV, and CD spectral data. Each isomer was stable for at least 5 d in its neutral aqueous solution. Reversible protonation accompanying a color change was observed for each isomer in the pH range 2—7; this protonation did not accompany the cleavage of its partial cubane core. However, slow decomposition of each isomer was observed in its 60% HClO4 solution.
Cysteine188 Revealed as Being Critical for the Enzyme Activity of Arylmalonate Decarboxylase by Site-Directed Mutagenesis
Authors: Miyazaki Mamoru , Kakidani Hitoshi , Hanzawa Satoshi , Ohta Hiromichi
Published: June 2006

Arylmalonate decarboxylase (AMDase) catalyzes the asymmetric decarboxylation of α-aryl-α-methylmalonic acid. Since this enzyme is inhibited by SH-reagents, a cysteine residue is supposed to be involved at the catalytic site. Cloning of the gene which codes the enzyme revealed that this enzyme contains four cysteine residues. Titration of free SH groups by p-(chloromercurio)benzoate disclosed that all four Cys are in the reduced form. In this study, four mutant enzymes (C101S, C148S, C171S, and C188S) were prepared, in which one of four cysteines was replaced by serine. The CD spectra indicated that the conformational differences of C101S and C188S compared to that of the native enzyme are not so significant. The catalytic activities of the four mutants were measured. Among these mutant enzymes, only C188S showed a drastic decrease in enzyme activity, indicating that cysteine188 is located at the active center of the enzyme. The catalytic activities of the other mutants are also discussed.
The conserved AAUAAA hexamer of the poly(A) signal can act alone to trigger a stable decrease in RNA polymerase II transcription velocity
Authors: Nag Anita , Narsinh Kazim , Kazerouninia Amir , Martinson Harold G.
Published: June 2006

In vivo the poly(A) signal not only directs 3′-end processing but also controls the rate and extent of transcription. Thus, upon crossing the poly(A) signal RNA polymerase II first pauses and then terminates. We show that the G/U-rich region of the poly(A) signal, although required for termination in vivo, is not required for poly(A)-dependent pausing either in vivo or in vitro. Consistent with this, neither CstF, which recognizes the G/U-rich element, nor the polymerase CTD, which binds CstF, is required for pausing. The only part of the poly(A) signal required to direct the polymerase to pause is the AAUAAA hexamer. The effect of the hexamer on the polymerase is long lasting—in many situations polymerases over 1 kb downstream of the hexamer continue to exhibit delayed progress down the template in vivo. The hexamer is the first part of the poly(A) signal to emerge from the polymerase and may play a role independent of the rest of the poly(A) signal in paving the way for subsequent events such as 3′-end processing and termination of transcription.
Negation and the role of gender and ethnic identity in the discourse of Malaysian children
Authors: Yip Cheng Karen Kow
Published: June 2006

This study is a qualitative study of Malaysian children aged between four and six years engaged in a story-telling task. The question posed in this piece of research, then, is the role played by gender and ethnic identity in discourse. If it does play a role, what, then, is the nature of this role? Listed below are the aims of this study:

1. To chart relatively uninterrupted discourse in story-telling among children aged between four and six.

2. To discover gender and ethnic differences in narrative forms, in particular, focus will be given to the use of negation.

3. To examine the role of gender and ethnic identity on the discourse of children.

The path taken by this study is to analyse discourse in story-telling. The aim is to examine the use of negation by children of both sexes and of two ethnic groups in Malaysia (Malays and Chinese) in the act of story-telling. This study is exciting in that actual transcriptions of the story-telling can be analyzed.
Malay ESL college students' spoken discourse: The use of formulaic expressions
Authors: Govindasamy Subramaniam , Kahn Mohana Nambiar
Published: June 2006

For communication purposes, formulaic expressions can be an easy and efficient way to impart information. Very often campaign slogans are built on using such expressions. Because the context and implications are transparent to the listening public, further explanations are usually not required. But once people get used to such a paratactic mode of expression, orally oriented language users may be lulled into thinking that, when they use such a mode of expression, there is no need for further elaboration of an issue at hand. This study examines whether literate Malays (undergraduates) use formulaic expressions in the spoken texts they produce. And in the event that they do, the study also hopes to determine the nature of topics that draws the use of such expressions. The results of the study show categorically that urban students do not use formulaic expressions. However, there is a tendency among rural students to use such expressions especially when discussing topics which are context reduced, i. e. when topics are more abstract.
Plato and the sympotic form in the Symposium of St Methodius of Olympus
Authors: Bril Alexander
Published: June 2006

Formal ist das Symposion des Methodios von Olympos ein Flickwerk, dessen Gestalt hauptsächlich auf dem Symposion Platons beruht. Sein Autor hat zwar Platon sehr viele Worte, Redensarten und Motive unmittelbar entnommen, aber er verrät in vielen Punkten seine Unkenntnis der echten Symposionkonventionen. Wenn man die platonische und methodianische Behandlung der sympotischen literarischen Gattung vergleicht, sieht man, daß diese Gattung zu Inhalt und Personen des Dialogs des Methodios nicht paßte, und daß es diesem Autor mißlang, die Entwicklung seiner theologisch-philosophischen Begriffe zu dem sympotischen Hintergrund in Beziehung zu setzen. Aus diesem Grund (und auch aus anderen Gründen) ist das Stück dramatisch und künstlerisch gänzlich erfolglos. Vielleicht durch seine Polemik gegen die Neoplatoniker, durch sein Interesse für die platonische Lehren (besonders über den ἔρως) und durch seine tiefe Liebe zu platonischer Sprache und Stil ist Methodios bewogen worden, die sympotische literarische Gattung anzunehmen.
The Ethics in Human Research Ethics
Authors: di Norcia Vincent
Published: June 2006

False, but common, assumptions about dilemmas in moral reasoning and the so-called fact/value dichotomy can impede the prosecution JERHRE's prime aim: Facilitating ethical problem solving in human research. Research ethics, and the development of moral science, demand better assumptions about ordinary everyday problem solving morality and the deep-seated connectedness of facts and values.
Research Sponsorship, Financial Relationships, and the Process of Research in Pharmaceutical Clinical Trials
Authors: Gardner William , Lidz Charles W.
Published: June 2006

The effects of sponsorship and financial relationships on the conduct of clinical trials were examined by surveying 321 authors who had published reports of pharmaceutical clinical trials. The survey asked about research sponsorship, financial relationships, who controlled the research, and who carried it out. When a commercial sponsor was the exclusive research sponsor, authors reported less control over and less contribution to the research, and more sponsor control and contribution, as compared with noncommercial or mixed sponsorship. Similarly, financial relationships with firms were associated with less author contribution to and more sponsor control over and contribution to the research. The results raise concerns about bias in the design, conduct, or reporting of research.
Anthropological Research in Light of Research-Ethics Review: Canadian Master's Theses, 1995–2004
Authors: van den Hoonaard Will C. , Connolly Anita
Published: June 2006

Despite claims that research-ethics review is changing or discouraging social research, there are no studies that have tested this assumption. Examining Canadian Master's theses in anthropology between 1995 and 2004, this paper explores the extent to which the theses represent a change in number, topic, or methodology in relation to formal ethics-review guidelines that came into force in Canada in 2001. ProQuest Digital Dissertations reveals that the number of theses has increased, and that there has not been a noticeable shift from research involving humans to research based on archival data, or theoretical or review theses. However, there has been a very significant increase in research that is called ethnography, but that relies exclusively on interviews. Possible reasons for the halving of percent of ethnographic or participant-observation research are explored.
The Anthropologist and the Crayons: Changing Our Focus from Avoiding Harm to Doing Good
Authors: Childress Herb
Published: June 2006

The ethical review process is aimed at protecting research participants, evaluating risk in relation to benefit, and, where possible, reducing risk to research participants (and by extension, to the sponsoring organizations). In practice, however, there is usually much focus on risk and little on benefit. However, social research presents an opportunity to give active benefits to many constituents: The research participants, the host community, the researcher and research team members, the sponsoring institution and funding agency, the academic community, and society at large. Even when benefits are considered, the proximal benefits—those that actually accrue during (and because of) the investigator's presence—are too often overlooked by both investigators and ethics committees in favor of the more distal benefits related to the contribution to knowledge. The research design and review processes can both be redirected to focus more centrally on imagining, creating and extending the benefits of our work.
New household waste recycling centre in Blackpool, UK
Authors: Cunningham L. S. , Conroy A.
Published: June 2006

This paper describes the design and construction of Blackpool Council's new household waste recycling centre. The scheme demonstrates the incorporation of sustainability considerations through design, construction and commissioning. Seeking to reduce the amount of household waste sent to landfill sites, the provision of a high-quality facility for recycling will encourage increased sustainability awareness and participation within the community. As a means of delivering a quality scheme, the challenge of ensuring high durability in combination with aesthetic and environmental enhancement has been met with innovation. Use of polymer fibre reinforcement in the heavy-duty apron slabs provides high durability under aggressive service loads. Elsewhere, incorporation of sub-surface skips facilitates spatial optimisation and allows significant noise attenuation with minimal visual impact. Where possible, materials won from the demolition of existing time-expired structures were incorporated in the new scheme or distributed for reuse elsewhere.
Cardiac Amyloidosis Due to Transthyretin Protein
Authors: Ruberg Frederick L. , Maurer Mathew S.
Published: March 2024

Importance

Systemic amyloidosis from transthyretin (ATTR) protein is the most common type of amyloidosis that causes cardiomyopathy.

Observations

Transthyretin (TTR) protein transports thyroxine (thyroid hormone) and retinol (vitamin A) and is synthesized predominantly by the liver. When the TTR protein misfolds, it can form amyloid fibrils that deposit in the heart causing heart failure, heart conduction block, or arrhythmia such as atrial fibrillation. The biological processes by which amyloid fibrils form are incompletely understood but are associated with aging and, in some patients, affected by inherited variants in the TTR genetic sequence. ATTR amyloidosis results from misfolded TTR protein deposition. ATTR can occur in association with normal TTR genetic sequence (wild-type ATTR) or with abnormal TTR genetic sequence (variant ATTR). Wild-type ATTR primarily manifests as cardiomyopathy while ATTR due to a genetic variant manifests as cardiomyopathy and/or polyneuropathy. Approximately 50 000 to 150 000 people in the US have heart failure due to ATTR amyloidosis. Without treatment, heart failure due to ATTR amyloidosis is associated with a median survival of approximately 5 years. More than 130 different inherited genetic variants in TTR exist. The most common genetic variant is Val122Ile (pV142I), an allele with an origin in West African countries, that is present in 3.4% of African American individuals in the US or approximately 1.5 million persons. The diagnosis can be made using serum free light chain assay and immunofixation electrophoresis to exclude light chain amyloidosis combined with cardiac nuclear scintigraphy to detect radiotracer uptake in a pattern consistent with amyloidosis. Loop diuretics, such as furosemide, torsemide, and bumetanide, are the primary treatment for fluid overload and symptomatic relief of patients with ATTR heart failure. An ATTR-directed therapy that inhibited misfolding of the TTR protein (tafamidis, a protein stabilizer), compared with placebo, reduced mortality from 42.9% to 29.5%, reduced hospitalizations from 0.7/year to 0.48/year, and was most effective when administered early in disease course.

Conclusions and Relevance

ATTR amyloidosis causes cardiomyopathy in up to approximately 150 000 people in the US and tafamidis is the only currently approved therapy. Tafamidis slowed progression of ATTR amyloidosis and improved survival and prevented hospitalization, compared with placebo, in people with ATTR-associated cardiomyopathy.
Uncovering domain motif interactions using high‐throughput protein–protein interaction detection methods
Authors: Idrees Sobia , Paudel Keshav Raj , Sadaf Tayyaba , Hansbro Philip M.
Published: March 2024

Protein–protein interactions (PPIs) are often mediated by short linear motifs (SLiMs) in one protein and domain in another, known as domain–motif interactions (DMIs). During the past decade, SLiMs have been studied to find their role in cellular functions such as post‐translational modifications, regulatory processes, protein scaffolding, cell cycle progression, cell adhesion, cell signalling and substrate selection for proteasomal degradation. This review provides a comprehensive overview of the current PPI detection techniques and resources, focusing on their relevance to capturing interactions mediated by SLiMs. We also address the challenges associated with capturing DMIs. Moreover, a case study analysing the BioGrid database as a source of DMI prediction revealed significant known DMI enrichment in different PPI detection methods. Overall, it can be said that current high‐throughput PPI detection methods can be a reliable source for predicting DMIs.
Homozygous variant in COQ7 causes autosomal recessive hereditary spastic paraplegia
Authors: Qiu Yusen , Xiong Ying , Wang Lulu , Zhu Min , Tan Dandan , Hong Daojun
Published: March 2024

Biallelic mutations in the coenzyme Q7 (COQ7) encoding gene were recently identified as a genetic cause of distal hereditary motor neuropathy. Here, we explored the clinical, electrophysiological, pathological, and genetic characteristics of a Chinese patient with spastic paraplegia associated with recessive variants in COQ7. This patient carried a novel c.322C>A (p.Pro108Thr) homozygous variant. Sural biopsy revealed mild mixed axonal and demyelinating degeneration. Immunoblotting showed a significant decrease in the COQ7 protein level in the patient's fibroblasts. This study confirmed that COQ7 variant as a genetic cause of HSP, and further extended spastic paraplegia to the phenotypic spectrum of COQ7‐related disorders.
Magical Transubstantiations: A Voyage to Italy
Authors: Wagner Aleksandra , Spiller Neil
Published: March 2024

Visiting Italy in 1978 as part of his own Grand Tour, Lebbeus Woods was able to see some of the treasures of the Renaissance and the Baroque. The ensuing mix of reality and imagination prompted the Editors of this 2, Aleksandra Wagner and Neil Spiller, to consider the visual travelogue –Cityscapes – in a similar manner, combining speculation and truth.
Evaluation on Mechanical Properties and Electrical Contact Behaviors for Au/Ni Composite Coating by Experiment and Finite Element Method
Authors: Wu Dao‐Yi , Zhou Xue , Ji Chen‐Song , Zhang Ming‐Xu , Zhai Guo‐Fu
Published: March 2024

Gold coatings are the most widely used protective layer for resisting surface oxidization and corrosion in various complex environments. However, the extremely low hardness, inferior load‐bearing capacity, and lack of an effective strategy for evaluating the elastic‐plastic behavior of gold coatings have greatly limited their further application. The main aim of this work is to investigate the effect of Ni doping on the microstructure, mechanical properties, and electrical contact stability of a coating based on an experimental method and finite element simulation. The strain‐hardening exponent model of the coating is established by employing a reverse analysis method based on the nanoindentation experiment until the reverse and forward loading curves are consistent, thereby determining the yield strength. The results indicate that Ni doping is conducive to enhancing the mechanical properties under the premise of ensuring low contact resistance. The hardness (3.3–4.2 GPa) and yield strength (524.3–689.8 MPa) of the Au1−xNix composite coating with a Ni content of 4 at–8 at% is more than twice as high as that of pure Au. The electrical contacts deposited by the Au1−xNix coatings maintain a low contact resistance range (1.12–3.29 mΩ) at a contact force of 10 gf.
Solar‐Driven Selective Oxidation Over Bismuth‐Based Semiconductors: From Prolific Catalysts to Diverse Reactions
Authors: Li Shutao , Li Yuanrui , Huang Hongwei
Published: March 2024

Synthesis of organic compounds often necessitates rigorous reaction conditions or the involvement of hazardous oxidants, resulting in substantial energy consumption and considerable environmental damage. Photocatalytic selective oxidation represents a green and environmentally friendly way to obtain high‐value chemicals, which has developed rapidly in recent years. Bismuth‐based (Bi‐based) semiconductor materials have gained intense interest in selective organic synthesis due to their diverse crystal structures and compositions, tunable band structure, and outstanding photocatalytic performance. Herein, a systematic summary of the solar‐driven selective oxidation over varieties of Bi‐based semiconductors is provided. Initially, the reactive species involved in selective oxidation, Bi‐based materials widely used in photocatalytic selective oxidation, and the methods for synthesizing these Bi‐based materials are meticulously classified. Concerning their selective oxidation reactions, a variety of modification strategies, with a focus on the separation of photogenerated carriers and the regulation of reactive species is extensively documented. Highlights are the diverse applications and mechanism discussions of Bi‐based photocatalysts in the oxidation reactions, including alcohol oxidation, C─H bond activation, amine oxidation, and sulfide oxidation, as well as the coupling reactions with photoreduction. Finally, the future development prospects and challenges of Bi‐based photocatalysts in the field of selective oxidation is proposed, hoping to provide valuable insights and guidance for the design of photocatalysts for selective oxidation.