bluuebunny/crossref_metadata_2025 huggingface dataset:
The long‐wavelength geoid from three‐dimensional spherical models of thermal and thermochemical mantle convection
Authors: Liu Xi , Zhong Shijie
Published: May 2015

The Earth's long‐wavelength geoid anomalies have long been used to constrain the dynamics and viscosity structure of the mantle in an isochemical, whole mantle convection model. However, there is strong evidence that the seismically observed large low shear velocity provinces (LLSVPs) in the lower mantle underneath the Pacific and Africa are chemically distinct and likely denser than the ambient mantle. In this study, we have formulated dynamically self‐consistent 3‐D spherical mantle convection models to investigate how chemically distinct and dense piles above the core‐mantle boundary may influence the geoid. Our dynamic models with realistic mantle viscosity structure produce dominantly spherical harmonic degree‐2 convection, similar to that of the present‐day Earth. The models produce two broad geoid and topography highs over two major thermochemical piles in the lower mantle, consistent with the positive geoid anomalies over the Pacific and African LLSVPs. Our geoid analysis showed that the bottom layer with dense chemical piles contributes negatively to the total geoid, while the layer immediately above the chemical piles contributes positively to the geoid, canceling out the effect of the piles. Thus, the bottom part of the mantle, as a compensation layer, has zero net contribution to the total geoid, and the thickness of the compensation layer is ~1000 km or 2 to 3 times as thick as the chemical piles. Our results help constrain and interpret the large‐scale thermochemical structure of the mantle using surface observations of the geoid and topography, as well as seismic models of the mantle.
Injection‐induced seismicity: Poroelastic and earthquake nucleation effects
Authors: Segall P. , Lu S.
Published: May 2015

The standard model of injection‐induced seismicity considers changes in Coulomb strength due solely to changes in pore pressure. We consider two additional effects: full poroelastic coupling of stress and pore pressure, and time‐dependent earthquake nucleation. We model stress and pore pressure due to specified injection rate in a homogeneous, poroelastic medium. Stress and pore pressure are used to compute seismicity rate through the Dieterich (1994) model. For constant injection rate, the time to reach a critical seismicity rate scales with t ∼ r2/(cfc), where r is distance from the injector, c is hydraulic diffusivity, and fc is a factor that depends on mechanical properties, and weakly on r. The seismicity rate decays following a peak, consistent with some observations. During injection poroelastic coupling may increase or decrease the seismicity rate, depending on the orientation of the faults relative to the injector. If injection‐induced stresses inhibit slip, abrupt shut‐in can lead to locally sharp increases in seismicity rate; tapering the flux mitigates this effect. The maximum magnitude event has been observed to occur postinjection. We suggest the seismicity rate at a given magnitude depends on the nucleation rate, the size distribution of fault segments, and if the background shear stress is low, the time‐varying volume of perturbed crust. This leads to a rollover in frequency‐magnitude distribution for larger events, with a “corner” that increases with time. Larger events are absent at short times, but approach the background frequency with time; larger events occurring post shut‐in are thus not unexpected.
Accounting for dust aerosol size distribution in radiative transfer
Authors: Li Jiangnan , Min Qilong , Peng Yiran , Sun Zhian , Zhao Jian‐Qi
Published: May 2015

The impact of size distribution of mineral dust aerosol on radiative transfer was investigated using the Aerosol Robotic Network‐retrieved aerosol size distributions. Three methods for determining the aerosol optical properties using size distributions were discussed. The first is referred to as a bin method in which the aerosol optical properties are determined for each bin of the size distribution. The second is named as an assembly mean method in which the aerosol optical properties are determined with an integration of the aerosol optical parameters over the observed size distribution. The third is a normal parameterization method based on an assumed size distribution. The bin method was used to generate the benchmark results in the radiation calculations against the methods of the assembly mean, and parameterizations based on two size distribution functions, namely, lognormal and gamma were examined. It is seen that the assembly mean method can produce aerosol radiative forcing with accuracy of better than 1%. The accuracies of the parameterizations based on lognormal and gamma size distributions are about 25% and 5%, respectively. Both the lognormal and gamma size distributions can be determined by two parameters, the effective radius and effective variance. The better results from the gamma size distribution can be explained by a third parameter of skewness which is found to be useful for judging how close the assumed distribution is to the observation result. The parameterizations based on the two assumed size distributions are also evaluated in a climate model. The results show that the reflected solar fluxes over the desert areas determined by the scheme based on the gamma size distribution are about 1 W m−2 less than those from the scheme based on the lognormal size distribution, bringing the model results closer to the observations.
Reconstruction of an atmospheric tracer source in Fusion Field Trials: Analyzing resolution features
Authors: Singh Sarvesh Kumar , Turbelin Gregory , Issartel Jean‐Pierre , Kumar Pramod , Feiz Amir Ali
Published: May 2015

Reconstruction of unknown atmospheric releases using measured concentrations is an ill‐posed inverse problem. Due to insufficient measurements and dispersion model uncertainties, reliable interpretation of a retrieved source is limited by lack of resolution, nonuniqueness, and instability in the inverse solution. The study presents an optimality analysis, in terms of resolution, stability, and reliability, of an inverse solution given by a recently proposed inversion technique, called as renormalization. The inversion technique is based on an adjoint source‐receptor framework and construction of a weight function which interprets a priori information about the unknown release apparent to the monitoring network. The properties of weight function provide a perfect data resolution, maximum model resolution, and minimum variance (or stability) for the retrieved source. The reliability of the retrieved source is interpreted in view of the information derived from the geometry of the monitoring network. The inversion technique and resolution features are evaluated for a point source reconstruction using measurements from a recent dispersion experiment (Fusion Field Trials 2007) conducted at Dugway Proving Ground, Utah. With the real measurements, the point release is reconstructed within an average distance of 23 m from the true release where the average distance of the nearest receptor from the true source was 32 m. In all the trials, the point release is retrieved within 3–60 m Euclidean distance from their true location. The source strength is retrieved within a factor of 1.5 to the true release mass. The posterior uncertainty in the release parameters is observed to be within 20% of their mean value. The source localization features are resolved to its maximum extent feasible with the design of the monitoring network. The sensitivity studies are conducted to highlight the importance of receptors reporting zero concentration measurements and variations in the resolution features of the source retrieval with respect to the various arrangements of the receptors.
Lagrangian dust model simulations for a case of moist convective dust emission and transport in the western Sahara region during Fennec/LADUNEX
Authors: Sodemann H. , Lai T. M. , Marenco F. , Ryder C. L. , Flamant C. , Knippertz P. , Rosenberg P. , Bart M. , McQuaid J. B.
Published: May 2015

Due to the harshness and inaccessibility of desert regions, the uncertainties concerning the processes of dust mobilization at the surface, airborne transport, and sedimentation are still considerable, limiting the ability to perform model simulations. In June 2011, a comprehensive data set of ground‐based and airborne in situ measurements and remote sensing observations was acquired within the Fennec/Lagrangian Dust Source Inversion Experiment (LADUNEX) field campaign in the western Sahara region. Here we evaluate the ability of the state‐of‐the‐art Lagrangian particle dispersion model FLEXPART, newly fitted with a dust mobilization capability, to simulate dust transport in this region. We investigate a case where a large mesoscale convective system (MCS) triggered dust emissions in central Mali, which subsequently moved as a large cold pool dust front toward northern Mauritania. Specifying dust mobilization for this case is shown to be an important obstacle to simulating dust transport during this event, since neither the MCS nor the associated cold pool‐causing dust emission is represented in the meteorological analysis. Obtaining a realistic dust transport simulation for this case therefore requires an inversion approach using a manual specification of the dust sources supported by satellite imagery. When compared to in situ and remote sensing data from two aircraft, the Lagrangian dust transport simulations represent the overall shape and evolution of the dust plume well. While accumulation and coarse mode dust are well represented in the simulation, giant mode particles are considerably underestimated. Our results re‐emphasize that dust emission associated with deep moist convection remains a key issue for reliable dust model simulations in northern Africa.
Is it appropriate to model turbidity currents with the three‐equation model?
Authors: Hu Peng , Pähtz Thomas , He Zhiguo
Published: May 2015

The three‐equation model (TEM) was developed in the 1980s to model turbidity currents (TCs) and has been widely used ever since. However, its physical justification was questioned because self‐accelerating TCs simulated with the steady TEM seemed to violate the turbulent kinetic energy balance. This violation was considered as a result of very strong sediment erosion that consumes more turbulent kinetic energy than is produced. To confine bed erosion and thus remedy this issue, the four‐equation model (FEM) was introduced by assuming a proportionality between the bed shear stress and the turbulent kinetic energy. Here we analytically proof that self‐accelerating TCs simulated with the original steady TEM actually never violate the turbulent kinetic energy balance, provided that the bed drag coefficient is not unrealistically low. We find that stronger bed erosion, surprisingly, leads to more production of turbulent kinetic energy due to conversion of potential energy of eroded material into kinetic energy of the current. Furthermore, we analytically show that, for asymptotically supercritical flow conditions, the original steady TEM always produces self‐accelerating TCs if the upstream boundary conditions (“ignition” values) are chosen appropriately, while it never does so for asymptotically subcritical flow conditions. We numerically show that our novel method to obtain the ignition values even works for Richardson numbers very near to unity. Our study also includes a comparison of the TEM and FEM closures for the bed shear stress to simulation data of a coupled Large Eddy and Discrete Element Model of sediment transport in water, which suggests that the TEM closure might be more realistic than the FEM closure.
A forward analysis on the applicability of tracer breakthrough profiles in revealing the pore structure of tight gas sandstone and carbonate rocks
Authors: Mehmani Ayaz , Mehmani Yashar , Prodanović Maša , Balhoff Matthew
Published: May 2015

We explore tracer breakthrough profiles (TBP) as a macroscopic property to infer the pore‐space topology of tight gas sandstone and carbonate rocks at the core scale. The following features were modeled via three‐dimensional multiscale networks: microporosity within dissolved grains and pore‐filling clay, cementation in the absence and presence of microporosity (each classified into uniform, pore‐preferred, and throat‐preferred modes), layering, vug, and microcrack inclusion. A priori knowledge of the extent and location of each process was assumed to be known. With the exception of an equal importance of macropores and pore‐filling micropores, TBPs show little sensitivity to the fraction of micropores present. In general, significant sensitivity of the TBPs was observed for uniform and throat‐preferred cementation. Layering parallel to the fluid flow direction had a considerable impact on TBPs whereas layering perpendicular to flow did not. Microcrack orientations seemed of minor importance in affecting TBPs.
Organic contaminant transport and fate in the subsurface: Evolution of knowledge and understanding
Authors: Essaid Hedeff I. , Bekins Barbara A. , Cozzarelli Isabelle M.
Published: May 2015

Toxic organic contaminants may enter the subsurface as slightly soluble and volatile nonaqueous phase liquids (NAPLs) or as dissolved solutes resulting in contaminant plumes emanating from the source zone. A large body of research published in Water Resources Research has been devoted to characterizing and understanding processes controlling the transport and fate of these organic contaminants and the effectiveness of natural attenuation, bioremediation, and other remedial technologies. These contributions include studies of NAPL flow, entrapment, and interphase mass transfer that have advanced from the analysis of simple systems with uniform properties and equilibrium contaminant phase partitioning to complex systems with pore‐scale and macroscale heterogeneity and rate‐limited interphase mass transfer. Understanding of the fate of dissolved organic plumes has advanced from when biodegradation was thought to require oxygen to recognition of the importance of anaerobic biodegradation, multiple redox zones, microbial enzyme kinetics, and mixing of organic contaminants and electron acceptors at plume fringes. Challenges remain in understanding the impacts of physical, chemical, biological, and hydrogeological heterogeneity, pore‐scale interactions, and mixing on the fate of organic contaminants. Further effort is needed to successfully incorporate these processes into field‐scale predictions of transport and fate. Regulations have greatly reduced the frequency of new point‐source contamination problems; however, remediation at many legacy plumes remains challenging. A number of fields of current relevance are benefiting from research advances from point‐source contaminant research. These include geologic carbon sequestration, nonpoint‐source contamination, aquifer storage and recovery, the fate of contaminants from oil and gas development, and enhanced bioremediation.
Preparation and graft‐copolymerization of hydrogenated natural rubber in latex stage
Authors: Ha Nguyen Thu , Kaneda Keisuke , Naitoh Yoshitaka , Fukuhara Lina , Kosugi Kenichiro , Kawahara Seiichi
Published: May 2015

Preparation and graft‐copolymerization of hydrogenated natural rubber are performed in latex stage after removal of proteins from the rubber with urea and surfactant. Hydrogenation of deproteinized natural rubber (DPNR) latex is carried out with palladium catalyst under hydrogen atmosphere. The hydrogenated DPNR (HDPNR) is crosslinked with a peroxide followed by graft‐copolymerization of styrene (Sty) and acrylonitrile (AN) in latex stage in order to prepare a graft‐copolymer of crosslinked HDPNR with poly(Sty‐co‐AN) (HDPNR‐graft‐PSAN). Characterization of the products is performed by nuclear magnetic resonance spectroscopy. The conversion of hydrogenation is investigated with respect to the catalyst feed, acidity (pH), and dry rubber content. In the resulting HDPNR‐graft‐PSAN, mole fraction of AN and Sty is 1.4 and 5.8 mol %, respectively. The graft‐copolymer is used to improve properties of PSAN as an impact modifier. The Charpy impact strength of crosslinked HDPNR‐graft‐PSAN/PSAN is about eight times as high as that of PSAN. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 42435.
Plasmonic device based on a PAAm hydrogel/gold nanoparticles composite
Authors: Monteiro Johny Paulo , Predabon Sheila Maria , da Silva Cleiser Thiago Pereira , Radovanovic Eduardo , Girotto Emerson Marcelo
Published: May 2015

Stimuli‐resposive hydrogels, such as poly(acrylamide), are smart materials that can be loaded with gold nanoparticles to explore the localized surface plasmon resonance effect to develop an optical device. Here we used electropolymerized poly(acrylamide) hydrogel for entrapped gold nanoparticles into gel structure (composite) to prepare a plasmonic device. Sensing tests were performed; for this bovine serum albumin molecules were placed into the composite by diffusion from an aqueous solution. The presence of the molecules alters the refractive index around the gold nanoparticles, changing its resonance conditions. The plasmonic band shifted ∼3.8 nm when the composite was incubated at the 20 µg/mL bovine serum albumin solution, which is a result comparable to reports elsewhere using gold nanoparticles on glass substrates. The device showed that it was possible to detect significantly low concentrations up to 10 ng/mL of protein in aqueous solution. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 42449.
Photoinduced Formation of Peroxide Ions on La2O3 and Nd2O3 under O2: Effects of Excitation Wavelength and Crystal Structure
Authors: Jing Xiao‐Lian , She Wen‐Yu , Li Jian‐Mei , Chen Qing‐Chuan , Weng Wei‐Zheng , An Dong‐Li , Wan Hui‐Lin
Published: May 2015

Photoinduced formation of peroxide ions on La2O3 and Nd2O3 under O2 was studied by in‐situ microprobe Raman spectroscopy with attention focused on the effect of excitation wavelength and crystal structure on the O22− formation. It was found that photoexcitations at 633, 532, 514, and 325 nm can induce O22− formation over La2O3 at 450 °C. By contrast, photoexcitation at 785 nm does not cause formation of O22− up to 500 °C. Photoexcitation at 325 nm can induce O22− formation on cubic Nd2O3 at 25 °C, but cannot induce O22− formation on hexagonal Nd2O3 up to 200 °C. The significant difference in the behavior of O22− formation over the Nd2O3 samples of the two structures can be related to the difference in the capacity to adsorb O2. Since the number of oxygen vacancies in cubic Nd2O3 is larger than that in the hexagonal one, the former has a higher capacity than the latter to adsorb O2. As a result, cubic Nd2O3 is more favorable to the reaction of O2 with O2− to generate O22−. The structural similarity between cubic Nd2O3 and Nd2O2(O2) may be another factor in favor of peroxide formation.
Investigation on the Surface‐Confined Self‐Assembly Stabilized by Hydrogen Bonds of Urea and Amide Groups: Quantitative Analysis of Concentration Dependence of Surface Coverage
Authors: Nishitani Nobuhiko , Hirose Takashi , Matsuda Kenji
Published: May 2015

Formation of a hydrogen‐bond network via an amide group is a key driving force for the nucleation–elongation‐type self‐assembly that is often seen in biomolecules and artificial supramolecular assemblies. In this work, rod‐coil‐like aromatic compounds bearing an amide (1 a–3 a) or urea group (1 u–3 u) were synthesized, and their self‐assemblies on a 2‐D surface were investigated by scanning tunneling microscopy (STM). According to the quantitative analysis of the concentration dependence of the surface coverage, it was revealed that the strength of the hydrogen bond (i.e., amide or urea) and the number of non‐hydrogen atoms in a molecular component (i.e., size of core and length of alkyl side chain) play a primary role in determining the stabilization energy during nucleation and elongation processes of molecular ordering on the HOPG surface.
Three‐Component Supramolecular System with Multistimuli‐Responsive Properties in Water
Authors: Wang Bin , Liu Hua‐Ji , Fu Xiao‐Bin , Yao Yefeng , Chen Yu
Published: May 2015

Hyperbranched polyethylenimine terminated with isobutyramide groups (HPEI‐IBAm), 4‐(phenylazo)benzoic acid (PABA), and α‐cyclodextrin (α‐CD) were assembled together at pH≈7 to form the three‐component supramolecular complexes that were verified by 1H and 2D ROESY 1H NMR spectroscopy. UV/Vis spectrometric titration experiments showed that the content of α‐CD in the three‐component complexes was less than the feed amount and it was difficult for all the PABA units in the complexes to further form complexes with α‐CD. The obtained three‐component supramolecular complexes exhibited thermoresponsive properties in water. Increasing the α‐CD concentration led to a sharp increase in the cloud point temperature (Tcp) at the beginning, but after the [α‐CD]/[PABA] ratio was in the region of 1.3–1.6, the Tcp increased gradually When the concentration of α‐CD was low, a higher concentration of PABA led to a lower Tcp, however, the opposite was observed when the concentration of α‐CD was high. For the three‐component complex, increasing the α‐CD concentration at pH≈7 or at pH≈9 led to different Tcp temperatures. In the low α‐CD concentration range, adjusting the pH from ≈7–≈9 resulted in an increase in the Tcp, similar but not so pronounced as that of the two‐component system of HPEI‐IBAm/[PABA]. When the concentration of α‐CD was high, adjusting the pH from ≈7–≈9 decreased the Tcp; this observation is different to that of the two‐component system of HPEI‐IBAm/[PABA]. Reversible trans‐to‐cis photoisomerization of azobenzene units in the complexes occurred, following irradiation with UV or visible light. Trans‐to‐cis isomerization of azobenzene units decreased the Tcp. However, this result differed to that of the two‐component system of HPEI‐IBAm/PABA.
A simple method for expression and purification of Shiga toxin 1 (Stx1) with biological activities by using a single‐promoter vector and native signal peptide
Authors: Tu Wei , Li Tao , Wang Qin , Cai Kun , Gao Xiang , Wang Hui
Published: May 2015

The entire stx1 region from Escherichia coli O157:H7, containing two open reading frames (stx1a and stx1b), was cloned into pET‐32a with a single promoter. This region was transformed into E. coli TransB (DE3), which is a trxB and gor mutation strain. After expression in the E. coli periplasm in a completely soluble form, the rStx1 was purified and verified by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS‐PAGE), ELISA, and Western blot analysis. Our rStx1 have Vero cell median cytotoxic dose (CD50) and median lethal dose (LD50) values of approximately 30 ng and 1.5 µg, respectively. The final yield of the purified rStx1 ranged from 2 to 3 mg/L by one‐step nickel affinity gel column chromatography. This method is an easy approach to the large‐scale preparation of Stx1 at a reasonable cost.
Isoniazid‐induced polyneuropathy in a tuberculosis patient – implication for individual risk stratification with genotyping?
Authors: Stettner Mark , Steinberger Daniela , Hartmann Christian J. , Pabst Tatjana , Konta Lidija , Hartung Hans Peter , Kieseier Bernd C.
Published: May 2015

Background

Development of polyneuropathy (PNP) under treatment for tuberculosis (TB), including isoniazid (INH), is a highly relevant adverse drug effect. The NAT2 acetylation status is a predictor of potential toxic effects of INH. The question as to whether individual risk stratification by genotyping is useful to avoid suffering of patients and to lower costs for the health care system is of considerable clinical importance.

Case Presentation

After drug treatment for TB, including INH, a 23‐year‐old man developed severe PNP. During the treatment, laboratory results have been indicating incipient liver and renal injury. Later, molecular genetic analyses were performed and revealed a variation in the NAT2 gene and the c1/c2 genotype of the CYP2E1 gene, both described to contribute to an elevated risk for anti‐tuberculostatic‐induced liver damages (ATIL).

Conclusion

The combination of metabolizer genotypes should be taken into account as a cause for toxic effects and the development of PNP. Individual genotyping, performed before medication or at least if an elevation of liver parameters is observed, may reduce the risk of severe cases of PNP by early adjustment of treatment. Our case study indicates that evaluation of individual risk stratification with systematic pharmacogenetic genotyping of metabolizer gene combinations in the context of TB treatment should be addressed in clinical studies with larger cohorts.
An appraisal of the short lateral rotators of the hip joint
Authors: Yoo Sarang , Dedova Irina , Pather Nalini
Published: May 2015

The short lateral rotators (piriformis, obturator internus, superior and inferior gemelli, obturator internus, and quadratus femoris) are functionally important muscles, significantly contributing to hip joint stability. They act as “postural muscles”, holding the femoral head in the acetabulum during hip movements, thus are frequently monitored in gait analysis and for muscle rehabilitation post‐injury. Despite the need to precisely identify and repair these muscles for stability postoperatively, clinical complications have resulted from the inadequate and inconsistent understanding of their morphological and functional anatomy. Furthermore, the short lateral rotators have complex entheses (osteotendinous insertions on bone) and may be subject to overuse injury in sport. This study aims to review the reported morphology of the short lateral rotators in order to ascertain whether discrepancies exist in our understanding of these muscles, and if further investigation is required to aid in gait analysis, clinical management of hip pathologies, and prevention of overuse injuries. Following a literature search strategy, 59 primary references were retrieved from three databases, with additional 26 anatomical textbooks selected for critical evaluation. Numerous inaccuracies and inconsistencies in the anatomical descriptions of the attachments, patterns of innervation and actions exist, and often insufficiently supported by primary findings. There is also a paucity of information regarding the architectural pattern of the muscles, which would be useful in clarifying the function of these dynamic stabilizers of the hip joint. A better anatomical understanding of these muscles will better inform hip reconstruction and lead to improved surgical outcomes by reducing post‐operative complications. Clin. Anat. 28:800–812, 2015. © 2015 Wiley Periodicals, Inc.
C35 Hopanoid Side Chain Biosynthesis: Reduction of Ribosylhopane into Bacteriohopanetetrol by a Cell‐Free System Derived from Methylobacterium organophilum
Authors: Bodlenner Anne , Liu Wenjun , Hirsch Guillaume , Schaeffer Philippe , Blumenberg Martin , Lendt Ralf , Tritsch Denis , Michaelis Walter , Rohmer Michel
Published: May 2015

The major bacterial triterpenoids of the hopane series each consist of a C30 triterpene hopane moiety and an additional nonterpene C5 side chain derived from D‐ribose and linked through its C‐5 carbon atom to the hopane side chain. Bacteriohopanetetrol and aminobacteriohopanetriol are the most common representatives of this natural product series, adenosylhopane and ribosylhopane being putative precursors. Deuterium‐labelled ribosylhopane was obtained by hemisynthesis and converted into deuterium‐labelled bacteriohopanetetrol in the presence of NADPH, thus giving evidence of this as yet unknown precursor‐to‐product relationship in the bacterial hopanoid metabolic pathway.
Diversified Structural Basis of a Conserved Molecular Mechanism for pH‐Dependent Dimerization in Spider Silk N‐Terminal Domains
Authors: Otikovs Martins , Chen Gefei , Nordling Kerstin , Landreh Michael , Meng Qing , Jörnvall Hans , Kronqvist Nina , Rising Anna , Johansson Jan , Jaudzems Kristaps
Published: May 2015

Conversion of spider silk proteins from soluble dope to insoluble fibers involves pH‐dependent dimerization of the N‐terminal domain (NT). This conversion is tightly regulated to prevent premature precipitation and enable rapid silk formation at the end of the duct. Three glutamic acid residues that mediate this process in the NT from Euprosthenops australis major ampullate spidroin 1 are well conserved among spidroins. However, NTs of minor ampullate spidroins from several species, including Araneus ventricosus (AvMiSp NT), lack one of the glutamic acids. Here we investigate the pH‐dependent structural changes of AvMiSp NT, revealing that it uses the same mechanism but involves a non‐conserved glutamic acid residue instead. Homology modeling of the structures of other MiSp NTs suggests that these harbor different compensatory residues. This indicates that, despite sequence variations, the molecular mechanism underlying pH‐dependent dimerization of NT is conserved among different silk types.
Direct observation of tropomyosin binding to actin filaments
Authors: Schmidt William M. , Lehman William , Moore Jeffrey R.
Published: May 2015

Tropomyosin is an elongated α‐helical coiled coil that binds to seven consecutive actin subunits along the long‐pitch helix of actin filaments. Once bound, tropomyosin polymerizes end‐to‐end and both stabilizes F‐actin and regulates access of various actin‐binding proteins including myosin in muscle and nonmuscle cells. Single tropomyosin molecules bind weakly to F‐actin with millimolar Kd, whereas the end‐to‐end linked tropomyosin associates with about a 1000‐fold greater affinity. Despite years of study, the assembly mechanism of tropomyosin onto actin filaments remains unclear. In this study, we used total internal reflection fluorescence microscopy to directly monitor the cooperative binding of fluorescently labeled tropomyosin molecules to phalloidin‐stabilized actin filaments. We find that tropomyosin molecules assemble from multiple growth sites after random low‐affinity binding of single molecules to actin. As the length of the tropomyosin chain increases, the probability of detachment decreases, which leads to further chain growth. Tropomyosin chain extension is linearly dependent on the concentration of tropomyosin, occurring at approximately 100 monomers/(μM*s). The random tropomyosin binding to F‐actin leads to discontinuous end‐to‐end association where gaps in the chain continuity smaller than the required seven sequential actin monomers are available. Direct observation of tropomyosin detachment revealed the number of gaps in actin‐bound tropomyosin, the time course of gap annealing, and the eventual filament saturation process. © 2015 Wiley Periodicals, Inc.
Emerging roles of sumoylation in the regulation of actin, microtubules, intermediate filaments, and septins
Authors: Alonso Annabel , Greenlee Matt , Matts Jessica , Kline Jake , Davis Kayla J. , Miller Rita K.
Published: May 2015

Sumoylation is a powerful regulatory system that controls many of the critical processes in the cell, including DNA repair, transcriptional regulation, nuclear transport, and DNA replication. Recently, new functions for SUMO have begun to emerge. SUMO is covalently attached to components of each of the four major cytoskeletal networks, including microtubule‐associated proteins, septins, and intermediate filaments, in addition to nuclear actin and actin‐regulatory proteins. However, knowledge of the mechanisms by which this signal transduction system controls the cytoskeleton is still in its infancy. One story that is beginning to unfold is that SUMO may regulate the microtubule motor protein dynein by modification of its adaptor Lis1. In other instances, cytoskeletal elements can both bind to SUMO non‐covalently and also be conjugated by it. The molecular mechanisms for many of these new functions are not yet clear, but are under active investigation. One emerging model links the function of MAP sumoylation to protein degradation through SUMO‐targeted ubiquitin ligases, also known as STUbL enzymes. Other possible functions for cytoskeletal sumoylation are also discussed. © 2015 The Authors. Cytoskeleton Published by Wiley Periodicals, Inc.
Evidence for changes in beta‐ and gamma‐actin proportions during inner ear hair cell life
Authors: Andrade Leonardo R.
Published: May 2015

Cytoplasmic actin isoforms beta (β‐) and gamma (γ‐) perform crucial physiological roles in inner ear hair cells (HC). The stereocilium, which is structured by parallel actin filaments composed of both isoforms, is the responsive organelle to mechanical stimuli such as sound, gravity and head movements. Modifications in isoform proportions affect the function of the stereocilia as previously shown in genetic studies of mutant mice. Here, immunogold labeling TEM studies in mice showed that both β‐ and γ‐actin isoforms colocalize throughout stereocilia actin filaments, adherens junctions and cuticular plates as early as embryonic stage 16.5. Gold‐particle quantification indicated that there was 40% more γ‐ actin than β‐actin at E16.5. In contrast, β‐ and γ‐actin were equally concentrated in adult stereocilia of cochlear and vestibular HC. Interestingly, all actin‐based structures presented almost five‐fold more β‐actin than γ‐actin in 22 month‐ old mice, suggesting that γ‐actin is probably under‐expressed during the aging process. These data provide evidence of dynamic modifications of the actin isoforms in stereocilia, cuticular plates and cell junctions during the whole HC life. © 2015 Wiley Periodicals, Inc.
An over‐nonlocal implicit gradient‐enhanced damage‐plastic model for trabecular bone under large compressive strains
Authors: Hosseini Hadi S. , Horák Martin , Zysset Philippe K. , Jirásek Milan
Published: May 2015

Purpose: Investigation of trabecular bone strength and compaction is important for fracture risk prediction. At 1–2% compressive strain, trabecular bone undergoes strain softening, which may lead to numerical instabilities and mesh dependency in classical local damage‐plastic models. The aim of this work is to improve our continuum damage‐plastic model of bone by reducing the influence of finite element mesh size under large compression.

Methodology: This spurious numerical phenomenon may be circumvented by incorporating the nonlocal effect of cumulated plastic strain into the constitutive law. To this end, an over‐nonlocal implicit gradient model of bone is developed and implemented into the finite element software ABAQUS using a user element subroutine. The ability of the model to detect the regions of bone failure is tested against experimental stepwise loading data of 16 human trabecular bone biopsies.

Findings: The numerical outcomes of the nonlocal model revealed reduction of finite element mesh dependency compared with the local damage‐plastic model. Furthermore, it helped reduce the computational costs of large‐strain compression simulations.

Originality: To the best of our knowledge, the proposed model is the first to predict the failure and densification of trabecular bone up to large compression independently of finite element mesh size. The current development enables the analysis of trabecular bone compaction as in osteoporotic fractures and implant migration, where large deformation of bone plays a key role. Copyright © 2015 John Wiley & Sons, Ltd.
Dynamic flow characteristics in normal and asthmatic lungs
Authors: Kim Minsuok , Bordas Rafel , Vos Wim , Hartley Ruth A. , Brightling Chris E. , Kay David , Grau Vicente , Burrowes Kelly S.
Published: May 2015

Complex flow patterns exist within the asymmetric branching airway network in the lungs. These flow patterns are known to become increasingly heterogeneous during disease as a result of various mechanisms such as bronchoconstriction or alterations in lung tissue compliance. Here, we present a coupled model of tissue deformation and network airflow enabling predictions of dynamic flow properties, including temporal flow rate, pressure distribution, and the occurrence of reverse flows. We created two patient‐specific airway geometries, one for a healthy subject and one for a severe asthmatic subject, derived using a combination of high‐resolution CT data and a volume‐filling branching algorithm. In addition, we created virtually constricted airway geometry by reducing the airway radii of the healthy subject model. The flow model was applied to these three different geometries to solve the pressure and flow distribution over a breathing cycle. The differences in wave phase of the flows in parallel airways induced by asymmetric airway geometry and bidirectional interaction between intra‐acinar and airway network pressures were small in central airways but were more evident in peripheral airways. The asthmatic model showed elevated ventilation heterogeneity and significant flow disturbance. The reverse flows in the asthmatic model not only altered the local flow characteristics but also affected total lung resistance. The clinical significance of temporal flow disturbance on lung ventilation in normal airway model is obscure. However, increased flow disturbance and ventilation heterogeneity observed in the asthmatic model suggests that reverse flow may be an important factor for asthmatic lung function. Copyright © 2015 John Wiley & Sons, Ltd.
β‐Actin as a loading control: Less than 2 μg of total protein should be loaded
Authors: Chen Wei , Xu Wei‐Hua
Published: May 2015

For the purpose of data normalization in Western blot analysis, journal editors and reviewers usually require authors to reprobe the Western blot membrane with a β‐actin‐specific antibody after detecting the target protein. In most cases, however, β‐actin is overloaded, which results in a failure to detect differences in protein loading. In this study, we attempted to optimize the amount of protein loaded for β‐actin detection to permit suitable Western blot analysis data normalization. Our data suggest that less than 2 μg of total protein should be loaded when β‐actin is used as a loading control. We also suggest avoiding reprobing the membrane with a β‐actin‐specific antibody.
Shore platform lowering due to frost shattering during the 2009 winter at mesnil Val, English channel coast, NW France
Authors: Dewez T. J. B. , Regard V. , Duperret A. , Lasseur E.
Published: May 2015

In 2008–2009, a severe cold snap affected the otherwise temperate mid‐latitude coasts of the English Channel of France. In March 2009, we gathered rock spalling observations at Mesnil Val, NW France, to document the effect of frost on platform lowering in macro‐tidal environments. Six epochs of frost were recorded in 2 months, the two longest lasted 16 and 8 days, with minimum air temperature dropping to –9.5°C. Semi‐diurnal tides flood the entire platform, imposing up to 25 freeze–thaw cycles below –2.5°C, the freezing temperature of seawater. 19 cycles occurred at neap tidal elevation lasting at most 3.5 h. Our integrated observations indicate that these frost cycles were responsible for a platform lowering of about 0.8±0.5 mm during a single winter. No clear spatial trend appears, nor do macroscopic chalk types clearly stand out as being more susceptible to erosion. Assuming that the long‐term platform retreat model preserves a constant slope, frost shattering would then account for 10 to 20% of the expected annual platform erosion rate. Under more contrasted climates, frost is thus likely to be a prominent shaping process for rocky coastal platforms. Copyright © 2015 John Wiley & Sons, Ltd.
Assessing the transport of total phosphorus from a prairie river basin using SPARROW
Authors: Morales‐Marín Luis , Wheater Howard , Lindenschmidt Karl‐Erich
Published: May 2015

Recent changes in land use and new industrial developments in river basins around the world have raised serious concerns regarding future water quality. Assessment of regional nutrient export from river basins are needed in order to identify main nutrient sources and hydrological variables involved. The Red Deer River catchment in Alberta, Canada has been chosen as a test case to assess total phosphorus export regionally. Agricultural and livestock activities in the catchment have increased manure production and the supply of fertilizer to crops. Oil and gas exploitation has also increased the risk of surface water and groundwater contamination. The rapid population growth has not only lead to increases in water consumption and wastewater discharges but also to further construction of transportation infrastructure and the expansion of new urban developments. This has imposed hydraulic controls on waterways, affecting the catchment hydrology and changing the dynamics of sediment and nutrient transport. River ecosystems are not exempt from the negative effects of water quality deterioration. Downstream from the city of Red Deer, the physiology and reproduction habits of native fish species have changed because of high riverine productivity. Although improvements have been made to surface water quality standards by Alberta Environment, further research is needed in order to identify major nutrient sources and quantify nutrient export. The SPAtially Referenced Regression On Watershed model has therefore been used in this study of the Red Deer River catchment to assess regional water quality, in order to describe the spatial and temporal patterns of the processes that affect water quality. The model is suitable for interpreting monitoring data sets that suffer from network sparseness, bias and basin heterogeneity. Ultimately, the model could provide improved information to environmental agencies to guide future water quality management practices and policies. Copyright © 2015 John Wiley & Sons, Ltd.
Multidimensional persistence in biomolecular data
Authors: Xia Kelin , Wei Guo‐Wei
Published: May 2015

Persistent homology has emerged as a popular technique for the topological simplification of big data, including biomolecular data. Multidimensional persistence bears considerable promise to bridge the gap between geometry and topology. However, its practical and robust construction has been a challenge. We introduce two families of multidimensional persistence, namely pseudomultidimensional persistence and multiscale multidimensional persistence. The former is generated via the repeated applications of persistent homology filtration to high‐dimensional data, such as results from molecular dynamics or partial differential equations. The latter is constructed via isotropic and anisotropic scales that create new simiplicial complexes and associated topological spaces. The utility, robustness, and efficiency of the proposed topological methods are demonstrated via protein folding, protein flexibility analysis, the topological denoising of cryoelectron microscopy data, and the scale dependence of nanoparticles. Topological transition between partial folded and unfolded proteins has been observed in multidimensional persistence. The separation between noise topological signatures and molecular topological fingerprints is achieved by the Laplace–Beltrami flow. The multiscale multidimensional persistent homology reveals relative local features in Betti‐0 invariants and the relatively global characteristics of Betti‐1 and Betti‐2 invariants. © 2015 Wiley Periodicals, Inc.
Error‐Prone Repair of DNA Double‐Strand Breaks
Authors: Rodgers Kasey , McVey Mitch
Published: May 2015

Preserving the integrity of the DNA double helix is crucial for the maintenance of genomic stability. Therefore, DNA double‐strand breaks represent a serious threat to cells. In this review, we describe the two major strategies used to repair double strand breaks: non‐homologous end joining and homologous recombination, emphasizing the mutagenic aspects of each. We focus on emerging evidence that homologous recombination, long thought to be an error‐free repair process, can in fact be highly mutagenic, particularly in contexts requiring large amounts of DNA synthesis. Recent investigations have begun to illuminate the molecular mechanisms by which error‐prone double‐strand break repair can create major genomic changes, such as translocations and complex chromosome rearrangements. We highlight these studies and discuss proposed models that may explain some of the more extreme genetic changes observed in human cancers and congenital disorders. J. Cell. Physiol. 230: 15–24, 2016. © 2015 Wiley Periodicals, Inc.
Cell‐penetrating and endoplasmic reticulum‐locating TAT‐IL‐24‐KDEL fusion protein induces tumor apoptosis
Authors: Zhang Jian , Sun Aiyou , Xu Rui , Tao Xinyi , Dong Yuguo , Lv Xinxin , Wei Dongzhi
Published: May 2015

Interleukin‐24 (IL‐24) is a unique IL‐10 family cytokine that could selectively induce apoptosis in cancer cells without harming normal cells. Previous research demonstrated that intracellular IL‐24 protein induces an endoplasmic reticulum (ER) stress response only in cancer cells, culminating in apoptosis. In this study, we developed a novel recombinant fusion protein to penetrate into cancer cells and locate on ER. It is composed of three distinct functional domains, IL‐24, and the targeting domain of transactivator of transcription (TAT) and an ER retention four‐peptide sequence KDEL (Lys‐Asp‐Glu‐Leu) that link at its NH2 and COOH terminal, respectively. The in vitro results indicated that TAT‐IL‐24‐KDEL inhibited growth in bladder cancer cells, as well as in non‐small cell lung cancer cell line and breast cancer cell line, but the normal human lung fibroblast cell line was not affected, indicating the cancer specificity of TAT‐IL‐24‐KDEL. Western blot analysis showed that apoptosis activation was induced by TAT‐IL‐24‐KDEL through the ER stress‐mediated cell death pathway. Treatment with TAT‐IL‐24‐KDEL significantly inhibited the growth of human H460 xenografts in nude mice, and the tumor growth inhibition was correlated with increased hematoxylin and eosin (H&E) staining and terminal deoxynucleotidyl transferase‐mediated dUTP nick end labeling (TUNEL) staining. These findings suggest that the artificially designed recombinant fusion protein TAT‐IL‐24‐KDEL may be highly effective in cancer therapy and worthy of further evaluation and development. J. Cell. Physiol. 230: 84–93, 2016. © 2015 Wiley Periodicals, Inc.
Endotoxin‐stimulated Rat Hepatic Stellate Cells Induce Autophagy in Hepatocytes as a Survival Mechanism
Authors: Dangi Anil , Huang Chao , Tandon Ashish , Stolz Donna , Wu Tong , Gandhi Chandrashekhar R.
Published: May 2015

Bacterial lipopolysaccharide (LPS)‐stimulated hepatic stellate cells (HSCs) produce many cytokines including IFNβ, TNFα, and IL6, strongly inhibit DNA synthesis, but induce apoptosis of a small number of hepatocytes. In vivo administration of LPS (up to 10 mg/mL) causes modest inflammation and weight loss in rats but not mortality. We determined whether LPS‐stimulated HSCs instigate mechanisms of hepatocyte survival. Rats received 10 mg/kg LPS (i.p.) and determinations were made at 6 h. In vitro, HSCs were treated with 100 ng/mL LPS till 24 h. The medium was transferred to hepatocytes, and determinations were made at 0–12 h. Controls were HSC‐conditioned medium or medium‐containing LPS. LPS treatment of rats caused autophagy in hepatocytes, a physiological process for clearance of undesirable material including injured or damaged organelles. This was accompanied by activation of c‐Jun NH2 terminal kinase (JNK) and apoptosis of ∼4–5% of hepatocytes. In vitro, LPS‐conditioned HSC medium (LPS/HSC) induced autophagy in hepatocytes but apoptosis of only ∼10% of hepatocytes. While LPS/HSC stimulated activation of JNK (associated with cell death), it also activated NFkB and ERK1/2 (associated with cell survival). LPS‐stimulated HSCs produced IFNβ, and LPS/HSC‐induced autophagy in hepatocytes and their apoptosis were significantly inhibited by anti‐IFNβ antibody. Blockade of autophagy, on the other hand, strongly augmented hepatocyte apoptosis. While LPS‐stimulated HSCs cause apoptosis of a subpopulation of hepatocytes by producing IFNβ, they also induce cell survival mechanisms, which may be of critical importance in resistance to liver injury during endotoxemia. J. Cell. Physiol. 230: 94–105, 2016. © 2015 Wiley Periodicals, Inc.