bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical Study of the Uniformity of Balloon-Expandable Stent Deployment
Authors: Mortier P. , De Beule M. , Carlier S. G. , Van Impe R. , Verhegghe B. , Verdonck P.
Published: April 2008

Stents are small tubelike structures, implanted in coronary and peripheral arteries to reopen narrowed vessel sections. This endovascular intervention remains suboptimal, as the success rate is limited by restenosis. This renarrowing of a stented vessel is related to the arterial injury caused by stent-artery and balloon-artery interactions, and a local subsequent inflammatory process. Therefore, efforts to optimize the stent deployment remain very meaningful. Several authors have studied with finite element modeling the mechanical behavior of balloon-expandable stents, but none of the proposed models incorporates the folding pattern of the balloon. We developed a numerical model in which the CYPHER™ stent is combined with a realistic trifolded balloon. In this paper, the impact of several parameters such as balloon length, folding pattern, and relative position of the stent with respect to the balloon catheter on the free stent expansion has been investigated. Quantitative validation of the modeling strategy shows excellent agreement with data provided by the manufacturer and, therefore, the model serves as a solid basis for further investigations. The parametric analyses showed that both the balloon length and the folding pattern have a considerable influence on the uniformity and symmetry of the transient stent expansion. Consequently, this approach can be used to select the most appropriate balloon length and folding pattern for a particular stent design in order to optimize the stent deployment. Furthermore, it was demonstrated that small positioning inaccuracies may change the expansion behavior of a stent. Therefore, the placement of the stent on the balloon catheter should be accurately carried out, again in order to decrease the endothelial damage.
Does occupational success influence longevity among England test cricketers?
Authors: Boyle P J
Published: April 2008

Objective:

To determine whether the longevity of England test cricketers is influenced by occupational success, controlling for the influence of social background.

Design:

Archival survey.

Setting:

England.

Subjects:

Those 418 cricketers who played for England in a test match from the first test in 1876 to 1963 when the distinction between amateur and professional status was removed.

Main outcome measures:

Length of life.

Results:

Survival analysis of players born between 1827 and 1941 (349 dead, 69 alive) showed a significant relation between mortality and year of birth (p<0.001), amateur/professional status (p = 0.042) and the number of test matches played (p = 0.042). Captaining England was not related to survival.

Conclusion:

The link between longevity and both social background and occupational success is supported among test match cricketers. Amateur (or “gentlemen”) cricketers from more privileged social backgrounds survived longer than professionals (or “players”). The most successful cricketers who played in a larger number of tests lived longer than those who played in a smaller number of tests. Captaining England, which could be regarded as a form of occupational “control”, was not associated with longevity.
Maximal oxygen intake and independence in old age
Authors: Shephard R J
Published: April 2008

This brief review examines the likelihood that a deterioration of aerobic fitness will lead to a loss of independence in old age. The rate of deterioration of maximal aerobic power observed in middle-aged adults continues unabated during the retirement years. Loss of independence seems likely if maximal oxygen intake falls below a threshold of 18 ml/[kg.min] in men and 15 ml/[kg.min] in women, reached at 80–85 years. A regular programme of aerobic exercise can slow or reverse the functional deterioration, reducing the individual’s biological age by 10 or more years, and potentially prolonging independence by a similar amount. There remains a need to clarify the importance of decreasing aerobic fitness relative to other potential causes of dependency but, from the practical viewpoint, regular aerobic activity should be commended to elderly people since it can address many of the issues of both functional loss and chronic disease.
Evaluation of different ways of presenting LipL32 to the immune system with the aim of developing a recombinant vaccine against leptospirosis
Authors: Seixas Fabiana Kömmling , Fernandes Claudia Hartleben , Hartwig Daiane Drawanz , Conceição Fabricio Rochedo , Aleixo José Antônio Guimarães , Dellagostin Odir Antônio
Published: April 2008

Leptospirosis, caused by bacteria of the genus Leptospira , is a direct zoonosis with wide geographical distribution. The implications in terms of public health and the economical losses caused by leptospirosis justify the use of a vaccine against Leptospira in human or animal populations at risk. In this study, we used the external membrane protein LipL32 as a model antigen, as it is highly immunogenic. The LipL32 coding sequence was cloned into several expression vectors: (i) pTarget, to create a DNA vaccine; (ii) pUS973, pUS974, and pUS977 for expression in BCG (rBCG); and (iii) pAE, to express the recombinant protein in Escherichia coli , for a subunit vaccine. Mice were immunized with the various constructs, and the immune response was evaluated. The highest humoral immune response was elicited by the subunit vaccine (rLipL32). However, with rBCG, the titer was still rising at the end of the experiment. The serum of vaccinated animals was able to recognize LipL32 on the membrane of the Leptospira, detected by indirect immunofluorescence. A monoclonal antibody anti-LipL32 was shown to inhibit the growth of Leptospira in vitro, indicating potential protection induced by the LipL32 antigen.
Bacterial communities associated with the mucopolysaccharide layers of three coral species affected and unaffected with dark spots disease
Authors: Gil-Agudelo Diego L. , Fonseca Diana P. , Weil Ernesto , Garzón-Ferreira Jaime , Smith Garriet W.
Published: April 2008

Dark spots disease (DSD) is a relatively new coral disease that has become one of the most prevalent afflictions in the Caribbean Sea. To partially characterize bacterial communities associated with DSD, carbon utilization patterns of bacterial strains isolated from the surface mucopolysaccharide layers of healthy and DSD-affected Montastraea annularis , Montastraea faveolata , and Siderastrea siderea were compared with each other and with bacterial strains isolated from the water column by using cluster analysis. Differences between healthy and diseased corals were found and were greatest for M. annularis than for the other species. A metabolic group of bacteria similar to Vibrio carchariae was found to be unique to diseased samples. Inoculation experiments on healthy corals did not result in the development of disease signs. However, our results support the hypothesis that stress (in this case disease) alters the normal microbiota in the coral surface mucopolysaccaride layers. Studies are continuing to determine the pathogenic agent(s) responsible for DSD.
Identification and characterization of thermophilicSynechococcusspp. isolates from Asian geothermal springs
Authors: Jing Hongmei , Liu Hongbin , Pointing Stephen B.
Published: April 2008

Two thermophilic cyanobacterial strains, Ts and Bs, collected from Asian geothermal springs were identified morphologically and phylogenetically as Synechococcus in the order Chroococcales and were isolated into axenic cultures. In addition to the high similarities between their full 16S rRNA gene sequences, both strains also shared similar pigment profiles and fatty acid compositions but with varied ratios. Strain Ts had elevated levels of photoprotective pigments such as carotenoid and scytonemin even after prolonged culture under identical laboratory conditions, whereas strain Bs produced more chlorophyll a per unit cell volume, perhaps resulting from UV adaptation in the natural habitats. In addition, strain Ts had more content than strain Bs in terms of the total fatty acids and the proportion of unsaturated fatty acids. Neither isolate was able to fix nitrogen, and they had zero susceptibility to ampicillin and streptomycin.
Conditions that allow for effective transfer of membrane proteins onto nitrocellulose membrane in Western blots
Authors: Abeyrathne Priyanka D. , Lam Joseph S.
Published: April 2008

A major hurdle in characterizing bacterial membrane proteins by Western blotting is the ineffectiveness of transferring these proteins from sodium dodecyl sulfate – polyacrylamide gel electrophoresis (SDS–PAGE) gel onto nitrocellulose membrane, using standard Western blot buffers and electrophoretic conditions. In this study, we compared a number of modified Western blotting buffers and arrived at a composition designated as the SDS–PAGE-Urea Lysis buffer. The use of this buffer and specific conditions allowed the reproducible transfer of highly hydrophobic bacterial membrane proteins with 2–12 transmembrane-spanning segments as well as soluble proteins onto nitrocellulose membranes. This method should be broadly applicable for immunochemical studies of other membrane proteins.
Cycloheximide resistance in the Lipomycetaceae revisited
Authors: Müller W.J. , Albertyn J. , Smit M.S.
Published: April 2008

Cycloheximide (CYH) is a heterocyclic, glutarimide antibiotic that is a potent inhibitor of protein biosynthesis in most eukaryotes. This study demonstrated that yeasts from all species of the Lipomycetaceae, with the exception of Dipodascopsis spp., can grow in the presence of up to 5 g·L–1 CYH — a concentration that is five times higher than the accepted “highest” concentration of 1 g·L–1 used in physiological tests for yeast identification. Lipomycetaceous yeasts are known to utilize heterocyclic nitrogen-containing compounds such as thymine as sole nitrogen source. CYH contains a glutarimide ring, which is chemically similar to thymine. We investigated the possibility that CYH resistance in the Lipomycetaceae might be due to an ability to degrade CYH and use it as the sole nitrogen source. However, we were unable to demonstrate significant growth on CYH as sole nitrogen source. When thymine was used as positive control, we could demonstrate its utilization as sole nitrogen source.
Extracellular enzymatic activities of basidiomycetous yeasts isolated from glacial and subglacial waters of northwest Patagonia (Argentina)
Authors: Brizzio Silvia , Turchetti Benedetta , de García Virginia , Libkind Diego , Buzzini Pietro , van Broock María
Published: April 2008

As part of a project aimed at the selection of cold-adapted yeasts expressing biotechnologically interesting features, the extracellular enzymatic activity (EEA) of basidiomycetous yeasts isolated from glacial and subglacial waters of northwest Patagonia (Argentina) was investigated. Ninety-one basidiomycetous yeasts (belonging to the genera Cryptococcus , Leucosporidiella , Dioszegia , Mrakia , Rhodotorula , Rhodosporidium , Sporobolomyces , Sporidiobolus , Cystofilobasidium , and Udeniomyces ) were screened for extracellular amylolytic, proteolytic, lipolytic, esterasic, pectinolytic, chitinolytic, and cellulolytic activities. Over 15% of the strains exhibited three or more different EEAs at 4 °C and more than 63% had at least two EEAs at the same temperature. No chitinolytic or cellulolytic activities were detected at 4 and 20 °C. Cell-free supernatants exhibited significantly higher (P < 0.01) protease and lipase activities at ≤10 °C, or even at 4 °C. In light of these findings, cold environments of Patagonia (Argentina) may be considered a potential source of cold-adapted yeasts producing industrially relevant cold-active enzymes.
Comparison of element levels in minimal and complex yeast media
Authors: Abelovska Lenka , Bujdos Marek , Kubova Jana , Petrezselyova Silvia , Nosek Jozef , Tomaska Lubomir
Published: April 2008

The cellular functions are strongly influenced by the composition of the environment. In particular, phenotypes of microbial strains are modulated by concentrations of ions in the culture medium, and differences in element levels may be responsible for a phenotypic variability observed when microbial strains are grown on synthetic versus complex media. In this report, we analyzed the levels of nine elements (magnesium, potassium, sodium, calcium, iron, copper, manganese, zinc, and phosphorus) and sulphate ions in commercially available peptone and yeast extract and compared them with those in yeast nitrogen base routinely used for preparation of synthetic minimal media. We observed that whereas some elements are present at similar levels, the levels of others differ by a factor as high as 20. The observed differences should be taken into account when interpreting different phenotypes observed for microbial strains grown on synthetic versus complex media.
Pathway of phytate dephosphorylation by β-propeller phytases of different origins
Authors: Greiner Ralf , Lim Boon L. , Cheng Chiwai , Carlsson Nils-Gunnar
Published: April 2008

Using a combination of high-performance ion chromatography analysis and kinetic studies, the pathway of myo-inositol hexakisphosphate dephosphorylation by the β-propeller phytase of Shewanella oneidensis was established, which was then compared with that of Bacillus subtilis 168, Bacillus amyloliquefaciens ATCC 15841, and B. amyloliquefaciens 45 β-propeller phytases. The data demonstrate that all of these β-propeller phytases dephosphorylate myo-inositol hexakisphosphate in a stereospecific way by sequential removal of phosphate groups via d-Ins(1,2,4,5,6)P5, Ins(2,4,5,6)P4 to finally Ins(2,4,6)P3. Thus, the β-propeller phytases prefer the hydrolysis of every second phosphate over that of adjacent ones. This finding does not support previous phytate degradation models proposed by J. Kerovuo, J. Rouvinen, and F. Hatzack (2000. Biochem. J. 352: 623–628) and R. Greiner, A. Farouk, M. Larsson Alminger, and N.G. Carlsson (2002. Can. J. Microbiol. 48: 986–994) , but seems to fit with the structural model given by S. Shin, N.C. Ha, B.C. Oh, T.K. Oh, and B.H. Oh (2001. Structure, 9: 851–858) .
Production of small, acid-soluble spore proteins inClostridium perfringensnonfoodborne gastrointestinal disease isolates
Authors: Raju Deepa , Sarker Mahfuzur R.
Published: April 2008

The molecular basis for the differences in heat resistance between spores of Clostridium perfringens food-borne versus nonfoodborne isolates remains unknown. Since a recent study demonstrated the role of small, acid-soluble spore proteins (SASPs) in heat resistance of spores of food-borne isolates, in the current study, we evaluated the expression of SASP-encoding genes (ssp) and the production of SASPs in nonfoodborne isolates. Our results demonstrated the presence of all three ssp genes in five surveyed nonfoodborne isolates. A β-glucuronidase assay showed that these ssp genes are expressed specifically during sporulation. Furthermore, nonfoodborne isolate F4969 produced SASPs at a level similar to that of food-borne isolate SM101. Collectively, these results suggest that the difference in the levels of heat resistance between spores of food-borne and the nonfoodborne isolates is not the result of impaired expression of ssp genes and (or) decreased production of SASPs in nonfoodborne isolates.
Effect of sunlight on the infectivity ofCryptosporidium parvumin seawater
Authors: Nasser Abid M. , Telser Lital , Nitzan Yeshayahu
Published: April 2008

The prevalence of pathogenic microorganisms in seawater can result in waterborne and food borne outbreaks. This study was performed to determine the effect of sunlight and salinity on the die-off of Cryptosporidium parvum . Cryptosporidium parvum oocysts, Escherichia coli , and MS2 coliphage were seeded into tap water and seawater samples and then exposed to sunlight. The die-off of C. parvum in seawater, as measured by infectivity, was greater under sunlight (–3.08 log10) than under dark conditions (–1.31 log10). While, no significant difference was recorded in the die-off of C. parvum, under dark conditions, in tap water as compared to seawater (P < 0.05), indicating that the synergistic effect of salinity and sunlight was responsible for the enhanced die-off in seawater. The die-off of MS2 coliphage and E. coli was greater than that observed for C. parvum under all tested conditions. This indicates that these microorganisms cannot serve as indicators for the presence of C. parvum oocysts in seawaters. The results of the study suggest that C. parvum can persist as infectious oocysts for a long time in seawater and can thus pose a serious hazard by direct and indirect contact with humans.
Protein–DNA interactions at theSulfolobusspindle-shaped virus-1 (SSV1) T5 and T6 gene promoters
Authors: Qureshi Sohail A.
Published: April 2008

Ultraviolet irradiation upregulates transcription from the Sulfolobus spindle-shaped virus 1 (SSV-1) T5, Tind, and T6 genes promoters and also triggers viral DNA replication, but nothing is known about the proteins involved in this process. A notable feature of T5 and T6 promoters is that they contain 4 copies of a highly conserved DNA sequence 5′-ATAGATAGAGT-3′; 2 copies of this repeat are found in tandem upstream of the A-box, whereas 2 additional tandem copies span the initiator region from which transcription originates. By employing electrophoretic mobility gel-shift assays (EMSAs) and chemical modification interference analyses, I have identified a protein STRIP (SSV-1 T5/T6 region-interacting protein) in Sulfolobus shibatae extract that binds specifically to this sequence. Unique to S. shibatae, STRIP induces a 28° bend in DNA. Surprisingly, despite the fact that STRIP binding masks the initiator region and can potentially interfere with preinitiation complex assembly, it does not appear to effect transcription driven from T5 and T6 promoters in vitro. Based on these results, I discuss the potential roles of STRIP in T5 and T6 transcription and in initiating SSV-1 DNA replication.
In vivo characterization of thermal stabilities of Aeropyrum pernix cellular components by differential scanning calorimetry
Authors: Milek Igor , Črnigoj Miha , Ulrih Nataša Poklar , Kaletunç Gönül
Published: April 2008

Revival studies of Aeropyrum pernix show that the viability of cells and cell recovery after heat treatment depends on the temperature of treatment. Differential scanning calorimetry (DSC) is used to analyze the relative thermal stabilities of cellular components of A. pernix and to identify the cellular components responsible for the observed lag phase and reduced maximum growth following a heat treatment. DSC thermograms show 5 visible endothermic transitions with 2 major transitions. DSC analysis of isolated crude ribosomes aids the assignment of the 2 major peaks observed in whole-cell thermograms to denaturation of ribosomal structures. A comparison of partial and immediate full rescan thermograms of A. pernix whole cells indicates that both major peaks represent irreversible thermal transitions. A DNA peak is also identified in the whole-cell thermogram by comparison with the optical data of isolated pure DNA. DNA melting is shown to be irreversible in dilute solution, whereas it is partially reversible in whole cells, owing at least in part, to restricted volume effects. In contrast to mesophilic organisms, hyperthermophilic A. pernix ribosomes are more thermally stable than DNA, but in both organisms, irreversible changes leading to cell death occur owing to ribosomal denaturation.
Osmolarity affects Bvg-mediated virulence regulation by Bordetella pertussis
Authors: Stenson Trevor H. , Peppler Mark S.
Published: April 2008

Bordetella pertussis dramatically alters its phenotype by sensing its environment via the BvgAS regulatory system. Increased concentrations of specific chemicals are used in vitro to induce modulation of the bacterium from the Bvg+virulent phenotype to a fully Bvg–phenotype. Varied expression of sets of Bvg-regulated molecules depends on the modulating capacity of the environment. We examined the effect of a number of chemicals on the modulating capacity of B. pertussis growth media, both alone and in combination with known modulators. It was demonstrated that under certain conditions the Bvg-intermediate protein, BipA, is coexpressed with the Bvg–antigen, VraA. This demonstrates that the patterns of molecules expressed in the different phenotypes of B. pertussis are more fluid than has previously been demonstrated. The in vitro modulator, sulfate, was found to be a relatively inefficient modulator of our Tohama I-derived B. pertussis strain. However, addition of nicotinic acid, MgCl2, or sucrose in combination with relatively low sulfate concentrations resulted in effective modulation. This suggests that multiple signals may affect modulation through the BvgAS system or possibly through other regulatory networks. In addition, the cooperative modulating effect of sucrose implicates osmolarity as an environmental stimulus that affects phenotypic modulation.
Induction and preliminary characterization of a novel halophage SNJ1 from lysogenic Natrinema sp. F5
Authors: Mei Yunjun , Chen Jin , Sun Dongchang , Chen Dong , Yang Yang , Shen Ping , Chen Xiangdong
Published: April 2008

Halophage SNJ1 was induced with mitomycin C from Natrinema sp. strain F5. The phage produces plaques on Natrinema sp. strain J7 only. The phage has a head of about 67 nm in diameter and a tail of 570 nm in length and belongs morphologically to the family Siphoviridae. The phage is strongly salt dependent; NaCl concentration affects the integrity of SNJ1, phage adsorption, and plaque formation. The optimal NaCl concentration for phage adsorption and plaque formation is 30% and 25%, respectively.
Menaquinone reduction by an HMT2-like sulfide dehydrogenase from Bacillus stearothermophilus
Authors: Shibata Hiroomi , Suzuki Kuniyuki , Kobayashi Shigeki
Published: April 2008

The gene-encoding HMT2-like sulfide dehydrogenase from Bacillus stearothermophilus JCM2501 was amplified and expressed in Escherichia coli and the enzymatic features were examined. The enzyme was detected mainly in the membrane fraction. It catalyzed the sulfide-dependent menaquinone (MK) reduction showing special enzymatic features distinct from other sulfide–quinone oxidoreductases (SQRs) from autotrophic bacteria. The purified protein from E. coli brought about the sulfide-dependent 2,3-dimethyl-1,4-naphthoquinone (DMN) reduction in vitro. The reduction was accelerated in the presence of either cyanide or 2-mercaptoethanol and phospholipids. The high reduction was followed by a change in Kmvalues for sulfide and DMN. The purified enzyme utilized MK as an electron acceptor in the membrane fraction from E. coli. Under anaerobic conditions, sulfide was oxidized with reduction of fumarate or nitrate via the MK pool. The dehydrogenase was different from SQR in autotrophic bacteria in terms of the low affinity for sulfide and the activity enhancement in the presence of cyanide or 2-mercaptoethanol. The sulfide oxidation via MK in the cellular membrane of Gram-positive bacteria was certified.
The antioxidants dimethylsulfoxide and dimethylthiourea affect the immediate adhesion responses of larval haemocytes from 3 lepidopteran insect species
Authors: Dunphy Gary B. , Chen Genhui , Webster John M.
Published: April 2008

Antioxidants, dimethylsulfoxide (DMSO) and dimethylthiourea (DMTU), at concentrations not affecting the viability of blood cells (haemocytes) from the larval stage of 3 lepidopteran insects — Galleria mellonella , Lymantria dispar , and Malacosoma disstria — differed in their influence on the innate binding of haemocytes to glass, bacteria to haemocytes, and on humoral responses to alien materials. In vitro DMSO had little effect, whereas DMTU substantially impaired the adhesion of the haemocyte types, the plasmatocytes and granular cells, to slides as well as the attachment of Bacillus subtilis to these haemocytes. Although both antioxidants increased lysozyme and phenoloxidase activities, there was no correlation of enzyme activity and haemocyte adhesion responses, possibly reflecting sequestered radicals. Nitric oxide and hydroxyl radicals offset the DMTU effect. In the absence of antioxidants, inactivate protein kinases A (PKA) and C (PKC) enhanced haemocyte aggregation. In general, DMSO, as opposed to DMTU, did not alter the effects of PKA and PKC activators and inhibitors on haemocyte aggregation or of PKC and PKA activities. High concentrations of DMSO and all levels of DMTU, although inhibiting PKA and PKC, inhibited haemocyte adhesion to slides. Comparable results occurred for DMTU-treated haemocytes incubated with B. subtilis. In vivo DMSO, unlike DMTU, did not impair plasmatocyte or granular cell responses to foreign materials, including bacterial removal from the haemolymph and nodulation.
Induction of oxalate decarboxylase by oxalate in a newly isolated Pandoraea sp. OXJ-11 and its ability to protect against Sclerotinia sclerotiorum infection
Authors: Jin Zhao-Xia , Wang Changhai , Chen Wenfu , Chen Xiaoyi , Li Xianzhen
Published: April 2008

Pandoraea sp. OXJ-11 has been shown to produce an oxalate decarboxylase. The enzyme could be induced by increasing the oxalate in the medium. An increasing concentration of yeast extract was able to stimulate the cell growth but could not increase the specific oxalate decarboxylase activity. The oxalate decarboxylase was produced maximally at 25–35 °C and pH 4.0–9.0, favoring its potential application in protection of host plants from oxalate-producing phytopathogens. The influence of glucose on the induction of oxalate decarboxylase by oxalate was examined, and it was found that glucose inhibited the production of the oxalate decarboxylase. Resistance results showed that Pandoraea sp. OXJ-11 was capable of suppressing Sclerotinia sclerotiorum infection on detached leaflets of Brassica napus plants.
Immune complexes in early Lyme disease
Authors: Lenčáková Daniela , Štefančíková Astéria , Ivanová Renáta , Peťko Branislav
Published: April 2008

The study investigated the presence of Borrelia -specific antibodies captured in immune complexes (ICs) in patients with early Lyme disease manifested by erythema migrans. Out of 18 patients, 15 (83.3%) tested positive for polyethylene glycol-precipitated ICs containing IgM antibodies, while only 4 (22.2%) were IgG positive. These results are in accordance with our findings obtained by standard ELISA and recombinant blot, which indicated that ICs might be used for serological diagnosis of the early disease.
Serological profiling with Chlamycheck, a commercial multiplex recombinant antigen Western blot assay of chlamydial infections
Authors: Radouani Fouzia , Maile Julia , Betsou Fotini
Published: April 2008

A new chlamydial test system, the Chlamycheck assay, which uses 4 purified recombinant antigens of Chlamydia trachomatis and Chlamydophila pneumoniae and one antigen of Chlamydophila psittaci , has been developed and commercialized. We investigated the reactivities of the recombinant antigens with sera from a group of 30 patients with acute Chlamydia trachomatis infection, 88 patients consulting for sexually transmitted infections, and 46 patients with serological evidence of Chlamydophila pneumoniae infection. The results obtained from human and infected mouse sera suggest that Chlamycheck serology against multiple proteins may provide additional useful information that is not available by conventional whole elementary body microimmunofluorescence or single-antigen enzyme-linked immunosorbent assay serology. Specific serological profiles were associated with acute versus past Chlamydia trachomatis infection or with Chlamydia trachomatis primo-infection versus infection in a Chlamydophila pneumoniae history context.
A THEORETICAL STUDY ABOUT THE ELECTRONIC COOPERATIVE EFFECT ON HYDROCYANIDE CHAINS USING DFT CALCULATIONS AND AIM TOPOLOGICAL PARAMETERS
Authors: DE OLIVEIRA BOAZ GALDINO , DE ARAÚJO REGIANE DE CÁSSIA MARITAN UGULINO , SOARES VERNECK MAIA , RAMOS MOZART NEVES
Published: April 2008

A theoretical investigation about the cooperative effect on ( HCN )nhomo and ( HCN )n⋯ HF heterochains was performed in terms of structural parameters and topological properties obtained in concordance with the protocol of Bader's atoms in molecules theory. Initially, the hydrogen bonding distances, electronic densities, and Laplacian descriptors were used to characterize small ( HCN )nand ( HCN )n⋯ HF chains formed by n = 2–4 units of HCN . Hydrogen bond distances and distribution of charge density have revealed that the cooperative effect on ( HCN )n⋯ HF heterochains is ruled by the polarity of the extreme hydrofluoric acid species. Furthermore, we investigated larger homo and heterochain systems formed by n = 2–8 molecules of HCN . In this insight, the drastic polarized effect caused by HF molecule which was considered very substantial at prior, in fact is seriously limited by an excessive number of HCN molecules connected to the heterochain. This leads to a stabilization of the ( N ⋯ HF ) hydrogen bonds with invariable electronic density in the range of [Formula: see text]. In this stage and henceforth, the cooperative effect is re-established with n = 4 molecules of HCN . Thereby, the electronic density of the hydrogen bonds become unaltered within the ( HCN )n⋯ HF heterochains.
THEORETICAL STUDY OF HYDROGEN BONDED CLUSTERS OF AMMONIA AND FULMINIC ACID
Authors: ZABARDASTI ABEDIEN , AMANI SAEID , SALEHNASSAJ MARYAM , KIANFARD ALI H.
Published: April 2008

Ab initio and density functional calculations are used to analyze the interaction between a molecule of fulminic acid with one, two, three, and four molecules of ammonia along with a 2:2 complex at B3LYP/6-311++G(d, p) and MP2/6-311++G(d, p) computational levels. Cooperative effect (CE) in terms of stabilization energy of clusters is calculated and discussed as well. For the studied clusters, the CE is increased with increasing cluster size. Red shifts of H – C stretching frequency for complexes involving HCNO as H -donor are predicted. Atom in molecules is used to analyze the cooperative effect on topological parameters.
UNSYMMETRICAL AND SYMMETRICAL ONE-RANGE ADDITION THEOREMS FOR SLATER TYPE ORBITALS AND COULOMB–YUKAWA-LIKE CORRELATED INTERACTION POTENTIALS OF INTEGER AND NONINTEGER INDICES
Authors: GUSEINOV I. I.
Published: April 2008

Using one-center expansion relations for the Slater type orbitals (STOs) of noninteger principal quantum numbers in terms of integer nSTOs derived in this study with the help of ψa-exponential type orbitals (ψa-ETOs, a = 1, 0, -1, -2,…), the general formulas through the integer nSTOs are established for the unsymmetrical and symmetrical one-range addition theorems for STOs and Coulomb–Yukawa-like correlated interaction potentials (CIPs) with integer and noninteger indices. The final results are especially useful for the computations of arbitrary multicenter multielectron integrals that arise in the Hartree–Fock–Roothaan (HFR) approximation and also in the correlated methods based upon the use of STOs as basis functions.
A DFT STUDY ON THE REACTION MECHANISM OF SrO + CH4
Authors: QIN SONG , YANG HUA-QING , QIN SONG , XU JIAN , TANG DIAN-YONG , HU CHANG-WEI
Published: April 2008

The reaction mechanism of SrO + CH 4 has been investigated on a singlet spin state potential energy surface at the B3LYP/SDD, AUG-cc-pVQZ//B3LYP/SDD, 6-311+G(2df, 2p) levels of theory. Initially, the reactants give two molecule–molecule complexes: (i) a collinear C – H approach to O -end of the Sr – O bond forming SrOCH 4 molecular complex with C 3v symmetry, and (ii) a side-on to side-on approach of C – H bond to Sr – O forming OSrCH 4 molecular complex with C 1 symmetry. From SrOCH 4, the SrOH + CH 3 radicals are formed by the direct abstraction of a hydrogen atom from CH 4 moiety. From OSrCH 4, the gas-phase methane to methanol conversion by SrO is suggested to involve the SrO insertion into a C – H bond of CH 4 to produce the hydroxy and methoxy intermediates, HOSrCH 3 and HSrOCH 3, and the reaction pathway via the hydroxy intermediate ( HOSrCH 3) is energetically more favorable than the other one via the methoxy intermediate ( HSrOCH 3). These channels to form ( SrOH + CH 3) and ( Sr + CH 3 OH ) are expected to compete with each other, and the formation of methyl radical via the direct Sr – C cleavage from HOSrCH 3 is energetically more preferable. On the other hand, the intermediates HSrOCH 3 and HOSrCH 3 are predicted to be the energetically preferred configuration in the reaction of Sr + CH 3 OH , which is precisely the reverse reaction of methane hydroxylation. For the reaction of MO ( M = Mg , Ca , Sr ) with CH 4, the two main reaction pathways, methyl formation via a-TS1 and hydroxyl intermediate formation via b-TS1, are expected to compete with each other, and the preference of methyl formation pathway via a-TS1 would follow the sequence: MgO > CaO > SrO .
THEORETICAL STUDIES ON THE FORMATION MECHANISM AND STRUCTURE OF PENTAFULVENONE AND AZAFULVENONE
Authors: PAN XIU-MEI , JIA XIU-JUAN , LIU YING , SUN HAO , SU ZHONG-MIN , WANG RONG-SHUN
Published: April 2008

The formation mechanisms of pentafulvenone and azafulvenone were extensively investigated at the B3LYP/6-311++G** level and the potential energy surfaces were drawn out. Ketene pentafulvenone (A) and 3-carbonyl-3H-pyrrole (C) can be formed by eliminating N 2 from the diazo ketone via α elimination reaction and ketene 2-carbonyl-2H-pyrrole (B), 4-carbonyl-4H-imidazole (D), and 2-carbonyl-2H-imidazole (E) were formed by the elimination of water or methanol from pyrrole-2-carboxylic acid (rB) and carboxylate (rD and rE) via β elimination reaction. The structures of these monomers were compared and showed some information about the bond changed characters. The structure investigation indicated that the C = C bond is activated when the nitrogen atom locates in the ortho position of the C = C = O part, and therefore ortho-monomers are more facile to react. The difference of the amount and stability of the corresponding dimers are caused by differing the position and number of nitrogen atom and the variety of the ortho-dimer is complicated. In addition, the infrared spectra of the title species were also analyzed including the vibrational frequencies, IR relative intensities, and vibrational mode assignment.
A COMPARISON OF DIFFUSION-LIMITED CURRENT AT MICROELECTRODES OF VARIOUS GEOMETRIES
Authors: SENTHAMARAI R. , RAJENDRAN L.
Published: April 2008

In this paper, we present a critical evaluation of the influence of geometry on the behavior of the transient current at all ultramicroelectrodes. The nonsteady-state chronoamperometric diffusion limited current of various microelectrodes (circular disc, circular ring, elliptical disc, elliptical ring, band, hemicylinder, hemisphere, hemioblate and hemiprolate electrodes) are compared. Here, the area of the entire electrode is fixed and time variables are also normalized with respect to area. The chronoamperometric current for short and long time for all microelectrodes are given in tabular as well as graphical form also.
2D/3D-QSAR STUDY ON ANALOGUES OF 2-METHOXYESTRADIOL WITH ANTICANCER ACTIVITY
Authors: LIAO SI YAN , QIAN LI , CHEN JIN CAN , SHEN YONG , ZHENG KANG CHENG
Published: April 2008

Two-dimensional (2D) and three-dimensional (3D) quantitative structure–activity relationships (QSARs) of 23 analogs of 2-Methoxyestradiol with anticancer activity (expressed as p GI50) against MCF-7 human breast cancer cells have been studied by using a combined method of the DFT, MM2 and statistics for 2D, as well as the comparative molecular field analysis (CoMFA) for 3D. The established 2D-QSAR model in training set shows not only significant statistical quality, but also predictive ability, with the square of adjusted correlation coefficient [Formula: see text] and the square of the cross-validation coefficient (q2= 0.779). The same model was further applied to predict p GI50values of the four compounds in the test set, and the resulting [Formula: see text] being as high as 0.827, further confirms that this 2D-QSAR model has high predictive ability for this kind of compound. The 3D-QSAR model also shows good correlative and predictive capabilities in terms of R2(0.927) and q2(0.786) obtained from CoMFA model. The results that 2D- and 3D-QSAR analyses accord with each other, suggest that the electrostatic interaction plays a decisive role in determining the anticancer activity of the studied compounds, and that increasing the negative charge of substituent R2and the positive charge of substituents linking to C17as well as decreasing the size of substituent R1are advantageous to improving the cytotoxicity. Such results can offer some useful theoretical references for directing the molecular design and understanding the action mechanism of this kind of compound with anticancer activity.
THE VERTEX PI AND SZEGED INDICES OF AN INFINITE FAMILY OF FULLERENES
Authors: ASHRAFI A. R. , GHORBANI M. , JALALI M.
Published: April 2008

The topological index of a graph G is a numeric quantity related to G which is invariant under automorphisms of G. In this paper, the vertex PI and Szeged indices of an infinite family of fullerenes are computed.
A GLOBAL OPTIMIZATION SCHEME: KERNEL REPLICA EXCHANGE SIMULATION METHOD FOR PROTEIN FOLDING
Authors: MU YUGUANG , YANG YE , XU WEIXIN
Published: April 2008

A global optimization scheme which utilizes the framework of replica-exchange simulation and replaces the system exchange probability for jumping between different temperature replicas with the kernel exchange probability is brought out. The kernel exchange probability is calculated by taking into account the kernel part interaction, including protein–protein interactions only, with protein–solvent and solvent–solvent interactions approximated by a continuum solvation model. All the configurations are sampled with potential energies explicitly considering water molecules during the simulation while the energies obtained from continuum solvation model play as a scoring function to rank the conformation during the exchange process. It is shown that this method gives nearly identical total potential energy distribution in the solvated alanine dipeptide system compared with the results of the standard replica-exchange simulation in which much more number of replicas has to be employed. This optimization method is highly demonstrated in successfully folding a β-hairpin peptide, C-terminus (residue 41-56) of protein G, from the extended structure to native conformation.
Structural Biology of the Tumor Suppressor p53
Authors: Joerger Andreas C. , Fersht Alan R.
Published: April 2008

The tumor suppressor protein p53 induces or represses the expression of a variety of target genes involved in cell cycle control, senescence, and apoptosis in response to oncogenic or other cellular stress signals. It exerts its function as guardian of the genome through an intricate interplay of independently folded and intrinsically disordered functional domains. In this review, we provide insights into the structural complexity of p53, the molecular mechanisms of its inactivation in cancer, and therapeutic strategies for the pharmacological rescue of p53 function in tumors. p53 emerges as a paradigm for a more general understanding of the structural organization of modular proteins and the effects of disease-causing mutations.
Macromolecular Modeling with Rosetta
Authors: Das Rhiju , Baker David
Published: April 2008

Advances over the past few years have begun to enable prediction and design of macromolecular structures at near-atomic accuracy. Progress has stemmed from the development of reasonably accurate and efficiently computed all-atom potential functions as well as effective conformational sampling strategies appropriate for searching a highly rugged energy landscape, both driven by feedback from structure prediction and design tests. A unified energetic and kinematic framework in the Rosetta program allows a wide range of molecular modeling problems, from fibril structure prediction to RNA folding to the design of new protein interfaces, to be readily investigated and highlights areas for improvement. The methodology enables the creation of novel molecules with useful functions and holds promise for accelerating experimental structural inference. Emerging connections to crystallographic phasing, NMR modeling, and lower-resolution approaches are described and critically assessed.
Single-Molecule Studies of RNA Polymerase: Motoring Along
Authors: Herbert Kristina M. , Greenleaf William J. , Block Steven M.
Published: April 2008

Single-molecule techniques have advanced our understanding of transcription by RNA polymerase (RNAP). A new arsenal of approaches, including single-molecule fluorescence, atomic-force microscopy, magnetic tweezers, and optical traps (OTs) have been employed to probe the many facets of the transcription cycle. These approaches supply fresh insights into the means by which RNAP identifies a promoter, initiates transcription, translocates and pauses along the DNA template, proofreads errors, and ultimately terminates transcription. Results from single-molecule experiments complement the knowledge gained from biochemical and genetic assays by facilitating the observation of states that are otherwise obscured by ensemble averaging, such as those resulting from heterogeneity in molecular structure, elongation rate, or pause propensity. Most studies to date have been performed with bacterial RNAP, but work is also being carried out with eukaryotic polymerase (Pol II) and single-subunit polymerases from bacteriophages. We discuss recent progress achieved by single-molecule studies, highlighting some of the unresolved questions and ongoing debates.
Access to Civil Justice and Race, Class, and Gender Inequality
Authors: Sandefur Rebecca L.
Published: April 2008

Access to civil justice is a perspective on the experiences that people have with civil justice events, organizations, or institutions. It focuses on who is able or willing to use civil law and law-like processes and institutions (who has access) and with what results (who receives what kinds of justice). This article reviews what we know about access to civil justice and race, social class, and gender inequality. Three classes of mechanisms through which inequality may be reproduced or exacerbated emerge: the unequal distribution of resources and costs, groups’ distinct subjective orientations to law or to their experiences, and differential institutionalization of group or individual interests. Evidence reveals that civil justice experiences can be an important engine in reproducing inequalities and deserve greater attention from inequality scholars. However, the inequality-conserving picture in part reflects scholars’ past choices about what to study: Much research has focused narrowly on the use of formal legal means to solve problems or advance interests, or it has considered the experience only of relatively resource-poor, lower status, or otherwise less privileged groups. Thus, we often lack the information necessary to compare systematically groups’ experiences to each other or the impact of law to that of other means of managing conflicts or repairing harm.
Strategies and Stakeholders: Minority Recruitment in Cancer Genetics Research
Authors: James Rosalina D. , Yu Joon-Ho , Henrikson Nora B. , Bowen Deborah J. , Fullerton Stephanie M.
Published: April 2008

The Cancer Genetics Network (CGN) is one of a growing number of large-scale registries designed to facilitate investigation of genetic and environmental contributions to health and disease. Despite compelling scientific and social justice arguments that recommend diverse participation in biomedical research, members of ethnic minority groups continue to be chronically underrepresented in such projects. The CGN studies reported in this issue used strategies well documented to increase minority participation in research activities, including use of community-targeted materials, addressing community trust concerns, and the adoption of personalized and flexible research protocols. Here, we review the outcome of these efforts to increase minority recruitment to the CGN, and ask what lessons the findings suggest for future minority recruitment initiatives.
BRCA1 and BRCA2 Risk Perceptions among African American Women at Increased Risk for Hereditary Breast-Ovarian Cancer
Authors: Kessler Lisa , Domchek Susan , Stopfer Jill , Halbert Chanita Hughes
Published: April 2008

Objectives: To describe BRCA1 or BRCA2 (BRCA1/2) risk perceptions among African American women at increased risk for hereditary breast-ovarian cancer and to identify factors having independent associations with these perceptions. Methods: Risk perceptions were evaluated by self-report during a structured telephone interview among African American women (n = 162) at increased risk for hereditary cancer who were recruited from oncology clinics, general medical practices, and community oncology resources. Results: The majority of women (75%) believed that it was likely that they had a BRCA1/2 mutation. Women ages 50 and younger and those with greater cancer-specific worry were most likely to believe that they had a BRCA1/2 mutation. Conclusions: Although BRCA1/2 risk perceptions may be consistent with objective risk levels among African American women, discussion about the basis of risk perceptions may enhance provision of genetic counseling and testing in this population.
Partnership with an African American Sorority to Enhance Participation in Cancer Genetics Research
Authors: Olsen Sharon J. , Malvern Kathryn T. , May Betty J. , Jenkins Issie L. , Griffin Constance A.
Published: April 2008

Background/Aims: Reduced minority participation in clinical research challenges researchers to consider novel recruitment modalities. This study describes a formal partnership between the National Educational Foundation of the Zeta Phi Beta Sorority and the Mid-Atlantic Cancer Genetics Network. The goal was to enhance awareness about inherited breast cancer and to increase enrollment in the national Cancer Genetics Network. Methods: In this descriptive, pilot study, two recruitment strategies across four states were undertaken: an onsite educational session at four Annual State Leadership Conferences and a 2-tiered direct mail campaign to the sorority membership. Results: Recruitment methods targeted over 1,200 well-educated African American women. Of the 279 attendees at the state conference educational sessions, only 3 women meeting the high risk eligibility requirement enrolled. Direct mail recruitment elicited 24 eligible women. Lessons learned are described. Conclusion: Despite low accrual, the partnership laid a foundation for broader collaboration with the Zeta Phi Beta Sorority. In the future, collaboration with minority sororities and fraternities as part of standard registry recruitment should be explored.
Factors Associated with African Americans’ Enrollment in a National Cancer Genetics Registry
Authors: Skinner C.S. , Schildkraut J.M. , Calingaert B. , Hoyo C. , Crankshaw S.S. , Fish L. , Susswein L. , Jasper C. , Reid L.
Published: April 2008

This study explored whether reactions to the Cancer Genetics Network (CGN) or CGN enrollment differed by receipt of a standard informational brochure versus a targeted version addressing factors previously associated with African Americans’ health behavior decisions and research participation. The 262 participants, identified through tumor registries or clinic contacts, were mailed brochures and completed phone interviews. When asked whether – based on the brochure – they were or were not ‘leaning toward’ CGN enrollment, about 75% of both standard and targeted groups reported leaning toward. When given the opportunity at the end of the interview, 68% enrolled in the CGN. Trust was strongly related to enrollment. Less education, less satisfaction with cancer care, and individualistic rather than collective orientation were associated with lower trust. Education was also bivariately associated with enrollment, but mediation analysis indicated that the operational mechanism of education’s influence on enrollment was through trust.