bluuebunny/crossref_metadata_2025 huggingface dataset:
Infrared spectra of protonated polycyclic aromatic hydrocarbon molecules: Azulene
Authors: Zhao Dawei , Langer Judith , Oomens Jos , Dopfer Otto
Published: November 2009

The infrared (IR) spectrum of protonated azulene (AzuH+, C10H9+) has been measured in the fingerprint range (600–1800 cm−1) by means of IR multiple photon dissociation (IRMPD) spectroscopy in a Fourier transform ion cyclotron resonance mass spectrometer equipped with an electrospray ionization source using a free electron laser. The potential energy surface of AzuH+ has been characterized at the B3LYP/6-311G∗∗ level in order to determine the global and local minima and the corresponding transition states for interconversion. The energies of the local and global minima, the dissociation energies for the lowest-energy fragmentation pathways, and the proton affinity have been evaluated at the CBS-QB3 level. Comparison with calculated linear IR absorption spectra supports the assignment of the IRMPD spectrum to C4-protonated AzuH+, the most stable of the six distinguishable C-protonated AzuH+ isomers. Comparison between Azu and C4-AzuH+ reveals the effects of protonation on the geometry, vibrational properties, and the charge distribution of these fundamental aromatic molecules. Calculations at the MP2 level indicate that this technique is not suitable to predict reliable IR spectra for this type of carbocations even for relatively large basis sets. The IRMPD spectrum of protonated azulene is compared to that of isomeric protonated naphthalene and to an astronomical spectrum of the unidentified IR emission bands.
Inside the ordering room: characteristics of women's in-home sex toy parties, facilitators and sexual communication
Authors: Herbenick Debra , Reece Michael , Hollub Ariane
Published: November 2009

Background: Previous research suggests that adult bookstores are a unique way through which individuals may learn about sexuality or practice sexual communication. Recently, the woman-oriented in-home sex toy party industry has rapidly expanded in several countries. The purpose of this study was to document the characteristics of the parties, the women who run the parties (‘facilitators’) and facilitator-consumer communication about sexual health topics.
Methods: Female facilitators for a large in-home sex toy party company in the USA were invited to participate in an anonymous, cross-sectional online survey.
Results: A total of 1197 completed surveys were received. Most respondents were white (85.2%), heterosexual (91.6%), had at least some college education (76.3%) and were married (59.4%). Most parties were held in another woman’s home (88.3%), lasted 1–2 h (72.2%) and had 10 or fewer women in attendance (65.1%). At their most recent party facilitated, most respondents were asked questions about increasing desire/arousal (75.3%), orgasm (57.8%), desire discrepancy (56.4%), erection and ejaculation (73.8%), and vaginal dryness and lubrication (64.5%). Respondents who encountered sexual health questions or disclosures by consumers (those that were more ‘askable’) scored significantly higher on the Sexual Opinion Survey, indicating greater erotophilia.
Conclusions: Results suggest that female in-home sex toy party facilitators have the potential to provide a diverse group of women with opportunities to access sexuality information, products and communication and that facilitators’ ‘askability’ is related to erotophilia. Implications for sexual health professionals are discussed.
Sexual risk-taking in the general population of Sweden (1989 - 2007)
Authors: Herlitz Claes
Published: November 2009

Background: The aim of the study was to assess changes in sexual attitudes and sexual behaviour related to HIV/sexually transmissible infections (STI) during a long period of intensive efforts by the Swedish authorities to curb the spread of HIV. Methods: We conducted mailed questionnaire surveys in random samples of the Swedish general population in 1989, 1994, 1997, 2000, 2003 and 2007 (total n = 16773). Each sample consisted of some 4000–6000 participants aged 16–44 years, stratified by age: 16–17, 18–19, 20–24, 25–34 and 35–44 years. The overall participation rate was 61.6% (for men, 53.5%; for women, 69.9%). Results: Between 1989 and 1994, the proportion of participants holding a restrictive view on sexual intercourse outside a stable relationship decreased significantly. The surveys since 1994 do not show any change in that respect. The prevalence of several sexual partners increased significantly throughout the period of study. The prevalence of casual sexual intercourse without the use of a condom also increased significantly from 1989 until 2003, but decreased slightly between 2003 and 2007. This change in sexual behaviour was more prominent in women than among men. The prevalence of several sexual partners and casual sexual intercourse without the use of a condom was significantly higher for the younger than for the older age cohorts. Conclusions: The study demonstrates the need for a continuous preventive campaign against HIV/STI in the general population in Sweden, particularly among young people.
Metronidazole resistance in Trichomonas vaginalis from highland women in Papua New Guinea
Authors: Upcroft Jacqueline A. , Dunn Linda A. , Wal Tilda , Tabrizi Sepehr , Delgadillo-Correa Maria G. , Johnson Patricia J. , Garland Suzanne , Siba Peter , Upcroft Peter
Published: November 2009

Background: The prevalence of the sexually transmissible protozoan parasite Trichomonas vaginalis in the highlands of Papua New Guinea (PNG) has been reported to be as high as 46% and although not previously studied in Papua New Guinea, clinical resistance against metronidazole (Mz), the drug most commonly used to treat trichomoniasis, is well documented worldwide. This study was primarily aimed at assessing resistance to Mz in T. vaginalis strains from the Goroka region. Methods: Consenting patients presenting at the Goroka Base Hospital Sexually Transmitted Diseases (STD) Clinic and local women were asked to provide two vaginal swabs: one for culturing of the parasite; and one for polymerase chain reaction detection of T. vaginalis, Chlamydia trachomatis and Neisseria gonorrhoeae. T. vaginalis isolates were assayed for Mz susceptibility and a selection was genotyped. Results: The prevalence of T. vaginalis was determined to be 32.9% by culture and polymerase chain reaction of swabs among 82 local women and patients from the STD clinic. An unexpectedly high level of in vitro Mz resistance was determined with 17.4% of isolates displaying unexpectedly high resistance to Mz. The ability to identify isolates of T. vaginalis by genotyping was confirmed and the results revealed a more homogeneous T. vaginalis population in Papua New Guinea compared with isolates from elsewhere. Conclusion: T. vaginalis is highly prevalent in the Goroka region and in vitro Mz resistance data suggest that clinical resistance may become an issue.
The role of drugs during group sex among gay men in Australia
Authors: Prestage Garrett , Grierson Jeffrey , Bradley Jack , Hurley Michael , Hudson Jeff
Published: November 2009

Background: Drug use has been associated with risk behaviour among gay men. We examined the use of drugs and sexual risk behaviour among homosexually-active men who engaged in group sex in Australia. Methods: We used an anonymous, self-complete survey about participants’ most recent occasion of group sex with other men and in-depth interviews with a small number of these survey participants. The 746 men who reported having engaged in group sex within the previous 6 months were included in these analyses. Results: Among 746 men who engaged in group sex within the previous 6 months, 63.0% reported using illicit drugs at the group sex encounter. Men commonly reported using drugs specifically to enhance their sexual experience and to intensify the pleasure of that experience. After controlling for each drug type and other risk factors, only use of methamphetamine (odds ratio = 1.74, confidence interval = 1.06–2.88, P = 0.030) and having more than five drinks (odds ratio = 2.41, confidence interval = 1.34–4.33, P = 0.003) were independently associated with unprotected anal intercourse with non-HIV seroconcordant partners in multivariate analysis. Conclusion: Methamphetamine and heavy alcohol use are associated with increased sexual risk behaviour among men who engage in group sex. Within more ‘adventurous’ gay community subcultures, drug use is often for the explicit purpose of enhancing the sexual experience and this complex relationship may be key to understanding HIV risk among these men.
An HIV-1 integrase genotype assay for the detection of drug resistance mutations
Authors: Hearps Anna C. , Greengrass Vicki , Hoy Jennifer , Crowe Suzanne M.
Published: November 2009

Background: The integrase inhibitors (e.g. Raltegravir) are a new class of antiretroviral drugs that have recently become available for the treatment of patients with multi-drug resistant HIV-1 within Australia. The emergence of mutations that confer resistance to the integrase inhibitors has been observed in vivo; however, no commercial genotyping assay is currently available to screen for resistance to these drugs. Methods: The HIV-1 integrase gene was amplified from plasma-derived HIV-1 viral RNA via reverse transcription-polymerase chain reaction and genotype determined via population DNA sequencing. Drug resistance mutations and polymorphisms were detected using the Stanford University online HIV database. Assay sensitivity and reproducibility were determined using clinical and laboratory-derived samples. Results: Our in-house assay was capable of genotyping the integrase gene from all samples tested (n = 30) of HIV-1 subtypes B, C, D, F, CFR01_AE and CRF02_AG and can amplify the integrase region from plasma samples containing as few as 50 HIV RNA copies/mL. The assay is highly reproducible (average nucleotide concordance = 99.6%, n = 4) and is capable of detecting resistance-associated mutations. Conclusions:This assay is suitable for routine drug resistance screening of plasma samples from HIV-infected patients receiving integrase inhibitor antiretroviral drugs and also serves as a useful research tool.
Condom failure among men receiving sexually transmissible infection clinic services, Cape Town, South Africa
Authors: Kalichman Seth C. , Simbayi Leickness C. , Cain Demetria , Jooste Sean
Published: November 2009

Background: Condoms offer the most realistic and available protection against sexually transmissible infections (STIs), including HIV infection. The protective benefits of condoms are, however, compromised by breaks and tears. The objective of the present study was to examine condom failure and associated behavioural risk factors among men at high-risk for HIV transmission in South Africa. Methods: Men (n = 431) receiving STI treatment services at a public clinic completed computer assisted interviews and STI clinic chart abstraction over a 1-year observation period. Results: One in three male STI clinic patients reported a history of condom failure. Condom failure was associated with sexual exchange, alcohol and other drug use, and higher rates of unprotected vaginal intercourse. Men with a history of condom failure were significantly more likely to have an STI diagnosis 1 month before the baseline interview and were significantly more likely to be diagnosed with an STI over the subsequent year. Conclusion: Condom failures are common among STI clinic patients and pose a threat for increased HIV transmission risks.
Adipose-specific deletion of
autophagy-related gene 7
(
atg7
) in mice reveals a role in adipogenesis
Authors: Zhang Yong , Goldman Scott , Baerga Rebecca , Zhao Yun , Komatsu Masaaki , Jin Shengkan
Published: November 2009

White adipocytes have a unique structure in which nearly the entire cell volume is occupied by one large lipid droplet. However, the molecular and cellular processes involved in the cytoplasmic remodeling necessary to create this structure are poorly defined. Autophagy is a membrane trafficking process leading to lysosomal degradation. Here, we investigated the effect of the deletion of an essential autophagy gene,
autophagy-related gene 7
(
atg7
), on adipogenesis. A mouse model with a targeted deletion of
atg7
in adipose tissue was generated. The mutant mice were slim and contained only 20% of the mass of white adipose tissue (WAT) found in wild-type mice. Interestingly, ≈50% of the mutant white adipocytes were multilocular. The mutant white adipocytes were smaller with a larger volume of cytosol and contained more mitochondria. These cells exhibited altered fatty acid metabolism with increased rates of β-oxidation and reduced rates of hormone-induced lipolysis. Consistently, the mutant mice had lower fed plasma concentrations of fatty acids and the levels decreased at faster rates upon insulin stimuli. These mutant mice exhibited increased insulin sensitivity. The mutant mice also exhibited markedly decreased plasma concentrations of leptin but not adiponectin, lower plasma concentrations of triglyceride and cholesterol, and they had higher levels of basal physical activity. Strikingly, these mutant mice were resistant to high-fat-diet-induced obesity. Taken together, our results indicate that
atg7
, and by inference autophagy, plays an important role in normal adipogenesis and that inhibition of autophagy by disrupting the
atg7
gene has a unique anti-obesity and insulin sensitization effect.
MAP kinases
MPK9
and
MPK12
are preferentially expressed in guard cells and positively regulate ROS-mediated ABA signaling
Authors: Jammes Fabien , Song Charlotte , Shin Dongjin , Munemasa Shintaro , Takeda Kouji , Gu Dan , Cho Daeshik , Lee Sangmee , Giordo Roberta , Sritubtim Somrudee , Leonhardt Nathalie , Ellis Brian E. , Murata Yoshiyuki , Kwak June M.
Published: November 2009

Reactive oxygen species (ROS) mediate abscisic acid (ABA) signaling in guard cells. To dissect guard cell ABA-ROS signaling genetically, a cell type-specific functional genomics approach was used to identify 2 MAPK genes,
MPK9
and
MPK12
, which are preferentially and highly expressed in guard cells. To provide genetic evidence for their function,
Arabidopsis
single and double TILLING mutants that carry deleterious point mutations in these genes were isolated. RNAi-based gene-silencing plant lines, in which both genes are silenced simultaneously, were generated also. Mutants carrying a mutation in only 1 of these genes did not show any altered phenotype, indicating functional redundancy in these genes. ABA-induced stomatal closure was strongly impaired in 2 independent RNAi lines in which both
MPK9
and
MPK12
transcripts were significantly silenced. Consistent with this result,
mpk9-1
/
12-1
double mutants showed an enhanced transpirational water loss and ABA- and H
2
O
2
-insensitive stomatal response. Furthermore, ABA and calcium failed to activate anion channels in guard cells of
mpk9-1
/
12-1
, indicating that these 2 MPKs act upstream of anion channels in guard cell ABA signaling. An
MPK12-YFP
fusion construct rescued the ABA-insensitive stomatal response phenotype of
mpk9-1
/
12-1
, demonstrating that the phenotype was caused by the mutations. The MPK12 protein is localized in the cytosol and the nucleus, and ABA and H
2
O
2
treatments enhance the protein kinase activity of MPK12. Together, these results provide genetic evidence that
MPK9
and
MPK12
function downstream of ROS to regulate guard cell ABA signaling positively.
A single plant resistance gene promoter engineered to recognize multiple TAL effectors from disparate pathogens
Authors: Römer Patrick , Recht Sabine , Lahaye Thomas
Published: November 2009

Plant pathogenic bacteria of the genus
Xanthomonas
inject transcription-activator like (TAL) effector proteins that manipulate the hosts' transcriptome to promote disease. However, in some cases plants take advantage of this mechanism to trigger defense responses. For example, transcription of the pepper
Bs3
and rice
Xa27
resistance (
R
) genes are specifically activated by the respective TAL effectors AvrBs3 from
Xanthomonas campestris
pv.
vesicatoria
(
Xcv
), and AvrXa27 from
X. oryzae
pv.
oryzae
(
Xoo
). Recognition of AvrBs3 was shown to be mediated by interaction with the corresponding
UPT
(
UP
regulated by
T
AL effectors) box
UPT
AvrBs3
present in the promoter
R
gene
Bs3
from the dicot pepper. In contrast, it was not known how the
Xoo
TAL effector AvrXa27 transcriptionally activates the matching
R
gene
Xa27
from the monocot rice. Here we identified a 16-bp
UPT
AvrXa27
box present in the rice
Xa27
promoter that when transferred into the
Bs3
promoter confers AvrXa27-dependent inducibility. We demonstrate that polymorphisms between the
UPT
AvrXa27
box of the AvrXa27-inducible
Xa27
promoter and the corresponding region of the noninducible
xa27
promoter account for their distinct inducibility and affinity, with respect to AvrXa27. Moreover, we demonstrate that three functionally distinct
UPT
boxes targeted by separate TAL effectors retain their function and specificity when combined into one promoter. Given that many economically important xanthomonads deliver multiple TAL effectors, the engineering of
R
genes capable of recognizing multiple TAL effectors provides a potential approach for engineering broad spectrum and durable disease resistance.
Diseases.
Authors: Coates L. , Zhou ErXun Zhou ErXun , Sittigul C.
Published: November 2009

This chapter describes the following diseases infecting longan and litchi (Litchi chinensis): soilborne diseases (rot caused by Armillaria mellea, litchi decline, and longan decline); diseases in nurseries (caused by Fusarium, Pythium and Rhizoctonia species); foliar, floral, fruit, stem and preharvest diseases (algal spot caused by Cephaleuros virescens, corky bark caused by F. decemcellulare [Nectria rigidiuscula], downy blight caused by Peronophythora litchii, branch blight and fruit rot caused by Lasiodiplodia theobromae, pepper spot caused by Colletotrichum gloeosporioides [Glomerella cingulata], leaf blight caused by Phomopsis species, Phytophthora-incited diseases, sooty mould and black mildew, witches' broom, and minor foliar and stem diseases); and postharvest diseases (anthracnose caused by Colletotrichum species, stem end rot, and other postharvest diseases). Information on symptoms, morphology of causal agents, vectors (insects and nematodes), and control strategies (mainly cultural and chemical) is provided.
Speaking, writing, and memory span in children: Output modality affects cognitive performance
Authors: Grabowski Joachim
Published: November 2009

Low‐level processes of children's written language production are cognitively more costly than those involved in speaking. This has been shown by French authors who compared oral and written memory span performance. The observed difficulties of children's, but not of adults' low‐level processes in writing may stem from graphomotoric as well as from orthographic inadequacies. We report on five experiments designed to replicate and expand the original results. First, the French results were successfully replicated for German third‐graders, and for university students. Then, the developmental changes of the cognitive costs of writing were examined during primary school, comparing the performance of second‐ and fourth‐graders. Next, we show that unpractised writing modes, which were experimentally induced, also lead to a decrease of memory performance in adults, which supports the assumption that a lack of graphomotoric automation is responsible for the observed effects in children. However, unpractised handwriting yields clearer results than unpractised typing. Lastly, we try to separate the influences of graphomotoric as opposed to orthographic difficulties by having the words composed through pointing on a “spelling board”. This attempt, however, has not been successful, probably because the pointing to letters introduced other low‐level costs. In sum, throughout the four years of primary school, German children show worse memory span performance in writing compared to oral recall, with an overall increase in both modalities. Thus, writing had not fully caught up with speaking regarding the implied cognitive costs by the end of primary school. Therefore, conclusions relate to the question of how to assess properly any kind of knowledge and abilities through language production.
Mindfulness-Based Relapse Prevention for Substance Use Disorders: A Pilot Efficacy Trial
Authors: Bowen Sarah , Chawla Neharika , Collins Susan E. , Witkiewitz Katie , Hsu Sharon , Grow Joel , Clifasefi Seema , Garner Michelle , Douglass Anne , Larimer Mary E. , Marlatt Alan
Published: November 2009

The current study is the first randomized-controlled trial evaluating the feasibility and initial efficacy of an 8-week outpatient Mindfulness-Based Relapse Prevention (MBRP) program as compared to treatment as usual (TAU). Participants were 168 adults with substance use disorders who had recently completed intensive inpatient or outpatient treatment. Assessments were administered pre-intervention, post-intervention, and 2 and 4 months post-intervention. Feasibility of MBRP was demonstrated by consistent homework compliance, attendance, and participant satisfaction. Initial efficacy was supported by significantly lower rates of substance use in those who received MBRP as compared to those in TAU over the 4-month post-intervention period. Additionally, MBRP participants demonstrated greater decreases in craving, and increases in acceptance and acting with awareness as compared to TAU. Results from this initial trial support the feasibility and initial efficacy of MBRP as an aftercare approach for individuals who have recently completed an intensive treatment for substance use disorders.
Mindfulness Training and Stress Reactivity in Substance Abuse: Results from a Randomized, Controlled Stage I Pilot Study
Authors: Brewer Judson A. , Sinha Rajita , Chen Justin A. , Michalsen Ravenna N. , Babuscio Theresa A. , Nich Charla , Grier Aleesha , Bergquist Keri L. , Reis Deidre L. , Potenza Marc N. , Carroll Kathleen M. , Rounsaville Bruce J.
Published: November 2009

Stress is important in substance use disorders (SUDs). Mindfulness training (MT) has shown promise for stress-related maladies. No studies have compared MT to empirically validated treatments for SUDs. The goals of this study were to assess MT compared to cognitive behavioral therapy (CBT) in substance use and treatment acceptability, and specificity of MT compared to CBT in targeting stress reactivity. Thirty-six individuals with alcohol and/or cocaine use disorders were randomly assigned to receive group MT or CBT in an outpatient setting. Drug use was assessed weekly. After treatment, responses to personalized stress provocation were measured. Fourteen individuals completed treatment. There were no differences in treatment satisfaction or drug use between groups. The laboratory paradigm suggested reduced psychological and physiological indices of stress during provocation in MT compared to CBT. This pilot study provides evidence of the feasibility of MT in treating SUDs and suggests that MT may be efficacious in targeting stress.
'Guilty knowledge': ethical aporia emergent in the research practice of educational development practitioners
Authors: Williams K. F.
Published: November 2009

Research into the practice of academics serves to inform higher education development (HED) theory and interventions, and is important for the development of the professional knowledge of the HED practitioner. Through such research HED practitioners gain access to what in another context
is referred to as 'guilty knowledge'. The complex ethical and methodological challenges faced by HED researchers 'researching in their own backyard' may often be underestimated or overlooked in research proposals and practice. I propose that Heidegger's conceptualisation of aporia may
extend our awareness beyond ethical customs and procedures to the underlying ontological nature of research ethics.
Emerging discourses within the English 'choice advice' policy network
Authors: Exley Sonia
Published: November 2009

This paper examines regulating discourses 'spoken' within the complex multi-sector network of educational policy and provision that has grown from a recent introduction of choice advisers in England. Choice advice documentation from across the network is examined and four discursive
themes are identified: equity; parental responsibility; independence/impartiality; and realism. The paper suggests that choice advice – as an English policy case illustrating broader social and political trends – superficially promotes empowerment for disadvantaged parents with
a depoliticised, managerial approach while disempowering them by diverting attention away from wider stratification and shifting responsibility for educational quality away from the state.
On establishing a modus vivendi: the exercise of agency in decisions to participate or not participate in higher education
Authors: Kahn Peter
Published: November 2009

It is becoming increasingly clear that the notion of 'removing barriers' offers a limited foundation for widening participation to higher education. Drawing on realist social theory, we consider how decisions to participate or not participate form part of a process to establish a modus
vivendi or 'way of life' for oneself. We explore factors that affect how individuals pursue courses of action around entry into potentially alien educational contexts. Our analysis suggests that interventions designed to widen participation should take account of different modes of reflexive
deliberation, underpinning social and cultural structures, and a range of notions of human flourishing.
Phase Behavior of Liquid Crystals Formed in [C12mim]CI/H2O and [C12mim]CI/Alcohols Systems
Authors: Pei Mei-shan , Wu Zhi-yan , Wang Lu-yan , Wu Xin-zhou , Tao Xu-tang
Published: November 2009

Phase behaviors of different binary systems involving 1-dodecyl-3-methylimidazolium chloride ([C12mim]Cl) and H2O, [C12mim]Cl and different alcohols (1-butanol, 1-pentanol, 1-hexanol and 1-octanol) are investigated at 25 C. Hexagonal liquid crystal phase (H1) is identified in [C12mim]Cl/H2O system, and lamellar liquid-crystalline (L) phase is found in [C12mim]Cl/alcohols systems by using polarized optical microscopy and small-angle X-ray scattering techniques. The formation of such phases is considered as a synergetic result of the solvatophobic force and the hydrogen-bonded network comprising an imidazolium ring, chloride ion and water (or alcohols), which can be confirmed by Fourier transform infrared spectra. It is noticeable that in [C12mim]Cl/1-octanol system, the lattice spacings of lamellar phase increase with increasing C12mimCl concentration, which is opposite to the results of [C12mim]Cl/H2O system. This may result mainly from stronger static repulsion among hydrophilic headgroups of imidazolium salts arranged in the bilayers of lamellar structures. Further measurements by differential scanning calorimetry indicate that the lamellar phase is stable within a wide temperature range above room temperature. However, the lattice spacings decrease with the increase of temperature, which may be due to the softening of the hydrocarbon chain of [C12mim]Cl molecules. In different alcohols systems, it is found that the lamellar lyotropic liquid crystal structure is easier to be formed when the carbon chain length becomes longer.
Using PVP/SDS Complex as a Probe to Study the Inclusion Complex of -cyclodextrin with SDS in Aqueous Solution
Authors: Chen Xiao-ming , Yang Hai-yang , He Ping-sheng
Published: November 2009

PVP/SDS complex was applied as a probe to study the interaction between -cyclodextrin (-CD) and sodium dodecyl sulfate (SDS) in aqueous solution. It has been found that a critical concentration, namely cS, exists in the relative viscosity of solution containing PVP/SDS complex versus -CD concentration plot. As the -CD concentration is less than cS, the relative viscosity of solution decreases sharply by adding -CD into solution successively. On the other hand, as the -CD concentration is greater than cS, the relative viscosity of solution increases gradually by adding -CD into solution. The decrease of the relative viscosity of solution containing PVP/SDS in the presence of -CD is just due to the inclusion complex of -CD with the guest molecule SDS. And, this inclusion interaction takes down SDS from the PVP chains in solution. The ratio of the host molecule -CD to the guest molecule SDS can be calculated from cS. In our experiment the inclusion ratio of -CD to SDS is 1/1. The further experimental results indicate that cS is associated with SDS but free from PVP in PVP/SDS complex. However, the inclusion ratio of -GD to SDS has proved to be independent of either SDS or PVP in PVP/SDS complex.
Automatic clustering of docking poses in virtual screening process using self-organizing map
Authors: Bouvier Guillaume , Evrard-Todeschi Nathalie , Girault Jean-Pierre , Bertho Gildas
Published: November 2009

Motivation: Scoring functions provided by the docking software are still a major limiting factor in virtual screening (VS) process to classify compounds. Score analysis of the docking is not able to find out all active compounds. This is due to a bad estimation of the ligand binding energies. Making the assumption that active compounds should have specific contacts with their target to display activity, it would be possible to discriminate active compounds from inactive ones with careful analysis of interatomic contacts between the molecule and the target. However, compounds clustering is very tedious due to the large number of contacts extracted from the different conformations proposed by docking experiments.

Results: Structural analysis of docked structures is processed in three steps: (i) a Kohonen self-organizing map (SOM) training phase using drug–protein contact descriptors followed by (ii) an unsupervised cluster analysis and (iii) a Newick file generation for results visualization as a tree. The docking poses are then analysed and classified quickly and automatically by AuPosSOM (Automatic analysis of Poses using SOM). AuPosSOM can be integrated into strategies for VS currently employed. We demonstrate that it is possible to discriminate active compounds from inactive ones using only mean protein contacts' footprints calculation from the multiple conformations given by the docking software. Chemical structure of the compound and key binding residues information are not necessary to find out active molecules. Thus, contact–activity relationship can be employed as a new VS process.

Availability: AuPosSOM is available at http://www.aupossom.com.

Contact:  contact@aupossom.com; gildas.bertho@parisdescartes.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Strategic Voting in Plurality Elections
Authors: Kselman Daniel , Niou Emerson
Published: November 2009

This paper extends theCalculus of Votingof McKelvey and Ordeshook, providing the first direct derivation of the conditions under which voters will votestrategically: choose their second-most preferred candidate in order to prevent their least-preferred candidate from winning. Addressing this theoretical problem is important, as nearly all empirical research on strategic voting either implicitly or explicitly tests hypotheses which originate from this seminal model. The formal result allows us toisolate the subset of voters to which strategic voting hypotheses properly applyand in turn motivates a critical reevaluation of past empirical work. In making this argument, we develop a unified and parsimonious framework for understanding competing models of tactical voter choice. The typology helps to elucidate the methodological difficulties in studying tactical behavior when faced with heterogeneous explanatory models and suggests the need for both theoretical caution and more precise data instruments in future empirical work.
Bond anisotropy and cohesion of wet granular materials
Authors: Radjai Farhang , Richefeu Vincent
Published: November 2009

We analyse the Coulomb cohesion of wet granular materials and its relationship with the distribution of capillary bonds between particles. We show that, within a harmonic representation of the bond and force states, the shear strength can be expressed as a state equation in terms of internal anisotropy parameters. This formulation involves a dependence of the shear strength on loading direction and leads to the fragile behaviour of granular materials. The contact dynamics simulations of a wet material, in which a capillary force law is prescribed, are in excellent agreement with the predictions of this model. We find that the fragile character decreases as the local adhesion is increased or the mean stress is decreased.
Traumatic endophthalmitis caused by Staphylococcus gallinarum
Authors: Tibra Nand Kishore , Jalali Subhadra , Reddy Ashok Kumar , Narayanan Raja , Agarwal Rupesh
Published: November 2009

Herein, we describe what we believe to be the first case of traumatic endophthalmitis caused by Staphylococcus gallinarum, following injury with an iron nail. The patient was successfully treated by vitrectomy and intravitreal injection of cefazolin and vancomycin.
Killing of adherent oral microbes by a non-thermal atmospheric plasma jet
Authors: Rupf Stefan , Lehmann Antje , Hannig Matthias , Schäfer Barbara , Schubert Andreas , Feldmann Uwe , Schindler Axel
Published: November 2009

Atmospheric plasma jets are being intensively studied with respect to potential applications in medicine. The aim of this in vitro study was to test a microwave-powered non-thermal atmospheric plasma jet for its antimicrobial efficacy against adherent oral micro-organisms. Agar plates and dentin slices were inoculated with 6 log10 c.f.u. cm−2 of Lactobacillus casei, Streptococcus mutans and Candida albicans, with Escherichia coli as a control. Areas of 1 cm2 on the agar plates or the complete dentin slices were irradiated with a helium plasma jet for 0.3, 0.6 or 0.9 s mm−2, respectively. The agar plates were incubated at 37 °C, and dentin slices were vortexed in liquid media and suspensions were placed on agar plates. The killing efficacy of the plasma jet was assessed by counting the number of c.f.u. on the irradiated areas of the agar plates, as well as by determination of the number of c.f.u. recovered from dentin slices. A microbe-killing effect was found on the irradiated parts of the agar plates for L. casei, S. mutans, C. albicans and E. coli. The plasma-jet treatment reduced the c.f.u. by 3–4 log10 intervals on the dentin slices in comparison to recovery rates from untreated controls. The microbe-killing effect was correlated with increasing irradiation times. Thus, non-thermal atmospheric plasma jets could be used for the disinfection of dental surfaces.
A 2-oxoacid dehydrogenase complex of Haloferax volcanii is essential for growth on isoleucine but not on other branched-chain amino acids
Authors: Sisignano Marco , Morbitzer Daniel , Gätgens Jochem , Oldiges Marco , Soppa Jörg
Published: November 2009

The halophilic archaeonHaloferax volcaniicontains three operons encoding 2-oxoacid dehydrogenase complexes (OADHCs) OADHC1–OADHC3. However, the biological role of these OADHCs is not known as previous studies have demonstrated that they cannot use any of the known OADHC substrates. Even the construction of single mutants in all threeoadhcoperons, reported recently, could not identify a substrate. Therefore, all three possible double mutants and a triple mutant were generated, and single, double and triple mutants were compared to the wild-type. The four mutants devoid of a functional OADHC1 had a reduced growth yield during nitrate-respirative growth on tryptone. A metabolome analysis of the medium after growth of the triple mutant in comparison to the wild-type revealed that the mutant was unable to degrade isoleucine and leucine, in contrast to the wild-type. It was shown thatoadhc1mutants were unable to grow in synthetic medium on isoleucine, in contrast to the other mutants and the isogenic parent strain. However, all strains grew indistinguishably on valine and leucine. The transcript of theoadhc1operon was highly induced during growth on isoleucine. However, attempts to detect enzymic activity were unsuccessful, while the branched-chain OADHC (BCDHC) ofPseudomonas putidacould be measured easily. Therefore, the growth capability of the triple mutant and the wild-type on the two first degradation intermediates of isoleucine was tested and provided further evidence that OADHC is involved in isoleucine degradation. Taken together, the results indicate that OADHC1 is a specialized BCDHC that uses only one (or maximally two) of the three branched-chain 2-oxoacids, in contrast to BCDHCs from other species.
The Type 2C protein phosphatase FgPtc1p of the plant fungal pathogen Fusarium graminearum is involved in lithium toxicity and virulence
Authors: JIANG LINGHUO , YANG JINGRAN , FAN FEIYU , ZHANG DAJUN , WANG XULI
Published: November 2009

Type 2C protein phosphatases (PP2Cs) are monomeric protein serine/threonine phosphatases that play various roles in eukaryotic organisms. In this study, we characterized the PP2C encoded by FgPTC1 in Fusarium graminearum, the major causal agent of Fusarium head blight on wheat and barley. We found that deletion of FgPTC1 delays the mycelium growth of F. graminearum in response to lithium. Consistently, FgPTC1 complemented the function of ScPTC1 in lithium toxicity in Saccharomyces cerevisiae. Furthermore, we showed that deletion of FgPTC1 attenuated the virulence of F. graminearum on wheat. Therefore, FgPTC1 plays an important role in regulating the hyphal growth and virulence of F. graminearum.
Pepino mosaic virus: a successful pathogen that rapidly evolved from emerging to endemic in tomato crops
Authors: HANSSEN INGE M. , THOMMA BART P. H. J.
Published: November 2009

Taxonomy: Pepino mosaic virus (PepMV) belongs to the Potexvirus genus of the Flexiviridae family.

Physical properties: PepMV virions are nonenveloped flexuous rods that contain a monopartite, positive‐sense, single‐stranded RNA genome of 6.4 kb with a 3′ poly‐A tail. The genome contains five major open reading frames (ORFs) encoding a 164‐kDa RNA‐dependent RNA polymerase (RdRp), three triple gene block proteins of 26, 14 and 9 kDa, and a 25‐kDa coat protein.

Genome diversity: Four PepMV genotypes, with an intergenotype RNA sequence identity ranging from 78% to 95%, can be distinguished: the original Peruvian genotype (LP); the European (tomato) genotype (EU); the American genotype US1; and the Chilean genotype CH2.

Transmission: PepMV is very efficiently transmitted mechanically, and a low seed transmission rate has been demonstrated. In addition, bumblebees have been associated with viral transmission.

Host range: Similar to other Potexviruses, PepMV has a rather narrow host range that is thought to be largely restricted to species of the Solanaceae family. After originally being isolated from pepino (Solanum muricatum), PepMV has been identified in natural infections of the wild tomato species S. chilense, S. chmielewskii, S. parviflorum and S. peruvianum. PepMV is causing significant problems in the cultivation of the glasshouse tomato Solanum lycopersicum, and has been identified in weeds belonging to various plant families in the vicinity of tomato glasshouses.

Symptomatology: PepMV symptoms can be very diverse. Fruit marbling is the most typical and economically devastating symptom. In addition, fruit discoloration, open fruit, nettle‐heads, leaf blistering or bubbling, leaf chlorosis and yellow angular leaf spots, leaf mosaic and leaf or stem necrosis have been associated with PepMV. The severity of PepMV symptoms is thought to be dependent on environmental conditions, as well as on the properties of the viral isolate. Minor nucleotide sequence differences between isolates from the same genotype have been shown to lead to enhanced aggressiveness and symptomatology.

Control: Prevention of infection through strict hygiene measures is currently the major strategy for the control of PepMV in tomato production. Cross‐protection can be effective, but only under well‐defined and well‐controlled conditions, and the effectiveness depends strongly on the PepMV genotype.
microRNA expression in erythropoiesis and erythroid disorders
Authors: Lawrie Charles H.
Published: November 2009

MicroRNAs are a recently discovered class of small (c. 22 nt) naturally occurring non‐coding RNA molecules that regulate gene expression through binding to the un‐translated region of target mRNA. MicroRNAs play key roles in many cellular pathways including haematopoiesis and aberrant expression is a common feature of haematological malignancies. Whilst other areas of haematopoiesis have been extensively reviewed the involvement of microRNAs in red cell production (erythropoiesis) and disorders of this pathway is lacking. In this review the rapidly accumulating evidence that points to the major role microRNAs play in both erythropoiesis and erythroid disorders is discussed.
Polo‐like‐kinase 1 (PLK1) as a molecular target to overcome SYK‐mediated resistance of B‐lineage acute lymphoblastic leukaemia cells to oxidative stress
Authors: Uckun Fatih M. , Ozer Zahide , Qazi Sanjive , Tuel‐Ahlgren Lisa , Mao Chen
Published: November 2009

SYK tyrosine kinase has emerged as a master regulator of cellular resistance to oxidative stress (OS) by mediating the activation of the anti‐apoptotic nuclear factor κB and phosphatidylinositol‐3 kinase/AKT pathways after OS exposure. Here, we present unprecedented experimental evidence that polo‐like kinase 1 (PLK1) is the upstream regulator of SYK in B‐lineage acute lymphoblastic leukaemia (ALL) cells. Selective inhibition of PLK‐1 with the leflunomide metabolite analogue α‐cyano‐β‐hydroxy‐β‐methyl‐N‐[4‐(trifluoromethoxy) phenyl]‐propenamide/LFM‐A12 abolished the resistance of B‐lineage ALL cells to OS by preventing the activation of the anti‐apoptotic SYK signal transduction pathway. Notably, LFM‐A12 treatments at non‐cytotoxic concentrations resulted in marked augmentation of clonogenic death in resistant human B‐lineage ALL cell lines challenged with OS. Further, LFM‐A12 augmented OS‐induced apoptosis of chemotherapy‐resistant primary leukaemic cells from relapsed B‐lineage ALL patients in vitro and markedly potentiated the in vivo anti‐leukaemic activity of total body irradiation (TBI) against leukaemia‐initiating cells in severe combined immunodeficient mouse xenograft models of B‐lineage ALL. This study is the first to identify PLK1 as a regulator of SYK tyrosine kinase and a molecular target to overcome SYK‐mediated resistance of B‐lineage ALL cells to OS.
Unrelated stem cell transplantation after reduced intensity conditioning for patients with multiple myeloma relapsing after autologous transplantation
Authors: Kröger Nicolaus , Shimoni Avichai , Schilling Georgia , Schwerdtfeger Rainer , Bornhäuser Martin , Nagler Arnon , Zander Axel R. , Heinzelmann Marion , Brand Ronald , Gahrton Gösta , Morris Curly , Niederwieser Dietger , De Witte Theo
Published: November 2009

From 2002 to 2007, 49 myeloma patients who relapsed following autologous SCT were included in a prospective multicenter trial to determine the efficacy of a reduced melphalan/fludarabine regimen followed by allogeneic SCT from unrelated donors. All patients showed leucocyte and platelet engraftment after a median of 15 and 19 d, respectively. Grade II–IV acute graft‐versus‐host disease (GvHD) occurred in 25% of patients and 35% had chronic GvHD. Overall response rate at day 100 was 95% including 46% complete remission (CR). Cumulative incidence of non‐relapse mortality at 1 year was 25% [95% confidence interval (CI): 13–37%] and was significantly lower for human leucocyte antigen (HLA)‐matched compared to ‐mismatched SCT (10% vs. 53%, P = 0·001). The cumulative incidence of relapse at 3 years was 55% (95% CI: 40–70%). After a median follow up of 43 months, the estimated 5‐year progression‐free and overall survival rates were 20% and 26% respectively and were significantly better for matched in CR at day 100 (41% vs. 7%, P = 0·04 and 56% vs. 16%, P = 0·02). We conclude that optimal donor selection is mandatory for a low non‐relapse mortality and high relapse incidence, which remains a major concern, should be improved by including post‐transplant strategies to upgrade remission status.
Practical prebiotics, probiotics and synbiotics for allergists: how useful are they?
Authors: Johannsen H. , Prescott S. L.
Published: November 2009

With the advent of the hygiene hypothesis, probiotics have provided an avenue of hope in curbing the allergic epidemic. The initial enthusiasm has been tempered by recognition of the inherent complexities of this approach. This review examines the current clinical evidence and practical issues in using probiotics and related products, for the prevention and treatment of allergic disease. So far, probiotics have shown more promise, albeit limited, in the primary prevention of allergic disease rather than in the treatment of established disease. These effects have largely been limited to the prevention of early childhood conditions such as eczema, with no consistent effects on other allergic outcomes. There is emerging evidence that clinical effects may be strain specific, but again these findings have been inconsistent. While there have been several meta‐analyses to examine probiotics in both the prevention and the treatment of allergic disease, these have been hampered by significant heterogeneity between studies, including wide variations in the strains used, the methods and timing of administration and the age and assessment of allergic outcomes. In any case, these have also become outdated by a series of new studies published in the last year. Although it is not yet clear exactly how the growing number of new studies will modify the results of meta‐analyses, it is likely that these will add yet further heterogeneity that will continue to make interpretation of pooled data difficult. At this stage, the effects of prebiotics, synbiotics and postbiotics are even less clear. Thus, while there is little doubt that microbiota modulate immune development and can prevent the allergic phenotype, the optimal way of achieving this is far from clear. Given the current level of evidence, it is not appropriate to recommend prebiotics/probiotics/synbiotics or postbiotics as a part of standard therapy or for the prevention of any allergic conditions. Further studies are needed to address the growing speculation that supplementation with a single probiotic strain may be oversimplistic and that approaches that have a more global effect on colonization may be warranted.
Histamine, histamine receptors and their role in immune pathology
Authors: Jutel M. , Akdis M. , Akdis C. A.
Published: November 2009

The important roles of histamine in body physiology and various pathologic events have been well established, whereas new and exciting findings are still being uncovered. Histamine is not only the major mediator of the acute inflammatory and immediate hypersensitivity responses, but has also been demonstrated to affect chronic inflammation and regulate several essential events in the immune response. The diverse effects of histamine on immune regulation are due to the differential expression and regulation of four histamine receptors (HR) and their distinct intracellular signals. Differences in the affinities of these receptors are highly decisive on the biological effects of histamine and agents that target HRs. In particular, the discovery of reciprocal regulation of T cell activity by H1 and H2 receptor activation indicating histamine‐cytokine cross‐talk, as well as the characterization of the fourth histamine receptor (HR4) and its expression on numerous immune and inflammatory cells have prompted a re‐evaluation of the actions of histamine. This accounts for a new potential for HR antagonists and agonists in targeting various immunopathologic conditions.