bluuebunny/crossref_metadata_2025 huggingface dataset:
Peptide Inhibitors of the amyloidogenesis of IAPP: verification of the hairpin‐binding geometry hypothesis
Authors: Sivanesam Kalkena , Shu Irene , Huggins Kelly N. L. , Tatarek‐Nossol Marianna , Kapurniotu Aphrodite , Andersen Niels H.
Published: June 2016

Versions of a previously discovered β‐hairpin peptide inhibitor of IAPP aggregation that are stabilized in that conformation, or even forced to remain in the hairpin conformation by a backbone cyclization constraint, display superior activity as inhibitors. The cyclized hairpin, cyclo‐WW2, displays inhibitory activity at substoichiometric concentrations relative to this amyloidogenic peptide. The hairpin‐binding hypothesis stands confirmed.
Depletion of autophagy receptor p62/SQSTM1 enhances the efficiency of gene delivery in mammalian cells
Authors: Tsuchiya Megumi , Ogawa Hidesato , Koujin Takako , Kobayashi Shouhei , Mori Chie , Hiraoka Yasushi , Haraguchi Tokuko
Published: June 2016

Novel methods that increase the efficiency of gene delivery to cells will have many useful applications. Here, we report a simple approach involving depletion of p62/SQSTM1 to enhance the efficiency of gene delivery. The efficiency of reporter gene delivery was remarkably higher in p62‐knockout murine embryonic fibroblast (MEF) cells compared with normal MEF cells. This higher efficiency was partially attenuated by ectopic expression of p62. Furthermore, siRNA‐mediated knockdown of p62 clearly increased the efficiency of transfection of murine embryonic stem (mES) cells and human HeLa cells. These data indicate that p62 acts as a key regulator of gene delivery.
Simultaneous and common‐volume lidar observations of K/Na layers and temperature at Arecibo Observatory (18°N, 67°W)
Authors: Yue Xianchang , Zhou Qihou , Yi Fan , Friedman Jonathan , Raizada Shikha , Tepley Craig
Published: June 2016

We present the first simultaneous and common‐volume observations of mesospheric K and Na densities and temperature conducted by a K Doppler lidar and a Na lidar at the Arecibo Observatory (18.35°N, 66.75°W), Puerto Rico. Measurements reported here were conducted on three nights with 9, 6, and 7 h of observations in December 2003 and January 2004. The behaviors of the Na and K layer and the temperature variations showed that the bottom edges of the Na and K layers matched one another almost exactly. Layer peak and column densities increased/decreased together with temperature for the Na layer, but not for the K layer. The correlation between temperature and density fluctuations was strongly positive at and just below the peak altitude of the nightly mean density profile but transitioned to negative several kilometers above the respective peak of either Na or K. The peak densities of the sporadic Na and K layers occurring at low altitudes did not behave in the same manner especially when the background temperature decreased. We discuss, qualitatively, the impact of dynamical and chemical effects on the behaviors of the Na and K layers. Our analysis suggests that wave‐induced dynamical transport can account for the observed correlations between temperature, Na density, and K density fluctuations. Dynamical transport and wave‐induced chemical transport have similar effects on the behaviors of the Na and K layers. The resulting differences in Na and K layers are qualitatively consistent with different dependences on temperature of the Na and K chemistries.
On the electrostatic field created at ground level by a halo
Authors: Pérez‐Invernón F. J. , Gordillo‐Vázquez F. J. , Luque A.
Published: June 2016

We investigate the effect of halo activity on the electrostatic field measured at ground level. We use electrostatic arguments as well as self‐consistent simulations to show that, due to the screening charge in the ionosphere, the distant electrostatic field created by the uncompensated charge in a thundercloud decays exponentially rather than as the third power of the distance. Furthermore, significative ionization around the lower edge of the ionosphere slightly reduces the electrostatic field at ground level. We conclude that halos do not extend the range of detectability of lightning‐induced electrostatic fields.
Slow shock and rotational discontinuity in MHD and Hall MHD models with anisotropic pressure
Authors: Hau L.‐N. , Wang B.‐J.
Published: June 2016

Pressure anisotropy may modify the characteristics of magnetohydrodynamic (MHD) waves, in particular, the slow mode wave and the corresponding shocks and discontinuities. In this study the formation of slow shocks (SSs) in anisotropic plasmas is examined by solving the gyrotropic MHD and Hall MHD equations numerically for one‐dimensional Riemann problem. The MHD shocks and discontinuities are generated by imposing a finite normal magnetic field on the Harris type current sheet with a guide magnetic By component. It is shown that anomalous SSs moving faster than the intermediate wave or with positive density‐magnetic field correlation may be generated in gyrotropic MHD and Hall MHD models. Moreover, for some parameter values SSs may exhibit upstream wave trains with right‐handed polarization in contrast with the earlier prediction that SSs shall possess downstream left‐hand polarized wave trains based on the isotropic Hall MHD theory. For the cases of By ≠ 0, SSs with increased density and decreased magnetic field followed by noncoplanar intermediate mode or rotational discontinuity (RD)‐like structures similar to the compound SS‐RD structures observed in space plasma environments may possibly form in symmetric and asymmetric current layers. The Walén relation of these anomalous RDs without the correction of pressure anisotropy may significantly be violated.
Subsidence rates at the southern Salton Sea consistent with reservoir depletion
Authors: Barbour Andrew J. , Evans Eileen L. , Hickman Stephen H. , Eneva Mariana
Published: June 2016

Space geodetic measurements from the Envisat satellite between 2003 and 2010 show that subsidence rates near the southeastern shoreline of the Salton Sea in Southern California are up to 52mmyr−1greater than the far‐field background rate. By comparing these measurements with model predictions, we find that this subsidence appears to be dominated by poroelastic contraction associated with ongoing geothermal fluid production, rather than the purely fault‐related subsidence proposed previously. Using a simple point source model, we suggest that the source of this proposed volumetric strain is at depths between 1.0 km and 2.4 km (95% confidence interval), comparable to generalized boundaries of the Salton Sea geothermal reservoir. We find that fault slip on two previously imaged tectonic structures, which are part of a larger system of faults in the Brawley Seismic Zone, is not an adequate predictor of surface velocity fields because the magnitudes of the best fitting slip rates are often greater than the full plate boundary rate and at least 2 times greater than characteristic sedimentation rates in this region. Large‐scale residual velocity anomalies indicate that spatial patterns predicted by fault slip are incompatible with the observations.
Identification of dominant source of errors in developing streamflow and groundwater projections under near‐term climate change
Authors: Seo S. B. , Sinha T. , Mahinthakumar G. , Sankarasubramanian A. , Kumar M.
Published: June 2016

Uncertainties in projecting the changes in hydroclimatic variables (i.e., temperature and precipitation) under climate change partly arises from the inability of global circulation models (GCMs) in explaining the observed changes in hydrologic variables. Apart from the unexplained changes by GCMs, the process of customizing GCM projections to watershed scale through a model chain—spatial downscaling, temporal disaggregation, and hydrologic model—also introduces errors, thereby limiting the ability to explain the observed changes in hydrologic variability. Toward this, we first propose metrics for quantifying the errors arising from different steps in the model chain in explaining the observed changes in hydrologic variables (streamflow and groundwater). The proposed metrics are then evaluated using a detailed retrospective analyses in projecting the changes in streamflow and groundwater attributes in four target basins that span across a diverse hydroclimatic regimes over the U.S. Sunbelt. Our analyses focused on quantifying the dominant sources of errors in projecting the changes in eight hydrologic variables—mean and variability of seasonal streamflow, mean and variability of 3 day peak seasonal streamflow, mean and variability of 7 day low seasonal streamflow, and mean and standard deviation of groundwater depth—over four target basins using an Penn state Integrated Hydrologic Model (PIHM) between the period 1956–1980 and 1981–2005. Retrospective analyses show that small/humid (large/arid) basins show increased (reduced) uncertainty in projecting the changes in hydrologic attributes. Further, changes in error due to GCMs primarily account for the unexplained changes in mean and variability of seasonal streamflow. On the other hand, the changes in error due to temporal disaggregation and hydrologic model account for the inability to explain the observed changes in mean and variability of seasonal extremes. Thus, the proposed metrics provide insights on how the error in explaining the observed changes being propagated through the model under different hydroclimatic regimes.
Probing ionospheric structures using the LOFAR radio telescope
Authors: Mevius M. , van der Tol S. , Pandey V. N. , Vedantham H. K. , Brentjens M. A. , de Bruyn A. G. , Abdalla F. B. , Asad K. M. B. , Bregman J. D. , Brouw W. N. , Bus S. , Chapman E. , Ciardi B. , Fernandez E. R. , Ghosh A. , Harker G. , Iliev I. T. , Jelić V. , Kazemi S. , Koopmans L. V. E. , Noordam J. E. , Offringa A. R. , Patil A. H. , van Weeren R. J. , Wijnholds S. , Yatawatta S. , Zaroubi S.
Published: June 2016

LOFAR is the LOw‐Frequency Radio interferometer ARray located at midlatitude (52°53′N). Here we present results on ionospheric structures derived from 29 LOFAR nighttime observations during the winters of 2012/2013 and 2013/2014. We show that LOFAR is able to determine differential ionospheric total electron content values with an accuracy better than 0.001 total electron content unit = 1016m−2 over distances ranging between 1 and 100 km. For all observations the power law behavior of the phase structure function is confirmed over a long range of baseline lengths, between 1 and 80 km, with a slope that is, in general, larger than the 5/3 expected for pure Kolmogorov turbulence. The measured average slope is 1.89 with a one standard deviation spread of 0.1. The diffractive scale, i.e., the length scale where the phase variance is 1rad2, is shown to be an easily obtained single number that represents the ionospheric quality of a radio interferometric observation. A small diffractive scale is equivalent to high phase variability over the field of view as well as a short time coherence of the signal, which limits calibration and imaging quality. For the studied observations the diffractive scales at 150 MHz vary between 3.5 and 30 km. A diffractive scale above 5 km, pertinent to about 90% of the observations, is considered sufficient for the high dynamic range imaging needed for the LOFAR epoch of reionization project. For most nights the ionospheric irregularities were anisotropic, with the structures being aligned with the Earth magnetic field in about 60% of the observations.
Physical mixtures as simple and efficient alternative to alloy carriers in chemical looping processes
Authors: More Amey , Veser Götz
Published: June 2016

Chemical looping combustion is a clean combustion technology for fossil or renewable fuels. In a previous demonstration, chemical looping was applied to CO2 activation via reduction to CO with concurrent production of synthesis gas (CO + H2) from CH4 via rationally designed Fe‐Ni alloys. Here, it is demonstrated that that a simple physical mixture can even outperform the equivalent alloy based on an intricate gas phase mediated coupling between the two metals: Ni cracks methane to carbon and H2. The latter then reduces iron oxide carrier, forming steam, which gasifies the carbon deposits on Ni to produce a mixture of CO + H2, thus regenerating the active Ni surface. It was suggested that the principle demonstrated here—the gas phase‐mediated coupling of two solid reactants with distinct functionalities—should be applicable broadly toward oxidation reactions and hence opens a new avenue for rational design of chemical looping processes. © 2016 American Institute of Chemical Engineers AIChE J, 63: 51–59, 2017
Cohesive grains: Bridging microlevel measurements to macrolevel flow behavior via surface roughness
Authors: Liu Peiyuan , LaMarche Casey Q. , Kellogg Kevin M. , Leadley Stuart , Hrenya Christine M.
Published: June 2016

Significance Understanding fine‐particle flows relies on van der Waals cohesion modeling, requiring a method to consider measured surface roughness. A robust scheme to extract roughness parameters from AFM surface maps, achieving accurate predictions of microscale measured cohesion is proposed. Macroscale quantitative agreement is demonstrated by comparing defluidization predictions to measurements, which are sensitive to cohesion and system‐size independent. Agreement in both microscale and macroscale comparisons highlights the role of individual particle properties on bulk granular systems. © 2016 American Institute of Chemical Engineers AIChE J, 62: 3529–3537, 2016
Kinetic study of hydrogen peroxide decomposition at high temperatures and concentrations in two capillary microreactors
Authors: Shang Minjing , Noël Timothy , Su Yuanhai , Hessel Volker
Published: June 2016

On the background of the direct adipic acid synthesis from cyclohexene and H2O2, a kinetic model was derived for the H2O2 decomposition catalyzed by sodium tungstate at high H2O2 concentrations and high temperatures. A perfluoroalkoxy (PFA) and a stainless steel micro‐flow capillary match commonly used microreactor materials. In the PFA capillary, the decomposition of hydrogen peroxide increased with residence time, reaction temperature and catalyst loading. The reaction order with respect to hydrogen peroxide and sodium tungstate was zero and one, respectively. Simulated data fit well with experimental data in the PFA capillary. While showing a similar trend as that in the PFA capillary, the stainless steel capillary exhibited much higher reaction rates. The steel surface participated in the decomposition process as a heterogeneous catalyst. Key influencing factors of the H2O2 decomposition provided some clues on the reaction mechanism of the adipic acid synthesis and its process optimization. © 2016 American Institute of Chemical Engineers AIChE J, 63: 689–697, 2017
Cellulose acetate ultrafiltration membranes reinforced by cellulose nanocrystals: Preparation and characterization
Authors: Zhou Jianjun , Chen Jin , He Ming , Yao Jianfeng
Published: June 2016

Cellulose nanocrystals (CNCs) were used as a sustainable additive to improve the hydrophilicity, permeability, antifouling, and mechanical properties of blend membranes. Different CNC loadings (0–1.2 wt %) in cellulose acetate (CA) membranes were studied. The blend membranes were prepared by a phase‐inversion process, and their chemical structure and morphological properties were characterized by attenuated total reflectance–Fourier transform infrared spectroscopy, scanning electron microscopy, porosity, and mean pore size and contact angle measurement. The blend membranes became more porous and more interconnected after the addition of CNCs. The thickness of the top layer decreased and a few large holes in the porous substrate appeared with increasing CNC loading. In comparison with the pure CA membranes, the pure water flux of the blend membranes increased with increasing CNC loading. It reaches a maximum value of 76 L m−2 h−1 when the CNC loading was 0.5 wt %. The antifouling properties of the CA membrane were significantly improved after the addition of CNCs, and the flux recovery ratio value increased to 68% with the addition of 0.5 wt % CNCs. In comparison with that of the pure CA membranes, the tensile strength of the composite membranes increased by 47%. This study demonstrated the importance of using sustainable CNCs to achieve great improvements in the physical and chemical performance of CA ultrafiltration membranes and provided an efficient method for preparing high‐performance membranes. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 43946.
Facile UV‐curing technique to establish a 3D‐grafted poly(ethylene glycol) layer on an epoxy resin base for underwater applications
Authors: Yang Yang , Luo Huali , Yang Jinlong , Huang Daofen , Zhou Shuxue
Published: June 2016

Construction of a highly hydrophilic polymer surface with excellent long‐term stability underwater is a great challenge. In this paper, a facile ultraviolet (UV) curing technique was employed to realize the three‐dimensional (3D) grafting of poly(ethylene glycol) diacrylate (PEGDA, molecular weight: 400, 600, and 1000 g/mol) on a bisphenol A epoxy acrylate (BEA) sheet. The cross section morphology, surface chemical composition, and wettability of the sheets were monitored using an optical microscope, an attenuated total reflectance Fourier transform infrared spectroscope, and a water contact angle analyzer, respectively. The PEGDA‐grafted epoxy sheets displayed a highly hydrophilic surface and meanwhile possessed excellent stability underwater, despite the molecular weight of PEGDA. In contrast, the PEGDA/BEA blend sheets are easily damaged underwater, due to strong swelling. In addition, the PEGDA1000‐grafted BEA sheet demonstrated good antifouling performance in a natural marine environment. Nevertheless, its long‐term antifouling is not satisfactory, being presumably due to hydrolysis or biodegradation of the PEG segments. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 43972.
Covalent integration of differently structured polyester polyols improves the toughness and strength of cationically polymerized, amorphous epoxy networks
Authors: Arnebold Andre , Wellmann Stefanie , Hartwig Andreas
Published: June 2016

The structure–property relationship of polyester polyols in cationically polymerized, amorphous epoxy‐based copolymers is investigated. An epoxy resin is polymerized in the presence of structurally different polyesters. These resulting copolymers show improved tensile strength and toughness. The optimal epoxide/polyester ratio depends on the structure of the polyesters. Poly(δ‐valerolactone) (PVL) reveals the highest ester group density of the investigated polyesters, which enhances physical interactions with the epoxide during polymerization as well as in the network. Furthermore, PVL leads to outstanding tensile strength, strain at break, and toughness. Among all polyester polyols examined, PVL leads to the highest gel fraction or, in other words, the most complete integration into the epoxy network. This work shows that polyesters that are present in the reactive system should be covalently integrated into the polymer network as completely as possible to obtain good mechanical properties of the amorphous copolymer. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 43986.
Ancillary contributions of heterologous biotin protein ligase and carbonic anhydrase for CO2 incorporation into 3‐hydroxypropionate by metabolically engineered Pyrococcus furiosus
Authors: Lian Hong , Zeldes Benjamin M. , Lipscomb Gina L. , Hawkins Aaron B. , Han Yejun , Loder Andrew J. , Nishiyama Declan , Adams Michael W.W. , Kelly Robert M.
Published: June 2016

Acetyl‐Coenzyme A carboxylase (ACC), malonyl‐CoA reductase (MCR), and malonic semialdehyde reductase (MRS) convert HCO3− and acetyl‐CoA into 3‐hydroxypropionate (3HP) in the 3‐hydroxypropionate/4‐hydroxybutyrate carbon fixation cycle resident in the extremely thermoacidophilic archaeon Metallosphaera sedula. These three enzymes, when introduced into the hyperthermophilic archaeon Pyrococcus furiosus, enable production of 3HP from maltose and CO2. Sub‐optimal function of ACC was hypothesized to be limiting for production of 3HP, so accessory enzymes carbonic anhydrase (CA) and biotin protein ligase (BPL) from M. sedula were produced recombinantly in Escherichia coli to assess their function. P. furiosus lacks a native, functional CA, while the M. sedula CA (Msed_0390) has a specific activity comparable to other microbial versions of this enzyme. M. sedula BPL (Msed_2010) was shown to biotinylate the β‐subunit (biotin carboxyl carrier protein) of the ACC in vitro. Since the native BPLs in E. coli and P. furiosus may not adequately biotinylate the M. sedula ACC, the carboxylase was produced in P. furiosus by co‐expression with the M. sedula BPL. The baseline production strain, containing only the ACC, MCR, and MSR, grown in a CO2‐sparged bioreactor reached titers of approximately 40 mg/L 3HP. Strains in which either the CA or BPL accessory enzyme from M. sedula was added to the pathway resulted in improved titers, 120 or 370 mg/L, respectively. The addition of both M. sedula CA and BPL, however, yielded intermediate titers of 3HP (240 mg/L), indicating that the effects of CA and BPL on the engineered 3HP pathway were not additive, possible reasons for which are discussed. While further efforts to improve 3HP production by regulating gene dosage, improving carbon flux and optimizing bioreactor operation are needed, these results illustrate the ancillary benefits of accessory enzymes for incorporating CO2 into 3HP production in metabolically engineered P. furiosus, and hint at the important role that CA and BPL likely play in the native 3HP/4HB pathway in M. sedula. Biotechnol. Bioeng. 2016;113: 2652–2660. © 2016 Wiley Periodicals, Inc.
Production of citramalate by metabolically engineered Escherichia coli
Authors: Wu Xianghao , Eiteman Mark A.
Published: June 2016

Citramalic acid (citramalate) is a five carbon hydroxy‐dicarboxylic acid and potential precursor for the production of methacrylic acid from renewable resources. We examined citramalate production in Escherichia coli expressing the citramalate synthase gene cimA. Although, knockouts in ldhA coding lactate dehydrogenase and glcB/aceB coding malate synthase did not benefit citramalate accumulation, knockouts in gltA coding citrate synthase, and ackA coding acetate kinase significantly increased citramalate accumulation compared to the control strain. A fed‐batch process in a controlled fermenter using a glucose feed resulted in 46.5 g/L citramalate in 132 h with a yield of 0.63 g/g, over 75% of the theoretical maximum yield from glucose of 0.82 g/g. Biotechnol. Bioeng. 2016;113: 2670–2675. © 2016 Wiley Periodicals, Inc.
Molecular basis of substrate recognition and specificity revealed in family 12 glycoside hydrolases
Authors: Calzado Felipe , Prates Erica T. , Gonçalves Thiago A. , Rubio Marcelo V. , Zubieta Mariane P. , Squina Fabio M. , Skaf Munir S. , Damásio André R.L.
Published: June 2016

Fungal GH12 enzymes are classified as xyloglucanases when they specifically target xyloglucans, or promiscuous endoglucanases when they exhibit catalytic activity against xyloglucan and β‐glucan chains. Several structural and functional studies involving GH12 enzymes tried to explain the main patterns of xyloglucan activity, but what really determines xyloglucanase specificity remains elusive. Here, three fungal GH12 enzymes from Aspergillus clavatus (AclaXegA), A. zonatus (AspzoGH12), and A. terreus (AtEglD) were studied to unveil the molecular basis for substrate specificity. Using functional assays, site‐directed mutagenesis, and molecular dynamics simulations, we demonstrated that three main regions are responsible for substrate selectivity: (i) the YSG group in loop 1; (ii) the SST group in loop 2; and (iii) loop A3‐B3 and neighboring residues. Functional assays and sequence alignment showed that while AclaXegA is specific to xyloglucan, AtEglD cleaves β‐glucan, and xyloglucan. However, AspzoGH12 was also shown to be promiscuous contrarily to a sequence alignment‐based prediction. We find that residues Y111 and R93 in AtEglD harbor the substrate in an adequate orientation for hydrolysis in the catalytic cleft entrance and that residues Y19 in AclaXegA and Y30 in AspzoGH12 partially compensate the absence of the YSG segment, typically found in promiscuous enzymes. The results point out the multiple structural factors underlying the substrate specificity of GH12 enzymes. Biotechnol. Bioeng. 2016;113: 2577–2586. © 2016 Wiley Periodicals, Inc.
Investigating strain dependency in the production of aromatic compounds in Saccharomyces cerevisiae
Authors: Suástegui Miguel , Guo Weihua , Feng Xueyang , Shao Zengyi
Published: June 2016

Although Saccharomyces cerevisiae is the most highly domesticated yeast, strain dependency in biotechnological processes still remains as a common, yet poorly understood phenomenon. To investigate this, the entrance to the aromatic amino acid biosynthetic pathway was compared in four commonly used S. cerevisiae laboratory strains. The strains were engineered to accumulate shikimate by overexpressing a mutant version of the pentafunctional ARO1 enzyme with disrupted activity in the shikimate kinase subunit. Carbon tracing and 13C metabolic flux analysis combined with quantitative PCR, revealed that precursor availability and shikimate production were dramatically different in the four equally engineered strains, which were found to be correlated with the strains’ capacity to deal with protein overexpression burden. By implementing a strain‐dependent approach, the genetic platform was reformulated, leading to an increase in yield and titer in all strains. The highest producing strain, INVSc1‐SA3, produced 358 mg L−1 of shikimate with a yield of 17.9 mg g−1glucose. These results underline the importance of strain selection in developing biological manufacturing processes, demonstrate the first case of high production of shikimate in yeast, and provide an appropriate platform for strain selection for future production of aromatic compounds. Biotechnol. Bioeng. 2016;113: 2676–2685. © 2016 Wiley Periodicals, Inc.
A comparison between data requirements and availability for calibrating predictive ecological models for lowland UK woodlands: learning new tricks from old trees
Authors: Evans Matthew R. , Moustakas Aristides
Published: June 2016

Woodlands provide valuable ecosystem services, and it is important to understand their dynamics. To predict the way in which these might change, we need process‐based predictive ecological models, but these are necessarily very data intensive. We tested the ability of existing datasets to provide the parameters necessary to instantiate a well‐used forest model (SORTIE) for a well‐studied woodland (Wytham Woods). Only five of SORTIE's 16 equations describing different aspects of the life history and behavior of individual trees could be parameterized without additional data collection. One age class – seedlings – was completely missed as they are shorter than the height at which Diameter at Breast Height (DBH) is measured. The mensuration of trees has changed little in the last 400 years (focussing almost exclusively on DBH) despite major changes in the nature of the source of value obtained from trees over this time. This results in there being insufficient data to parameterize process‐based models in order to meet the societal demand for ecological prediction. We do not advocate ceasing the measurement of DBH, but we do recommend that those concerned with tree mensuration consider whether additional measures of trees could be added to their data collection protocols. We also see advantages in integrating techniques such as ground‐based LIDAR or remote sensing techniques with long‐term datasets to both preserve continuity with what has been performed in the past and to expand the range of measurements made.
Shifts in leaf litter breakdown along a forest–pasture–urban gradient in Andean streams
Authors: Iñiguez‐Armijos Carlos , Rausche Sirkka , Cueva Augusta , Sánchez‐Rodríguez Aminael , Espinosa Carlos , Breuer Lutz
Published: June 2016

Tropical montane ecosystems of the Andes are critically threatened by a rapid land‐use change which can potentially affect stream variables, aquatic communities, and ecosystem processes such as leaf litter breakdown. However, these effects have not been sufficiently investigated in the Andean region and at high altitude locations in general. Here, we studied the influence of land use (forest–pasture–urban) on stream physico‐chemical variables (e.g., water temperature, nutrient concentration, and pH), aquatic communities (macroinvertebrates and aquatic fungi) and leaf litter breakdown rates in Andean streams (southern Ecuador), and how variation in those stream physico‐chemical variables affect macroinvertebrates and fungi related to leaf litter breakdown. We found that pH, water temperature, and nutrient concentration increased along the land‐use gradient. Macroinvertebrate communities were significantly different between land uses. Shredder richness and abundance were lower in pasture than forest sites and totally absent in urban sites, and fungal richness and biomass were higher in forest sites than in pasture and urban sites. Leaf litter breakdown rates became slower as riparian land use changed from natural to anthropogenically disturbed conditions and were largely determined by pH, water temperature, phosphate concentration, fungal activity, and single species of leaf‐shredding invertebrates. Our findings provide evidence that leaf litter breakdown in Andean streams is sensitive to riparian land‐use change, with urban streams being the most affected. In addition, this study highlights the role of fungal biomass and shredder species (Phylloicus; Trichoptera and Anchytarsus; Coleoptera) on leaf litter breakdown in Andean streams and the contribution of aquatic fungi in supporting this ecosystem process when shredders are absent or present low abundance in streams affected by urbanization. Finally, we summarize important implications in terms of managing of native vegetation and riparian buffers to promote ecological integrity and functioning of tropical Andean stream ecosystems.
Antioxidant effect of leaf extracts from Cressa cretica against oxidation process in soybean oil
Authors: Afshari Afsaneh , Sayyed‐Alangi S. Zahra
Published: June 2016

Phenolic compounds from Cressa cretica leaves were extracted using different solvents (water and ethanol 70%) during 3–24 h by immersion method and were determined according to the Folin–Ciocalteu method. The antioxidant activities of the extracts were investigated by 1,1‐diphenyl‐2‐picryl hydrazyl (DPPH) radical scavenging, ferric reduction activity potential and total antioxidant capacity assays compared with synthetic antioxidant namely BHT. The results were shown that the most total phenol content was outcome of the ethanolic extract after 18 h (68.512 ± 0.36 mg gallic acid/g dry extract) extraction. The results of different assays for determination of antioxidant potential of the extracts as well as their EC50 values were indicated antioxidant activities in order: BHT>ethanolic extract>aqueous extract. Also, the antioxidant activities were enhanced with increasing of the extracts and BHT concentrations. The results of Peroxide value (PV) and Thiobarbituric acid (TBA) tests were revealed that the ethanolic extract with various concentrations (200–1000 ppm) were suppressed the oxidation of soybean oil. The highest oxidation inhibitor was belonged to 1000 ppm concentration of the ethanolic extract so that can be good alternative for BHT.
BioActivities of Coturnix japonica (quail) egg yolk and albumen against physiological stress
Authors: Oladipo Gideon O. , Ibukun Emmanuel O.
Published: June 2016

Cold and immobilization stressors can generate oxidative stress as well as skeletal muscle fatigue. Free radicals cause oxidative degradation of lipids, proteins, nucleic acids, and carbohydrates molecules thereby compromising cell integrity and function. Coturnix japonica (quail) egg had been described as being very functional biochemically, due to the essential biomolecules it contains in very regulated quantity. This study was designed to evaluate the in vitro antioxidant activity of extracts of quail egg yolk and the albumen. The assessment of the antioxidant potentials was typified using the total antioxidant capacity, and ABTS, DPPH (1‐diphenyl‐2‐picrylhydrazyl) and hydroxyl radicals scavenging activities. Others are reducing power, metal chelating and lipid peroxidation inhibition activities. The antistress activities of quail egg yolk and albumen were evaluated on hepatopathic enzymes as well as endogenous antioxidant enzymes. The total antioxidant activities of the yolk extract (YE) and the albumen extracts (AE) were, respectively, 186.57 ± 6.441 mg/g and 172 ± 10.690 mg/g AAE (Ascorbic Acid Equivalent). The YE exhibited significant, potent and appreciable antioxidant activities than AE in a concentration‐dependent manner. The study confirmed that quail egg yolk contained highly antioxidative bioactive compounds not present in albumen, contributing to its (yolk) overall antioxidant and anti‐inflammatory (antistress) properties, thus necessitating their (albumen and yolk) beneficial effects in the management of oxidative and inflammatory conditions.
Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST
Authors: Ramsey Steven , Nguyen Crystal , Salomon‐Ferrer Romelia , Walker Ross C. , Gilson Michael K. , Kurtzman Tom
Published: June 2016

The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on surfaces, we have incorporated Grid Inhomogeneous Solvation Theory (GIST) into the CPPTRAJ toolset of AmberTools. GIST is a grid‐based implementation of Inhomogeneous Fluid Solvation Theory, which analyzes the output from molecular dynamics simulations to map out solvation thermodynamic and structural properties on a high‐resolution, three‐dimensional grid. The CPPTRAJ implementation, called GIST‐cpptraj, has a simple, easy‐to‐use command line interface, and is open source and freely distributed. We have also developed a set of open‐source tools, called GISTPP, which facilitate the analysis of GIST output grids. Tutorials for both GIST‐cpptraj and GISTPP can be found at ambermd.org. © 2016 Wiley Periodicals, Inc.
Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide‐and‐conquer, density‐functional tight‐binding, and massively parallel computation
Authors: Nishizawa Hiroaki , Nishimura Yoshifumi , Kobayashi Masato , Irle Stephan , Nakai Hiromi
Published: June 2016

The linear‐scaling divide‐and‐conquer (DC) quantum chemical methodology is applied to the density‐functional tight‐binding (DFTB) theory to develop a massively parallel program that achieves on‐the‐fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC‐DFTB potential energy surface are implemented to the program called DC‐DFTB‐K. A novel interpolation‐based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC‐DFTB‐K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC‐DFTB‐K program, a single‐point energy gradient calculation of a one‐million‐atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc.
Associations between brain white matter integrity and disease severity in obstructive sleep apnea
Authors: Tummala Sudhakar , Roy Bhaswati , Park Bumhee , Kang Daniel W. , Woo Mary A. , Harper Ronald M. , Kumar Rajesh
Published: June 2016

Obstructive sleep apnea (OSA) is characterized by recurrent upper airway blockage, with continued diaphragmatic efforts to breathe during sleep. Brain structural changes in OSA appear in various regions, including white matter sites that mediate autonomic, mood, cognitive, and respiratory control. However, the relationships between brain white matter changes and disease severity in OSA are unclear. This study examines associations between an index of tissue integrity, magnetization transfer (MT) ratio values (which show MT between free and proton pools associated with tissue membranes and macromolecules), and disease severity (apnea‐hypopnea index [AHI]) in OSA subjects. We collected whole‐brain MT imaging data from 19 newly diagnosed, treatment‐naïve OSA subjects (50.4 ± 8.6 years of age, 13 males, AHI 39.7 ± 24.3 events/hr], using a 3.0‐Tesla MRI scanner. With these data, whole‐brain MT ratio maps were calculated, normalized to common space, smoothed, and correlated with AHI scores by using partial correlation analyses (covariates, age and gender;P< 0.005). Multiple brain sites in OSA subjects, including superior and inferior frontal regions, ventral medial prefrontal cortex and nearby white matter, midfrontal white matter, insula, cingulate and cingulum bundle, internal and external capsules, caudate nuclei and putamen, basal forebrain, hypothalamus, corpus callosum, and temporal regions, showed principally lateralized negative correlations (P< 0.005). These regions showed significant correlations even with correction for multiple comparisons (cluster‐level, family‐wise error,P< 0.05), except for a few superior frontal areas. Predominantly negative correlations emerged between local MT values and OSA disease severity, indicating potential usefulness of MT imaging for examining the OSA condition. These findings indicate that OSA severity plays a significant role in white matter injury. © 2016 Wiley Periodicals, Inc.
Leptin suppresses adenosine triphosphate‐induced impairment of spinal cord astrocytes
Authors: Li Baoman , Qi Shuang , Sun Guangfeng , Yang Li , Han Jidong , Zhu Yue , Xia Maosheng
Published: June 2016

Spinal cord injury (SCI) causes long‐term disability and has no clinically effective treatment. After SCI, adenosine triphosphate (ATP) may be released from neuronal cells and astrocytes in large amounts. Our previous studies have shown that the extracellular release of ATP increases the phosphorylation of cytosolic phospholipase A2 (cPLA2) and triggers the rapid release of arachidonic acid (AA) and prostaglandin E2 (PGE2) via the stimulation of epidermal growth factor receptor (EGFR) and the downstream phosphorylation of extracellular‐regulated protein kinases 1 and 2. Leptin, a glycoprotein, induces the activation of the Janus kinase (JAK2)/signal transducers and activators of transcription‐3 (Stat3) pathway via the leptin receptor. In this study, we found that 1) prolonged leptin treatment suppressed the ATP‐stimulated release of AA and PGE2 from cultured spinal cord astrocytes; 2) leptin elevated the expression of caveolin‐1 (Cav‐1) via the JAK2/Stat3 signaling pathway; 3) Cav‐1 blocked the interaction between Src and EGFR, thereby inhibiting the phosphorylation of EGFR and cPLA2 and attenuating the release of AA or PGE2; 4) pretreatment with leptin decreased ;he level of apoptosis and the release of interleukin‐6 from cocultured neurons and astrocytes; and 5) leptin improved the recovery of locomotion in mice after SCI. Our results highlight leptin as a promising therapeutic agent for SCI. © 2016 Wiley Periodicals, Inc.
Excess River Sedimentation at Bridges in the Raya Graben (Northern Ethiopia)
Authors: Demissie Biadgilgn , Billi Paolo , Frankl Amaury , Haile Mitiku , Nyssen Jan
Published: June 2016

This study investigates the temporal variability and effects of bio‐climatic factors and bridges on local hydro‐geomorphic conditions that cause excess sedimentation and flood hazard in ephemeral rivers of the Raya graben (northern Ethiopia). Normalized difference vegetation index (NDVI) was analyzed using Landsat imageries of 1972, 1986, 2000, 2005, 2010, and 2014. Daily rainfall data of three meteorological stations were considered to analyze the temporal trends and return time intervals of rainfall intensity in 24 h. Stream‐bed gradient and bed material grain size were measured in 20 river reaches. Results show that the maximum NDVI values were recorded in the time interval from 2000 to 2014. Nevertheless, during this decade, the study bridges experienced the largest excess sedimentation, in some bridges up to 1·6 m. Different factors to account for it are discussed as no evidence of rainfall pattern, accountable for an increase in sediment delivery from the headwaters, is found. The field data show that channel narrowing at bridges is the main cause of thick upstream sedimentation and of increasing frequency of overbank flows during the last 15 years. A simple hydraulic approach is presented to explain the variability of sediment deposition at bridges and change in bed material grain size between the main stem and the reach right upstream of the bridge. Copyright © 2016 John Wiley & Sons, Ltd.
Resting and Reemergent Tongue Tremor as Presenting Symptoms of Parkinson's Disease
Authors: Fabbri Margherita , Abreu Luis , Santos Telma , Ferreira Joaquim J.
Published: June 2016

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FOXJ2 controls meiosis during spermatogenesis in male mice
Authors: Miao Hui , Miao Cong‐Xiu , Li Na , Han Jing
Published: June 2016

Spermatogenesis is a highly complex cell differentiation process necessary for production of haploid spermatozoa. Central to this unique process is spermatocyte meiosis. FOXJ2 (Forkhead box J2), a FOX transcription factor, is specifically expressed in meiotic spermatocytes in adult mouse testes, so we used a germ cell specific conditional knockout model (Foxj2flox/flox, Mvh‐Cre) to explore its role in spermatogenesis. Loss of FOXJ2 in the male germ line led to meiotic arrest and complete infertility. Although, DNA double‐strand breaks (DSBs) were initiated, Foxj2‐deficient spermatocytes failed to form chromosomal synapses and perform DSB repair. Furthermore, Foxj2‐deficient spermatocytes contained significantly less mRNA encoding DSB repair‐associated factors (Rad18, Rad51, Brca1, Brca2, and Tex15) and meiotic arrest‐related proteins (Fzr1, Hsp70‐2, Spata22, Eif4g3, and Zpac); in contrast, no change was observed in the expression of spermatogonia markers (Gfra1, Zbtb16, and c‐Kit) and germ cell markers (Dazl, Mvh, and Tra98). Taken together, FOXJ2 appears to promote meiotic progression in male mice by a mechanism that needs further investigation. Mol. Reprod. Dev. 83: 684–691, 2016 © 2016 Wiley Periodicals, Inc.
Ante Mortem Cranial Trepanation in the Late Bronze Age in Western Siberia
Authors: Slepchenko S. M. , Vybornov A. V. , Slavinsky V. S. , Tsybankov A. A. , Matveev V. E.
Published: June 2016

We report a case study of cranial trepanation in a male subject 30 to 40 years of age from the Nefteprovod II burial ground in the Anzhevsk archeological site. This burial dates back to the Late Bronze Age, in particular the Karasuk culture located in the Minusinsk Basin on the Yenisei River and on the upper reaches of the Ob River. The left parietal bone had an opening with evident signs of bone healing, as well as signs of inflammatory reaction from both bone plates of the calvarium. The strongest signs of inflammation were located around the trepanation opening at the exocranium, suggesting that it occurred after, rather than before, the operation.

Although trepanation was the main cause for the development of the changes noted in the preceding texts, there are no reasons to believe that the subject died from complications arising from infection after trepanation. The patient survived and later died for reasons that may never be determined. Medical necessity was the most likely justification for trepanation. Immersion in altered states of consciousness may also have been a necessary part of the trepanation process as a mode of sedation, along with other shamanic practices, such as consumption of psychotropic substances or ecstatic dance. These data, together with reports of other ante mortem burials, raised questions about the application of anaesthesia and possible techniques of cranial trepanation. These issues and possible postoperative complications are discussed in the following text. Copyright © 2016 John Wiley & Sons, Ltd.
Synthesis of novel tri‐benzoxazine and effect of phenolic nucleophiles on its ring‐opening polymerization
Authors: Nalakathu Kolanadiyil Sini , Azechi Motohisa , Endo Takeshi
Published: June 2016

A trifunctional benzoxazine, 1,3,5‐tris(3‐phenyl‐3,4‐dihydro‐2H‐benzo[1,3]oxazin‐6‐yl)benzene (T‐Bz) was synthesized and in an effort to reduce its curing temperature (curing maxima at 238 °C), it was mixed with various phenolic nucleophiles such as phenol (PH), p‐methoxy phenol (MPH), 2‐methyl resorcinol (MR), hydroquinone (HQ), pyrogallol (PG), 2‐naphthol (NPH), 2,7‐dihydroxy naphthalene (DHN), and 1,1'‐bi‐2‐naphthol (BINOL). The influence of these phenolic nucleophiles on ring‐opening polymerization temperature of T‐Bz was examined by DSC and FTIR analysis. T‐Bz undergoes a complete ring‐opening addition reaction in the presence of bi‐ and trifunctional phenolic nucleophiles (MR/HQ/PG/DHN) at 140 °C (heated for 3 h) and forms a networked polybenzoxazine (NPBz). The NPBzs showed a high thermal stability with Td20 of 350–465 °C and char yield of 67–78% at 500 °C; however, a diminutive weight loss (6.9–9.8%) was observed at 150–250 °C (Td5: 215–235 °C) due to degradation of phenolic end groups. This article also gives an insight on how the traces of phenolic impurities can alter the thermal properties of pure benzoxazine monomer as well as its corresponding polymer. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 2811–2819
Preparation of ureido group bearing polymers and their upper critical solution temperature in water
Authors: Fujihara Ami , Itsuki Kohei , Shimada Naohiko , Maruyama Atsushi , Sagawa Naoya , Shikata Toshiyuki , Yusa Shin‐Ichi
Published: June 2016

Poly(2‐ureidoethylmethacrylate) (PUEMn) was synthesized via reversible addition‐fragmentation chain transfer (RAFT) radical polymerization and following polymer reaction. We prepared two PUEMn samples with different degrees of polymerization (n = 100 and 49). The polymers exhibited upper critical solution temperature (UCST) in phosphate‐buffered saline (PBS) solution. The phase separation temperature (Tp) in PBS can be controlled ranging from 17 to 55 °C by changing molecular weight of the polymer, polymer concentration, and adding NaCl concentration. The polymers in PBS formed coacervate drops by liquid–liquid phase separations below Tp. Results of the dielectric relaxation measurement, the hydration number per monomeric unit was 5 above Tp. Based on a fluorescence study, the polymer formed slightly hydrophobic environments below Tp. The liquid–liquid phase separation was occurred presumably because of weak hydrophobic interactions and intermolecularly hydrogen bonding interactions between the pendant ureido groups. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 2845–2854
One‐pot, solvent‐free, metal‐free synthesis and UCST‐based purification of poly(ethylene oxide)/poly‐ε‐caprolactone block copolymers
Authors: Ianiro Alessandro , Jiménez‐Pardo Isabel , Esteves A. Catarina C. , Tuinier Remco
Published: June 2016

A fast, one pot, solvent‐free and metal‐free synthesis of poly‐ε‐caprolactone and poly(ethylene oxide) block copolymers is reported. Copolymers with different molar mass, different hydrophilic to lipophilic balance, high degree of conversion and narrow molar mass dispersity have been obtained by organocatalyzed ring opening polymerization of ε‐caprolactone in presence of mono‐ or diol‐poly(ethylene oxide) as initiator and fumaric acid as catalyst. A new biocompatible and environmental friendly purification method is presented, exploiting the upper critical solution temperature of these class of copolymers in ethanol. The phase diagrams of the synthesized copolymers in ethanol are also reported. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem.2016,54, 2992–2999