bluuebunny/crossref_metadata_2025 huggingface dataset:
Accumulating and Remembering the Details of Neutral and Emotional Natural Scenes
Authors: Melcher David
Published: August 2010

In contrast to our rich sensory experience with complex scenes in everyday life, the capacity of visual working memory is thought to be quite limited. Here our memory has been examined for the details of naturalistic scenes as a function of display duration, emotional valence of the scene, and delay before test. Individual differences in working memory and long-term memory for pictorial scenes were examined in experiment 1. The accumulation of memory for emotional scenes and the retention of these details in long-term memory were investigated in experiment 2. Although there were large individual differences in performance, memory for scene details generally exceeded the traditional working memory limit within a few seconds. Information about positive scenes was learned most quickly, while negative scenes showed the worst memory for details. The overall pattern of results was consistent with the idea that both short-term and long-term representations are mixed together in a medium-term ‘online’ memory for scenes.
Local and Global Processing in Savant Artists with Autism
Authors: Pring Linda , Ryder Nicola , Crane Laura , Hermelin Beate
Published: August 2010

We explored the hypothesis that an enhanced local processing style is characteristic of both art and autism spectrum disorder (ASD) by examining local and global processing in savant artists with ASD. Specifically, savant artists were compared against non-talented individuals with ASD or mild/moderate learning difficulties (MLD), as well as artistically talented or non-talented students, on the block-design task and meaningful and abstract versions of the embedded figures test (EFT). Results demonstrated that there were no significant differences between the meaningful and abstract versions of the EFT, in any of the groups. This suggests that the primary process governing performance on this task was perceptual (local), rather than conceptual (global). More interestingly, the savant artists performed above the level of the ASD and MLD groups on the block-design test, but not the EFT. Despite both the block-design task and the EFT measuring local processing abilities, we suggest that this result is due to the block-design task being an active construction task (requiring the conversion of a visual input into a motor output), whereas the EFT is a passive recognition task. Therefore, although an enhanced local processing style is an important aspect of savant artistic talent, motor control also appears to be a necessary skill.
Evidence for arsenic-driven redox chemistry in a wetland system: a field voltammetric study
Authors: Haffert L. , Sander S. G. , Hunter K. A. , Craw D.
Published: August 2010

Environmental context.The speciation of the toxic element arsenic directly controls its environmental mobility and toxicity. The current study took place on site in an historic mine processing environment that is extremely arsenic-rich and comparatively sulfur-deficient. When arsenic is one of the major chemical components, redox state and pH of the chemical system are closely linked to arsenic speciation.
Abstract.This study investigates the chemistry of the AsIII–AsV redox couple in association with As-rich processing residues (up to 40 wt%) from a historic gold mine in New Zealand. The site provides a unique natural laboratory of a sulfide-free chemical system driven by arsenolite dissolution. Field based cathodic stripping voltammetry, which circumvents post-sampling preservation issues, was successfully applied to analyse the AsIII to the microgram level. The AsIII–AsV redox couple, in particular the oxidation of AsIII, was found to have a noticeable influence on system pH and EH. The As redox pair itself is controlled by a range of processes, which were identified for the varying aqueous environments present on the studied site.
Audit of paired anal cytology and histopathology outcomes in patients referred to a public sexual health clinic
Authors: Williams Vincent M. , Metcalf Cecily , French Martyn A. , McCloskey Jenny C.
Published: August 2010

Background: The level of agreement between anal cytology and histopathology is not clear with only a few studies evaluating the reliability of anal specimen reporting. Australian data in relation to this are limited. Methods: The results of paired anal cytology and histopathology specimens received between 2002 and 2008 from patients who were referred within the sexual health clinic were retrieved from the anatomical pathology database. A total of 248 paired samples from 154 (21 females, 133 males) participants were extracted. Concurrent high risk human papilloma virus (hrHPV) DNA assay and HIV status for the study group were also collected. Data were tabulated according to reported grade of squamous abnormality based on the Bethesda system. Using the biopsy result as the gold standard the specificity, sensitivity, positive predictive value (PPV) and negative predictive value (NPV) for cytology were calculated and the association between grade of abnormality, HIV status and hrHPV infection estimated. Results: Concordance between cytology and histology showed that in 204 (85%) paired samples both tests were categorised as abnormal (Kappa statistic 0.73, P = 0.013). The cytology result showed a sensitivity of 96%, specificity 14%, PPV 89% and NPV 31% when compared with histopathology. HrHPV assay was positive in 192 (80%) samples. High-grade squamous abnormalities were reported in biopsy specimens from 60% (n = 42/67) of HIV-positive subjects and 25% (n = 22/87) of HIV-negative subjects. HIV-positive individuals were more likely to be hrHPV positive, odds ratio (OR) 6.21 [95% confidence interval (CI) 2.69 to 14.34], when compared with HIV-negative subjects. Conclusion: Anal cytology is highly sensitive for the detection of abnormal squamous cells. While cytology has low specificity for predicting the grade of abnormality compared with biopsy outcome, its application as a screening method in asymptomatic at risk populations warrants further study.
Cervical cancer vaccine development
Authors: Frazer Ian H.
Published: August 2010

Cervical cancer is initiated by infection of cervical epithelium with human papillomavirus. Vaccines have been developed, incorporating papillomavirus viral capsids and alum based adjuvants. In extensive clinical trials these vaccines have been shown safe and effective in preventing infection with, and disease caused by, the papillomavirus genotypes they incorporate, in women not already infected. These vaccines have the potential to reduce the global burden of cervical cancer by up to 70%.
Cytology and cervical cancer surveillance in an era of human papillomavirus vaccination
Authors: Budd Alison C. , Sturrock Christine J.
Published: August 2010

Cytological and cancer surveillance will provide the most effective indications of short-term effects and long-term outcomes of the introduction of the human papillomavirus (HPV) vaccine in Australia. This article outlines how this surveillance is proposed to occur through the established national monitoring mechanisms of the National Cervical Screening Program in the annual Australian Institute of Health and Welfare (AIHW) publication ‘Cervical screening in Australia’. Cytological surveillance will be possible principally through cytology data provided annually by the state and territory cervical cytology registers, and it is expected that these data will provide the earliest and most comprehensive indications of effects from the HPV vaccine. Some potential issues in interpreting these data are also discussed, including the potentially confounding effects of the introduction of new National Health and Medical Research Council guidelines ‘Screening to prevent cervical cancer: guidelines for the management of asymptomatic women with screen-detected abnormalities’ some 9 months before the introduction of the vaccine. Cancer surveillance over the long term will be possible using cervical cancer incidence data reported annually for the National Cervical Screening Program in ‘Cervical screening in Australia’ using data sourced from the Australian Cancer Database. In a final discourse, the HPV vaccine and cervical screening are discussed concurrently, and the importance of continued cervical screening in the HPV vaccine era emphasised.
Global reduction of cervical cancer with human papillomavirus vaccines: insights from the hepatitis B virus vaccine experience
Authors: Heffernan Margaret E. , Garland Suzanne M. , Kane Mark A.
Published: August 2010

Background: Worldwide, prophylactic vaccines against two major human cancers are now commercially available: hepatitis B virus (HBV) vaccines (first licensed in 1982) against primary hepatocellular carcinoma and human papillomavirus (HPV) vaccines (first licensed 2006) against cervical cancer. Initial implementation strategies for HBV vaccination were not successful in preventing disease in the community: it took 15 years for significant global reduction in the burden of this disease. Methods: We compare and contrast HBV vaccine experiences to challenges for successful global HPV vaccination strategies, and make recommendations accordingly. Results: Lessons from HBV immunisation for successful outcomes with HPV immunisation showed that several factors need to be met: (i) the engagement of key stakeholders in all aspects of planning and delivery of HPV vaccine strategies; (ii) understanding the specific characteristics of targeted population groups; (iii) global cooperation and support with WHO recommendations; (iv) Government supported mass immunization programs and cooperation between public and private entities; (v) affordable HPV vaccines for some regions; (vi) culturally appropriate and diverse public education programs in targeted health promotion strategies; (vii) pro-active health providers and parents in encouraging adolescents to undertake HPV vaccination; and (vii) eventual immunisation of infants. Conclusions: The key to success will be affordable, readily deliverable HPV vaccines to young girls as universal campaigns.
'It's a logistical nightmare!' Recommendations for optimising human papillomavirus school-based vaccination experience
Authors: Robbins Spring Chenoa Cooper , Bernard Diana , McCaffery Kirsten , Skinner S. Rachel
Published: August 2010

Introduction: To date, no published studies examine procedural factors of the school-based human papillomavirus (HPV) vaccination program from the perspective of those involved. This study examines the factors that were perceived to impact optimal vaccination experience. Methods: Schools across Sydney were selected to reflect a range of vaccination coverage at the school level and different school types to ensure a range of experiences. Semi-structured focus groups were conducted with girls; and one-on-one interviews were undertaken with parents, teachers and nurses until saturation of data in all emergent themes was reached. Focus groups and interviews explored participants’ experiences in school-based HPV vaccination. Transcripts were analysed, letting themes emerge. Results: Themes related to participants’ experience of the organisational, logistical and procedural aspects of the vaccination program and their perceptions of an optimal process were organised into two categories: (1) preparation for the vaccination program and (2) vaccination day strategies. In (1), themes emerged regarding commitment to the process from those involved, planning time and space for vaccinations, communication within and between agencies, and flexibility. In (2), themes included vaccinating the most anxious girls first, facilitating peer support, use of distraction techniques, minimising waiting time girls, and support staff. Discussion: A range of views exists on what constitutes an optimal school-based program. Several findings were identified that should be considered in the development of guidelines for implementing school-based programs. Future research should evaluate how different approaches to acquiring parental consent, and the use of anxiety and fear reduction strategies impact experience and uptake in the school-based setting.
What can surveillance of genital warts tell us?
Authors: Fairley Christopher K. , Donovan Basil
Published: August 2010

In this Review, we describe the recent epidemiology of genital warts and postulate what the future may hold as a result of the introduction of the quadrivalent human papillomavirus (HPV) vaccine. HPV types 6 or 11 are responsible for most cases and they develop in about two-thirds of women a few months after HPV 6 or 11 infections are first detected by polymerase chain reaction. Surveillance data, cohort studies and cross-sectional surveys suggest that the annual incidence of genital warts exceeds 1% and serological studies suggest cumulative risk up to 40 years of age for HPV 6 or 11 is over 25%. The quadrivalent HPV vaccine is highly effective against genital warts and Australian surveillance data in the 2 years after the introduction of the vaccine have shown large declines in younger women and to a lesser degree heterosexual men. No significant changes in older women or men who have sex with men were seen. Given the success of Australia’s catch-up program it will not be long before we know if the basic reproductive number for genital warts holds the prospect of elimination. However, if genital warts stabilise at a lower, but not very low, rate we will know that elimination will not be possible without vaccination of males.
Unresolved questions concerning human papillomavirus infection and transmission: a modelling perspective
Authors: Regan David G. , Philp David J. , Waters Edward K.
Published: August 2010

Mathematical transmission models are widely used to forecast the potential impact of interventions such as vaccination and to inform the development of health policy. Effective vaccines are now available for the prevention of cervical cancer and other diseases attributable to human papillomavirus (HPV). Considerable uncertainties remain regarding the characterisation of HPV infection and its sequelae, infectivity, and both vaccine-conferred and naturally-acquired immunity. In this review, we discuss the key knowledge gaps that impact on our ability to develop accurate models of HPV transmission and vaccination.
miRNA-based mechanism for the commitment of multipotent progenitors to a single cellular fate
Authors: Mann Mati , Barad Omer , Agami Reuven , Geiger Benjamin , Hornstein Eran
Published: August 2010

When stem cells and multipotent progenitors differentiate, they undergo fate restriction, enabling a single fate and blocking differentiation along alternative routes. We herein present a mechanism whereby such unequivocal commitment is achieved, based on microRNA (miRNA)-dependent repression of an alternative cell fate. We show that the commitment of monocyte RAW264.7 progenitors to active macrophage differentiation involves rapid up-regulation of miR-155 expression, which leads to the suppression of the alternative pathway, namely RANK ligand-induced osteoclastogenesis, by repressing the expression of MITF, a transcription factor essential for osteoclast differentiation. A temporal asymmetry, whereby miR-155 expression precedes and overrides the activation of the osteoclast transcriptional program, provides the means for coherent macrophage differentiation, even in the presence of osteoclastogenic signals. Based on these findings, we propose that miRNA may provide a general mechanism for the unequivocal commitment underlying stem cell differentiation.
Translations for dubbing as dynamic texts
Authors: Matamala Anna
Published: August 2010

This article aims to describe how written translations of audiovisual products change along the dubbing process until they reach the audience, focusing mainly on the synchronisation stage. The corpus is made up of the first reel of the Catalan and Spanish translations of three different films released in 2006 (Casino Royale, Good night, and good luck, and The Da Vinci Code).

After a brief summary of the dubbing process and a short overview of the approaches to synchronisation found in the literature, the specific strategies found in a bottom-up analysis are highlighted, offering both a wide analysis of the general changes throughout the process and a closer analysis of the specific changes that occur in the synchronisation stage. A comparison of the strategies found in Catalan and Spanish is also included in order to assess whether different languages result in different strategies.
Cultural loss in the English translation of Chinese poetry
Authors: Yang Liu
Published: August 2010

Translation is to reproduce the meaning and style of a source language text in a target language text in consideration of the cultural differences. Because of dramatic differences between the cultures, translators have to sacrifice something, such as time, religious connotation, and the wording of the original poem to obtain its aesthetic value and its original beauty. In this paper the author examines the poetry translation focusing on the basic concepts of cultural translation and the difficulties of Chinese poetry translation, and special attentions are paid on losses and the strategies in the translation. Beginning from the basic concepts of cultural translation, the paper expounds the essence of the cultural translation in order to lay a sound foundation for the following analysis of the poetry translation. In Part 2, the paper points out the difficulties of Chinese poetry translation that arise from the differences between Chinese and English cultures .Part 3 is a tentative analysis of the losses in the English translation of Chinese poetry and categorizes the losses into four groups:the loss of time;the loss of religious connotation ;the loss in wording; the loss of allusion. To address the losses, the author proposes several strategies such as free translation , transfer of allusion and annotation.
Failure to agree is not a failure
Authors: Preminger Omer
Published: August 2010

Based on the patterns of phi-agreement with post-verbal subjects in Hebrew, I argue against the idea that failure to establish a phi-agreement relation between a phi-probe and its putative target (e.g., due to intervention) results in ungrammaticality, or a “crash”; at the same time, I demonstrate that phi-agreement also cannot be optional. At first glance, these two claims—that phi-agreement is neither optional, nor does its failure result in ungrammaticality—might seem contradictory. However, I argue that there is a third possibility, which is in fact the only one that can account for the data under consideration: phi-agreement must be attempted by every phi-probe; but if it fails (e.g., due to the presence of an intervener), its failure is systematically tolerated. tolerated.
Interpretation of fast measurements of plasma potential, temperature and density in SOL of ASDEX Upgrade
Authors: Horacek J. , Adamek J. , Müller H.W. , Seidl J. , Nielsen A.H. , Rohde V. , Mehlmann F. , Ionita C. , Havlíčková E.
Published: August 2010

This paper focuses on interpretation of fast (1 µs) and local (2–4 mm) measurements of plasma density, potential and electron temperature in the edge plasma of tokamak ASDEX Upgrade. Steady-state radial profiles demonstrate the credibility of the ball-pen probe. We demonstrate that floating potential fluctuations measured by a Langmuir probe are dominated by plasma electron temperature rather than potential. Spatial and temporal scales are found consistent with expectations based on interchange-driven turbulence. Conditionally averaged signals found for both potential and density are also consistent; however, those for temperature show an unexpected ∼4 mm wide decrease by 10% at the very centre of a blob. In the wall shadow, temperature measured by the swept Langmuir probe yields values ∼10 eV, whilst the ball-pen temperature gradient is more steep and credible, dropping down to ∼1 eV.
Feedback control of ECRH polarization on LHD
Authors: Felici F. , Shimozuma T. , Kubo S. , Yoshimura Y. , Takahashi H. , Igami H. , Goodman T.P. , Seki T. , Tsuchiya H. , Ito S. , Mizuno Y. , Sauter O. , Mutoh T.
Published: August 2010

The polarization of electron cyclotron resonance heating (ECRH) waves, set by the orientation of a pair of corrugated mirror polarizers in the transmission line, determines the degree of coupling to O- and X-modes in the plasma and has an important effect on the first-pass absorption. Existing methods for determining the required polarization have been found adequate in most experiments. However, as the pulse length is increased it becomes increasingly important to maximize the first-pass absorption while the plasma or injection conditions change or when there can be significant O- to X-mode power coupling during propagation, particularly in the edge plasma region of a stellarator. This has motivated the development of a dedicated feedback control system which is able to adjust the polarizers' angles settings during the discharge in order to maintain the highest possible absorption. An extremum seeking controller is shown to successfully recover the optimum polarization setting during long-pulse ECRH experiments on the Large Helical Device (LHD).

Corrections were made to this article on 02 September 2010. 'The' was removed before LHD in several places.
Impact of gyro-motion and sheath acceleration on the flux distribution on rough surfaces
Authors: Schmid K. , Mayer M. , Adelhelm C. , Balden M. , Lindig S.
Published: August 2010

As was already observed experimentally, the erosion of tungsten (W) coated graphite (C) tiles in ASDEX-Upgrade (AUG) exhibits regular erosion patterns on the micrometre rough surfaces whose origin is not fully understood: surfaces inclined towards the magnetic field direction show strong net W erosion while surfaces facing away from the magnetic field are shadowed from erosion and may even exhibit net W deposition. This paper presents a model which explains the observed erosion/deposition pattern. It is based on the calculation of ion trajectories dropping through the plasma sheath region to the rough surface with combined magnetic and electrical fields. The surface topography used in the calculations is taken from atomic force microscope measurement of real AUG tiles. The calculated erosion patterns are directly compared with secondary electron microscopy images of the erosion zones from the same location. The erosion on surfaces inclined towards the magnetic field is due to ions from the bulk plasma which enter the sheath gyrating along the magnetic field lines, while the deposition of W on surfaces facing away from the magnetic field is due to promptly re-deposited W that is ionized still within the magnetic pre-sheath.
The Sodium/Proton Exchanger NHE8 Regulates Late Endosomal Morphology and Function
Authors: Lawrence Scott P. , Bright Nicholas A. , Luzio J. Paul , Bowers Katherine
Published: August 2010

The pH and lumenal environment of intracellular organelles is considered essential for protein sorting and trafficking through the cell. We provide the first evidence that a mammalian NHE sodium (potassium)/proton exchanger, NHE8, plays a key role in the control of protein trafficking and endosome morphology. At steady state, the majority of epitope-tagged NHE8 was found in the trans-Golgi network of HeLa M-cells, but a proportion was also localized to multivesicular bodies (MVBs). Depletion of NHE8 in HeLa M-cells with siRNA resulted in the perturbation of MVB protein sorting, as shown by an increase in epidermal growth factor degradation. Additionally, NHE8-depleted cells displayed striking perinuclear clustering of endosomes and lysosomes, and there was a ninefold increase in the cellular volume taken up by LAMP1/LBPA-positive, dense MVBs. Our data points to a role for the ion exchange activity of NHE8 being required to maintain endosome morphology, as overexpression of a nonfunctional point mutant protein (NHE8 E225Q) resulted in phenotypes similar to those seen after siRNA depletion of endogenous NHE8. Interestingly, we found that depletion of NHE8, despite its function as a sodium (potassium)/proton antiporter, did not affect the overall pH inside dense MVBs.
Sprouty Proteins Inhibit Receptor-mediated Activation of Phosphatidylinositol-specific Phospholipase C
Authors: Akbulut Simge , Reddi Alagarsamy L. , Aggarwal Priya , Ambardekar Charuta , Canciani Barbara , Kim Marianne K.H. , Hix Laura , Vilimas Tomas , Mason Jacqueline , Basson M. Albert , Lovatt Matthew , Powell Jonathan , Collins Samuel , Quatela Steven , Phillips Mark , Licht Jonathan D.
Published: August 2010

Sprouty (Spry) proteins are negative regulators of receptor tyrosine kinase signaling; however, their exact mechanism of action remains incompletely understood. We identified phosphatidylinositol-specific phospholipase C (PLC)-γ as a partner of the Spry1 and Spry2 proteins. Spry–PLCγ interaction was dependent on the Src homology 2 domain of PLCγ and a conserved N-terminal tyrosine residue in Spry1 and Spry2. Overexpression of Spry1 and Spry2 was associated with decreased PLCγ phosphorylation and decreased PLCγ activity as measured by production of inositol (1,4,5)-triphosphate (IP3) and diacylglycerol, whereas cells deficient for Spry1 or Spry1, -2, and -4 showed increased production of IP3at baseline and further increased in response to growth factor signals. Overexpression of Spry 1 or Spry2 or small-interfering RNA-mediated knockdown of PLCγ1 or PLCγ2 abrogated the activity of a calcium-dependent reporter gene, suggesting that Spry inhibited calcium-mediated signaling downstream of PLCγ. Furthermore, Spry overexpression in T-cells, which are highly dependent on PLCγ activity and calcium signaling, blocked T-cell receptor-mediated calcium release. Accordingly, cultured T-cells from Spry1 gene knockout mice showed increased proliferation in response to T-cell receptor stimulation. These data highlight an important action of Spry, which may allow these proteins to influence signaling through multiple receptors.
Activation of Akt Is Essential for the Propagation of Mitochondrial Respiratory Stress Signaling and Activation of the Transcriptional Coactivator Heterogeneous Ribonucleoprotein A2
Authors: Guha Manti , Fang Ji-Kang , Monks Robert , Birnbaum Morris J. , Avadhani Narayan G.
Published: August 2010

Mitochondrial respiratory stress (also called mitochondrial retrograde signaling) activates a Ca2+/calcineurin-mediated signal that culminates in transcription activation/repression of a large number of nuclear genes. This signal is propagated through activation of the regulatory proteins NFκB c-Rel/p50, C/EBPδ, CREB, and NFAT. Additionally, the heterogeneous ribonucleoprotein A2 (hnRNPA2) functions as a coactivator in up-regulating the transcription of Cathepsin L, RyR1, and Glut-4, the target genes of stress signaling. Activation of IGF1R, which causes a metabolic switch to glycolysis, cell invasiveness, and resistance to apoptosis, is a phenotypic hallmark of C2C12 myoblasts subjected to mitochondrial stress. In this study, we report that mitochondrial stress leads to increased expression, activation, and nuclear localization of Akt1. Mitochondrial respiratory stress also activates Akt1-gene expression, which involves hnRNPA2 as a coactivator, indicating a complex interdependency of these two factors. Using Akt1−/−mouse embryonic fibroblasts and Akt1 mRNA-silenced C2C12 cells, we show that Akt1-mediated phosphorylation is crucial for the activation and recruitment of hnRNPA2 to the enhanceosome complex. Akt1 mRNA silencing in mtDNA-depleted cells resulted in reversal of the invasive phenotype, accompanied by sensitivity to apoptotic stimuli. These results show that Akt1 is an important regulator of the nuclear transcriptional response to mitochondrial stress.
Integrin-mediated Cell Attachment Induces a PAK4-dependent Feedback Loop Regulating Cell Adhesion through Modified Integrin αvβ5 Clustering and Turnover
Authors: Li Zhilun , Lock John G. , Olofsson Helene , Kowalewski Jacob M. , Teller Steffen , Liu Yajuan , Zhang Hongquan , Strömblad Staffan
Published: August 2010

Cell-to-extracellular matrix adhesion is regulated by a multitude of pathways initiated distally to the core cell–matrix adhesion machinery, such as via growth factor signaling. In contrast to these extrinsically sourced pathways, we now identify a regulatory pathway that is intrinsic to the core adhesion machinery, providing an internal regulatory feedback loop to fine tune adhesion levels. This autoinhibitory negative feedback loop is initiated by cell adhesion to vitronectin, leading to PAK4 activation, which in turn limits total cell–vitronectin adhesion strength. Specifically, we show that PAK4 is activated by cell attachment to vitronectin as mediated by PAK4 binding partner integrin αvβ5, and that active PAK4 induces accelerated integrin αvβ5 turnover within adhesion complexes. Accelerated integrin turnover is associated with additional PAK4-mediated effects, including inhibited integrin αvβ5 clustering, reduced integrin to F-actin connectivity and perturbed adhesion complex maturation. These specific outcomes are ultimately associated with reduced cell adhesion strength and increased cell motility. We thus demonstrate a novel mechanism deployed by cells to tune cell adhesion levels through the autoinhibitory regulation of integrin adhesion.
Module-based prediction approach for robust inter-study predictions in microarray data
Authors: Mi Zhibao , Shen Kui , Song Nan , Cheng Chunrong , Song Chi , Kaminski Naftali , Tseng George C.
Published: August 2010

Motivation: Traditional genomic prediction models based on individual genes suffer from low reproducibility across microarray studies due to the lack of robustness to expression measurement noise and gene missingness when they are matched across platforms. It is common that some of the genes in the prediction model established in a training study cannot be matched to another test study because a different platform is applied. The failure of inter-study predictions has severely hindered the clinical applications of microarray. To overcome the drawbacks of traditional gene-based prediction (GBP) models, we propose a module-based prediction (MBP) strategy via unsupervised gene clustering.

Results:  K-means clustering is used to group genes sharing similar expression profiles into gene modules, and small modules are merged into their nearest neighbors. Conventional univariate or multivariate feature selection procedure is applied and a representative gene from each selected module is identified to construct the final prediction model. As a result, the prediction model is portable to any test study as long as partial genes in each module exist in the test study. We demonstrate that K-means cluster sizes generally follow a multinomial distribution and the failure probability of inter-study prediction due to missing genes is diminished by merging small clusters into their nearest neighbors. By simulation and applications of real datasets in inter-study predictions, we show that the proposed MBP provides slightly improved accuracy while is considerably more robust than traditional GBP.

Availability:  http://www.biostat.pitt.edu/bioinfo/

Contact:  ctseng@pitt.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ancient death-grip leaf scars reveal ant–fungal parasitism
Authors: Hughes David P. , Wappler Torsten , Labandeira Conrad C.
Published: August 2010

Parasites commonly manipulate host behaviour, and among the most dramatic examples are diverse fungi that cause insects to die attached to leaves. This death-grip behaviour functions to place insects in an ideal location for spore dispersal from a dead body following host death. Fossil leaves record many aspects of insect behaviour (feeding, galls, leaf mining) but to date there are no known examples of behavioural manipulation. Here, we document, to our knowledge, the first example of the stereotypical death grip from 48 Ma leaves of Messel, Germany, indicating the antiquity of this behaviour. As well as probably being the first example of behavioural manipulation in the fossil record, these data support a biogeographical parallelism between mid Eocene northern Europe and recent southeast Asia.
Bernhard Hermann Neumann AC. 15 October 1909 — 21 October 2002
Authors: Praeger Cheryl E.
Published: August 2010

Bernhard Hermann Neumann was born and educated in Berlin. He held doctorates from Berlin and Cambridge, and mathematical positions at universities in Cardiff, Hull, Manchester and the Australian National University (ANU) in Canberra. Whereas his move to the UK in 1932 was a result of the difficulties he faced as a Jew in finding employment in Germany, his move to Australia in 1962 was to set up a new research Department of Mathematics at the Institute of Advanced Studies at ANU. Bernhard Neumann was famous both for his seminal research work in algebra and also for his strong support of all endeavours in mathematics. His scholarly publications span more than 70 years. His honours include election to the Fellowships of the Royal Society and of the Australian Academy of Science, appointment as Companion of the Order of Australia, and numerous honorary doctorates. To Bernhard it was important to share and spread the joy of doing mathematics.
Jeffrey Barry Harborne. 1 September 1928 — 21 July 2002
Authors: Prebble John N.
Published: August 2010

Jeffrey Harborne made a major contribution to the discipline of phytochemistry. Originally an organic chemist, he became an academic leader in the biochemistry of secondary metabolites, particularly flavonoids and also other plant phenols. He contributed significantly to areas at the interface between chemistry and traditional areas of plant science, systematics and ecology. His early research was influential on the rise in importance of both plant chemotaxonomy and biochemical ecology.
Christopher John Lamb CBE. 19 March 1950 — 21 August 2009
Authors: Chory Joanne , Casey Rod
Published: August 2010

Chris Lamb was one of the most influential plant biologists of his time. He was director of the Plant Biology Laboratory at the Salk Institute and of the John Innes Centre, two of the world's leading plant and microbial research institutions. He was recognized by the Institute for Scientific Information as one of the most highly cited researchers worldwide in plant and animal science. His field of study was plant–pathogen interactions, and he made seminal contributions to the understanding of the molecular basis of plant defence. His efforts led to discoveries such as how cell wall composition influences microbial entry, which plant genes are rapidly induced on infection, and the role of reactive oxygen and nitrogen intermediates in plant defence signalling. His work demonstrated a number of links between defence responses in plants and in animals. He believed that plant and microbial science research could be used to improve the world, and he took his belief to the local communities, to regional and national media and to Westminster. He had a skill for talent spotting, and one of his major legacies is the number of careers that he nurtured and are now flourishing at universities and institutes across the world.
Growth factor delivery-based tissue engineering: general approaches and a review of recent developments
Authors: Lee Kangwon , Silva Eduardo A. , Mooney David J.
Published: August 2010

The identification and production of recombinant morphogens and growth factors that play key roles in tissue regeneration have generated much enthusiasm and numerous clinical trials, but the results of many of these trials have been largely disappointing. Interestingly, the trials that have shown benefit all contain a common denominator, the presence of a material carrier, suggesting strongly that spatio-temporal control over the location and bioactivity of factors after introduction into the body is crucial to achieve tangible therapeutic effect. Sophisticated materials systems that regulate the biological presentation of growth factors represent an attractive new generation of therapeutic agents for the treatment of a wide variety of diseases. This review provides an overview of growth factor delivery in tissue engineering. Certain fundamental issues and design strategies relevant to the material carriers that are being actively pursued to address specific technical objectives are discussed. Recent progress highlights the importance of materials science and engineering in growth factor delivery approaches to regenerative medicine.
Nanoscale thermodynamics of biological interfacial tension
Authors: Fernández Ariel
Published: August 2010

The interfacial tension of biological water, a promoter of biomolecular interactions, is difficult to determine because of the inhomogeneous nanoscale patterns that make up the surface of biomolecules. These patterns modulate solubility in peculiar manners, enabling specific associations while preventing phase separation or precipitation. In this work, we derive de novo the nanoscale thermodynamics associated with the creation of biological interfaces and validate the results against experimentally identified complex interfaces. Interfacial tension is shown to be generated by hot spots of red-shifted dielectric relaxation. The most common spots involve hindered polar hydration. Taken collectively, these patches contribute more to the interfacial tension than the better known non-polar cavities with nanometre curvature, where our results agree with the established length-scale dependence of hydrophobicity. The thermodynamic results are validated by showing that the inferred patches of interfacial tension actually promote biomolecular associations.
Validation of the energy-balance approach to curve-shaped shear-band propagation in soil
Authors: Saurer Erich , Puzrin Alexander M.
Published: August 2010

Progressive and catastrophic failure in soils has been commonly associated with the phenomenon of shear-band propagation. This is a challenging topic, both in terms of understanding and simulation. Most existing studies have focused on the propagation of planar shear bands. This paper is an attempt to analytically model the rate of progressive shear-band propagation in shear-blade tests, especially designed to produce curved shear bands in dense silty sand. The simplified analytical solution is based on fracture mechanics energy balance and on limiting equilibrium approaches. The analytical solution is validated against experimental data. Comparison shows that, despite the simplifications, the energy-balance approach is a useful tool in modelling the rate of non-planar shear-band propagation, both qualitatively and quantitatively.
The evolution of punishment through reputation
Authors: Santos Miguel dos , Rankin Daniel J. , Wedekind Claus
Published: August 2010

Punishment of non-cooperators has been observed to promote cooperation. Such punishment is an evolutionary puzzle because it is costly to the punisher while beneficial to others, for example, through increased social cohesion. Recent studies have concluded that punishing strategies usually pay less than some non-punishing strategies. These findings suggest that punishment could not have directly evolved to promote cooperation. However, while it is well established that reputation plays a key role in human cooperation, the simple threat from a reputation of being a punisher may not have been sufficiently explored yet in order to explain the evolution of costly punishment. Here, we first show analytically that punishment can lead to long-term benefits if it influences one's reputation and thereby makes the punisher more likely to receive help in future interactions. Then, in computer simulations, we incorporate up to 40 more complex strategies that use different kinds of reputations (e.g. from generous actions), or strategies that not only include punitive behaviours directed towards defectors but also towards cooperators for example. Our findings demonstrate that punishment can directly evolve through a simple reputation system. We conclude that reputation is crucial for the evolution of punishment by making a punisher more likely to receive help in future interactions, and that experiments investigating the beneficial effects of punishment in humans should include reputation as an explicit feature.
Divergence and ontogenetic coupling of larval behaviour and thermal reaction norms in three closely related butterflies
Authors: Berger David , Friberg Magne , Gotthard Karl
Published: August 2010

Genetic trade-offs such as between generalist–specialist strategies can be masked by changes in compensatory processes involving energy allocation and acquisition which regulation depends on the state of the individual and its ecological surroundings. Failure to account for such state dependence may thus lead to misconceptions about the trade-off structure and nature of constraints governing reaction norm evolution. Using three closely related butterflies, we first show that foraging behaviours differ between species and change remarkably throughout ontogeny causing corresponding differences in the thermal niches experienced by the foraging larvae. We further predicted that thermal reaction norms for larval growth rate would show state-dependent variation throughout development as a result of selection for optimizing feeding strategies in the respective foraging niches of young and old larvae. We found substantial developmental plasticity in reaction norms that was species-specific and reflected the different ontogenetic niche shifts. Any conclusions regarding constraints on performance curves or species-differentiation in thermal physiology depend on when reaction norms were measured. This demonstrates that standardized estimates at single points in development, or in general, allow variation in only one ecological dimension, may sometimes provide incomplete information on reaction norm constraints.
Stacking Multiple Transgenes at a Selected Genomic Site via Repeated Recombinase-Mediated DNA Cassette Exchanges
Authors: Li Zhongsen , Moon Bryan P. , Xing Aiqiu , Liu Zhan-Bin , McCardell Richard P. , Damude Howard G. , Falco S. Carl
Published: August 2010

Recombinase-mediated DNA cassette exchange (RMCE) has been successfully used to insert transgenes at previously characterized genomic sites in plants. Following the same strategy, groups of transgenes can be stacked to the same site through multiple rounds of RMCE. A gene-silencing cassette, designed to simultaneously silence soybean (Glycine max) genes fatty acid ω-6 desaturase 2 (FAD2) and acyl-acyl carrier protein thioesterase 2 (FATB) to improve oleic acid content, was first inserted by RMCE at a precharacterized genomic site in soybean. Selected transgenic events were subsequently retransformed with the second DNA construct containing a Yarrowia lipolytica diacylglycerol acyltransferase gene (DGAT1) to increase oil content by the enhancement of triacylglycerol biosynthesis and three other genes, a Corynebacterium glutamicum dihydrodipicolinate synthetase gene (DHPS), a barley (Hordeum vulgare) high-lysine protein gene (BHL8), and a truncated soybean cysteine synthase gene (CGS), to improve the contents of the essential amino acids lysine and methionine. Molecular characterization confirmed that the second RMCE successfully stacked the four overexpression cassettes to the previously integrated FAD2-FATB gene-silencing cassette. Phenotypic analyses indicated that all the transgenes expressed expected phenotypes.
Estimation of time‐varying price elasticity in 1970–1997 Japanese raw milk supply by structural time‐series model
Authors: Komaki Toru , Penzer Jeremy
Published: August 2010

The price elasticity of raw milk supply in Japan is estimated over time by a structural time‐series model in state space form, and the changes in elasticity are tested by the diagnosing test of de John and Penzer in 1998. The supply function is modeled with a local linear trend and a strictly exogenous autoregressive distributed lag price. The seasonality in the data is adjusted by a structural time‐series model. In the 1970–1997 period, there were major dairy policy changes in Japan: a production adjustment, related penalties, and two‐tier pricing. Hokkaido is the region that mainly provides the supply of raw milk for milk products, while Tofuken is the region that mainly produces drinking milk. The estimated price elasticity in Hokkaido became stable after imposition of the production adjustment. On the other hand, price elasticity in Tofuken became stable after the inflation of the mid‐1970s. Price elasticity is estimated to be more inelastic as well as more likely to converge in inelasticity in Hokkaido than in Tofuken. We discuss the relationship between changes in dairy policy and changes in price elasticity.
Differences in agricultural returns: an empirical test of efficiency in factor input allocation using Vietnamese data
Authors: Linde‐Rahr Martin
Published: August 2010

We study whether rural households in Vietnam allocate their factor inputs efficiently. Factor returns and technical rates of substitution (TRS) between production activities are compared. We estimate two translog production functions and conduct three tests: First we test the equality of bootstrapped returns. Second, we use a bootstrapped t‐test comparing the equality of TRS. Finally, we derive a set of nonlinear restrictions on our estimated parameters, which, if held, would imply that we cannot reject efficiency. The article concentrates on the allocation of factors between the cultivation of the two most important agricultural crops—sugar cane and rice. We cannot reject the possibility that households are efficient in their input allocation. These results are consistent and stable over different estimation techniques and support the assumption of profit maximization.
The determinants of vinegrowers employment and policy implications: the case of a Greek island
Authors: Papadopoulos Athanasios P. , Papanikos Gregory T.
Published: August 2010

This study investigates the employment of vinegrowers on a Greek island (Samos) where there exist attractive alternative employment opportunities, particularly in the tourist sector. The recent dramatic decline in the number of vinegrowers has been of great concern particularly to wine producers, policy makers, and local authorities because such a pattern has had, and most importantly will have, serious economic, social, and environmental implications. The focus of this paper is on two issues. First, some descriptive statistics on the demographics of vinegrowers and characteristics of vineyards are presented and second, a probit model is developed to identify the demographic and other determinants of the probability of off‐farm and off‐vineyard work participation. The most important source of data information is primary data collected by the authors, using a questionnaire, which was completed by a representative sample of vinegrowers from the island of Samos. The empirical findings suggest that the promotion of vinegrowing requires policies that will enlarge the size of vineyards, promote investments in human and physical capital, and improve the public infrastructure.
Toward understanding household preference for consumption characteristics of millet varieties: a case study from western Niger
Authors: Ndjeunga Jupiter , Nelson Carl H.
Published: August 2010

In this study, we evaluate the preference of consumers in Niger for different tuwo or couscous characteristics using a random utility‐based choice experiment, ordered probit analysis, and tree‐based partitioning. Data were collected through a structured survey administered at four sites. Preferences are estimated for three products (couscous, fermented tuwo, and nonfermented tuwo) made from five pearl millet cutivars. We provide relative valuation for different traits by type of product. Results show that product taste, color, and textural attributes are important, especially for tuwo and couscous. Probit and partitioning results show that taste and color are the first attributes that consumers use to distinguish more preferred millet food products from less preferred millet food products. This should provide some direction for millet breeding programs and food processing of millet.