bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrography and estimation of density currents in the southern part of the Bay of Campeche, Mexico
Authors: Monreal-Gómez MA , Salas-de-León DA , Padilla-Pilotze AR , Alatorre-Mendieta MA
Published: November 2017

This paper reports the temperature, salinity and sigma-t distributions at the surface, 10 and 30 m depth, derived from data obtained in the autumn of 1987 in the southern part of the Bay of Campeche, as well as the density distribution along two cross sections which intersect near the most important river system in the region. Based on density field data, density driven currents and the vertical stratification were estimated, the latter by means of the potential energy anomaly. A strong haline gradient, that dominates the sigma-t distribution and is associated with the discharge of the rivers in the region, was observed. The calculated potential energy anomaly had a maximum value of 70 J m–3 near the mouth of the Grijalva-Usumacinta system and the San Pedro and San Pablo rivers. The surface current induced by the density gradient was estimated at 11.2 cm s–1 northeastward. On the other hand, the distribution of isohalines and isopycnals at the surface and 10 m depth showed certain symmetry with respect to a normal axis to the coast. This axis was displaced towards the west of the mouth of the Grijalva-Usumacinta system, suggesting the existence of a littoral current in the east-west direction.
Post-nursery growout potential of Penaeus vannamei in an intensive raceway system
Authors: Robertson L , Samocha T , Gregg K , Lawrence A
Published: November 2017

A 49-day intensive growth trial in 70 m2 raceways under a greenhouse was conducted with Penaeus vannamei (stocked at an average weight of 80 mg and density of 223-299 ind./m2). Shrimp grew at an average rate of 0.94 to 1.19 g/week. They were harvested at a mean size of 6.5 to 8.1 g with the biomass produced reaching 1.36 to 1.56 kg/m2 and survival ranging from 78 to 83%. As biomass increased, the management of water recirculation and water exchange became more intensified. Seawater was replaced initially at a rate of 3%/day and increased to 400% daily during the final week of the study. Although this trial was undertaken during the spring in Texas when ambient morning water temperatures ranged from 18.3 to 28.3ºC, temperatures in the raceways were maintained with a mean daily low temperature of 26.8ºC and mean daily high of 29.8ºC. Shrimp cultured simultaneously in outdoor ponds were smaller (4.3 to 5.0 g) and had lower growth (0.62 to 0.71 g/week). Results obtained in this trial indicate that a larger juvenile can be produced for pond stocking and suggest that P. vannamei can be cultured successfully in this intensive raceway system to a marketable size.
Analysis of the benthic infauna from Bahia de San Quintin, Baja California, with emphasis on its use in impact assessment studies
Authors: Calderón-Aguilera LE
Published: November 2017

An ecological analysis of benthic polychaete assemblages is presented. Samples were collected at ll stations in July, September and December 1981, and February and May 1982. Thirty-nine species in 21 families of polychaetes were identified. Spatial variations may be due to microhabitats and/or the intrinsic biology of the species. The abundance increased in spring because of reproduction and recruitment. The values of the Shannon diversity index were as high as 3.1 and 0.9 for evenness. Clusters among stations could not be identified which may have been because of the dominance of five species (Exogone occidentalis, Pseudopolydora kempi, Scoloplos acmeceps, Prionospio heterobranchia and Neanthes arenaceodentata) and the relative abundance of secondary species. The abundance, number of species and evenness were not significant (p > > 0.05) when correlated with the content of organic matter and sediment particle size. The log-normal distributions of individuals among species did not detect pollution-induced changes in the community. The benthic community in Bahía de San Quintín was found to be at or near equilibrium which may be the result of a relatively high resilience to disturbance. A qualitative assessment of the possible impact of domestic sewage on the infauna and an outline for the ecological management of the bay are presented.
Effect of turbulent kinetic energy on the spatial distribution of chlorophyll a in a small coastal lagoon
Authors: Santamaría-del-Ángel E , Millán-Núñez R , Cajal-Medrano R
Published: November 2017

In order to observe the effect of turbulent kinetic energy (TKE) on the spatial distribution of chlorophyll a, four spatial variations were analysed (two during high and two during low tide) on 15 and 16 April, 1989 in Puerto Don Juan. Observations were made of buoy drifts and tidal height, and surface water samples were taken at 20 stations to determine chlorophyll a concentration in each variation. A pattern for ebb conditions is inferred, which shows a direct relationship between a smooth bottom slope and a high concentration of chlorophyll a. For flow conditions, the relationship is inverse. We suggest that the higher concentrations of chlorophyll a are due to a simple mechanical process of accumulation in areas with certain morphological characteristics that attenuate the TKE. That is, the speed of transport of the phytoplankton that enters the lagoon decreases on reaching areas of low TKE, causing stagnation of the particles. This long-term pattern produces high concentrations in the inner part of the lagoon, resulting in higher concentrations of chlorophyll a at the innermost stations. When the tide begins to ebb, these patches of high concentration are transported to the outer part of the lagoon.
The role of mitochondrial ROS in the aging brain
Authors: Stefanatos Rhoda , Sanz Alberto
Published: November 2017

The brain is the most complex human organ, consuming more energy than any other tissue in proportion to its size. It relies heavily on mitochondria to produce energy and is made up of mitotic and postmitotic cells that need to closely coordinate their metabolism to maintain essential bodily functions. During aging, damaged mitochondria that produce less ATP and more reactive oxygen species (ROS) accumulate. The current consensus is that ROS cause oxidative stress, damaging mitochondria and resulting in an energetic crisis that triggers neurodegenerative diseases and accelerates aging. However, in model organisms, increasing mitochondrial ROS (mtROS) in the brain extends lifespan, suggesting that ROS may participate in signaling that protects the brain. Here, we summarize the mechanisms by which mtROS are produced at the molecular level, how different brain cells and regions produce different amounts of mtROS, and how mtROS levels change during aging. Finally, we critically discuss the possible roles of ROS in aging as signaling molecules and damaging agents, addressing whether age‐associated increases in mtROS are a cause or a consequence of aging.
The Impact of the AMOC Resumption in the Western South Atlantic Thermocline at the Onset of the Last Interglacial
Authors: Santos Thiago P. , Lessa Douglas O. , Venancio Igor M. , Chiessi Cristiano M. , Mulitza Stefan , Kuhnert Henning , Albuquerque Ana Luiza S.
Published: November 2017

After glacial terminations, large amounts of heat and salt were transferred from low to high latitudes, which is a crucial phenomenon for the reestablishment of the Atlantic Meridional Overturning Circulation (AMOC). However, how different glacial terminations evolved in the (sub)tropics is still poorly documented. Here we use foraminifera oxygen (δ18O) and carbon (δ13C) stable isotopes to show that the North Atlantic heat piracy, following the AMOC resumption at the early Last Interglacial, affected the thermocline δ18O levels of the subtropical western South Atlantic. Because of the cooling imposed by this process, glacial δ18O persisted in the thermocline for ~7 kyr after the onset of the Last Interglacial, dampening the effect of sea level rise usually imprinted on foraminifera δ18O during terminations. Faunal composition and δ13C also suggest the existence of a colder and thicker South Atlantic Central Water coeval with the AMOC recovery. This process apparently did not occur during the last deglaciation.
Inflated Uncertainty in Multimodel‐Based Regional Climate Projections
Authors: Madsen Marianne Sloth , Langen Peter L. , Boberg Fredrik , Christensen Jens Hesselbjerg
Published: November 2017

Multimodel ensembles are widely analyzed to estimate the range of future regional climate change projections. For an ensemble of climate models, the result is often portrayed by showing maps of the geographical distribution of the multimodel mean results and associated uncertainties represented by model spread at the grid point scale. Here we use a set of CMIP5 models to show that presenting statistics this way results in an overestimation of the projected range leading to physically implausible patterns of change on global but also on regional scales. We point out that similar inconsistencies occur in impact analyses relying on multimodel information extracted using statistics at the regional scale, for example, when a subset of CMIP models is selected to represent regional model spread. Consequently, the risk of unwanted impacts may be overestimated at larger scales as climate change impacts will never be realized as the worst (or best) case everywhere.
Dependence of Electromagnetic Ion Cyclotron Wave Occurrence on North‐South Orientation of Interplanetary Magnetic Field: THEMIS Observations
Authors: Park Jong‐Sun , Shue Jih‐Hong , Kim Khan‐Hyuk
Published: November 2017

We investigate the L‐MLT (i.e., L‐shall versus magnetic local time) distributions of electromagnetic ion cyclotron (EMIC) waves, using the Time History of Events and Macroscale Interactions during Substorms data from 2009 to 2014, under prolonged (more than 4 h) intervals of northward and southward interplanetary magnetic fields (IMFs). H‐band EMIC waves show high occurrence in the dawn‐to‐postnoon sector (0400–1600 MLT) at L > ~7 for northward IMFs. On the other hand, for southward IMFs, H‐band EMIC waves occur in the morning‐to‐afternoon sector (0700–1500 MLT), and no strong wave activity is found in the dawn sector (0400–0700 MLT). H‐band EMIC waves are frequently observed in the region where the ambient temperature anisotropy for ~1–25 keV ions is high. He‐band EMIC waves show high occurrence in the noon‐to‐dusk sector (1100–2000 MLT) for both IMF BZ conditions. In the dusk sector, however, the high occurrence region is shifted into the inner L‐shell for southward IMFs (L < 8) in contrast to that observed for northward IMFs (L < 10). He‐band EMIC waves are shown to be generated in the region where the total plasma density is high (especially near the plasmapause). The occurrence rates of EMIC waves are lower overall for southward IMFs than for northward IMFs for both H‐band and He‐band waves. We suggest that an increase of heavy ion (i.e., He+ and O+) concentration is likely associated with low occurrence rates in both frequency bands for southward IMFs.
Electron Flux Dropouts at L ∼ 4.2 From Global Positioning System Satellites: Occurrences, Magnitudes, and Main Driving Factors
Authors: Boynton R. J. , Mourenas D. , Balikhin M. A.
Published: November 2017

Dropouts in electron fluxes at L ∼ 4.2 were investigated for a broad range of energies from 120 keV to 10 MeV, using 16 years of electron flux data from Combined X‐ray Dosimeter on board Global Positioning System (GPS) satellites. Dropouts were defined as flux decreases by at least a factor 4 in 12 h, or 24 h during which a decrease by at least a factor of 1.5 must occur during each 12 h time bin. Such fast and strong dropouts were automatically identified from the GPS electron flux data and statistics of dropout magnitudes, and occurrences were compiled as a function of electron energy. Moreover, the Error Reduction Ratio analysis was employed to search for nonlinear relationships between electron flux dropouts and various solar wind and geomagnetic activity indices, in order to identify potential external causes of dropouts. At L ∼ 4.2, the main driving factor for the more numerous and stronger 1–10 MeV electron dropouts turns out to be the southward interplanetary magnetic field Bs, suggesting an important effect from precipitation loss due to combined electromagnetic ion cyclotron and whistler mode waves in a significant fraction of these events, supplementing magnetopause shadowing and outward radial diffusion which are also effective at lower energies.
Van Allen Probes Measurements of Energetic Particle Deep Penetration Into the Low L Region (L < 4) During the Storm on 8 April 2016
Authors: Zhao H. , Baker D. N. , Califf S. , Li X. , Jaynes A. N. , Leonard T. , Kanekal S. G. , Blake J. B. , Fennell J. F. , Claudepierre S. G. , Turner D. L. , Reeves G. D. , Spence H. E.
Published: November 2017

Using measurements from the Van Allen Probes, a penetration event of tens to hundreds of keV electrons and tens of keV protons into the low L shells (L < 4) is studied. Timing and magnetic local time (MLT) differences of energetic particle deep penetration are unveiled and underlying physical processes are examined. During this event, both proton and electron penetrations are MLT asymmetric. The observed MLT difference of proton penetration is consistent with convection of plasma sheet protons, suggesting enhanced convection during geomagnetic active times to be the cause of energetic proton deep penetration during this event. The observed MLT difference of tens to hundreds of keV electron penetration is completely different from tens of keV protons and cannot be well explained by inward radial diffusion, convection of plasma sheet electrons, or transport of trapped electrons by enhanced convection electric field represented by the Volland‐Stern model or a uniform dawn‐dusk electric field model based on the electric field measurements. It suggests that the underlying physical mechanism responsible for energetic electron deep penetration, which is very important for fully understanding energetic electron dynamics in the low L shells, should be MLT localized.
Seismicity During the Initial Stages of the Guy‐Greenbrier, Arkansas, Earthquake Sequence
Authors: Yoon Clara E. , Huang Yihe , Ellsworth William L. , Beroza Gregory C.
Published: November 2017

We analyze the background seismicity, initiation, and earliest stages of the Guy‐Greenbrier, Arkansas, earthquake sequence, which was potentially induced by wastewater injection starting in July 2010, during the 3 month time period 1 June to 1 September 2010. High‐resolution observations of low‐magnitude seismicity, and the high‐quality Arkansas public well database, facilitate detailed analysis of spatial and temporal correlations between earthquakes, wastewater injection, and hydraulic fracturing. We detected 14,604 earthquakes, with magnitudes −1.5≤ML≤2.9, using two sensitive, waveform similarity‐based event detection methods in parallel: Fingerprint And Similarity Thresholding, and template matching. We located the 1,740 largest earthquakes that form 16 spatially compact clusters, using P and S phases from 3 stations with the double‐difference relocation algorithm and an improved velocity model constrained by the location of quarry blasts. We enhanced the temporal resolution of these event clusters by assigning smaller unlocated events to a cluster based on waveform similarity. Most clustered earthquakes during this time were both spatially and temporally correlated with hydraulic fracturing stimulation at several production wells. For one cluster, microseismicity was correlated with individual stages of stimulation. Many other wells had no detectable nearby seismicity during stimulation. We found a smaller number of events located on the Guy‐Greenbrier Fault that were likely induced by wastewater injection. The concurrent presence of seismicity induced by hydraulic fracturing and wastewater injection presents a challenge for attribution and seismic hazard characterization, but the combination of precision seismology and high‐quality well information allows us to disentangle the effects of these two processes.
The Climate Response to Stratospheric Aerosol Geoengineering Can Be Tailored Using Multiple Injection Locations
Authors: MacMartin Douglas G. , Kravitz Ben , Tilmes Simone , Richter Jadwiga H. , Mills Michael J. , Lamarque Jean‐Francois , Tribbia Joseph J. , Vitt Francis
Published: November 2017

By injecting different amounts of SO2 at multiple different latitudes, the spatial pattern of aerosol optical depth (AOD) can be partially controlled. This leads to the ability to influence the climate response to geoengineering with stratospheric aerosols, providing the potential for design. We use simulations from the fully coupled whole‐atmosphere chemistry climate model CESM1(WACCM) to demonstrate that by appropriately combining injection at just four different locations, 30°S, 15°S, 15°N, and 30°N, then three spatial degrees of freedom of AOD can be achieved: an approximately spatially uniform AOD distribution, the relative difference in AOD between Northern and Southern Hemispheres, and the relative AOD in high versus low latitudes. For forcing levels that yield 1–2°C cooling, the AOD and surface temperature response are sufficiently linear in this model so that the response to different combinations of injection at different latitudes can be estimated from single‐latitude injection simulations; nonlinearities associated with both aerosol growth and changes to stratospheric circulation will be increasingly important at higher forcing levels. Optimized injection at multiple locations is predicted to improve compensation of CO2‐forced climate change relative to a case using only equatorial aerosol injection (which overcools the tropics relative to high latitudes). The additional degrees of freedom can be used, for example, to balance the interhemispheric temperature gradient and the equator to pole temperature gradient in addition to the global mean temperature. Further research is needed to better quantify the impacts of these strategies on changes to long‐term temperature, precipitation, and other climate parameters.
Stratospheric Dynamical Response and Ozone Feedbacks in the Presence of SO2 Injections
Authors: Richter Jadwiga H. , Tilmes Simone , Mills Michael J. , Tribbia Joseph J. , Kravitz Ben , MacMartin Douglas G. , Vitt Francis , Lamarque Jean‐Francois
Published: November 2017

Injections of sulfur dioxide into the stratosphere are among several proposed methods of solar radiation management. Such injections could cool the Earth's climate. However, they would significantly alter the dynamics of the stratosphere. We explore here the stratospheric dynamical response to sulfur dioxide injections ∼5 km above the tropopause at multiple latitudes (equator, 15°S, 15°N, 30°S and 30°N) using a fully coupled Earth system model, Community Earth System Model, version 1, with the Whole Atmosphere Community Climate Model as its atmospheric component (CESM1(WACCM)). We find that in all simulations, the tropical lower stratosphere warms primarily between 30°S and 30°N, regardless of injection latitude. The quasi‐biennial oscillation (QBO) of the tropical zonal wind is altered by the various sulfur dioxide injections. In a simulation with a 12 Tg yr−1 equatorial injection, and with fully interactive chemistry, the QBO period lengthens to ∼3.5 years but never completely disappears. However, in a simulation with specified (or noninteractive) chemical fields, including O3 and prescribed aerosols taken from the interactive simulation, the oscillation is virtually lost. In addition, we find that geoengineering does not always lengthen the QBO. We further demonstrate that the QBO period changes from 24 to 12–17 months in simulations with sulfur dioxide injections placed poleward of the equator. Our study points to the importance of understanding and verifying of the complex interactions between aerosols, atmospheric dynamics, and atmospheric chemistry as well as understanding the effects of sulfur dioxide injections placed away from the Equator on the QBO.
Examining the Impact of Smoke on Frontal Clouds and Precipitation During the 2002 Yakutsk Wildfires Using the WRF‐Chem‐SMOKE Model and Satellite Data
Authors: Lu Zheng , Sokolik Irina N.
Published: November 2017

In 2002, an enormous amount of smoke has been emitted from Yakutsk wildfires. In this study, we examine the impact of smoke on cloud properties and precipitation associated with frontal systems using the WRF‐Chem‐SMOKE model and satellite data. The smoke emissions are computed using the fire radiative power technique. Smoke particles are represented as an internal mixture of organic matter (OM), black carbon (BC), and other inorganic matter, and their microphysical and radiative effects are explicitly modeled. After examining the fire activities, we identified two fire periods (FP1 and FP2). During FP1, in the cloud deck with the high cloud droplet number concentration (CDNC), but the relatively small amount of ice nuclei (IN), the rain and snow water contents (RWC and SWC) were strongly reduced, because of suppressed collision‐coalescence and riming processes. The cloud cells acquired the longer lifetime and traveled farther downwind. During FP2, in the cloud deck with relatively high CDNC and IN, RWC was reduced; however, the large amounts of IN triggered the glaciation indirect effect and leaded to increased SWC. Due to the competing effects of CDNC and IN, changes in the cloud lifetime were small. Consequently, smoke‐induced changes in the total cloudiness cause a dipole feature. After the smoke was nearly consumed during FP1, the large‐scale dynamics of the frontal system was altered by smoke. The onset of the precipitation was delayed by 1 day. In FP2, the onset of the precipitation was not delayed but occurred at different locations, and the area‐averaged precipitation was slightly reduced (~0.5 mm/day).
Improving Global Gross Primary Productivity Estimates by Computing Optimum Light Use Efficiencies Using Flux Tower Data
Authors: Madani Nima , Kimball John S. , Running Steven W.
Published: November 2017

In the light use efficiency (LUE) approach of estimating the gross primary productivity (GPP), plant productivity is linearly related to absorbed photosynthetically active radiation assuming that plants absorb and convert solar energy into biomass within a maximum LUE (LUEmax) rate, which is assumed to vary conservatively within a given biome type. However, it has been shown that photosynthetic efficiency can vary within biomes. In this study, we used 149 global CO2 flux towers to derive the optimum LUE (LUEopt) under prevailing climate conditions for each tower location, stratified according to model training and test sites. Unlike LUEmax, LUEopt varies according to heterogeneous landscape characteristics and species traits. The LUEopt data showed large spatial variability within and between biome types, so that a simple biome classification explained only 29% of LUEopt variability over 95 global tower training sites. The use of explanatory variables in a mixed effect regression model explained 62.2% of the spatial variability in tower LUEopt data. The resulting regression model was used for global extrapolation of the LUEopt data and GPP estimation. The GPP estimated using the new LUEopt map showed significant improvement relative to global tower data, including a 15% R2 increase and 34% root‐mean‐square error reduction relative to baseline GPP calculations derived from biome‐specific LUEmax constants. The new global LUEopt map is expected to improve the performance of LUE‐based GPP algorithms for better assessment and monitoring of global terrestrial productivity and carbon dynamics.
The Northern Gulf of Mexico During OAE2 and the Relationship Between Water Depth and Black Shale Development
Authors: Lowery Christopher M. , Cunningham Robert , Barrie Craig D. , Bralower Timothy , Snedden John W.
Published: November 2017

Despite their name, Oceanic Anoxic Events (OAEs) are not periods of uniform anoxia and black shale deposition in ancient oceans. Shelf environments account for the majority of productivity and organic carbon burial in the modern ocean, and this was likely true in the Cretaceous as well. However, it is unlikely that the mechanisms for such an increase were uniform across all shelf environments. Some, like the northwest margin of Africa, were characterized by strong upwelling, but what might drive enhanced productivity on shelves not geographically suited for upwelling? To address this, we use micropaleontology, carbon isotopes, and sedimentology to present the first record of Oceanic Anoxic Event 2 (OAE2) from the northern Gulf of Mexico shelf. Here OAE2 occurred during the deposition of the well‐oxygenated, inner neritic/lower estuarine Lower Tuscaloosa Sandstone. The overlying organic‐rich oxygen‐poor Marine Tuscaloosa Shale is entirely Turonian in age. We trace organic matter enrichment from the Spinks Core into the deepwater Gulf of Mexico, where wireline log calculations and public geochemical data indicate organic enrichment and anoxia throughout the Cenomanian‐Turonian boundary interval. Redox change and organic matter preservation across the Gulf of Mexico shelf were driven by sea level rise prior to the early Turonian highstand, which caused the advection of nutrient‐rich, oxygen‐poor waters onto the shelf. This results in organic matter mass accumulation rates 1–2 orders of magnitude lower than upwelling sites like the NW African margin, but it likely occurred over a much larger geographic area, suggesting that sea level rise was an important component of the overall increase in carbon burial during OAE2.
Big Data
Authors: Yandell Brian S.
Published: November 2017

This article discusses what Big Data is/are, its relation to data science, and the importance of team research to make sense of Big Data. Machine learning is briefly described, but the emphasis is on human learning and perceiving training in Big Data as an ongoing process. The roles of open source and data repositories are addressed, as is the value of data‐rich story telling.
Model Averaging
Authors: Claeskens Gerda
Published: November 2017

A model‐averaged estimator is composed of estimators, each obtained from a different model, that are weighted and summed. There are different ways of setting the weights. The weights can be deterministic or random. Frequentist methods for the weights may be based on the values of an information criterion or may be the result of some optimization procedure. Fully Bayesian methods for model averaging incorporate prior information on the models and the parameters therein. Model averaging is used to avoid choosing a single estimator or improve individual estimators' performances.
G‐Estimation
Authors: Moodie Erica E.M. , Stephens David A. , Wallace Michael P.
Published: November 2017

G‐estimation is a tool for estimating structural nested models, which offer causal parameters for the effect of time‐dependent exposures under the assumption of no unmeasured confounding. Similar to traditional regression models, structural nested models are typically conditional rather than marginal. G‐estimation has seen relatively little uptake in the statistical and applied literature, perhaps because it was originally presented for time‐to‐event outcomes with estimates traditionally found using grid search methods. However, G‐estimation gained some popularity in the context of dynamic treatment regimes and is, in fact, straightforward to understand and implement. It can also be shown to be equivalent to the familiar approach of propensity score regression under linear structural nested models.
Modeling of Seed Dormancy
Authors: Allen Phil S. , Benech‐Arnold Roberto L. , Batlla Diego , Bradford Kent J.
Published: November 2017

The sections in this article are

Introduction

Types and Phenology of Seed Dormancy

Environmental Control of Dormancy

Approaches to Modeling Seed Dormancy

Examples of Seed Dormancy Models

Population‐Based Threshold Models of Seed Dormancy

Conclusions and Future Directions
A Merging of Paths: Abscisic Acid and Hormonal Cross‐Talk in the Control of Seed Dormancy Maintenance and Alleviation
Authors: Feurtado J. Allan , Kermode Allison R.
Published: November 2017

The sections in this article are

Introduction

Abscisic Acid

Gibberellin

Light Interactions

Ethylene

Auxin and Cytokinin

Brassinosteroids

G‐Protein Signaling Reveals Integration ofGA,BR,ABA, and Sugar Responses

Profiling of Hormone Metabolic Pathways inArabidopsisMutants Reveals Cross‐Talk

Summary and Future Directions
De‐Repression of Seed Germination byGASignaling
Authors: Steber Camille M.
Published: November 2017

The sections in this article are

Introduction

Control of Germination byGASignaling

The Role of the Ubiquitin–Proteasome Pathway inGASignaling

IsRGL2a ‘Master Regulator’ of Seed Germination?

Sleepy1is a Positive Regulator of Seed Germination inArabidopsis

DoDELLAProteins Have a Conserved Role in Seed Germination?

Future Directions
Mechanisms and Genes Involved in GerminationSensu Stricto
Authors: Nonogaki Hiroyuki , Chen Feng , Bradford Kent J.
Published: November 2017

The sections in this article are

Introduction

Imbibition and Water Relations of Seed Germination

Testa/Endosperm Restraint and Embryo Growth Potential

Approaches to Identify Additional Genes Involved in Germination
Sugar and Abscisic Acid Regulation of Germination and Transition to Seedling Growth
Authors: Dekkers Bas J.W. , Smeekens Sjef C.M.
Published: November 2017

The sections in this article are

Introduction

ABASignaling during Germination and Early Seedling Growth

Sugar Signaling Represses Germination and the Transition to Vegetative Growth

Conclusions

Acknowledgments
Plant Proteomics: Challenges and Resources
Authors: Heazlewood Joshua L. , Millar A. Harvey
Published: November 2017

The sections in this article are

Introduction

Challenges

Resources

Future

Acknowledgements
Structural Proteomics
Authors: Wrobel Russell L. , Bingman Craig A. , Jeon Won Bae , Song Jikui , Vinarov Dmitriy A. , Frederick Ronnie O. , Aceti David J. , Sreenath Hassan K. , Zolnai Zsolt , Vojtik Frank C. , Bitto Eduard , Fox Brian G. , Phillips George N. , Markley John L.
Published: November 2017

The sections in this article are

Introduction

Project Data Handling:Sesame

ORFCloning

E.coli Cell‐Based Protein Production Pipeline

Wheat Germ Cell‐Free Protein Production

Mass Spectrometry of Purified Proteins for Quality Assurance and Analysis

Crystallomics andX‐Ray Structure Determination

NMRScreening and Structure Determination

Illustrative Structures and Functional Implications

Acknowledgements
Proteome Analysis for the Study of Developmental Processes in Plants
Authors: Rajjou Loïc , Gallardo Karine , Job Claudette , Job Dominique
Published: November 2017

The sections in this article are

Introduction

Examples of Proteome Analyses of Plant Development

Conclusions and Perspectives
Proteomics of Plant Mitochondria
Authors: Bykova Natalia V. , Møller Ian M.
Published: November 2017

The sections in this article are

Mitochondria as Attractive Targets for Subcellular Proteomics

Methods and Approaches Briefly for Identification of Proteins

Mitochondrial Proteins Identified

Stress‐Responsive Proteins and Redox Regulation

Protein Phosphorylation and Signal Transduction

Concluding Remarks
Chromatin‐Associated ArchitecturalHMGAandHMGBProteins Assist Transcription Factor Function
Authors: Grasser Klaus D. , Launholt Dorte
Published: November 2017

The sections in this article are

Introduction

HMGAProteins

HMGBProteins

Dynamic Interaction of HistoneH1andHMGProteins with Chromatin

HMGAandHMGBProteins as Architectural Assistant Factors

Acknowledgements
A model for predicting the dose to the parotid glands based on their relative overlapping with planning target volumes during helical radiotherapy
Authors: Millunchick Cheryl H. , Zhen Heming , Redler Gage , Liao Yixiang , Turian Julius V.
Published: November 2017

The sparing of the parotid glands in the treatment of head and neck cancers is of clinical relevance as high doses to the salivary glands may result in xerostomia. Xerostomia is a major cause of decreased quality of life for head and neck patients. This paper explores the relationship between the overlap of the target volumes and their expansions with the parotid glands for helical delivery plans and their ability to be spared. Various overlapping volumes were examined, and an overlap with a high statistical relevance was found. A model that predicts exceeding tolerance parotid mean dose based on its fractional overlapping volume with PTVs was developed. A fractional overlapping volume of 0.083 between the parotid gland and the high dose PTV plus 5 mm expansion – was determined to be the threshold value to predict parotid Dmean > 26 Gy for parotids that overlap with the high dose PTV plus 5 mm expansion. If the parotid gland only overlaps with the intermediate dose target (and/or low dose target) and the overlapping volume of the parotid gland and the intermediate dose target is less than 25%, the parotid mean dose is likely less than 26 Gy. If the parotid overlaps with the low dose target only then the mean dose to the parotid is likely to be less than 26 Gy. This finding will prove as a very useful guide for the physicians and planners involved in the planning process to know prior whether the parotid glands will be able to be spared with the current set of target volumes or if revisions are necessary. This work will serve as a helpful guide in the planning process of head and neck target cases.
Vibration Damping of Carbon Nanotube Assembly Materials
Authors: Zhao Jingna , Wang Fulin , Zhang Xin , Liang Linjie , Yang Xueqin , Li Qingwen , Zhang Xiaohua
Published: November 2017

Vibration reduction is of great importance in various engineering applications, and a material that exhibits good vibration damping along with high strength and modulus has become more and more vital. Owing to the superior mechanical property of carbon nanotube (CNT), new types of vibration damping material can be developed. This paper presents recent advancements, including our progresses, in the development of high‐damping macroscopic CNT assembly materials, such as forests, gels, films, and fibers. In these assemblies, structural deformation of CNTs, zipping and unzipping at CNT connection nodes, strengthening and welding of the nodes, and sliding between CNTs or CNT bundles are playing important roles in determining the viscoelasticity, and elasticity as well. Toward the damping enhancement, strategies for micro‐structure and interface design are also discussed.
Reversible Switching of Spiropyran Molecules in Direct Contact With a Bi(111) Single Crystal Surface
Authors: Nickel Fabian , Bernien Matthias , Kraffert Kai , Krüger Dennis , Arruda Lucas M. , Kipgen Lalminthang , Kuch Wolfgang
Published: November 2017

Photochromic molecular switches immobilized by direct contact with surfaces typically show only weak response to optical excitation, which often is not reversible. In contrast, here, it is shown that a complete and reversible ring‐opening and ring‐closing reaction of submonolayers of spironaphthopyran on the Bi(111) surface is possible. The ring opening to the merocyanine isomer is initiated by ultraviolet light. Switching occurs in a two‐step process, in which after optical excitation, an energy barrier needs to be overcome to convert to the merocyanine form. This leads to a strong temperature dependence of the conversion efficiency. Switching of the merocyanine isomer back to the closed form is achieved by a temperature increase. Thus, the process can be repeated in a fully reversible manner, in contrast to previously studied nitrospiropyran molecules on surfaces. This is attributed to the destabilization of the merocyanine isomer by the electron‐donating nature of the naphtho group and the reduced van der Waals interaction of the Bi(111) surface. The result shows that molecules designed for switching in solutions need to be modified to function in direct contact with a surface.
Photoelectrochemically Active and Environmentally Stable CsPbBr3/TiO2 Core/Shell Nanocrystals
Authors: Li Zhi‐Jun , Hofman Elan , Li Jian , Davis Andrew Hunter , Tung Chen‐Ho , Wu Li‐Zhu , Zheng Weiwei
Published: November 2017

Inherent poor stability of perovskite nanocrystals (NCs) is the main impediment preventing broad applications of the materials. Here, TiO2 shell coated CsPbBr3 core/shell NCs are synthesized through the encapsulation of colloidal CsPbBr3 NCs with titanium precursor, followed by calcination at 300 °C. The nearly monodispersed CsPbBr3/TiO2 core/shell NCs show excellent water stability for at least three months with the size, structure, morphology, and optical properties remaining identical, which represent the most water‐stable inorganic shell passivated perovskite NCs reported to date. In addition, TiO2 shell coating can effectively suppress anion exchange and photodegradation, therefore dramatically improving the chemical stability and photostability of the core CsPbBr3 NCs. More importantly, photoluminescence and (photo)electrochemical characterizations exhibit increased charge separation efficiency due to the electrical conductivity of the TiO2 shell, hence leading to an improved photoelectric activity in water. This study opens new possibilities for optoelectronic and photocatalytic applications of perovskites‐based NCs in aqueous phase.
Fast Setting Silk Fibroin Bioink for Bioprinting of Patient‐Specific Memory‐Shape Implants
Authors: Costa João B. , Silva‐Correia Joana , Oliveira Joaquim M. , Reis Rui L.
Published: November 2017

The pursuit for the “perfect” biomimetic and personalized implant for musculoskeletal tissue regeneration remains a big challenge. 3D printing technology that makes use of a novel and promising biomaterials can be part of the solution. In this study, a fast setting enzymatic‐crosslinked silk fibroin (SF) bioink for 3D bioprinting is developed. Their properties are fine‐tuned and different structures with good resolution, reproducibility, and reliability can be fabricated. Many potential applications exist for the SF bioinks including 3D bioprinted scaffolds and patient‐specific implants exhibiting unique characteristics such as good mechanical properties, memory‐shape feature, suitable degradation, and tunable pore architecture and morphology.
Plasmonic Metalens for Narrowband Dual‐Focus Imaging
Authors: Williams Calum , Montelongo Yunuen , Wilkinson Timothy D.
Published: November 2017

A new type of metalens with the capability to selectively focus narrowband light is reported at different focal planes depending on polarization. Two zone planes with two different focal lengths are spatially multiplexed and encoded in the subwavelength regime with arrays of orthogonal silver nanostructures, which are designed to exhibit strong wavelength‐ and polarization‐dependent scattering profiles. Using this principle, imaging under white‐light illumination with independent focal planes is experimentally demonstrated for each polarization at the narrowband resonant wavelength. Furthermore, each focal plane can be dynamically controlled with an output polarizer. In contrast to conventional refractive and diffractive optical elements, functional metalenses allow additional control over wavelength and polarization properties of light for a wide range of applications.
Flexible and Stretchable Biobatteries: Monolithic Integration of Membrane‐Free Microbial Fuel Cells in a Single Textile Layer
Authors: Pang Sumiao , Gao Yang , Choi Seokheun
Published: November 2017

The fabrication and performance of a flexible and stretchable microbial fuel cell (MFC) monolithically integrated into a single sheet of textile substrate are reported. The single‐layer textile MFC uses Pseudomonas aeruginosa (PAO1) as a biocatalyst to produce a maximum power of 6.4 µW cm−2 and current density of 52 µA cm−2, which are substantially higher than previous textile‐MFCs and are similar to other flexible paper‐based MFCs. The textile MFC demonstrates a stable performance with repeated stretching and twisting cycles. The membrane‐less single‐chamber configuration drastically simplifies the fabrication and improves the performance of the MFC. A conductive and hydrophilic anode in a 3D fabric microchamber maximizes bacterial electricity generation from a liquid environment and a silver oxide/silver solid‐state cathode reduces cathodic overpotential for fast catalytic reaction. A simple batch fabrication approach simultaneously constructs 35 individual devices, which will revolutionize the mass production of textile MFCs. This stretchable and twistable power device printed directly onto a single textile substrate can establish a standardized platform for textile‐based biobatteries and will be potentially integrated into wearable electronics in the future.
A branch and bound algorithm to solve large‐scale multistage stochastic programs with endogenous uncertainty
Authors: Christian Brianna , Cremaschi Selen
Published: November 2017

The growth in computation complexity of multistage stochastic programs (MSSPs) with problem size often prevents its application to real‐world size problems. We present two variants of branch‐and‐bound algorithm, which reduce the resource requirements for the generation and solution of large‐scale MSSPs with endogenous uncertainty. Both variants use Knapsack‐problem based Decomposition Algorithm (Christian and Cremaschi, Comput Chem Eng. 2015;74:34–47) to generate feasible solutions and primal bounds. First variant (PH‐KDA) uses a progressive hedging dual‐bounding approach; the second (OSS‐KDA) solves the MSSP removing all nonanticipativity constraints. Both variants were used to solve several instances of the pharmaceutical clinical trial planning problem. The first iteration of both algorithms provides a feasible solution, and a primal bound and a dual bound for the problem. Although the dual‐bounds of OSS‐KDA were generally weaker than PH‐KDA, they are generated considerably faster. For the seven‐product case the OSS‐KDA generated a solution with a gap of 9.92% in 115 CPU seconds. © 2017 American Institute of Chemical Engineers AIChE J, 64: 1262–1271, 2018
Uncertainty‐conscious methodology for process performance assessment in biopharmaceutical drug product manufacturing
Authors: Casola Gioele , Sugiyama Hirokazu , Siegmund Christian , Mattern Markus
Published: November 2017

This work presents an uncertainty‐conscious methodology for the assessment of process performance—for example, run time—in the manufacturing of biopharmaceutical drug products. The methodology is presented as an activity model using the type 0 integrated definition (IDEF0) functional modeling method, which systematically interconnects information, tools, and activities. In executing the methodology, a hybrid stochastic–deterministic model that can reflect operational uncertainty in the assessment result is developed using Monte Carlo simulation. This model is used in a stochastic global sensitivity analysis to identify tasks that had large impacts on process performance under the existing operational uncertainty. Other factors are considered, such as the feasibility of process modification based on Good Manufacturing Practice, and tasks to be improved is identified as the overall output. In a case study on cleaning and sterilization processes, suggestions were produced that could reduce the mean total run time of the processes by up to 40%. © 2017 American Institute of Chemical Engineers AIChE J, 64: 1272–1284, 2018
Three‐Dimensional Anionic Cyclodextrin‐Based Covalent Organic Frameworks
Authors: Zhang Yuanyuan , Duan Jiyun , Ma Dou , Li Pengfei , Li Siwu , Li Haiwei , Zhou Junwen , Ma Xiaojie , Feng Xiao , Wang Bo
Published: November 2017

Three‐dimensional covalent organic frameworks (3D COFs) are promising crystalline materials with well‐defined structures, high porosity, and low density; however, the limited choice of building blocks and synthetic difficulties have hampered their development. Herein, we used a flexible and aliphatic macrocycle, namely γ‐cyclodextrin (γ‐CD), as the soft struts for the construction of a polymeric and periodic 3D extended network, with the units joined via tetrakis(spiroborate) tetrahedra with various counterions. The inclusion of pliable moieties in the robust open framework endows these CD‐COFs with dynamic features, leading to a prominent Li ion conductivity of up to 2.7 mS cm−1 at 30 °C and excellent long‐term Li ion stripping/plating stability. Exchanging the counterions within the pores can effectively modulate the interactions between the CD‐COF and CO2 molecules.
Glass Microsphere‐Supported Giant Vesicles for the Observation of Self‐Reproduction of Lipid Boundaries
Authors: Fiore Michele , Maniti Ofelia , Girard‐Egrot Agnes , Monnard Pierre‐Alain , Strazewski Peter
Published: November 2017

Growth and division experiments on phospholipid boundaries were carried out using glass microsphere‐supported phospholipid (DOPC) giant vesicles (GVs) fed with a fatty acid solution (oleic acid) at two distinct feeding rates. Both fast and slow feeding methods produced daughter GVs. Under slow feeding conditions the membrane growth process (evagination, buds, filaments) was observed in detail by fluorescence microscopy. The density difference between supported mother vesicles and newly formed daughter vesicles allowed their easy separation. Mass spectrometric analysis of the resulting mother and daughter GVs showed that the composition of both vesicle types was a mixture of original supported phospholipids and added fatty acids reflecting the total composition of amphiphiles after the feeding process. Thus, self‐reproduction of phospholipid vesicles can take place under preservation of the lipid composition but different aggregate size.
Donor–σ–Acceptor Motifs: Thermally Activated Delayed Fluorescence Emitters with Dual Upconversion
Authors: Geng Yan , D'Aleo Anthony , Inada Ko , Cui Lin‐Song , Kim Jong Uk , Nakanotani Hajime , Adachi Chihaya
Published: November 2017

A family of organic emitters with a donor–σ–acceptor (D‐σ‐A) motif is presented. Owing to the weakly coupled D‐σ‐A intramolecular charge‐transfer state, a transition from the localized excited triplet state (3LE) and charge‐transfer triplet state (3CT) to the charge‐transfer singlet state (1CT) occurred with a small activation energy and high photoluminescence quantum efficiency. Two thermally activated delayed fluorescence (TADF) components were identified, one of which has a very short lifetime of 200–400 ns and the other a longer TADF lifetime of the order of microseconds. In particular, the two D‐σ‐A materials presented strong blue emission with TADF properties in toluene. These results will shed light on the molecular design of new TADF emitters with short delayed lifetimes.
Record High‐Nuclearity Polyoxoniobates: Discrete Nanoclusters {Nb114}, {Nb81}, and {Nb52}, and Extended Frameworks Based on {Cu3Nb78} and {Cu4Nb78}
Authors: Jin Lu , Zhu Zeng‐Kui , Wu Yan‐Lan , Qi Yan‐Jie , Li Xin‐Xiong , Zheng Shou‐Tian
Published: November 2017

A series containing the highest nuclearity polyoxoniobate (PONb) nanoclusters, ranging from dimers to tetramers, has been obtained. They include one 114‐nuclear {Li8⊂Nb114O316}, one 81‐nuclear {Li3K⊂Nb81O225}, and one 52‐nuclear {H4Nb52O150}. The Nb nuclearity of these PONbs is remarkably larger than those of all known high‐nuclearity PONbs (≤32). Furthermore, the introduction of 3d Cu2+ ions can lead to the generation of extended inorganic–organic hybrid frameworks built from novel, high‐nuclearity, nanoscale heterometallic PONb building blocks {H3Cu3Nb78O222} or {H3Cu4(en)Nb78O222}. These building blocks also contain the largest number of Nb centers of any heterometallic PONbs reported to date. The synthesis of new‐type PONbs has long been a challenging subject in PONb chemistry.