bluuebunny/crossref_metadata_2025 huggingface dataset:
Neurons in the pigeon nidopallium caudolaterale signal the selection and execution of perceptual decisions
Authors: Lengersdorf Daniel , Pusch Roland , Güntürkün Onur , Stüttgen Maik C.
Published: August 2014

Sensory systems provide organisms with information on the current status of the environment, thus enabling adaptive behavior. The neural mechanisms by which sensory information is exploited for action selection are typically studied with mammalian subjects performing perceptual decision‐making tasks, and most of what is known about these mechanisms at the single‐neuron level is derived from cortical recordings in behaving monkeys. To explore the generality of neural mechanisms underlying perceptual decision making across species, we recorded single‐neuron activity in the pigeon nidopallium caudolaterale (NCL), a non‐laminated associative forebrain structure thought to be functionally equivalent to mammalian prefrontal cortex, while subjects performed a visual categorisation task. We found that, whereas the majority of NCL neurons unspecifically upregulated or downregulated activity during stimulus presentation, ~20% of neurons exhibited differential activity for the sample stimuli and predicted upcoming choices. Moreover, neural activity in these neurons was ramping up during stimulus presentation and remained elevated until a choice was initiated, a response pattern similar to that found in monkey prefrontal and parietal cortices in saccadic choice tasks. In addition, many NCL neurons coded for movement direction during choice execution and differentiated between choice outcomes (reward and punishment). Taken together, our results implicate the NCL in the selection and execution of operant responses, an interpretation resonating well with the results of previous lesion studies. The resemblance of the response patterns of NCL neurons to those observed in mammalian cortex suggests that, despite differing neural architectures, mechanisms for perceptual decision making are similar across classes of vertebrates.
Restless legs syndrome is associated with cardio/cerebrovascular events and mortality in end‐stage renal disease
Authors: Lin C.‐H. , Sy H.‐N. , Chang H.‐W. , Liou H.‐H. , Lin C.‐Y. , Wu V.‐C. , Wu S.‐L. , Chang C.‐C. , Chiu P.‐F. , Li W.‐Y. , Lin S.‐Y. , Wu K.‐D. , Chen Y.‐M. , Wu R.‐M.
Published: August 2014

Background and purpose

Earlier studies suggested an association between idiopathic restless legs syndrome (RLS) and cardiovascular diseases. However, the risk of cardiovascular events in patients with secondary RLS due to end‐stage renal disease (ESRD) is unclear. Our aim was to examine whether ESRD patients with RLS had an increased risk of cardio/cerebrovascular events and mortality.

Methods

In all, 1093 ESRD patients were recruited between 2009 and 2010. The diagnosis and severity of RLS were assessed in a face‐to‐face interview. The occurrence of cardio/cerebrovascular events and death were confirmed by medical record review. The association between RLS and the outcomes of interest was examined using an adjusted multivariate Cox regression model.

Results

After a mean follow‐up period of 3.7 ± 0.8 years, ESRD patients with RLS had a significantly higher risk of developing cardiovascular events and strokes [adjusted hazard ratio (aHR) 2.82, 95% confidence interval (CI) 2.02–4.11, and aHR 2.41, 95% CI 1.55–3.75, respectively] compared with patients without RLS. Increasing RLS severity was associated with an increasing likelihood of cardiovascular events [mild RLS severity, aHR 1.71 (95% CI 1.02–2.87); moderate, 2.79 (1.64–4.66); severe, 2.85 (1.99–4.46)] and strokes [mild, 1.89 (0.87–4.16); moderate, 2.42 (1.50–3.90); severe, 2.64 (1.49–4.91)] in a dose‐dependent manner. RLS also increased the risk of total mortality in patients with ESRD [aHR 1.53 (95% CI 1.07–2.18), P = 0.02]; this association attenuated slightly after stratification by individual RLS severity category [mild RLS severity, aHR 1.44 (95% CI 0.78–2.67); moderate, 1.49 (0.98–2.55); severe, 2.03 (0.93–4.45)].

Conclusions

ESRD patients with RLS demonstrated an increased likelihood of cardio/cerebrovascular events and mortality.
The rise of endogeneity in multilevel models: A theoretical assessment of the role of stratification
Authors: Mostafa Tarek
Published: August 2014

This paper studies the role of stratification in the rise of endogeneity bias in multilevel models. The theory is illustrated using educational stratification and its implications on the estimation of multilevel education production functions. Educational stratification results from the functioning of the education market; it transforms a continuum of student characteristics into a continuum of tuition fees. These fees enter students' utility functions and determine the school they attend and its quality. In other words, student characteristics are the major determinants of school quality and the two are correlated. In this paper, I analyze how these correlations arise and what their implications are for multilevel estimation of education production functions. The major problem posed by such correlations is cross‐level endogeneity bias. The theory developed in this paper can be extended to any economic phenomenon that exhibits stratification or nesting of smaller units within larger units (employees within firms, residents within neighborhoods, etc.).
Burden of Stroke in Puerto Rico
Authors: Zevallos Juan , Santiago Fernando , González Juan , Rodríguez Abiezer , Pericchi Luis , Rodríguez-Mercado Rafael , Nobo Ulises
Published: August 2014

Stroke is the fifth leading cause of death and the first cause of long-term disability in Puerto Rico. Trained staff reviewed and independently validated the medical records of patients who had been hospitalized with possible stroke at any of the 20 largest hospitals located in Puerto Rico during 2007, 2009, and 2011. The mean age of the 5005 newly diagnosed stroke patients (51·2% female) was 70 years. At the time of hospitalization, women were 41/2 years older, were less likely to be married (60·2% vs. 39·9%, P < 0·001), smoked less (5·8% vs. 13·4%, P < 0·001), and had significantly higher proportion of diabetes (56·0% vs. 54·8%), hypertension (89·1% vs. 85·0%), and low density lipoprotein-cholesterol (LDL-Chol) > 100 mg/dL (65·7% vs. 57·5%) P < 0·05. Ischemic stroke represented 75% of all types of strokes. Atrial fibrillation was mentioned in 7·9% of the medical records. The risk for dying before discharge was similar for both genders, but was 40% higher for women than for men at one-year follow-up: age-adjusted odds ratio = 1·4 (95% confidence interval = 1·2–1·5).
A field test of a model for the stability of androdioecy in the freshwater shrimp, Eulimnadia texana
Authors: Weeks S. C. , Benvenuto C. , Reed S. K. , Duff R. J. , Duan Z.‐H. , David P.
Published: August 2014

The evolution of hermaphroditism from dioecy is a poorly studied transition. Androdioecy (the coexistence of males and hermaphrodites) has been suggested as an intermediate step in this evolutionary transition or could be a stable reproductive mode. Freshwater crustaceans in the genus Eulimnadia have reproduced via androdioecy for 24+ million years and thus are excellent organisms to test models of the stability of androdioecy. Two related models that allow for the stable maintenance of males and hermaphrodites rely on the counterbalancing of three life history parameters. We tested these models in the field over three field seasons and compared the results to previous laboratory estimates of these three parameters. Male and hermaphroditic ratios within years were not well predicted using either the simpler original model or a version of this model updated to account for differences between hermaphroditic types (‘monogenic’ and ‘amphigenic’ hermaphrodites). Using parameter estimates of the previous year to predict the next year's sex ratios revealed a much better fit to the original relative to the updated version of the model. Therefore, counter to expectations, accounting for differences between the two hermaphroditic types did not improve the fit of these models. At the moment, we lack strong evidence that the long‐term maintenance of androdioecy in these crustaceans is the result of a balancing of life history parameters; other factors, such as metapopulation dynamics or evolutionary constraints, may better explain the 24+ million year maintenance of androdioecy in clam shrimp.
Adaptive cyanogenesis clines evolve recurrently through geographical sorting of existing gene deletions
Authors: Kooyers N. J. , Olsen K. M.
Published: August 2014

Identifying the genetic basis of parallel phenotypic evolution provides insight into the process of adaptation and evolutionary constraint. White clover (Trifolium repens) has evolved climate‐associated adaptive clines in cyanogenesis (the ability to produce hydrogen cyanide upon tissue damage) in several world regions where it has been introduced. Gene‐deletion polymorphisms at the CYP79D15 and Li loci underlie the presence/absence of the cyanogenic phenotype. Both loci have undergone multiple independent gene‐deletion events, which are identifiable through molecular signatures in flanking regions. To investigate whether cyanogenesis clines in introduced populations have evolved through the sorting of standing genetic variation or de novo gene deletions, we examined cyanogenesis gene‐flanking regions in three world regions. In comparison with native Eurasian populations, we find no evidence for novel gene deletion events in any introduced region, which suggests that these adaptive clines have evolved through the geographical sorting of pre‐existing genetic variation.
Automated thresholding and analysis of microCT scanned bread dough
Authors: JENSEN S. , SAMANTA S. , CHAKRABARTI‐BELL S. , REGENAUER‐LIEB K. , SIDDIQUE K.H.M. , WANG S.
Published: August 2014

Computer aided x‐ray microtomography is an increasingly popular method to investigate the structure of materials. Continuing improvements in the technique are resulting in increasingly larger data sets. The analysis of these data sets generally involves executing a static workflow for multiple samples and is generally performed manually by researchers. Executing these processes requires a significant time investment. A workflow which is able to automate the activities of the user would be useful. In this work, we have developed an automated workflow for the analysis of microtomography scanned bread dough data sets averaging 5 GB in size. Comparing the automated workflow with the manual workflow indicates a significant amount of the time spent (33% in the case of bread dough) on user interactions in manual method. Both workflows return similar results for porosity and pore frequency distribution. Finally, by implementing an automated workflow, users save the time which would be required to manually execute the workflow. This time can be spent on more productive tasks.
Oral health‐related quality of life of removable partial denture wearers and related factors
Authors: Shaghaghian S. , Taghva M. , Abduo J. , Bagheri R.
Published: August 2014

This study aims to investigate the oral health‐related quality of life (OHRQoL) in a group of removable partial denture (RPD) wearers in Shiraz (Iran), using the Persian version of the Oral Health Impact Profile (OHIP‐14). Two hundred removable partial denture wearers had completed a questionnaire regarding patients' demographic characteristics and denture‐related factors. In addition, the OHIP‐14 questionnaire was filled out by interviewing the patients. Two measures of interpreting the OHIP‐14 scales were utilised: OHIP‐14 sum and OHIP‐14 prevalence. The relationship of the patients' demographic characteristics and denture‐related factors, with their OHRQoL was investigated. The mean OHIP‐14 sum and OHIP‐14 prevalence of RPD wearers were 13·80 (±10·08) and 44·5%, respectively. The most problematic aspects of OHIP‐14 were physical disability and physical pain. Twenty‐seven percentage and 24% of participants had reported meal interruption and eating discomfort, respectively. OHIP‐14 prevalence and OHIP‐14 sum were found to be significantly associated with factors representing RPD wearer's oral health such as self‐reported oral health and frequency of denture cleaning. Furthermore, OHIP‐14 prevalence and OHIP‐14 sum were significantly associated with factors related to frequency of denture use such as hours of wearing the denture during the day and wearing the denture while eating and sleeping. Therefore, it can be concluded that the OHRQoL of the patients of the study was generally not optimal and found to be strongly associated with oral health.
Outcomes of human immunodeficiency virus‐infected children after anti‐retroviral therapy in Malaysia
Authors: Moy Fong Siew , Fahey Paul , Nik Yusoff Nik K , Razali Kamarul A , Nallusamy Revathy ,   the TREAT Asia Pediatric HIV Observational Database (TApHOD)
Published: August 2014

Aims

To describe outcome and examine factors associated with mortality among human immunodeficiency virus (HIV)‐infected children in Malaysia after anti‐retroviral therapy (ART).

Methods

Retrospective and prospective data collected through March 2009 from children in four different states in Malaysia enrolled in TREAT Asia's Pediatric HIV Observational Database were analysed.

Results

Of 347 children in the cohort, only 278 (80.1%) were commenced on ART. The median CD4 count and median age at baseline prior to ART was 272 cells/μL and 4.2 years (interquartile range (IQR): 1.4, 7.4 years), respectively. The median duration of follow‐up was 3.7 years (IQR: 1.8, 6.0) with 32 deaths giving a crude mortality rate of 2.86 per 100 child‐years. The mortality rate highest in the first 6 months of ART was 10.62 per 100 child‐years and declined to 1.83 per 100 child‐years thereafter. On univariate analyses, only baseline median CD4 percentage, weight for age z score, height for age z score and anaemia were significantly associated with mortality. Upon including all four of these predictors into a single multivariate model, only weight for age z score remained statistically significantly predictive of mortality.

Conclusions

Children commenced on ART had high mortality in the first 6 months especially in those with low CD4 percentage, wasting and anaemia. Poor nutritional status is an important independent predictor of mortality in this study. Besides initiating ART therapy, nutritional support and intervention must receive the utmost attention.
Melatonin regulates proteomic changes during leaf senescence in Malus hupehensis
Authors: Wang Ping , Sun Xun , Xie Yinpeng , Li Mingjun , Chen Wei , Zhang Sheng , Liang Dong , Ma Fengwang
Published: August 2014

Despite the relationship between melatonin and aging, the overall changes and regulation of proteome profiling by long‐term melatonin exposure during leaf senescence is not well understood. In this study, leaf senescence in Malus hupehensis plants was delayed when exogenous melatonin was regularly applied to the roots for 2 months compared with natural leaf senescence. Proteins of samples 0 and 50 day for both treatments were extracted and labeled with TMT regents before being examined via NanoLC‐MS/MS. The proteomics data showed that 622 and 309 proteins were altered by senescence and melatonin, respectively. Our GO analysis by Blast2GO revealed that most of the altered proteins that are involved in major metabolic processes exhibited hydrolase activity and were mainly located in the plastids. These proteins were classified into several senescence‐related functional categories, including degradation of macromolecules, redox and stress responses, transport, photosynthesis, development, and other regulatory proteins. We found that melatonin treatment led to the downregulation of proteins that are normally upregulated during senescence. The melatonin‐related delay in senescence might have occurred due to the altering of proteins involved in processes associated with senescence. And as well, there are many unknown regulatory proteins possibly being involved in the melatonin's function. This study is the first to demonstrate changes at the proteome level in response to exogenous melatonin in plants. Our findings provide a set of informative and fundamental data about the role of melatonin in apple leaf senescence.
The effect of different concentrations of linseed oil or fish oil in the maternal diet on the fatty acid composition and oxidative status of sows and piglets
Authors: Tanghe S. , Missotten J. , Raes K. , De Smet S.
Published: August 2014

N‐3 polyunsaturated fatty acids (PUFA) are essential for foetal development. Hence, including n‐3 PUFA in the sow diet can be beneficial for reproduction. Both the amount and form (precursor fatty acids vs. long chain PUFA) of supplementation are important in this respect. Furthermore, including n‐3 PUFA in the diet can have negative effects, such as decreased arachidonic acid (ARA) concentration and increased oxidative stress. This study aimed to compare the efficacy to increase eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) concentrations in the piglet, when different concentrations of linseed oil (LO, source of precursor α‐linolenic acid) or fish oil (FO, source of EPA and DHA) were included in the maternal diet. Sows were fed a palm oil diet or a diet including 0.5% or 2% LO or FO from day 45 of gestation until weaning. Linoleic acid (LA) was kept constant in the diets to prevent a decrease in ARA, and all diets were supplemented with α‐tocopherol acetate (150 mg/kg) and organic selenium (0.4 mg/kg) to prevent oxidative stress. Feeding 0.5% LO or 0.5% FO to the sows resulted in comparable EPA concentrations in the 5‐day old piglet liver, but both diets resulted in lower EPA concentrations than when 2% LO was fed. The highest EPA concentration was obtained when 2% FO was fed. The DHA level in the piglet liver could only be increased when FO, but not LO, was fed to the sows. The 2% FO diet had no advantage over the 0.5% FO diet to increase DHA in the piglet. Despite the constant LA concentration in the sow diet, a decrease in ARA could not be avoided when LO or FO were included in the diet. Feeding 2% FO to the sows increased the malondialdehyde concentration (marker for lipid peroxidation) in sow plasma, but not in piglets.
Monetary Policy and Forward Guidance in the UK
Authors: Miles David
Published: August 2014

This paper assesses the case for the use of more explicit forward guidance on monetary policy in the UK. Such a policy was introduced in the middle of 2013. The economic conditions at that time meant that the rule adopted by the Monetary Policy of the Bank of England helped avert some risks to the emerging recovery.
Has Weak Lending and Activity in the UK been Driven by Credit Supply Shocks?
Authors: Barnett Alina , Thomas Ryland
Published: August 2014

This paper investigates the role of credit supply shocks in driving the weakness in UK banks’ lending and economic activity during the various UK financial crises since 1966. It uses a structural VAR analysis to identify credit supply shocks separately from standard macroeconomic shocks. It finds that credit supply shocks can account for most of the weakness in bank lending since the onset of the recent financial crisis and 1/3 – 1/2 of the fall in GDP relative to its historic trend. It also finds that credit supply shocks behave more like aggregate supply shocks than aggregate demand shocks.
The Future of the Eurozone
Authors: De Grauwe Paul , Ji Yuemei
Published: August 2014

We argue first that the Eurozone crisis has left a legacy of unsustainable government debt levels. These will continue to exert a deflationary dynamics in the Eurozone except if creditor nations are willing to contemplate a debt restructuring. Second, we argue that the institutional innovations since the start of the debt crisis fall short of what is needed to solve the design failures of the Eurozone. In addition, they are not sustainable, mainly because they have led to a situation where bureaucratic institutions have been vested with more responsibilities without a concomitant increase in the democratic legitimacy of these institutions. We conclude that the Euro crisis is not over.
Variation in soil aluminium tolerance genes is associated with local adaptation to soils at the Park Grass Experiment
Authors: Gould Billie , McCouch Susan , Geber Monica
Published: August 2014

Studies of the wild grass Anthoxanthum odoratum at the long‐term Park Grass Experiment (PGE, Harpenden, UK) document a well‐known example of rapid plant evolution in response to environmental change. Repeated fertilizer applications have acidified the soil in some experimental plots over the past 150+ years, and Anthoxanthum subpopulations have quickly become locally adapted. Early reciprocal transplants showed subpopulation differentiation specifically in response to soil aluminium (Al) toxicity across the experiment, even at small (30 m) spatial scales. Almost 40 years after its original measurement, we reassessed the degree of local adaptation to soil Al at the PGE using updated phenotyping methods and identified genes with variation linked to the tolerance trait. Root growth assays show that plants are locally adapted to soil Al at both the seedling and adult growth stages, but to a smaller extent than previously inferred. Among a large suite of candidate loci that were previously shown to have Al‐sensitive expression differences between sensitive and tolerant plants, three loci contained SNPs that are associated with both Al tolerance and soil acidity: an Al‐sensitive malate transporter (ALMT), a tonoplast intrinsic protein (TIP) and the putative homolog of the rice cell‐wall modification gene STAR1. Natural genetic variation at these loci is likely to have contributed to the recent rapid evolution at PGE. Continued study of Al tolerance variants in Anthoxanthum will allow us to test hypotheses about the nature and source of genetic variation that enables some species to adapt to soil acidification and other types of rapid environmental change.
Pleiotrophin inhibits melanogenesis via Erk1/2‐MITF signaling in normal human melanocytes
Authors: Choi Woo Jong , Kim Misun , Park Ji‐Youn , Park Tae Jun , Kang Hee Young
Published: August 2014

Pleiotrophin (PTN) is a secreted heparin‐binding protein that is involved in various biological functions of cell growth and differentiation. Little is known about the effects of PTN on the melanocyte function and skin pigmentation. In this study, we investigated whether PTN would affect melanogenesis. PTN was expressed in melanocytes and fibroblasts of human skin. Transfection studies revealed that PTN decreased melanogenesis, probably through MITF degradation via Erk1/2 activation in melanocytes. The inhibitory action of PTN in pigmentation was further confirmed in ex vivo cultured skin and in the melanocytes cocultured with fibroblasts. These findings suggest that PTN is a crucial factor for the regulation of melanogenesis in the skin.
The effect of peatland drainage and rewetting (ditch blocking) on extracellular enzyme activities and water chemistry
Authors: Peacock M. , Jones T. G. , Airey B. , Johncock A. , Evans C. D. , Lebron I. , Fenner N. , Freeman C.
Published: August 2014

Extensive areas of European peatlands have been drained by digging ditches in an attempt to improve the land, resulting in increased carbon dioxide fluxes to the atmosphere and enhanced fluvial dissolved organic carbon (DOC) concentrations. Numerous peatland restoration projects have been initiated which aim to raise water tables by ditch blocking, thus reversing drainage‐induced carbon losses. It has been suggested that extracellular hydrolase and phenol oxidase enzymes are partly responsible for controlling peatland carbon dynamics and that these enzymes are affected by environmental change. The aim of this study was to investigate how drainage and ditch blocking affect enzyme activities and water chemistry in a Welsh blanket bog, and to study the relationship between enzyme activity and water chemistry. A comparison of a drained and undrained site showed that the drained site had higher phenol oxidase and hydrolase activities, and lower concentrations of phenolic compounds which inhibit hydrolase enzymes. Ditch blocking had little impact upon enzyme activities; although hydrolase activities were lowered 4–9 months after restoration, the only significant difference was for arylsulphatase. Finally, we noted a negative correlation between β‐glucosidase activity and DOC concentrations, and a positive correlation between arylsulphatase activity and sulphate concentration. Phenol oxidase activity was negatively correlated with DOC concentrations in pore water, but for ditch water phenol oxidase correlated negatively with the ratio of phenolics to DOC. Our results imply that drainage could exacerbate gaseous and fluvial carbon losses and that peatland restoration may not reverse the effects, at least in the short term.
The gibberellin biosynthetic genes AtKAO1 and AtKAO2 have overlapping roles throughout Arabidopsis development
Authors: Regnault Thomas , Davière Jean‐Michel , Heintz Dimitri , Lange Theo , Achard Patrick
Published: August 2014

Ent‐kaurenoic acid oxidase (KAO), a class of cytochrome P450 monooxygenases of the subfamily CYP88A, catalyzes the conversion of ent‐kaurenoic acid (KA) to gibberellin (GA) GA12, the precursor of all GAs, thereby playing an important role in determining GA concentration in plants. Past work has demonstrated the importance of KAO activity for growth in various plant species. In Arabidopsis, this enzyme is encoded by two genes designated KAO1 and KAO2. In this study, we used various approaches to determine the physiological roles of KAO1 and KAO2 throughout plant development. Analysis of gene expression pattern reveals that both genes are mainly expressed in germinating seeds and young developing organs, thus suggesting functional redundancy. Consistent with this, kao1 and kao2 single mutants are indistinguishable from wild‐type plants. By contrast, the kao1 kao2 double mutant exhibits typical non‐germinating GA‐dwarf phenotypes, similar to those observed in the severely GA‐deficient ga1‐3 mutant. Phenotypic characterization and quantitative analysis of endogenous GA contents of single and double kao mutants further confirm an overlapping role of KAO1 and KAO2 throughout Arabidopsis development.
Solidification of Phase Change Materials Infiltrated in Porous Media in Presence of Voids
Authors: Moeini Sedeh Mahmoud , Khodadadi J. M.
Published: August 2014

Infiltration of phase change materials (PCM) into highly conductive porous structures effectively enhances the thermal conductivity and phase change (solidification and melting) characteristics of the resulting thermal energy storage (TES) composites. However, the infiltration process contributes to formation of voids as micron-size air bubbles within the pores of the porous structure. The presence of voids negatively affects the thermal and phase change performance of TES composites due to the thermophysical properties of air in comparison with PCM and porous structure. This paper investigates the effect of voids on solidification of PCM, infiltrated into the pores of graphite foam as a highly conductive porous medium with interconnected pores. A combination of the volume-of-fluid (VOF) and enthalpy-porosity methods was employed for numerical investigation of solidification. The proposed method takes into account the variation of density with temperature during phase change and is able to predict the volume shrinkage (volume contraction) during the solidification of liquids. Furthermore, the presence of void and the temperature gradient along the liquid–gas interface (the interface between void and PCM) can trigger thermocapillary effects. Thus, Marangoni convection was included during the solidification process and its importance was elucidated by comparing the results among cases with and without thermocapillary effects. The results indicated that the presence of voids within the pores causes a noticeable increase in solidification time, with a sharper increase for cases without thermocapillary convection. For verification purposes, the amount of volume shrinkage during the solidification obtained from numerical simulations was compared against the theoretical volume change due to the variation of density for several liquids with contraction and expansion during the freezing process. The two sets of results exhibited good agreement.
Probabilistic Analysis of the Secondary Air System of a Low-Pressure Turbine
Authors: Brack Stefan , Muller Yannick
Published: August 2014

The present investigation aims at performing a probabilistic analysis of the secondary air system (SAS) of a three-stage low-pressure turbine rotor in a jet engine. Geometrical engine to engine variations due to the tolerance of the different parts as well as the variation of engine performance parameters are taken into account to analyze the impact on the aerodynamic behavior of the SAS. Three main functions of the SAS have been investigated at one engine condition—takeoff. At first the variation of the turbine rotor cooling flow consumption was studied. Second, the axial bearing loads were considered and finally the system was analyzed with regard to its robustness toward disk space hot gas ingestion. To determine the uncertainty in the accomplishment of these tasks and to identify the major variation drivers, a Latin hypercube sampling (LHS) method coupled with the correlation coefficient analysis was applied to the 1D flow model. The incapability of the correlation coefficient analysis to deal with functional relationships of not monotonic behavior or strong interaction effects was compensated by additionally applying in such cases an elementary effect analysis to determine the influential variables. As the 1D flow model cannot consider thermal and centrifugal growth effects, a simple mathematical model was deduced from the physical dependencies enhancing the 1D flow model to approximately capture the impact of these effects on the labyrinth seals. Results showed that the cooling mass flow and axial bearing load are both normally distributed while their uncertainties are mainly induced by the uncertainties of the state variable of the primary air system. The investigated chamber temperature ratio to analyze the hot gas ingestion showed a not normally distributed histogram and a strong influence of interaction terms. Therefore, the results of the correlation coefficient analysis were complemented with the results of an elementary effect analysis.
Early allopolyploid evolution in the post-Neolithic
Brassica napus
oilseed genome
Authors: Chalhoub Boulos , Denoeud France , Liu Shengyi , Parkin Isobel A. P. , Tang Haibao , Wang Xiyin , Chiquet Julien , Belcram Harry , Tong Chaobo , Samans Birgit , Corréa Margot , Da Silva Corinne , Just Jérémy , Falentin Cyril , Koh Chu Shin , Le Clainche Isabelle , Bernard Maria , Bento Pascal , Noel Benjamin , Labadie Karine , Alberti Adriana , Charles Mathieu , Arnaud Dominique , Guo Hui , Daviaud Christian , Alamery Salman , Jabbari Kamel , Zhao Meixia , Edger Patrick P. , Chelaifa Houda , Tack David , Lassalle Gilles , Mestiri Imen , Schnel Nicolas , Le Paslier Marie-Christine , Fan Guangyi , Renault Victor , Bayer Philipp E. , Golicz Agnieszka A. , Manoli Sahana , Lee Tae-Ho , Thi Vinh Ha Dinh , Chalabi Smahane , Hu Qiong , Fan Chuchuan , Tollenaere Reece , Lu Yunhai , Battail Christophe , Shen Jinxiong , Sidebottom Christine H. D. , Wang Xinfa , Canaguier Aurélie , Chauveau Aurélie , Bérard Aurélie , Deniot Gwenaëlle , Guan Mei , Liu Zhongsong , Sun Fengming , Lim Yong Pyo , Lyons Eric , Town Christopher D. , Bancroft Ian , Wang Xiaowu , Meng Jinling , Ma Jianxin , Pires J. Chris , King Graham J. , Brunel Dominique , Delourme Régine , Renard Michel , Aury Jean-Marc , Adams Keith L. , Batley Jacqueline , Snowdon Rod J. , Tost Jorg , Edwards David , Zhou Yongming , Hua Wei , Sharpe Andrew G. , Paterson Andrew H. , Guan Chunyun , Wincker Patrick
Published: August 2014

The genomic origins of rape oilseed

Many domesticated plants arose through the meeting of multiple genomes through hybridization and genome doubling, known as polyploidy. Chalhoub
et al.
sequenced the polyploid genome of
Brassica napus
, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed (canola), kale, and rutabaga.
B. napus
has undergone multiple events affecting differently sized genetic regions where a gene from one progenitor species has been converted to the copy from a second progenitor species. Some of these gene conversion events appear to have been selected by humans as part of the process of domestication and crop improvement.

Science
, this issue p.
950
A photon steers a photon with an atom
Authors: Rempe Gerhard
Published: August 2014

Nonlinear optics with single quanta of light and matter becomes reality

[Also see Report by

Shomroni
et al.

]
Carbon cycling in the Arctic
Authors: Tranvik Lars
Published: August 2014

Sunlight drives the emission of carbon from arctic waters

[Also see Report by

Cory
et al.

]
Glacier retreat crosses a line
Authors: Marshall Shawn
Published: August 2014

Mountain glacier loss since the 1970s has mostly been caused by human influences on climate change

[Also see Report by

Marzeion
et al.

]
The cancer drug that almost wasn't
Authors: Garber Ken
Published: August 2014

After years in drug development limbo, a compound that interrupts cell division has revitalized a troubled area of cancer research.
Detection of Antibodies to the Biofilm Exopolysaccharide of Histophilus somni following Infection in Cattle by Enzyme-Linked Immunosorbent Assay
Authors: Pan Yu , Fisher Taylor , Olk Christina , Inzana Thomas J.
Published: August 2014

An enzyme-linked immunosorbent assay (ELISA) was developed to detect bovine antibodies to
Histophilus somni
exopolysaccharide (EPS), which is created during biofilm formation. When an index value of 0.268 was used, the sensitivity of the assay for infected calves was 90.5% at 3 weeks postinfection, but the number of positive animals increased by week 4. The specificity of the assay for healthy calves was 92.5%. The EPS ELISA may aid in identifying calves with
H. somni
diseases.
Single-Molecule Long-Read 16S Sequencing To Characterize the Lung Microbiome from Mechanically Ventilated Patients with Suspected Pneumonia
Authors: Toma Ian , Siegel Marc O. , Keiser John , Yakovleva Anna , Kim Alvin , Davenport Lionel , Devaney Joseph , Hoffman Eric P. , Alsubail Rami , Crandall Keith A. , Castro-Nallar Eduardo , Pérez-Losada Marcos , Hilton Sarah K. , Chawla Lakhmir S. , McCaffrey Timothy A. , Simon Gary L.
Published: August 2014

In critically ill patients, the development of pneumonia results in significant morbidity and mortality and additional health care costs. The accurate and rapid identification of the microbial pathogens in patients with pulmonary infections might lead to targeted antimicrobial therapy with potentially fewer adverse effects and lower costs. Major advances in next-generation sequencing (NGS) allow culture-independent identification of pathogens. The present study used NGS of essentially full-length PCR-amplified 16S ribosomal DNA from the bronchial aspirates of intubated patients with suspected pneumonia. The results from 61 patients demonstrated that sufficient DNA was obtained from 72% of samples, 44% of which (27 samples) yielded PCR amplimers suitable for NGS. Out of the 27 sequenced samples, only 20 had bacterial culture growth, while the microbiological and NGS identification of bacteria coincided in 17 (85%) of these samples. Despite the lack of bacterial growth in 7 samples that yielded amplimers and were sequenced, the NGS identified a number of bacterial species in these samples. Overall, a significant diversity of bacterial species was identified from the same genus as the predominant cultured pathogens. The numbers of NGS-identifiable bacterial genera were consistently higher than identified by standard microbiological methods. As technical advances reduce the processing and sequencing times, NGS-based methods will ultimately be able to provide clinicians with rapid, precise, culture-independent identification of bacterial, fungal, and viral pathogens and their antimicrobial sensitivity profiles.
In Vitro
Activity of Ceftolozane-Tazobactam as Determined by Broth Dilution and Agar Diffusion Assays against Recent U.S. Escherichia coli Isolates from 2010 to 2011 Carrying CTX-M-Type Extended-Spectrum β-Lactamases
Authors: Estabrook Mark , Bussell Brianne , Clugston Susan L. , Bush Karen
Published: August 2014

Ceftolozane MIC
50
/MIC
90
s were 4/8 μg/ml when tested against 26 CTX-M-14-type-producing isolates and 64/>64 μg/ml against 219 CTX-M-15-type-producing isolates. The addition of 4 μg/ml tazobactam lowered the ceftolozane MIC
50
/MIC
90
s to ≤0.25/0.5 μg/ml by broth microdilution and Etest. The zone diameters for the ceftolozane-tazobactam disks were 23 to 29 mm for 92.2% of the isolates.
Sensitivity of Surveillance Testing for Multidrug-Resistant Gram-Negative Bacteria in the Intensive Care Unit
Authors: Ridgway Jessica P. , Peterson Lance R. , Thomson Richard B. , Miller Becky A. , Wright Marc-Oliver , Schora Donna M. , Robicsek Ari
Published: August 2014

We tested intensive care unit patients for colonization with multidrug-resistant Gram-negative bacilli (MDR GNB) and compared the results with those of concurrent clinical cultures. The sensitivity of the surveillance test for detecting MDR GNB was 58.8% (95% confidence interval, 48.6 to 68.5%). Among 133 patients with positive surveillance tests, 61% had no prior clinical culture with MDR GNB.
Multiple Groups of Endogenous Epsilon-Like Retroviruses Conserved across Primates
Authors: Brown Katherine , Emes Richard D. , Tarlinton Rachael E.
Published: August 2014

Several types of cancer in fish are caused by retroviruses, including those responsible for major outbreaks of disease, such as walleye dermal sarcoma virus and salmon swim bladder sarcoma virus. These viruses form a phylogenetic group often described as the epsilonretrovirus genus. Epsilon-like retroviruses have become endogenous retroviruses (ERVs) on several occasions, integrating into germ line cells to become part of the host genome, and sections of fish and amphibian genomes are derived from epsilon-like retroviruses. However, epsilon-like ERVs have been identified in very few mammals. We have developed a pipeline to screen full genomes for ERVs, and using this pipeline, we have located over 800 endogenous epsilon-like ERV fragments in primate genomes. Genomes from 32 species of mammals and birds were screened, and epsilon-like ERV fragments were found in all primate and tree shrew genomes but no others. These viruses appear to have entered the genome of a common ancestor of Old and New World monkeys between 42 million and 65 million years ago. Based on these results, there is an ancient evolutionary relationship between epsilon-like retroviruses and primates. Clearly, these viruses had the potential to infect the ancestors of primates and were at some point a common pathogen in these hosts. Therefore, this result raises questions about the potential of epsilonretroviruses to infect humans and other primates and about the evolutionary history of these retroviruses.

IMPORTANCE
Epsilonretroviruses are a group of retroviruses that cause several important diseases in fish. Retroviruses have the ability to become a permanent part of the DNA of their host by entering the germ line as endogenous retroviruses (ERVs), where they lose their infectivity over time but can be recognized as retroviruses for millions of years. Very few mammals are known to have epsilon-like ERVs; however, we have identified over 800 fragments of endogenous epsilon-like ERVs in the genomes of all major groups of primates, including humans. These viruses seem to have circulated and infected primate ancestors 42 to 65 million years ago. We are now interested in how these viruses have evolved and whether they have the potential to infect modern humans or other primates.
The Herpes Simplex Virus 2 Virion-Associated Ribonuclease vhs Interferes with Stress Granule Formation
Authors: Finnen Renée L. , Hay Thomas J. M. , Dauber Bianca , Smiley James R. , Banfield Bruce W.
Published: August 2014

In a previous study, it was observed that cells infected with herpes simplex virus 2 (HSV-2) failed to accumulate stress granules (SGs) in response to oxidative stress induced by arsenite treatment. As a follow-up to this observation, we demonstrate here that disruption of arsenite-induced SG formation by HSV-2 is mediated by a virion component. Through studies on SG formation in cells infected with HSV-2 strains carrying defective forms of UL41, the gene that encodes vhs, we identify vhs as a virion component required for this disruption. Cells infected with HSV-2 strains producing defective forms of vhs form SGs spontaneously late in infection. In addition to core SG components, these spontaneous SGs contain the viral immediate early protein ICP27 as well as the viral serine/threonine kinase Us3. As part of these studies, we reexamined the frameshift mutation known to reside within the UL41 gene of HSV-2 strain HG52. We demonstrate that this mutation is unstable and can rapidly revert to restore wild-type UL41 following low-multiplicity passaging. Identification of the involvement of virion-associated vhs in the disruption of SG formation will enable mechanistic studies on how HSV-2 is able to counteract antiviral stress responses early in infection. In addition, the ability of Us3 to localize to stress granules may indicate novel roles for this viral kinase in the regulation of translation.

IMPORTANCE
Eukaryotic cells respond to stress by rapidly shutting down protein synthesis and storing mRNAs in cytoplasmic stress granules (SGs). Stoppages in protein synthesis are problematic for all viruses as they rely on host cell machinery to synthesize viral proteins. Thus, many viruses target SGs for disruption or modification. Infection by herpes simplex virus 2 (HSV-2) was previously observed to disrupt SG formation induced by oxidative stress. In this follow-up study, we identify virion host shutoff protein (vhs) as a viral protein involved in this disruption. The identification of a specific viral protein involved in disrupting SG formation is a key step toward understanding how HSV-2 interacts with these antiviral structures. Additionally, this understanding may provide insights into the biology of SGs that may find application in studies on human motor neuron degenerative diseases, like amyotrophic lateral sclerosis (ALS), which may arise as a result of dysregulation of SG formation.
Sapovirus Translation Requires an Interaction between VPg and the Cap Binding Protein eIF4E
Authors: Hosmillo Myra , Chaudhry Yasmin , Kim Deok-Song , Goodfellow Ian , Cho Kyoung-Oh
Published: August 2014

Sapoviruses of the
Caliciviridae
family of small RNA viruses are emerging pathogens that cause gastroenteritis in humans and animals. Molecular studies on human sapovirus have been hampered due to the lack of a cell culture system. In contrast, porcine sapovirus (PSaV) can be grown in cell culture, making it a suitable model for understanding the infectious cycle of sapoviruses and the related enteric caliciviruses. Caliciviruses are known to use a novel mechanism of protein synthesis that relies on the interaction of cellular translation initiation factors with the virus genome-encoded viral protein genome (VPg) protein, which is covalently linked to the 5′ end of the viral genome. Using PSaV as a representative member of the
Sapovirus
genus, we characterized the role of the viral VPg protein in sapovirus translation. As observed for other caliciviruses, the PSaV genome was found to be covalently linked to VPg, and this linkage was required for the translation and the infectivity of viral RNA. The PSaV VPg protein was associated with the 4F subunit of the eukaryotic translation initiation factor (eIF4F) complex in infected cells and bound directly to the eIF4E protein. As has been previously demonstrated for feline calicivirus, a member of the
Vesivirus
genus, PSaV translation required eIF4E and the interaction between eIF4E and eIF4G. Overall, our study provides new insights into the novel mechanism of sapovirus translation, suggesting that sapovirus VPg can hijack the cellular translation initiation mechanism by recruiting the eIF4F complex through a direct eIF4E interaction.

IMPORTANCE
Sapoviruses, which are members of the
Caliciviridae
family, are one of the causative agents of viral gastroenteritis in humans. However, human sapovirus remains noncultivable in cell culture, hampering the ability to characterize the virus infectious cycle. Here, we show that the VPg protein from porcine sapovirus, the only cultivatable sapovirus, is essential for viral translation and functions via a direct interaction with the cellular translation initiation factor eIF4E. This work provides new insights into the novel protein-primed mechanism of calicivirus VPg-dependent translation initiation.
Analysis of the Highly Diverse Gene Borders in Ebola Virus Reveals a Distinct Mechanism of Transcriptional Regulation
Authors: Brauburger Kristina , Boehmann Yannik , Tsuda Yoshimi , Hoenen Thomas , Olejnik Judith , Schümann Michael , Ebihara Hideki , Mühlberger Elke
Published: August 2014

Ebola virus (EBOV) belongs to the group of nonsegmented negative-sense RNA viruses. The seven EBOV genes are separated by variable gene borders, including short (4- or 5-nucleotide) intergenic regions (IRs), a single long (144-nucleotide) IR, and gene overlaps, where the neighboring gene end and start signals share five conserved nucleotides. The unique structure of the gene overlaps and the presence of a single long IR are conserved among all filoviruses. Here, we sought to determine the impact of the EBOV gene borders during viral transcription. We show that readthrough mRNA synthesis occurs in EBOV-infected cells irrespective of the structure of the gene border, indicating that the gene overlaps do not promote recognition of the gene end signal. However, two consecutive gene end signals at the VP24 gene might improve termination at the VP24-L gene border, ensuring efficient L gene expression. We further demonstrate that the long IR is not essential for but regulates transcription reinitiation in a length-dependent but sequence-independent manner. Mutational analysis of bicistronic minigenomes and recombinant EBOVs showed no direct correlation between IR length and reinitiation rates but demonstrated that specific IR lengths not found naturally in filoviruses profoundly inhibit downstream gene expression. Intriguingly, although truncation of the 144-nucleotide-long IR to 5 nucleotides did not substantially affect EBOV transcription, it led to a significant reduction of viral growth.

IMPORTANCE
Our current understanding of EBOV transcription regulation is limited due to the requirement for high-containment conditions to study this highly pathogenic virus. EBOV is thought to share many mechanistic features with well-analyzed prototype nonsegmented negative-sense RNA viruses. A single polymerase entry site at the 3′ end of the genome determines that transcription of the genes is mainly controlled by gene order and
cis
-acting signals found at the gene borders. Here, we examined the regulatory role of the structurally unique EBOV gene borders during viral transcription. Our data suggest that transcriptional regulation in EBOV is highly complex and differs from that in prototype viruses and further the understanding of this most fundamental process in the filovirus replication cycle. Moreover, our results with recombinant EBOVs suggest a novel role of the long IR found in all filovirus genomes during the viral replication cycle.