bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental and modeling study of O and Cl atoms surface recombination reactions in O2 and Cl2 plasmas
Authors: Stafford Luc , Guha Joydeep , Khare Rohit , Mattei Stefano , Boudreault Olivier , Clain Boris , Donnelly Vincent M.
Published: May 2010

In low-pressure plasmas commonly used in materials processing, plasma–wall inter-actions play a crucial role in the evolution of the plasma properties both over time and across large-area wafers. We have recently studied the heterogeneous recombination of O and Cl atoms on reactor walls in O2 and Cl2 plasmas through both experiments and modeling. The Langmuir–Hinshelwood (i.e., delayed) recombination was investigated using a “spinning-wall” technique in which a portion of the substrate surface is periodically exposed to an inductively coupled plasma and to a differentially pumped chamber where either Auger electron spectroscopy (AES) or line-of-sight mass spectrometry (MS) is used to detect surface and desorbing species. In this paper, a review of the various effects driving the O and Cl atoms recombination dynamics on anodized aluminum (AA) and stainless steel (SS) surfaces is presented. It is shown that recombination probabilities, γ, can vary following plasma exposure due to surface conditioning. In Cl2 plasmas, γ was also found to depend on the Cl-to-Cl2 number density ratio, a mechanism ascribed to a competition for adsorption sites between Cl and Cl2. We have also determined the recombination rates of Cl atoms in Cl2 high-density plasmas sustained by electromagnetic surface waves by comparing the measured degrees of dissociation of Cl2 to those predicted by an isothermal fluid model. For a reactor with large SS and quartz surfaces exposed to the plasma, γ values and their dependence on the Cl-to-Cl2 number density ratio were consistent with those obtained from the rotating substrate technique. Similar values were obtained for plasmas sustained in a quartz discharge tube. It is expected that for plasmas sustained in or adjacent to a silica tube or plate, the Cl atoms recombination coefficient becomes independent of chamber wall material due to reactor seasoning, producing a silicon-oxychloride layer.
Bizet in Khayelitsha: U-Carmen eKhayelitsha as audio-visual transculturation
Authors: Davies James , Dovey Lindiwe
Published: May 2010

This article takes as its focus Mark Dornford-May's film operaU-Carmen eKhayelitsha(Dornford-May 2005), set in the South African township of Khayelitsha and based on Bizet's opra comiqueCarmen. The authors of the article approach the film opera in a self-consciously audio-visual and interdisciplinary way, paying attention at once to its operatic, filmic and socio-political worlds. They prefer not to rehearse arguments in favour of the politics of gender and sexuality, as is usual in the Carmen on film literature. Rather, an adaptation of Fernando Ortiz's concept of transculturation proves a useful theoretical frame for the study. The way in whichU-Carmen eKhayelitshastrives for operatic authenticity (faithfully rendering Bizet) and filmic authenticity (faithfully rendering the township) forces a collision between two conceits of cultural difference. The authors argue that the binaries of sight and sound, stereotypes of low and high, local and global, present and past, Africa and opera, textual and contextual are both forcefully articulated and troubled in this film opera. These disarticulations, far from jettisoning the filmic effect, explainU-Carmen eKhayelitsha'senormous vitality, restlessness and enabling energy. In the end, the authors argue that the operatic text and township context are de-cultured and then re-cultured in ways that evince powerfully emotional processes of transcultural change.
Negotiating identities: representations of childhood in Senegalese cinema
Authors: Bradbury Marina
Published: May 2010

This article offers a critique of reductive paradigms that pit the West against Africa by means of specific analysis of representations of childhood in early and contemporary Senegalese fiction films. Since children are by nature malleable and impressionable, and the notion of childhood
itself unstable, children as characters and symbols provide a challenging and engaging way of dealing with issues of identity and a crisis of representation within an African screen media context. The article discusses to what extent audio-visual African representations of childhood allow
African directors to reclaim autonomous yet hybrid identities on behalf of Africans, and argues that cinematic representations of childhood are key to building a more positive, multi-faceted vision of Africa, African cultures and African identities.
They stole the show!: Indian films in coastal Tanzania, 1950s1980s
Authors: Fair Laura
Published: May 2010

Utilizing rare and innovative source materials, including hundreds of interviews and survey responses, as well as box-office receipts and archival sources, this article provides path-breaking insights into the history of audience preferences in Tanzania from the 1950s to the 1980s. It reveals a long-term passion for Indian films amongst Tanzanians of all class, ethnic and gender backgrounds, and explores the nature of movie-going in Tanzania. This article also describes innovative exhibition practices inspired by the overwhelming audience demand for Indian films, such as reeling and a black market trade in cinema tickets. While hinting at the complex reasons why Indian films became so popular among East African audiences, the article adds to the increasingly vocal calls for recognition of the place of both audiences and non-western producers and distributors in our understanding of global media flows.
Zen and the art of film narrative: towards a transcendental realism in film
Authors: Knudsen Erik
Published: May 2010

Nations and peoples are largely the stories they feed themselves. If they tell themselves stories that are lies, they will suffer the consequences of those lies. If they tell themselves stories that face their own truths, they will free their histories for future
flowerings. (Okri 1995: 21)

What defines the classic narrative is also at the root of its limitations; an epistemology that ties it to a material and psychological paradigm governed by largely explicable laws of cause and effect. Such notions
as character motivation, narrative aims, obstacles, climax and so on have evolved to become as overwhelmingly dominant in cinema as the dogma of reason which subsequently the industrial age solidified. It is from this that the moving-image medium emerged: empirical evidence of motivations,
mechanistic notions of causes and effects and scientifically based including the pseudosciences of psychology and sociology that provide justifications for events and actions all serve to reinforce the dominance of the classic narrative's role in the storytelling of the developed world.

In
this article, I shall call for a different perspective on cinematic narrative form; not with a view to discussing what film generally is, but to make some general suggestions of what it could be, particularly from the perspective of a film-maker trying to transcend the limitations of the classic
narrative. The motive is to try and understand how, in practice, one may evolve narrative forms in such a way as to deal with experiences not sufficiently touched by the classic form, as it is currently generally practised in cinema. I shall, in particular, look at the relationship between
emotions and feelings and their relationship to narrative structure and bring into this examination some notions and ideas from Zen Buddhism to re-evaluate that relationship. The issues I hope to raise are about paradigms and I shall therefore deliberately base my discussion on general assertions
and eclectic contextualization.
Who Writes British Films: A Summary on the UKFC Report and a Call for Further Research
Authors: Rogers Susan
Published: May 2010

In 2007 I was commissioned by the UK Film Council to investigate the background and employment experience of screenwriters credited on a random selection of recent UK films. The resulting report, Writing British Films Who Writes British Films and How They are Recruited, confirmed
some widely-held views and uncovered much new information. The UK Film Council's first studies had revealed that many of the beliefs about screenwriting, expressed in interviews within the British film industry, to be anecdotal or based on unsubstantiated fact and to an extent, myth, confirming
the scarcity of research in this field. The following is a summary and a reflection on the findings revealed in the report.
Reviews
Authors: Papia Dan , Pallant C.J , Ormrod Joan , Millard Kathryn
Published: May 2010

SCRIPT CULTURE AND THE AMERICAN SCREENPLAY, KEVIN ALEXANDER BOON (2008) Detroit, MI: Wayne State University Press, 230 pp., ISBN: 9780814332634 (pbk), 19.95

JAMES WHALE'S DRACULA'S DAUGHTER: AN ALTERNATIVE HISTORY FOR CLASSIC FILM MONSTERS, PHILIP J. RILEY
(2009) Albany, GA: BearManor, 176 pp., ISBN: 9781593934750 (pbk), 15.40

HORROR SCREENWRITING: THE NATURE OF FEAR, DEVIN WATSON (2009) Studio City, CA: Michael Wiese Productions, 232 pp., ISBN: 9781932907605 (pbk), 14.99

BASICS ANIMATION: SCRIPTWRITING, PAUL
WELLS (2007) Lausanne, Switzerland: Ava Publishing, 183 pp., ISBN-13: 9782940373161 (pbk), 17.95
Opportunism as the Inhibiting Trigger for Developing Long-Term-Oriented Western Exporter–Hong Kong Importer Relationships
Authors: Barnes Bradley R. , Leonidou Leonidas C. , Siu Noel Y.M. , Leonidou Constantinos N.
Published: May 2010

Notwithstanding the extensive literature on opportunism in buyer–seller relationships, scant empirical attention has been given to this issue in both international and Chinese contexts. Using a sample of 202 Hong Kong Chinese importers, this article highlights the harmful effect of Western exporters’ opportunism on importers’ long-term orientation through the intervening role of key behavioral constructs. The study confirms almost all hypothesized associations between the constructs examined, indicating that an exporter's opportunistic behavior reduces trust and generates conflict. In turn, low trust reduces commitment, and conflict impedes communication. Low levels of both commitment and communication reduce importers’ satisfaction, which inhibits their long-term orientation. The importer's proactive initiation of the relationship moderates the link between opportunism and trust but not that of opportunism with conflict. The study also confirms the moderating role of importer dependence and exporters’ marketing adaptation on the association of satisfaction with long-term orientation. The authors find moderating effects on this association through the Chinese constructs of renqing and mianzi, albeit in the opposite direction to that hypothesized.
Dynamic changes in N-terminal pro-brain natriuretic peptide in acute coronary syndromes treated with percutaneous coronary intervention: a marker of ischemic burden, reperfusion and outcome
Authors: Buchner Stefan , Debl Kurt , Barlage Stefan , Griese Daniel , Fredersdorf Sabine , Jeron Andreas , Lubnow Matthias , Müller Thomas , Muders Frank , Holmer Stephan , Riegger Günter A.J. , Luchner Andreas
Published: May 2010

Background: Whereas N-terminal pro-brain natriuretic peptide (NT-proBNP) is approved for risk stratification of patients with acute coronary syndromes (ACS), short-term temporal changes in NT-proBNP concentrations and the optimal time points for sampling are not clear. The purpose of this study was to better define the short-term changes in NT-proBNP in relation to clinical presentation, reperfusion and prognostic value in patients with ACS, as well as to identify the optimum time points for sampling.

Methods: We studied daily plasma concentrations of NT-proBNP in 133 unselected patients with myocardial infarction (n=65), stable coronary artery disease (CAD, n=46) and no CAD (n=22) who underwent coronary angiography.

Results: Patients with non-ST-elevation myocardial infarction (NSTEMI) presented with markedly higher NT-proBNP than patients with ST-elevation myocardial infarction (STEMI) [1305 (741–3208) ng/L vs. 170 (70–424) ng/L, p<0.001]. Also, time to presentation from onset of pain was much longer in NSTEMI as compared to STEMI (>48 h vs. <6 h, p<0.001). Patients with NSTEMI also presented with higher NT-proBNP as compared with CAD [224 (98–732) ng/L] and no CAD [47 (26–102) ng/L; p<0.001, NSTEMI vs. both]. Following successful percutaneous coronary intervention [thrombolysis in myocardial infarction (TIMI) 3-flow established], NT-proBNP increased markedly within 24 h in patients with STEMI [718 (379–1338) ng/L, p<0.01 vs. 0 h], whereas no change in NT-proBNP was noted in patients with NSTEMI [1190 (1010–2024) ng/L, p=0.88 vs. 0 h]. In both STEMI and NSTEMI, NT-proBNP decreased significantly 96 h after successful reperfusion [STEMI –52%, 372 (189–610) ng/L, p<0.05; NSTEMI –52%, 613 (365–724) ng/L, p<0.05]. Unsuccessful reperfusion (TIMI<3) was associated with unchanged or increased NT-proBNP. NT-proBNP at 96 h and peak NT-proBNP further displayed a strong correlation with cardiac troponin T (r=0.64 and r=0.54, p<0.001), a marker of infarct size, and NT-proBNP at 96 h was a strong predictor of long-term prognosis (hazard ratio 7.29, p=0.025).

Conclusions: In patients with NSTEMI, NT-proBNP may be increased as high as concentrations usually associated with acute congestive heart failure despite the absence of clinical signs. In contrast, patients with STEMI and short time to presentation may present with completely normal NT-proBNP, but dramatic short-term increases following reperfusion. NT-proBNP reflects ischemic burden, reperfusion success and prognosis, and the current data support repetitive sampling in patients with ACS.

Clin Chem Lab Med 2010;48:875–81.
Molecular diagnostics: between chips and customized medicine
Authors: Castaldo Giuseppe , Lembo Francesca , Tomaiuolo Rossella
Published: May 2010

Recently there has been an explosive increase in molecular diagnostics. This is due to translational research on the molecular basis of human diseases, and to technological developments that have resulted in efficient procedures for extensive analysis of the human genome. However, a large body of data on the genome is still difficult to interpret at the clinical level. For many monogenic diseases, “modifier” genes, inherited independently of the disease gene interact, thereby resulting in a distinct phenotype for each patient. Multigenic diseases depend on complex interactions between genes and the environment. Response to drugs and side effects are modulated by gene variants. The same is true for the response to nutrients. All these interactions, which vary from patient to patient, led to the concept of “personalized medicine”. Our genome consists of 25,000 genes, a surprisingly low number when compared to other species. Therefore, the complex phenotype of humans depends on a number of mechanisms that regulate gene expression, which, in turn, may be altered resulting in disease. For example, DNA methylation modulates the level of gene expression, and altered methylation of some genes is related to human neoplasias. MicroRNAs regulate the expression of a myriad of genes, and mounting evidence indicates that this mechanism may be impaired in human diseases. Finally, the relationships between genetics and human behavior are starting to be elucidated. For example, suicide may be related to alterations of methylation of specific genes. To conclude: the chip-wide analysis of human genomes is becoming easier, but the understanding of molecular genetics that confirmed the real “uniqueness” of each genome is an excellent opportunity for laboratory medicine to reposition the patient at the heart of the medical process.

Clin Chem Lab Med 2010;48:973–82.
The prevalence of preanalytical errors in a Croatian ISO 15189 accredited laboratory
Authors: Simundic Ana-Maria , Nikolac Nora , Vukasovic Ines , Vrkic Nada
Published: May 2010

Background: The preanalytical phase is the most common source of laboratory errors. The goal of this descriptive study was to analyze the prevalence and type of preanalytical errors in relation to the site of sample collection (inpatient vs. outpatient) and the type of laboratory unit (hematology and coagulation vs. biochemistry). For the biochemistry unit, the data were also analyzed relative to the type of the analysis (stat vs. routine).

Methods: We retrospectively analyzed the sample and test request form error rate for a 1-year period, from January to December 2008.

Results: The frequency of the sample errors differed significantly between the emergency and routine biochemistry unit (0.69% vs. 2.14%; p<0.0001), and between inpatients and outpatients (1.12% vs. 1.36%; p=0.0006). Hemolysis was the most frequent sample error, accounting for 65% of all unsuitable specimens in the emergency biochemistry unit. The total sample error rate did not differ between hematology and coagulation vs. the biochemistry unit. The frequency of test request form errors differed significantly with respect to the sample collection site (p<0.0001), laboratory unit (p<0.0001) and type of the analysis (p<0.0001). Errors in the test request form were least frequent in the outpatient unit (2.98%) and most frequent in the routine biochemistry unit (65.94%).

Conclusions: Sample and test request form errors in our laboratory are occurring with a frequency comparable to that reported by others. Continuous educational action is needed for all stakeholders involved in laboratory testing to improve the quality of the preanalytical phase of the total testing process.

Clin Chem Lab Med 2010;48:1009–14.
Non-destructive assessment of green density and moisture condition in plantation-grown radiata pine (Pinus radiata D. Don.) by increment core measurements
Authors: Chan Julian Moreno , Raymond Carolyn A. , Walker John C.
Published: May 2010

A novel protocol for non-destructive assessment of green density and moisture content via increment cores was validated for young (8–10 years) and mature trees (36 years) of radiata pine (Pinus radiata D. Don.). Initial procedures involved comparing 5- and 12-mm cores with fresh disks taken from young trees at breast height and felled during the winter, as well as methods for rehydrating the wood cores. Subsequently, the best method (12-mm cores) was validated with material collected in summer from both young and mature trees. The protocols developed require separate processing of sapwood and heartwood, and soaking the sapwood for 24 h to replace the moisture lost while coring. For young trees, bark-to-pith 12-mm cores accounted for between 64% and 66% of variation in green density of sapwood and between 51% and 72% of saturation percentage, as measured by destructively sampled disks. For mature trees, the average of two sides of 12-mm bark-to-bark cores accounted for 73% of variation in green density of sapwood, and 56% of saturation percentage as measured by destructive wedges. One or both sides of a bark-to-bark core accounted for between 72% and 80% of variation in whole-section green density, and between 70% and 79% of variation in sapwood percentage. The number of heartwood rings was better predicted from the average of two sides of the cores (R2 of 0.71). Whole-tree values (lower two logs) for sapwood green density and saturation were better predicted from the average of both sides of the bark-to-bark core (R2 of 0.76 and 0.57, respectively). Whole-tree values for whole-section green density could be predicted either by one side or two sides of the cores (R2 for 1 or 2 sides of 0.77 and 0.81). Finally, whole-tree sapwood volumetric percent was better predicted by the average of two sides of the cores (R2 of 0.81).
Impact of organosilicon treatments on the wood-water relationship of solid wood
Authors: De Vetter Liesbeth , Van den Bulcke Jan , Van Acker Joris
Published: May 2010

The interaction of wood with water is a primary factor for degradation of the substrate. Organosilicons are known to behave like a water repellent, thus they are in discussion as protecting agents for wood used outdoors. In the present paper, the influence of water on organosilicon treated material was investigated. Solid Scots pine sapwood was impregnated or treated superficially with low concentrations of organosilicons and evaluated for several water related characteristics. The results confirm the water repellent properties of organosilicons as the polysiloxane film increases the contact angle between water and the wood substrate. However, they do not influence the total uptake of moisture but can change the rate at which moisture is taken up, and as such, prolong the service life of the substrate. In general, impregnated specimens behave better than dipped ones. To gain more insight in the exact behavior, continuous moisture uptake experiments are needed in real outdoor exposure tests.
Creep behavior of bamboo under various desorption conditions
Authors: Tsubaki Takashi , Nakano Takato
Published: May 2010

Longitudinal bending creep during desorption, which is also referred to as mechano-sorptive creep, was measured under various desorption conditions for moso bamboo (Phyllostachys pubescens) to clarify the effect of the conditions and the specimen part. The results showed that the mechano-sorptive effect appeared not only in wood but also in bamboo, and that its effect was reduced by an increase in the volume fraction of the bundle sheath in the cross-sectional area. The results of this experiment suggest that mechano-sorptive behavior is related to the amorphous matrix in bamboo components.
A computational study of pyrolysis reactions of lignin model compounds
Authors: Elder Thomas
Published: May 2010

Enthalpies of reaction for the initial steps in the pyrolysis of lignin have been evaluated at the CBS-4m level of theory using fully substituted β-O-4 dilignols. Values for competing unimolecular decomposition reactions are consistent with results previously published for phenethyl phenyl ether models, but with lowered selectivity. Chain propagating reactions of free radicals with a closed-shell dilignol are dominated by structures in which extensive electron delocalization occurs.
Acoustic emission measurements and lattice simulations of microfracture events in spruce
Authors: Nagy Edwin , Landis Eric N. , Davids William G.
Published: May 2010

A statistical lattice model was developed to investigate the energy associated with damage and failure of wood. The model incorporates several important morphological aspects of wood such as grain direction, early wood percentage and grain geometry. The model was developed to investigate progressive damage under enforced boundary displacements and has been adapted to predict fracture energy related phenomena. In this particular study, notched specimens were loaded in uniaxial tension while monitored by a passive acoustic emission (AE) measurement system. The energy associated with the mechanical damage was measured by the AE instruments and compared with the energy released by ruptured elements in the lattice model. Cumulative energy release was tracked as a function of specimen load and deformation in both model and experiment. A ratio was established between the cumulative AE energy released at the first drop in load and the cumulative fracture energy released when the model load-deformation relationship becomes significantly non-linear. An additional ratio was established between the total fracture energy measured prior to 50% of peak strain and the total fracture energy measured prior to peak strain. The magnitudes of these energy release ratios vary owing to a change in failure modes between the short model and the larger specimens; however, the shape of the AE energy release curve up to failure coincides well with that predicted by the model simulations.
Statistical Design and Analysis of RNA Sequencing Data
Authors: Auer Paul L , Doerge R W
Published: May 2010

Next-generation sequencing technologies are quickly becoming the preferred approach for characterizing and quantifying entire genomes. Even though data produced from these technologies are proving to be the most informative of any thus far, very little attention has been paid to fundamental design aspects of data collection and analysis, namely sampling, randomization, replication, and blocking. We discuss these concepts in an RNA sequencing framework. Using simulations we demonstrate the benefits of collecting replicated RNA sequencing data according to well known statistical designs that partition the sources of biological and technical variation. Examples of these designs and their corresponding models are presented with the goal of testing differential expression.
Fine Mapping in 94 Inbred Mouse Strains Using a High-Density Haplotype Resource
Authors: Kirby Andrew , Kang Hyun Min , Wade Claire M , Cotsapas Chris , Kostem Emrah , Han Buhm , Furlotte Nick , Kang Eun Yong , Rivas Manuel , Bogue Molly A , Frazer Kelly A , Johnson Frank M , Beilharz Erica J , Cox David R , Eskin Eleazar , Daly Mark J
Published: May 2010

The genetics of phenotypic variation in inbred mice has for nearly a century provided a primary weapon in the medical research arsenal. A catalog of the genetic variation among inbred mouse strains, however, is required to enable powerful positional cloning and association techniques. A recent whole-genome resequencing study of 15 inbred mouse strains captured a significant fraction of the genetic variation among a limited number of strains, yet the common use of hundreds of inbred strains in medical research motivates the need for a high-density variation map of a larger set of strains. Here we report a dense set of genotypes from 94 inbred mouse strains containing 10.77 million genotypes over 121,433 single nucleotide polymorphisms (SNPs), dispersed at 20-kb intervals on average across the genome, with an average concordance of 99.94% with previous SNP sets. Through pairwise comparisons of the strains, we identified an average of 4.70 distinct segments over 73 classical inbred strains in each region of the genome, suggesting limited genetic diversity between the strains. Combining these data with genotypes of 7570 gap-filling SNPs, we further imputed the untyped or missing genotypes of 94 strains over 8.27 million Perlegen SNPs. The imputation accuracy among classical inbred strains is estimated at 99.7% for the genotypes imputed with high confidence. We demonstrated the utility of these data in high-resolution linkage mapping through power simulations and statistical power analysis and provide guidelines for developing such studies. We also provide a resource of in silico association mapping between the complex traits deposited in the Mouse Phenome Database with our genotypes. We expect that these resources will facilitate effective designs of both human and mouse studies for dissecting the genetic basis of complex traits.
Molecular Genetic Analysis of Chd3 and Polytene Chromosome Region 76B-D in Drosophila melanogaster
Authors: Cooper Monica T , Conant Alexander W , Kennison James A
Published: May 2010

The Drosophila melanogaster Chd3 gene encodes a member of the CHD group of SNF2/RAD54 ATPases. CHD proteins are conserved from yeast to man and many are subunits of chromatin-remodeling complexes that facilitate transcription. Drosophila CHD3 proteins are not found in protein complexes, but as monomers that remodel chromatin in vitro. CHD3 colocalize with elongating RNA polymerase II on salivary gland polytene chromosomes. Since the role of Chd3 in development was unknown, we isolated and characterized the essential genes within the 640-kb region of the third chromosome (polytene chromosome region 76B-D) that includes Chd3. We recovered mutations in 24 genes that are essential for zygotic viability. We found that transposon-insertion mutants for 46% of the essential genes are included in the Drosophila Gene Disruption Project collection. None of the essential genes that we identified are in a 200-kb region that includes Chd3. We generated a deletion of Chd3 by targeted gene replacement. This deletion had no effect on either viability or fertility.
The Rate and Spectrum of Spontaneous Mutations in a Plant RNA Virus
Authors: Tromas Nicolas , Elena Santiago F
Published: May 2010

Knowing mutation rates and the molecular spectrum of spontaneous mutations is important to understanding how the genetic composition of viral populations evolves. Previous studies have shown that the rate of spontaneous mutations for RNA viruses widely varies between 0.01 and 2 mutations per genome and generation, with plant RNA viruses always occupying the lower side of this range. However, this peculiarity of plant RNA viruses is based on a very limited number of studies. Here we analyze the spontaneous mutational spectrum and the mutation rate of Tobacco etch potyvirus, a model system of positive sense RNA viruses. Our experimental setup minimizes the action of purifying selection on the mutational spectrum, thus giving a picture of what types of mutations are produced by the viral replicase. As expected for a neutral target, we found that transitions and nonsynonymous (including a few stop codons and small deletions) mutations were the most abundant type. This spectrum was notably different from the one previously described for another plant virus. We have estimated that the spontaneous mutation rate for this virus was in the range 10−6−10−5 mutations per site and generation. Our estimates are in the same biological ballpark that previous values reported for plant RNA viruses. This finding gives further support to the idea that plant RNA viruses may have lower mutation rates than their animal counterparts.
Expression Quantitative Trait Loci: Replication, Tissue- and Sex-Specificity in Mice
Authors: van Nas Atila , Ingram-Drake Leslie , Sinsheimer Janet S , Wang Susanna S , Schadt Eric E , Drake Thomas , Lusis Aldons J
Published: May 2010

By treating the transcript abundance as a quantitative trait, gene expression can be mapped to local or distant genomic regions relative to the gene encoding the transcript. Local expression quantitative trait loci (eQTL) generally act in cis (that is, control the expression of only the contiguous structural gene), whereas distal eQTL act in trans. Distal eQTL are more difficult to identify with certainty due to the fact that significant thresholds are very high since all regions of the genome must be tested, and confounding factors such as batch effects can produce false positives. Here, we compare findings from two large genetic crosses between mouse strains C3H/HeJ and C57BL/6J to evaluate the reliability of distal eQTL detection, including “hotspots” influencing the expression of multiple genes in trans. We found that >63% of local eQTL and >18% of distal eQTL were replicable at a threshold of LOD > 4.3 between crosses and 76% of local and >24% of distal eQTL at a threshold of LOD > 6. Additionally, at LOD > 4.3 four tissues studied (adipose, brain, liver, and muscle) exhibited >50% preservation of local eQTL and >17% preservation of distal eQTL. We observed replicated distal eQTL hotspots between the crosses on chromosomes 9 and 17. Finally, >69% of local eQTL and >10% of distal eQTL were preserved in most tissues between sexes. We conclude that most local eQTL are highly replicable between mouse crosses, tissues, and sex as compared to distal eQTL, which exhibited modest replicability.
Analysis of Multiple Ethyl Methanesulfonate-MutagenizedCaenorhabditis elegansStrains by Whole-Genome Sequencing
Authors: Sarin Sumeet , Bertrand Vincent , Bigelow Henry , Boyanov Alexander , Doitsidou Maria , Poole Richard J , Narula Surinder , Hobert Oliver
Published: May 2010

Whole-genome sequencing (WGS) of organisms displaying a specific mutant phenotype is a powerful approach to identify the genetic determinants of a plethora of biological processes. We have previously validated the feasibility of this approach by identifying a point-mutated locus responsible for a specific phenotype, observed in an ethyl methanesulfonate (EMS)-mutagenized Caenorhabditis elegans strain. Here we describe the genome-wide mutational profile of 17 EMS-mutagenized genomes as assessed with a bioinformatic pipeline, called MAQGene. Surprisingly, we find that while outcrossing mutagenized strains does reduce the total number of mutations, a striking mutational load is still observed even in outcrossed strains. Such genetic complexity has to be taken into account when establishing a causative relationship between genotype and phenotype. Even though unintentional, the 17 sequenced strains described here provide a resource of allelic variants in almost 1000 genes, including 62 premature stop codons, which represent candidate knockout alleles that will be of further use for the C. elegans community to study gene function.
Whole-Genome Profiling of Mutagenesis inCaenorhabditis elegans
Authors: Flibotte Stephane , Edgley Mark L , Chaudhry Iasha , Taylor Jon , Neil Sarah E , Rogula Aleksandra , Zapf Rick , Hirst Martin , Butterfield Yaron , Jones Steven J , Marra Marco A , Barstead Robert J , Moerman Donald G
Published: May 2010

Deep sequencing offers an unprecedented view of an organism's genome. We describe the spectrum of mutations induced by three commonly used mutagens: ethyl methanesulfonate (EMS), N-ethyl-N-nitrosourea (ENU), and ultraviolet trimethylpsoralen (UV/TMP) in the nematode Caenorhabditis elegans. Our analysis confirms the strong GC to AT transition bias of EMS. We found that ENU mainly produces A to T and T to A transversions, but also all possible transitions. We found no bias for any specific transition or transversion in the spectrum of UV/TMP-induced mutations. In 10 mutagenized strains we identified 2723 variants, of which 508 are expected to alter or disrupt gene function, including 21 nonsense mutations and 10 mutations predicted to affect mRNA splicing. This translates to an average of 50 informative mutations per strain. We also present evidence of genetic drift among laboratory wild-type strains derived from the Bristol N2 strain. We make several suggestions for best practice using massively parallel short read sequencing to ensure mutation detection.
Genome-Wide Association Studies and the Problem of Relatedness Among Advanced Intercross Lines and Other Highly Recombinant Populations
Authors: Cheng Riyan , Lim Jackie E , Samocha Kaitlin E , Sokoloff Greta , Abney Mark , Skol Andrew D , Palmer Abraham A
Published: May 2010

Model organisms offer many advantages for the genetic analysis of complex traits. However, identification of specific genes is often hampered by a lack of recombination between the genomes of inbred progenitors. Recently, genome-wide association studies (GWAS) in humans have offered gene-level mapping resolution that is possible because of the large number of accumulated recombinations among unrelated human subjects. To obtain analogous improvements in mapping resolution in mice, we used a 34th generation advanced intercross line (AIL) derived from two inbred strains (SM/J and LG/J). We used simulations to show that familial relationships among subjects must be accounted for when analyzing these data; we then used a mixed model that included polygenic effects to address this problem in our own analysis. Using a combination of F2 and AIL mice derived from the same inbred progenitors, we identified genome-wide significant, subcentimorgan loci that were associated with methamphetamine sensitivity, (e.g., chromosome 18; LOD = 10.5) and non-drug-induced locomotor activity (e.g., chromosome 8; LOD = 18.9). The 2-LOD support interval for the former locus contains no known genes while the latter contains only one gene (Csmd1). This approach is broadly applicable in terms of phenotypes and model organisms and allows GWAS to be performed in multigenerational crosses between and among inbred strains where familial relatedness is often unavoidable.
Serial Measurements of Lung Function in a Cohort of Young Children With Bronchopulmonary Dysplasia
Authors: Fakhoury Khoulood F. , Sellers Charles , Smith E. O'Brian , Rama Jennifer A. , Fan Leland L.
Published: May 2010

OBJECTIVE:

We aimed to prospectively and longitudinally measure lung function in a cohort of children with bronchopulmonary dysplasia (BPD) during their first 3 years of life.

METHODS:

Forty-four children with BPD with a mean (±SD) gestational age of 25.6 (±1.7) weeks and birth weight of 0.767 (±0.2) kg underwent serial measurements of lung function (maximum flow at functional residual capacity [VmaxFRC] and functional residual capacity [FRC]) at 6, 12, and 24 months after initial discharge from the neonatal care unit.

RESULTS:

Compared with normative data, children with BPD had low partial expiratory airflow, measured by VmaxFRC, with mean z score (±SD) of −1.92 (±1.04), −1.79 (±1.5), and −1.67 (±1.5) at 6, 12, and 24 months, respectively. Over time there was no significant improvement in z scores (P = .66), and 45% of the patients had a z score value of less than −2 (2 SDs below the mean) at the end of the study. FRC measurements steadily and significantly increased over time. Partial expiratory flow showed no correlation with gestational age, birth weight, or length of mechanical ventilation. Mean FRC was significantly higher in children who were using bronchodilators and inhaled steroids but showed no correlation with clinical symptoms. Bronchodilator response was initially present in 30% of the patients and declined to 20% at the end of the study.

CONCLUSIONS:

During the first 3 years of life, children with mostly moderate-to-severe BPD continue to show significant abnormalities with airflow limitation according to lung-function testing.
Defining the Reference Range for Oxygen Saturation for Infants After Birth
Authors: Dawson Jennifer A. , Kamlin C. Omar F. , Vento Maximo , Wong Connie , Cole Tim J. , Donath Susan M. , Davis Peter G. , Morley Colin J.
Published: May 2010

OBJECTIVE:

The goal was to define reference ranges for pulse oxygen saturation (Spo2) values in the first 10 minutes after birth for infants who received no medical intervention in the delivery room.

METHODS:

Infants were eligible if a member of the research team was available to record Spo2 immediately after birth. Infants were excluded if they received supplemental oxygen or any type of assisted ventilation. Spo2 was measured with a sensor applied to the right hand or wrist as soon as possible after birth; data were collected every 2 seconds.

RESULTS:

We studied 468 infants and recorded 61650 Spo2 data points. The infants had a mean ± SD gestational age of 38 ± 4 weeks and birth weight of 2970 ± 918 g. For all 468 infants, the 3rd, 10th, 50th, 90th, and 97th percentile values at 1 minute were 29%, 39%, 66%, 87%, and 92%, respectively, those at 2 minutes were 34%, 46%, 73%, 91%, and 95%, and those at 5 minutes were 59%, 73%, 89%, 97%, and 98%. It took a median of 7.9 minutes (interquartile range: 5.0–10 minutes) to reach a Spo2 value of >90%. Spo2 values for preterm infants increased more slowly than those for term infants. We present percentile charts for all infants, term infants of ≥37 weeks, preterm infants of 32 to 36 weeks, and extremely preterm infants of <32 weeks.

CONCLUSION:

These data represent reference ranges for Spo2 in the first 10 minutes after birth for preterm and term infants.
Special Health Care Needs of Infants Born at the Limits of Viability
Authors: Stephens Bonnie E. , Tucker Richard , Vohr Betty R.
Published: May 2010

OBJECTIVE:

The objective of this study was to compare rates of survival and special health care needs (SHCN) from discharge to 18 months' corrected age between infants who were born between 22 and 24 weeks and 25 and 27 weeks and to determine predictors and persistence of SHCN.

METHODS:

Data were collected on 508 infants who were born between 22 and 27 weeks from January 1, 1998, to December 31, 2002 at Women and Infants Hospital. SHCN was defined as need for home oxygen, medication, monitor, gastrostomy tube, or ventriculoperitoneal shunt. χ2 was used to compare rates of survival and SHCN between groups. Regression analyses explored predictors of SHCN and their persistence.

RESULTS:

Survival at 22 to 24 weeks was 53% vs 90% at 25 to 27 weeks. There were no 22-week survivors. Survivors at 23 to 24 weeks were more likely to be discharged on oxygen, a monitor, or medications; remain on oxygen or a monitor or require tube feeds at 18 months; and have a SHCN at any time than survivors who were born at 25 to 27 weeks. The strongest predictor of SHCN at discharge was chronic lung disease and at 18 months was public health insurance.

CONCLUSIONS:

Rates of SHCN were high for infants who were born at the limits of viability. Although rates decreased with increasing age, 40% had persistent SCHN at 18 months. The association of public health insurance with persistent SHCN indicates a need for comprehensive health care and support services for infants with combined biological and environmental risks.
Prophylactic or Early Selective Surfactant Combined With nCPAP in Very Preterm Infants
Authors: Sandri Fabrizio , Plavka Richard , Ancora Gina , Simeoni Umberto , Stranak Zbyněk , Martinelli Stefano , Mosca Fabio , Nona José , Thomson Merran , Verder Henrik , Fabbri Laura , Halliday Henry ,   for the CURPAP Study Group
Published: May 2010

OBJECTIVE:

Early surfactant followed by extubation to nasal continuous positive airway pressure (nCPAP) compared with later surfactant and mechanical ventilation (MV) reduce the need for MV, air leaks, and bronchopulmonary dysplasia. This randomized, controlled trial investigated whether prophylactic surfactant followed by nCPAP compared with early nCPAP application with early selective surfactant would reduce the need for MV in the first 5 days of life.

METHODS:

A total of 208 inborn infants who were born at 25 to 28 weeks' gestation and were not intubated at birth were randomly assigned to prophylactic surfactant or nCPAP within 30 minutes of birth. Outcomes were assessed within the first 5 days of life and until death or discharge of the infants from hospital.

RESULTS:

Thirty-three (31.4%) infants in the prophylactic surfactant group needed MV in the first 5 days of life compared with 34 (33.0%) in the nCPAP group (risk ratio: 0.95 [95% confidence interval: 0.64–1.41]; P = .80). Death and type of survival at 28 days of life and 36 weeks' postmenstrual age and incidence of main morbidities of prematurity (secondary outcomes) were similar in the 2 groups. A total of 78.1% of infants in the prophylactic surfactant group and 78.6% in the nCPAP group survived in room air at 36 weeks' postmenstrual age.

CONCLUSIONS:

Prophylactic surfactant was not superior to nCPAP and early selective surfactant in decreasing the need for MV in the first 5 days of life and the incidence of main morbidities of prematurity in spontaneously breathing very preterm infants on nCPAP.
Legg-Calvé-Perthes Disease and Risks for Cardiovascular Diseases and Blood Diseases
Authors: Hailer Yasmin D. , Montgomery Scott M. , Ekbom Anders , Nilsson Olof S. , Bahmanyar Shahram
Published: May 2010

OBJECTIVE:

We hypothesized that patients with Legg-Calvé-Perthes disease (LCPD) might have higher risks of cardiovascular and blood diseases.

METHODS:

A total of 3141 patients, 2 to 15 years of age, with LCPD diagnosed between 1965 and 2005 were identified with the Swedish Inpatient Register. A total of 15 595 individuals without LCPD were selected randomly from among the Swedish general population, with matching according to year of birth, age, gender, and region of residence. Cox proportional-hazard regression analyses, with adjustment for socioeconomic index, were used to estimate relative risks. The patients also were compared with their same-gender siblings.

RESULTS:

Patients with LCPD had a hazard ratio (HR) of 1.70 (95% confidence interval [CI]: 1.39–2.09) for cardiovascular diseases, compared with individuals without LCPD. The point estimate was slightly higher among subjects >30 years of age at the follow-up (HR: 2.10 [95% CI: 1.52–2.91]). There were statistically significantly higher risks for blood diseases, including anemias and coagulation defects (HR: 1.41 [95% CI: 1.07–1.86]), which were more pronounced among subjects >30 years of age at the follow-up (HR: 2.70 [95% CI: 1.50–4.84]). Patients also had statistically significantly higher risks of hypertensive disease (HR: 2.97 [95% CI: 1.87–4.72]) and nutritional anemia (HR: 2.92 [95% CI: 1.58–5.40]). Analyses using siblings as the comparison group showed consistent results for cardiovascular diseases.

CONCLUSION:

The results are consistent with the hypothesis that an insufficient blood supply to the femoral head, attributable to vascular pathologic conditions, is involved in the pathogenesis of LCPD.
A abordagem proibicionista em desconstrução: compreensão fenomenológica existencial do uso de drogas
Authors: Sodelli Marcelo
Published: May 2010

O presente artigo pretende, por meio do pensamento da fenomenologia existencial, desconstruir o modelo proibicionista ao uso de drogas. Ao compreender o homem como um ser inacabado, sempre entregue ao seu próprio cuidado, o estudo caminhará na direção de demonstrar a incompatibilidade dos objetivos proibicionistas com o modo singular de ser do homem. Demonstraremos que é a própria condição existencial do homem que gera o que nomearemos como "vulnerabilidade existencial", condição esta impossível de ser modificada. Com efeito, argumentaremos que qualquer abordagem preventiva que tenha como princípio fundamental erradicar o uso de drogas já estaria fadada ao fracasso. Fundamentando-nos ainda neste posicionamento, rejeitaremos a compreensão proibicionista que o "uso de drogas" é sempre e invariavelmente um comportamento desviante (patologia). Por fim, o estudo aponta para a importância do desenvolvimento de uma nova abordagem preventiva que absorva de modo integral a singularidade da condição humana (vulnerabilidade existencial), rompendo definitivamente com os preceitos proibicionistas, a saber, a abordagem de redução de danos.
Comparison between two household surveys on psychotropic drug use in Brazil: 2001 and 2004
Authors: Fonseca Arilton Martins , Galduróz José Carlos Fernandes , Noto Ana Regina , Carlini Elisaldo Luiz de Araújo
Published: May 2010

CEBRID (Brazilian Center of Information on Psychotropic Drugs) conducted two household surveys on drug use in Brazil, the first in 2001 and the second in 2005, making it possible for researchers, for the first time ever, to have a timeline comparison using this type of methodology. The universe studied corresponded to the Brazilian population living in 107 Brazilian cities with more than 200.00 inhabitants. 8,589 people were interviewed in the first survey in 2001, and 7,939 people in the second. Data on prevalence of lifetime use for psychotropic drugs showed that there was a significant increase only in the number of people who had made lifetime use of psychotropic substances (including tobacco and alcohol). In 2001, 19.4% of the interviewees reported having used some type of drug, and the ranking of lifetime drug use in 2004 was 22.8%, a statistically significant increase. There was also a statistically significant increase in lifetime use of alcohol and tobacco in comparison between the two surveys.