bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Epstein-Barr Virus Mutant Produces Immunogenic Defective Particles Devoid of Viral DNA
Authors: Pavlova Sophia , Feederle Regina , Gärtner Kathrin , Fuchs Walter , Granzow Harald , Delecluse Henri-Jacques 
Published: December 2012

ABSTRACT

Virus-like particles (VLPs) from hepatitis B and human papillomaviruses have been successfully used as preventative vaccines against these infectious agents. These VLPs consist of a self-associating capsid polymer formed from a single structure protein and are devoid of viral DNA. Since virions from herpesviruses consist of a large number of molecules of viral and cellular origin, generating VLPs from a subset of these would be a particularly arduous task. Therefore, we have adopted an alternative strategy that consists of producing DNA-free defective virus particles in a cell line infected by a herpesvirus mutant incapable of packaging DNA. We previously reported that an Epstein-Barr virus (EBV) mutant devoid of the terminal repeats (ΔTR) that act as packaging signals in herpesviruses produces substantial amounts of VLPs and of light particles (LPs). However, ΔTR virions retained some infectious genomes, and although these mutants had lost their transforming abilities, this poses potential concerns for clinical applications. Therefore, we have constructed a series of mutants that lack proteins involved in maturation and assessed their ability to produce viral DNA-free VLP/LPs. Some of the introduced mutations were deleterious for capsid maturation and virus production. However, deletion of BFLF1/BFRF1A or of BBRF1 resulted in the production of DNA-free VLPs/LPs. The ΔBFLF1/BFRF1A viruses elicited a potent CD4
+
T-cell response that was indistinguishable from the one obtained with wild-type controls. In summary, the defective particles produced by the ΔBFLF1/BFRF1A mutant fulfill the criteria of efficacy and safety expected from a preventative vaccine.
Structure of a Dengue Virus Envelope Protein Late-Stage Fusion Intermediate
Authors: Klein Daryl E. , Choi Jason L. , Harrison Stephen C. 
Published: December 2012

ABSTRACT
The final stages of dengue virus fusion are thought to occur when the membrane-proximal stem drives the transmembrane anchor of the viral envelope protein (E) toward the fusion loop, buried in the target cell membrane. Crystal structures of E have lacked this essential stem region. We expressed and crystallized soluble mutant forms of the dengue virus envelope protein (sE) that include portions of the juxtamembrane stem. Their structures represent late-stage fusion intermediates. The proximal part of the stem has both intra- and intermolecular interactions, so the chain “zips up” along the trimer seam. The penultimate interaction we detected involves the conserved residue F402, which has hydrophobic contacts with a conserved surface on domain II. These interactions do not require any larger-scale changes in trimer packing. The techniques for expression and crystallization of sE containing stem reported here may allow further characterization of the final stages of flavivirus fusion.
Lateral variation in sandstone lithofacies from conventional core, Scotian Basin: implications for reservoir quality and connectivity 1This article is one of a series of papers published in this CJES Special Issue on the theme of Mesozoic–Cenozoic geology of the Scotian Basin. 2Geological Survey of Canada Contribution 20120021.
Authors: Gould Kathleen M. , Piper David J.W. , Pe-Piper Georgia 
Published: December 2012

Facies analysis in outcrops on land is strongly dependent on the lateral variability of lithofacies. Interpretation of conventional core in wells relies principally on the vertical succession of lithofacies. To better understand depositional environments and reservoir sandstone connectivity, the lithofacies of reservoir sandstones sampled in conventional core were correlated laterally through two sets of closely spaced wells in the Scotian Basin: in the Barremian–Albian succession around the Panuke–Cohasset field and in the Late Jurassic succession west of the Venture field. Regional correlation by gamma logs is confirmed by lithologically similar transgressive units including shelly mudstones or coals. A standard scheme of lithofacies and recognition of three types of parasequences were used for comparisons between wells. Some transgressive surfaces are of limited extent and may represent delta distributary switching and subsidence rather than regional changes in sea level. Major sandstone packets extend at least 10–30 km laterally, but commonly show lateral changes in lithofacies, and some are bounded by the margins of incised valleys. Such packages show poor correlation of lithofacies with porosity and permeability, probably because of the variable effects of diagenesis. Lateral transitions from tidal estuary sandstones in Panuke B-90 to thick-bedded river-mouth turbidites in Lawrence D-14, over a distance of 15 km, demonstrates the scale of delta lobes and confirms that sharp-based sandstone beds are turbidites related to river floods, not storm deposits. Similar lateral transitions in the Venture field are on a similar scale and pass distally into prodeltaic muddy landslide deposits.
The effects of water currents on walleye (Sander vitreus) eggs and larvae and implications for the early survival of walleye in Lake Erie
Authors: Humphrey Sarah , Zhao Yingming , Higgs Dennis 
Published: December 2012

Advection of teleost early life stages from nursery habitats can greatly impact year-class strength. Few studies test the effects of current on retention in freshwater fish eggs and larvae, so we used walleye (Sander vitreus) to assess current effects throughout egg and larval development and the role of substrate on egg retention. Eggs were removed from sand substrates at currents of 12 cm·s–1, but much higher speeds were required for removal from tile or stones. Larvae exhibited biphasic swimming ability, with slow swimming below 21 mm total length and rapidly increasing ability above 21 mm. These data necessitate adjusting models currently used to link water current and nursery advection in this and similar species, as the current effects were clearly substrate- and size-dependent.
Food restriction prior to release reduces precocious maturity and improves migration tendency of Atlantic salmon (Salmo salar) smolts
Authors: Vainikka Anssi , Huusko Riina , Hyvärinen Pekka , Korhonen Pekka K. , Laaksonen Tapio , Koskela Juha , Vielma Jouni , Hirvonen Heikki , Salminen Matti 
Published: December 2012

Since food availability is known to affect both the precocious maturation and start of feeding migration in wild juvenile salmonids, we examined if a reduction in otherwise plentiful feeding in hatcheries could improve migration tendency and the subsequent survival of released Atlantic salmon (Salmo salar) smolts. A reduction in diet lipid content and feed ration (FR) the previous spring and in FR in the winter prior to release proved efficient; spring-diet treatment halved the proportion of mature males in the autumn prior to release, and a reduction in FR in the winter prior to release decreased latency before leaving the stocking site. In addition, a reduction in FR in winter affected the onset of migration, improved migration speed, and defined the direction of migration downstream in controlled experiments. However, diet manipulations neither affected the swimming endurance nor improved the generally poor tag recapture rates. We conclude that reduced FR at specific times could be used to reduce both precocious male maturity and improve the migration tendency of released salmon.
MicroRNAs Play a Big Role in Regulating Ovarian Cancer–Associated Fibroblasts and the Tumor Microenvironment
Authors: Chou Jonathan , Werb Zena 
Published: December 2012

Abstract
Summary: Mitra and colleagues analyzed microRNA expression profiles of fibroblasts isolated from ovarian cancer patients, searching for dysregulated microRNAs in the stromal compartment of human cancer. They found that decreased miR-31 and miR-214 and increased miR-155 expression can reprogram normal fibroblasts into tumor-promoting cancer-associated fibroblasts. They identified CCL5, a protumorigenic chemokine that is highly expressed in tumors, as a key target of miR-214, thus showing that microRNA perturbation in the stromal microenvironment can affect tumor growth. Cancer Discov; 2(12); 1078–80. ©2012 AACR.
Commentary on Mitra et al., p. 1100
Chest Compression–Only Cardiopulmonary Resuscitation for Out-of-Hospital Cardiac Arrest With Public-Access Defibrillation
Authors: Iwami Taku , Kitamura Tetsuhisa , Kawamura Takashi , Mitamura Hideo , Nagao Ken , Takayama Morimasa , Seino Yoshihiko , Tanaka Hideharu , Nonogi Hiroshi , Yonemoto Naohiro , Kimura Takeshi 
Published: December 2012

Background—
It remains unclear which is more effective to increase survival after out-of-hospital cardiac arrest in those with public-access defibrillation, bystander-initiated chest compression–only cardiopulmonary resuscitation (CPR) or conventional CPR with rescue breathing.

Methods and Results—
A nationwide, prospective, population-based observational study covering the whole population of Japan and involving consecutive out-of-hospital cardiac arrest patients with resuscitation attempts has been conducted since 2005. We enrolled all out-of-hospital cardiac arrests of presumed cardiac origin that were witnessed and received shocks with public-access automated external defibrillation (AEDs) by bystanders from January 1, 2005, to December 31, 2009. The main outcome measure was neurologically favorable 1-month survival. We compared outcomes by type of bystander-initiated CPR (chest compression–only CPR and conventional CPR with compressions and rescue breathing). Multivariable logistic regression was used to assess the relationship between the type of CPR and a better neurological outcome. During the 5 years, 1376 bystander-witnessed out-of-hospital cardiac arrests of cardiac origin in individuals who received CPR and shocks with public-access AEDs by bystanders were registered. Among them, 506 (36.8%) received chest compression–only CPR and 870 (63.2%) received conventional CPR. The chest compression–only CPR group (40.7%, 206 of 506) had a significantly higher rate of 1-month survival with favorable neurological outcome than the conventional CPR group (32.9%, 286 of 870; adjusted odds ratio, 1.33; 95% confidence interval, 1.03–1.70).

Conclusions—
Compression-only CPR is more effective than conventional CPR for patients in whom out-of-hospital cardiac arrest is witnessed and shocked with public-access defibrillation. Compression-only CPR is the most likely scenario in which lay rescuers can witness a sudden collapse and use public-access AEDs.
Performance and Technique of Coherent 2-μm Differential Absorption and Wind Lidar for Wind Measurement
Authors: Iwai Hironori , Ishii Shoken , Oda Ryoko , Mizutani Kohei , Sekizawa Shinya , Murayama Yasuhiro 
Published: December 2012

Abstract
A coherent 2-μm differential absorption and wind lidar (Co2DiaWiL) has been built with a high-power Q-switched Tm,Hm:YLF laser to measure CO2 concentration and radial wind speed. The performance of the Co2DiaWiL is described and analyzed, with a view to demonstrating system capabilities for remote measurements of wind velocities in the atmospheric boundary layer and free troposphere. Bias in the velocity measurements was estimated at −0.0069 m s−1 using measurements from a stationary hard target. The Co2DiaWiL achieved a velocity precision of 0.12 m s−1, derived from the magnitude of random error in radial wind velocity measurements. These measurements were made for ranges out to 20–25 km by using a horizontally fixed beam mode for average times of 1 min. Quantitative intercomparisons of 1-min averages between the Co2DiaWiL and a sonic anemometer revealed a correlation coefficient of 0.99. This study demonstrated measurements of horizontal wind profiles, by making radial wind velocity measurements with the Co2DiaWiL using conical scanning. Profile differences at higher levels could be attributed to probable large horizontal separations of the radiosondes and the low signal-to-noise ratio of the Co2DiaWiL. A pseudo-dual-Doppler technique was developed to retrieve horizontal wind components with a single-Doppler lidar and a steering mirror. Intercomparisons of the 1-min-averaged u and υ components from the pseudo-dual-Doppler lidar measurements with those from the sonic anemometer revealed correlation coefficients of 0.84 and 0.83, respectively.
Delivering Climate Services: Organizational Strategies and Approaches for Producing Useful Climate-Science Information
Authors: McNie Elizabeth C. 
Published: December 2012

Abstract
Despite numerous and widespread calls for more “useful” climate-science information to inform policy, most climate science is still produced in a way that is consistent with the “linear model” of research that favors pure basic research over other approaches, resulting in missed opportunities to link useful climate science with decision makers. To improve the ability to adapt to a changing climate, it is necessary to improve the linkages between the production and supply of climate-science information with users’ needs to ensure that the climate science is contextual, credible, trusted, and understood by the users. This paper reports on research that evaluated how three Regional Integrated Sciences and Assessments (RISA) programs produced useful climate information for improved decision support in a variety of sectors. Research indicates that these organizations utilized several processes and approaches to produce useful climate information, including identifying users’ information needs; translating, communicating, and sharing knowledge; producing and situating social capital; building capacity in the user community to understand and utilize the climate-science information; and maintaining a flexible and nimble organization guided by strong leadership. The process of linking the production and supply of climate-science information with users’ demands is a complex, highly contextual social process that requires ample resources and time management, research agendas that are “end to end” and can respond to changing contexts, and organizational commitment to support “use-inspired” research. Additional research is needed to improve evaluation methods and metrics used to assess climate-service organizations.
High rate of transplacental infection and transmission of Neospora caninum following experimental challenge of cattle at day 210 of gestation
Authors: Benavides Julio , Katzer Frank , Maley Stephen W , Bartley Paul M , Cantón Germán , Palarea-Albaladejo Javier , Purslow Caroline A , Pang Yvonne , Rocchi Mara S , Chianini Francesca , Buxton David , Innes Elisabeth A 
Published: December 2012

AbstractIn order to investigate the pathogenesis of neosporosis following a primary infection in late pregnancy, cattle were subcutaneously challenged with 5 × 108Neospora caninum(NC1 isolate) tachyzoites at day 210 of gestation and serial necropsies were then carried out at 14, 28, 42 and 56 days post-infection (dpi). No abortions occurred and all the foetuses were viable at the time of euthanasia. There was a high rate of vertical transmission, as parasites were detected by immunohistochemical labelling and PCR in all the foetuses from 28 dpi. Focal necrotic lesions were observed in the placentomes of the placenta from 28 dpi and showed resolution during later time points, denoted by infiltration of inflammatory cells at 42 dpi and fibrosis at 56 dpi. Foetuses at 28 and 42 dpi showed scarce and isolated lesions which are unlikely to represent a threat to foetal viability. No lesions were observed in the foetuses at 14 or 56 dpi suggesting control of the infection and resolution of the lesions by maternal and foetal immune responses. Once infection was established, it could not be cleared from the host and vertical transmission of the parasite occurred in all infected hosts. Parasite was detected in the placenta at 28 dpi, while in previous experimental infections of cattle at day 70 and 140 of gestation using the same challenge model, it was already present at day 14 post infection. This suggests that a change in the maternal immune response plays a crucial role in limiting the initial infection during the last term of pregnancy.
Drosophila king tubby (ktub) mediates light-induced rhodopsin endocytosis and retinal degeneration
Authors: Chen Shu-Fen , Tsai Yu-Chen , Fan Seng-Sheen 
Published: December 2012

Background

Background
The tubby (tub) and tubby-like protein (tulp) genes encode a small family of proteins found in many organisms. Previous studies have shown that TUB and TULP genes in mammalian involve in obesity, neural development, and retinal degeneration. The purpose of this study was to investigate the role of Drosophila king tubby (ktub) in rhodopsin 1 (Rh1) endocytosis and retinal degeneration upon light stimulation.

Results

Drosophila ktub mutants were generated using imprecise excision. Wild type and mutant flies were raised in dark or constant light conditions. After a period of light stimulation, retinas were dissected, fixed and stained with anti-Rh1 antibody to reveal Rh1 endocytosis. Confocal and transmission electron microscope were used to examine the retinal degeneration. Immunocytochemical analysis shows that Ktub is expressed in the rhabdomere domain under dark conditions. When flies receive light stimulation, the Ktub translocates from the rhabdomere to the cytoplasm and the nucleus of the photoreceptor cells. Wild type photoreceptors form Rh1-immunopositive large vesicles (RLVs) shortly after light stimulation. In light-induced ktub mutants, the majority of Rh1 remains at the rhabdomere, and only a few RLVs appear in the cytoplasm of photoreceptor cells. Mutation of norpA allele causes massive Rh1 endocytosis in light stimulation. In ktub and norpA double mutants, however, Rh1 endocytosis is blocked under light stimulation. This study also shows that ktub and norpA double mutants rescue the light-induced norpA retinal degeneration. Deletion constructs further demonstrate that the Tubby domain of the Ktub protein participates in an important role in Rh1 endocytosis.

Conclusions
The results in this study delimit the novel function of Ktub in Rh1 endocytosis and retinal degeneration.
Molecular phylogeny of microhylid frogs (Anura: Microhylidae) with emphasis on relationships among New World genera
Authors: de Sá Rafael O , Streicher Jeffrey W , Sekonyela Relebohile , Forlani Mauricio C , Loader Simon P , Greenbaum Eli , Richards Stephen , Haddad Célio F B 
Published: December 2012

AbstractBackgroundOver the last ten years we have seen great efforts focused on revising amphibian systematics. Phylogenetic reconstructions derived from DNA sequence data have played a central role in these revisionary studies but have typically under-sampled the diverse frog family Microhylidae. Here, we present a detailed phylogenetic study focused on expanding previous hypotheses of relationships within this cosmopolitan family. Specifically, we placed an emphasis on assessing relationships among New World genera and those taxa with uncertain phylogenetic affinities (i.e.,incertae sedis).ResultsOne mitochondrial and three nuclear genes (about 2.8 kb) were sequenced to assess phylogenetic relationships. We utilized an unprecedented sampling of 200 microhylid taxa representing 91% of currently recognized subfamilies and 95% of New World genera. Our analyses do not fully resolve relationships among subfamilies supporting previous studies that have suggested a rapid early diversification of this clade. We observed a close relationship betweenSynapturanusandOtophryneof the subfamily Otophryninae. Within the subfamily Gastrophryninae relationships between genera were well resolved.ConclusionOtophryninae is distantly related to all other New World microhylids that were recovered as a monophyletic group, Gastrophryninae. Within Gastrophryninae, five genera were recovered as non-monophyletic; we propose taxonomic re-arrangements to render all genera monophyletic. This hypothesis of relationships and updated classification for New World microhylids may serve as a guide to better understand the evolutionary history of this group that is apparently subject to convergent morphological evolution and chromosome reduction. Based on a divergence analysis calibrated with hypotheses from previous studies and fossil data, it appears that microhylid genera inhabiting the New World originated during a period of gradual cooling from the late Oligocene to mid Miocene.
Feasibility of using 454 pyrosequencing for studying quasispecies of the whole dengue viral genome
Authors: Chin-inmanu Kwanrutai , Suttitheptumrong Aroonroong , Sangsrakru Duangjai , Tangphatsornruang Sithichoke , Tragoonrung Somvong , Malasit Prida , Tungpradabkul Sumalee , Suriyaphol Prapat 
Published: December 2012

Abstract

Background
Dengue is the world's most common mosquito-borne viral disease. Poor proofreading by RNA polymerase during its replication results in the accumulation of mutations in its genome. This leads to a diversity of genotypes in the viral population termed quasispecies. Quasispecies play an important role in disease severity. The study of quasispecies in dengue has been hindered because of the requirement for large amounts of cloning and sequencing, which could be overcome by 454 pyrosequencing. In this study, we attempted to demonstrate the feasibility of using 454 pyrosequencing to study genome diversity of dengue virus quasispecies by sequencing a pool of known dengue viral strains.

Results
Two sets of dengue DNA templates were sequenced by 454/Roche GS FLX. The total number of reads for data 1 and data 2 were 54,440 and 134,441, with average lengths of 221 and 232 bp, respectively. Reads containing ambiguous base Ns were excluded (6.00% in data 1, 7.05% in data 2). More than 99% of reads could be aligned back to the correct serotypes by BLAST. The reads covered the whole genome without any gaps, and the minimum coverage depth was 50×. Frequencies of known strains detected from each data set were highly correlated with the input ratios. We also explored criteria for filtering error reads and artifacts from true variations.

Conclusions
This study showed that 454 pyrosequencing, coupled with our analysis procedure, could sequence the whole genome of dengue virus with good coverage. The ratio of detected variants in the sequencing data reflected the starting ratio, proving that the proposed technique could be used to study the frequencies of variants in quasispecies.
The prevalence of anal human papillomavirus among young HIV negative men who have sex with men
Authors: Zou Huachun , Fairley Christopher K , Hocking Jane S , Garland Suzanne M , Grulich Andrew E , Chen Marcus Y 
Published: December 2012

Abstract
Men who have sex with men (MSM) especially those who are HIV positive are at risk for HPV-associated anal cancer. We systematically reviewed studies with data on the prevalence of vaccine preventable anal HPV among men who have sex with men aged 25 or younger and identified 6 studies. None of these studies were specifically designed to determine the prevalence of HPV in this population. Available data, albeit limited, suggest many young MSM may not already be HPV infected. Further studies using representative sampling focused on teenage MSM are required to confirm this.