bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Aerial Insecticide Spraying on West Nile Virus Disease—North-Central Texas, 2012
Authors: Ruktanonchai Duke J. , Stonecipher Shelley , Lindsey Nicole , McAllister Janet , Pillai Satish K. , Horiuchi Kalanthe , Delorey Mark , Biggerstaff Brad J. , Sidwa Tom , Zoretic James , Nasci Roger , Fischer Marc , Hills Susan L.
Published: April 2014

During 2012, four north-central Texas counties experienced high West Nile virus (WNV) disease incidence. Aerial insecticide spraying was conducted in two counties. To evaluate the effect of spraying on WNV disease, we calculated incidence rate ratios (IRRs) in treated and untreated areas by comparing incidence before and after spraying; for unsprayed areas, before and after periods were defined by using dates from a corresponding sprayed area. In treated areas, WNV neuroinvasive disease incidence before and after spraying was 7.31/100,000 persons and 0.28/100,000 persons, respectively; the IRR was 26.42 (95% confidence interval [CI]: 12.42–56.20). In untreated areas, the before and after incidence was 4.80/100,000 persons and 0.45/100,000 persons, respectively; the IRR was 10.57 (95% CI: 6.11–18.28). The ratio of IRRs was 2.50 (95% CI: 0.98–6.35). Disease incidence decreased in both areas, but the relative change was greater in aerial-sprayed areas.
Whole Genome Analysis of Sierra Nevada Virus, a Novel Mononegavirus in the Family Nyamiviridae
Authors: Rogers Matthew B. , Cui Lijia , Fitch Adam , Popov Vsevolod , Travassos da Rosa Amelia P. A. , Vasilakis Nikos , Tesh Robert B. , Ghedin Elodie
Published: April 2014

A novel mononegavirus was isolated in 1975 from ticks (Ornithodoros coriaceus) collected during investigation of an outbreak of epizootic bovine abortion (EBA) in northern California. It was originally designated “bovine abortion-tick virus” (BA-T virus). The EBA is now known to be associated with a deltaproteobacterium infection, and not a virus. The BA-T virus had remained uncharacterized until now. We have determined by electron microscopy, serology, and genome sequencing that the BA-T virus is a fourth member of the newly proposed family Nyamiviridae, and we have renamed it Sierra Nevada virus (SNVV). Although antigenically distinct, phylogenetically SNVV is basal to Nyamanini virus (NYMV) and Midway virus (MIDWV), two other tick-borne agents. Although NYMV was found to infect land birds, and MIDWV seabirds, it is presently unknown whether SNVV naturally infects birds or mammals.
Retrieval of characteristic parameters for water vapour transmittance in the development of ground-based sun–sky radiometric measurements of columnar water vapour
Authors: Campanelli M. , Nakajima T. , Khatri P. , Takamura T. , Uchiyama A. , Estelles V. , Liberti G. L. , Malvestuto V.
Published: April 2014

Abstract. Sun–sky radiometers are instruments created for aerosol study, but they can measure in the water vapour absorption band allowing the estimation of columnar water vapour in clear sky simultaneously with aerosol characteristics, with high temporal resolution. A new methodology is presented for estimating calibration parameters (i.e. characteristic parameters of the atmospheric transmittance and solar calibration constant) directly from the sun–sky radiometer measurements. The methodology is based on the hypothesis that characteristic parameters of the atmospheric transmittance are dependent on vertical profiles of pressure, temperature and moisture occurring at each site of measurement. To obtain the parameters from the proposed methodology some seasonal independent measurements of columnar water vapour taken over a large range of solar zenith angle simultaneously with the sun–sky radiometer measurements, are needed. In this work high time resolution columnar water vapour measurements by GPS were used as independent data set, but also the case when such measurements are not available was considered by developing the surface humidity method (SHM). This methodology makes it possible to retrieve the needed independent data set of columnar water vapour using the standard surface meteorological observations (temperature, pressure and relative humidity) more readily available. The time pattern of columnar water vapour from sun–sky radiometer retrieved using both the methodologies was compared with simultaneous measurements from microwave radiometer, radiosondings and GPS. Water vapour from sun–sky radiometer, obtained using GPS independent measurements, was characterized by an error varying from 1% up to 5%, whereas water vapour from SHM showed an error from 1% up to 11%, depending on the local columnar water occurring at the site during the year. These errors were estimated by comparing water vapour series from sun–sky radiometer against measurements taken by GPS at a nearby station. The accordance between retrievals from sun–sky radiometer and simultaneous measurements from the other instruments was found always within the error both in the case of SHM and of the GPS independent data set. Water vapour obtained using characteristic parameters of the atmospheric transmittance dependent on water vapour was also compared against GPS retrievals, showing a clear improvement with respect to the case when these parameters are kept fixed.
The impact of spectral resolution on satellite retrieval accuracy of CO2 and CH4
Authors: Galli A. , Guerlet S. , Butz A. , Aben I. , Suto H. , Kuze A. , Deutscher N. M. , Notholt J. , Wunch D. , Wennberg P. O. , Griffith D. W. T. , Hasekamp O. , Landgraf J.
Published: April 2014

Abstract. The Fourier-transform spectrometer on board the Japanese GOSAT (Greenhouse gases Observing SATellite) satellite offers an excellent opportunity to study the impact of instrument resolution on retrieval accuracy of CO2 and CH4. This is relevant to further improve retrieval accuracy and to optimize the cost–benefit ratio of future satellite missions for the remote sensing of greenhouse gases. To address this question, we degrade GOSAT measurements with a spectral resolution of ≈ 0.24 cm−1 step by step to a resolution of 1.5 cm−1. We examine the results by comparing relative differences at various resolutions, by referring the results to reference values from the Total Carbon Column Observing Network (TCCON), and by calculating and inverting synthetic spectra for which the true CO2 and CH4 columns are known. The main impacts of degrading the spectral resolution are reproduced for all approaches based on GOSAT measurements; pure forward model errors identified with simulated measurements are much smaller. For GOSAT spectra, the most notable effect on CO2 retrieval accuracy is the increase of the standard deviation of retrieval errors from 0.7 to 1.0% when the spectral resolution is reduced by a factor of six. The retrieval biases against atmospheric water abundance and air mass become stronger with decreasing resolution. The error scatter increase for CH4 columns is less pronounced. The selective degradation of single spectral windows demonstrates that the retrieval accuracy of CO2 and CH4 is dominated by the spectral range where the absorption lines of the target molecule are located. For both GOSAT and synthetic measurements, retrieval accuracy decreases with lower spectral resolution for a given signal-to-noise ratio, suggesting increasing interference errors.
Variability of the transport of anthropogenic CO2 at the Greenland–Portugal OVIDE section: controlling mechanisms
Authors: Zunino P. , Garcia-Ibañez M. I. , Lherminier P. , Mercier H. , Rios A. F. , Pérez F. F.
Published: April 2014

Abstract. The interannual to decadal variability in the transport of anthropogenic CO2 (Cant) across the subpolar North Atlantic (SPNA) is investigated, using summer data of the FOUREX and OVIDE high-resolution transoceanic sections, from Greenland to Portugal, occupied six times from 1997 to 2010. The transport of Cant across this section, Tcant hereafter, is northward, with a mean value of 254 ± 29 kmol s−1 over the 1997–2010 period. We find that Tcant undergoes interannual variability, masking any trend different from 0 for this period. In order to understand the mechanisms controlling the variability of Tcant across the SPNA, we propose a new method that quantifies the transport of Cant caused by the diapycnal and isopycnal circulation. The diapycnal component yields a large northward transport of Cant (400 ± 29 kmol s−1) that is partially compensated by a southward transport of Cant caused by the isopycnal component (−171 ± 11 kmol s−1), mainly localized in the Irminger Sea. Most importantly, the diapycnal component is found to be the main driver of the variability of Tcant across the SPNA. Both the Meridional Overturning Circulation (computed in density coordinates, MOCσ) and the Cant increase in the water column have an important effect on the variability of the diapycnal component and of Tcant itself. Based on this analysis, we propose a simplified estimator for the variability of Tcant based on the intensity of the MOCσ and on the difference of Cant between the upper and lower limb of the MOCσ (ΔCant). This estimator shows a good consistency with the diapycnal component of Tcant, and help to disentangle the effect of the variability of both the circulation and the Cant increase on the Tcant variability. We find that ΔCant keeps increasing over the past decade, and it is very likely that the continuous Cant increase in the water masses will cause an increase in Tcant across the SPNA at long timescale. Nevertheless, at the timescale analyzed here (1997–2010), the MOCσ controls the Tcant variability, blurring any Tcant trend. Extrapolating the observed ΔCant increase rate and considering the predicted slow-down of 25% of the MOCσ, Tcant across the SPNA is expected to increase by 430 kmol s−1 during the 21st century. Consequently, an increase in the storage rate of Cant in the SPNA could be envisaged.
Presence of Prochlorococcus in the aphotic waters of the western Pacific Ocean
Authors: Jiao N. , Luo T. , Zhang R. , Yan W. , Lin Y. , Johnson Z. I. , Tian J. , Yuan D. , Yang Q. , Zheng Q. , Sun J. , Hu D. , Wang P.
Published: April 2014

Abstract. Prochlorococcus, the smallest but most abundant marine primary producer, plays an important role in carbon cycling of the global ocean. As a phototroph, Prochlorococcus is thought to be confined to the euphotic zone, with commonly observed maximum depths of ~ 150–200 m, but here we show for the first time the substantial presence of Prochlorococcus populations in the dark ocean ("deep Prochlorococcus" hereafter). Intensive studies at the Luzon Strait in the western Pacific Ocean show that the deep Prochlorococcus populations are exported from the euphotic zone. Multiple physical processes including internal solitary waves could be responsible for the transportation. These findings reveal a novel mechanism for picoplankton carbon export other than the known mechanisms such as sinking of phytodetritus and aggregates or grazing-mediated transportation.
Disparities between Phaeocystis in situ and optically-derived carbon biomass and growth rates: potential effect on remote-sensing primary production estimates
Authors: Peperzak L. , van der Woerd H. J. , Timmermans K. R.
Published: April 2014

Abstract. The oceans play a pivotal role in the global carbon cycle. Unfortunately, the daily production of organic carbon, the product of phytoplankton standing stock and growth rate cannot be measured globally by discrete oceanographic methods. Instead, optical proxies from Earth-orbiting satellites must be used. To test the accuracy of optically-derived proxies of phytoplankton physiology and growth rate, standard ex situ data from the wax and wane of a Phaeocystis bloom in laboratory mesocosms were compared with hyperspectral reflectance data. Chlorophyll biomass could be estimated accurately from reflectance using specific chlorophyll absorption algorithms. However, the conversion of chlorophyll (Chl) to carbon (C) was obscured by the observed increase in C : Chl under nutrient-limited growth. C : Chl was inversely correlated (r2 = 0.88) with Photosystem II quantum efficiency (Fv/Fm), the in situ fluorometric oceanographic proxy for growth rate. In addition, the optical proxy for growth rate, the quantum efficiency of fluorescence ϕ was linearly correlated to Fv/Fm (r2 = 0.84), but not – as by definition – by using total phytoplankton absorption, because during nutrient-limited growth the concentrations of non-fluorescent light-absorbing pigments increased. As a consequence, none of the three proxies (C : Chl, Fv/Fm, φ) was correlated to carbon or cellular phytoplankton growth rates. Therefore, it is concluded that although satellite derived estimates of chlorophyll biomass may be accurate, physiologically-induced non-linear shifts in growth rate proxies may obscure accurate phytoplankton growth rates and hence global carbon production estimates.
Bacterial production and transformation of dissolved neutral sugars and amino acids in seawater
Authors: Jørgensen L. , Lechtenfeld O. , Benner R. , Middelboe M. , Stedmon C. A.
Published: April 2014

Abstract. Dissolved organic matter (DOM) in the ocean consists of a heterogeneous mixture of molecules, most of which are of unknown origin. Neutral sugars and amino acids are among the few recognizable biomolecules in DOM, and the molecular composition of these biomolecules is shaped primarily by biological production and degradation processes. This study provides insight into the bioavailability of biomolecules as well as the chemical composition of DOM produced by bacteria. The molecular compositions of neutral sugars and amino acids were investigated in DOM produced by bacteria and in DOM remaining after long-term bacterial degradation. Results from bioassay incubations (32 days) with natural and artificial seawater, indicate that the molecular compositions following bacterial degradation are not strongly influenced by the initial substrate or bacterial community. The molecular composition of neutral sugars released by bacteria was characterized by a high glucose content (47 mol%) and heterogeneous contributions from other neutral sugars (3–14 mol%). DOM remaining after bacterial degradation was characterized by a high galactose content (33 mol%), followed by glucose (22 mol%) and the remaining neutral sugars (7–11 mol%). The ratio of D-amino acids to L-amino acids increased during the experiments as a response to bacterial degradation, and after 32 days the D/L ratios of aspartic acid, glutamic acid, serine and alanine reached around 0.79, 0.32, 0.30 and 0.51 in all treatments, respectively. The striking similarity in neutral sugar and amino acid compositions between natural and artificial seawater samples, suggests that the microbial carbon pump also applies for neutral sugars and amino acids and that bacterially-produced biomolecules persist for long periods in the ocean.
GPCC Drought Index – a new, combined, and gridded global drought index
Authors: Ziese M. , Schneider U. , Meyer-Christoffer A. , Schamm K. , Vido J. , Finger P. , Bissolli P. , Pietzsch S. , Becker A.
Published: April 2014

Abstract. The Global Precipitation Climatology Centre Drought Index (GPCC-DI) provides estimations of precipitation anomalies with respect to long term statistics. It is a combination of the Standardized Precipitation Index with adaptations from Deutscher Wetterdienst (SPI-DWD) and the Standardized Precipitation Evapotranspiration Index (SPEI). Precipitation data were taken from the Global Precipitation Climatology Centre (GPCC) and temperature data from NOAA's Climate Prediction Center (CPC). The GPCC-DI is available with several averaging periods of 1, 3, 6, 9, 12, 24 and 48 months for different applications. Since spring 2013, the GPCC-DI is calculated operationally and available back to January 2013. Typically it is released at the 10th day of the following month, depending on the availability of the input data. It is calculated on a~regular grid with 1° spatial resolution. All averaging periods are integrated into one netCDF-file for each month. This dataset can be referenced by the DOI:10.5676/DWD_GPCC/DI_M_100 and is available free of charge from the GPCC website ftp://ftp.dwd.de/pub/data/gpcc/html/gpcc_di_doi_download.html.
Modelling of primary aerosols in the chemical transport model MOCAGE: development and evaluation of aerosol physical parameterizations
Authors: Sič B. , El Amraoui L. , Marécal V. , Josse B. , Arteta J. , Guth J. , Joly M. , Hamer P.
Published: April 2014

Abstract. This paper deals with recent improvements to the chemical transport model of Météo-France MOCAGE that consists of updates to different aerosol parameterizations. MOCAGE only contains primary aerosol species. We introduced important changes to the aerosol parameterization concerning emissions, wet deposition and sedimentation. For the emissions, size distribution and wind calculations are modified for desert dust aerosols, and a surface sea temperature dependant source function is introduced for sea salt aerosols. Wet deposition is modified toward a more physically realistic representation by introducing re-evaporation of falling rain and snowfall scavenging, and by changing in-cloud scavenging scheme along with calculations of precipitation cloud cover and rain properties. The sedimentation scheme update includes changes regarding the stability and viscosity calculations. Independent data from satellites (MODIS, SEVIRI), the ground (AERONET), and a model inter-comparison project (AeroCom) is compared with MOCAGE simulations and showed that the introduced changes brought a significant improvement on aerosol representation, properties and global distribution. Emitted quantities of desert dust and sea salt, as well their lifetimes, moved closer towards values of AeroCom estimates and the multi-model average. When comparing the model simulations with MODIS aerosol optical depth (AOD) observations over the oceans, the updated model configuration shows a decrease in the bias (from 0.032 to 0.002) and a better correlation (from 0.062 to 0.322) in terms of the geographical distribution and the temporal variability. The updates corrected a strong positive bias in the sea salt representation at high latitudes (from 0.153 to 0.026), and a negative bias in the desert dust representation in the African dust outflow region (from −0.179 to −0.051). The updates in sedimentation produced a modest difference; the bias with MODIS data from 0.002 in the updated configuration went to 0.003 in the updated configuration only without the sedimentation updates. Yet, the updates in the emissions and the wet deposition made a stronger impact on the results; the bias was 0.041 and 0.032 in updated configurations only without emission, and wet deposition updates, respectively. Also, the lifetime, the extent, and the strength of the episodic aerosol events are better reproduced in the updated configuration. The wet deposition processes and the differences between the various configurations that were tested greatly influence the representation of the episodic events. However, wet deposition is not a continuous process; it has a local and episodic signature and its representation depends strongly on the precipitation regime in the model.
Climate information based streamflow and rainfall forecasts for Huai River basin using hierarchical Bayesian modeling
Authors: Chen X. , Hao Z. , Devineni N. , Lall U.
Published: April 2014

Abstract. A Hierarchal Bayesian model is presented for one season-ahead forecasts of summer rainfall and streamflow using exogenous climate variables for east central China. The model provides estimates of the posterior forecasted probability distribution for 12 rainfall and 2 streamflow stations considering parameter uncertainty, and cross-site correlation. The model has a multi-level structure with regression coefficients modeled from a common multi-variate normal distribution resulting in partial pooling of information across multiple stations and better representation of parameter and posterior distribution uncertainty. Covariance structure of the residuals across stations is explicitly modeled. Model performance is tested under leave-10-out cross-validation. Frequentist and Bayesian performance metrics used include receiver operating characteristic, reduction of error, coefficient of efficiency, rank probability skill scores, and coverage by posterior credible intervals. The ability of the model to reliably forecast season-ahead regional summer rainfall and streamflow offers potential for developing adaptive water risk management strategies.
Daytime identification of summer hailstorm cells from MSG data
Authors: Merino A. , López L. , Sánchez J. L. , García-Ortega E. , Cattani E. , Levizzani V.
Published: April 2014

Abstract. Identifying deep convection is of paramount importance, as it may be associated with extreme weather phenomena that have significant impact on the environment, property and populations. A new method, the hail detection tool (HDT), is described for identifying hail-bearing storms using multispectral Meteosat Second Generation (MSG) data. HDT was conceived as a two-phase method, in which the first step is the convective mask (CM) algorithm devised for detection of deep convection, and the second a hail mask algorithm (HM) for the identification of hail-bearing clouds among cumulonimbus systems detected by CM. Both CM and HM are based on logistic regression models trained with multispectral MSG data sets comprised of summer convective events in the middle Ebro Valley (Spain) between 2006 and 2010, and detected by the RGB (red-green-blue) visualization technique (CM) or C-band weather radar system of the University of León. By means of the logistic regression approach, the probability of identifying a cumulonimbus event with CM or a hail event with HM are computed by exploiting a proper selection of MSG wavelengths or their combination. A number of cloud physical properties (liquid water path, optical thickness and effective cloud drop radius) were used to physically interpret results of statistical models from a meteorological perspective, using a method based on these "ingredients". Finally, the HDT was applied to a new validation sample consisting of events during summer 2011. The overall probability of detection was 76.9 % and the false alarm ratio 16.7 %.
Using records from submarine, aircraft and satellite to evaluate climate model simulations of Arctic sea ice thickness
Authors: Stroeve J. , Barrett A. , Serreze M. , Schweiger A.
Published: April 2014

Abstract. Arctic sea ice thickness distributions from models participating in the World Climate Research Programme Coupled Model Intercomparison Project Phase 5 are evaluated against observations from submarines, aircraft and satellites. While it's encouraging that the mean thickness distributions from the models are in general agreement with observations, the spatial patterns of sea ice thickness are poorly represented in most models. The poor spatial representation of thickness patterns is associated with a failure of models to represent details of the mean atmospheric circulation pattern that governs the transport and spatial distribution of sea ice. The climate models as a whole also tend to underestimate the rate of ice volume loss from 1979 to 2013, though the multi-model ensemble mean trend remains within the uncertainty of that from the Pan-Arctic Ice Ocean Modeling and Assimilation System. These results raise concerns regarding the ability of CMIP5 models to realistically represent the processes driving the decline of Arctic sea ice and project the timing of when a seasonally ice-free Arctic may be realized.
Binzasara: Music and Dance at Sensōji in Edo/Tōkyō
Authors: Groemer Gerald
Published: April 2014

Dengaku, literally “field music” or “field entertainment,” figures as one of the most important genres of traditional Japanese music, that is, music developed in Japan before the Meiji period (1868–1912). Dengaku has played a role in ceremonies at major religious institutions since at least the twelfth century and continues to be performed at many locations today, including the Kasuga Wakamiya shrine in Nara prefecture, the Nachi shrine in Wakayama prefecture, the Mikachi Hachiman shrine in Fukuchiyama (Kyōto-fu), the Yasaka shrine in Yasaka-chō (Kyōto-fu), the Hie shrine in Yashiro (Kyoto), the Ωji shrine in Tōkyō-to, the Kanasayama shrines in Ibaraki prefecture, Mōtsūji in Hiraizumi (Iwate prefecture), Sensōji in downtown Tokyo, and other religious institutions throughout the land.
Non-invasive Ventilation for Acute Respiratory Failure
Authors: Ferrari Rodolfo , Giostra Fabrizio , Agostinelli Daniela , Cavazza Mario
Published: April 2014

Giant steps are what Non-Invasive Mechanical Ventilation (NIMV) has taken in the last decades for the treatment of Acute Respiratory Failure. NIMV is safe and effective when applied early to carefully selected patients not meeting criteria for invasive ventilation. A well-fitting interface, close monitoring, coaching and clear information provided to patients, and a trained and skilled team available throughout the 24-h period are crucial factors to get to the best outcome, to reduce morbility and mortality associated to endotracheal intubation. Moving from the essential questions, in this review we focused on the key points to know and understand NIMV in some lights and shadows. What is NIMV and what do we mean speaking about NIMV? Which kind of NIMV is it suitable? Why NIMV works? Who is the right patient, and who is the right doctor, for NIMV? When to start NIMV? Where to perform NIMV? How to carry out NIMV? How long to go on with NIMV?
p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-κB complexes
Authors: Krawczyk Michal , Emerson Beverly M
Published: April 2014

Deregulated expression of COX-2 has been causally linked to development, progression, and outcome of several types of human cancer. We describe a novel fundamental level of transcriptional control of COX-2 expression. Using primary human mammary epithelial cells and monocyte/macrophage cell lines, we show that the chromatin boundary/insulator factor CTCF establishes an open chromatin domain and induces expression of a long non-coding RNA within the upstream promoter region of COX-2. Upon induction of COX-2 expression, the lncRNA associates with p50, a repressive subunit of NF-κB, and occludes it from the COX-2 promoter, potentially facilitating interaction with activation-competent NF-κB p65/p50 dimers. This enables recruitment of the p300 histone acetyltransferase, a domain-wide increase in histone acetylation and assembly of RNA Polymerase II initiation complexes. Our findings reveal an unexpected mechanism of gene control by lncRNA-mediated repressor occlusion and identify the COX-2-lncRNA, PACER, as a new potential target for COX-2-modulation in inflammation and cancer.
Repair of naturally occurring mismatches can induce mutations in flanking DNA
Authors: Chen Jia , Miller Brendan F , Furano Anthony V
Published: April 2014

‘Normal’ genomic DNA contains hundreds of mismatches that are generated daily by the spontaneous deamination of C (U/G) and methyl-C (T/G). Thus, a mutagenic effect of their repair could constitute a serious genetic burden. We show here that while mismatches introduced into human cells on an SV40-based episome were invariably repaired, this process induced mutations in flanking DNA at a significantly higher rate than no mismatch controls. Most mutations involved the C of TpC, the substrate of some single strand-specific APOBEC cytidine deaminases, similar to the mutations that can typify the ‘mutator phenotype’ of numerous tumors. siRNA knockdowns and chromatin immunoprecipitation showed that TpC preferring APOBECs mediate the mutagenesis, and siRNA knockdowns showed that both the base excision and mismatch repair pathways are involved. That naturally occurring mispairs can be converted to mutators, represents an heretofore unsuspected source of genetic changes that could underlie disease, aging, and evolutionary change.
Age- and diet-associated metabolome remodeling characterizes the aging process driven by damage accumulation
Authors: Avanesov Andrei S , Ma Siming , Pierce Kerry A , Yim Sun Hee , Lee Byung Cheon , Clish Clary B , Gladyshev Vadim N
Published: April 2014

Aging is thought to be associated with increased molecular damage, but representative markers vary across conditions and organisms, making it difficult to assess properties of cumulative damage throughout lifespan. We used nontargeted metabolite profiling to follow age-associated trajectories of >15,000 metabolites in Drosophila subjected to control and lifespan-extending diets. We find that aging is associated with increased metabolite diversity and low-abundance molecules, suggesting they include cumulative damage. Remarkably, the number of detected compounds leveled-off in late-life, and this pattern associated with survivorship. Fourteen percent of metabolites showed age-associated changes, which decelerated in late-life and long-lived flies. In contrast, known metabolites changed in abundance similarly to nontargeted metabolites and transcripts, but did not increase in diversity. Targeted profiling also revealed slower metabolism and accumulation of lifespan-limiting molecules. Thus, aging is characterized by gradual metabolome remodeling, and condition- and advanced age-associated deceleration of this remodeling is linked to mortality and molecular damage.
Periodic DNA patrolling underlies diverse functions of Pif1 on R-loops and G-rich DNA
Authors: Zhou Ruobo , Zhang Jichuan , Bochman Matthew L , Zakian Virginia A , Ha Taekjip
Published: April 2014

Pif1 family helicases are conserved from bacteria to humans. Here, we report a novel DNA patrolling activity which may underlie Pif1’s diverse functions: a Pif1 monomer preferentially anchors itself to a 3′-tailed DNA junction and periodically reel in the 3′ tail with a step size of one nucleotide, extruding a loop. This periodic patrolling activity is used to unfold an intramolecular G-quadruplex (G4) structure on every encounter, and is sufficient to unwind RNA-DNA heteroduplex but not duplex DNA. Instead of leaving after G4 unwinding, allowing it to refold, or going beyond to unwind duplex DNA, Pif1 repeatedly unwinds G4 DNA, keeping it unfolded. Pif1-induced unfolding of G4 occurs in three discrete steps, one strand at a time, and is powerful enough to overcome G4-stabilizing drugs. The periodic patrolling activity may keep Pif1 at its site of in vivo action in displacing telomerase, resolving R-loops, and keeping G4 unfolded during replication, recombination and repair.
Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons
Authors: Jonkers Iris , Kwak Hojoong , Lis John T
Published: April 2014

Production of mRNA depends critically on the rate of RNA polymerase II (Pol II) elongation. To dissect Pol II dynamics in mouse ES cells, we inhibited Pol II transcription at either initiation or promoter-proximal pause escape with Triptolide or Flavopiridol, and tracked Pol II kinetically using GRO-seq. Both inhibitors block transcription of more than 95% of genes, showing that pause escape, like initiation, is a ubiquitous and crucial step within the transcription cycle. Moreover, paused Pol II is relatively stable, as evidenced from half-life measurements at ∼3200 genes. Finally, tracking the progression of Pol II after drug treatment establishes Pol II elongation rates at over 1000 genes. Notably, Pol II accelerates dramatically while transcribing through genes, but slows at exons. Furthermore, intergenic variance in elongation rates is substantial, and is influenced by a positive effect of H3K79me2 and negative effects of exon density and CG content within genes.
Coming soon to a screen near you
Authors: Harrison Melissa
Published: April 2014

As eLife starts to publish the accepted versions of certain Research Articles, we explain what happens once a manuscript has been accepted for publication.
Efeito residual de herbicidas na cultura do crambe em sucessão
Authors: Timossi Paulo César , Silva Werley Soares , Lima Suzete Fernandes , Alves Valdiney Ferreira , Almeida Dieimisson Paulo
Published: April 2014

Herbicidas aplicados em um sistema de produção com cultivos em sucessão podem apresentar efeito residual, na cultura subsequente, causando injúrias na cultura em sucessão. Tal efeito é denominado de carryover, o qual é importante o conhecimento para o planejamento e recomendação de sucessão de culturas. O trabalho objetivou avaliar o efeito carryover da associação de herbicidas utilizados na dessecação para cultivo de soja, em Crambe abyssinica, cultivar FMS-Brilhante, cultivada em sucessão. O experimento foi instalado e conduzido em delineamento experimental de blocos casualizado, com oito tratamentos e três repetições. Os tratamentos foram: glyphosate (1.300 g e.a. ha-1), glyphosate + 2,4-D (1.300 g e.a. + 1.005 g e.a. ha-1), glyphosate + (paraquat + diuron) [1.300 g e.a. + (600 + 300 g i.a. ha-1)], glyphosate + carfentrazone-ethyl (1.300 g e.a. + 40 g i.a. ha-1), glyphosate + saflufenacil (1.300 g e.a. + 24,5 g i.a. ha-1), glyphosate + flumioxazyn (1.300 g e.a. + 35 g i.a. ha-1), glyphosate + diclosulam (1.300 g e.a. + 25 g i.a. ha-1), glyphosate + chlorimuron-ethyl (1.300 g e.a. + 20 g i.a. ha-1). Após a colheita da soja (120 DAS - dias após a semeadura), semeou-se a cultura do crambe. As avaliações basearam-se na determinação da população de plantas (aos 30 DAS), massa seca no florescimento (45 DAS) e determinação de características agronômicas (90 DAS) da cultura do crambe. Conclui-se que a associação de glyphosate aos herbicidas residuais utilizados no sistema plante e aplique da cultura da soja, não afetaram negativamente a cultura do crambe, em solo de textura argilosa.
Controle químico e caracterização da superfície foliar de Conyza bonariensis e C. canadensis (Asteraceae)
Authors: Inacio Estela Maris , Monquero Patricia Andrea
Published: April 2014

O gênero Conyza inclui aproximadamente 60 espécies de plantas distribuídas em quase todo o mundo. As espécies Conyza canadensis e C. bonariensis destacam-se por infestarem áreas abandonadas, pastagens, culturas perenes e lavouras anuais. Os objetivos desse trabalho foram: (1) caracterizar a superfície foliar de C. bonariensis e C. canadensis através da microscopia eletrônica de varredura; (2) determinar o controle destas plantas com o uso do herbicida glyphosate em associação com herbicidas de distintos mecanismos de ação. Para analisar a superfície foliar foram retirados dois segmentos de aproximadamente 50 mm2 da região mediana das folhas jovens de C. bonariensis e C. canadensis, porém totalmente expandidas para análise em microscópio eletrônico de varredura. No estudo de controle químico foi utilizado o delineamento experimental inteiramente casualizado com quatro repetições, os herbicidas foram aplicados em pós-emergência com as plantas apresentando de três a quatro pares de folhas verdadeiras. Os tratamentos utilizados foram glyphosate (0,42 kg ha-1), em associação com amônio - glufosinato (0,50 kg ha-1), 2,4-D (1,0 kg ha-1), bentazon (0,72 kg ha-1), chlorimuron-ethyl (0,15 kg ha-1), carfentrazone-ethyl (0,03 kg ha-1), metribuzin (0,48 kg ha-1) e sulfentrazone (0,60 kg ha-1), além dos mesmos herbicidas aplicados isoladamente e um tratamento testemunha. Ambas as espécies são anfiestomáticas, apresentam estômatos na superfície adaxial e abaxial, possuem tricomas tectores unicelulares e pluricelulares, sendo que a espécie C. bonariensis possui visualmente maior quantidade de tricomas na face adaxial. Para C. bonariensis, os tratamentos de amônio-glufosinato e a associação de glyphosate com amônio-glufosinato, bentazon, chlorimuron-ethyl e metribuzin foram os mais efetivos no controle. Para C. canadensis os tratamentos mais eficientes no controle foram: glyphosate + amônio-glufosinato, glyphosate + bentazon, e glyphosate + metribuzin.
Artificial Leaves
Authors: Centi Gabriele , Perathoner Siglinda
Published: April 2014

The development of an artificial leaf that collects sunlight, water, and carbon oxide and then transforms them into useful chemicals/fuels in the same manner as a natural one is one of society's grand challenges for the use of renewable energy and sustainable development. This KOE article analyzes the recent progresses in this field (up to mid‐2013), with particular attention to the design and development of system approaches to artificial leaf devices and some of the related critical components. The aspects that are discussed are (
1
) natural versus artificial leaves, (
2
) the elements of an artificial leaf, (
3
) the possible approaches in developing an artificial leaf, (
4
) the development of the catalytic functionalities, (
5
) the advanced cell design in an artificial leaf, and finally (
6
) the artificial leaf plant design.
Cassini nightside observations of the oscillatory motion of Saturn's northern auroral oval
Authors: Bunce E. J. , Grodent D. C. , Jinks S. L. , Andrews D. J. , Badman S. V. , Coates A. J. , Cowley S. W. H. , Dougherty M. K. , Kurth W. S. , Mitchell D. G. , Provan G.
Published: April 2014

In recent years we have benefitted greatly from the first in‐orbit multi‐wavelength images of Saturn's polar atmosphere from the Cassini spacecraft. Specifically, images obtained from the Cassini UltraViolet Imaging Spectrograph (UVIS) provide an excellent view of the planet's auroral emissions, which in turn give an account of the large‐scale magnetosphere‐ionosphere coupling and dynamics within the system. However, obtaining near‐simultaneous views of the auroral regions with in situ measurements of magnetic field and plasma populations at high latitudes is more difficult to routinely achieve. Here we present an unusual case, during Revolution 99 in January 2009, where UVIS observes the entire northern UV auroral oval during a 2 h interval while Cassini traverses the magnetic flux tubes connecting to the auroral regions near 21 LT, sampling the related magnetic field, particle, and radio and plasma wave signatures. The motion of the auroral oval evident from the UVIS images requires a careful interpretation of the associated latitudinally “oscillating” magnetic field and auroral field‐aligned current signatures, whereas previous interpretations have assumed a static current system. Concurrent observations of the auroral hiss (typically generated in regions of downward directed field‐aligned current) support this revised interpretation of an oscillating current system. The nature of the motion of the auroral oval evident in the UVIS image sequence, and the simultaneous measured motion of the field‐aligned currents (and related plasma boundary) in this interval, is shown to be related to the northern hemisphere magnetosphere oscillation phase. This is in agreement with previous observations of the auroral oval oscillatory motion.
Diagenetic compaction experiments on simulated anhydrite fault gouge under static conditions
Authors: Pluymakers Anne M. H. , Peach Colin J. , Spiers Christopher J.
Published: April 2014

Faults that crosscut subsurface CO2 storage systems offer potential leakage pathways, especially if fault reactivation and dilation occur. After reactivation, however, newly formed fault gouge is expected to gradually compact and seal as a function of time. To estimate the time scale on which this occurs, the processes that control compaction must be understood. We performed uniaxial compaction experiments on simulated anhydrite fault gouge to investigate the deformation mechanisms that operate under postslip conditions in faulted anhydrite caprocks. This involved constant stress (5–12 MPa) and stress stepping experiments (5/7.5/10 MPa) performed at 80°C, under dry and wet conditions, on fault gouge samples prepared from crushed natural anhydrite sieved into different grain size fractions in the range 20–500 µm. Dry samples showed little to no compaction creep, whereas wet samples (i.e., flooded with presaturated CaSO4 solution) showed rapid compaction. Our mechanical data and microstructural observations on wet samples suggest that for fine grain sizes (<50 µm) and low stresses, gouge compaction is controlled by diffusion‐controlled pressure solution. With increasing grain size and stress, fluid‐assisted subcritical microcracking becomes dominant. Pressurizing solution‐flooded samples with CO2 (15 MPa) led to no significant effect on compaction rates in fine‐grained material, but it decreased compaction rates in coarse samples. Since fine grain sizes are expected in reactivated faults, we infer that pressure solution will dominate in anhydrite (cap)rocks, with extrapolation of our lab data to reservoir conditions suggesting sealing time scales of a few decades.
Redox Chemistry and Electrochemistry of Homoleptic Metal Phenolates
Authors: Fabrizi de Biani Fabrizia , Corsini Maddalena , Zanello Piero
Published: April 2014

The redox chemistry of aryl alcohols, or phenols, is of great interest because of their involvement in important biological and industrial processes. Phenol and its substituted analogs are facile one‐electron reducing agents that are often involved in electrochemical, photochemical and radiation chemical electron transfer reactions. For these and many other reasons the interest of chemists in the metal phenolates has always been lively and a huge number of these complexes are known. In this chapter we describe the redox behavior of the more restricted set of homoleptic aryloxide complexes. The peculiarities of phenolates as ligands make them usually unable to stabilize a metal in different redox states and, very often, reduction of the metal is accompanied by the release of one or more of the ligands and/or by the formation of polynuclear compounds. This may give rise to a complicated pattern in the redox chemistry of these complexes, but may also open the way to a rich, redox‐driven, chemistry of this class of compounds, which, apparently, is still largely unexplored.
Analytical Aspects of Metal Phenolates
Authors: Zabicky Jacob
Published: April 2014

The analytical methods are approached in three ways: (i) detection and quantitation of specific metal phenolates, especially the simpler ones used in industry; (ii) methods of detection and quantitation involving selective formation of a complex of the analyte with a phenolic ligand, taking advantage of special properties of the complex (optical, luminescent, electrochemical, phase transfer, etc.); (iii) certain metal–phenolate complexes act as analytical tools, specifically interacting as hosts with the analyte or by interchanging the metal ions and undergoing changes of properties (optical, luminescent, electrochemical, etc.) that can be applied to detection or quantitation. Although in approaches (ii) and (iii) the main subject is selective metal cation recognition, some attention is also paid to selective recognition of anions and molecules. For completeness of the analytical methods covered by phenolic reagents or complexes, specific recognition of ammonium ions, and especially quaternary ammonium ones, is discussed in a special section.
Positively Charged Selenium‐ and Tellurium‐Stabilized Species
Authors: Sato Soichi
Published: April 2014

Cationic chalcogenium species have attracted some attention due to the ability of these highly electropositive centers to interact with organic molecules or to provide strong π‐accepter ligands for transition metals. Though the cationic selenium and tellurium species are very useful for organic synthesis, most of the naked cationic chalcogen species, with the exception of tricoordinated chalcogenium salt (R3Ch+, Ch = chalcogen atoms), are unstable and difficult to isolate as a result of their intrinsic high reactivity. However, if the cationic chalcogen species are supported by the coordination of neighboringp‐block elements bearing a lone electron pair, they are often stabilized dramatically. Several cationic selenium and tellurium species which are naturally unstable have been synthesized and isolated by the intra‐ and intermolecular coordination of various ligands. The main purpose of this chapter is to introduce the recent progress of positively charged selenium and tellurium species, mainly focused on the dicationic selenium(II, IV, VI) and tellurium(II, IV, VI) species, which are stabilized by the coordination withp‐block elements.
Organic Conductors Containing Selenium and Tellurium
Authors: Vilela Filipe , Vobecka Zuzana , Skabara Peter J.
Published: April 2014

In recent years, efforts have been made to introduce the heavier chalcogens into aromatic organic molecules that obey the Huckel rule (4n+2π‐electrons), with a view to promoting and exploring their effect on electronic properties such as conductivity, magnetism, HOMO/LUMO energy levels, etc. Some of the fundamental properties of selenium and tellurium differ significantly from those of oxygen and sulfur, giving rise to disparities between the structures and properties of heavier chalcogen conducting materials when compared to their oxygen and sulfur‐rich counterparts. In this chapter, we will focus on the state‐of‐the‐art of selenium‐ and/or tellurium‐rich derivatives of chalcogenophenes and tetrathiafulvalene that have been developed and studied for their application as organic conductors. Herein are presented carefully chosen examples and studies that illustrate how chalcogen chemistry and the replacement of oxygen and sulfur by the heavier selenium and tellurium chalcogens is used in the design and manipulation of electroactive materials, and ultimately how it affects suitability for molecular device applications. Finally, we will discuss the current state‐of‐the‐art of these aromatic systems and the challenges presented in the synthesis and application of these materials in the field of organic electronics.
Rearrangements of Organoselenium and Organotellurium Compounds
Authors: Niyomura Osamu , Murai Toshiaki
Published: April 2014

This chapter has reviewed two types of rearrangements of compounds involving seleno‐ and tellurocarbonyl groups. First, focus has been laid on the rearrangement of a proton, that is tautomerization. Several types of tautomerizations such as selone/selenol and tellone/tellurol (keto/enol type isomerization), chalcogenocarboxylic acids (selenol/selenoxo and tellurol/telluroxo isomerization), and selenoamidate/selenoimidate and telluroamidate/telluroimidate are described. The seleno‐ and tellurocarbonyl groups have generally been understood to be less stable than the corresponding carbonyl and thiocarbonyl groups. Nevertheless, in many cases, chalcogenoxo forms are readily generated. Intramolecular and intermolecular hydrogen bonds also play crucial roles in these tautomerizations. Several theoretical approaches to the tautomerizations are also introduced. Many of them are in accordance with experimental results.

Second, selenium and tellurium versions of Claisen rearrangements are discussed. Seleno‐ and telluro‐ Claisen rearrangements generally precede milder than ordinary rearrangement and the sulfur version. In the rearrangement generating seleno‐ and telluoraldehdyes, these reactive species are trapped with dienes and alkenes. The availability of the rearrangement involving selenoamides and selenotihoic acid S‐esters as synthetic tools has been shown, in particular, for the construction of quaternary carbon centers. Despite these experimental developments, theoretical studies on seleno‐ and telluro‐Claisen rearrangement have yet to be achieved.