bluuebunny/crossref_metadata_2025 huggingface dataset:
Binge Drinking and Unsafe Sex: A Study of Narcology Hospital Patients from St. Petersburg, Russia
Authors: Raj A. , Cheng D. M. , Krupitsky E. M. , Levenson S. , Egorova V. Y. , Meli S. , Zvartau E. E. , Samet J. H.
Published: July 2009

The purpose of this study was to assess the association between binge alcohol use and unprotected sex in Russian substance users. Participants ( N = 181) were narcology hospital patients assessed on demographics, alcohol use, risky sex, and sexually transmitted disease/human immunodeficiency virus (STD/HIV) diagnoses. Adjusted generalized estimating equations (GEEs) logistic regression analysis examined the association between binge drinking and same-day unprotected sex across each of the past 30 days, per participant ( N = 5430 observations). Participants were age 18 to 55 years, 75% male, and 64% binge drinking. Sex trade was reported by 27%; history of STDs by 43%; and HIV by 15%. One fourth of daily observations included sex; 88% of these involved unprotected sex. Binge drinking was not associated with same-day unprotected sex (adjusted odds ratio [ORadj] = 1.0, 95% confidence interval [CI] = 0.7–1.4, χ2(1, N = 5219) = 0.01, ns). Findings document substantial HIV/STD risk and prevalence among Russian narcology patients, but no link between binge drinking and unprotected sex in this population, possibly due to very low rates of condom use generally.
Survey of Alcohol and Other Drug Use Attitudes and Behaviors in Nursing Students
Authors: Baldwin Jeffrey N. , Bartek Jean K. , Scott David M. , Davis-Hall R. Ellen , DeSimone Edward M.
Published: July 2009

Statewide nursing student alcohol and other drug (AOD) use attitudes and behaviors were assessed. Response was 929/2017 (46%) (practical nursing [ n = 173/301] 57.3%; diploma and associate degree in nursing [ n = 282/417] 67.6%; bachelor of science in nursing [ n = 474/1299] 36.5%). Nearly 44% reported inadequate substance abuse education. Past-year AOD use included tobacco 36.9%, marijuana 6.8%, sedatives 4.6%, and opioids 2.6%. Past-year AOD-related events included blackouts 19.8%, class/work under the influence 6.3%, patient care under the influence 3.9%, lowered grades/job evaluations 6.6%, and legal charges 3.6%. Heavy drinking was reported by 28.9%. Practical nursing (PN) students most often reported tobacco use and sedative use, whereas Bachelor of Science in nursing (BSN) students most often reported marijuana use. Family histories of alcohol-related problems and drug-related problems were reported, respectively, by 48.1% and 19.2% of respondents; 51.1% reported at least one of these. PN students most often reported such family histories. Nursing educational systems should proactively address student AOD prevention, education, and assistance.
Masked priming effect reflects evidence accumulated by the prime
Authors: Kinoshita Sachiko , Norris Dennis
Published: July 2009

In the same–different match task, masked priming is observed with the same responses but not different responses. Norris and Kinoshita's (2008) Bayesian reader account of masked priming explains this pattern based on the same principle as that explaining the absence of priming for nonwords in the lexical decision task. The pattern of priming follows from the way the model makes optimal decisions in the two tasks; priming does not depend on first activating the prime and then the target. An alternative explanation is in terms of a bias towards responding “same” that exactly counters the facilitatory effect of lexical access. The present study tested these two views by varying both the degree to which the prime predicts the response and the visibility of the prime. Unmasked primes produced effects expected from the view that priming is influenced by the degree to which the prime predicts the response. In contrast, with masked primes, the size of priming for the same response was completely unaffected by predictability. These results rule out response bias as an explanation of the absence of masked priming for different responses and, in turn, indicate that masked priming is not a consequence of automatic lexical access of the prime.
Segmentation by lexical subtraction in Hungarian speakers of second-language English
Authors: White Laurence , Melhorn James F. , Mattys Sven L.
Published: July 2009

Using cross-modal form priming, we compared the use of stress and lexicality in the segmentation of spoken English by native English speakers (L1) and by native Hungarian speakers of second-language English (L2). For both language groups, lexicality was found to be an effective segmentation cue. That is, spoken disyllabic word fragments were stronger primes in a subsequent visual word recognition task when preceded by meaningful words than when preceded by nonwords: For example, the first two syllables of corridor were a more effective prime for visually presented corridor when heard in the phrase anythingcorri than in imoshingcorri. The stress pattern of the prime (strong–weak vs. weak–strong) did not affect the degree of priming. For L1 speakers, this supports previous findings about the preferential use of high-level segmentation strategies in clear speech. For L2 speakers, the lexical strategy was employed regardless of L2 proficiency level and instead of exploiting the consistent stress pattern of their native language. This is clear evidence for the primacy and robustness of segmentation by lexical subtraction even in individuals whose lexical knowledge is limited.
Annexin A2 Regulates Phagocytosis of Photoreceptor Outer Segments in the Mouse Retina
Authors: Law Ah-Lai , Ling Qi , Hajjar Katherine A. , Futter Clare E. , Greenwood John , Adamson Peter , Wavre-Shapton Silène T. , Moss Stephen E. , Hayes Matthew J.
Published: July 2009

The daily phagocytosis of shed photoreceptor outer segments by pigment epithelial cells is critical for the maintenance of the retina. In a subtractive polymerase chain reaction analysis, we found that functional differentiation of human ARPE19 retinal pigment epithelial (RPE) cells is accompanied by up-regulation of annexin (anx) A2, a major Src substrate and regulator of membrane–cytoskeleton dynamics. Here, we show that anx A2 is recruited to the nascent phagocytic cup in vitro and in vivo and that it fully dissociates once the phagosome is internalized. In ARPE19 cells depleted of anx A2 by using small interfering RNA and in ANX A2−/−mice the phagocytosis of outer segments was impaired, and in ANX A2−/−mice there was an accumulation of phagocytosed outer segments in the RPE apical processes, indicative of retarded phagosome transport. We show that anx A2 is tyrosine phosphorylated at the onset of phagocytosis and that the synchronized activation of focal adhesion kinase and c-Src is abnormal in ANX A2−/−mice. These findings reveal that anx A2 is involved in the circadian regulation of outer segment phagocytosis, and they provide new insight into the protein machinery that regulates phagocytic function in RPE cells.
Divergent S Phase Checkpoint Activation Arising from Prereplicative Complex Deficiency Controls Cell Survival
Authors: Lau Eric , Chiang Gary G. , Abraham Robert T. , Jiang Wei
Published: July 2009

The DNA replication machinery plays additional roles in S phase checkpoint control, although the identities of the replication proteins involved in checkpoint activation remain elusive. Here, we report that depletion of the prereplicative complex (pre-RC) protein Cdc6 causes human nontransformed diploid cells to arrest nonlethally in G1-G1/S and S phase, whereas multiple cancer cell lines undergo G1-G1/S arrest and cell death. These divergent phenotypes are dependent on the activation, or lack thereof, of an ataxia telangiectasia and Rad3-related (ATR)-dependent S phase checkpoint that inhibits replication fork progression. Although pre-RC deficiency induces chromatin structural alterations in both nontransformed and cancer cells that normally lead to ATR checkpoint activation, the sensor mechanisms in cancer cells seem to be compromised such that higher levels of DNA replication stress/damage are required to trigger checkpoint response. Our results suggest that therapy-induced disruption of pre-RC function might exert selective cytotoxic effects on tumor cells in human patients.
Population integrity and connectivity in Northwest Atlantic herring: a review of assumptions and evidence
Authors: Stephenson Robert L. , Melvin Gary D. , Power Michael J.
Published: July 2009

Stephenson, R. L., Melvin, G. D., and Power, M. J. 2009. Population integrity and connectivity in Northwest Atlantic herring: a review of assumptions and evidence. – ICES Journal of Marine Science, 66: 1733–1739. The issue of herring population structure has been debated for more than a century. Population integrity and connectivity have become an increasingly important problem for both resource evaluation (e.g. concern for the use of appropriate modelling approaches) and management (e.g. increasing attention to the preservation of within-species diversity and the complexity of mixed-stock fisheries). In recent decades, there has been considerable advancement in the scientific information related to herring population structure, but papers continue to demonstrate a spectrum of conclusions related to population integrity and connectivity at various scales. We review herring stock structure in the western Atlantic, specifically addressing the assumptions currently being used in management and the validity of scientific evidence on which these assumptions are based. Herring of the western Atlantic exhibit considerable population discreteness and limited connectivity on the temporal and spatial scales that are of relevance to management. Maintaining the resulting population complexity is a challenge, particularly because preservation of within-species diversity is an important element of an ecosystem approach to management.
Fuzzy diel patterns in catchability of deep-water species on the continental margin
Authors: Bahamon Nixon , Sardà Francesc , Aguzzi Jacopo
Published: July 2009

Bahamon, N., Sardà, F., and Aguzzi, J. 2009. Fuzzy diel patterns in catchability of deep-water species on the continental margin. – ICES Journal of Marine Science, 66: 2211–2218. Exploited deep-water fish communities on continental margins are poorly understood in terms of variations in species composition and abundance by depth and season as a response to diel changes in light intensity and length of photoperiod. Innovative fuzzy clustering and traditional agglomerative hierarchical clustering methods were applied to data from bottom trawls collected continuously for 4 d in October and June, on the shelf (100–110 m) and upper slope (400–430 m). Fuzzy clustering was more effective than hierarchical clustering at characterizing diel variations in catches from the upper slope because the species assemblage did not show a distinct day and night structure. On the shelf, the species assemblages shifted abruptly between a diurnal and a nocturnal structure at sunset and sunrise, and the two clustering methods yielded similar results. Endobenthic decapods with marked crepuscular-nocturnal emergence from the substratum were mostly responsible for this pattern. No clearly discernible diel pattern was found with the dampening of light intensity with depth, weakening the behavioural response of endobenthos to the day–night cycle. The results indicated that the regulatory effect of the light cycle on diel activity rhythms weakens with depth.
Type IV Pili Are Required for Virulence, Twitching Motility, and Biofilm Formation of Acidovorax avenae subsp. citrulli
Authors: Bahar Ofir , Goffer Tal , Burdman Saul
Published: July 2009

Acidovorax avenae subsp. citrulli is the causal agent of bacterial fruit blotch (BFB), a threatening disease of watermelon, melon, and other cucurbits. Despite the economic importance of BFB, relatively little is known about basic aspects of the pathogen's biology and the molecular basis of its interaction with host plants. To identify A. avenae subsp. citrulli genes associated with pathogenicity, we generated a transposon (Tn5) mutant library on the background of strain M6, a group I strain of A. avenae subsp. citrulli, and screened it for reduced virulence by seed-transmission assays with melon. Here, we report the identification of a Tn5 mutant with reduced virulence that is impaired in pilM, which encodes a protein involved in assembly of type IV pili (TFP). Further characterization of this mutant revealed that A. avenae subsp. citrulli requires TFP for twitching motility and wild-type levels of biofilm formation. Significant reductions in virulence and biofilm formation as well as abolishment of twitching were also observed in insertional mutants affected in other TFP genes. We also provide the first evidence that group I strains of A. avenae subsp. citrulli can colonize and move through host xylem vessels.
A Multiplex PCR System for the Specific Detection of Cylindrocarpon liriodendri, C. macrodidymum, and C. pauciseptatum from Grapevine
Authors: Alaniz Sandra , Armengol Josep , García-Jiménez José , Abad-Campos Paloma , León Maela
Published: July 2009

Cylindrocarpon liriodendri and C. macrodidymum are the causal agents of grapevine black foot disease. Recently, a third species, C. pauciseptatum, has been isolated from roots of grapevine showing decline symptoms. Currently, reliable identification of isolates of these species through phenotypical characteristics has not been possible. The polymerase chain reaction (PCR)-based method developed in this study allows a quick and easy detection of Cylindrocarpon spp. associated with grapevine. Three primer pairs annealing to variable, partly species-specific sites of the internal transcribed spacer regions amplified species-specific PCR fragments of different sizes in C. liriodendri, C. macrodidymum, and C. pauciseptatum in a multiplex assay with DNA obtained with both quick and traditional extraction methods. They did not generate any PCR product in other fungal trunk pathogens or contaminants commonly associated with grapevines. When universal fungal ITS primers were used in a nested multiplex PCR, the three primer pairs also detected C. liriodendri, C. macrodidymum, and C. pauciseptatum in total DNA extracted from roots of inoculated grapevines. The designed methods can be used for the diagnosis of these fungi from pure culture or infected grapevines.
Distribution of Genets of Perenniporia subacida in Stands of Chamaecyparis obtusa (Japanese Cypress) Determined by AFLP Fingerprints and Somatic Incompatibility
Authors: Tabata Masanobu , Suyama Yoshihisa , Abe Yasuhisa
Published: July 2009

The clonal structure of Perenniporia subacida, a wood-rotting basidiomycete, was studied in a 30-year-old stand (site A; 1 ha) and a 43-year-old stand (site B; 0.5 ha) of Chamaecyparis obtusa in northern Kagawa Prefecture, Japan. A total of 110 isolates from decayed trees, stumps, wooden fences, logs, and mycelial mats were analyzed by amplified fragment length polymorphism (AFLP) and somatic incompatibility test (SIT). The results of AFLP, which agreed with those of SIT, revealed that the P. subacida population consisted of at least 17 genets at site A and 6 genets at site B. Individual genets were found in 1 to 9 trees at site A and in 1 to 7 trees at site B. One particular genet had spread over a distance of 70 m. Root contacts were observed among roots of decaying stumps and living trees at both sites. White mycelial mats were often found where roots made contact between stumps and neighboring trees. These results suggest that P. subacida spreads vegetatively over significant distances through root contacts.
Elucidation of the Roles of Blackcurrant reversion virus and Phytoplasma in the Etiology of Full Blossom Disease in Currants
Authors: Špak Josef , Kubelková Darina , Přibylová Jaroslava , Špaková Vlastimila , Petrzik Karel
Published: July 2009

To determine the roles of phytoplasmas and Blackcurrant reversion virus (BRV) in the etiology of full blossom disease (FBD), we conducted graft and dodder transmission experiments. Scions from FBD-affected Ribes rubrum were grafted onto red currants, white currants, and black currants. Red and white cultivars revealed symptoms of FBD, whereas blackcurrant displayed symptoms of BRV. No differences in symptoms were observed between plants infected with BRV only and those infected with BRV and phytoplasma. Aster yellows phytoplasma subgroup 16SrI-C was transferred from FBD-infected red currants to periwinkle, where symptoms of green and yellow petal were observed. Back-transmission of phytoplasma to currant seedlings of red and black currant was not successful. Scions of periwinkle infected with aster yellows phytoplasmas of subgroup 16SrI-C and 16SrI-B, which were bottle-, bark-, and approach-grafted onto seedlings of red and black currant, resulted in positive but symptomless transmission of phytoplasma to red currant. We conclude that FBD symptoms are induced by BRV rather than by phytoplasma, which was originally described as the causal agent of FBD.
A Phytoplasma Associated with an Outbreak of an Unusual Disease of Chrysanthemum in China in 2008
Authors: Min H. , Hu S. B. , Li Z. N. , Wu Y. F. , Zhang C. P. , Wei T.
Published: July 2009

In August of 2008, a disease of chrysanthemum (Dendranthema morifolium (Ramat.) Tzvel) caused losses of 70 to 80% in one of the largest chrysanthemum gardens in Yangling, Shanxi Province, China. Chrysanthemum plants in nearby areas also were affected to various degrees. Symptoms included flattened stems, shortening of internodes, yellowing of leaf margins, root death, and dwarfing of plants. Affected plants eventually collapsed. On the basis of these symptoms, a phytoplasma was suspected. Total nucleic acids were extracted from 0.5 g of phloem tissue from stems of eight symptomatic and eight asymptomatic plants by the cetyltrimethylammoniumbromide (CTAB) method (1). To amplify phytoplasma DNA, primer pairs R16mF2/R16mR1, followed by R16F2n/R16R1 (2), were used in a nested PCR. A final amplicon product (1.2 kb) was obtained from all symptomatic plants but not from asymptomatic ones. Restriction fragment length polymorphism (RFLP) analyses of R16F2n/R16R1 amplicons with MseI, AluI, HhaI, HaeIII, KpnI, RsaI, and HpaII endonucleases indicated that all symptomatic plants, but none of the asymptomatic plants, contained a phytoplasma strain of group 16SrI, subgroup B (3). A search of rDNA sequences in GenBank revealed a similarity (>99%) to aster yellow phytoplasma, 16SrI group, thereby confirming strain identity based on RFLP analysis. These results indicate the disease of chrysanthemum is associated with a phytoplasma related to the aster yellow phytoplasma group. Sequences were deposited in GenBank (Accession No. FJ543467). A vector of this phytoplasma in chrysanthemum has not been identified.

References: (1) E. Angelini et al. Vitis 40:79, 2001. (2) D. E. Gundersen and I.-M. Lee. Phytopathol. Mediterr. 35:144, 1996. (3) I. M. Lee et al. Int. J. Syst. Evol. Microbiol. 48:1153, 1998.
First Report of Verticillium Wilt of Grapevine (Vitis vinifera) Caused by Verticillium dahliae in China
Authors: Zhang L. , Zhang G. L. , Qian X. , Li G. Y.
Published: July 2009

Verticillium dahliae Kleb. causes Verticillium wilt in large numbers of crops all over the world. Common symptoms caused by the pathogen include yellowing, wilting of leaves, and discoloration in vascular tissue of the stem. In June 2007, symptoms of Verticillium wilt were observed in a grapevine (Vitis vinifera) field in the Shihezi Region of Xinjiang. To isolate the pathogen, stem segments (0.5 cm long) were surface sterilized with 1% HgCl2 for 1 min and then dipped in 70% ethanol for 10 s. The sterilized tissues were rinsed with sterile water and incubated in the dark for 7 days at 25°C on potato dextrose agar (PDA) medium. The fungus growing from the diseased tissue showed dark colonies that produced verticillate conidiophores with two to three layers with colorless, ovoid, unicellular conidia and small, black microsclerotia, which are characteristics of V. dahliae (3). To confirm its identity, ribosomal DNA fragments (regions ITS1, 5.8S rDNA, and ITS4) were PCR amplified with primer pair ITS1/ITS4 (4) and sequenced (GenBank Accession No. FJ475122). Sequential analysis revealed that the rDNA region of the fungus isolated from grapevine was identical to that of a Greek strain of V. dahliae (GenBank Accession No. AF104926). Furthermore, the specific fragment (1,500 bp) of nondefoliating pathotype of V. dahliae (1) was PCR amplified from 24 grapevine isolates of V. dahliae collected in Xinjiang, indicating that the V. dahliae pathogen from Xinjiang is a nondefoliating pathotype. To verify the causal role of the isolated fungus, pathogenicity assays were conducted on 1-year-old seedlings of the Centennial seedless cultivar. Trimmed roots were submerged in a conidial suspension (1 × 106 conidia/ml) for 30 min and sterile tap water was used as a control. The seedlings were transplanted into a pot containing 2:1 sterile mixture of peat/perlite (vol/vol). Plants were grown in a greenhouse at 25°C. Six Verticillium isolates were found to cause the same symptoms as in fields 50 days after inoculation. V. dahliae was successfully reisolated from the stems of inoculated plants. Control seedlings inoculated in sterile tap water remained healthy. Because grapevine (Vitis vinifera) is an economically important crop for fruit and winemaking material in Xinjiang, Verticillium wilt poses a threat. The disease has been previously reported in the United States (2), but to our knowledge, this is the first report from China.

References: (1) E. Pérez Artés et al. Eur. J. Plant Pathol. 106:507, 2000. (2) W. C. Schnathorst and A. C. Goheen. Plant Dis. Rep. 61:909, 1977. (3) H. C. Smith. N. Z. J. Agric. Res. 8:450, 1965. (4) T. J. White et al. PCR Protocols. Academic Press, San Diego, CA, 1990.
Soybean Rust Caused by Phakopsora pachyrhizi Detected in the State of Campeche on the Yucatan Peninsula, Mexico
Authors: de Jesús Yáñez Morales Ma. , Martínez I. Alanis , Rocha J. Manuel Soto , Malvick D. K. , Kurle J. E. , Floyd C. M. , Krupa S. V.
Published: July 2009

Soybean rust caused by Phakopsora pachyrhizi Syd. & P. Syd is a destructive foliar disease of soybean (Glycine max L), which was first confirmed in North America in Louisiana during 2004 (4). Soybean rust (SBR) has also been reported late in the growing season as far north as Illinois, Indiana, and Iowa. SBR was first confirmed in Mexico in 2005 in the state of San Luis Potosi on soybean (3) and subsequently reported in the states of Tamaulipas, Veracruz, and the southwestern coast of Chiapas. Symptoms of SBR were observed on leaves of multiple, nearly mature soybean plants near the city of Campeche (19.72796°N, 90.0771°W) on the Gulf Coast of the Yucatan Peninsula during November 2008. Angular and irregular chlorotic lesions on leaves contained necrotic spots and pale brown, erumpent, cone-like uredinia with a central opening. Ellipsoid to obovoid, echinulate, light tan urediniospores (10 to 13 × 16 to 18 μm) were observed microscopically. DNA was extracted from leaf tissue containing uredinia and from asymptomatic tissue with the DNeasy Plant Mini Kit (Qiagen, Valencia, CA). P. pachyrhizi was confirmed in the symptomatic leaves by a PCR assay with Ppm1/Ppa2 primers, but not from the asymptomatic leaves (1). Subsequently, the DNA extracted from symptomatic and asymptomatic leaf tissues was tested again in another laboratory by a specific quantitative PCR assay (1), and positive results for the presence of soybean rust were obtained only from the symptomatic tissue. As a final confirmatory step, amplified DNA from the PCR assay was sequenced, and the results matched P. pachyrhizi sequences in the GenBank database. To our knowledge, these observations confirm for the first time the presence of P. pachyrhizi in the state of Campeche of southern Mexico. Although it was confirmed on soybean during 2008, it is not known how long the pathogen has been present or which other hosts may be infected there. The presence of SBR on the Yucatan Peninsula is significant because of its potential effects on local plant hosts. In addition, the climate allows possible year-round survival of the pathogen and long-distance transport of urediniospores to the United States. Potential transport of SBR spores from this part of Mexico to the United States has been reported through the application of NOAA's HYSPLIT (Hybrid Single Particle Lagrangian Integrated Transport) model and atmospheric back-trajectory analysis (2).

References: (1) R. D. Frederick et al. Phytopathology 92:217, 2002. (2) S. V. Krupa et al. Plant Dis. 90:1254, 2006. (3) A. C. Rodriguez et al. Plant Dis. 90:1260, 2006. (4) R. W. Schneider et al. Plant Dis. 89:774, 2005.
Sex-ratio biasing towards daughters among lower-ranking co-wives in Rwanda
Authors: Pollet Thomas V. , Fawcett Tim W. , Buunk Abraham P. , Nettle Daniel
Published: July 2009

There is considerable debate as to whether human females bias the sex ratio of their offspring as a function of their own condition. We apply the Trivers–Willard prediction—that mothers in poor condition will overproduce daughters—to a novel measure of condition, namely wife rank within a polygynous marriage. Using a large-scale sample of over 95 000 Rwandan mothers, we show that lower-ranking polygynous wives do indeed have significantly more daughters than higher-ranking polygynous wives and monogamously married women. This effect remains when controlling for potential confounds such as maternal age. We discuss these results in reference to previous work on sex-ratio adjustment in humans.
Evidence of an evolutionary precursor to human language affixation in a non-human primate
Authors: Endress Ansgar D. , Cahill Donal , Block Stefanie , Watumull Jeffrey , Hauser Marc D.
Published: July 2009

Human language, and grammatical competence in particular, relies on a set of computational operations that, in its entirety, is not observed in other animals. Such uniqueness leaves open the possibility thatcomponentsof our linguistic competence are shared with other animals, having evolved for non-linguistic functions. Here, we explore this problem from a comparative perspective, asking whether cotton-top tamarin monkeys (Saguinus oedipus) can spontaneously (no training) acquire an affixation rule that shares important properties with our inflectional morphology (e.g. the rule that adds–edto create the past tense, as in the transformation ofwalkintowalk-ed). Using playback experiments, we show that tamarins discriminate between bisyllabic items that start with a specific ‘prefix’ syllable and those that end with the same syllable as a ‘suffix’. These results suggest that some of the computational mechanisms subserving affixation in a diversity of languages are shared with other animals, relying on basic perceptual or memory primitives that evolved for non-linguistic functions.
Atomic-scale dynamics inside living cells explored by neutron scattering
Authors: Jasnin Marion
Published: July 2009

Single-particle neutron spectroscopy has contributed important experimental data on molecular dynamics in biological systems. The technique provides information on atomic and molecular motions in macromolecules on the picosecond to the nanosecond time scale, which are essential to biological function. Here, we report on recent neutron measurements performed directly in living cells by using isotope labelling to explore the dynamics of specific cellular components. The paper proposes an integrated view of results on atomic-scale cell water dynamics, internal and global macromolecular motions and solvent isotope effect on macromolecular dynamics. The work established the specific usefulness of the neutron scattering technique to get insight into biologically relevant dynamical features, in particular through comparative measurements. The method developed can now be applied to look for dynamical signatures related to cell characteristics in many different cell types and organelles.
Oxidative stress and inflammation response after nanoparticle exposure: differences between human lung cell monocultures and an advanced three-dimensional model of the human epithelial airways
Authors: Müller Loretta , Riediker Michael , Wick Peter , Mohr Martin , Gehr Peter , Rothen-Rutishauser Barbara
Published: July 2009

Combustion-derived and manufactured nanoparticles (NPs) are known to provoke oxidative stress and inflammatory responses in human lung cells; therefore, they play an important role during the development of adverse health effects. As the lungs are composed of more than 40 different cell types, it is of particular interest to perform toxicological studies with co-cultures systems, rather than with monocultures of only one cell type, to gain a better understanding of complex cellular reactions upon exposure to toxic substances. Monocultures of A549 human epithelial lung cells, human monocyte-derived macrophages and monocyte-derived dendritic cells (MDDCs) as well as triple cell co-cultures consisting of all three cell types were exposed to combustion-derived NPs (diesel exhaust particles) and to manufactured NPs (titanium dioxide and single-walled carbon nanotubes). The penetration of particles into cells was analysed by transmission electron microscopy. The amount of intracellular reactive oxygen species (ROS), the total antioxidant capacity (TAC) and the production of tumour necrosis factor (TNF)-α and interleukin (IL)-8 were quantified. The results of the monocultures were summed with an adjustment for the number of each single cell type in the triple cell co-culture. All three particle types were found in all cell and culture types. The production of ROS was induced by all particle types in all cell cultures except in monocultures of MDDCs. The TAC and the (pro-)inflammatory reactions were not statistically significantly increased by particle exposure in any of the cell cultures. Interestingly, in the triple cell co-cultures, the TAC and IL-8 concentrations were lower and the TNF-α concentrations were higher than the expected values calculated from the monocultures. The interplay of different lung cell types seems to substantially modulate the oxidative stress and the inflammatory responses after NP exposure.
Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states inAspergillus flavusurate oxidase
Authors: Oksanen E. , Blakeley M. P. , Bonneté F. , Dauvergne M. T. , Dauvergne F. , Budayova-Spano M.
Published: July 2009

Urate oxidase (Uox) catalyses the oxidation of urate to allantoin and is used to reduce toxic urate accumulation during chemotherapy. X-ray structures of Uox with various inhibitors have been determined and yet the detailed catalytic mechanism remains unclear. Neutron crystallography can provide complementary information to that from X-ray studies and allows direct determination of the protonation states of the active-site residues and substrate analogues, provided that large, well-ordered deuterated crystals can be grown. Here, we describe a method and apparatus used to grow large crystals of Uox (Aspergillus flavus) with its substrate analogues 8-azaxanthine and 9-methyl urate, and with the natural substrate urate, in the presence and absence of cyanide. High-resolution X-ray (1.05–1.20 Å) and neutron diffraction data (1.9–2.5 Å) have been collected for the Uox complexes at the European Synchrotron Radiation Facility and the Institut Laue-Langevin, respectively. In addition, room temperature X-ray data were also collected in preparation for joint X-ray and neutron refinement. Preliminary results indicate no major structural differences between crystals grown in H2O and D2O even though the crystallization process is affected. Moreover, initial nuclear scattering density maps reveal the proton positions clearly, eventually providing important information towards unravelling the mechanism of catalysis.
Prospective virtual screening with Ultrafast Shape Recognition: the identification of novel inhibitors of arylamineN-acetyltransferases
Authors: Ballester Pedro J. , Westwood Isaac , Laurieri Nicola , Sim Edith , Richards W. Graham
Published: July 2009

There is currently a shortage of chemical molecules that can be used as bioactive probes to study molecular targets and potentially as starting points for drug discovery. One inexpensive way to address this problem is to use computational methods to screen a comprehensive database of small molecules to discover novel structures that could lead to alternative and better bioactive probes. Despite that pleasing logic the results have been somewhat mixed. Here we describe a virtual screening technique based on ligand–receptor shape complementarity, Ultrafast Shape Recognition (USR). USR is specifically applied to identify novel inhibitors of arylamineN-acetyltransferases by computationally screening almost 700 million molecular conformers in a time- and resource-efficient manner. A small number of the predicted active compounds were purchased and tested obtaining a confirmed hit rate of 40 per cent which is an outstanding result for a prospective virtual screening.
Unsupervised training of Bayesian networks for data clustering
Authors: Pham Duc Truong , Ruz Gonzalo A.
Published: July 2009

This paper presents a new approach to the unsupervised training of Bayesian network classifiers. Three models have been analysed: the Chow and Liu (CL) multinets; the tree-augmented naive Bayes; and a new model called the simple Bayesian network classifier, which is more robust in its structure learning. To perform the unsupervised training of these models, the classification maximum likelihood criterion is used. The maximization of this criterion is derived for each model under the classification expectation–maximization (EM) algorithm framework. To test the proposed unsupervised training approach, 10 well-known benchmark datasets have been used to measure their clustering performance. Also, for comparison, the results for thek-means and the EM algorithm, as well as those obtained when the three Bayesian network classifiers are trained in a supervised way, are analysed. A real-world image processing application is also presented, dealing with clustering of wood board images described by 165 attributes. Results show that the proposed learning method, in general, outperforms traditional clustering algorithms and, in the wood board image application, the CL multinets obtained a 12 per cent increase, on average, in clustering accuracy when compared with thek-means method and a 7 per cent increase, on average, when compared with the EM algorithm.
Venturi effect on slotted metamaterial interfaces: broadband tunnelling
Authors: Monzon Cesar
Published: July 2009

We demonstrate the existence of broadband anomalous transmission of electromagnetic (EM) waves through an electrically very narrow aperture in a thin metal plate backed by left-handed media (LHM). It is shown that the incoming energy is simply squeezed through the aperture, without any reflection, regardless of how small the physical aperture is. Analogous to the Venturi effect in fluids, the EM energy behaves as an incompressible fluid, flowing through the constriction (aperture), as if the wave character of EM was lost. This counterintuitive tunnelling effect is not related to resonances and is impossible to achieve with naturally occurring materials. Analysis indicates that a cascaded waveguide implementation, in the form of a slotted metallized LHM wall, retains the exotic broadband transparency character. Applications for a device with these properties abound in the RF/microwave/THz/optical ranges, to which the analysis can be scaled. To complement this analysis, a proposal for achieving broadband LHM is also included.
Thermodynamic control on the climate of intense tropical cyclones
Authors: Chan Johnny C. L.
Published: July 2009

How thermodynamic factors control the climate of intense tropical cyclones (TCs) is investigated by examining the relationship between the seasonally averaged maximum potential intensity (MPI, used as a representative index of the thermodynamic forcing) over an ocean basin where TCs form and the seasonal frequency of occurrence of intense TCs. It is found that only in the Atlantic does the MPI have a statistically significant relationship with the number of intense TCs, explaining about 40 per cent of the variance. In other ocean basins, there is either no correlation or the correlation is not statistically significant. In other words, only in the Atlantic are thermodynamic factors responsible, but still only to a certain extent, for the climate variations of intense TCs. In other ocean basins, it appears that the dynamic factors are much more dominant. Such a conclusion has important implications in considering whether global warming may influence the future climate of intense TCs for the following reason. Although it has been generally accepted that the thermodynamic energy available in the atmosphere is likely to increase under global warming, the results from this study suggest that such an increase does not necessarily imply a concomitant increase in the number of intense TCs, because how the dynamic factors will vary are still not clear. Until we can demonstrate that the dynamic factors will also become more favourable for TC intensification, it remains uncertain whether the frequency of occurrence of intense TCs will increase under a global warming scenario.
Domain walls and double bubbles
Authors: Gillard Mike , Sutcliffe Paul
Published: July 2009

We study configurations of intersecting domain walls in a Wess–Zumino model with three vacua. We introduce a volume-preserving flow and show that its static solutions are configurations of intersecting domain walls that form double bubbles, that is, minimal area surfaces which enclose and separate two prescribed volumes. To illustrate this field theory approach to double bubbles, we use domain walls to reconstruct the phase diagram for double bubbles in the flat square two-torus and also construct all known examples of double bubbles in the flat cubic three-torus.
Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation
Authors: Balloux François , Handley Lori-Jayne Lawson , Jombart Thibaut , Liu Hua , Manica Andrea
Published: July 2009

There is an ongoing discussion in the literature on whether human mitochondrial DNA (mtDNA) evolves neutrally. There have been previous claims for natural selection on human mtDNA based on an excess of non-synonymous mutations and higher evolutionary persistence of specific mitochondrial mutations in Arctic populations. However, these findings were not supported by the reanalysis of larger datasets. Using a geographical framework, we perform the first direct test of the relative extent to which climate and past demography have shaped the current spatial distribution of mtDNA sequences worldwide. We show that populations living in colder environments have lower mitochondrial diversity and that the genetic differentiation between pairs of populations correlates with difference in temperature. These associations were unique to mtDNA; we could not find a similar pattern in any other genetic marker. We were able to identify two correlated non-synonymous point mutations in the
ND3
and
ATP6
genes characterized by a clear association with temperature, which appear to be plausible targets of natural selection producing the association with climate. The same mutations have been previously shown to be associated with variation in mitochondrial pH and calcium dynamics. Our results indicate that natural selection mediated by climate has contributed to shape the current distribution of mtDNA sequences in humans.
Pleiotropic Modulation of Carbon and Nitrogen Metabolism in Arabidopsis Plants Overexpressing theNAD kinase2Gene
Authors: Takahashi Hideyuki , Takahara Kentaro , Hashida Shin-nosuke , Hirabayashi Takayuki , Fujimori Tamaki , Kawai-Yamada Maki , Yamaya Tomoyuki , Yanagisawa Shuichi , Uchimiya Hirofumi
Published: July 2009

Nicotinamide nucleotides (NAD and NADP) are important cofactors in many metabolic processes in living organisms. In this study, we analyzed transgenic Arabidopsis (Arabidopsis thaliana) plants that overexpress NAD kinase2 (NADK2), an enzyme that catalyzes the synthesis of NADP from NAD in chloroplasts, to investigate the impacts of altering NADP level on plant metabolism. Metabolite profiling revealed that NADP(H) concentrations were proportional to NADK activity in NADK2 overexpressors and in the nadk2 mutant. Several metabolites associated with the Calvin cycle were also higher in the overexpressors, accompanied by an increase in overall Rubisco activity. Furthermore, enhanced NADP(H) production due to NADK2 overexpression increased nitrogen assimilation. Glutamine and glutamate concentrations, as well as some other amino acids, were higher in the overexpressors. These results indicate that overexpression of NADK2 either directly or indirectly stimulates carbon and nitrogen assimilation in Arabidopsis under restricted conditions. Importantly, since neither up-regulation nor down-regulation of NADK2 activity affected the sum amount of NAD and NADP or the redox state, the absolute level of NADP and/or the NADP/NAD ratio likely plays a key role in regulating plant metabolism.
(Homo)glutathione Depletion Modulates Host Gene Expression during the Symbiotic Interaction betweenMedicago truncatulaandSinorhizobium meliloti
Authors: Pucciariello Chiara , Innocenti Gilles , Van de Velde Willem , Lambert Annie , Hopkins Julie , Clément Mathilde , Ponchet Michel , Pauly Nicolas , Goormachtig Sofie , Holsters Marcelle , Puppo Alain , Frendo Pierre
Published: July 2009

Under nitrogen-limiting conditions, legumes interact with symbiotic rhizobia to produce nitrogen-fixing root nodules. We have previously shown that glutathione and homoglutathione [(h)GSH] deficiencies impaired Medicago truncatula symbiosis efficiency, showing the importance of the low M  r thiols during the nodulation process in the model legume M. truncatula. In this study, the plant transcriptomic response to Sinorhizobium meliloti infection under (h)GSH depletion was investigated using cDNA-amplified fragment length polymorphism analysis. Among 6,149 expression tags monitored, 181 genes displayed significant differential expression between inoculated control and inoculated (h)GSH depleted roots. Quantitative reverse transcription polymerase chain reaction analysis confirmed the changes in mRNA levels. This transcriptomic analysis shows a down-regulation of genes involved in meristem formation and a modulation of the expression of stress-related genes in (h)GSH-depleted plants. Promoter-β-glucuronidase histochemical analysis showed that the putative MtPIP2 aquaporin might be up-regulated during nodule meristem formation and that this up-regulation is inhibited under (h)GSH depletion. (h)GSH depletion enhances the expression of salicylic acid (SA)-regulated genes after S. meliloti infection and the expression of SA-regulated genes after exogenous SA treatment. Modification of water transport and SA signaling pathway observed under (h)GSH deficiency contribute to explain how (h)GSH depletion alters the proper development of the symbiotic interaction.
Therapeutic efficacy of Bifidobacterium longum‐mediated human granulocyte colony‐stimulating factor and/or endostatin combined with cyclophosphamide in mouse‐transplanted tumors
Authors: Zhu Li‐Ping , Yin Yan , Xing Jing , Li Chen , Kou Lei , Hu Bi , Wu Zhi‐Wei , Wang Jian‐Jun , Xu Gen‐Xing
Published: July 2009

Granulocyte colony‐stimulating factor (GCSF) is frequently used as an adjunctive agent in tumor chemotherapy. Bifidobacterium longums (B. longum) attracted researchers’ interests due to its enhancement of immunity and selective location in solid tumors. B. longum‐pBV22210‐endostatin (Endo) was proved to have a definite inhibitive effect on tumor growth in our previous study. In the present study, we evaluated the effects of B. longum‐pBV22210‐GCSF and/or B. longum‐pBV22210‐Endo combined with cyclophosphamide (CTX) on H22 and S180 tumor‐bearing mice. Based on our previous work, the plasmid pBV22210‐GCSF was constructed and transformed by electroporation into B. longum. The B. longum‐pBV22210‐GCSF and/or B. longum‐pBV22210‐Endo combined with CTX were applied to treat H22 and S180 tumor‐bearing mice. A leukocyte count was carried out and the tumor inhibition rate was calculated after treatment. In our study, CTX combined with B. longum‐pBV22210‐GCSF significantly raised the leukocyte level of tumor‐bearing mice, while combined with B. longum‐pBV22210‐GCSF alone or B. longum‐pBV22210‐Endo alone combinations with CTX inhibited tumor growth by over 65%. The results showed that B. longum‐pBV22210‐GCSF had an effective antagonistic effect on bone marrow inhibited by CTX and could inhibit tumor growth when it was combined with B. longum‐pBV22210‐Endo and CTX. Our results provide an enhanced understanding of B. longum and GCSF as well as their potential as an adjunctive approach in cancer gene therapy. (Cancer Sci 2009; 100: 1986–1990)
Neurological complication analysis of 1000 ultrasound guided peripheral nerve blocks for elective orthopaedic surgery: a prospective study*
Authors: Fredrickson M. J. , Kilfoyle D. H.
Published: July 2009

Little data exists regarding the frequency of neurological complications following ultrasound guided peripheral nerve blockade. Therefore, we studied single injection and continuous ultrasound guided interscalene, supraclavicular, infraclavicular, femoral and sciatic nerve blocks in patients undergoing orthopaedic extremity surgery. All patients were contacted during postoperative weeks 2–4 and questioned for numbness or altered sensation anywhere in the involved extremity, and pain or weakness unrelated to surgery. The presumed aetiology of symptoms was based on the collective agreement of principal investigator, primary surgeon and a neurologist. Multivariate analysis was performed for characteristics potentially important in the causation of neurological complications. Of 1010 consecutive blocks, successful follow up between weeks 2 and 4 occurred in 98.6%. New, all‐cause, neurological symptoms were present in 56/690 blocks (8.2%) at day 10, 37/1010 (3.7%) at 1 month and 6/1010 (0.6%) at 6 months. Most symptoms were due to causes unrelated to the block. Of 452 patients directly questioned at the time of the block, new neurological symptoms were more common in patients who experienced procedure‐induced paraesthesia (odds ratio = 1.7, p = 0.029). The postoperative neurological symptom rate in this series is very similar to those previously reported following traditional techniques.
An assessment of the efficiency of the Glostavent® ventilator
Authors: Bailey T. M. , Webster S. , Tully R. , Eltringham R. , Bourdeaux C.
Published: July 2009

In parts of the world where supplies of oxygen and electricity are erratic, ventilating patients’ lungs can be problematic. Should the electricity supply fail, gas driven ventilators have an advantage as they can continue functioning. However, many are extravagant in their requirement for the driving gas. The Glostavent® ventilator was designed to minimise these requirements. We measured the duration of ventilation achieved by the Glostavent ventilator using an E‐size oxygen cylinder at a range of minute volumes, and the inspired oxygen concentration achieved by recycling the driving gas. The period of mechanical ventilation from a single E‐size cylinder ranged from 11 h 8 min (SD 4 min) with a minute volume of 7 l.min−1 to 18 h 15 min (SD 7 min) with a minute volume of 3 l.min−1. The mean fractional inspired oxygen concentration achieved by recycling the driving gas without further inspired oxygen supplementation was 0.33. We conclude that the Glostavent ventilator performs as efficiently and cost effectively as predicted.