bluuebunny/crossref_metadata_2025 huggingface dataset:
JULES-crop: a parametrisation of crops in the Joint UK Land Environment Simulator
Authors: Osborne T. , Gornall J. , Hooker J. , Williams K. , Wiltshire A. , Betts R. , Wheeler T.
Published: October 2014

Abstract. Studies of climate change impacts on the terrestrial biosphere have been completed without recognition of the integrated nature of the biosphere. Improved assessment of the impacts of climate change on food and water security requires the development and use of models not only representing each component but also their interactions. To meet this requirement the Joint UK Land Environment Simulator (JULES) land surface model has been modified to include a generic parametrisation of annual crops. The new model, JULES-crop, is described and evaluation at global and site levels for the four globally important crops; wheat, soy bean, maize and rice is presented. JULES-crop demonstrates skill in simulating the inter-annual variations of yield for maize and soy bean at the global level, and for wheat for major spring wheat producing countries. The impact of the new parametrisation, compared to the standard configuration, on the simulation of surface heat fluxes is largely an alteration of the partitioning between latent and sensible heat fluxes during the later part of the growing season. Further evaluation at the site level shows the model captures the seasonality of leaf area index and canopy height better than in standard JULES. However, this does not lead to an improvement in the simulation of sensible and latent heat fluxes. The performance of JULES-crop from both an earth system and crop yield model perspective is encouraging however, more effort is needed to develop the parameterisation of the model for specific applications. Key future model developments identified include the specification of the yield gap to enable better representation of the spatial variability in yield.
IceChrono v1: a probabilistic model to compute a common and optimal chronology for several ice cores
Authors: Parrenin F.
Published: October 2014

Abstract. Polar ice cores provides exceptional archives of past environmental conditions. Dating ice and air bubbles/hydrates in ice cores is complicated since it involves different dating methods: modeling of the sedimentation process (accumulation of snow at surface, densification of snow into ice with air trapping and ice flow), use of dated horizons by comparison to other well dated targets (other dated paleo-archives or calculated variations of Earth's orbital parameters), use of dated depth intervals, use of Δdepth information (depth shift between synchronous events in the ice matrix and its air/hydrate content), use of stratigraphic links in between ice cores (ice-ice, air-air or mix ice-air links). Here I propose IceChrono v1, a new probabilistic model to combine these different kinds of chronological information to obtain a common and optimized chronology for several ice cores, as well as its confidence interval. It is based on the inversion of three quantities: the surface accumulation rate, the Lock-In Depth (LID) of air bubbles and the vertical thinning function. IceChrono is similar in scope to the Datice model, but has differences on the mathematical, numerical and programming point of views. I apply IceChrono on two dating experiments. The first one is similar to the AICC2012 experiment and I find similar results than Datice within a few centuries, which is a confirmation of both IceChrono and Datice codes. The second experiment involves only the Berkner ice core in Antarctica and I produce the first dating of this ice core. IceChrono v1 is freely available under the GPL v3 open source license.
Derivation and Long-Term Culture of Transgene-Free Human Induced Pluripotent Stem Cells on Synthetic Substrates
Authors: Villa-Diaz Luis Gerardo , Kim Jin Koo , Lahann Joerg , Krebsbach Paul H.
Published: October 2014

We describe a platform to derive, culture, and differentiate genomically stable, transgene-free human induced pluripotent stem cells (iPSCs) on a fully synthetic polymer substrate made of a grafted zwitterionic hydrogel: poly2-(methacryloyloxy)ethyl dimethyl-(3-sulfopropyl) ammonium hydroxide (PMEDSAH). Three independent transgene-free iPSC lines derived in these conditions demonstrated continuous self-renewal, genomic stability, and pluripotency in vitro and in vivo after up to 9 months of continuous in vitro culture on PMEDSAH-grafted plates. Together, these data demonstrate the strength this alternative platform offers to generate and maintain human iPSCs for regenerative medicine.
Future Research Directions for Soil Carbon Modeling
Authors: Todd‐Brown K. , Luo Y.
Published: October 2014

Soil carbon is a recent but critical sub‐component of Earth system models that contributes significant uncertainty to carbon cycle simulations in the current Intergovernmental Panel on Climate Change (IPCC) assessment. Understanding and reducing this uncertainty is a high priority for the next round of IPCC assessments. To this end, experts in soil carbon dynamics gathered in Breckenridge, Colo., for 3 days to discuss next steps for global soil carbon modeling.
2014 AGU Election Results
Authors: McPhaden Mike , Branch Benjamin Dewayne , Brigham‐Grette Julie , Carroll Mary Anne , Fucugauchi Jaime Urrutia , Green Harry , Kavner Abby , McEntee Chris , Enderlein Cheryl
Published: October 2014

Congratulations to the following members who were elected to leadership positions that will begin on 1 January 2015.
Contribution of Weddell Gyre to Global Overturning Circulation
Authors: Wendel JoAnna
Published: October 2014

The Southern Ocean plays a pivotal role in the Global Overturning Circulation (GOC), which transports warm, light water from the tropics to the poles, where it becomes cool, dense, and capable of influencing the global transport of carbon, nutrients, and energy.
Deep water recycling through time
Authors: Magni Valentina , Bouilhol Pierre , van Hunen Jeroen
Published: October 2014

We investigate the dehydration processes in subduction zones and their implications for the water cycle throughout Earth's history. We use a numerical tool that combines thermo‐mechanical models with a thermodynamic database to examine slab dehydration for present‐day and early Earth settings and its consequences for the deep water recycling. We investigate the reactions responsible for releasing water from the crust and the hydrated lithospheric mantle and how they change with subduction velocity (vs), slab age (a) and mantle temperature (Tm). Our results show that faster slabs dehydrate over a wide area: they start dehydrating shallower and they carry water deeper into the mantle. We parameterize the amount of water that can be carried deep into the mantle, W (×105 kg/m2), as a function of vs (cm/yr), a (Myrs), and Tm (°C):
. We generally observe that a 1) 100°C increase in the mantle temperature, or 2) ∼15 Myr decrease of plate age, or 3) decrease in subduction velocity of ∼2 cm/yr all have the same effect on the amount of water retained in the slab at depth, corresponding to a decrease of ∼2.2×105 kg/m2 of H2O. We estimate that for present‐day conditions ∼26% of the global influx water, or 7×108 Tg/Myr of H2O, is recycled into the mantle. Using a realistic distribution of subduction parameters, we illustrate that deep water recycling might still be possible in early Earth conditions, although its efficiency would generally decrease. Indeed, 0.5–3.7 × 108 Tg/Myr of H2O could still be recycled in the mantle at 2.8 Ga.
Observation of the spread of slow deformation in Greece following the breakup of the slab
Authors: Durand Virginie , Bouchon Michel , Floyd Michael A. , Theodulidis Nikos , Marsan David , Karabulut Hayrullah , Schmittbuhl Jean
Published: October 2014

Over the past two decades, geophysical observations have shown that earthquakes can trigger other earthquakes, raising the possibility that earthquake interaction plays an important role in the earth's deformation. We analyze here a “storm” of earthquakes in Greece and show that their interaction provides remarkable insight into the mechanics of one of the fastest deforming continental region in the world. A rupture of the African slab initiates a cascade of large earthquakes and a long episode of slow slip marking the downward plunge of the slab, the concomitant rollback of the subduction, and the subsequent detachment of southern Greece from the Eurasian plate. Intense crustal deformation, indicative of the resulting plate stretching, follows. This slow deformation which spreads in a few months over more than 500 km lasts ~3 years and triggers earthquakes. The observations also show that the retreat of the African subduction is the motor of the Aegean deformation.
Distinct patterns of seasonal Greenland glacier velocity
Authors: Moon Twila , Joughin Ian , Smith Ben , van den Broeke Michiel R. , van de Berg Willem Jan , Noël Brice , Usher Mika
Published: October 2014

Predicting Greenland Ice Sheet mass loss due to ice dynamics requires a complete understanding of spatiotemporal velocity fluctuations and related control mechanisms. We present a 5 year record of seasonal velocity measurements for 55 marine‐terminating glaciers distributed around the ice sheet margin, along with ice‐front position and runoff data sets for each glacier. Among glaciers with substantial speed variations, we find three distinct seasonal velocity patterns. One pattern indicates relatively high glacier sensitivity to ice‐front position. The other two patterns are more prevalent and appear to be meltwater controlled. These patterns reveal differences in which some subglacial systems likely transition seasonally from inefficient, distributed hydrologic networks to efficient, channelized drainage, while others do not. The difference may be determined by meltwater availability, which in some regions may be influenced by perennial firn aquifers. Our results highlight the need to understand subglacial meltwater availability on an ice sheet‐wide scale to predict future dynamic changes.
Properties of light‐absorbing aerosols in the Nagoya urban area, Japan, in August 2011 and January 2012: Contributions of brown carbon and lensing effect
Authors: Nakayama Tomoki , Ikeda Yuka , Sawada Yuuki , Setoguchi Yoshitaka , Ogawa Shuhei , Kawana Kaori , Mochida Michihiro , Ikemori Fumikazu , Matsumoto Kiyoshi , Matsumi Yutaka
Published: October 2014

The optical properties of aerosols at 405 and 781 nm were measured in an urban site in Nagoya, Japan, in August 2011 and in January 2012 using a photoacoustic spectrometer. Comparison of the absorption coefficient at 781 nm of aerosols that did and did not pass through a thermo‐denuder showed that an increase in black carbon (BC) light absorption due to the coating of non‐refractory materials (i.e., the lensing effect) was small (on average, 10%) in August and negligible in January. The effective density distributions for the particles that did and did not pass through the thermo‐denuder, which were measured simultaneously in August, suggested that the majority of BC particles sampled had a minimal coating. The small lensing effect observed can be explained partly by assuming that a large portion of non‐refractory materials was mixed externally with BC. The contribution of direct light absorption by organic matter (OM) that vaporized at temperatures below 300°C to the total light absorption at 405 nm was negligible in August, but those by OM that vaporized below 300 and 400°C averaged 11 and 17%, respectively, in January. The larger contribution of light‐absorbing OM in January is likely due to the greater contribution of OM originating from the burning of biomass, including biofuel and agricultural residue, in Japan, northern China, or Siberia, during the winter.
On the relationship between continuing current and positive leader growth
Authors: Lapierre Jeff L. , Sonnenfeld Richard G. , Edens Harald E. , Stock Mike
Published: October 2014

It has long been speculated that the source of continuing current (CC) for a negative cloud‐to‐ground flash is provided by the growth of its positive leader into negative charge regions. In this study, data from the Langmuir Electric Field Array (LEFA) and Lightning Mapping Array (LMA) are used to investigate these speculations. LEFA and LMA data provide a way to estimate the occurrence and duration of CC and channel growth throughout a flash, respectively. By connecting LMA VHF sources onto contiguous channels, the growth of the positive leader associated with each return stroke is inferred. A linear correlation between positive‐channel growth and CC duration is found, providing evidence that the positive leader grows with a constant velocity, but no obvious correlation of this velocity with CC occurrence is found. Each return stroke is then sorted by its channel growth rate and further identified by its CC type. This analysis also provides no identifiable correlation linking the positive‐channel growth rate to CC occurrence or duration. Finally, the positive‐channel growth rate for the whole flash is calculated in 10 ms windows so that any trends occurring before, during, or after the CC can be observed. This analysis too shows no correlation, which implies that positive‐channel growth is not the primary mechanism that determines CC occurrence and duration.
Hydroxyl layer: Mean state and trends at midlatitudes
Authors: Grygalashvyly M. , Sonnemann G. R. , Lübken F.‐J. , Hartogh P. , Berger U.
Published: October 2014

Based on an advanced model of excited hydroxyl relaxation we calculate trends of number densities and altitudes of the OH*‐layer during the period 1961–2009. The OH*‐model takes into account all major chemical processes such as the production by H + O3, deactivation by O, O2, and N2, spontaneous emission, and removal by chemical reactions. The OH*‐model is coupled with a chemistry‐transport model (CTM). The dynamical part (Leibniz Institute Model of the Atmosphere, LIMA) adapts ECMWF/ERA‐40 data in the troposphere‐stratosphere. The change of greenhouse gases (GHGs) such as CH4, CO2, O3, and N2O is parameterized in LIMA/CTM. The downward shift of the OH*‐layer in geometrical altitudes occurs entirely due to shrinking (mainly in the mesosphere) as a result of cooling by increasing CO2 concentrations. In order to identify the direct chemical effect of GHG changes on OH*‐trends under variable solar cycle conditions, we consider three cases: (a) variable GHG and Lyman‐α fluxes, (b) variable GHG and constant Lyman‐α fluxes, and (c) constant GHG and Lyman‐α. At midlatitudes, shrinking of the middle atmosphere descends the OH*‐layer by ~ −300 m/decade in all seasons. The direct chemical impact of GHG emission lifts up the OH*‐layer by ~15–25 m/decade depending on season. Trends of the thermal and dynamical state within the layer lead to a trend of OH* height by ~ ±100 m/decade, depending on latitude and season. Trends in layer altitudes lead to differences between temperature trends within the layer, at constant pressure, and at constant altitude, respectively, of typically 0.5 to 1 K/decade.
Optical wavelength conversion via optomechanical coupling in a silica resonator
Authors: Dong Chunhua , Fiore Victor , Kuzyk Mark C. , Tian Lin , Wang Hailin
Published: October 2014

In an optomechanical resonator, an optically active mechanical mode can couple to any of the optical resonances via radiation pressure. This unique property can enable a remarkable phenomenon: conversion of optical fields via optomechanical coupling between vastly different wavelengths. Here we expand an earlier experimental study [Science 338, 1609 (2012)] on classical wavelength conversion of coherent optical fields by coupling two optical modes to a mechanical breathing mode in a silica resonator. Heterodyne detection of the converted optical fields shows that the wavelength conversion process is coherent and bidirectional. The conversion efficiency obtained features a distinct saturation behavior that arises from optomechanical impedance matching. A measurement of the coherent mechanical excitation involved in the wavelength conversion process also provides additional insight on the underlying optomechanical interactions.
A Molecular Copper Catalyst for Electrochemical Water Reduction with a Large Hydrogen‐Generation Rate Constant in Aqueous Solution
Authors: Zhang Peili , Wang Mei , Yang Yong , Yao Tianyi , Sun Licheng
Published: October 2014

The copper complex [(bztpen)Cu](BF4)2 (bztpen=N‐benzyl‐N,N′,N′‐tris(pyridin‐2‐ylmethyl)ethylenediamine) displays high catalytic activity for electrochemical proton reduction in acidic aqueous solutions, with a calculated hydrogen‐generation rate constant (kobs) of over 10000 s−1. A turnover frequency (TOF) of 7000 h−1 cm−2 and a Faradaic efficiency of 96 % were obtained from a controlled potential electrolysis (CPE) experiment with [(bztpen)Cu]2+ in pH 2.5 buffer solution at −0.90 V versus the standard hydrogen electrode (SHE) over two hours using a glassy carbon electrode. A mechanism involving two proton‐coupled reduction steps was proposed for the dihydrogen generation reaction catalyzed by [(bztpen)Cu]2+.
Direct Evidence for a Peroxide Intermediate and a Reactive Enzyme–Substrate–Dioxygen Configuration in a Cofactor‐free Oxidase
Authors: Bui Soi , von Stetten David , Jambrina Pablo G. , Prangé Thierry , Colloc'h Nathalie , de Sanctis Daniele , Royant Antoine , Rosta Edina , Steiner Roberto A.
Published: October 2014

Cofactor‐free oxidases and oxygenases promote and control the reactivity of O2 with limited chemical tools at their disposal. Their mechanism of action is not completely understood and structural information is not available for any of the reaction intermediates. Near‐atomic resolution crystallography supported by in crystallo Raman spectroscopy and QM/MM calculations showed unambiguously that the archetypical cofactor‐free uricase catalyzes uric acid degradation via a C5(S)‐(hydro)peroxide intermediate. Low X‐ray doses break specifically the intermediate C5OO(H) bond at 100 K, thus releasing O2 in situ, which is trapped above the substrate radical. The dose‐dependent rate of bond rupture followed by combined crystallographic and Raman analysis indicates that ionizing radiation kick‐starts both peroxide decomposition and its regeneration. Peroxidation can be explained by a mechanism in which the substrate radical recombines with superoxide transiently produced in the active site.
Xenon(II) Polyfluoridotitanates(IV): Synthesis and Structural Characterization of [Xe2F3]+ and [XeF]+ Salts
Authors: Radan Kristian , Goreshnik Evgeny , Žemva Boris
Published: October 2014

Thermal reaction between XeF2 and excess TiF4 resulted in the unexpected formation of a highly ionized XeII species. The products [Xe2F3][Ti8F33] and [XeF]2[Ti9F38] represent the first examples of [Xe2F3]+ and [XeF]+ compounds, which differ from known XeII salts containing discrete fluoride anions with pentavalent metalloid/metal centers. A new structural type of 2D polyanion [Ti8F33]− and the formation and structure of the novel 1D [Ti9F38]2− are discussed. Both products were characterized by single‐crystal X‐ray analysis and Raman spectroscopy.
Molecular‐Level Understanding of the Photocatalytic Activity Difference between Anatase and Rutile Nanoparticles
Authors: Kim Wooyul , Tachikawa Takashi , Moon Gun‐hee , Majima Tetsuro , Choi Wonyong
Published: October 2014

The generation of oxidants on illuminated photocatalysts and their participation in subsequent reactions are the main basis of the widely investigated photocatalytic processes for environmental remediation and selective oxidation. Here, the generation and the subsequent diffusion of .OH from the illuminated TiO2 surface to the solution bulk were directly observed using a single‐molecule detection method and this molecular phenomenon could explain the different macroscopic behavior of anatase and rutile in photocatalysis. The mobile .OH is generated on anatase but not on rutile. Therefore, the photocatalytic oxidation on rutile is limited to adsorbed substrates whereas that on anatase is more facile and versatile owing to the presence of mobile .OH. The ability of anatase to generate mobile .OH is proposed as a previously unrecognized key factor that explains the common observations that anatase has higher activity than rutile for many photooxidative reactions.
Coumarin‐Based Fluorogenic Probes for No‐Wash Protein Labeling
Authors: Chen Yingche , Clouthier Christopher M. , Tsao Kelvin , Strmiskova Miroslava , Lachance Hugo , Keillor Jeffrey W.
Published: October 2014

A fluorescent protein‐labeling strategy was developed in which a protein of interest (POI) is genetically tagged with a short peptide sequence presenting two Cys residues that can selectively react with synthetic fluorogenic reagents. These fluorogens comprise a fluorophore and two maleimide groups that quench fluorescence until they both undergo thiol addition during the labeling reaction. Novel fluorogens were prepared and kinetically characterized to demonstrate the importance of a methoxy substituent on the maleimide in suppressing reactivity with glutathione, an intracellular thiol, while maintaining reactivity with the dithiol tag. This system allows the rapid and specific labeling of intracellular POIs.
Nasal Anatomy of the Non‐mammaliaform Cynodont Brasilitherium riograndensis (Eucynodontia, Therapsida) Reveals New Insight into Mammalian Evolution
Authors: Ruf Irina , Maier Wolfgang , Rodrigues Pablo G. , Schultz Cesar L.
Published: October 2014

The mammalian nasal cavity is characterized by a unique anatomy with complex internal features. The evolution of turbinals was correlated with endothermic and macrosmatic adaptations in therapsids and in early mammals, which is still apparent in their twofold function (warming and moistening of air, olfaction). Fossil evidence for the transformation from the nonmammalian to the mammalian nasal cavity pattern has been poor and inadequate. Ossification of the cartilaginous nasal capsule and turbinals seems to be a feature that occurred only very late in synapsid evolution but delicate ethmoidal bones are rarely preserved. Here we provide the first µCT investigation of the nasal cavity of the advanced non‐mammaliaform cynodont Brasilitherium riograndensis from the Late Triassic of Southern Brazil, a member of the sister‐group of mammaliaforms, in order to elucidate a critical anatomical transition in early mammalian evolution. Brasilitherium riograndensis already had at least partially ossified turbinals as remnants of the nasoturbinal and the first ethmoturbinal are preserved. The posterior nasal septum is partly ossified and contributes to a mesethmoid. The nasal cavity is posteriorly expanded and forms a distinctive pars posterior (ethmoidal recess) that is ventrally separated from the nasopharyngeal duct by a distinct lamina terminalis. Thus, our observations clearly demonstrate that principal features of the mammalian nasal cavity were already present in the sister‐group of mammaliaforms. Anat Rec, 297:2018–2030, 2014. © 2014 Wiley Periodicals, Inc.
Morphology of the Nasal Capsule of Primates—With Special Reference to Daubentonia and Homo
Authors: Maier Wolfgang , Ruf Irina
Published: October 2014

Primitive mammals are considered macrosmatic. They have very large and complicated nasal capsules, nasal cavities with extensive olfactory epithelia, and relatively large olfactory bulbs. The complicated structures of the nasal capsule follow a relatively conservative “bauplan,” which is normally easy to see in earlier fetal stages; especially in altricial taxa it differentiates well into postnatal life. As anteriormost part of the chondrocranium, the nasal capsule is at first cartilaginous. Most of it ossifies endochondrally, but “appositional bone” (“Zuwachsknochen”) is also common. Many fetal structures become resorbed. Together, all surviving bone structures form the ethmoid bone, but cartilages of the external nose and of the vomeronasal complex can persist throughout life. We describe in detail the anatomy of Daubentonia madagascariensis based on a fetal stage (41 mm HL) and an adult skull was analyzed by µCT. We found that the nasal capsule of this species is by far the most complicated one of all extant Primates. We also describe older fetuses of Homo sapiens (35 and 63 mm HL) as representative of a derived primate. The most significant feature of man—and probably of all anthropoids—is the complete loss of the recessus frontoturbinalis and its associated structures. It can be demonstrated that the evolutionary reductions within the primate nasal capsule mainly affect those structures associated with olfaction, whereas cartilages that are important for the biomechanics of the facial skull of the fetus persist. Anat Rec, 297:1985–2006, 2014. © 2014 Wiley Periodicals, Inc.
Mapping the Nasal Airways: Using Histology to Enhance CT‐Based Three‐Dimensional Reconstruction in Nycticebus
Authors: Deleon Valerie Burke , Smith Timothy D.
Published: October 2014

Three‐dimensional reconstructions of imaging data are an increasingly common approach for studying anatomical structure. However, certain aspects of anatomy, including microscopic structure and differentiating tissue types, continue to benefit from traditional histological analyses. We present here a detailed methodology for combining data from microCT and histological imaging to create 3D virtual reconstructions for visualization and further analyses. We used this approach to study the distribution of olfactory mucosa on ethmoturbinal I of an adult pygmy slow loris, Nycticebus pygmaeus. MicroCT imaging of the specimen was followed by processing, embedding, and sectioning for histological analysis. We identified corresponding features in the CT and histological data, and used these to reconstruct the plane of section in the CT volume. The CT volume was then digitally re‐sliced, such that orthogonal sections of the CT image corresponded to histological sections. Histological images were annotated for the features of interest (in this case, the contour of soft tissue on ethmoturbinal I and the extent of olfactory mucosa), and annotations were transferred to binary masks in the CT volume. These masks were combined with density‐based surface reconstructions of the skull to create an enhanced 3D virtual reconstruction, in which the bony surfaces are coded for mucosal function. We identified a series of issues that may be raised in this approach, for example, deformation related to histological processing, and we make recommendations for addressing these issues. This method provides an evidence‐based approach to 3D visualization and analysis of microscopic features in an anatomic context. Anat Rec, 297:2113–2120, 2014. © 2014 Wiley Periodicals, Inc.
Computational Fluid Dynamics as Surgical Planning Tool: A Pilot Study on Middle Turbinate Resection
Authors: Zhao Kai , Malhotra Prashant , Rosen David , Dalton Pamela , Pribitkin Edmund A
Published: October 2014

Controversies exist regarding the resection or preservation of the middle turbinate (MT) during functional endoscopic sinus surgery. Any MT resection will perturb nasal airflow and may affect the mucociliary dynamics of the osteomeatal complex. Neither rhinometry nor computed tomography (CT) can adequately quantify nasal airflow pattern changes following surgery. This study explores the feasibility of assessing changes in nasal airflow dynamics following partial MT resection using computational fluid dynamics (CFD) techniques. We retrospectively converted the pre‐ and postoperative CT scans of a patient who underwent isolated partial MT concha bullosa resection into anatomically accurate three‐dimensional numerical nasal models. Pre‐ and postsurgery nasal airflow simulations showed that the partial MT resection resulted in a shift of regional airflow towards the area of MT removal with a resultant decreased airflow velocity, decreased wall shear stress and increased local air pressure. However, the resection did not strongly affect the overall nasal airflow patterns, flow distributions in other areas of the nose, nor the odorant uptake rate to the olfactory cleft mucosa. Moreover, CFD predicted the patient's failure to perceive an improvement in his unilateral nasal obstruction following surgery. Accordingly, CFD techniques can be used to predict changes in nasal airflow dynamics following partial MT resection. However, the functional implications of this analysis await further clinical studies. Nevertheless, such techniques may potentially provide a quantitative evaluation of surgical effectiveness and may prove useful in preoperatively modeling the effects of surgical interventions. Anat Rec, 297:2187–2195, 2014. © 2014 Wiley Periodicals, Inc.
Breathing Life Into Dinosaurs: Tackling Challenges of Soft‐Tissue Restoration and Nasal Airflow in Extinct Species
Authors: Bourke Jason M. , Ruger Porter WM. , Ridgely Ryan C. , Lyson Tyler R. , Schachner Emma R. , Bell Phil R. , Witmer Lawrence M.
Published: October 2014

The nasal region plays a key role in sensory, thermal, and respiratory physiology, but exploring its evolution is hampered by a lack of preservation of soft‐tissue structures in extinct vertebrates. As a test case, we investigated members of the “bony‐headed” ornithischian dinosaur clade Pachycephalosauridae (particularlyStegoceras validum) because of their small body size (which mitigated allometric concerns) and their tendency to preserve nasal soft tissues within their hypermineralized skulls. Hypermineralization directly preserved portions of the olfactory turbinates along with an internal nasal ridge that we regard as potentially an osteological correlate for respiratory conchae. Fossil specimens were CT‐scanned, and nasal cavities were segmented and restored. Soft‐tissue reconstruction of the nasal capsule was functionally tested in a virtual environment using computational fluid dynamics by running air through multiple models differing in nasal soft‐tissue conformation: a bony‐bounded model (i.e., skull without soft tissue) and then models with soft tissues added, such as a paranasal septum, a scrolled concha, a branched concha, and a model combining the paranasal septum with a concha. Deviations in fluid flow in comparison to a phylogenetically constrained sample of extant diapsids were used as indicators of missing soft tissue. Models that restored aspects of airflow found in extant diapsids, such as appreciable airflow in the olfactory chamber, were judged as more likely. The model with a branched concha produced airflow patterns closest to those of extant diapsids. These results from both paleontological observation and airflow modeling indicate thatS. validumand other pachycephalosaurids could have had both olfactory and respiratory conchae. Although respiratory conchae have been linked to endothermy, such conclusions require caution in that our re‐evaluation of the reptilian nasal apparatus indicates that respiratory conchae may be more widespread than originally thought, and other functions, such as selective brain temperature regulation, could be important. Anat Rec, 297:2148–2186, 2014. © 2014 Wiley Periodicals, Inc.
Evolutionary and bioinformatic analysis of the spike glycoprotein gene of H120 vaccine strain protectotype of infectious bronchitis virus from India
Authors: Kamble Nitin Machindra , Pillai Aravind S. , Gaikwad Satish S. , Shukla Sanjeev Kumar , Khulape Sagar Aashok , Dey Sohini , Mohan C. Madhan
Published: October 2014

The infectious bronchitis virus is a causative agent of avian infectious bronchitis (AIB), and is is an important disease that produces severe economic losses to the poultry industry worldwide. Recent AIB outbreaks in India have been associated with poor growth in broilers, drop in egg production, and thin egg shells in layers. The complete spike gene of Indian AIB vaccine strain was amplified and sequenced using a conventional reverse transcription polymerase chain reaction and is submitted to the GenBank (accession no KF188436). Phylogenetic analysis revealed that the vaccine strain currently used belongs to H120 genotype, an attenuated strain of Massachusetts (Mass) serotype. Nucleotide and amino acid sequence comparisons have shown that the reported spike gene from Indian isolates have 71.8%–99% and 71.4%–96.9% genetic similarity with the sequenced H120 strain. The study identifies live attenuated IBV vaccine strain, which is routinely used for vaccination, for the first time. Based on nucleotide and amino acid relatedness studies of the vaccine strain with reported IBV sequences from India, it is shown that the current vaccine strain is efficient in controlling the IBV infection. Continuous monitoring of IBV outbreaks by sequencing for genotyping and in vivo cross protection studies for serotyping is not only important for epidemiological investigation but also for evaluation of efficacy of the current vaccine.
Molecular chaperones (TrxA, SUMO, Intein, and GST) mediating expression, purification, and antimicrobial activity assays of plectasin in Escherichia coli
Authors: Chen Xin , Shi Jiawei , Chen Rui , Wen Yaoan , Shi Yu , Zhu Zhe , Guo Songwen , Li Ling
Published: October 2014

Plectasin (PS) is the first defensin to be isolated from a fungus, the saprophytic ascomycete Pseudoplectania nigrella, and active against Streptococcus pneumoniae and S. aureus, including antibiotic‐resistant pathogens. To establish a bacterium‐based production system, we compared the efficiency of four molecular chaperones and corresponding cleavage to the expression and purification of plectasin. The results showed that the yield of plectasin combined with thioredoxin A (TrxA) and small ubiquitin‐related modifier (SUMO) was at a higher level (0.0356 and 0.0358 g L−1, respectively) than that with intein (0.0238 g L−1) and glutathione‐S‐transferase (GST) (0.0243 g L−1). TrxA–plectasin, SUMO–plectasin, and 2–plectasin were cleaved at the correct site and purified, but their considerable amount was not cleaved and remained as a fusion peptide. The antimicrobial activity of plectasin cleaved from SUMO—plectasin against methicillin‐resistant Staphylococcus aureus (MRSA), penicillin‐resistant S. pneumoniae (PRSP), and vancomycin‐resistant enterococci (VRE)—was stronger than ampicillin (Amp) for the same amount of substance (P ≤ 0.05). This is the first study to complete and compare the effect of different molecular chaperones and corresponding cleavage with the expression and purification of plectasin in the Escherichia coli expression system, which laid the foundation for future research and may develop the application and production of plectasin.
Influence of substrate composition on human embryonic stem cell differentiation and extracellular matrix production in embryoid bodies
Authors: Laperle Alex , Masters Kristyn S. , Palecek Sean P.
Published: October 2014

Stem cells reside in specialized niches in vivo. Specific factors, including the extracellular matrix (ECM), in these niches are directly responsible for maintaining the stem cell population. During development, components of the stem cell microenvironment also control differentiation with precise spatial and temporal organization. The stem cell microenvironment is dynamically regulated by the cellular component, including stem cells themselves. Thus, a mechanism exists whereby stem cells modify the ECM, which in turn affects the fate of the stem cell. In this study, we investigated whether the type of ECM initially adsorbed to the culture substrate can influence the composition of the ECM deposited by human embryonic stem cells (hESCs) differentiating in embryoid bodies, and whether different ECM composition and deposition profiles elicit distinct differentiation fates. We have shown that the initial ECM environment hESCs are exposed to affects the fate decisions of those cells and that this initial ECM environment is constantly modified during the differentiation process. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:212–219, 2015
Simple micropatterning method for enhancing fusion efficiency and responsiveness to electrical stimulation of C2C12 myotubes
Authors: Takayama Yuzo , Wagatsuma Akira , Hoshino Takayuki , Mabuchi Kunihiko
Published: October 2014

Cultured myotubes induced in vitro from myoblast cell lines have been widely used to investigate muscle functional properties and disease‐related biological phenotypes. Until now, several cell patterning techniques have been applied to regulate in vitro myotube structures. However, these previous studies required specific geometry patterns or soft materials for inducing efficient myotube formation. Thus, more simple and easy handling method will be promising. In this study, we aimed to provide a method to form C2C12 myotubes with regulated sizes and orientations in simple line patterns. We used a poly(dimethylsiloxane) (PDMS) stamp and a 2‐methacryloyloxyethyl phosphorylcholine (MPC) polymer solution to fabricate line patterns for myotube formation onto a culture dish. We confirmed that C2C12 myotubes of well‐defined size and orientation were reproducibly formed. In particular, myotubes formed in the micropatterned lines showed the increased fusion efficiency. Then, functional dynamics in the micropatterned myotubes were detected and analyzed using a calcium imaging method. We confirmed micropatterning in line patterns enhanced the responsiveness of myotubes to external electrical stimulations. These results indicate that micropatterning myoblasts with the MPC polymer is a simple and effective method to form functional myotube networks. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:220–225, 2015
Iron(III)‐porphyrin Complex FeTSPP: A Versatile Water‐soluble Catalyst for Oxidations in Organic Syntheses, Biorenewables Degradation and Environmental Applications
Authors: Böhm Philipp , Gröger Harald
Published: October 2014

The metal complex FeTSPP (5,10,15,20‐tetrakis‐(4‐sulfonato‐phenyl)‐porphyrin‐iron(III) chloride; also denoted as FeTPPS), which consists of an iron(III) center ion (an environmentally advantageous metal) and a highly water‐soluble heme ligand, represents an exciting and already broadly applied catalyst in the area of “green” oxidation reactions in aqueous media. This commercially available iron catalyst shows a high oxidation potential for many substrates. Further advantages are its high stability and ability not to aggregate in aqueous solution. This Minireview gives an overview of the structural properties of FeTSPP in aqueous solution and selected applications as an oxidation catalyst for organic syntheses, biorenewable degradations, and environmental applications.
Zirconium Materials from Mixed Dicarboxylate Linkers: Enhancing the Stability for Catalytic Applications
Authors: Rasero‐Almansa Antonia M. , Corma Avelino , Iglesias Marta , Sánchez Félix
Published: October 2014

We report the synthesis of two series of zirconium‐based metal–organic frameworks from solutions composed of a mixed‐ligand system (naphthalene dicarboxylic acid/4‐amino‐2,6‐naphthalenedicarboxylic acid or [1,1′‐biphenyl]‐4,4′‐dicarboxylic acid (BPDC)/2‐amino‐[1,1′‐biphenyl]‐4,4′‐dicarboxylic acid). Materials synthesized with low loadings of functionalized linkers exhibit higher long‐term chemical stability and similarly high thermal stability relative to those with 100 % amino linkers. These materials and their corresponding rhodium derivatives prove excellent catalysts in one‐pot reactions. Moreover, the recycling experiments demonstrate an interesting prospect for the long‐term reusability of these catalysts.
Preparation of Chemically Modified RNA Origami Nanostructures
Authors: Endo Masayuki , Takeuchi Yosuke , Emura Tomoko , Hidaka Kumi , Sugiyama Hiroshi
Published: October 2014

In nucleic acid nanotechnology, designed RNA molecules are widely explored because of their usability originating from RNA’s structural and functional diversity. Herein, a method to design and prepare RNA nanostructures by employing DNA origami strategy was developed. A single‐stranded RNA scaffold and staple RNA strands were used for the formation of RNA nanostructures. After the annealing of the mixtures, 7‐helix bundled RNA tile and 6‐helix bundled RNA tube structures were observed as predesigned shapes. These nanostructures were easily functionalized by introducing chemical modification to the RNA scaffolds. The DNA origami method is extended and utilized to construct RNA nanostructures.
Fractional Reactive Extraction for Symmetrical Separation of 4‐Nitro‐D,L‐Phenylalanine in Centrifugal Contactor Separators: Experiments and Modeling
Authors: Tang Kewen , Wen Ping , Zhang Panliang , Huang Yan
Published: October 2014

The enantioselective liquid–liquid extraction of 4‐nitro‐D,L‐phenylalanine (D,L‐Nphy) using PdCl2{(s)‐BINAP} as extractant in dichloroethane was studied experimentally in a countercurrent cascade of 10 centrifugal contactor separators (CCSs) at 5°C, involving flow ratio, extractant concentration, and Cl− concentration. The steady‐state enantiomeric excess (ee) in both stream exits was 90.86% at a 93.29% yield. The predicted value was modeled using an equilibrium stage approach. The correlation between model and experiment was satisfactory. The model was applied to optimize the production of both enantiomers in >97% ee and >99% ee. 14 stages and 16 stages are required for 97% ee and 99% ee for both enantiomers, respectively. Chirality 27:75–81, 2015. © 2014 Wiley Periodicals, Inc.
Study of Al2O3 addition to synthetic Ca‐based sorbents for CO2 sorption capacity and stability in cyclic operations
Authors: Karami Davood , Mahinpey Nader
Published: October 2014

Synthetic CaO sorbents were prepared using alumina as a sintering inhibitor via a simple precipitation method. The effects of three mixing procedures on the physical properties and CO2 capture performance of the sorbents were examined. The cyclic CO2 capture performance of the sorbent derived from the precipitation of calcium salts over colloidal alumina (highly dispersed alumina gel) showed the best performance of the three mixing methods. It was found that variation of alumina‐to‐CaO ratios did not significantly change the sintering influence on the sorbent capacity in cyclic operations. CaO particles homogeneously mingled with alumina at higher ratios. Sintering prevention, however, was not observed. This important observation indicates that alumina appeared to merely act as a binder for the fabrication of mechanically enhanced strength particles that are suitable for large‐scale operations. It was determined that CO2 uptake was not dependent on either the mixing technique or the type of synthetic materials incorporated into a sorbent in cyclic operation. The sorbent derived from the precipitation of calcium salts over colloidal alumina with an alumina‐to‐CaO ratio of 20:80 achieved the highest CO2 uptake of 13.1 moles/kg sorbent for half an hour of carbonation in the first cycle and retained a sorption capacity of 6.5 moles/kg sorbent after 17 successive cycles (50 % activity loss), which is in agreement with the reported results. It was demonstrated that the quantity of CO2 uptake increased moderately with decreasing sorbent particle sizes. The effect of pressure on sorbent CO2 uptake was insignificant.
Assessment of denitrification using electrocoagulation process
Authors: Yehya Tania , Balla Wafaa , Chafi Mohammed , Audonnet Fabrice , Vial Christophe , Essadki Abdelhafid , Gourich Bouchaib
Published: October 2014

The objectives were to study the applicability of electrocoagulation (EC) for the denitrification of drinking water and to determine the main mechanisms of pollution removal. Electrolysis in the intensiostatic mode was applied to a synthetic water representative of potable water in which the concentration of nitrate ions was varied up to 200 mg/L. The respective influences of process parameters, initial concentration of nitrates, and initial pH were investigated. Experimental results show that EC removes efficiently nitrates, following first‐order kinetics. A two‐step mechanism was established: it consisted of the electroreduction of nitrates into ammonium on the cathode, followed by the adsorption of ammonium on the precipitated oxyhydroxides. Adsorption exhibited a zero‐order mechanism. The rates of the two mechanisms were proportional to electrical charge loading and to the total amount of aluminum released in water, as current did not modify significantly the surface area of precipitates. However, adsorption was impaired by the increase of pH resulting from the electroreduction of nitrates, whereas the electrochemical step was insensitive to pH. While the electroreduction of nitrates is known to be far more expensive than biological denitrification, aluminum hydroxides formed during EC present interesting adsorption properties for ammonium removal.
The Role of Hydroxyl Group Acidity on the Activity of Silica‐Supported Secondary Amines for the Self‐Condensation of n‐Butanal
Authors: Shylesh Sankaranarayanapillai , Hanna David , Gomes Joseph , Canlas Christian G. , Head‐Gordon Martin , Bell Alexis T.
Published: October 2014

The catalytic activity of secondary amines supported on mesoporous silica for the self‐condensation of n‐butanal to 2‐ethylhexenal can be altered significantly by controlling the Brønsted acidity of MOH species present on the surface of the support. In this study, MOH (M=Sn, Zr, Ti, and Al) groups were doped onto the surface of SBA‐15, a mesoporous silica, prior to grafting secondary propyl amine groups on to the support surface. The catalytic activity was found to depend critically on the synthesis procedure, the nature and amount of metal species introduced and the spatial separation between the acidic sites and amine groups. DFT analysis of the reaction pathway indicates that, for weak Brønsted acid groups, such as SiOH, the rate‐limiting step is CC bond formation, whereas for stronger Brønsted acid groups, such as Ti and Al, hydrolysis of iminium species produced upon CC bond formation is the rate‐limiting step. Theoretical analysis shows further that the apparent activation energy decreases with increasing Brønsted acidity of the MOH groups, consistent with experimental observation.
Cost‐Effective Synthesis of Amine‐Tethered Porous Materials for Carbon Capture
Authors: Lu Weigang , Bosch Mathieu , Yuan Daqiang , Zhou Hong‐Cai
Published: October 2014

A truly cost‐effective strategy for the synthesis of amine‐tethered porous polymer networks (PPNs) has been developed. A network containing diethylenetriamine (PPN‐125‐DETA) exhibits a high working capacity comparable to current state‐of‐art technology (30 % monoethanolamine solutions), yet it requires only one third as much energy for regeneration. It has also been demonstrated to retain over 90 % capacity after 50 adsorption–desorption cycles of CO2 in a temperature‐swing adsorption process. The results suggest that PPN‐125‐DETA is a very promising new material for carbon capture from flue gas streams.
The RanGEFBj1 promotes prospero nuclear export and neuroblast self‐renewal
Authors: Joy Tasha , Hirono Keiko , Doe Chris Q.
Published: October 2014

Drosophila larval neuroblasts are a model system for studying stem cell self‐renewal and differentiation. Here, we report a novel role for the Drosophila gene Bj1 in promoting larval neuroblast self‐renewal. Bj1 is the guanine‐nucleotide exchange factor for Ran GTPase, which regulates nuclear import/export. Bj1 transcripts are highly enriched in larval brain neuroblasts (in both central brain and optic lobe), while Bj1 protein is detected in both neuroblasts and their neuronal progeny. Loss of Bj1 using both mutants or RNAi causes a progressive loss of larval neuroblasts, showing that Bj1 is required to maintain neuroblast numbers. Loss of Bj1 does not result in neuroblast apoptosis, but rather leads to abnormal nuclear accumulation of the differentiation factor Prospero, and premature neuroblast differentiation. We conclude that the Bj1 RanGEF promotes Prospero nuclear export and neuroblast self‐renewal. © 2014 Wiley Periodicals, Inc. Develop Neurobiol 75: 485–493, 2015