bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection and reconstruction of large‐scale coherent flow structures in gravel‐bed rivers
Authors: Franca Mário J. , Lemmin Ulrich
Published: July 2014

Large‐scale flow structures (LSFS) in the streamwise direction are important features of gravel‐bed river flows, because they may contribute to sediment transport and gas exchange. In the present study, these structures are detected using Huang's empirical mode decomposition and reconstructed with phase‐averaging techniques based on a Hilbert transform of the velocity signal. The analysis is based on the fluctuating component of 15 quasi‐instantaneous velocity profiles measured with a three‐dimensional (3D) acoustic Doppler velocity profiler (ADVP) in an armoured gravel‐bed river with a low relative submergence of 2.9 (ratio between flow depth and bed grain diameter). LSFS were identified in most of the measured profiles and consistently showed similar features. We were able to characterize the geometry of these large‐scale coherent structures: the front has a vertical linear shift in the time domain and a vertical profile corresponding to a first quarter moon with the apex situated at z/h ≈ 0.4. In the vertical, the front scales with flow depth h, and in the streamwise direction, LSFS scale with three to seven times the mean flow depth. On the bed, the effect of LSFS is a periodic non‐linear variation of the friction velocity on average between 0.90 and 1.10 times the mean value. A model for the friction velocity cycle resulting from LSFS oscillation is presented. Copyright © 2014 John Wiley & Sons, Ltd.
The effect of El Niño Southern Oscillation cycles on the decadal scale suspended sediment behavior of a coastal dry‐summer subtropical catchment
Authors: Gray Andrew B. , Pasternack Gregory B. , Watson Elizabeth B. , Warrick Jonathan A. , Goñi Miguel A.
Published: July 2014

Rivers display temporal dependence in suspended sediment–water discharge relationships. Although most work has focused on multi‐decadal trends, river sediment behavior often displays sub‐decadal scale fluctuations that have received little attention. The objectives of this study were to identify inter‐annual to decadal scale fluctuations in the suspended sediment–discharge relationship of a dry‐summer subtropical river, infer the mechanisms behind these fluctuations, and examine the role of El Niño Southern Oscillation climate cycles. The Salinas River (California) is a moderate sized (11 000 km2), coastal dry‐summer subtropical catchment with a mean discharge (Qmean) of 11.6 m3 s−1. This watershed is located at the northern most extent of the Pacific coastal North America region that experiences increased storm frequency during El Niño years. Event to inter‐annual scale suspended sediment behavior in this system was known to be influenced by antecedent hydrologic conditions, whereby previous hydrologic activity regulates the suspended sediment concentration–water discharge relationship. Fine and sand suspended sediment in the lower Salinas River exhibited persistent, decadal scale periods of positive and negative discharge corrected concentrations. The decadal scale variability in suspended sediment behavior was influenced by inter‐annual to decadal scale fluctuations in hydrologic characteristics, including: elapsed time since small (~0.1 × Qmean), and moderate (~10 × Qmean) threshold discharge values, the number of preceding days that low/no flow occurred, and annual water yield. El Niño climatic activity was found to have little effect on decadal‐scale fluctuations in the fine suspended sediment–discharge relationship due to low or no effect on the frequency of moderate to low discharge magnitudes, annual precipitation, and water yield. However, sand concentrations generally increased in El Niño years due to the increased frequency of moderate to high magnitude discharge events, which generally increase sand supply. Copyright © 2014 John Wiley & Sons, Ltd.
Effects of single and multiple applications of glyphosate or aminopyralid on simple constructed plant communities
Authors: Pfleeger Thomas , Blakeley-Smith Matthew , Lee E. Henry , King George , Plocher Milton , Olszyk David
Published: July 2014

To determine effects of multiple applications of herbicides on small constructed plant communities, Prunella vulgaris L.var. lanceolata Fern, Festuca roemeri (Pavlick) Alexeev, Clarkia amoena (Lehm.) Nels., and Cynosurus echinatus L. were grown together in small field plots. Plants were treated with glyphosate at target concentrations of 0 × , 0.01 × , 0.1 × , and 0.2× a field application rate (FAR) of 1122 g ha−1 active ingredient (a.i.) for 3 yr in 1 location, and for 2 yr in a second location. Plants also were treated with aminopyralid at 0 × , 0.037 × , 0.136 × , and 0.5× FAR of 123 g ha−1 a.i. for 2 yr in 2 locations. Plants received 1, 2, or 3 applications of each herbicide each year. Species and community responses depended on herbicide concentration and number of applications. With glyphosate, plant volume (modified formula for a cone) tended to decrease for all species (especially C. echinatus), and the decreases generally became larger with more applications. Plant communities exposed to the 2 greatest concentrations initially differed from controls but then appeared to recover. With aminopyralid, C. amoena was essentially eliminated from the communities, especially at the 2 greatest FARs, whereas the other 3 species tended to have significant increases in volume, especially at the 2 smallest FARs. With aminopyralid, increasing numbers of applications produced variable results, and the plant community volume never tended to recover. Environ Toxicol Chem 2014;33:2368–2378. Published 2014 Wiley Periodicals Inc., on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America.
Methylated phenanthrenes are more potent than phenanthrene in a bioassay of human aryl hydrocarbon receptor (AhR) signaling
Authors: Sun Yue , Miller Charles A. , Wiese Thomas E. , Blake Diane A.
Published: July 2014

Alkylated polycyclic aromatic hydrocarbons (APAHs) are abundant in petroleum, but data regarding their toxicological properties are limited. A survey of all monomethylated phenanthrene structures revealed that they were 2 times to 5 times more potent than phenanthrene for activation of human aryl hydrocarbon receptor in a yeast bioassay. Phenanthrenes with equatorial methyl groups had the greatest potency. The greater potency of the methylated phenanthrenes highlights the need for more toxicological data on APAHs. Environ Toxicol Chem 2014;33:2363–2367. © 2014 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.
Lead toxicity to Lemna minor predicted using a metal speciation chemistry approach
Authors: Antunes Paula M.C. , Kreager Nancy J.
Published: July 2014

In the present study, predictive measures for Pb toxicity and Lemna minor were developed from bioassays with 7 surface waters having varied chemistries (0.5–12.5 mg/L dissolved organic carbon, pH of 5.4–8.3, and water hardness of 8–266 mg/L CaCO3). As expected based on water quality, 10%, 20%, and 50% inhibitory concentration (IC10, IC20, and IC50, respectively) values expressed as percent net root elongation (%NRE) varied widely (e.g., IC20s ranging from 306 nM to >6920 nM total dissolved Pb), with unbounded values limited by Pb solubility. In considering chemical speciation, %NRE variability was better explained when both Pb hydroxides and the free lead ion were defined as bioavailable (i.e., f{OH}) and colloidal Fe(III)(OH)3 precipitates were permitted to form and sorb metals (using FeOx as the binding phase). Although cause and effect could not be established because of covariance with alkalinity (p = 0.08), water hardness correlated strongly (r2 = 0.998, p < 0.0001) with the concentration of total Pb in true solution ([Pb]T_True solution). Using these correlations as the basis for predictions (i.e., [Pb]T_True solution vs water hardness and %NRE vs f{OH}), IC20 and IC50 values produced were within a factor of 2.9 times and 2.2 times those measured, respectively. The results provide much needed effect data for L. minor and highlight the importance of chemical speciation in Pb-based risk assessments for aquatic macrophytes. Environ Toxicol Chem 2014;33:2225–2233. © 2014 SETAC
Hydrological footprints of urban developments in the Lake Simcoe watershed, Canada: a combined paired‐catchment and change detection modelling approach
Authors: Oni Stephen K. , Futter Martyn N. , Buttle James , Dillon Peter J.
Published: July 2014

Urban sprawl and regional climate variability are major stresses on surface water resources in many places. The Lake Simcoe watershed (LSW) Ontario, Canada, is no exception. The LSW is predominantly agricultural but is experiencing rapid population growth because of its proximity to the Greater Toronto area. This has led to extensive land use changes that have impacted its water resources and altered run‐off patterns in some rivers draining to the lake. Here, we use a paired‐catchment approach, hydrological change detection modelling and remote sensing analysis of satellite images to evaluate the impacts of land use change on the hydrology of the LSW (1994 to 2008). Results show that urbanization increased up to 16% in Lovers Creek, the most urban‐impacted catchment. Annual run‐off from Lovers Creek increased from 239 to 442 mm/year in contrast to the reference catchment (Black River at Washago) where run‐off was relatively stable with an annual mean of 474 mm/year. Increased annual run‐off from Lovers Creek was not accompanied by an increase in annual precipitation. Discriminant function analysis suggests that early (1992–1997; pre‐major development) and late (2004–2009; fully urbanized) periods for Lovers Creek separated mainly based on model parameter sets related to run‐off flashiness and evapotranspiration. As a result, parameterization in either period cannot be used interchangeably to produce credible run‐off simulations in Lovers Creek because of greater scatter between the parameters in canonical space. Separation of early and late‐period parameter sets for the reference catchment was based on climate and snowmelt‐related processes. This suggests that regional climatic variability could be influencing hydrologic change in the reference catchment, whereas urbanization amplified the regional natural hydrologic changes in urbanizing catchments of the LSW. Copyright © 2014 John Wiley & Sons, Ltd.
Osteogenic Cell Cultures Cannot Utilize Exogenous Sources of Synthetic Polyphosphate for Mineralization
Authors: Ariganello Marianne B. , Omelon Sidney , Variola Fabio , Wazen Rima M. , Moffatt Pierre , Nanci Antonio
Published: July 2014

Phosphate is critical for mineralization and deficiencies in the regulation of free phosphate lead to disease. Inorganic polyphosphates (polyPs) may represent a physiological source of phosphate because they can be hydrolyzed by biological phosphatases. To investigate whether exogenous polyP could be utilized for mineral formation, mineralization was evaluated in two osteogenic cell lines, Saos‐2 and MC3T3, expressing different levels of tissue non‐specific alkaline phosphatase (tnALP). The role of tnALP was further explored by lentiviral‐mediated overexpression in MC3T3 cells. When cells were cultured in the presence of three different phosphate sources, there was a strong mineralization response with β‐glycerophosphate (βGP) and orthophosphate (Pi) but none of the cultures sustained mineralization in the presence of polyP (neither chain length 17‐Pi nor 42‐Pi). Even in the presence of mineralizing levels of phosphate, low concentrations of polyP (50 μM) were sufficient to inhibit mineral formation. Energy‐dispersive X‐ray spectroscopy confirmed the presence of apatite‐like mineral deposits in MC3T3 cultures supplemented with βGP, but not in those with polyP. While von Kossa staining was consistent with the presence or absence of mineral, an unusual Alizarin staining was obtained in polyP‐treated MC3T3 cultures. This staining pattern combined with low Ca:P ratios suggests the persistence of Ca‐polyP complexes, even with high residual ALP activity. In conclusion, under standard culture conditions, exogenous polyP does not promote mineral deposition. This is not due to a lack of active ALP, and unless conditions that favor significant processing of polyP are achieved, its mineral inhibitory capacity predominates. J. Cell. Biochem. 115: 2089–2102, 2014. © 2014 Wiley Periodicals, Inc.
Contrast‐enhanced endoscopic ultrasonography can predict a higher malignant potential of gastrointestinal stromal tumors by visualizing large newly formed vessels
Authors: Yamashita Yasunobu , Kato Jun , Ueda Kazuki , Nakamura Yasushi , Abe Hiroko , Tamura Takashi , Itonaga Masahiro , Yoshida Takeichi , Maeda Hiroki , Moribata Kosaku , Niwa Toru , Maekita Takao , Iguchi Mikitaka , Tamai Hideyuki , Ichinose Masao
Published: July 2014

Background

The aim of this study was to elucidate the histologic and clinical implications of detection of intratumoral vessels on contrast‐enhanced endoscopic ultrasonography (CE‐EUS) in gastrointestinal stromal tumors (GISTs).

Methods

Thirteen patients with a GIST, all of whom were referred for surgery, underwent presurgical CE‐EUS. The malignant potential, assessed according to the modified Fletcher risk classification system, and the histologic degree of angiogenesis were compared with the presence or absence of intratumoral vessels on CE‐EUS.

Results

Of the six tumors with intratumoral vessels observed on CE‐EUS, five were intermediate‐ or high‐risk GISTs, and the remaining seven negative cases were categorized as very low risk or low risk. The presence of intratumoral vessels on CE‐EUS was significantly correlated with a higher‐risk classification (p = 0.005). On histologic examination, all GISTs having visualized vessels incorporated vessels of more than 500 μm in diameter. The large intratumoral vessels of the five intermediate‐ or high‐risk GISTs lacked elastic fibers, suggesting that they were neovascular in nature. These higher‐risk tumors were also found, by immunohistochemical analysis, to have high expression of vascular endothelial growth factor.

Conclusions

Intratumoral vessels observed in GISTs on CE‐EUS are correlated with a higher degree of angiogenesis, resulting in higher malignant potential. © 2014 Wiley Periodicals, Inc. J Clin Ultrasound, 43:89–97, 2015
In vivo monitoring of intracellular chloroplast movements in intact leaves of c4 plants using two‐photon microscopy
Authors: Ryu Jeongeun , Nam Hyoseok , Kim Hae Koo , Joo Yongjoon , Lee Sang Joon , Kim Ki Hean
Published: July 2014

Dynamic changes in the spatial distribution of chloroplasts are essential for optimizing photosynthetic capacity under changing light conditions. Light‐induced movement of chloroplasts has been widely investigated, but most studies were conducted on isolated tissues or protoplasts. In this study, a two‐photon microscopy (TPM) system was adapted to monitor the intracellular 3‐dimensional (3D) movements of chloroplasts in intact leaves of plants during dark to light transitions. The TPM imaging was based on autofluorescence of chlorophyll generated by a femto‐second Ti:Sapphire laser. All chloroplasts did not exhibit the same motion in response to irradiation variation. In the sub‐epidermal mesophyll cells, chloroplasts generally moved away from the surface following blue light treatment, however many chloroplasts did not show any movement. Such spatial heterogeneity in chloroplast motility underlines the importance of monitoring intracellular orientation and movement of individual chloroplasts across intact leaves. Our investigation shows that the 3D imaging of chloroplasts using TPM can help to understand the changes in local photosynthetic capacity in intact leaves under changing environmental conditions. Microsc. Res. Tech. 77:806–813, 2014. © 2014 Wiley Periodicals, Inc.
Current approaches in evolution: From molecules to cells and organisms
Authors: Thattai Mukund , Peisajovich Sergio G.
Published: July 2014

This is an exciting time to be an evolutionary biologist. Indeed, it is difficult to keep up with all the studies that fall under the broad category of “Evolution” since they span species, traits, and scales of organization. This special issue gives a flavor of exciting new approaches in evolutionary biology, but also emphasizes universal themes. The reviews contained here discuss important aspects of molecular evolution at multiple scales, from individual proteins to complex regulatory networks, as well as from unicellular organisms to macroscopic traits in animals. Though the model systems are diverse, the issues addressed are fundamental: the origin of evolutionary novelties, and the forces that drive them to fixation. J. Exp. Zool. (Mol. Dev. Evol.) 322B: 465–467, 2014. © 2014 Wiley Periodicals, Inc.
Sensitivity of soil moisture initialization for decadal predictions under different regional climatic conditions in Europe
Authors: Khodayar S. , Sehlinger A. , Feldmann H. , Kottmeier Ch.
Published: July 2014

The impact of soil initialization is investigated through perturbation simulations with the regional climate model Consortium for Small‐scale Modelling (COSMO) and the Climate Limited‐area Modelling (COSMO–CLM). The focus of the investigation is to assess the sensitivity of simulated extreme periods, dry and wet, to soil moisture initialization in different climatic regions over Europe and to establish the necessary spin‐up time within the framework of decadal predictions for these regions. Sensitivity experiments consisted of a reference simulation from 1968 to 1999 and five simulations from 1972 to 1983. The Effective Drought Index (EDI) is used to select and quantify drought status in the reference run to establish the simulation time period for the sensitivity experiments. Different soil initialization procedures are investigated. The sensitivity of the decadal predictions to soil moisture initial conditions is investigated through the analysis of water cycle components' (WCC) variability. In an episodic timescale, the local effects of soil moisture on the boundary layer and the propagated effects on the large‐scale dynamics are analysed. The results show: (1) COSMO–CLM reproduces the observed features of the drought index. (2) Soil moisture initialization exerts a relevant impact on WCC, e.g. precipitation distribution and intensity. (3) Regional characteristics strongly impact the response of the WCC. Precipitation and evapotranspiration deviations are larger for humid regions. (4) The initial soil conditions (wet/dry), the regional characteristics (humid/dry) and the annual period (wet/dry) play a key role in the time that soil needs to restore quasi‐equilibrium and the impact on the atmospheric conditions. Humid areas, and for all regions, a humid initialization, exhibit shorter spin‐up times, also soil reacts more sensitive when initialized during dry periods. (5) The initial soil perturbation may markedly modify atmospheric pressure field, wind circulation systems and atmospheric water vapour distribution affecting atmospheric stability conditions, thus modifying precipitation intensity and distribution even several years after the initialization.
Neonatal medical exposures and characteristics of low birth weight hepatoblastoma cases: A report from the Children's Oncology Group
Authors: Turcotte Lucie M. , Georgieff Michael K. , Ross Julie A. , Feusner James H. , Tomlinson Gail E. , Malogolowkin Marcio H. , Krailo Mark D. , Miller Nicole , Fonstad Rachel , Spector Logan G.
Published: July 2014

Background

Hepatoblastoma is a malignancy of young children. Low birth weight is associated with significantly increased risk of hepatoblastoma and neonatal medical exposures are hypothesized as contributors. This study represents the largest case–control study of hepatoblastoma to date and aimed to define the role of neonatal exposures in hepatoblastoma risk among low birth weight children.

Procedure

Incident hepatoblastoma cases who were born <2,500 g (N = 60), diagnosed between 2000 and 2008, were identified through the Children's Oncology Group. Controls were recruited through state birth registries (N = 51). Neonatal medical exposures were abstracted from medical records. Subjects from the Vermont Oxford Network were used for further comparisons, as were existing reports on neonatal medical exposures.

Results

Case–control comparisons were hindered by poor matching within birth weight strata. Cases were smaller and received more aggressive neonatal treatment compared to controls, and reflected high correlation levels between birth weight and treatments. Similar difficulty was encountered when comparing cases to Vermont Oxford Network subjects; cases were smaller and required more aggressive neonatal therapy. Furthermore, it appears hepatoblastoma cases were exposed to a greater number of diagnostic X‐rays than in case series previously reported in the neonatal literature.

Conclusions

This study presents the largest case series of hepatoblastoma in <2,500 g birth weight infants with accompanying neonatal medical exposure data. Findings confirm that birth weight is highly correlated with exposure intensity, and neonatal exposures are themselves highly correlated, which hampers the identification of a causal exposure among hepatoblastoma cases. Experimental models or genetic susceptibility testing may be more revealing of etiology. Pediatr Blood Cancer 2014;61:2018–2023. © 2014 Wiley Periodicals, Inc.
Managing Structural and Dynamic Complexity: A Tale of Two Projects
Authors: Brady Tim , Davies Andrew
Published: July 2014

Previous research suggests complexity may be a significant factor in a project's failure to achieve cost, time, and quality objectives. In this paper, we examine the project complexity literature to develop a simple framework consisting of structural and dynamic complexity. We use this to compare the complexity of two successful construction megaprojects–-Heathrow Terminal 5 and the London 2012 Olympic Park–-to consider how the complexity in the two projects was managed. Our analysis reveals differences in the approach to managing structural and dynamic complexity, but identifies common factors that may help project managers achieve positive outcomes for their complex projects.
Synthesis and characterization of double hydrophilic block copolymers containing semi‐rigid and flexible segments
Authors: Savage Alice M. , Ullrich Elizabeth , Chin Stacey M. , Kiernan Zachary , Kost Caitlyn , Turner S. Richard
Published: July 2014

3‐Methyl‐(E)‐stilbene (3MSti) and 4‐(diethylamino)‐(E)‐stilbene (DEASti) monomers are synthesized and polymerized separately with maleic anhydride (MAn) in a strictly alternating fashion using reversible addition‐fragmentation chain transfer (RAFT) polymerization techniques. The optimal RAFT chain transfer agents (CTAs) for each copolymerization affect the reaction kinetics and CTA compatibilities. Psuedo‐first order polymerization kinetics are demonstrated for the synthesis of poly((3‐methyl‐(E)‐stilbene)‐alt‐maleic anhydride) (3MSti‐alt‐MAn) with a thiocarbonylthio CTA (methyl 2‐(dodecylthiocarbonothioylthio)−2‐methylpropionate, TTCMe). In contrast, a dithioester CTA (cumyl dithiobenzoate, CDB) controls the synthesis of poly((4‐(diethylamino)‐(E)‐stilbene)‐alt‐maleic anhydride) (DEASti‐alt‐MAn) with pseudo‐first order polymerization kinetics. DEASti‐alt‐MAn is chain extended with 4‐acryloylmorpholine (ACMO) to synthesize diblock copolymers and subsequently converted to a double hydrophilic polyampholyte block copolymers (poly((4‐(diethylamino)‐(E)‐stilbene)‐alt‐maleic acid))‐b‐acryloylmorpholine) (DEASti‐alt‐MA)‐b‐ACMO) via acid hydrolysis. The isoelectric point and dissociation behavior of these maleic acid‐containing copolymers are determined using ζ‐potential and acid–base titrations, respectively. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015, 53, 219–227
From reactor to rheology in industrial polymers
Authors: Read Daniel J.
Published: July 2014

This article reviews current efforts towards quantitative prediction of rheological properties of industrial polymer resins, based upon their polydisperse branched molecular structure. This involves both an understanding of how reactor and reaction conditions influence the distribution of chain lengths and branch placement (which is the province of reactor engineering) and an understanding of how the molecular structures in turn give rise to the rheology (the province of polymer physics). Both fields are reviewed at an introductory level, focussing in particular on developments in theoretical prediction of rheology for both entangled model polymers and industrial polymers. Finally, we discuss three classes of reaction for which the fields of reactor engineering and polymer physics have been truly combined to produce predictions from reactor to rheology. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys.2015,53, 123–141
Symptoms of posttraumatic stress in Australian women with ovarian cancer
Authors: Shand Lyndel K. , Brooker Joanne E. , Burney Sue , Fletcher Jane , Ricciardelli Lina A.
Published: July 2014

Objective

The aim of the study was to assess the prevalence and nature of symptoms of posttraumatic stress disorder (PTSD) in women with ovarian cancer. A further aim was to examine the demographic, medical and psychosocial factors associated with PTSD symptoms.

Method

One hundred and eight women with ovarian cancer were assessed for PTSD, quality of life, depression, anxiety, posttraumatic growth, optimism, coping and social support.

Results

Clinically significant symptoms were experienced by 9.25% of participants for PTSD, 5.6% for depression and 13.9% for anxiety. Poorer quality of life was associated with total PTSD symptoms, and avoidance and intrusive symptoms. Depression was associated with avoidance and intrusive symptoms. Anxiety was associated with total, avoidance, intrusive and hyperarousal symptoms. Finally, coping by substance use/self‐blame was associated with total, avoidance and hyperarousal PTSD symptoms.

Conclusions

Levels of PTSD in women with ovarian cancer were equivalent to that of the general population. Poorer quality of life, depression, anxiety and maladaptive coping, characterised by avoidance, substance use and self‐blame, were associated with increased symptoms of PTSD. Copyright © 2014 John Wiley & Sons, Ltd.
Double trouble—Buffer selection and His‐tag presence may be responsible for nonreproducibility of biomedical experiments
Authors: Majorek Karolina A. , Kuhn Misty L. , Chruszcz Maksymilian , Anderson Wayne F. , Minor Wladek
Published: July 2014

The availability of purified and active protein is the starting point for the majority of in vitro biomedical, biochemical, and drug discovery experiments. The use of polyhistidine affinity tags has resulted in great increases of the efficiency of the protein purification process, but can negatively affect structure and/or activity measurements. Similarly, buffer molecules may perturb the conformational stability of a protein or its activity. During the determination of the structure of a Gcn5‐related N‐acetyltransferase (GNAT) from Pseudomonas aeruginosa (PA4794), we found that both HEPES and the polyhistidine affinity tag bind (separately) in the substrate‐binding site. In the case of HEPES, the molecule induces conformational changes in the active site, but does not significantly affect enzyme activity. In contrast, the uncleaved His‐tag does not induce major conformational changes but acts as a weak competitive inhibitor of peptide substrate. In two other GNAT enzymes, we observed that the presence of the His‐tag had a strong influence on the activity of these proteins. The influence of protein preparation on functional studies may affect the reproducibility of experiments in other laboratories, even when changes between protocols seem at first glance to be insignificant. Moreover, the results presented here show how critical it is to adjust the experimental conditions for each protein or family of proteins, and investigate the influence of these factors on protein activity and structure, as they may significantly alter the effectiveness of functional characterization and screening methods. Thus, we show that a polyhistidine tag and the buffer molecule HEPES bind in the substrate‐binding site and influence the conformation of the active site and the activity of GNAT acetyltransferases. We believe that such discrepancies can influence the reproducibility of some experiments and therefore could have a significant “ripple effect” on subsequent studies.
Dopamine‐induced α‐synuclein oligomers show self‐ and cross‐propagation properties
Authors: Planchard Matthew S. , Exley Sarah E. , Morgan Sarah E. , Rangachari Vijayaraghavan
Published: July 2014

Amyloid aggregates of α‐synuclein (αS) protein are the predominant species present within the intracellular inclusions called Lewy bodies in Parkinson's disease (PD) patients. Among various aggregates, the low‐molecular weight ones broadly ranging between 2 and 30 mers are known to be the primary neurotoxic agents responsible for the impairment of neuronal function. Recent research has indicated that the neurotransmitter dopamine (DA) is one of the key physiological agents promoting and augmenting αS aggregation, which is thought to be a significant event in PD pathologenesis. Specifically, DA is known to induce the formation of soluble oligomers of αS, which in turn are responsible for inducing several important cellular changes leading to cellular toxicity. In this report, we present the generation, isolation, and biophysical characterization of five different dopamine‐derived αS oligomers (DSOs) ranging between 3 and 15 mers, corroborating previously published reports. More importantly, we establish that these DSOs are also capable of replication by self‐propagation, which leads to the replication of DSOs upon interaction with αS monomers, a process similar to that observed in mammilian prions. In addition, DSOs are also able to cross‐propagate amyloid‐β (Aβ) aggregates involved in Alzheimer's disease (AD). Interestingly, while self‐propagation of DSOs occur with no net gain in protein structure, cross‐propagation proceeds with an overall gain in β‐sheet conformation. These results implicate the involvement of DSOs in the progression of PD, and, in part, provide a molecular basis for the observed co‐existence of AD‐like pathology among PD patients.
Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake
Authors: Kumar Abhinav , Punta Marco , Axelrod Herbert L. , Das Debanu , Farr Carol L. , Grant Joanna C. , Chiu Hsiu‐Ju , Miller Mitchell D. , Coggill Penelope C. , Klock Heath E. , Elsliger Marc‐André , Deacon Ashley M. , Godzik Adam , Lesley Scott A. , Wilson Ian A.
Published: July 2014

Crystal structures of three members (BACOVA_00364 from Bacteroides ovatus, BACUNI_03039 from Bacteroides uniformis and BACEGG_00036 from Bacteroides eggerthii) of the Pfam domain of unknown function (DUF4488) were determined to 1.95, 1.66, and 1.81 Å resolutions, respectively. The protein structures adopt an eight‐stranded, calycin‐like, β‐barrel fold and bind an endogenous unknown ligand at one end of the β‐barrel. The amino acids interacting with the ligand are not conserved in any other protein of known structure with this particular fold. The size and chemical environment of the bound ligand suggest binding or transport of a small polar molecule(s) as a potential function for these proteins. These are the first structural representatives of a newly defined PF14869 (DUF4488) Pfam family.
The gas‐dynamic synthesis of diamond by thermal activation
Authors: Emelyanov Alexei , Rebrov Aleksey , Yudin Ivan
Published: July 2014

The study presents results on deposition of diamond structures from high‐velocity flows of carbon‐containing a gas mixture activated by hot surfaces. Important problems were solved by creation of the reactor using a spiral of heat‐resistant material, inserted into the chamber with an inlet nozzle. The possibilities of diamond synthesis in wide parameters ranges (pressure from 10−4to 100 Torr, flow rates from 500 to 3000 sccm, substrate temperature from 1100 to 1600 K) have been studied experimentally. For analysis of the hydrogen flow, the direct simulation Monte Carlo (DSMC) method was used. The activation–deactivation influence of reactor surfaces has been taken into account. The results of diamond crystal synthesis are presented for the cases of joint and separated H2and CH4gas delivery. Due to retaining the catalytic tungsten properties in the case of separated gas delivery, an increasing growth rate of diamond crystals was discovered.
Assessing the prediction accuracy of cure in the Cox proportional hazards cure model: an application to breast cancer data
Authors: Asano Junichi , Hirakawa Akihiro , Hamada Chikuma
Published: July 2014

A cure rate model is a survival model incorporating the cure rate with the assumption that the population contains both uncured and cured individuals. It is a powerful statistical tool for prognostic studies, especially in cancer. The cure rate is important for making treatment decisions in clinical practice. The proportional hazards (PH) cure model can predict the cure rate for each patient. This contains a logistic regression component for the cure rate and a Cox regression component to estimate the hazard for uncured patients. A measure for quantifying the predictive accuracy of the cure rate estimated by the Cox PH cure model is required, as there has been a lack of previous research in this area. We used the Cox PH cure model for the breast cancer data; however, the area under the receiver operating characteristic curve (AUC) could not be estimated because many patients were censored. In this study, we used imputation‐based AUCs to assess the predictive accuracy of the cure rate from the PH cure model. We examined the precision of these AUCs using simulation studies. The results demonstrated that the imputation‐based AUCs were estimable and their biases were negligibly small in many cases, although ordinary AUC could not be estimated. Additionally, we introduced the bias‐correction method of imputation‐based AUCs and found that the bias‐corrected estimate successfully compensated the overestimation in the simulation studies. We also illustrated the estimation of the imputation‐based AUCs using breast cancer data. Copyright © 2014 John Wiley & Sons, Ltd.
How to ensure that your research works
Authors: Petit Annie
Published: July 2014

Top ten reasons why your social listening research is missing the mark
Topographic control of stratified flows: upstream jets, blocking and isolating layers
Authors: Winters Kraig B. , Armi Laurence
Published: July 2014

Optimal solutions to the nonlinear, hydrostatic, Boussinesq equations are developed for steady, density-stratified, topographically controlled flows characterized by blocking and upstream influence. These flows are jet-like upstream of an isolated obstacle and are contained within an asymmetric, thinning stream tube that is accelerated as it passes over the crest. A stagnant, nearly uniform-density isolating layer, surrounded by a bifurcated uppermost streamline, separates the accelerated flow from an uncoupled flow above. The flows are optimal in the sense that, for a given stratification, the solutions maximize the topographic rise above the blocking level required for hydraulic control while minimizing the total energy of the flow. Hydraulic control is defined mathematically by the asymmetry of the accelerated flow as it passes the crest. A subsequent analysis of the Taylor–Goldstein equation shows that these sheared, non-uniformly stratified flows are indeed subcritical upstream, critical at the crest, and supercritical downstream with respect to gravest-mode, long internal waves. The flows obtained are relevant to arrested wedge flows, selective withdrawal, stratified towing experiments, tidal flow over topography and atmospheric flows over mountains.
The Saint with Indra's Sword: Khruubaa Srivichai and Buddhist Millenarianism in Northern Thailand
Authors: Bowie Katherine
Published: July 2014

Despite a growing literature revealing the presence of millenarian movements in both Theravada and Mahayana Buddhist societies, scholars have been remarkably reluctant to consider the role of messianic beliefs in Buddhist societies. Khruubaa Srivichai (1878–1938) is the most famous monk of northern Thailand and is widely revered as atonbun, or saint. Althoughtonbunhas been depoliticized in the modern context, the term also refers to a savior who is an incarnation of the coming Maitreya Buddha. In 1920 Srivichai was sent under arrest to the capital city of Bangkok to face eight charges. This essay focuses on the charge that he claimed to possess the god Indra's sword. Although this charge has been widely ignored, it was in fact a charge of treason. In this essay, I argue that the treason charge should be understood within the context of Buddhist millenarianism. I note the saint/savior tropes in Srivichai's mytho-biography, describe the prevalence of millenarianism in the region, and detail the political economy of the decade of the 1910s prior to Srivichai's detention. I present evidence to show that the decade was characterized by famine, dislocation, disease, and other disasters of both natural and social causes. Such hardships would have been consistent with apocalyptic omens in the Buddhist repertoire portending the advent of Maitreya. Understanding Srivichai in this millenarian context helps to explain both the hopes of the populace and the fears of the state during that tumultuous decade.
Resource Politics and State-Society Relations: Why Are Certain States More Inclusive than Others?
Authors: Sato Jin
Published: July 2014

Why do some states resort to more exclusive top-down management of natural resources, while others tend to be more inclusive and solicit participation from civil society? By rejecting the simple characterization of the state within the narrow spectrum of “weak” and “strong,” this article investigates resource-mediated relations in the peripheral social groups that the state has sought to transform as part of the process of modernization. Focusing on Siam and Japan, I highlight alternative explanations based on ethnicity and labor, bureaucratic mindset, and agro-ecological conditions. I argue that the more embedded nature of the labor force in resources sectors made it necessary for the Japanese government to engage with marginal people, whereas the enclave nature of such sectors in Siam allowed elites to establish a distinctively exclusive system. While the Japanese state quickly learned to accommodate people at the fringes through its recognition and acceptance of existing customs in the management of resources, and even facilitated the creation of local organizations such as forest unions, the Siamese were consistently more exclusionary and even oppressed indigenous groups living at the state's territorial periphery. Resource interventions targeted at the fringes of land and society in Japan and Siam produced lasting effects on state-society relations that have extended far beyond their original intention of securing resource procurement. Understanding the historical roots of such relations offers a fresh perspective from which to explain why state inaction prevails in the present debate on state devolution in Thailand.
Genetic diversity and population structure of wild soybean (Glycine sojaSieb. and Zucc.) accessions in Korea
Authors: Kim Kil Hyun , Lee Seukki , Seo Min-Jung , Lee Gi-An , Ma Kyung-Ho , Jeong Soon-Chun , Lee Suk-Ha , Park Eui Ho , Kwon Young-Up , Moon Jung-Kyung
Published: July 2014

Genetic variation in wild soybean (Glycine sojaSieb. and Zucc.) is a valuable resource for crop improvement efforts. Soybean is believed to have originated from China, Korea, and Japan, but little is known about the diversity or evolution of Korean wild soybean. Therefore, in this study, we evaluated the genetic diversity and population structure of 733G. sojaaccessions collected in Korea using 21 simple sequence repeat (SSR) markers. The SSR loci produced 539 alleles (25.7 per locus) with a mean genetic diversity of 0.882 in these accessions. Rare alleles, those with a frequency of less than 5%, represented 75% of the total number. This collection was divided into two populations based on the principal coordinate analysis. Accessions from population 1 were distributed throughout the country, whereas most of the accessions from population 2 were distributed on the western side of the Taebaek and Sobaek mountains. The KoreanG. sojacollection evaluated in this study should provide useful background information for allele mining approach and breeding programmes to introgress alleles into the cultivated soybean (G. max(L). Merr.) from wild soybean.
Circadian clock and photoperiodic flowering genes in adzuki bean (Vigna angularis [Willd.] Ohwi & H. Ohashi)
Authors: Kim Moon Young , Kang Yang Jae , Lee Taeyoung , Lee Suk-Ha
Published: July 2014

Adzuki bean (Vigna angularis [Willd.] Ohwi & H. Ohashi) is one of the most important legume crops cultivated in East Asia and northern South Asia. Despite its agronomic importance, the lack of available sequence information has made it difficult to improve important agronomic traits. In the present study, we performed de novo assembly of transcript sequences produced by short-read sequencing to construct 59,860 full-length protein-coding sequences in adzuki bean. These genes were subjected to a BLASTP search to identify putative homologues of the 84 Arabidopsis genes involved in the circadian clock and photoperiodic flowering pathway. A large proportion of these Arabidopsis genes were found to be conserved in adzuki bean. However, there were no homologues of six genes including FLOWER LOCUS D (FD) and LEAFY (LFY). Furthermore, the phylogenetic relationships of 25 highly homologous matches to CONSTANS (CO) or CONSTANS-LIKE (COL) of Arabidopsis indicated the lack of a CO orthologue in adzuki bean. FLOWER LOCUS T (FT) and its homologues were found to have two homologous counterparts in adzuki bean. This study provides primary genetic resources that may be useful for producing adzuki bean with improved flowering and fruiting performance in response to environmental changes.
Genome-wide expression analysis in a dwarf soybean mutant
Authors: Zhang Feng , Shen Yanting , Sun Shi , Guo Jianqiu , Li Congcong , Wu Cunxiang , Li Qing , Nian Hai , Huang Xianzhong , Tian Zhixi , Han Tianfu
Published: July 2014

Plant height is important for crop yield improvement. In this study, a dwarf mutant, Gmdwarf1, was screened from a γ-ray-treated soybean population. Compared with the wild type, the mutant exhibited later germination, smaller and darker green leaves, and less-elongated shoots. Genome-wide transcriptome detection through RNA-seq analysis revealed that not only gibberellin-related genes but many other genes involved in hormone biosynthetic pathways were also significantly influenced in the mutant. We presumed that Gmdwarf1 might play essential roles in the plant hormone pathways. Future functional analysis of this dwarf mutant would help us to understand the underlying mechanisms and be beneficial for improving soybean yield.
Molecular nature of chemically and physically induced mutants in plants: a review
Authors: Nawaz Zarqa , Shu Qingyao
Published: July 2014

More than 3200 new mutant varieties have been bred and used by millions of farmers, which has significantly contributed to world food security. A lot more mutants have also served as tools for gene discovery and functional analysis. Recent genomic approaches including TILLING (Targeting Induced Local Lesions In Genome) have enabled screening of mutations at the molecular level. This review describes the molecular nature of chemically and physically induced mutations and their repercussions. Analyses of TILLING reports indicate that chemically induced mutations are mostly nucleotide substitutions, but that mutation frequencies fluctuate among plant species ranging from one DNA lesion per 300 kbp inArabidopsisto one DNA lesion per 30 kbp in bread wheat, which reciprocate with an increase in ploidy levels. The majority (>95%) of chemically induced DNA lesions are silent or missense mutations. Mutations induced by physical mutagens seem to be more diverse, including single-nucleotide substitutions, insertions, inversions and translocations, although short deletions ( < 15 bp) are relatively more predominant. The proportion of complex mutations (translocation, inversions, etc.) may increase with an increase in the linear energy transfer of radiations. In addition, the implications of these findings for the roles of induced mutants in breeding and gene function analysis are briefly discussed.
Cloning and characterization of Ku70 and Ku80 homologues involved in DNA repair process in wheat (Triticum aestivum L.)
Authors: Gu Jiayu , Wang Qing , Cui Meng , Han Bing , Guo Huijun , Zhao Linshu , Xie Yongdun , Song Xiyun , Liu Luxiang
Published: July 2014

Error-prone repair of radiation-induced DNA double-strand breaks (DSBs) results in DNA mutation that is essential for mutation breeding. Non-homologous end joining might be the principal DSB repair mechanism in eukaryotes, which is mediated and activated by Ku protein, a heterodimer of 70 and 80 kDa subunits. In this study, on the basis of complementary DNA (cDNA), the genomic sequences of TaKu70 and TaKu80 genes in all the three genomes of wheat were characterized. Only single-nucleotide substitutions and no insertions or deletions were detected in the exons of TaKu70 and TaKu80 genes. The size of the introns exhibited a slight variation between the sequences. Yeast two-hybrid analysis demonstrated that TaKu70 and TaKu80 formed a heterodimer, and electrophoretic mobility shift assays revealed that this heterodimer bound to double-stranded DNA, but not to single-stranded DNA. The quantitative polymerase chain reaction analysis revealed that the expression of TaKu70 and TaKu80 genes was up-regulated under γ-ray irradiation in a dose-dependent manner in the seedlings of wheat. These results suggest that TaKu70 and TaKu80 form a functional heterodimer and are associated with the repair of the induced DSBs in wheat.
De novo transcriptome assembly of Vitis flexuosa grapevines inoculated with Elsinoe ampelina
Authors: Ahn Soon Young , Kim Seon Ae , Jo Sung Hwan , Yun Hae Keun
Published: July 2014

In this study, the transcriptome of Vitis flexuosa leaves inoculated with Elsinoe ampelina was analysed to identify useful genes and elucidate their function and differential expression patterns through assembly and annotation gene ontology of data from sequencing short reads on the Illumina platform. We assembled ~121 million high-quality trimmed reads using Velvet and Oases with optimal parameters into a non-redundant set of 70,899 transcripts ( ≥ 200 bp in length). The transcripts exhibited an average length of 1138 bp and a N50 length of 1695 bp, with the largest contig length being 9623 bp. Functional categorization revealed the conservation of genes involved in various molecular functions, including protein binding (21.1%) and oxidoreductase activity (11.7%), in V. flexuosa. The V. flexuosa transcript set generated in this study will serve as a resource for gene discovery and development of functional molecular markers.