bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental investigation of shell modes in two-dimensional phononic crystal consisting of hollow cylinders
Authors: Mei Xuefei , Liu Gangqiang , He Zhaojian , Yu Liangbo , Yu Zhenhua , Ke Manzhu , Liu Zhengyou
Published: March 2010

We experimentally demonstrate the flexural shell modes of thin-walled hollow steel cylinders immersed in water. For a two-dimensional square-arranged phononic crystal consisting of such hollow cylinders, two flat bands are created because of the coupling of the shell modes among neighboring cylinders. The narrow bands associated with shell-modes are first validated by experiment. In particular, by analyzing the transmission spectra, band-structure, and eigen-pressure field distribution, we give detailed discussion on the anisotropic coupling behavior of the two flat bands with external incident plane waves.
Valence electron energy-loss spectroscopy of ultrathin SrTiO3 films grown on silicon (100) single crystal
Authors: Su Dong , Yang Bo , Jiang Nan , Sawicki M. , Broadbridge C. , Couillard M. , Reiner J. W. , Walker F. J. , Ahn C. H. , Zhu Yimei
Published: March 2010

Valence electron energy-loss spectroscopy is used to investigate the plasmon excitations of ultrathin SrTiO3 sandwiched between amorphous Si and crystalline Si. Two plasmon excitations were observed, one at 15.8 eV and the other at 28.7 eV. Our calculations, based on dielectric-function theory, suggest that the former peak originates from the coupling of the Si layers and is related to the geometry of the structure, and the latter peak results from the SrTiO3 bulk plasmon after a redshift. Our findings demonstrate the value of valence electron energy-loss spectroscopy in detecting a local change in the effective electron mass.
Quantum grow—A quantum dynamics sampling approach for growing potential energy surfaces and nonadiabatic couplings
Authors: Godsi Oded , Collins Michael A. , Peskin Uri
Published: March 2010

A quantum sampling algorithm for the interpolation of diabatic potential energy matrices by the Grow method is introduced. The new procedure benefits from penetration of the wave packet into classically forbidden regions, and the accurate quantum mechanical description of nonadiabatic transitions. The increased complexity associated with running quantum dynamics is reduced by using approximate low order expansions of the nuclear wave function within a Multi-configuration time-dependent Hartree scheme during the Grow process. The sampling algorithm is formulated and applied for three representative test cases, demonstrating the recovery of analytic potentials by the interpolated ones, and the convergence of a dynamic observable.
Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface
Authors: Park Jae Hyun , Aluru N. R.
Published: March 2010

In this paper, we investigate, using molecular dynamics simulations, the conformation and diffusion of longer and shorter single-strand DNA (ssDNA) as a function of water film thickness. While the conformation of the shorter ssDNA is significantly affected and the diffusion is suppressed with reduction in water film thickness, the conformation and diffusion of the longer DNA is not influenced. We explain our observations by considering the competition between stacking interaction of bases and solvation tendency of ssDNA. This paper suggests an approach to control the surface motion of ssDNA in nanoscale water films using film thickness.
Enhanced magnetic moments of alkali metal coated Sc clusters: New magnetic superatoms
Authors: Pradhan Kalpataru , Reveles J. Ulises , Sen Prasenjit , Khanna S. N.
Published: March 2010

It is shown that the magnetic moments of Sc atoms can be significantly enhanced by combining them with alkali atoms. We present results of first principles electronic structure calculations of ScNan (1≤n≤12) clusters that indicate that a ScNa12 cluster consisting of a Sc atom surrounded by 12 Na atoms forming a compact icosahedral structure has a spin magnetic moment of 3μB that is three times that of an isolated Sc atom. This unusual behavior is analyzed in terms of the filling of the supershells 1S, 1P,… controlled by the nature and size of the alkali atoms and the more localized Sc 3d orbitals that hybridize weakly with Na sp orbitals. It is shown that even larger magnetic moments could be attained by controlling the relative position of 1S, 1P, and 3d states. Indeed, our studies indicate large magnetic moment five times that of an isolated Sc atom in the ScK12 and ScCs12 clusters, in which the 3d orbitals of Sc adopt a half-filled configuration, while the clusters are stabilized by filled 1S2, 1P6, and 2S2 shells, the features making them as new magnetic superatoms.
Frequency-resolved temperature imaging of integrated circuits with full field heterodyne interferometry
Authors: Suck S. Y. , Tessier G. , Warnasooriya N. , Babuty A. , De Wilde Y.
Published: March 2010

We report a fast imaging method based on full field heterodyne interferometry for the purpose of frequency resolved temperature imaging. An integrated circuit is supplied with a modulated current resulting into a temperature modulation. The frequency content for this modulation is detected using an object beam and a reference beam, frequency-shifted to create a beating of the interference pattern. We obtain frequency domain spectra of the temperature with excellent precision.
Evidences of evanescent Bloch waves in phononic crystals
Authors: Romero-García V. , Sánchez-Pérez J. V. , Castiñeira-Ibáñez S. , Garcia-Raffi L. M.
Published: March 2010

We show both experimentally and theoretically the evanescent behavior of modes in the band gap of finite phononic crystal (PC). Based on experimental and numerical data we obtain the imaginary part of the wave vector in good agreement with the complex band structures obtained by the extended plane wave expansion. The calculated and measured acoustic field of a localized mode out of the point defect inside the PC presents also evanescent behavior. The correct understanding of evanescent modes is fundamental for designing narrow filters and waveguides based on PCs with defects.
Alignment of Ba–O divacancies as a mechanism for polarization imprint in BaTiO3 as revealed by first principles and classical molecular dynamics simulations
Authors: Ma Ying , Liu Bainian , Zhou Yichun , Ding Jianwen
Published: March 2010

Periodic arrays of Ba–O divacancies in BaTiO3 were studied using both first principles calculations and molecular dynamics simulations. It is found that the 2nd-neighbor complexes that are aligned along the direction of the spontaneous polarization have the lowest formation energies. The symmetry between the up and down polarization states is broken, which is manifested by a vertical shift in the polarization-voltage hysteresis loop. Systems containing randomly distributed Ba–O pairs were also studied and the shift in the hysteresis loop is negligible, which suggests that the alignment of polar Ba–O divacancies is responsible for the polarization imprint in ferroelectric BaTiO3.
Terahertz nanoresonators: Giant field enhancement and ultrabroadband performance
Authors: Park H. R. , Park Y. M. , Kim H. S. , Kyoung J. S. , Seo M. A. , Park D. J. , Ahn Y. H. , Ahn K. J. , Kim D. S.
Published: March 2010

Transmission of terahertz (THz) electromagnetic waves through a series of nanoresonator arrays punctured in a thin metallic film is investigated. Over 30% of normalized transmitted amplitude is observed with only 0.18% of aperture-coverage, implying an electric field enhancement of 170. Increasing the coverage to 0.6% results in a 90% normalized amplitude, with a broader line width. Inspired by log-periodic antenna, we put ten nanoresonators with four different lengths per unit cell, succeeding in an ultrabroadband THz filter with one decade width between 0.2 and 2.0 THz.
Effects of silicon and germanium adsorbed on graphene
Authors: Aktürk E. , Ataca C. , Ciraci S.
Published: March 2010

Based on the first-principles plane wave calculations, we studied the adsorption of Si and Ge on graphene. We found that these atoms are bound to graphene at the bridge site with a significant binding energy, while many other atoms are bound at the hollow site above the center of hexagon. It is remarkable that these adatoms may induce important changes in the electronic structure of graphene even at low coverage. Semimetallic graphene becomes metallized and attains a magnetic moment. The combination of adatom orbitals with those of π- and π∗-states of bare graphene is found responsible for these effects.
Electronic transport in chemical vapor deposited graphene synthesized on Cu: Quantum Hall effect and weak localization
Authors: Cao Helin , Yu Qingkai , Jauregui L. A. , Tian J. , Wu W. , Liu Z. , Jalilian R. , Benjamin D. K. , Jiang Z. , Bao J. , Pei S. S. , Chen Yong P.
Published: March 2010

We report on electronic properties of graphene synthesized by chemical vapor deposition (CVD) on copper then transferred to SiO2/Si. Wafer-scale (up to 4 in.) graphene films have been synthesized, consisting dominantly of monolayer graphene as indicated by spectroscopic Raman mapping. Low temperature transport measurements are performed on microdevices fabricated from such CVD graphene, displaying ambipolar field effect (with on/off ratio ∼5 and carrier mobilities up to ∼3000 cm2/V s) and “half-integer” quantum Hall effect, a hall-mark of intrinsic electronic properties of monolayer graphene. We also observe weak localization and extract information about phase coherence and scattering of carriers.
Illusion media: Generating virtual objects using realizable metamaterials
Authors: Jiang Wei Xiang , Ma Hui Feng , Cheng Qiang , Cui Tie Jun
Published: March 2010

We propose a class of optical transformation media, illusion media, which render the enclosed object invisible and generate one or more virtual objects as desired. We apply the proposed media to design a microwave device, which transforms an actual object into two virtual objects. Such an illusion device exhibits unusual electromagnetic behavior as verified by full-wave simulations. Different from the published illusion devices which are composed of left-handed materials with simultaneously negative permittivity and permeability, the proposed illusion media have finite and positive permittivity and permeability. Hence the designed device could be realizable using artificial metamaterials.
Production of ultradense deuterium: A compact future fusion fuel
Authors: Badiei Shahriar , Andersson Patrik U. , Holmlid Leif
Published: March 2010

Ultradense deuterium as a nuclear fuel in laser-ignited inertial confinement fusion appears to have many advantages. The density of ultradense deuterium D(−1) is as high as 140 kg cm−3 or 1029 cm−3. This means that D(−1) will be very useful as a target fuel, circumventing the complex and unstable laser compression stage. We show that the material is stable apart from the oscillation between two forms, and can exist for days in the laboratory environment. We also demonstrate that an amount of D(−1) corresponding to tens of kilojoules is produced in each experiment. This may be sufficient for break-even.
Structural and optoelectronic properties of germanium-rich islands grown on silicon using molecular beam epitaxy
Authors: Nataraj L. , Sustersic N. , Coppinger M. , Gerlein L. F. , Kolodzey J. , Cloutier S. G.
Published: March 2010

We report on the structural and optoelectronic properties of self-assembled germanium-rich islands grown on silicon using molecular beam epitaxy. Raman, photocurrent, photoluminescence, and transient optical spectroscopy measurements suggest significant built-in strains and a well-defined interface with little intermixing between the islands and the silicon. The shape of these islands depends on the growth conditions and includes pyramid, dome, barn-shaped, and superdome islands. Most importantly, we demonstrate that these germanium-rich islands provide efficient light emission at telecommunication wavelengths on a complementary metal-oxide semiconductor-compatible platform.
Skin, Affect, Aggregation: Guattarian Variations on Fanon
Authors: Saldanha Arun
Published: March 2010

Geography has turned to phenomenology, poststructuralism, and psychoanalysis to understand human bodies in non-Cartesian terms as always-already positioned within social formations. But how exactly do we conceive of the constitution of many bodies at once? Specifically, how do bodies ‘aggregate’ into racial formations? ‘The body’ is not a target of socialization—racializing, gendering, disciplining—as if it sits alone until its senses and viscera are stirred by the environment. Bodies never come alone. Racial formations are from the start phenomena of collective embodiment, not ideological structures that secondarily have corporeal effects. In this paper I will argue that racial difference (like all social relations) is a reality involving the interactions, imaginations, and biologies of human bodies. First, Frantz Fanon's influential theory of racialization and racial difference is recast in an embodied framework through one of his own examples. This framework will be construed through the concept of affect in Baruch Spinoza, the phenomenology of Michel Henry, and the ‘machinic’ approach to psychoanalysis suggested by Félix Guattari. Aggregation is thereafter explained through the contemporary Spinozism of Antonio Negri and population biology. Finally, the political implications of a machinic theory of race are explored using another concrete example from Fanon.
Inextinguishable Fibres: Demolition and the Vital Materialisms of Asbestos
Authors: Gregson Nicky , Watkins Helen , Calestani Melania
Published: March 2010

This paper forwards a performative reading of asbestos in economies of disposal. It argues that materials need to be thought through transformative states, not just stable states, and that materials’ performativity varies according to material states. As a radical intervention in form, demolition is one such transformative state, which disturbs and animates materials. Relatively unconsidered in the academic literature, demolition is argued to be the means to an endless source of surprise in the built environment as well as a singular and multiple practice entailing the dissolution of form, the purposeful reduction and dismantling of large-scale objects, salvage and remediation work, and a host of micropractices, including cutting, tearing, sorting, and separating. The paper illustrates asbestos' interventions in demolition activities, using as its exemplar the case of ship breaking in the EU. More broadly, the paper works with asbestos to show that material properties are not fixed but processual, relational, and distributed. The paper also flags some key questions for the emergent debate on vital materialisms, highlighting the difficulties materials like asbestos pose for thinking through enchantment and generosity; the importance of thinking a vital materialism through remediation as well as salvage; and the need to extend an ethics founded on generosity to encompass respect, humility, responsibility, and surprise towards those materials that most threaten human life.
Stakeholders' views on the routine use of n-of-1 trials to improve clinical care and to make resource allocation decisions for drug use
Authors: Nikles Jane , Mitchell Geoffrey K. , Clavarino Alexandra , Yelland Michael J. , Del Mar Christopher B.
Published: March 2010

N-of-1 trials are empirical formal tests using a within-patient randomised, double-blind, cross-over comparison of drug and placebo (or another drug), which we adapted to study individual patients’ responses as a clinical tool to guide clinical management. We administered semi-structured interviews to gauge stakeholder perspectives on the possibility of using routine n-of-1 trials for this purpose. Stakeholders included government and non-government health care sector, and patient, clinician and consumer, organisations. Stakeholders supported more widespread implementation of n-of-1 trials, in a targeted fashion, with some caveats. Barriers to their widespread implementation included constraints on doctors’ time, doctors’ acceptance, drug company acceptance, patient willingness, and cost. Strategies for overcoming barriers included conditional Pharmaceutical Benefits Scheme listing if cost-effective. There was little consensus on which model of n-of-1 trial implementation would be most effective. We discuss different approaches to addressing the several concerns raised to enable widespread introduction of n-of-1 trials into routine clinical practice as a decision tool.
What is known about the topic?No previous publications have explored methods of implementation and gathered stakeholder’s views on widespread use of n-of-1 trials.
What does this paper add?N-of-1 trials could have a role in making resource allocation decisions for medications, and in guiding treatment choices for patients.
What are the implications for practitioners?There is potential for n-of-1 trials to be used more widely, including as part of normal medical practice for targeted illnesses and groups of patients. This could deliver clinical and economic benefits throughout the health care system.
Spirituality and health: an exploratory study of hospital patients' perspectives
Authors: Hilbers Julieanne , Haynes Abby S. , Kivikko Jennifer G.
Published: March 2010

The relationship between spirituality/religion and health is receiving increasing academic interest, but few studies have explored the experience of Australians. This paper presents data from an exploratory survey of patients and families in a public teaching hospital in Sydney. The findings show that the majority of hospital service users: •believe there are links between spirituality/religion and health; •believe that rituals and customs can help people when they are sick/suffering; •have valued practices associated with their beliefs; •feel it is helpful for health staff to know their patients’ beliefs; •are willing to be asked about their beliefs; or •want hospital staff to respect and support the beliefs and practices of all patients. Spirituality and religion, and the beliefs and practices associated with them, were found to be eclectic, individualised and evolving in response to life events such as loss and health crises. This paper concludes that a person-centred framework of health practice includes attention to the religious/spiritual dimension of patients and their families. What is known about the topic?There is a rapidly developing body of research that demonstrates an increasing awareness of the important links between religion and health, but is limited in Australian application. What does this paper add?This paper provides contextually relevant qualitative and quantitative data on patient perspectives, including how patients wish to be treated by health staff in relation to their beliefs and practices. The Australian perspective also provides a valuable counterpoint to US-dominated research in the global community. What are the implications for practitioners?The research findings indicate that practitioners need to recognise and respond to the role of religious and spiritual beliefs and practices in patients’ health journeys. The discussion suggests some practical ways of doing this which sit comfortably within the patient-centred approach.
A population study on Indigenous hospitalisations for interpersonal violence
Authors: Meuleners Lynn B. , Lee Andy H. , Hendrie Delia , Fraser Michelle
Published: March 2010

Indigenous people experience a disproportionately high burden of interpersonal violence. This paper compares the demographic characteristics and injury circumstances of male and female Indigenous Australians hospitalised due to interpersonal violence in Western Australia over a 15-year period. A population-based, retrospective study of all hospitalisations due to interpersonal violence for Indigenous people in WA was undertaken using the linked 1990–2004 data from the WA Mortality Database and the Hospital Morbidity Data System. The majority of Indigenous hospitalisations were for females (56.3%). Female victims were more likely to be admitted due to maltreatment and rape (11.9%). Age profiles, residential location and length of hospital stay were similar between both sexes. The results indicate higher rates of hospitalisation and readmissions for interpersonal violence in WA among Indigenous females than males. There may potentially be different risk factors for each sex and further investigation will have public health benefits. What is known about the topic?Indigenous people experience a disproportionately high burden of interpersonal violence compared with non-Indigenous people. In contrast to the general population, Indigenous females are hospitalised for interpersonal violence at a higher rate than their male counterparts. What does this paper add?This study used population-based data to compare the different characteristics between Indigenous male and female hospitalisations due to interpersonal violence in Western Australia. Females were hospitalised at nearly 1.3 times the rate of males and comprised the majority (65%) of hospitalisations for those admitted more than once. What are the implications for practitioners?The results provide policy makers and planners with a basis for making informed decisions on where to specifically target resources so as to reverse the increasing burden of interpersonal violence on Indigenous communities. In addition, more rigorous prospective investigation is required to determine the contributing factors of interpersonal violence hospitalisations for Indigenous people.
Getting evidence into obstetric practice: appropriate timing of elective caesarean section
Authors: Nicholl Michael C. , Cattell Miriam A.
Published: March 2010

There is considerable variation in the timing of elective pre-labour caesarean section at term where there is no immediate threat to the life of the mother or baby. Given the outcomes, elective or pre-labour caesarean section ought not be offered or performed before 39 completed weeks’ gestation. Primary data sources indicated that the rate of term elective caesarean sections with no medical indication undertaken before 39 weeks’ gestation at our institution was ~30% in 2005 and 2006. A project was undertaken during the 6-month period from March 2007 to August 2007 with the aim of reducing this rate to 10%. Over the 6-month period, the rate of elective caesarean section with no medical indication done before 39 weeks’ gestation in the target group fell to 10%. Over the same timeframe the number of admissions to the neonatal nursery of term babies born by caesarean section at less than 39 weeks fell to zero. Although the numbers are small and not statistically significant, this work suggests implementation across larger jurisdictions or states could result in significant improvements in clinical outcomes.
What is known about the topic? The risk of neonatal respiratory morbidity is increased in babies born by caesarean section before labour, but this risk decreases after 39 completed weeks’ gestation.
What does this paper add? This case study reports on a project that was successful in reducing the number of caesarean sections with no medical indication undertaken before 39 weeks’ gestation, with a corresponding decrease in neonatal nursery admissions.
What are the implications for practitioners?A change in the booking process, with empowerment of delivery suite staff to refer on to the Clinical Director any booking for a caesarean section where there was no clinical indication for delivery before 39 weeks’ gestation, may be a useful tactic in other hospitals.
Over the rainbow: direct payments and social inclusion
Authors: Donoghue Jed , Taylor Chris
Published: March 2010

This paper examines the impact of direct payments on social isolation. We define what social isolation means, and then evaluate the role of direct payments in the provision of social services in the United Kingdom. Social isolation is a particular problem for older people. In Australia there are an increasing number of older residents who are isolated, but would benefit from having greater choice in terms of how they access and receive social services. Increased access to direct payments could help to reduce waiting lists for traditional social services and address gaps in service provision.
What is known about the topic?International research indicates that in some cases direct payments or self-directed service provision helps to reduce social isolation.
What does this paper add?The authors argue that based on the available evidence, a system incorporating direct payments would have health benefits for older adults living in the community.
What are the implications for practitioners?The paper concludes by suggesting that directs payments have the capacity to reduce social isolation in Australia.
Talking EPC - speech pathologists' views of the Enhanced Primary Care items four years on
Authors: Skeat Jemma , Morgan Angela , Nickless Tristan
Published: March 2010

Background.Allied health professionals have provided services under Enhanced Primary Care (EPC) since 2004; however, the experiences and views of AHPs about the initiative and how it has been utilised have not been well explored. Objective.We examined speech pathologists’ views and experiences under EPC. Methods.A survey of speech pathologists in private practice who provide services under EPC was undertaken. Results.Speech pathologists provide EPC services to a wide range of clients with communication and swallowing disorders. The five EPC sessions provide a ‘starting point’ for therapy for some clients, and supplement existing therapy for others. Speech pathologists expressed concern about the accessibility of the program, and its understanding and use in practice, but noted that the program can be valuable for clients who are able to negotiate the hurdles, and for themselves in terms of increased referrals and collaboration with general practitioners. Conclusions.Education around eligibility, access, and reporting requirements is needed for clients, GPs and allied health professionals in order to reduce the frustrating aspects of this program, and support its ongoing use. What is known about the topic?The Enhanced Primary Care (EPC) program relies on collaboration between general practitioners and allied health professionals, and aims to improve the management of chronic and complex conditions in the community. The experiences and views of allied health professionals (AHPs) in implementing the EPC program since 2004 are important to inform evaluation of the effectiveness, usefulness and value of the program. What does this paper add?We explored speech pathologists’ perspectives on EPC, including their experiences and views about the program. The paper informs understanding of the use of EPC in practice, for example, how sessions are provided to clients over the 12-month period, as well as how those who use it – allied health professionals – perceive the value and practicality of this program. What are the implications for practitioners?Education for GPs, clients and AHPs is needed to facilitate a more efficient and effective use of EPC. Policy makers should consider the views and experiences of AHPs when reviewing the EPC initiative, in order to understand aspects such as the accessibility of the programs for clients, and the perceived value for AHPs.
The future of community-centred health services in Australia: lessons from the mental health sector
Authors: Rosen Alan , Gurr Roger , Fanning Paul
Published: March 2010

•It is apparent that hospital-dominated health care produces limited health outcomes and is an unsustainable health care system strategy. •Community-centred health care has been demonstrated to be a more cost-efficient and cost-effective alternative to hospital-centred care, particularly for prevention and care of persistent, long-term or recurrent conditions. Nevertheless, hospital-centred services continue to dominate health care services in Australia, and some state governments have presided over a retreat from, or even dismantling of, community health services. •The reasons for these trends are explored. •The future of community health services in Australia is uncertain, and in some states under serious threat. We consider lessons from the partial dismantling of Australian community mental health services, despite a growing body of Australian and international studies finding in their favour. •Community-centred health services should be reconceptualised and resourced as the centre of gravity of local, effective and affordable health care services for Australia. A growing international expert consensus suggests that such community-centred health services should be placed in the centre of their communities, closely linked or collocated where possible with primary health care, and functionally integrated with their respective hospital-based services. What is known about the topic?Community-centred health care has been widely demonstrated to be a more cost-efficient and cost-effective alternative to hospital-centred care, particularly for prevention and care of persistent, long-term or recurrent conditions, e.g. in mental health service systems. A growing international expert consensus suggests that such community-centred health services should be placed in the centre of their communities, closely linked or collocated where possible with primary health care, and functionally integrated with their respective hospital-based services. What does this paper add?Despite this global consensus, hospital-centred services continue to dominate health care services in Australia, and some state governments have presided over a retreat from, or even dismantling of, community health services. The reasons for these trends and possible solutions are explored. What are the implications for practitioners?Unless this trend is reversed, the loss of convenient public access to community health services at shopping and transport hubs and the consequent compromising of intensive home-based clinical care, will lead to a deterioration of preventative interventions and the health care of long-term conditions, contrary to international studies and reviews.
Concentration Depth Profiles of Inorganic Ions at Liquid Surfaces
Authors: Andersson Gunther
Published: March 2010

For a decade, it has been discussed whether or not inorganic ions like iodide or bromide adsorb preferentially at liquid surfaces. Thermodynamic relationships cannot be used to derive detailed information about the molecular structure of surfaces. Thus, it is import to investigate the structure of liquid surfaces directly. Neutral Impact Collision Ion Scattering Spectroscopy is one of the very few techniques that can be used to determine directly the molecular structure of liquid surfaces.
Computational Photobiology and Beyond
Authors: Schapiro Igor , Ryazantsev Mikhail N. , Ding Wan Jian , Huntress Mark M. , Melaccio Federico , Andruniow Tadeusz , Olivucci Massimo
Published: March 2010

In this paper we review the results of a group of computational studies of the spectroscopy and photochemistry of light-responsive proteins. We focus on the use of quantum mechanics/molecular mechanics protocols based on a multiconfigurational quantum chemical treatment. More specifically, we discuss the use, limitations, and application of the ab initio CASPT2//CASSCF protocol that, presently, constitutes the method of choice for the investigation of excited state organic molecules, most notably, biological chromophores and fluorophores. At the end of this Review we will also see how the computational investigation of the visual photoreceptor rhodopsin is providing the basis for the design of light-driven artificial molecular devices.
A phylogenetic analysis for the South-east Asian mite harvestman family Stylocellidae (Opiliones:Cyphophthalmi) – a combined analysis using morphometric and molecular data
Authors: Clouse Ronald M. , de Bivort Benjamin L. , Giribet Gonzalo
Published: March 2010

In an effort to place type specimens lacking molecular data into a phylogenetic framework ahead of a taxonomic revision, we used morphometric data, both alone and in combination with a molecular dataset, to generate phylogenetic hypotheses under the parsimony criterion for 107 members of the South-east Asian mite harvestman family Stylocellidae (Arachnida: Opiliones: Cyphophthalmi). For the morphometric analyses, we used undiscretised characters, analysed for independence and collapsed by principal components analysis (PCA) when dependent. Two challenges not previously encountered in the use of this method were (a) handling terminals with missing data, necessitated by the inclusion of old and damaged type specimens, and (b) controlling for extreme variation in size. Custom scripts for independence analysis were modified to accommodate missing data whereby placeholder numbers were used during PCA for missing measurements. Size was controlled in four ways: choosing characters that avoided misleading size information and were easily scaled; using only locally scaled measurements; adjusting ratios by y-intercepts; and collapsing dependent characters into one. These steps removed enough size information that miniaturised and large species, suspected from molecular and discrete morphological studies to be closely related, were closely placed using morphometric data alone. Both morphometric and combined analyses generated relationships that positioned type specimens in agreement with taxonomic expectations and our knowledge of the family from prior studies. The hypotheses generated here provide new direction in linking molecular analyses with established taxonomy in this large group of South-east Asian arachnids.
The economic implications of alternative publishing models
Authors: Houghton John W. , Oppenheim Charles
Published: March 2010

A knowledge economy has been defined as one in which the generation and exploitation of knowledge has come to play the predominant part in the creation of wealth. It is not simply about pushing back the frontiers of knowledge; it is also about the more effective use and exploitation of all types of knowledge in all manner of economic activities. One key question is whether there are new opportunities and new models for scholarly publishing that might better serve researchers and more effectively communicate and disseminate research findings. Building on previous work, this paper looks at the costs and potential benefits of alternative models for scientific and scholarly publishing, describing the approach and methods used and summarising the findings of a study undertaken for the Joint Information Systems Committee (JISC) in the United Kingdom. It concludes that different publishing models can make a material difference to the costs faced and benefits realised from research communication, and it seems likely that more open access to findings from publicly funded research would have substantial net benefits.
Is grammaticality inferred from global similarity? Comment on Jamieson and Mewhort (2009)
Authors: Kinder Annette
Published: March 2010

In a recent article, Jamieson and Mewhort (2009) proposed a novel account of artificial grammar learning (AGL), which is based on a multitrace model of episodic memory, the Minerva 2 model. According to this account, test performance in AGL is based on an assessment of global similarity of the test strings to the memory traces of the training strings. In this article, simulation studies are presented, showing for three different AGL experiments that the predictions of the Minerva 2 model strikingly deviate from participants’ performance. It is argued that participants’ test performance is not generally based on general similarity.
Humanities and social science journals: a pilot study of eight US associations
Authors: WALTHAM Mary
Published: March 2010

The paper summarizes the findings of a pilot study for the National Humanities Alliance, including the methodology, research tools, analysis, and initial conclusions about the publishing business of eight association published humanities and social sciences journals in the context of a move to an open access (author/producer pays) publishing model. The eight disciplines represented by these journals are modern languages, history, religion, economics, sociology, anthropology, politics and statistics. Specific tools were developed for the study to enable like‐for‐like comparison of the journals. Detailed information on current trends in revenue, costs, and surplus is included. Significant differences between HSS and STM journals are reviewed. Open access to research articles on publication as the ‘gold’ author/producer‐pays approach would not be sustainable for this sample of HSS journals for reasons articulated in the report. Further studies using the tools and methodology developed are required to broaden and confirm these results.
Book Reviews
Authors: OKERSON Ann
Published: March 2010

Licensing Digital Content: A Practical Guide for Librarians, 2nd edn Lesley Ellen Harris Chicago, American Library Association, 2009, 170 pp. ISBN 9780838909928, US$57, pbk
From Rabbit Reticulocytes to Clam Oocytes: In Search of the System That Targets Mitotic Cyclins for Degradation
Authors: Hershko Avram
Published: March 2010

By the late 1980s, the basic biochemistry of ubiquitin-mediated protein degradation had already been elucidated by studies that used reticulocyte lysates. However, the scope and biological functions of this system remained largely obscure. Therefore, I became interested at that time in the mechanisms by which mitotic cyclins are degraded in exit from mitosis. Using a cell-free system from clam oocytes that faithfully reproduced cell cycle stage–specific degradation of cyclins, we identified in 1995 a large ubiquitin ligase complex that targets mitotic cyclins for degradation. Subsequent studies in many laboratories showed that this ubiquitin ligase, now called the anaphase-promoting complex/cyclosome, has centrally important roles in many aspects of cell cycle control.
The Spectraplakin Short Stop Is an Actin–Microtubule Cross-Linker That Contributes to Organization of the Microtubule Network
Authors: Applewhite Derek A. , Grode Kyle D. , Keller Darby , Zadeh Alireza Dehghani , Slep Kevin C. , Rogers Stephen L.
Published: March 2010

The dynamics of actin and microtubules are coordinated in a variety of cellular and morphogenetic processes; however, little is known about the molecules mediating this cytoskeletal cross-talk. We are studying Short stop (Shot), the sole Drosophila spectraplakin, as a model actin–microtubule cross-linking protein. Spectraplakins are an ancient family of giant cytoskeletal proteins that are essential for a diverse set of cellular functions; yet, we know little about the dynamics of spectraplakins and how they bridge actin filaments and microtubules. In this study we describe the intracellular dynamics of Shot and a structure–function analysis of its role as a cytoskeletal cross-linker. We find that Shot interacts with microtubules using two different mechanisms. In the cell interior, Shot binds growing plus ends through an interaction with EB1. In the cell periphery, Shot associates with the microtubule lattice via its GAS2 domain, and this pool of Shot is actively engaged as a cross-linker via its NH2-terminal actin-binding calponin homology domains. This cross-linking maintains microtubule organization by resisting forces that produce lateral microtubule movements in the cytoplasm. Our results provide the first description of the dynamics of these important proteins and provide key insight about how they function during cytoskeletal cross-talk.
PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene–disease associations
Authors: Denny Joshua C. , Ritchie Marylyn D. , Basford Melissa A. , Pulley Jill M. , Bastarache Lisa , Brown-Gentry Kristin , Wang Deede , Masys Dan R. , Roden Dan M. , Crawford Dana C.
Published: March 2010

Motivation: Emergence of genetic data coupled to longitudinal electronic medical records (EMRs) offers the possibility of phenome-wide association scans (PheWAS) for disease–gene associations. We propose a novel method to scan phenomic data for genetic associations using International Classification of Disease (ICD9) billing codes, which are available in most EMR systems. We have developed a code translation table to automatically define 776 different disease populations and their controls using prevalent ICD9 codes derived from EMR data. As a proof of concept of this algorithm, we genotyped the first 6005 European–Americans accrued into BioVU, Vanderbilt's DNA biobank, at five single nucleotide polymorphisms (SNPs) with previously reported disease associations: atrial fibrillation, Crohn's disease, carotid artery stenosis, coronary artery disease, multiple sclerosis, systemic lupus erythematosus and rheumatoid arthritis. The PheWAS software generated cases and control populations across all ICD9 code groups for each of these five SNPs, and disease-SNP associations were analyzed. The primary outcome of this study was replication of seven previously known SNP–disease associations for these SNPs.

Results: Four of seven known SNP–disease associations using the PheWAS algorithm were replicated with P-values between 2.8 × 10−6 and 0.011. The PheWAS algorithm also identified 19 previously unknown statistical associations between these SNPs and diseases at P < 0.01. This study indicates that PheWAS analysis is a feasible method to investigate SNP–disease associations. Further evaluation is needed to determine the validity of these associations and the appropriate statistical thresholds for clinical significance.

Availability:The PheWAS software and code translation table are freely available at http://knowledgemap.mc.vanderbilt.edu/research.

Contact:  josh.denny@vanderbilt.edu
Bayesian Combination of State Polls and Election Forecasts
Authors: Lock Kari , Gelman Andrew
Published: March 2010

A wide range of potentially useful data are available for election forecasting: the results of previous elections, a multitude of preelection polls, and predictors such as measures of national and statewide economic performance. How accurate are different forecasts? We estimate predictive uncertainty via analysis of data collected from past elections (actual outcomes, preelection polls, and model estimates). With these estimated uncertainties, we use Bayesian inference to integrate the various sources of data to form posterior distributions for the state and national two-party Democratic vote shares for the 2008 election. Our key idea is to separately forecast the national popular vote shares and the relative positions of the states. More generally, such an approach could be applied to study changes in public opinion and other phenomena with wide national swings and fairly stable spatial distributions relative to the national average.
Familial Aggregation in Children Affected by Functional Gastrointestinal Disorders
Authors: Buonavolontà R , Coccorullo P , Turco R , Boccia G , Greco L , Staiano A
Published: March 2010

Background and Aims:

Adults with irritable bowel syndrome may often have a first‐degree relative with abdominal pain and bowel problems. The aims of this study were to evaluate the prevalence of functional gastrointestinal disorders (FGIDs) in parents and siblings of children affected by FGIDs, the psychological profile of both children and parents affected by FGIDs, and whether independent factors could influence the prevalence of FGIDs in parents of children with and without FGIDs.

Subjects and Methods:

One hundred three patients affected by FGIDs according to Rome III criteria and/or their parents and siblings filled out validated questionnaires for gastrointestinal (GI) symptoms, depression, and anxiety. These patients were compared with 65 age‐ and sex‐matched controls referred to the Primary Care Center of the Department of Paediatrics at the University of Naples “Federico II” for non‐GI symptoms.

Results:

The parents of children with FGIDs showed a significantly (P < 0.0001) higher prevalence of FGIDs compared with the parents of children without FGIDs. No significant differences between the groups were observed for marital status, parental occupation, education level, standard of living, and presence of anxiety and/or depression. An association between the children's and their parents' type of GI disorders was found in 33.9% (35/103) of patients. In particular, an association between the children's and mother's type of GI disorders was found in 25.2% (26/103) of patients.

Conclusions:

To our knowledge, our study is the first to demonstrate that a large number of mothers of children with FGIDs have the same FGIDs as their children.
Orange But Not Apple Juice Enhances Ferrous Fumarate Absorption in Small Children
Authors: Balay Kimberly S , Hawthorne Keli M , Hicks Penni D , Griffin Ian J , Chen Zhensheng , Westerman Mark , Abrams Steven A
Published: March 2010

Objective:

Ferrous fumarate is a common, inexpensive iron form increasingly used instead of ferrous sulfate as a food iron supplement. However, few data exist as to whether juices enhance iron absorption from ferrous fumarate.

Subjects and Methods:

We studied 21 children, ages 4.0 to 7.9 years using a randomized crossover design. Subjects consumed a small meal including a muffin containing 4 mg 57Fe as ferrous fumarate and either apple (no ascorbic acid) or orange juice (25 mg ascorbic acid). They were separately given a reference dose of 58Fe (ferrous sulfate) with ascorbic acid.

Results:

Iron absorption increased from 5.5% ± 0.7% to 8.2% ± 1.2%, P < 0.001 from the muffins given with orange juice compared with muffins given with apple juice. The absorption of ferrous fumarate given with orange juice and enhancement of absorption by the presence of juice were significantly positively related to height, weight, and age (P < 0.01 for each). Although iron absorption from ferrous fumarate given with apple juice was significantly inversely associated with the (log transformed) serum ferritin, the difference in absorption between juice types was not (P > 0.9).

Conclusions:

These data demonstrate an overall benefit to iron absorption from ferrous fumarate provided with orange juice. The effect was age related such that in children older than 6 years of age, there was a nearly 2‐fold increase in iron absorption from ferrous fumarate given with orange juice.
Home Management of Acute Diarrhoea in Czech Children
Authors: Kudlova Eva
Published: March 2010

Objectives:

The aim of the study was to investigate home management of childhood acute diarrhoea.

Methods:

A cross‐sectional questionnaire study was conducted in Prague, Czech Republic. The caregivers of 210 children ages 6 to 59 months were approached in public places and interviewed about the knowledge and use of oral rehydration solution (ORS) and about management of the child's last episode of diarrhoea.

Results:

Maternal knowledge of ORS (27.6%) and ORS use (1.9% during the child's last episode of diarrhoea) were low. They were positively associated with education level but not with the source of advice. Small volumes of ORS given and its refusal were issues. Increased amounts of fluid offered to 60% of children were significantly associated with higher maternal education and relatives/friends (76%) as a source of advice rather than a paediatrician (57.9%), the most frequent source of advice (78.1%). Black tea was the most common fluid given (86.2%) followed by plain or mineral water (41.9%). Breast‐feeding of all breast‐fed children was continued; low‐lactose formula was given in 1 case only. Withholding food was rare (5.2%), but the diet of 75.2% cases was modified. Drugs were given to 52.4% children, most frequently smectite and/or probiotics, and antimicrobials were given to 6.4% cases.