bluuebunny/crossref_metadata_2025 huggingface dataset:
Cloud-resolving simulations of mercury scavenging and deposition in thunderstorms
Authors: Nair U. S. , Wu Y. , Holmes C. D. , Ter Schure A. , Kallos G. , Walters J. T.
Published: October 2013

Abstract. This study examines dynamical and microphysical features of convective clouds that affect mercury (Hg) wet scavenging and concentrations in rainfall. Using idealized numerical model simulations in the Regional Atmospheric Modeling System (RAMS), we diagnose vertical transport and scavenging of soluble Hg species – gaseous oxidized mercury (GOM) and particle-bound mercury (HgP), collectively Hg(II) – in thunderstorms under typical environmental conditions found in the Northeast and Southeast United States (US). Mercury scavenging efficiencies from various initial altitudes are diagnosed for a case study of a typical strong convective storm in the Southeast US. Assuming that soluble mercury concentrations are initially vertically uniform, the model results suggest that 60% of mercury deposited to the surface in rainwater originates from above the boundary layer (> 2 km). The free troposphere could supply a larger fraction of mercury wet deposition if GOM and HgP concentrations increase with altitude. We use radiosonde observations in the Northeast and Southeast to characterize three important environmental characteristics that influence thunderstorm morphology: convective available potential energy (CAPE), vertical shear (0–6 km) of horizontal wind (SHEAR) and precipitable water (PW). The Southeast US generally has lower SHEAR and higher CAPE and PW. We then use RAMS to test how PW and SHEAR impact mercury scavenging and deposition, while keeping the initial Hg(II) concentrations fixed in all experiments. We found that the mercury concentration in rainfall is sensitive to SHEAR with the nature of sensitivity differing depending upon the PW. Since CAPE and PW cannot be perturbed independently, we test their combined influence using an ensemble of thunderstorm simulations initialized with environmental conditions for the Northeast and Southeast US. These simulations, which begin with identical Hg(II) concentrations, predict higher mercury concentrations in rainfall from thunderstorms forming in the environmental conditions over the Southeast US compared to the Northeast US. A final simulation of a stratiform rain event produces lower mercury concentrations than in thunderstorms forming in environments typical of the Southeast US. The stratiform cloud scavenges mercury from the lowest ~ 4 km of the atmosphere, while thunderstorms scavenge up to ~ 10 km.
Impact of external industrial sources on the regional and local air quality of Mexico Megacity
Authors: Almanza V. H. , Molina L. T. , Li G. , Fast J. , Sosa G.
Published: October 2013

Abstract. The air quality of megacities can be influenced by external emissions sources on both global and regional scale, and at the same time their outflow emissions can exert an important impact to the surrounding environment. The present study evaluates an SO2 peak observed on 24 March 2006 at the suburban supersite T1 and ambient air quality monitoring stations located in the north region of the Mexico City Metropolitan Area (MCMA) during MILAGRO campaign. We found that this peak could be related to an important episodic emission event from Tizayuca region, northeast of the MCMA. Back trajectories analyses suggest that the emission event started in the early morning at 04:00 LST and lasted for about 9 h. The estimated emission rate is noticeably high, about 2 kg s−1. This finding suggests the possibility of "overlooked" emission sources in this region that could influence the air quality of the MCMA. This further motivated us to study the cement plants, including those in the State of Hidalgo and in the State of Mexico, and we found that they can contribute in the NE region of the basin (about 41.7%), at the suburban supersite T1 (41.23%) and at some monitoring stations their contribution can be even higher than from the Tula Industrial Complex. The contribution of Tula Industrial Complex to regional ozone levels is estimated. The model suggests low contribution to the MCMA (1 ppb to 4 ppb) and slightly higher at the suburban T1 (6 ppb) and rural T2 (5 ppb) supersites. However, the contribution could be as high as 10 ppb in the upper northwest region of the basin and in the southwest and south-southeast regions of State of Hidalgo. In addition, a first estimate of the potential contribution from flaring activities to regional ozone levels is presented. Emission rates are estimated with a CFD combustion model. Results suggest that up to 30% of the total regional ozone from TIC could be related to flaring activities. Finally, the influence in SO2 levels from technological changes in the existing refinery is briefly discussed. These changes are due to the upcoming construction of a new refinery in Tula. The combination of emission reductions in the power plant, the refinery and in local sources in the MCMA could result in higher reductions on the average SO2 concentration. Reductions in external sources tend to affect more the northern part of the basin (−16.35% to −45.58%), whilst reductions of urban sources in the megacity tend to diminish SO2 levels substantially in the central, southwest, and southeast regions (−30.71% to −49.75%).
A new stratospheric and tropospheric NO2 retrieval algorithm for nadir-viewing satellite instruments: applications to OMI
Authors: Bucsela E. J. , Krotkov N. A. , Celarier E. A. , Lamsal L. N. , Swartz W. H. , Bhartia P. K. , Boersma K. F. , Veefkind J. P. , Gleason J. F. , Pickering K. E.
Published: October 2013

Abstract. We describe a new algorithm for the retrieval of nitrogen dioxide (NO2) vertical columns from nadir-viewing satellite instruments. This algorithm (SP2) is the basis for the Version 2.1 OMI This algorithm (SP2) is the basis for the Version 2.1 Ozone Monitoring Instrument (OMI) NO2 Standard Product and features a novel method for separating the stratospheric and tropospheric columns. NO2 Standard Product and features a novel method for separating the stratospheric and tropospheric columns. The approach estimates the stratospheric NO2 directly from satellite data without using stratospheric chemical transport models or assuming any global zonal wave pattern. Tropospheric NO2 columns are retrieved using air mass factors derived from high-resolution radiative transfer calculations and a monthly climatology of NO2 profile shapes. We also present details of how uncertainties in the retrieved columns are estimated. The sensitivity of the retrieval to assumptions made in the stratosphere–troposphere separation is discussed and shown to be small, in an absolute sense, for most regions. We compare daily and monthly mean global OMI NO2 retrievals using the SP2 algorithm with those of the original Version 1 Standard Product (SP1) and the Dutch DOMINO product. The SP2 retrievals yield significantly smaller summertime tropospheric columns than SP1, particularly in polluted regions, and are more consistent with validation studies. SP2 retrievals are also relatively free of modeling artifacts and negative tropospheric NO2 values. In a reanalysis of an INTEX-B validation study, we show that SP2 largely eliminates an ~20% discrepancy that existed between OMI and independent in situ springtime NO2 SP1 measurements.
Investigation of ground-based microwave radiometer calibration techniques at 530 hPa
Authors: Maschwitz G. , Löhnert U. , Crewell S. , Rose T. , Turner D. D.
Published: October 2013

Abstract. Ground-based microwave radiometers (MWR) are becoming more and more common for remotely sensing the atmospheric temperature and humidity profile as well as path-integrated cloud liquid water content. The calibration accuracy of the state-of-the-art MWR HATPRO-G2 (Humidity And Temperature Profiler – Generation 2) was investigated during the second phase of the Radiative Heating in Underexplored Bands Campaign (RHUBC-II) in northern Chile (5320 m above mean sea level, 530 hPa) conducted by the Atmospheric Radiation Measurement (ARM) program conducted between August and October 2009. This study assesses the quality of the two frequently used liquid nitrogen and tipping curve calibrations by performing a detailed error propagation study, which exploits the unique atmospheric conditions of RHUBC-II. Both methods are known to have open issues concerning systematic offsets and calibration repeatability. For the tipping curve calibration an uncertainty of ±0.1 to ±0.2 K (K-band) and ±0.6 to ±0.7 K (V-band) is found. The uncertainty in the tipping curve calibration is mainly due to atmospheric inhomogeneities and the assumed air mass correction for the Earth curvature. For the liquid nitrogen calibration the estimated uncertainty of ±0.3 to ±1.6 K is dominated by the uncertainty of the reflectivity of the liquid nitrogen target. A direct comparison between the two calibration techniques shows that for six of the nine channels that can be calibrated with both methods, they agree within the assessed uncertainties. For the other three channels the unexplained discrepancy is below 0.5 K. Systematic offsets, which may cause the disagreement of both methods within their estimated uncertainties, are discussed.
Site-specific climate analysis elucidates revegetation challenges for post-mining landscapes in eastern Australia
Authors: Audet P. , Arnold S. , Lechner A. M. , Baumgartl T.
Published: October 2013

Abstract. In eastern Australia, the availability of water is critical for the successful rehabilitation of post-mining landscapes and climatic characteristics of this diverse geographical region are closely defined by factors such as erratic rainfall and periods of drought and flooding. Despite this, specific metrics of climate patterning are seldom incorporated into the initial design of current post-mining land rehabilitation strategies. Our study proposes that a few common rainfall parameters can be combined and rated using arbitrary rainfall thresholds to characterise bioregional climate sensitivity relevant to the rehabilitation these landscapes. This approach included assessments of annual rainfall depth, average recurrence interval of prolonged low intensity rainfall, average recurrence intervals of short or prolonged high intensity events, median period without rain (or water-deficit) and standard deviation for this period in order to address climatic factors such as total water availability, seasonality and intensity – which were selected as potential proxies of both short- and long-term biological sensitivity to climate within the context of post-disturbance ecological development and recovery. Following our survey of available climate data, we derived site "climate sensitivity" indexes and compared the performance of 9 ongoing mine sites: Weipa, Mt. Isa and Cloncurry, Eromanga, Kidston, the Bowen Basin (Curragh), Tarong, North Stradbroke Island, and the Newnes Plateau. The sites were then ranked from most-to-least sensitive and compared with natural bioregional patterns of vegetation density using mean NDVI. It was determined that regular rainfall and relatively short periods of water-deficit were key characteristics of sites having less sensitivity to climate – as found among the relatively more temperate inland mining locations. Whereas, high rainfall variability, frequently occurring high intensity events, and (or) prolonged seasonal drought were primary indicators of sites having greater sensitivity to climate – as found among the semi-arid central-inland sites. Overall, the manner in which these climatic factors are identified and ultimately addressed by land managers and rehabilitation practitioners could be a key determinant of achievable success at given locations at the planning stages of rehabilitation design.
10Be in late deglacial climate simulated by ECHAM5-HAM – Part 2: Isolating the solar signal from 10Be deposition
Authors: Heikkilä U. , Shi X. , Phipps S. J. , Smith A. M.
Published: October 2013

Abstract. This study investigates the effect of deglacial climate on the deposition of the solar proxy 10Be globally, and at two specific locations, the GRIP site at Summit, Central Greenland, and the Law Dome site in coastal Antarctica. The deglacial climate is represented by three 30 yr time slice simulations of 10 000 BP (years before present = 1950 CE), 11 000 BP and 12 000 BP, compared with a preindustrial control simulation. The model used is the ECHAM5-HAM atmospheric aerosol–climate model, driven with sea surface temperatures and sea ice cover simulated using the CSIRO Mk3L coupled climate system model. The focus is on isolating the 10Be production signal, driven by solar variability, from the weather or climate driven noise in the 10Be deposition flux during different stages of climate. The production signal varies on lower frequencies, dominated by the 11yr solar cycle within the 30 yr time scale of these experiments. The climatic noise is of higher frequencies. We first apply empirical orthogonal functions (EOF) analysis to global 10Be deposition on the annual scale and find that the first principal component, consisting of the spatial pattern of mean 10Be deposition and the temporally varying solar signal, explains 64% of the variability. The following principal components are closely related to those of precipitation. Then, we apply ensemble empirical decomposition (EEMD) analysis on the time series of 10Be deposition at GRIP and at Law Dome, which is an effective method for adaptively decomposing the time series into different frequency components. The low frequency components and the long term trend represent production and have reduced noise compared to the entire frequency spectrum of the deposition. The high frequency components represent climate driven noise related to the seasonal cycle of e.g. precipitation and are closely connected to high frequencies of precipitation. These results firstly show that the 10Be atmospheric production signal is preserved in the deposition flux to surface even during climates very different from today's both in global data and at two specific locations. Secondly, noise can be effectively reduced from 10Be deposition data by simply applying the EOF analysis in the case of a reasonably large number of available data sets, or by decomposing the individual data sets to filter out high-frequency fluctuations.
Rainfall and temperature estimation for a data sparse region
Authors: Wilby R. L. , Yu D.
Published: October 2013

Abstract. Humanitarian and development agencies face difficult decisions about where and how to prioritise climate risk reduction measures. These tasks are especially challenging in regions with few meteorological stations, complex topography and extreme weather events. In this study, we blend surface meteorological observations, remotely sensed (TRMM and NDVI) data, physiographic indices, and regression techniques to produce gridded maps of annual mean precipitation and temperature, as well as parameters for site-specific, daily weather generation in Yemen. Maps of annual means were cross-validated and tested against independent observations. These replicated known features such as peak rainfall totals in the highlands and western escarpment, as well as maximum temperatures along the coastal plains and interior. The weather generator reproduced daily and annual diagnostics when run with parameters from observed meteorological series for a test site at Taiz. However, when run with interpolated parameters, the frequency of wet days, mean wet-day amount, annual totals and variability were underestimated. Stratification of sites for model calibration improved representation of the growing season's rainfall totals. Future work should focus on a wider range of model inputs to better discriminate controls exerted by different landscape units.
Household water use and conservation models using Monte Carlo techniques
Authors: Cahill R. , R. Lund J. , DeOreo B. , Medellín-Azuara J.
Published: October 2013

Abstract. The increased availability of end use measurement studies allows for mechanistic and detailed approaches to estimating household water demand and conservation potential. This study simulates water use in a single-family residential neighborhood using end-water-use parameter probability distributions generated from Monte Carlo sampling. This model represents existing water use conditions in 2010 and is calibrated to 2006–2011 metered data. A two-stage mixed integer optimization model is then developed to estimate the least-cost combination of long- and short-term conservation actions for each household. This least-cost conservation model provides an estimate of the upper bound of reasonable conservation potential for varying pricing and rebate conditions. The models were adapted from previous work in Jordan and are applied to a neighborhood in San Ramon, California in the eastern San Francisco Bay Area. The existing conditions model produces seasonal use results very close to the metered data. The least-cost conservation model suggests clothes washer rebates are among most cost-effective rebate programs for indoor uses. Retrofit of faucets and toilets is also cost-effective and holds the highest potential for water savings from indoor uses. This mechanistic modeling approach can improve understanding of water demand and estimate cost-effectiveness of water conservation programs.
Variability of extreme precipitation over Europe and its relationships with teleconnection patterns
Authors: Casanueva A. , Rodríguez-Puebla C. , Frías M. D. , González-Reviriego N.
Published: October 2013

Abstract. A growing interest in extreme precipitation has spread through the scientific community due to the effects of global climate change on the hydrological cycle and their threat on natural systems more than averaged climatic values. Understanding the variability of hydrological indices and their association to atmospheric processes could help to project the frequency and severity of extremes. This paper evaluates the trend of three precipitation extremes: the number of consecutive dry/wet days (CDD/CWD) and the quotient of the precipitation in days where daily precipitation exceeds the 95th percentile of the reference period and the total amount of precipitation (or contribution of very wet days, R95pTOT). The aim of this study is twofold. First, extreme indicators are compared against accumulated precipitation (RR) over Europe in terms of trends using non-parametric approaches. Second, we analyse the geographic opposite trends found over different parts of Europe by considering their relationships with large-scale processes, using different teleconnection patterns. The study is accomplished for the four seasons using the gridded E-OBS dataset developed within the EU ENSEMBLES project. Different patterns of variability were found for CWD and CDD in winter and summer, with north-south and east–west configurations, respectively. We consider physical factors to understand the extremes variability by linking large-scale processes and hydrological extremes. Opposite association with the North Atlantic Oscillation in winter and summer, and the relationships with the Scandinavian, East Atlantic patterns and El Niño/Southern Oscillation events in spring and autumn gave insight into the trend differences. Significant relationships were found between the Atlantic Multidecadal Oscillation and very extreme precipitation (R95pTOT) during the whole year. The largest extreme anomalies were analysed by composite maps using atmospheric variables and sea surface temperature. The association of extreme precipitation indices and large-scale variables found in this work could pave the way of new possibilities for the projection of extremes in downscaling techniques.
New empirical stiffness equations for corner-filleted flexure hinges
Authors: Meng Q. , Li Y. , Xu J.
Published: October 2013

Abstract. This paper investigates the existing stiffness equations for corner-filleted flexure hinges. Three empirical stiffness equations for corner-filleted flexure hinges (each fillet radius, r, equals to 0.1 l; l, the length of a corner-filleted flexure hinge) are formulated based on finite element analysis results for the purpose of overcoming these investigated limitations. Three comparisons made with the existing compliance/stiffness equations and finite element analysis (FEA) results indicate that the proposed empirical stiffness equations enlarge the range of rate of thickness (t, the minimum thickness of a corner-filleted flexure hinge) to length (l), t/l (0.02 ≤ t/l ≤ 1) and ensure the accuracy for each empirical stiffness equation under large deformation. The errors are within 6% when compared to FEA results.
Assessment of heat sources on the control of fast flow of Vestfonna Ice Cap, Svalbard
Authors: Schäfer M. , Gillet-Chaulet F. , Gladstone R. , Pettersson R. , Pohjola V. A. , Strozzi T. , Zwinger T.
Published: October 2013

Abstract. The dynamic regime of Svalbard's Nordaustlandet ice caps is dominated by fast flowing outlet glaciers, making assessment of their response to climate change challenging. A key element of the challenge lies in the fact that the motion of fast outlet glaciers occurs largely through basal sliding, and is governed by physical processes at the glacier bed, processes that are difficult both to observe and to simulate. Up to now, most of the sliding laws used in ice flow models were based on uniform parameters with a condition on temperature to identify regions of basal sliding. However these models are usually not able to reproduce observed velocities with sufficient accuracy. With the development of inverse methods, it is now common to infer a spatially varying field of sliding parameters from surface ice-velocity observations. These parameter distributions usually reflect a high spatial variability and represent valuable information to understand and test various hypotheses on physical processes involved in sliding. However, in these models, basal sliding is uncoupled from the thermal regime of basal ice and the evolution of the sliding parameters in prognostic simulations remains problematic. Here we explore the role of different heat sources (friction heating, strain heating and latent heat through percolation of melt water) on the development of sliding and fast flow through thermomechanical coupling on Nordaustlandet outlet glaciers. We focus on Vestfonna with a special emphasis on Franklinbreen, a fast flowing outlet glacier which has been observed to accelerate between 1995 and 2008 and possibly already prior to 1995. We try to reconcile the impacts of temperature and heat sources on basal friction coefficients inferred from observed surface velocities during these two periods. Our simulations reproduce a temperature profile from borehole measurements, allowing an interpretation of the vertical temperature structure in terms of temporal evolution of climate. We identify firn heating as a crucial heat source to explain Vestfonna's temperature distribution, especially in the thick areas in the center. However, friction heating is the dominant heat source at the bed of fast flowing outlet glaciers. Our findings do not support a purely temperature dependent sliding law for Vestfonna, implying that hydrology and/or sediment physics need to be represented in order to simulate fast flowing outlet glaciers.
Fuchs’ Superficial Marginal Keratitis Managed with Circumferential Marginal Corneoscleral Lamellar Patch Graft
Authors: Mejía Luis F. , Santamaría Juan P. , Gaviria Ana M. , Rodríguez Ana M.
Published: October 2013

Purpose

To report a case of Fuchs’ superficial marginal keratitis managed with circumferential marginal corneoscleral lamellar patch graft.

Methods

Interventional case report.

Results

A 34-year-old man presented with several years’ history of ill-defined symptoms of binocular ocular irritation associated with vision loss, mostly in the left eye. A superior marginal corneal thinning was found at biomicroscopy of the left eye, with 2 finely vascularized descemetoceles, and a gray epithelial demarcation line without lipid infiltrates. The right eye was clinically normal. Anterior segment optical coherence tomography demonstrated an important corneal thinning from the 7 o'clock to 3 o'clock positions, without scleral involvement. A circumferential marginal corneoscleral lamellar patch graft was done involving 3 mm of sclera and 3 mm of cornea.

Conclusions

Fuchs’ superficial marginal keratitis is a rare entity, mostly affecting young adults. It should be considered part of a spectrum of corneal thinning disorders, together with Terrien's marginal degeneration. Definitive treatment with a marginal corneoscleral lamellar patch graft with or without conjunctival autograft is suggested.
Amino acid content and biomass productivity of selected weed species as an indicator of their response to herbicide stress
Authors: Kieloch Renata , Sadowski Jerzy , Domaradzki Krzysztof
Published: October 2013

Biomass reduction and amino acid content in plants of Papaver rhoeas L. and Stellaria media L. were investigated to evaluate response of these species to herbicide stress under various temperature (25/16 and 8/2 oC) and relative humidity (50 and 75%) regimes. Weeds were treated with tribenuron methyl (15 g × ha-1), a mixture of 2.4-D with florasulam (180 + 3.75 g × ha-1), and a mixture of 2.4-D with dicamba (1252.5 + 97.5 g × ha-1). The fresh weight of weeds and the content of free branched-chain amino acids (valine, leucine and isoleucine) in plant tissue were recorded. Tribenuron methyl was the herbicide that most limited biomass productivity, regardless of weed species and climate conditions. S. media was more sensitive to herbicides than P. rhoeas. Weed response to herbicides was dependent on temperature, but not on relative humidity. Tribenuron methyl applied to both weed species under various temperature regimes caused significant amino acid deficiency. The reduction in amino acid content in plants of P. rhoeas was greater at warm temperature compared to the cold regime due to stronger reaction to tribenuron methyl applied under these conditions. In most of cases, the mixture of 2.4-D + dicamba induced overproduction of amino acids.
When 19 is greater than 92
Authors: Zeitels Lauren R , Mendell Joshua T
Published: October 2013

The gene miR-17-92 encodes six different microRNAs, with one of these acting as an internal brake that opposes the oncogenic activity of the others in some cancer contexts.
A year in the life of eLife
Authors: Schekman Randy , Watt Fiona M , Weigel Detlef
Published: October 2013

Improving the peer review process, overcoming the limitations of print journals and providing open access to the very best work in the life and biomedical sciences are three highlights of our first year.
Selecting the Right Similarity‐Scoring Matrix
Authors: Pearson William R.
Published: October 2013

Protein sequence similarity searching programs like BLASTP, SSEARCH, and FASTA use scoring matrices that are designed to identify distant evolutionary relationships (BLOSUM62 for BLAST, BLOSUM50 for SSEARCH and FASTA). Different similarity scoring matrices are most effective at different evolutionary distances. “Deep” scoring matrices like BLOSUM62 and BLOSUM50 target alignments with 20% to 30% identity, while “shallow” scoring matrices (e.g., VTML10 to VTML80) target alignments that share 90% to 50% identity, reflecting much less evolutionary change. While “deep” matrices provide very sensitive similarity searches, they also require longer sequence alignments and can sometimes produce alignment overextension into nonhomologous regions. Shallower scoring matrices are more effective when searching for short protein domains, or when the goal is to limit the scope of the search to sequences that are likely to be orthologous between recently diverged organisms. Likewise, in DNA searches, the match and mismatch parameters set evolutionary look‐back times and domain boundaries. In this unit, we will discuss the theoretical foundations that drive practical choices of protein and DNA similarity scoring matrices and gap penalties. Deep scoring matrices (BLOSUM62 and BLOSUM50) should be used for sensitive searches with full‐length protein sequences, but short domains or restricted evolutionary look‐back require shallower scoring matrices. Curr. Protoc. Bioinform. 43:3.5.1‐3.5.9. © 2013 by John Wiley & Sons, Inc.
An Overview of RNA Sequence Analyses: Structure Prediction, ncRNA Gene Identification, and RNAi Design
Authors: Stormo Gary D.
Published: October 2013

This unit briefly describes the two fundamentally different methods for predicting RNA structures. The first is to find that structure with the minimum free energy of folding, as predicted by various thermodynamic parameters related to base‐pair stacking, loop lengths, and other features. If one has only a single sequence, this thermodynamic approach is the best available method. The second fundamental approach to RNA structure prediction is to use multiple, homologous sequences for which one can infer a common structure, and then try and predict a structure common to all of the sequences. Such an approach is referred to as a comparative method or phylogenetic method of RNA structure prediction. Curr. Protoc. Bioinform. 43:12.1.1‐12.1.3. © 2013 by John Wiley & Sons, Inc.
Evidence of parallel denitrification and nitrite oxidation in the ODZ of the Arabian Sea from paired stable isotopes of nitrate and nitrite
Authors: Gaye Birgit , Nagel Birgit , Dähnke Kirstin , Rixen Tim , Emeis Kay‐Christian
Published: October 2013

The Arabian Sea is a major oceanic nitrogen sink, and its oxygen‐deficient zone (ODZ) extends from 150 m to 1200 m water depth. To identify the dominant transformation processes of reactive nitrogen and to quantify the amounts of nitrogen turned over in the different reactions of the nitrogen cycle, we use paired data on stable isotope ratios of nitrogen and oxygen in nitrate and nitrite measured at four near‐coastal and five open ocean stations in the Arabian Sea. We find significant nitrate reduction and denitrification between 100 m and 400 m in the open Arabian Sea, which are most intense in the eastern and northern part of the basin, and estimate that about 50% of initial nitrate is being reduced either to dinitrogen gas (denitrification) or to nitrite (nitrate reduction) in the core zone of denitrification. Nitrite accumulates in concentrations above 4 µM in the water column of the eastern and northern Arabian Sea. Large differences in isotopic ratios of nitrate and nitrite and a decoupling of their stable nitrogen and oxygen isotopes can be explained by the reoxidation of nitrite. The observed decoupling of the paired isotopes may be due to the exchange of oxygen of nitrite with oxygen from ambient water. In agreement with model estimates from the literature, about 25% of the nitrate initially reduced to nitrite is returned to the nitrate pool by nitrification in the upper and lower denitrification layer while 40% is denitrified.
Paleoproxy data track how El Niño changes nutrient availability
Authors: Schultz Colin
Published: October 2013

The 1997–1998 El Niño was one of the strongest on record, and the installation of a widespread sensor network in the Pacific before its onset meant that it was also one of the best studied. The El Niño phase of the El Niño–Southern Oscillation (ENSO) brings reduced upwelling of deeper water and leads to warmer sea surface temperatures in the tropical Pacific Ocean. During the 1997–1998 El Niño, shipboard measurements showed that this reduced upwelling caused nutrient availability in the region to drop by roughly half. However, putting in context the effect of this El Niño on nutrient variability and ocean productivity is difficult because high temporal resolution measurements for earlier El Niño events are in short supply.
The Madden‐Julian oscillation detected in Aquarius salinity observations
Authors: Grunseich Gary , Subrahmanyam Bulusu , Wang Bin
Published: October 2013

The Madden‐Julian Oscillation (MJO) impacts a wide range of weather and climate phenomena. Current global coupled ocean‐atmospheric general circulation models exhibit considerable shortcomings in representing and predicting the MJO, specifically its initiation, due to a lack of in situ observations. Here we show, for the first time, that the MJO propagation can be detected from the newly launched NASA Aquarius Salinity mission. The magnitude and extent of sea surface salinity (SSS) variations during the MJO is established, providing a useful tool for data assimilation into models to correctly represent both oceanic and atmospheric processes during intraseasonal variations. Salinity observation allows for atmospheric conditions to be inferred from freshwater flux, on which surface salinity is highly dependent. Increased observations of global SSS from the Aquarius mission will be particularly valuable in remote regions of the tropics and will increase our dynamical understanding and advance prediction of the MJO through model improvement.
Climate and carbon cycle response to the 1815 Tambora volcanic eruption
Authors: Kandlbauer J. , Hopcroft P. O. , Valdes P. J. , Sparks R. S. J.
Published: October 2013

The sulphur released by the 1815 Tambora volcanic eruption resulted in a net cooling after the eruption. The cold climate was responsible for crop failures, leading to serious famine and high food prices in Europe and North America. The year 1816 became known as the “year without summer”. We performed a series of climate simulations with the UK Met Office model HadGEM2‐ES to assess the climate and carbon cycle consequences of the eruption. The model shows a temperature decrease of 1 ± 0.1°C and global precipitation decrease of 3.7% in 1816. The following net primary productivity (NPP) increase is caused by strongly reduced plant respiration and supports the overall increase in land carbon storage after the eruption. Most of the carbon is taken up by the soil reservoir, mainly due to increased litter influx. Overall, the change of combined land and ocean carbon implies an atmospheric CO2 decrease of over 6 ppmv. C3 and C4 grasses, used here as an analogy for crops, revealed globally increasing productivity for C3 grasses/crops (e.g., wheat) by ≥8%, while C4 grasses/crops (e.g., maize) decreased by over 12%. Regional positive C3 and negative C4 NPP are mainly found in the tropics and midlatitudes, whereas positive C4 NPP areas are distributed in marginal areas. Negative C3 grasses anomalies are found in high‐elevation and high‐latitude regions. These findings highlight the importance of including process‐based vegetation or crop model components to represent the potentially nonlinear dependencies on climatic changes.
Conditions for successful data assimilation
Authors: Chorin Alexandre J. , Morzfeld Matthias
Published: October 2013

We show, using idealized models, that numerical data assimilation can be successful only if an effective dimension of the problem is not excessive. This effective dimension depends on the noise in the model and the data, and in physically reasonable problems, it can be moderate even when the number of variables is huge. We then analyze several data assimilation algorithms, including particle filters and variational methods. We show that well‐designed particle filters can solve most of those data assimilation problems that can be solved in principle and compare the conditions under which variational methods can succeed to the conditions required of particle filters. We also discuss the limitations of our analysis.
An overview of the Geoengineering Model Intercomparison Project (GeoMIP)
Authors: Kravitz Ben , Robock Alan , Forster Piers M. , Haywood James M. , Lawrence Mark G. , Schmidt Hauke
Published: October 2013

The Geoengineering Model Intercomparison Project (GeoMIP) was designed to determine robust climate system model responses to solar geoengineering. GeoMIP currently consists of four standardized simulations involving reduction of insolation or increased amounts of stratospheric sulfate aerosols. Three more experiments involving marine cloud brightening are planned. This project has improved confidence in the expected climate effects of geoengineering in several key areas, such as the effects of geoengineering on spatial patterns of temperature and the spatial distribution of precipitation, especially extreme precipitation events. However, GeoMIP has also highlighted several important research gaps, such as the effects on terrestrial net primary productivity and the importance of the CO2 physiological effect in determining the hydrologic cycle response to geoengineering. Future efforts will endeavor to address these gaps, as well as encourage cooperation with the chemistry modeling communities, the impact assessment communities, and other groups interested in model output.
Mass‐wasting features and processes in Vesta's south polar basin Rheasilvia
Authors: Otto Katharina A. , Jaumann Ralf , Krohn Katrin , Matz Klaus‐Dieter , Preusker Frank , Roatsch Thomas , Schenk Paul , Scholten Frank , Stephan Katrin , Raymond Carol A. , Russell Christopher T.
Published: October 2013

The Rheasilvia crater is Vesta's largest impact basin. It is a 500 km diameter complex crater centered near the south pole and overlying the 400 km diameter impact basin Veneneia. Using Framing Camera (FC) data from the Dawn spacecraft's Low Altitude Mapping Orbit (20 m/pixel) and a digital terrain model derived from High Altitude Mapping Orbit stereo data, we identified various mass‐wasting features within the south polar region. These features include intra‐crater mass movements, flow‐like and creep‐like structures, slumping areas, landslides, and curved radial and concentric ridges. Intra‐crater mass‐wasting features are represented by lobate slides, talus material, dark patches on the crater wall, spurs along the crater rim and boulders. Slumping areas develop in compact material, whereas landslides form in relatively loose material. Both may be triggered by seismic shaking induced by impacts. Intra‐crater mass wasting and slid and slumped materials are homogeneously distributed throughout the basin. Slumping and sliding processes have contributed most efficiently to basin degradation. Flow‐like and creep‐like features originate from granular material and cluster between 0°E and 90°E, an area exposing shocked and fractured material from the Rheasilvia impact event. The radial curved ridges are likely to be remnants of the early Rheasilvia collapse process, when radially moving masses were deflected by the Coriolis Effect. The concentric ridges are artifacts from the crater rim collapse. Curved ridges at the intersection of Rheasilvia and Veneneia, and on Rheasilvia's central peak, may also have been influenced by the Rheasilvia basin relaxation process, and an oblique impact, respectively.
Analysis of polygonal cracking patterns in chloride‐bearing terrains on Mars: Indicators of ancient playa settings
Authors: El‐Maarry M. R. , Pommerol A. , Thomas N.
Published: October 2013

The ancient southern highlands on Mars (~3.5 Gyr old) contain > 600 regions that display spectral evidence in the infrared for the presence of chloride‐bearing materials. Many of these locations were previously reported to display polygonal cracking patterns. We studied more than 80 of the chloride‐bearing terrains using high‐resolution (0.25–0.5 m/pixel) images, as well as near‐infrared spectral data, to characterize the surface textures and the associated cracking patterns and mineralogies. Our study indicates that ~75% of the studied locations display polygonal cracks that resemble desiccation cracks, while some resemble salt expansion/thrust polygons. Furthermore, we detect, spectrally, the presence of smectites in association with ~30% of the studied fractured terrains. We note that smectites are a special class of swelling clay minerals that can induce formation of large desiccation cracks. As such, we suggest that the cracking patterns are indicative of the presence of smectite phyllosilicates even in the absence of spectral confirmation. Our results suggest that many chloride‐bearing terrains have a lacustrine origin and a geologic setting similar to playas on Earth. Such locations would have contained ephemeral lakes that may have undergone repeated cycles of desiccation and recharging by a near‐surface fluctuating water table in order to account for the salt‐phyllosilicates associations. These results have notable implications for the ancient hydrology of Mars. We propose that the morphologies and sizes of the polygonal cracks can be used as paleoenvironmental, as well as lithological, indicators that could be helpful in planning future missions.
Introduction to Shop‐Floor Control
Authors: Trentesaux Damien , Prabhu Vittaldas V.
Published: October 2013

Shop‐floor control (SFC) is an important element in managing manufacturing system operations in order to faithfully execute production plans. In this article, the functions and challenges encountered in typical SFC systems are presented along with their evolution from classical centralized approaches to more distributed approaches. An example of modern SFC is used to illustrate the manner in which such systems increasingly encompass manufacturing execution system and supervisory control and data acquisition levels of enterprise architectures. Some recent developments in feedback control approaches for SFC are also presented along with architectural, functional, technological, and human‐centric considerations.
Pure Cutting‐Plane Algorithms and their Convergence
Authors: Gade Dinakar , Küçükyavuz Simge
Published: October 2013

Cutting‐plane methods solve a mixed‐integer program (MIP) by iteratively adding a valid linear inequality that violates a fractional solution of a linear relaxation of the problem. This article surveys cutting‐plane algorithms for different subclasses of MIPs and addresses whether these algorithms converge to an optimal solution of MIP in finitely many steps.
Robustness for Operations Research and Decision Aiding
Authors: Roy Bernard
Published: October 2013

This article begins with a succinct presentation of what operations research and decision aiding (OR‐DA) seeks to accomplish and then goes on to develop two examples. The section titled “What Is Robustness in OR‐DA?,” which explains why the search for robustness is a major concern in the field, details the meaning of the qualifier robust, as used in this article. The two requirements presented in the section titled “Two Requirements to Meet the Concern for Robustness Properly” must be considered appropriately, if the concern is to be addressed properly. The section titled “A Framework Schema to Meet the Concern for Robustness” deals with the framework schema wherein the standard answers to the concern can be found. The sections titled “Other Ways of Defining the Concept of ‘Robust Solutions”’ and “The Concept of ‘Robust Conclusions”’ provide an overview of less traditional approaches.

Robustness for OR‐DA is a subject that has given rise to many publications over the last several years. I will first present the focus of OR‐DA and deal with two examples that will be developed further in my article. I will go on to explain why robustness is a major concern in OR‐DA, which will lead me to underscore the two requirements that must be tackled to deal with this concern properly. Then, I will present the framework schema for most research and the way that the concept of a robust solution is usually addressed. In the sections titled “Other Ways of Defining the Concept of ‘Robust Solutions”’ and “The Concept of ‘Robust Conclusions”’, I will examine the most recent research outside the schema, with other definitions of robust solutions and other types of answers (robust conclusions).
Fuzzy Measures and Integrals in Multicriteria Decision Analysis
Authors: Grabisch Michel
Published: October 2013

So far, the weighted sum has been the most popular way of aggregating criteria. We present the Choquet integral with respect to a fuzzy measure as an alternative. The fuzzy measure represents weights of importance on every group of criteria, and the Choquet integral generalizes the weighted sum and the ordered weighted average (OWA). The Shapley value and the interaction index permit to analyze and understand the behavior of the model.k‐additive fuzzy measures are submodels of polynomial size, which are sufficient in practice, and permit to represent the interaction between criteria.
Phage Selection of Peptide “Microantibodies”
Authors: Fujiwara Daisuke , Fujii Ikuo
Published: October 2013

A bioactive peptide capable of inhibiting protein‐protein interactions has the potential to be a molecular tool for biological studies and a therapeutic by disrupting aberrant interactions involved in diseases. We have developed combinatorial libraries of peptides with helix‐loop‐helix structure, from which the isolated peptides have the constrained structure to reduce entropy costs in binding, resulting in high binding affinities for target molecules. Previously, we designed a de novo peptide of helix‐loop‐helix structure that we termed a “microantibody.” Using the microantibody as a library scaffold, we have constructed a phage‐display library to successfully isolate molecular‐targeting peptides against a cytokine receptor (granulocyte colony‐stimulating factor receptor), a protein kinase (Aurora‐A), and a ganglioside (GM1). Protocols in this article describe a general procedure for the library construction and the library screening. Curr. Protoc. Chem. Biol. 5:171‐194 © 2013 by John Wiley & Sons, Inc.
Multiplexing High‐Content Flow (HCF) and Quantitative High‐Throughput Screening (qHTS) to Identify Compounds Capable of Decreasing Cell Viability, Activating Caspase 3/7, Expressing Annexin V, and Changing Mitochondrial Membrane Integrity
Authors: Mathews Lesley A. , Keller Jonathan M. , McKnight Crystal , Michael Sam , Shinn Paul , Liu Dongbo , Staudt Louis M. , Thomas Craig J. , Ferrer Marc
Published: October 2013

High‐content flow (HCF) screening systems, such as the iQue Screener and HTFC Screening System from IntelliCyt, have facilitated the implementation of flow cytometry assays for high‐throughput screening. HCF screening systems enable the use of smaller sample volumes and multiplexed assays to simultaneously assess different cellular parameters from a single well. This becomes invaluable when working with cells or compounds that are available in limited quantities or when conducting large‐scale screens. When assays can be miniaturized to a 384‐ or 1536‐well microplate format, it is possible to implement dose‐response‐based high‐throughput screens, also known as quantitative HTS or qHTS. This article describes how qHTS at the new National Center for Advancing Translational Science (NCATS) has been systematically coupled with the HTFC Screening System and Multimetric Apoptosis Screening Kit from IntelliCyt to biologically validate active compounds from primary cell proliferation screens using a model of diffuse large B cell lymphoma (DLBCL). Curr. Protoc. Chem. Biol. 5:195‐212 © 2013 by John Wiley & Sons, Inc.
An adaptive control scheme using multiple reference models
Authors: Tan Chang , Tao Gang , Qi Ruiyun
Published: October 2013

This paper develops an extended model reference adaptive control scheme to expand the capacity of state feedback state tracking adaptive control to handle the plant‐model matching uncertainties for single‐input LTI systems. The extended scheme is developed, using multiple reference model systems (only one of which is required to be able to match the controlled plant), and multiple controllers (which are updated from adaptive laws generated from multiple reference model systems based estimation errors), as two key features of such design to relax a plant‐model matching condition. A switching mechanism is constructed using those multiple estimation errors, capable of selecting the suitable control input from the multiple control signals, to achieve the desired system performance. An aircraft flight control example is presented to show the capacity of such design in relaxing a practical design condition. Copyright © 2013 John Wiley & Sons, Ltd.