bluuebunny/crossref_metadata_2025 huggingface dataset:
A longitudinal analysis of sociodemographic and health correlates of sexual health among HIV-infected men in the USA
Authors: Jeffries William L. , Zsembik Barbara A. , Peek Chuck W. , Uphold Constance R.
Published: November 2009

Background: Sexual health among HIV-infected men primarily has been examined in cross-sectional designs. Few have used longitudinal data to measure sexual health change or factors associated with change. Moreover, studies of HIV-infected men disproportionately focus on sexual risk behaviours. The present paper examines temporal changes in sexual health based on measures of sexual activity, erectile function, sex drive, and sex life satisfaction. Methods: Data from a prospective cohort study of HIV-infected men (n = 197) in the USA were used. Sexual health measures were based on self-reported sexual activity, erectile function, sex drive, and sex life satisfaction at 12- and 24-month follow-ups. Transition matrices described 1-year sexual health changes. Logistic regression models determined sociodemographic and health-related factors associated with change. Results: Men reported considerable change in sexual health during the year-long observation interval. Among men who experienced change, younger age, cohabitation, and higher CD4 counts were associated with greater sexual activity over time. Men with more depression symptoms had lower erectile function over time, and higher education and higher income were protective against temporal declines in sex drive and satisfaction. Less disease comorbidity was associated with 1-year improvements in sex life satisfaction. Conclusions: Some men in our sample experienced sexual health change, but stability was common for most. Temporal changes in sexual health varied according to age, cohabitation, education, income, and physical and mental health covariates. The present paper highlights the benefits of longitudinal investigations and multidimensional definitions of sexual health.
Acceptance of human papillomavirus vaccination among first year female university students in Hong Kong
Authors: Wong William C. W. , Fong Ben , Chan Paul K. S.
Published: November 2009

The present study assessed sexual behaviour, knowledge and attitudes among first year university students in order to identify factors that may affect their acceptance of human papillomavirus (HPV) vaccination. A cross-sectional survey was conducted at the Chinese University of Hong Kong in August 2006. The survey was a self-administered questionnaire comprising questions regarding general health, sexual behaviour, knowledge about HPV and cervical cancer, and attitudes towards vaccination. χ2, anova and logistic regression tests were used to identify associations between categories. Of 992 students, 63 (6.5%) reported having had sexual intercourse, 22.4% of whom had had more than one sexual partner and 36.5% had had unprotected sexual intercourse. A total of 70.8% of participants were willing to accept the HPV vaccine, with ‘willingness’ independently associated with age, having had sexual intercourse and beliefs regarding the effectiveness of vaccination (P < 0.05). Understanding the role of these influences can aid in the design of successful HPV education, prevention and vaccination programs.
Prevalence of Trichomonas vaginalis infection among young reproductive age women in India: implications for treatment and prevention
Authors: Madhivanan Purnima , Bartman Melissa T. , Pasutti Lauren , Krupp Karl , Arun Anjali , Reingold Arthur L. , Klausner Jeffrey D.
Published: November 2009

Background: Trichomonas vaginalis infection is the most common curable sexually transmissible infection (STI) worldwide. The present study describes the burden and correlates of T. vaginalis infection among young reproductive age women in Mysore, India. Methods: Between November 2005 and March 2006, sexually active women aged 15–30 years were recruited from low-income peri-urban and rural neighbourhoods of Mysore, India. Participants were interviewed and offered a physical examination and testing for T. vaginalis, bacterial vaginosis, vaginal candidiasis, Neisseria gonorrheoea and herpes simplex virus type-2 antibodies. Results: Of the 898 participating women, 76 had a T. vaginalis infection (8.5%, 95% confidence interval [95% CI]: 6.7–10.5%). Nearly all (98%) participants were married and most reported their spouse as their main sex partner. The mean age at marriage was 16.9 years (s.d. 2.9 years) and two-thirds of the sample reported having first sexual intercourse before the age of 19 years. Risk factors independently associated with T. vaginalis infection included early age at first intercourse (adjusted odds ratio [OR] 2.09; 95% CI: 1.09–4.00), concurrent bacterial vaginosis (OR 8.21; 95% CI: 4.30–15.66), vaginal candidiasis (OR 2.40; 95% CI: 1.48–3.89) and herpes simplex virus type-2 infection (OR 3.44; 95% CI: 1.97–6.02). Conclusion: The burden of T. vaginalis infection at 8.5% is relatively high among a community sample of young reproductive aged women. Because this infection increases the risk of HIV transmission and is associated with adverse pregnancy outcomes, there is a need for increased screening and treatment of this easily curable sexually transmissible infection in India.
High incidence of syphilis in HIV-positive homosexual men: data from two community-based cohort studies
Authors: Jin Fengyi , Prestage Garrett P. , Zablotska Iryna , Rawstorne Patrick , Imrie John , Kippax Susan C. , Donovan Basil , Templeton David J. , Kaldor John M. , Grulich Andrew E.
Published: November 2009

Background: Syphilis has re-emerged and become established in gay communities in most developed countries since the late 1990s. HIV infected men have been disproportionately affected by this endemic, but it is unclear whether this is due to behavioural or biological reasons. We report incidence and risk factors for syphilis in two community-based cohorts of HIV-negative and HIV-positive homosexual men in Sydney, Australia. Methods: Participants were recruited using similar community-based strategies in both cohorts and underwent annual face-to-face interviews. Syphilis screening was offered to all consenting participants at annual visits. Results: In the HIV-negative cohort, 21 men seroconverted to syphilis and one man had a syphilis re-infection during 2001–07, an incidence of 0.49 per 100 person-years (95% CI: 0.31–0.74). In the HIV-positive cohort during 2005–07, eight men seroconverted and one man had a syphilis re-infection, giving an incidence of 3.62 per 100 person-years (95% CI: 1.67–6.48). All nine reported a recent CD4 count of more than 350 cells µL–1. Syphilis incidence was significantly higher in the HIV-positive cohort after adjustment for age (hazard ratio (HR) = 9.20, 95% CI: 3.63–23.31). Unprotected anal intercourse (UAI) with HIV-positive partners was significantly associated with incident syphilis in both cohorts (HR = 4.45, 95% CI: 1.37–14.45 in HIV-negative; HR = 8.67, 95% CI: 1.03–72.76 in HIV-positive). Conclusion: Syphilis incidence was almost 10-fold higher in HIV-positive than in HIV-negative homosexual men, and it was not related to a CD4 count below 350 µL–1. UAI with HIV positive partners was of particular importance in the transmission of syphilis.
Wind-borne insects mediate directional pollen transfer between desert fig trees 160 kilometers apart
Authors: Ahmed Sophia , Compton Stephen G. , Butlin Roger K. , Gilmartin Philip M.
Published: November 2009

The question of how far pollen can move between plants has implications for topics as diverse as habitat fragmentation, conservation management, and the containment of genetically modified crops. The monoecious African fig tree
Ficus sycomorus
L. relies on the small, short-lived, night-flying, host-specific fig wasp
Ceratosolen arabicus
Mayr for pollination. We used microsatellite markers to characterize a geographically isolated riparian population of
F. sycomorus
growing along the Ugab River in the Namib Desert, Namibia, together with paternity analysis of seedlings from known mothers, to map pollen movement within this population. In this way we tracked insect movements between individually recognizable trees by means of their pollen cargo and documented the movement of
C. arabicus
between known trees separated by more than 160 km, with a mean distance for confirmed successful pollination events of 88.6 km. The predominant observed movement of pollinators was in a westerly direction, toward the sea, reflecting seasonal nighttime wind direction and the wind-borne dispersal of fig wasps. Our results suggest the existence of an extensive panmictic population of trees that are well suited to overcome the effects of geographical isolation.
Wet phases in the Sahara/Sahel region and human migration patterns in North Africa
Authors: Castañeda Isla S. , Mulitza Stefan , Schefuß Enno , Lopes dos Santos Raquel A. , Sinninghe Damsté Jaap S. , Schouten Stefan
Published: November 2009

The carbon isotopic composition of individual plant leaf waxes (a proxy for C
3
vs. C
4
vegetation) in a marine sediment core collected from beneath the plume of Sahara-derived dust in northwest Africa reveals three periods during the past 192,000 years when the central Sahara/Sahel contained C
3
plants (likely trees), indicating substantially wetter conditions than at present. Our data suggest that variability in the strength of Atlantic meridional overturning circulation (AMOC) is a main control on vegetation distribution in central North Africa, and we note expansions of C
3
vegetation during the African Humid Period (early Holocene) and within Marine Isotope Stage (MIS) 3 (≈50–45 ka) and MIS 5 (≈120–110 ka). The wet periods within MIS 3 and 5 coincide with major human migration events out of sub-Saharan Africa. Our results thus suggest that changes in AMOC influenced North African climate and, at times, contributed to amenable conditions in the central Sahara/Sahel, allowing humans to cross this otherwise inhospitable region.
Amyloid seeds formed by cellular uptake, concentration, and aggregation of the amyloid-beta peptide
Authors: Hu Xiaoyan , Crick Scott L. , Bu Guojun , Frieden Carl , Pappu Rohit V. , Lee Jin-Moo
Published: November 2009

One of the neuropathological hallmarks of Alzheimer's disease (AD) is the amyloid plaque, primarily composed of aggregated amyloid-beta (Aβ) peptide. In vitro, Aβ
1–42
, the major alloform of Aβ found in plaques, self-assembles into fibrils at micromolar concentrations and acidic pH. Such conditions do not exist in the extracellular fluid of the brain where the pH is neutral and Aβ concentrations are in the nanomolar range. Here, we show that extracellular soluble Aβ (sAβ) at concentrations as low as 1 nM was taken up by murine cortical neurons and neuroblastoma (SHSY5Y) cells but not by human embryonic kidney (HEK293) cells. Following uptake, Aβ accumulated in Lysotracker-positive acidic vesicles (likely late endosomes or lysosomes) where effective concentrations (>2.5 μM) were greater than two orders of magnitude higher than that in the extracellular fluid (25 nM), as quantified by fluorescence intensity using laser scanning confocal microscopy. Furthermore, SHSY5Y cells incubated with 1 μM Aβ
1–42
for several days demonstrated a time-dependent increase in intracellular high molecular weight (HMW) (>200 kDa) aggregates, which were absent in cells grown in the presence of Aβ
1–40
. Homogenates from these Aβ
1–42
-loaded cells were capable of seeding amyloid fibril growth. These results demonstrate that Aβ can be taken up by certain cells at low physiologically relevant concentrations of extracellular Aβ, and then concentrated into endosomes/lysosomes. At high concentrations, vesicular Aβ aggregates to form HMW species which are capable of seeding amyloid fibril growth. We speculate that extrusion of these aggregates may seed extracellular amyloid plaque formation during AD pathogenesis.
Processing of multiple-intron-containing pretRNA
Authors: Tocchini-Valentini Giuseppe D. , Fruscoloni Paolo , Tocchini-Valentini Glauco P.
Published: November 2009

Computational studies predict the simultaneous presence of two and even three introns in certain crenarchaeal tRNA genes. In these multiple-intron-containing pretRNAs, the introns are nested one inside the other and the pretRNA folds into a conformation that is anticipated to allow splicing of the last intron only after splicing the others. A set of operations, each consisting of two cleavages and one ligation, therefore needs to be carried out sequentially. PretRNAs containing multiple introns are predicted to fold, forming bulge–helix–bulge (BHB) and BHB-like motifs. The tRNA splicing endonuclease should recognize these motifs. To test this hypothetical scenario, we used the homotetrameric enzyme fromMethanocaldococcus jannaschii(METJA) and the heterotetrameric enzyme fromSulfolobus solfataricus(SULSO). On the basis of our previous studies, the METJA enzyme should cleave only the BHB structure motif, while the SULSO enzyme can in addition cleave variant substrate structures, like the bulge-helix-loop (BHL). We show here that the processing of multiple-intron-containing pretRNA can be observed in vitro.
Associations between Mindfulness and Implicit Cognition and Self-Reported Affect
Authors: Waters Andrew J. , Reitzel Lorraine R. , Cinciripini Paul , Li Yisheng , Marcus Marianne T. , Vidrine Jennifer Irvin , Wetter David W.
Published: November 2009

Theory suggests that mindful individuals exhibit enhanced attentional processing (e.g., attentional control) and that they maintain a detached perspective to problematic stimuli. For smokers, smoking and affective stimuli are problematic stimuli when they try to quit. In this cross-sectional study, smokers ( n = 158) completed 3 modified Stroop tasks (to assess attentional control), 3 Implicit Association Tests (IATs; to assess detached perspective), and a battery of self-report assessments. Degree of mindfulness was negatively associated ( P < .05) with self-reported negative affect, perceived stress, and depressive symptom severity, and positively associated ( P < .05) with positive affect. Degree of mindfulness was not associated with the ability to disengage attention from smoking or affective stimuli. On the depression IAT, more mindful participants exhibited a more negative IAT effect, suggesting that they may have developed a detached perspective to depression-related stimuli. Theoretical and clinical implications of the data are discussed.
Associations of Mindfulness with Nicotine Dependence, Withdrawal, and Agency
Authors: Vidrine Jennifer Irvin , Businelle Michael S. , Cinciripini Paul , Li Yisheng , Marcus Marianne T. , Waters Andrew J. , Reitzel Lorraine R. , Wetter David W.
Published: November 2009

Quitting smoking is a major life stressor that results in numerous aversive consequences, including persistently increased level of post-cessation negative affect and relapse. The identification of factors that may enhance behavioral and emotional regulation after quitting may be useful in enhancing quit rates and preventing relapse. One factor broadly linked with behavioral and emotional regulation is mindfulness. This study examined baseline associations of mindfulness with demographic variables, smoking history, dependence, withdrawal severity, and agency among 158 smokers enrolled in a cessation trial. Results indicated that mindfulness was negatively associated with level of nicotine dependence and withdrawal severity, and positively associated with a sense of agency regarding cessation. Moreover, mindfulness remained significantly associated with these measures even after controlling for key demographic variables. Results suggest that low level of mindfulness may be an important predictor of vulnerability to relapse among adult smokers preparing to quit; thus, mindfulness-based interventions may enhance cessation.
Translation, internationalisation and the university
Authors: Harris Suzy
Published: November 2009

The demands and challenges posed by the global economy help explain the growing importance of the internationalisation of higher education in European, national and institutional policy arenas. The discourse of internationalisation is driven primarily by economic factors, and an emphasis
on competition, standards and skills has shifted attention away from considering internationalisation in relation to the aims, values and the purpose of higher education. This paper considers the notion of translation as a way of thinking about internationalisation. Translation is normally
understood in relatively simple terms – as the transfer of meaning from one language to another – and it is seen primarily as a technical matter, albeit one that sometimes raises considerable difficulties. It is argued that that there is something limited and mistaken about this
way of thinking about translation. It is not only between languages that translation occurs but also within a language. The question of translation has to do with the nature of meaning, and meaning has been and must remain a central concern of higher education and the university.
Priceless conceptual thresholds: beyond the 'stuck place' in writing
Authors: Wisker Gina , Savin-Baden Maggi
Published: November 2009

This paper explores the idea of conceptual threshold crossing in the writing process and in particular stuck moments and the process of moving on, valuing the pricelessness of preliminality, the vision of a possible movement through a portal and the creative learning leap into focused,
formed writing. Our work to date is based on formal and less formal collections of narratives from academics who write, including ourselves, and from those who support and supervise the writing of both academic staff and doctoral students.
Monologue or dialogue? Stepping away from the abyss in higher education
Authors: Stern Julian
Published: November 2009

This paper investigates the possibilities of the use of dialogue, and the dangers of the use of monologue, in higher education in the early twenty-first century, in a period facing a number of smaller- and larger-scale crises – each interpreted as an 'abyss' of some kind. How
does higher education contribute, positively or negatively, to personal relationships and the risk of isolation and paranoia, institutional approaches to their own permanence, and broad economic-environmental problems? Each of these abysses is analysed in terms of dialogue, and a dialogic
approach in higher education is put forward as a way to help us step away from each abyss. Crises and conflicts throughout the twentieth century might have led to a decline in confidence in dialogic approaches in and beyond educational institutions. However, the opposite was the case, and
Martin Buber analysed dialogue in the midst of conflict, rather than simply when conflict was concluded. His mid-twentieth century analyses are used, here, to theorise contemporary dialogic higher education.
Validating a 3-Point Prediction Rule for Surgical Site Infection after Coronary Artery Bypass Surgery
Authors: Chen Luke F. , Anderson Deverick J. , Kaye Keith S. , Sexton Daniel J.
Published: November 2009

Background.

Surgical site infection (SSI) after coronary artery bypass graft (CABG) surgery is an increasing healthcare problem. Investigators from Australia proposed a new, 3-point scale that assesses SSI risk on the basis of diagnosis of diabetes mellitus and body mass index.

Objective.

To validate the Australian Clinical Risk Index among patients undergoing CABG surgery in the United States.

Design and Setting.

Nested case-control study involving patients undergoing CABG surgery at 9 hospitals during 1991-2002.

Patients.

Case patients were those who developed SSIs after CABG surgery. Control subjects were matched to case patients on the basis of hospital, age, and procedure date.

Methods.

Odds ratios (ORs) for SSIs were calculated for the comparison of case patients with control subjects for all risk categories determined using the Australian Clinical Risk Index and National Nosocomial Infections Surveillance System (NNIS) risk index. An adjusted area under the curve was used to compare predictive values among risk indices.

Results.

Four hundred sixty patients were studied, including 269 patients with SSI and 191 control subjects. NNIS risk group 2 was associated with increased rate of SSI (OR, 1.79; 95% confidence interval [CI], 1.19-2.67). No patient had an NNIS risk index of 3. The remaining NNIS categories were not predictive of infection. In contrast, an increase in Australian Clinical Risk Index was associated with an increase in risk of SSI (category 2: OR, 2.39 [95% CI, 1.33-4.29]; category 3: OR, 4.46 [95% CI, 1.83-10.85]).

Conclusions.

The NNIS risk index predicts the risk of SSI associated with many procedures, but it has limited use in predicting the risk of SSI after CABG surgery. The new Australian Clinical Risk Index stratified patients into discrete groups associated with increased risk of SSI. Data from our study support the use of this new risk index in the US population.
Field and temperature dependence of space charge injection in a silicone rubber
Authors: Rain P , Nguyen D H , Sylvestre A , Rowe S
Published: November 2009

The generation of space charges in a silicone elastomer has been characterized under dc voltage as a function of the temperature using the laser induced pressure pulse (LIPP) method. The analysis of the LIPP spectra has been detailed thanks to acoustical considerations, taking into account the reflection, attenuation and dispersion of the pressure wave. Both heterocharges and homocharges have been observed depending on the field magnitude (5 to 20 × 106 V m−1), polarization duration and temperature (20, 40 or 60 °C). With temperature increasing, charges are observed at lower fields. Heterocharges appear in less stressed conditions. Then, homocharges take the place of these heterocharges. Positive homocharges are observed in lower stressed conditions than negative homocharges. Mobility of these charges has not been observed below 60 °C.
Molecular Dynamics Simulation of Temperature-dependent Flexibility of Thermophilic Xylose Isomerase
Authors: Xu Wei , Cai Ping , Yan Ming , Xu Lin , Ouyang Ping-kai
Published: November 2009

The complex model of Thermus thermophilus xylose isomerase (TtXI) with D-xylose was constructed, and molecular dynamics (MD) simulations were carried out at 300 and 360 K for 10 ns by NAMD2.5. The radius of gyration (Rg), subunit interactions, and residue flexibility were analyzed. The results show that residues 6069, 142148, 169172, and 332340 have high flexibility at 300 and 360 K. Residues with higher flexibility at 360 K than that at 300 K can mainly be divided into two groups: one locates in the helix-loop-helix region consisting of residues 5580 in catalytic domain; the other at subunit interfaces. The Rg of catalytic domain at 360 K shows 0.16 A higher than that at 300 K, but Rg of small C-terminal domain has no obvious difference. The results indicate that enhanced Rg of catalytic domain may lead to the intense motion of the active site of TtXI and promote the D-xylose isomization reaction. Eight hydrogen bonds and five ion pairs are reduced at subunit interfaces at 360 K compared with 300 K, that may be the main reason for the decrease in rigidity and increase in activity at high temperature of TtXI. This result also help to explain the cold-adaption phenomenon of TtXI E372G mutant reported previously. Our results reveal the relationship between temperature and structure flexibility of TtXI, and play an important role in understanding the thermostability of thermophile protein with multiple subunits.
Molecular Modeling and Design of Arylthioindole Derivatives as Tubulin Inhibitors
Authors: Liao Si-yan , Miao Ti-fang , Chen Jin-can , Lu Hai-liang , Zheng Kang-cheng
Published: November 2009

Three-dimensional quantitative structure activity relationship (3D-QSAR) and docking studies of a series of arylthioindole derivatives as tubulin inhibitors against human breast cancer cell line MCF-7 have been carried out. An optimal 3D-QSAR model from the comparative molecular field analysis (CoMFA) for training set with significant statistical quality (R2 = 0.898) and predictive ability (q2 = 0.654) was established. The same model was further applied to predict pIC50 values of the compounds in test set, and the resulting predictive correlation coefficient R2(pred) reaches 0.816, further showing that this CoMFA model has high predictive ability. Moreover, the appropriate binding orientations and conformations of these compounds interacting with tubulin are located by docking study, and it is very interesting to find the consistency between the CoMFA field distribution and the 3D topology structure of active site of tubulin. Based on CoMFA along with docking results, some important factors improving the activities of these compounds were discussed in detail and were summarized as follows: the substituents R3R5 (on the phenyl ring) with higher electronegativity, the substituent R6 with higher electropositivity and bigger bulk, the substituent R7 with smaller bulk, and so on. In addition, five new compounds with higher activities have been designed. Such results can offer useful theoretical references for experimental works.
Continuum Model for Electronic Polarization Based on a Novel Dielectric Response Function
Authors: Wang Quan-de , Wu Han-yu , Fu Ke-xiang , Li Xiang-yuan
Published: November 2009

A generalized response function based on the use of dielectric spectra for dielectric relaxation process is derived. We apply the general response function to the special case in order to examine how special dielectric relaxation functions developed by other authors for solvent relaxation can be derived based on our formulations. Three typical solvents, water, methanol, and acetonitrile are used to investigate the electronic polarization processes of polar solvents. The solvent electronic polarization process is shown after a linear variation with the external electric field imposed on the solvent. The results show a conclusion that the electronic polarization of the solvents will accompany the electronic transition synchronously, without time lag.
Density Functional Theory Study on Organic Dye Sensitizers Containing Bis-dimethylfluorenyl Amino Benzofuran
Authors: Zhang Cai-rong , Liu Zi-jiang , Chen Yu-hong , Ma Jun , Chen Hong-shan , Zhang Mei-ling
Published: November 2009

The geometries, electronic structures, polarizabilities and hyperpolarizabilities, as well as the UV-Vis spectra of the two organic dye sensitizers containing bis-dimethylfluorenyl amino benzofuran were studied via density functional theory (DFT) and time-dependent DFT. The features of electronic absorption spectra were assigned on account of the agreement between the experiment and the calculations. The absorption bands in visible region are related to photoinduced electron transfer processes, and the dimethylfluorenyl amino benzo[b]furan groups are major chromophore that contributed to the sensitization of photo-to-current conversion. The role of vinylene group in geometry, electronic structure and spectra property is analyzed according to the comparative study of the dyes.
Efficient Stochastic Simulation Algorithm for Chemically Reacting Systems Based on Support Vector Regression
Authors: Peng Xin-jun , Wang Yi-fei
Published: November 2009

The stochastic simulation algorithm (SSA) accurately depicts spatially homogeneous well-stirred chemically reacting systems with small populations of chemical species and properly represents noise, but it is often abandoned when modeling larger systems because of its computational complexity. In this work, a twin support vector regression based stochastic simulations algorithm (TS3A) is proposed by combining the twin support vector regression and SSA, the former is a well-known robust regression method in machine learning. Numerical results indicate that this proposed algorithm can be applied to a wide range of chemically reacting systems and obtain significant improvements on efficiency and accuracy with fewer simulating runs over the existing methods.
Structures and Hydrogen Bonding Interactions in Urea-water System Studied by All-atom MD Simulation and Chemical Shifts in NMR Spectrum
Authors: Zhang Rong , Zhao Guan-sheng , Wu Wen-juan
Published: November 2009

The interactions and structures of the urea-water system are studied by an all-atom molecular dynamics (MD) simulation. The hydrogen-bonding network and the radial distribution functions are adopted in MD simulations. The structures of urea-water mixtures can be classified into different regions from the analysis of the hydrogen-bonding network. The urea molecule shows the certain tendency to the self-aggregate with the mole fraction of urea increasing. Moreover, the results of the MD simulations are also compare with the chemical shifts and viscosities of the urea aqueous solutions, and the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data such as chemical shifts of the hydrogen atom and viscosity.
Hydrogen Bonding Character Between the Glycine and BF4-
Authors: He Qin , Yang Jing , Meng Xiang-jun
Published: November 2009

The hydrogen bonding character between the BF4- and glycine was theoretically studied at the level of B3LYP/6;31+G*, single point energies were performed at the level of B3LYP/6311++G**. The relevant geometrical characteristics, energy properties, as well as the characters of the intramolecular hydrogen bonds have been studied. Atoms in molecule theory topological analysis indicated the (3,1) critical points for hydrogen bonds. In addition, the electron density and Laplacian were in the range suggested for the hydrogen bonds. Especially, the changes of atomic charge, dipole moment, enegry as well as volume of the hydrogen upon hydrogen bonds formation were systemitically discussed.
Quasi-classical Trajectory Study of the Intramolecular Isotope Effect in the Reaction O(3P)+H2/HD
Authors: Wei Qiang , Li Xing , Li Tie
Published: November 2009

Theoretical studies of the dynamics of the reactions O(3P)+H2/HD(v = 0, j = 0)OH+H have been performed with quasi-classical trajectory method (QCT) on an ab initio potential surface for the lowest triplet electronic state of H2O(3A). The QCT-calculated integral cross sections are in good agreement with the earlier time-dependent quantum mechanics results. The state-resolved rotational distributions reveal that the product OH rotational distributions for O+HD have a preference for populating highly internally excited states compared with the O+H2 reaction. Distributions of differential cross sections show that directions of scattering are strongly dependent on the choice of quantum state. The polarization dependent generalized differential cross-sections and the distributions were calculated and a pronounced isotopic effect is revealed. The calculated results indicate that the product polarization is very sensitive to the mass factor.
Transition Dipole, Charge Transfer, and Electron-hole Coherence in Two-photon Absorption: Visualizations with Two Dimensional Site and Three Dimensional Cube Representations
Authors: Li Yuan-zuo , Zhang Wen-qin , Zhao Xiao-hong , Ma Feng-cai , Chen Mao-du
Published: November 2009

The developed visualization methods of two dimensional (2D) site and three dimensional (3D) cube representations have been performed to show the orientation of transition dipole, charge transfer, and electron-hole coherence in two-photon absorption (TPA). The 3D cube representations of transition density can reveal visually the orientation and strength of transition dipole moment, and charge different density show the orientation of charge transfer in TPA. The 2D site representation can reveal visually the electron-hole coherence in TPA. The combination of 2D site and 3D cube representations provide clearly inspect into the charge transfer process and the contribution of excited molecular segments for TPA.
Radiation Vulcanization of Magnetorheological Elastomers Based on Silicone Rubber
Authors: Zhang Wei , Gong Xing-long , Li Jian-feng , Zhu Hong , Jiang Wan-quan
Published: November 2009

The fabrication of magnetorheological (MR) elastomers was studied by two vulcanization methods, including heat vulcanization (HV) and radiation vulcanization (RV), were employed to fabricate MRE samples. The dynamical mechanical properties were characterized by using a dynamic mechanic analyzer. In particular, both the MR effect and its durability were investigated. The experimental results showed that RV samples have large magneto-induced modulus, large zero-field modulus, and good durability property of MR effect. To explain these results, cubic deformation and plasticizer migration were analyzed. Large magneto-induced modulus of RV sample results from cubic deformation during vulcanization process. And the plasticizer migration results in better durability of MR effect.
Analysis and Verification on the Chain-like Model with Normal Distribution of Magnetorheological Elastomer
Authors: Yu Miao , Xia Yong-qiang , Yan Xiao-rui
Published: November 2009

Magnetorheological elastomer (MRE) is a new kind of smart materials, the rheological properties can be controlled rapidly by the external magnetic field. It is mainly composed of rubber and micron-sized ferromagnetic particles, which forms a chain-like structure. Therefore its mechanical, electric, and magnetic properties can be changed by the applied magnetic field, which is called as the magneto-induced effect. But this effect is not remarkable enough currently for the engineering application. So it is important for material preparation to optimize parameters to enhance the magneto-induced effect. In this work, based on chain-like model, some factors influencing the magneto-induced effect of MRE were analyzed theoretically by using dipole method with the normal distribution of chain's angle introduced. The factors included the oblique angle of particles chains, magnetic field intensity, and shear strain, etc. Some experiments were also carried out.
A Novel c-Jun N-terminal Kinase (JNK)-binding Protein WDR62 Is Recruited to Stress Granules and Mediates a Nonclassical JNK Activation
Authors: Wasserman Tanya , Katsenelson Ksenya , Daniliuc Sharon , Hasin Tal , Choder Mordechay , Aronheim Ami
Published: November 2009

The c-Jun N-terminal kinase (JNK) is part of a mitogen-activated protein kinase (MAPK) signaling cascade. Scaffold proteins simultaneously associate with various components of the MAPK signaling pathway and play a role in signal transmission and regulation. Here we describe the identification of a novel scaffold JNK-binding protein, WDR62, with no sequence homology to any of the known scaffold proteins. WDR62 is a ubiquitously expressed heat-sensitive 175-kDa protein that specifically associates with JNK but not with ERK and p38. Association between WDR62 and JNKs occurs in the absence and after either transient or persistent stimuli. WDR62 potentiates JNK kinase activity; however it inhibits AP-1 transcription through recruitment of JNK to a nonnuclear compartment. HEK-293T cells transfected with WDR62 display cytoplasmic granular localization. Overexpression of stress granule (SG) resident proteins results in the recruitment of endogenous WDR62 and activated JNK to SG. In addition, cell treatment with arsenite results in recruitment of WDR62 to SG and activated JNK to processing bodies (PB). JNK inhibition results in reduced number and size of SG and reduced size of PB. Collectively, we propose that JNK and WDR62 may regulate the dynamic interplay between polysomes SG and PB, thereby mediating mRNA fate after stress.
Mechanisms of Self-Organization of Cortical Microtubules in Plants Revealed by Computational Simulations
Authors: Allard Jun F. , Wasteneys Geoffrey O. , Cytrynbaum Eric N.
Published: November 2009

Microtubules confined to the two-dimensional cortex of elongating plant cells must form a parallel yet dispersed array transverse to the elongation axis for proper cell wall expansion. Some of these microtubules exhibit free minus-ends, leading to migration at the cortex by hybrid treadmilling. Collisions between microtubules can result in plus-end entrainment (“zippering”) or rapid depolymerization. Here, we present a computational model of cortical microtubule organization. We find that plus-end entrainment leads to self-organization of microtubules into parallel arrays, whereas catastrophe-inducing collisions do not. Catastrophe-inducing boundaries (e.g., upper and lower cross-walls) can tune the orientation of an ordered array to a direction transverse to elongation. We also find that changes in dynamic instability parameters, such as in mor1-1 mutants, can impede self-organization, in agreement with experimental data. Increased entrainment, as seen in clasp-1 mutants, conserves self-organization, but delays its onset and fails to demonstrate increased ordering. We find that branched nucleation at acute angles off existing microtubules results in distinctive sparse arrays and infer either that microtubule-independent or coparallel nucleation must dominate. Our simulations lead to several testable predictions, including the effects of reduced microtubule severing in katanin mutants.
Centromeric Localization of Dispersed Pol III Genes in Fission Yeast
Authors: Iwasaki Osamu , Tanaka Atsunari , Tanizawa Hideki , Grewal Shiv I.S. , Noma Ken-ichi
Published: November 2009

The eukaryotic genome is a complex three-dimensional entity residing in the nucleus. We present evidence that Pol III–transcribed genes such as tRNA and 5S rRNA genes can localize to centromeres and contribute to a global genome organization. Furthermore, we find that ectopic insertion of Pol III genes into a non-Pol III gene locus results in the centromeric localization of the locus. We show that the centromeric localization of Pol III genes is mediated by condensin, which interacts with the Pol III transcription machinery, and that transcription levels of the Pol III genes are negatively correlated with the centromeric localization of Pol III genes. This centromeric localization of Pol III genes initially observed in interphase becomes prominent during mitosis, when chromosomes are condensed. Remarkably, defective mitotic chromosome condensation by a condensin mutation, cut3-477, which reduces the centromeric localization of Pol III genes, is suppressed by a mutation in the sfc3 gene encoding the Pol III transcription factor TFIIIC subunit, sfc3-1. The sfc3-1 mutation promotes the centromeric localization of Pol III genes. Our study suggests there are functional links between the process of the centromeric localization of dispersed Pol III genes, their transcription, and the assembly of condensed mitotic chromosomes.
Target prediction and a statistical sampling algorithm for RNA–RNA interaction
Authors: Huang Fenix W. D. , Qin Jing , Reidys Christian M. , Stadler Peter F.
Published: November 2009

Motivation: It has been proven that the accessibility of the target sites has a critical influence on RNA–RNA binding, in general and the specificity and efficiency of miRNAs and siRNAs, in particular. Recently, O(N6) time and O(N4) space dynamic programming (DP) algorithms have become available that compute the partition function of RNA–RNA interaction complexes, thereby providing detailed insights into their thermodynamic properties.

Results: Modifications to the grammars underlying earlier approaches enables the calculation of interaction probabilities for any given interval on the target RNA. The computation of the ‘hybrid probabilities’ is complemented by a stochastic sampling algorithm that produces a Boltzmann weighted ensemble of RNA–RNA interaction structures. The sampling of k structures requires only negligible additional memory resources and runs in O(k·N3).

Availability: The algorithms described here are implemented in C as part of the rip package. The source code of rip2 can be downloaded from http://www.combinatorics.cn/cbpc/rip.html and http://www.bioinf.uni-leipzig.de/Software/rip.html.

Contact:  duck@santafe.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Management of obstructive renal failure caused by bilateral renal aspergilloma in an immunocompetent newborn
Authors: Martinez-Pajares J. D. , Martinez-Ferriz M. C. , Moreno-Perez D. , Garcia-Ramirez M. , Martin-Carballido S. , Blanch-Iribarne P.
Published: November 2009

Fungal infection of the kidneys is a rare condition that has been reported in premature babies and in diabetic or immunocompromised adult patients. Candida spp. is the most frequent micro-organism involved. This paper reports a case of an immunocompetent newborn with a bladder exstrophy who suffered from an acute renal failure caused by bilateral renal aspergilloma (Aspergillus flavus). The newborn was treated with amphotericin B urinary tract irrigation through bilateral nephrostomy catheters, combined with liposomal amphotericin B and voriconazole therapy, which improved his renal function. However, due to persistent fungal colonization, a long antifungal treatment and permanent ureterostomies were necessary to deal with new episodes of ureterorenal obstruction. As of November 2009, despite the renal injuries, renal function had been conserved. The management of the mechanical obstruction and the choice of antifungal drugs are discussed in this unusual case.
Tracking the geographical spread of avian influenza (H5N1) with multiple phylogenetic trees
Authors: Hovmöller Rasmus , Alexandrov Boyan , Hardman Jori , Janies Daniel
Published: November 2009

Avian influenza (H5N1) has been of great social and economic importance since it first infected humans in Hong Kong in 1997. A highly pathogenic strain has spread from China and has killed humans in east Asia, west Africa, south Asia, and the Middle East. Recently, several molecular phylogenetic studies have focused on the relationships of various clades of H5N1 and their spread over time, space, and various hosts. These studies examining the geographical spread of H5N1 have based their conclusions on a single tree. This tree often results from the analysis of the genomic segment coding for the haemagglutinin (HA) or neuraminidase (NA) proteins and a limited sample of viral isolates. Here we present the first study using multiple candidate trees to estimate geographical transmission routes of H5N1. In addition, we use all high‐quality HA and NA sequences available to the public as of June 2008. We estimated geographical transmission routes of H5N1 by optimizing multistate characters with states representing different geographical regions over a pool of presumed minimum‐length trees. We also developed means to visualize our results in Keyhole Markup Language (KML) for virtual globes. We provide these methods as a web application entitled “Routemap” (http://routemap.osu.edu). The resulting visualizations are akin to airline route maps but they depict the routes of spread of viral lineages. We compare our results with the results of previous studies. We focus on the sensitivity of results to sampling of tree space, character coding schemes, optimization methods, and taxon sampling. In conclusion, we find that using one tree and a single character optimization method will ignore many of the transmission routes indicated by genetic sequence and geographical data.

© The Willi Hennig Society 2009.
Glutathione S‐transferase M1 inhibits dexamethasone‐induced apoptosis in association with the suppression of Bim through dual mechanisms in a lymphoblastic leukemia cell line
Authors: Hosono Naoko , Kishi Shinji , Iho Sumiko , Urasaki Yoshimasa , Yoshida Akira , Kurooka Hisanori , Yokota Yoshifumi , Ueda Takanori
Published: November 2009

(Cancer Sci2010; 101: 767–773)

Glutathione S‐transferase μ (GSTM1) is mainly known as a detoxification enzyme but it has also been shown to be a negative regulator of apoptosis‐related signaling cascades. Recently GSTM1 has been reported to be a significant risk factor for hematological relapse in childhood acute lymphoblastic leukemia, although the underlying mechanism remains largely unknown. Glucocorticoids play a crucial role in the treatment of childhood acute lymphoblastic leukemia, therefore we hypothesized that GSTM1 plays important roles in glucocorticoid‐induced apoptotic pathways. To clarify the relationship betweenGSTM1and drug resistance,GSTM1was transfected into a T‐acute lymphoblastic leukemia cell line, CCRF‐CEM (CEM), and we established the GSTM1‐expressing cell lines CEM/M1‐4 and CEM/M1‐9. Transduction ofGSTM1into CEM selectively decreased cellular sensitivity to dexamethasone in a manner that was independent of glutathione conjugation, but was due to apoptosis inhibition. Dexamethasone‐induced p38‐MAPK and Bim activation were concomitantly suppressed. Interestingly, nuclear factor kappa b (NF‐κB) p50 activity was upregulated in GSTM1‐expressing CEM. Inhibition of NF‐κB by the pharmacological agent BAY11‐7082 greatly enhanced the sensitivity of the GSTM1‐expressing CEM to dexamethasone and was accompanied by an increase in Bim expression. Thus, we propose that GSTM1, a novel regulator of dexamethasone‐induced apoptosis, causes dexamethasone resistance by suppression of Bim through dual mechanisms of both downregulation of p38‐MAPK and upregulation of NF‐κB p50.
Aberrant DNA methylation in contrast with mutations
Authors: Ushijima Toshikazu , Asada Kiyoshi
Published: November 2009

Aberrant DNA methylation is known as an important cause of human cancers, along with mutations. Although aberrant methylation was initially speculated to be similar to mutations, it is now recognized that methylation is quite unlike mutations. Whereas the number of mutations in individual cancer cells is estimated to be ∼80, that of aberrant methylation of promoter CpG islands reaches several hundred to 1000. Although mutations of a specific gene are very few in non‐cancerous (thus polyclonal) tissues (usually at 1 × 10−5/cell), aberrant methylation of a specific gene can be present up to several 10% of cells. Mutagenic chemicals and radiation are well‐known inducers of mutations, whereas chronic inflammation is deeply involved in methylation induction. Although mutations are induced in mostly random genes, methylation is induced in specific genes depending on tissues and inducers. Methylation is potentially reversible, unlike mutations. These characteristics of methylation are opening up new fields of application and research. (Cancer Sci 2009)
The potential role of epigenetic therapy in multiple myeloma
Authors: Smith Emma M. , Boyd Kevin , Davies Faith E.
Published: November 2009

This review describes the role that epigenetic changes play in the pathogenesis of cancer, concentrating on the plasma cell malignancy multiple myeloma, and highlights recent findings regarding the efficacy of epigenetic therapeutic agents in laboratory studies and clinical trials. DNA methylation is altered in a wide range of cancers with hypermethylation of CpG islands associated with silencing of tumour suppressor genes. Genes found to be silenced by methylation in myeloma samples include VHL, TP53, CDKN2A, and TGFBR2. Myeloma is linked to the overexpression of a histone methylatransferase (MMSET) and inactivating mutations of a histone demethylase (UTX), suggesting that the regulation of histone methylation is a potential therapeutic target. Abnormal expression of histone deacetylases (HDACs) has been widely described in solid tumours and haematological malignancies. In myeloma, histone deacetylase inhibitors show promising results both in laboratory‐based cell culture studies and in clinical trials, where they demonstrate particularly good therapeutic outcome when administered in combination with other standard chemotherapeutic agents. The study of epigenetics shows great promise for understanding the alterations in gene expression that underlie malignancies and provides exciting novel drugable targets.