bluuebunny/crossref_metadata_2025 huggingface dataset:
Chondrule trace element geochemistry at the mineral scale
Authors: JACQUET Emmanuel , ALARD Olivier , GOUNELLE Matthieu
Published: December 2012

Abstract– We report trace element analyses from mineral phases in chondrules from carbonaceous chondrites (Vigarano, Renazzo, and Acfer 187), carried out by laser ablation inductively coupled plasma‐mass spectrometry. Results are similar in all three meteorites. Mesostasis has rare earth element (REE) concentrations of 10–20 × CI. Low‐Ca pyroxene has light REE (LREE) concentrations near 0.1 × CI and heavy REE (HREE) near 1 × CI, respectively. Olivine has HREE concentrations at 0.1–1 × CI and LREE around 10−2 × CI. The coarsest olivine crystals tend to have the most fractionated REE patterns, indicative of equilibrium partitioning. Low‐Ca pyroxene in the most pyroxene‐rich chondrules tends to have the lowest REE concentrations. Type I chondrules seem to have undergone a significant degree of batch crystallization (as opposed to fractional crystallization), which requires cooling rates slower than 1–100 K h−1. This would fill the gap between igneous calcium‐aluminum‐rich inclusions (CAIs) and type II chondrules. The anticorrelation between REE abundances and pyroxene mode may be understood as due to dilution by addition of silica to the chondrule melt, as in the gas‐melt interaction scenario of Libourel et al. (2006). The rapid cooling rate (of the order of 1000 K h−1) which seems recorded by low‐Ca pyroxene, contrasted with the more diverse record of olivine, may point to a nonlinear cooling history or suggest that formation of pyroxene‐rich chondrule margins was an event distinct from the crystallization of the interior.
HIV and the Moral Economy of Survival in an East African City
Authors: Prince Ruth
Published: December 2012

Based on fieldwork in the city of Kisumu, Kenya, the article examines the survival of HIV‐positive people on antiretroviral (ARV) medicines and situates this within broader moral economies of their lives—in matters of food, hunger, social relationships, and networks of care, including NGOs. Through locating survival at the level of individual adherence to medication, ARV programs medicalize it. Yet their focus on the intimate relation between medicine and food also opens up spaces in which the material conditions of life can be articulated. The article follows these spaces, from the clinic to the economy of NGO interventions and community‐based groups, paying attention to how hunger and material needs are visible in some spaces and invisible in others, and to how people have learned to articulate their “needs.” In this economy, HIV identities accrue moral and economic value, as through them people become visible to the flow of funds and the distribution of goods organized by NGOs.
Viability: A Cultural Calculus of Personhood at the Beginnings of Life
Authors: Christoffersen‐Deb Astrid
Published: December 2012

This article addresses birth and the recognition of personhood. It is about the calculated acts of recognition that take place at the beginnings of life when the obligation to protect and extend physical care is uncertain. It examines these dilemmas from the perspective of clinicians and scientists who assist in birth through their work with embryos, fetuses, and extremely premature infants in the United States. Through multisited ethnography and in‐depth interviews at a leading U.S. teaching hospital, this article argues that the concept of viability operates as a placeholder for the recognition of personhood at the beginnings of life. Articulated in a language of survival and stratified by gestational age, this article explores how viability is a central organizing principle in the management of birth. It aims to situate questions about the value of life to the maternity unit where patients and clinicians face choices about the kinds of viability—and as a result persons—that are possible and desired within the contemporary culture of hospital births.
Beyond an AFLP genome scan towards the identification of immune genes involved in plague resistance in Rattus rattus from Madagascar
Authors: Tollenaere C. , Jacquet S. , Ivanova S. , Loiseau A. , Duplantier J.‐M. , Streiff R. , Brouat C.
Published: December 2012

Genome scans using amplified fragment length polymorphism (AFLP) markers became popular in nonmodel species within the last 10 years, but few studies have tried to characterize the anonymous outliers identified. This study follows on from an AFLP genome scan in the black rat (Rattus rattus), the reservoir of plague (Yersinia pestis infection) in Madagascar. We successfully sequenced 17 of the 22 markers previously shown to be potentially affected by plague‐mediated selection and associated with a plague resistance phenotype. Searching these sequences in the genome of the closely related species Rattus norvegicus assigned them to 14 genomic regions, revealing a random distribution of outliers in the genome (no clustering). We compared these results with those of an in silico AFLP study of the R. norvegicus genome, which showed that outlier sequences could not have been inferred by this method in R. rattus (only four of the 15 sequences were predicted). However, in silico analysis allowed the prediction of AFLP markers distribution and the estimation of homoplasy rates, confirming its potential utility for designing AFLP studies in nonmodel species. The 14 genomic regions surrounding AFLP outliers (less than 300 kb from the marker) contained 75 genes encoding proteins of known function, including nine involved in immune function and pathogen defence. We identified the two interleukin 1 genes (Il1a and Il1b) that share homology with an antigen of Y. pestis, as the best candidates for genes subject to plague‐mediated natural selection. At least six other genes known to be involved in proinflammatory pathways may also be affected by plague‐mediated selection.
Differential introgression reveals candidate genes for selection across a spruce (Picea sitchensis × P. glauca) hybrid zone
Authors: Hamilton Jill A. , Lexer Christian , Aitken Sally N.
Published: December 2012

Differential patterns of introgression between species across ecological gradients provide a fine‐scale depiction of extrinsic and intrinsic factors that contribute to the maintenance of species barriers and adaptation across heterogeneous environments.

Introgression was examined for 721 individuals collected from the ecological transition zone spanning maritime to continental climates within the Picea sitchensis–Picea glauca contact zone using a panel of 268 candidate gene single nucleotide polymorphisms.

Geographic clines showed a strong spatial relationship between allele frequencies and both distance from the ocean along major rivers and mean annual precipitation, indicating a strong role for environmental selection. Interspecific patterns of differentiation using outlier tests revealed three candidate genes that may be targets of long‐term divergent selection between the parental species, although contemporary genomic clines within the hybrid zone suggested neutral patterns of introgression for these genes.

This study provides a fine‐scale analysis of locus‐specific introgression, identifying a suite of candidate loci that may be targets of extrinsic or intrinsic selection, with broad application in understanding local adaptation to climate.
Identification and mapping of adult‐plant stripe rust resistance in soft red winter wheat cultivar ‘USG 3555’
Authors: Christopher Mark D. , Liu Shuyu , Hall Marla D. , Marshall David S. , Fountain Myron O. , Johnson Jerry W. , Milus Eugene A. , Garland‐Campbell Kimberly A. , Chen Xianming , Griffey Carl A.
Published: December 2012

Little is known about the extent or diversity of resistance in soft red winter wheat (Triticum aestivum L.) to stripe rust, caused by the fungal pathogen Puccinia striiformis f.sp. tritici. The soft red winter (SRW) wheat cultivar ‘USG 3555’ has effective adult‐plant resistance to stripe rust, which was characterized in a population derived from ‘USG 3555’/‘Neuse’. The mapping population consisted of 99 recombinant inbred lines, which were evaluated for stripe rust infection type (IT) and severity to race PST‐100 in field trials in North Carolina in 2010 and 2011. Genome‐wide molecular‐marker screenings with 119 simple sequence repeats and 560 Diversity Arrays Technology (DArT) markers were employed to identify quantitative trait loci (QTL) for stripe rust resistance. QTL on chromosomes 1AS, 4BL and 7D of ‘USG 3555’ explained 12.8, 73.0 and 13.6% of the variation in stripe rust IT, and 13.5, 72.3 and 10.5% of the variation in stripe rust severity, respectively. Use of these and additional diagnostic markers for these QTL will facilitate the introgression of this source of stripe rust resistance into SRW wheat lines via marker‐assisted selection.
Down‐regulation of catalase activity allows transient accumulation of a hydrogen peroxide signal in Chlamydomonas reinhardtii
Authors: MICHELET LAURE , ROACH THOMAS , FISCHER BEAT B. , BEDHOMME MARIETTE , LEMAIRE STÉPHANE D. , KRIEGER‐LISZKAY ANJA
Published: December 2012

We provide evidence that a floodgate mechanism of ROS signalling that had been proposed to occur in mammalian cells may also take place in Chlamydomonas reinhardtii. When cells of C. reinhardtii were shifted from dark to high light, a transient increase in the level of hydrogen peroxide was observed which correlated with a reversible partial inactivation of catalase activity. This transient increase in the
H2O2 level seems to allow to activate H2O2‐dependent signaling pathways since changes in the expression level of H2O2 responsive genes such as HSP22C tightly followed the peak of H2O2.
The Photochemistry of Thymine in Frozen Aqueous Solution: Trimeric and Minor Dimeric Products
Authors: Shetlar Martin D. , Basus Vladimir J.
Published: December 2012

Early work identified three compounds, namely the c,s cyclobutane dimer, the so‐called (6‐4) photoproduct (5‐hydroxy‐6‐4′‐(5‐methylpyrimidin‐2′‐one)‐5,6‐dihydrothymine) and a trimer hydrate, as products formed upon UV irradiation of thymine in frozen aqueous solution. More recent work has shown that an (α‐4) product, namely α‐4′‐(5′‐methylpyrimidine‐2′‐one)‐thymine, is a likely product formed under these reaction conditions. During a thorough reinvestigation of the photochemistry of Thy in ice at −78.5°C, we found that a variety of other products could be detected. In addition to the c,s dimer, the other three known cyclobutane dimers, namely the c,a, t,s and t,a forms, are produced, although in considerably smaller amounts. The so‐called “spore product” of thymine (5,6‐dihydro‐5‐(α‐thyminyl)thymine) is likewise formed. Two other dimers have been identified as minor products; one of these has been determined to be 5‐(thymin‐3‐yl)‐5,6‐dihydrothymine and the other has been tentatively assigned to be a (5‐4) adduct (6‐hydroxy‐5‐4′‐(5‐methylpyrimidin‐2′‐one)‐5,6‐dihydrothymine). Compounds with the behavior expected of true trimeric compounds have been isolated via HPLC and characterized by mass spectrometry and photochemical behavior. One of these materials, putatively containing an oxetane ring, decomposes thermally to a secondary trimeric product that is then converted into the known trimer hydrate.
From support to pressure: The dynamics of social and governmental influences on environmental law enforcement inGuangzhouCity,China
Authors: Van Rooij Benjamin , Fryxell Gerald E. , Lo Carlos Wing‐Hung , Wang Wei
Published: December 2012

This paper examines how changes in governmental and social influences affect environmental enforcement in Guangzhou city, China, between 2000 and 2006. The paper finds that a form of “decentered regulation” has developed. Regulatory enforcement is no longer the sole affair of the government and the regulatory bureaucracy, but has been increasingly influenced by societal forces. The transformation over time shows the promises and limits of decentered regulation in Guangzhou's dynamic authoritarian setting. Analyzing a set of longitudinal survey data and qualitative interviews, the paper finds that by 2006, the rise of civil society and its increased support for protecting the environment had a double‐edged impact on the enforcement of environmental regulations. The paper demonstrates that on the one hand, by 2006, when government support for enforcement was low, societal forces developed an ability to counterbalance such lack of governmental support and positively influence enforcement. However, it also shows that when government support was high, a concurrent rise in societal support created a negative effect on enforcement. Thus too much societal support can become an enforcement burden.
Interleukin‐10 Gene Promoter and NFKB1 Promoter Insertion/Deletion Polymorphisms in Systemic Sclerosis
Authors: Salim P. H. , Jobim M. , Bredemeier M. , Chies J. A. B. , Brenol J. C. T. , Jobim L. F. , Xavier R. M.
Published: December 2012

Systemic sclerosis (SSc) is a connective tissue disease characterized by fibrotic, immunological and vascular abnormalities. Nuclear factor‐kB (NFKB), as a key transcription factor involved in the regulation of immune responses, appears to be a good candidate for studies on the pathogenesis of autoimmune diseases, as well as the interleukin‐10 (IL‐10) polymorphism, which other studies have suggested an association with SSc. Our objective was to study the association of NFKB and IL‐10 gene polymorphisms with SSc. One hundred and fifty‐one SSc patients and 147 healthy bone marrow donors were enrolled in a case–control study. Blood was collected for DNA extraction; typing of IL‐10 genes was made by polymerase chain reaction with sequence‐specific primers (PCR–SSP), and NFKB gene typing was made by restriction fragment length polymorphism (RFLP). Patients underwent clinical evaluation, serology, Doppler echocardiography and chest high‐resolution computed tomography. The frequency of IL‐10 (−1082) GG genotype was found to be significantly higher in SSc patients (36.4%) as compared to healthy controls (22.4%) (P = 0.012). The frequency of heterozygous genotype GA was significantly lower (P = 0.004) in patients (38.4%) in comparison with control subjects (55.8%). A predominance of the high‐producing IL‐10 phenotype (GCC+/GCC+) was observed in SSc patients compared with healthy controls (37.7% versus 24.5%, respectively; OR: 1.87, 95% CI: 1.10–3.19, P = 0.019). No significant difference was found in the allelic and genotype distribution of the NFKB promoter polymorphism between patients and controls. No statistically significant associations were found between IL‐10 or NFKB polymorphisms clinical and laboratory features of SSc. Our results confirmed the association of the high‐producing phenotype (GCC+/GCC+) with increased risk for SSc, but found no correlation with NFKB polymorphisms.
Whither Tobacco Studies?
Authors: Bell Kirsten
Published: December 2012

In recent years, tobacco research has become an increasingly politicized field, with ‘legitimate’ research on this topic expected to further the goals of tobacco control. This paper presents an overview of the state of field of social science studies on tobacco and critiques the growing polarity evident in scholarship on this topic. Moving beyond mainstream public health perspectives, I outline a body of research that challenges dominant understandings of tobacco use and tobacco control. This research can be classified into three main categories: studies that interrogate conceptions of why people smoke, those that examine the impacts of tobacco control policy on smokers, and studies embracing intellectual and philosophical perspectives (especially phenomenology and social constructionism) that place them outside of a public health frame. I end with a broader discussion of the growing instrumentalization of social science research and the need to resist prescriptions that seek to dictate the appropriate form and content of scholarly work.
ScRALF3, a secreted RALF‐like peptide involved in cell–cell communication between the sporophyte and the female gametophyte in a solanaceous species
Authors: Chevalier Eric , Loubert‐Hudon Audrey , Matton Daniel P.
Published: December 2012

Small peptides have been shown to regulate numerous aspects of plant development through cell–cell communication. These signaling events are particularly important during reproduction, regulating gamete development and embryogenesis. Rapid alkalinization factor (RALF)‐like genes, a large gene family that encodes secreted peptides, have specific or ubiquitous expression patterns. Previously, five RALF‐like genes with potential involvement during reproduction were isolated from Solanum chacoense. Here, we show that ScRALF3 is an important peptide regulator of female gametophyte development. Its expression, which is auxin‐inducible, is strictly regulated before and after fertilization. Down‐regulation of ScRALF3 expression by RNA interference leads to the production of smaller fruits that produce fewer seeds, due to improper development of the embryo sacs. Defects include loss of embryo sac nuclei polarization, as well as an increase in asynchronous division, accounting for cellular dysfunctions and premature embryo sac development arrest during megagametogenesis. ScRALF3 is expressed in the sporophytic tissue surrounding the embryo sac, the integument and the nucellus, as revealed by in situ hybridization and GUS staining. As expected for a secreted peptide, fluorescence from an ScRALF3–GFP fusion construct is detected throughout the secretory pathway. Therefore, the ScRALF3 secreted peptide may be directly involved in the regulation of multiple aspects of cell–cell communication between the female gametophyte and its surrounding sporophytic tissue during ovule development.
Dihedral Iwasawa theory of nearly ordinary quaternionic automorphic forms
Authors: Fouquet Olivier
Published: December 2012

Letπ(f) be a nearly ordinary automorphic representation of the multiplicative group of an indefinite quaternion algebraBover a totally real fieldFwith associated Galois representationρf. LetKbe a totally complex quadratic extension ofFembedding inB. Using families of CM points on towers of Shimura curves attached toBandK, we construct an Euler system forρf. We prove that it extends top-adic families of Galois representations coming from Hida theory and dihedral ℤdp-extensions. When this Euler system is non-trivial, we prove divisibilities of characteristic ideals for the main conjecture in dihedral and modular Iwasawa theory.
THE ETHNOGRAPHICISATION OF ANGLO-AMERICAN ANTHROPOLOGY:CAUSES AND CONSEQUENCES
Authors: Urry James
Published: December 2012

Anthropology, at least in terms of its emphasis on social and cultural life, is noted both within and outside the discipline for the quality of its ethnography. Ethnography, however, has come to mean different things within and outside anthropology. One dominant understanding is associated with ethnography as a distinct methodology involved with qualitative, local level research. Another concerns the product of such research – ethnographic accounts of social and cultural groups including the form of such texts as literary objects. How ethnography developed in the British and American traditions reveals how the discipline became more focussed on methodology and text than on theory. The contexts of this shift and its consequences for anthropological practice are considered with a suggestion that perhaps anthropologists are really ethnographers, not anthropologists, and perhaps a broader view of anthropology needs to be rediscovered.
THE LIMITS OF ETHNOGRAPHY VERSUS THE POVERTY OF THEORY:PATRON-CLIENT RELATIONS IN EUROPE RE-VISITED
Authors: Shore Cris
Published: December 2012

Calls for anthropology to move ‘beyond ethnography’ are not new, but the
frequency of their utterance suggests that they tend to go unheeded. A question increasingly asked today is ‘is it possible to do ethnography on an awkward scale’? (Comaroff and Comaroff 2003). In our increasingly globalized world, the material and moral conditions that animate local events are not easily captured by the ethnographer’s lens. In a recent critique, Paul Willis (2002) chastises anthropology for its lingering empiricism and persistent humanism, concluding with a plea for more ‘theoretically informed ethnographic studies’. This paper shares these concerns. Too often ‘social anthropology’ (the study of
human cultures and societies in its broadest sense) is conflated with ‘ethnography’, understood either as the process of participant-observation or fieldwork, or as the textual product arising from that experience: a case of the methodological tail wagging the theoretical dog. This paper sets out to demonstrate why going ‘beyond ethnography’ is necessary if we are to transcend the constraints of empiricism and make sense of wider socio-cultural patterns and processes. I illustrate my argument by reference to the European Commission, the European Union’s civil service, and the strengths and limitations of ethnography for understanding its complexity. While most local, ‘insider’ and ethnographic
accounts highlight the hybrid nature and ‘uniqueness’ of the Commission’s organizational culture – and still define the EU as an ‘inter-governmental’ body – I argue that a very different picture emerges when we use a wider theoretical lens that takes into account class and political economy perspectives. I also show how debates over EU institutions recall anthropological arguments over the analysis of patron-client relations: i.e. what appears from an ethnographic perspective as a loose set of inter-personal ties between individuals of unequal status and wealth often turns out to be, on reflection, an emergent class system and the beginnings of a process of state-formation.
THE ANTHROPOLOGIST AS CITIZEN
Authors: Metge Joan
Published: December 2012

In the ASAANZ’s Principles of Professional Responsibility ‘responsibility to the wider society’ comes second, immediately after ‘responsibility to research participants’. Anthropologists have a range of responsibilities to the wider society, including, but not restricted to, the responsibility of social criticism. Drawing on my own experience, I explore the varied history, difficulties and dilemmas of our attempts to carry out our responsibilities as citizens.
TURNING THE SUPER TANKER:BEYOND ETHNOGRAPHY AND INTO COLLABORATIVE LEARNING APPROACHES TO URBAN ENVIRONMENTAL MANAGEMENT
Authors: Scott Kathryn , Greenway Alison
Published: December 2012

This paper reflects on the place of ethnography in collaborative learning in
the context of urban environmental management. The Low Impact Urban
Design and Development (LIUDD) research programme is aimed at facilitating the uptake and implementation of low-impact principles, with a focus on improved approaches to storm-water management. Collaborative learning approaches include the use of case studies, learning groups and a web-based database. Place-based case studies are intended to showcase some examples of LIUDD and develop forums for refining research questions and developing innovative solutions. Ethnographic research approaches fit well with the process of collaborative learning, helping to understand how stakeholder groups
think about, evaluate, control and manage land and other resources. Organising and presenting this information in accessible formats, providing opportunities for stakeholders to reflect on and learn from each others’ practices and experiences, and facilitating critical dialogue aimed at transformative change are key aspects of the approach.
LUMPERS, SPLITTERS AND SAGGING PILLARS
Authors: Levine Hal B. , Glick With contributions from Paula Brown
Published: December 2012

Anthropologists have been narrowing the scope of the discipline for a long time. It has become less comparative, less concerned with wide-ranging questions about human nature, more narrowly ethnographic and increasingly relativistic. These trends have become strong enough in recent times to seriously undermine anthropology’s fundamental project – to understand social and cultural reality. Personal experiences with researching and writing about ethnicity, kinship, and questions of social scale are chronicled here in a paper that supports the need to move beyond ethnography in order to productively confront important issues. The section on scale contains contributions by Professor Paula Brown Glick, the well-known ethnographer of the Chimbu, who has recently received recognition of her lifetime achievements by the Association of Social Anthropologists of Oceania.
NEW ZEALAND'S BICULTURALISM AND THE DEVELOPMENT OF PUBLICLY FUNDED RONGOA (TRADITIONAL MAORI HEALING) SERVICES
Authors: O'Connor Tony
Published: December 2012

The establishment of publicly funded Rongoa services was made possible by a bicultural model of government. My aim was to examine how biculturalism played out through that process. To do that I drew on eighteen months of working with some Rongoa healers and three interviews with government employees developing Rongoa services. What emerged from the development process was a certain form of Rongoa that some Maori did not recognize as either ‘authentically Maori’ or particularly useful as a form of health care. There appeared to be limits as to how ‘Rongoa’s’ take on the public purse could be justified and hence how Rongoa could proceed into the future as a government funded health service. For Rongoa to form part of New Zealand’s publicly funded health system it had to be complementary to (as in different, but not too different) from the kinds of health concepts that had already been publicly validated. Silenced by the development process were some concepts, practices and relationships that said much about how cultural-pluralism in the field of health was managed under a bicultural model of government.
DEAD SERIOUS? FUNERAL DIRECTING IN NEW ZEALAND
Authors: Schafer Cyril
Published: December 2012

This article examines the history of funeral directing in New Zealand and
highlights a number of significant shifts in occupational orientation. The first identifiable transition involved the shift from undertaker to funeral director in the early twentieth century. Attempts to professionalise the occupation during this period parallel similar developments in the United States, and illustrate the increasing bureaucratisation and rationalisation of human disposal. A more recent shift has occurred in the past three decades. New Zealand funeral directors focused their attention primarily on grief management and emphasised the psychological value of funerary ritual. Funeral directors also played a significant role in personalising funerals and offering ‘life-centred’ funeral options. Despite the important influence of international industry developments, funeral directors in New Zealand have purveyed and promoted personalised post-mortem practices and attempted to distance New Zealand funerals from perceived ‘impersonal’ British practices, as well as the ‘excesses’ of North American obsequies.
PAKEHA TAONGA AND THE SOCIOLOGY OF DRESS
Authors: Webster Elaine
Published: December 2012

When in 2004 a Pakeha student was not allowed to wear her amethyst pendant to school, she claimed it as her taonga since it was spiritually and culturally significant to her. Through this she entered a cultural and political debate about what it means to be Pakeha, drawing on Maori cultural meanings to do so. Demonstrating the dynamic and transformational nature of culture, her actions contributed to constructs of cultural identity in Aotearoa New Zealand in a vital way, although her arguments to wear her pendant were never formally recognised. The ensuing struggle over cultural meanings and interpretations which her situation provoked has some parallels with that of Muslim schoolgirls in France wanting to wear headscarves to school, highlighting what it means to wear culture. Their claims are for diversity in the face of a dominant monoculturalism, exposed through this debate as defining cultural identity in its narrowest sense. The debate also exposes some beliefs about where Pakeha stand in relation to the Treaty of Waitangi.
Comparison between ZnO films grown by plasma-assisted atomic layer deposition using H2O plasma and O2 plasma as oxidant
Authors: Kawamura Yumi , Hattori Nozomu , Miyatake Naomasa , Uraoka Yukiharu
Published: December 2012

Zinc oxide (ZnO) thin films have attracted significant attention for application in thin film transistors (TFTs) due to their specific characteristics, such as high mobility and transparency. In this paper, the authors fabricated TFTs with ZnO thin films as channel layers deposited by plasma-assisted atomic layer deposition (PAALD) at 100 °C using two different plasma sources, water (H2O-plasma) and oxygen gas (O2-plasma), as oxidants, and investigated the effects of the plasma sources on TFT performances. The TFT with ZnO channel layer deposited with H2O-plasma indicated higher performances such as a field effect mobility (μ) of 1.1 cm2/Vs. Analysis of the ZnO films revealed that the residual carbon in the film deposited with H2O-plasma was lower than that of O2-plasma. In addition, the c-axis preferred orientation was obtained in the case of the ZnO film deposited with H2O-plasma. These results suggest that it is possible to fabricate high-performance ZnO TFTs at low temperatures by PAALD with H2O-plasma.
Four‐dimensional dose evaluation using deformable image registration in radiotherapy for liver cancer
Authors: Hoon Jung Sang , Min Yoon Sang , Ho Park Sung , Cho Byungchul , Won Park Jae , Jung Jinhong , Park Jin‐hong , Hoon Kim Jong , Do Ahn Seung
Published: December 2012

Purpose:

In order to evaluate the dosimetric impact of respiratory motion on the dose delivered to the target volume and critical organs during free‐breathing radiotherapy, a four‐dimensional dose was evaluated using deformable image registration (DIR).

Methods:

Four‐dimensional computed tomography (4DCT) images were acquired for 11 patients who were treated for liver cancer. Internal target volume‐based treatment planning and dose calculation (3D dose) were performed using the end‐exhalation phase images. The four‐dimensional dose (4D dose) was calculated based on DIR of all phase images from 4DCT to the planned image. Dosimetric parameters from the 4D dose, were calculated and compared with those from the 3D dose.

Results:

There was no significant change of the dosimetric parameters for gross tumor volume (p > 0.05). The increase Dmean and generalized equivalent uniform dose (gEUD) for liver were by 3.1% ± 3.3% (p = 0.003) and 2.8% ± 3.3% (p = 0.008), respectively, and for duodenum, they were decreased by 15.7% ± 11.2% (p = 0.003) and 15.1% ± 11.0% (p = 0.003), respectively. The Dmax and gEUD for stomach was decreased by 5.3% ± 5.8% (p = 0.003) and 9.7% ± 8.7% (p = 0.003), respectively. The Dmax and gEUD for right kidney was decreased by 11.2% ± 16.2% (p = 0.003) and 14.9% ± 16.8% (p = 0.005), respectively. For left kidney, Dmax and gEUD were decreased by 11.4% ± 11.0% (p = 0.003) and 12.8% ± 12.1% (p = 0.005), respectively. The NTCP values for duodenum and stomach were decreased by 8.4% ± 5.8% (p = 0.003) and 17.2% ± 13.7% (p = 0.003), respectively.

Conclusions:

The four‐dimensional dose with a more realistic dose calculation accounting for respiratory motion revealed no significant difference in target coverage and potentially significant change in the physical and biological dosimetric parameters in normal organs during free‐breathing treatment.
Arthropod Diversity in a Tropical Forest
Authors: Basset Yves , Cizek Lukas , Cuénoud Philippe , Didham Raphael K. , Guilhaumon François , Missa Olivier , Novotny Vojtech , Ødegaard Frode , Roslin Tomas , Schmidl Jürgen , Tishechkin Alexey K. , Winchester Neville N. , Roubik David W. , Aberlenc Henri-Pierre , Bail Johannes , Barrios Héctor , Bridle Jon R. , Castaño-Meneses Gabriela , Corbara Bruno , Curletti Gianfranco , Duarte da Rocha Wesley , De Bakker Domir , Delabie Jacques H. C. , Dejean Alain , Fagan Laura L. , Floren Andreas , Kitching Roger L. , Medianero Enrique , Miller Scott E. , Gama de Oliveira Evandro , Orivel Jérôme , Pollet Marc , Rapp Mathieu , Ribeiro Sérvio P. , Roisin Yves , Schmidt Jesper B. , Sørensen Line , Leponce Maurice
Published: December 2012

Assessing Creepy Crawlies

Arthropods are the most diverse group of terrestrial animal species, yet estimates of the total number of arthropod species have varied widely, especially for tropical forests.

Basset
et al.

(p.
1481
, see the cover) now provide more reliable estimates of total arthropod species richness in a tropical rainforest in Panama. Intensive sampling of a half hectare of forest yielded just over 6000 arthropod species. Scaling up this result to the whole forest suggests that the total species diversity lies between 17,000 and 40,000 species.
Hox
Genes Regulate Digit Patterning by Controlling the Wavelength of a Turing-Type Mechanism
Authors: Sheth Rushikesh , Marcon Luciano , Bastida M. Félix , Junco Marisa , Quintana Laura , Dahn Randall , Kmita Marie , Sharpe James , Ros Maria A.
Published: December 2012

Digit Determination

Pentadactyly has been an early and rapid innovation of tetrapods.

Sheth
et al.

(p.
1476
) report that a dramatic reduction in distally expressed
Hox
genes, in the absence of a functional morphogen signaling pathway, results in extreme polydactyly in mice. Mutant digits exhibited patterns reminiscent of the endoskeleton of fins, suggesting that an ancestral patterning mechanism has been deeply conserved in evolution.
A Universal Scaling for the Energetics of Relativistic Jets from Black Hole Systems
Authors: Nemmen R. S. , Georganopoulos M. , Guiriec S. , Meyer E. T. , Gehrels N. , Sambruna R. M.
Published: December 2012

So Different Yet So Similar

Gamma-ray bursts (GRBs) are associated with the collapse of stars into black holes. Blazars are a class of active galaxies powered by accretion onto central black holes with masses a million to a billion times that of the Sun.

Nemmen
et al.

(p.
1445
) show that, despite tremendous differences in luminosity and black hole mass, the relativistic jets produced in GRBs and blazars follow the same correlation between the kinetic power carried by the accelerated particles and the energy radiated away in the jet, suggesting that there may be a single mechanism for producing relativistic jets.
EZH2 Oncogenic Activity in Castration-Resistant Prostate Cancer Cells Is Polycomb-Independent
Authors: Xu Kexin , Wu Zhenhua Jeremy , Groner Anna C. , He Housheng Hansen , Cai Changmeng , Lis Rosina T. , Wu Xiaoqiu , Stack Edward C. , Loda Massimo , Liu Tao , Xu Han , Cato Laura , Thornton James E. , Gregory Richard I. , Morrissey Colm , Vessella Robert L. , Montironi Rodolfo , Magi-Galluzzi Cristina , Kantoff Philip W. , Balk Steven P. , Liu X. Shirley , Brown Myles
Published: December 2012

Alternative Role for EZH2

Epigenetic regulators are implicated in cancer progression and proposed as therapeutic targets.

Xu
et al.

(p.
1465
; see the Perspective by

Cavalli

) report that EZH2 (Enhancer of zeste homolog 2), a factor previously thought to exert its oncogenic function primarily as part of the polycomb repressive complex, acts through a distinct mechanism in cells of castration-resistant prostate cancer. Rather than exclusively silencing gene expression through histone methylation, EZH2 acts as a transcriptional coactivator. The activation function of EZH2 plays a critical role in the growth of castration-resistant prostate cancer cells, which could be relevant in future drug development.
Texture of Nanocrystalline Nickel: Probing the Lower Size Limit of Dislocation Activity
Authors: Chen Bin , Lutker Katie , Raju Selva Vennila , Yan Jinyuan , Kanitpanyacharoen Waruntorn , Lei Jialin , Yang Shizhong , Wenk Hans-Rudolf , Mao Ho-kwang , Williams Quentin
Published: December 2012

Strength Under Pressure

Above a lower cutoff value, shrinking the grain size of a metal tends to strengthen it because the overall increase in grain boundaries limits the activity of the dislocations as the material undergoes plastic deformation.

Chen
et al.

(p.
1448
) explore the question of whether this restriction in dislocation activity occurs when a metal is subjected to high pressures. Foils of nickel made from particles of different sizes were subjected to high pressures inside a diamond anvil cell. An increase in pressure extended dislocation activity to smaller grain sizes, indicating that pressure compensates for the inhibition of dislocation activity in small volumes.
A Steroid Receptor–MicroRNA Switch Regulates Life Span in Response to Signals from the Gonad
Authors: Shen Yidong , Wollam Joshua , Magner Daniel , Karalay Oezlem , Antebi Adam
Published: December 2012

Gonads and Life Span

Animals develop through successive life stages and have life spans that are determined by their genes and the environment. Yet how the molecular circuitry underlying life-stage structure relates to longevity is poorly understood.

Shen
et al.

(p.
1472
) now show that components of a steroid receptor-microRNA switch used for
Caenorhabditis elegans
developmental timing is co-opted to regulate adult longevity in response to signals from the reproductive system. Thus, the gonad can be coupled to metazoan life span via a developmental clock.
Rapid Folding of DNA into Nanoscale Shapes at Constant Temperature
Authors: Sobczak Jean-Philippe J. , Martin Thomas G. , Gerling Thomas , Dietz Hendrik
Published: December 2012

Speeding Up Nanoscale DNA Assembly

An impressive array of three-dimensional (3D) nanoscale objects has been assembled by folding a long, single-stranded DNA scaffold by binding of short DNA staples. However, these processes tend to be slow and inefficient.

Sobczak
et al.

(p.
1458
) examined the folding process with an intercalating fluorescence dye to measure the formation of double-stranded DNA in folding processes or single-stranded DNA in unfolding. Reaction conditions were identified that sped up folding by orders of magnitude and increased yields of the 3D nanoscale objects to nearly 100%.
Boldly Going Beyond Mathematics
Signals and Boundaries
Building Blocks for Complex Adaptive Systems

by John H. Holland

MIT Press, Cambridge, MA, 2012. 316 pp. $40, £27.95. ISBN 9780262017831.
Authors: Adami Christoph
Published: December 2012

Holland offers a framework for analyzing complex adaptive systems through considerations of the signals and boundaries among their evolving parts.
Sub-Nanosized Gold Catalysts
Authors: Hashmi A. Stephen K.
Published: December 2012

Small gold clusters catalyze water addition to alkynes at the high efficiencies required for bulk industrial applications.
A Controversial Close-Up of Humanity's Health
Authors: Cohen Jon
Published: December 2012

Kudos and criticism greet a landmark new report, filling the largest ever issue of
The Lancet
, on the global burden of disease.
Construction and Nonclinical Testing of a Puumala Virus Synthetic M Gene-Based DNA Vaccine
Authors: Brocato R. L. , Josleyn M. J. , Wahl-Jensen V. , Schmaljohn C. S. , Hooper J. W.
Published: December 2012

Puumala virus (PUUV) is a causative agent of hemorrhagic fever with renal syndrome (HFRS). Although PUUV-associated HFRS does not result in high case-fatality rates, the social and economic impact is considerable. There is no licensed vaccine or specific therapeutic to prevent or treat HFRS. Here we report the synthesis of a codon-optimized, full-length M segment open reading frame and its cloning into a DNA vaccine vector to produce the plasmid pWRG/PUU-M(s2). pWRG/PUU-M(s2) delivered by gene gun produced high-titer neutralizing antibodies in hamsters and nonhuman primates. Vaccination with pWRG/PUU-M(s2) protected hamsters against infection with PUUV but not against infection by related HFRS-associated hantaviruses. Unexpectedly, vaccination protected hamsters in a lethal disease model of Andes virus (ANDV) in the absence of ANDV cross-neutralizing antibodies. This is the first evidence that an experimental DNA vaccine for HFRS can provide protection in a hantavirus lethal disease model.
Kaposi's Sarcoma-Associated Herpesvirus Oncoprotein K13 Protects against B Cell Receptor-Induced Growth Arrest and Apoptosis through NF-κB Activation
Authors: Graham Ciaren , Matta Hittu , Yang Yanqiang , Yi Han , Suo Yulan , Tolani Bhairavi , Chaudhary Preet M.
Published: December 2012

Kaposi's sarcoma-associated herpesvirus (KSHV) has been linked to the development of Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease (MCD). We have characterized the role of KSHV-encoded viral FLICE inhibitory protein (vFLIP) K13 in the modulation of anti-IgM-induced growth arrest and apoptosis in B cells. We demonstrate that K13 protects WEHI 231, an immature B-cell line, against anti-IgM-induced growth arrest and apoptosis. The protective effect of K13 was associated with the activation of the NF-κB pathway and was deficient in a mutant K13 with three alanine substitutions at positions 58 to 60 (K13-58AAA) and a structural homolog, vFLIP E8, both of which lack NF-κB activity. K13 upregulated the expression of NF-κB subunit RelB and blocked the anti-IgM-induced decline in c-Myc and rise in p27Kip1that have been associated with growth arrest and apoptosis. K13 also upregulated the expression of Mcl-1, an antiapoptotic member of the Bcl2 family. Finally, K13 protected the mature B-cell line Ramos against anti-IgM-induced apoptosis through NF-κB activation. Inhibition of anti-IgM-induced apoptosis by K13 may contribute to the development of KSHV-associated lymphoproliferative disorders.
An AP-1 Binding Site in the Enhancer/Core Element of the HIV-1 Promoter Controls the Ability of HIV-1 To Establish Latent Infection
Authors: Duverger Alexandra , Wolschendorf Frank , Zhang Mingce , Wagner Fredric , Hatcher Brandon , Jones Jennifer , Cron Randall Q. , van der Sluis Renee M. , Jeeninga Rienk E. , Berkhout Ben , Kutsch Olaf
Published: December 2012

Following integration, HIV-1 in most cases produces active infection events; however, in some rare instances, latent infection events are established. The latter have major clinical implications, as latent infection allows the virus to persist despite antiretroviral therapy. Both the cellular factors and the viral elements that potentially determine whether HIV-1 establishes active or latent infection events remain largely elusive. We detail here the contribution of different long terminal repeat (LTR) sequences for the establishment of latent HIV-1 infection. Using a panel of full-length replication-competent virus constructs that reflect naturally occurring differences of HIV-1 subtype-specific LTRs and targeted LTR mutants, we found the primary ability of HIV-1 to establish latent infection in this system to be controlled by a four-nucleotide (nt) AP-1 element just upstream of the NF-κB element in the viral promoter. Deletion of this AP-1 site mostly deprived HIV-1 of the ability to establish latent HIV-1 infection. Extension of this site to a 7-nt AP-1 sequence massively promoted latency establishment, suggesting that this promoter region represents a latency establishment element (LEE). Given that these minimal changes in a transcription factor binding site affect latency establishment to such large extent, our data support the notion that HIV-1 latency is a transcription factor restriction phenomenon.
No Evidence of Xenotropic Murine Leukemia Virus-Related Virus Transmission by Blood Transfusion from Infected Rhesus Macaques
Authors: Williams Dhanya K. , Galvin Teresa A. , Gao Yamei , O'Neill Christina , Glasner Dustin , Khan Arifa S.
Published: December 2012

The discovery of xenotropic murine leukemia virus-related virus (XMRV) in human tissue samples has been shown to be due to virus contamination with a recombinant murine retrovirus. However, due to the unknown pathogenicity of this novel retrovirus and its broad host range, including human cell lines, it is important to understand the modes of virus transmission and develop mitigation and management strategies to reduce the risk of human exposure and infection. XMRV transmission was evaluated by whole-blood transfusion in rhesus macaques. Monkeys were infected with XMRV to serve as donor monkeys for blood transfers at weeks 1, 2, and 3 into naïve animals. The donor and recipient monkeys were evaluated for XMRV infection by nested PCR assays with nucleotide sequence confirmation, Western blot assays for development of virus-specific antibodies, and coculture of monkey peripheral blood mononuclear cells (PBMCs) with a sensitive target cell line for virus isolation. XMRV infection was demonstrated in the virus-injected donor monkeys, but there was no evidence of virus transmission by whole-blood transfusion to naïve monkeys based upon PCR analysis of PBMCs using XMRV-specific
gag
and
env
primers, Western blot analysis of monkey plasma up to 31 to 32 weeks after transfusion, and coculture studies using monkey PBMCs from various times after transfusion. The study demonstrates the lack of XMRV transmission by whole-blood transfusion during the acute phase of infection. Furthermore, analysis of PBMC viral DNA showed extensive APOBEC-mediated G-to-A hypermutation in a donor animal at week 9, corroborating previous results using macaques and supporting the possible restriction of XMRV replication in humans by a similar mechanism.
Intragenic Complementation of Hepatitis C Virus NS5A RNA Replication-Defective Alleles
Authors: Fridell Robert A. , Valera Lourdes , Qiu Dike , Kirk Melissa J. , Wang Chunfu , Gao Min
Published: December 2012

Hepatitis C virus NS5A has three structural domains, is required for RNA replication and virion assembly, and exists in hypo- and hyperphosphorylated forms. Accumulated data suggest that phosphorylation is involved in modulating NS5A functions. We performed a mutational analysis of highly conserved serine residues in the linker region between domains I and II of genotype 2a JFH1 NS5A. As with genotype 1b Con1 NS5A, we found that specific serine residues were important for efficient hyperphosphorylation of JFH1 NS5A. However, in contrast with Con1 replicons, we observed a positive correlation between hyperphosphorylation and JFH1 replicon replication. We previously demonstrated
trans
-complementation of a hyperphosphorylation-deficient, replication-defective JFH1 replicon. Our results suggested that the defective NS5A encoded by this replicon, while lacking one NS5A function, was capable of performing a separate replication function. In this report, we examined an additional set of replication-defective NS5A mutations in
trans
-complementation assays. While some behaved similarly to the S232I replicon, others displayed a unique
trans
-complementation phenotype, suggesting that NS5A
trans
-complementation can occur by two distinct modes. Moreover, we were able, for the first time, to demonstrate intragenic complementation of replication-defective NS5A alleles. Our results identified three complementation groups: group A, comprising mutations within NS5A domain I; group B, comprising mutations affecting serine residues important for hyperphosphorylation and a subset of the domain I mutations; and group C, comprising a single mutation within the C-terminal region of domain II. We postulate that these complementation groups define three distinct and genetically separable functions of NS5A in RNA replication.
A Novel Bacterium-Free Method for Generation of Flavivirus Infectious DNA by Circular Polymerase Extension Reaction Allows Accurate Recapitulation of Viral Heterogeneity
Authors: Edmonds Judith , van Grinsven Erinke , Prow Natalie , Bosco-Lauth Angela , Brault Aaron C. , Bowen Richard A. , Hall Roy A. , Khromykh Alexander A.
Published: December 2012

A novel bacterium-free approach for rapid assembly of flavivirus infectious cDNAs using circular polymerase extension reaction was applied to generate infectious cDNA for the virulent New South Wales isolate of the Kunjin strain of West Nile virus (KUNV) that recently emerged in Australia. Recovered virus recapitulated the genetic heterogeneity present in the original isolate. The approach was utilized to generate viral mutants with designed phenotypic properties and to identify E protein glycosylation as one of the virulence determinants.