bluuebunny/crossref_metadata_2025 huggingface dataset:
Increase in activation rate of Pro‐Tk‐subtilisin by a single nonpolar‐to‐polar amino acid substitution at the hydrophobic core of the propeptide domain
Authors: Yuzaki Kota , Sanda Yudai , You Dong‐Ju , Uehara Ryo , Koga Yuichi , Kanaya Shigenori
Published: October 2013

Tk‐subtilisin (Gly70‐Gly398) is a subtilisin homolog from Thermococcus kodakarensis. Active Tk‐subtilisin is produced from its inactive precursor, Pro‐Tk‐subtilisin (Gly1‐Gly398), by autoprocessing and degradation of the propeptide (Tk‐propeptide, Gly1‐Leu69). This activation process is extremely slow at moderate temperatures owing to high stability of Tk‐propeptide. Tk‐propeptide is stabilized by the hydrophobic core. To examine whether a single nonpolar‐to‐polar amino acid substitution at this core affects the activation rate of Pro‐Tk‐subtilisin, the Pro‐Tk‐subtilisin derivative with the Phe17→His mutation (Pro‐F17H), Tk‐propeptide derivative with the same mutation (F17H‐propeptide), and two active‐site mutants of Pro‐F17H (Pro‐F17H/S324A and Pro‐F17H/S324C) were constructed. The crystal structure of Pro‐F17H/S324A was nearly identical to that of Pro‐S324A, indicating that the mutation does not affect the structure of Pro‐Tk‐subtilisin. The refolding rate of Pro‐F17H/S324A and autoprocessing rate of Pro‐F17H/S324C were also nearly identical to those of their parent proteins (Pro‐S324A and Pro‐S324C). However, the activation rate of Pro‐F17H greatly increased when compared with that of Pro‐Tk‐subtilisin, such that Pro‐F17H is efficiently activated even at 40°C. The far‐UV circular dichroism spectrum of F17H‐propeptide did not exhibit a broad trough at 205–230 nm, which is observed in the spectrum of Tk‐propeptide. F17H‐propeptide is more susceptible to chymotryptic degradation than Tk‐propeptide. These results suggest that F17H‐propeptide is unfolded in an isolated form and is therefore rapidly degraded by Tk‐subtilisin. Thus, destabilization of the hydrophobic core of Tk‐propeptide by a nonpolar‐to‐polar amino acid substitution is an effective way to increase the activation rate of Pro‐Tk‐subtilisin.
The quark‐level linear σ model
Authors: Scadron M.D. , Rupp G. , Delbourgo R.
Published: October 2013

This review of the quark‐level linear σ model (QLLσM) is based upon the dynamical realization of the pseudoscalar and scalar mesons as a linear representation of SU(2)× SU(2) chiral symmetry, with the symmetry weakly broken by current quark masses. In its simplest SU(2) incarnation, with two non‐strange quark flavors and three colors, this nonperturbative theory, which can be selfconsistently bootstrapped in loop order, is shown to accurately reproduce a host of low‐energy observables with only one parameter, namely the pion decay constant fπ. Extending the scheme to SU(3) by including the strange quark, equally good results are obtained for many strong, electromagnetic, and weak processes just with two extra constants, viz. fK and <π |Hweak|K>. Links are made with the vector‐meson‐dominance model, the BCS theory of superconductivity, and chiral‐symmetry restoration at high temperature. Finally, these ideas are cautiously generalized to the electroweak sector, including the W, Z, and Higgs bosons, and also to CP violation.
Increased expression of putative cancer stem cell markers in the bone marrow of prostate cancer patients is associated with bone metastasis progression
Authors: Ricci Estelle , Mattei Eve , Dumontet Charles , Eaton Colby L. , Hamdy Freddy , van der Pluije Gabri , Cecchini Marco , Thalmann George , Clezardin Philippe , Colombel Marc
Published: October 2013

BACKGROUND

The number of cells positive for the α‐6 and α‐2 integrin subunits and the c‐Met receptor in primary tumors and bone biopsies from prostate cancer patients has been correlated with metastasis and disease progression. The objective of this study was to quantify disseminated tumour cells present in bone marrow in prostate cancer patients using specific markers and determine their correlation with metastasis and survival.

METHODS

Patients were included at different stage of prostate cancer disease, from localised to metastatic castration‐resistant prostate cancer. Healthy men were used as a control group. Bone marrow samples were collected and nucleated cells separated. These were stained for CD45, α‐2, α‐6 integrin subunits and c‐Met and samples were processed for analysis and quantification of CD45‐/α2+/α6+/c‐met + cells using flow cytometry. Clinical and pathological parameters were assessed and survival measured. Statistical analyses were made of associations between disease specific parameters, bone marrow flow cytometry data, prostate‐specific antigen (PSA) progression free survival and bone metastases progression free survival.

RESULTS

For all markers, the presence of more than 0.1% positive cells in bone marrow aspirates was significantly associated with the risk of biochemical progression, the risk of developing metastasis and death from prostate cancer.

CONCLUSIONS

Quantification of cells carrying putative stem cell markers in bone marrow is a potential indicator of disease progression. Functional studies on isolated cells are needed to show more specifically their property for metastatic spread in prostate cancer. Prostate 73:1738–1746, 2013. © 2013 Wiley Periodicals, Inc.
BCL::Fold—Protein topology determination from limited NMR restraints
Authors: Weiner Brian E. , Alexander Nathan , Akin Louesa R. , Woetzel Nils , Karakas Mert , Meiler Jens
Published: October 2013

When experimental protein NMR data are too sparse to apply traditional structure determination techniques, de novo protein structure prediction methods can be leveraged. Here, we describe the incorporation of NMR restraints into the protein structure prediction algorithm BCL::Fold. The method assembles discreet secondary structure elements using a Monte Carlo sampling algorithm with a consensus knowledge‐based energy function. New components were introduced into the energy function to accommodate chemical shift, nuclear Overhauser effect, and residual dipolar coupling data. In particular, since side chains are not explicitly modeled during the minimization process, a knowledge based potential was created to relate experimental side chain proton–proton distances to Cβ–Cβ distances. In a benchmark test of 67 proteins of known structure with the incorporation of sparse NMR restraints, the correct topology was sampled in 65 cases, with an average best model RMSD100 of 3.4 ± 1.3 Å versus 6.0 ± 2.0 Å produced with the de novo method. Additionally, the correct topology is present in the best scoring 1% of models in 61 cases. The benchmark set includes both soluble and membrane proteins with up to 565 residues, indicating the method is robust and applicable to large and membrane proteins that are less likely to produce rich NMR datasets. Proteins 2014; 82:587–595. © 2013 Wiley Periodicals, Inc.
Crystal structure of the N‐terminal methyltransferase‐like domain of anamorsin
Authors: Song Gaojie , Cheng Chongyun , Li Yang , Shaw Neil , Xiao Zhi‐Cheng , Liu Zhi‐Jie
Published: October 2013

Anamorsin is a recently identified molecule that inhibits apoptosis during hematopoiesis. It contains an N‐terminal methyltransferase‐like domain and a C‐terminal Fe‐S cluster motif. Not much is known about the function of the protein. To better understand the function of anamorsin, we have solved the crystal structure of the N‐terminal domain at 1.8 Å resolution. Although the overall structure resembles a typical S‐adenosylmethionine (SAM) dependent methyltransferase fold, it lacks one α‐helix and one β‐strand. As a result, the N‐terminal domain as well as the full‐length anamorsin did not show S‐adenosyl‐l‐methionine (AdoMet) dependent methyltransferase activity. Structural comparisons with known AdoMet dependent methyltransferases reveals subtle differences in the SAM binding pocket that preclude the N‐terminal domain from binding to AdoMet. The N‐terminal methyltransferase‐like domain of anamorsin probably functions as a structural scaffold to inhibit methyl transfers by out‐competing other AdoMet dependant methyltransferases or acts as bait for protein–protein interactions.Proteins 2014; 82:1066–1071. © 2013 Wiley Periodicals, Inc.
New semi‐synthesis of ubiquitin C‐terminal conjugate with 7‐amino‐4‐methylcoumarin
Authors: Li Yi‐Tong , Liang Jun , Li Jia‐Bin , Fang Ge‐Min , Huang Yong , Liu Lei
Published: October 2013

The ligation of peptide hydrazides at a Gly site carrying a removal auxiliary was found to be an efficient process. This technology was successfully used for the synthesis of ubiquitin C‐terminal conjugates. Recombinant Ub(1–75)‐NHNH2 was prepared through the hydrozinolysis of the Ub(1–75)‐intein fusion protein. It was ligated with a glycine derivative modified with an acid‐sensitive thiol auxiliary. The final acid treatment produced the desired bioactive ubiquitin conjugates in practical quantities. Thus, the method described here extends the protocols of expressed protein ligation. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.
Quantum transport through single atoms and molecules
Authors: Vitali L. , Wahl P. , Ohmann R. , Bork J. , Zhang Y. , Diekhöner L. , Kern K.
Published: October 2013

Experiments on quantum transport in a low temperature scanning tunneling microscope provide the possibility to study atomic and molecular contacts with well‐defined electrode‐geometry at least for one of the contacts, the surface. Here, we show for a number of examples, the strength of transport studies by STM. For single cobalt adatoms, we demonstrate the abrupt change in the width of the Kondo resonance of the cobalt adatom once the contact regime is reached. Differences of the mechanical properties of junctions with cobalt and gold adatoms are discussed. Finally, we show transport measurements and imaging with individual PVBA molecules.

Configurations in which we have investigated quantum transport: through a junction consisting of a single gold adatom, a single cobalt adatom, and a PVBA molecule between the tip of an STM and the surface.
Fabrication and photoluminescence properties of high‐quality ZnO film grown by solution‐vaporizing MOCVD
Authors: Ye Rongbin , Ohshima Eriko , Abe Takashi , Ohta Koji , Baba Mamoru
Published: October 2013

High‐quality ZnO film has been successfully grown on 2 inch c‐plane sapphire substrate using Zn(DPM)2 and O2 as zinc and oxygen sources by a solution‐vaporizing MOCVD technique. All films deposited at the substrate temperatures of 680 ∼ 760 °C were preferentially oriented along the (0001) direction and increasing the substrate temperature the full width at half maximum (FWHM) of the (0002) peak was decreased, as the crystallinity is improved. At the optimized substrate temperature of 740 °C the film showed the smallest FWHM was about 240 arcsec with the smoothest surface. In photoluminescence analysis of the film deposited at 740 °C, exciton emissions bound to the neutral donor (D0X) and two‐electron satellites (TES) emission dominated the edge emission region while phonon replicas of D0X and TES dominated the lower energy region with a weakly donor‐acceptor‐pair emission. Further, a comparatively negligible defect luminescence was observed, which indicated high‐quality ZnO film obtained. With increased temperature, the PL intensity of D0X and TES emissions decreased, which peaks shifts to the lower energy side, while the intensity of the free exciton emission increases and finally dominates the spectrum at room temperature. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fabrication of high‐mobility n ‐type carbon nanotube thin‐film transistors on plastic film
Authors: Yasunishi Tomohiro , Kishimoto Shigeru , Kauppinen Esko I. , Ohno Yutaka
Published: October 2013

We fabricated flexible n ‐type carbon nanotube thin‐film transistors on a plastic film by a simple transfer process and a solution‐based chemical doping technique with polyethyleneimine (PEI). There exists an optimal PEI concentration, which is determined by doping level and charge accumulation in the PEI layer. A high electron mobility of 70 cm2/Vs was achieved with an on/off ratio of 105 in ambient air. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Strain engineering of topological properties in lead‐salt semiconductors
Authors: Barone Paolo , Di Sante Domenico , Picozzi Silvia
Published: October 2013

Rock‐salt chalcogenide SnTe represents the simplest realization of a topological insulator where a crystal symmetry allows for the appearance of surface metallic states. Here, we theoretically predict that strain, as realized in thin films grown on (001) substrates, may induce a transition to a topological crystalline insulating phase in related lead‐salt chalcogenides. Furthermore, relevant topological properties of the surface states, such as the location of the Dirac cones on the surface Brillouin zone or the decay length of edge states, appear to be tunable with strain, with potential implications for technological devices benefiting from those additional degrees of freedom. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optimizing trial design in pharmacogenetics research: comparing a fixed parallel group, group sequential, and adaptive selection design on sample size requirements
Authors: Boessen Ruud , van der Baan Frederieke , Groenwold Rolf , Egberts Antoine , Klungel Olaf , Grobbee Diederick , Knol Mirjam , Roes Kit
Published: October 2013

Two‐stage clinical trial designs may be efficient in pharmacogenetics research when there is some but inconclusive evidence of effect modification by a genomic marker. Two‐stage designs allow to stop early for efficacy or futility and can offer the additional opportunity to enrich the study population to a specific patient subgroup after an interim analysis. This study compared sample size requirements for fixed parallel group, group sequential, and adaptive selection designs with equal overall power and control of the family‐wise type I error rate. The designs were evaluated across scenarios that defined the effect sizes in the marker positive and marker negative subgroups and the prevalence of marker positive patients in the overall study population. Effect sizes were chosen to reflect realistic planning scenarios, where at least some effect is present in the marker negative subgroup. In addition, scenarios were considered in which the assumed ‘true’ subgroup effects (i.e., the postulated effects) differed from those hypothesized at the planning stage. As expected, both two‐stage designs generally required fewer patients than a fixed parallel group design, and the advantage increased as the difference between subgroups increased. The adaptive selection design added little further reduction in sample size, as compared with the group sequential design, when the postulated effect sizes were equal to those hypothesized at the planning stage. However, when the postulated effects deviated strongly in favor of enrichment, the comparative advantage of the adaptive selection design increased, which precisely reflects the adaptive nature of the design. Copyright © 2013 John Wiley & Sons, Ltd.
Fourier transform ion cyclotron resonance mass spectrometric analysis of the green fraction of soil humic acids
Authors: Ikeya Kosuke , Sleighter Rachel L. , Hatcher Patrick G. , Watanabe Akira
Published: October 2013

RATIONALE

The green fraction of soil humic acids (HAs), designated Pg, contains 4,9‐dihydroxyperylene‐3,10‐quinone (DHPQ) as a chromophore. Although various naturally occurring DHPQ derivatives are known to occur and Pg‐like absorption is observed in the UV‐visible spectra of HAs from various types of soils worldwide, the chemical structure of Pg is still unknown.

METHODS

For a better understanding of the chemical composition of Pg, the pre‐isolated (crude Pg) and purified Pg (G2) samples and three soil HAs with different degrees of humification were analyzed using negative‐mode electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) at 12 Tesla. The Pg samples were characterized using H/C–O/C ratios and based on the type and magnitude of the molecular formulae having DHPQ or related compounds as a potential structure.

RESULTS

The H/C–O/C diagram indicated that most of the lipids, proteins, other aliphatics, and lignin‐like components were removed, while condensed aromatic components were concentrated during the purification process of crude Pg to G2 using Sephadex G‐50. More than 27 molecular formulae resembling DHPQ, DHPQ substituted with varying numbers of carboxyl and/or hydroxyl groups, and phenyl‐DHPQ derivatives were identified in both Pg samples. The peak magnitudes of these formulae in G2 (accounting for 40% of the total assigned magnitude) were greater than that in the crude Pg (21%). Most of the 27 molecular formulae were also detected in the three soil HAs, suggesting a common existence of Pg‐related compounds in various soil HAs.

CONCLUSIONS

The important molecular formulae of Pg components were estimated utilizing FTICRMS. Copyright © 2013 John Wiley & Sons, Ltd.
Methodology of automated ionosphere front velocity estimation for ground‐based augmentation of GNSS
Authors: Bang Eugene , Lee Jiyun
Published: October 2013

Extreme ionospheric anomalies occurring during severe ionospheric storms can pose integrity threats to Global Navigation Satellite System (GNSS) Ground‐Based Augmentation Systems (GBAS). Ionospheric anomaly threat models for each region of operation need to be developed to analyze the potential impact of these anomalies on GBAS users and develop mitigation strategies. Along with the magnitude of ionospheric gradients, the speed of the ionosphere “fronts” in which these gradients are embedded is an important parameter for simulation‐based GBAS integrity analysis. This paper presents a methodology for automated ionosphere front velocity estimation which will be used to analyze a vast amount of ionospheric data, build ionospheric anomaly threat models for different regions, and monitor ionospheric anomalies continuously going forward. This procedure automatically selects stations that show a similar trend of ionospheric delays, computes the orientation of detected fronts using a three‐station‐based trigonometric method, and estimates speeds for the front using a two‐station‐based method. It also includes fine‐tuning methods to improve the estimation to be robust against faulty measurements and modeling errors. It demonstrates the performance of the algorithm by comparing the results of automated speed estimation to those manually computed previously. All speed estimates from the automated algorithm fall within error bars of ± 30% of the manually computed speeds. In addition, this algorithm is used to populate the current threat space with newly generated threat points. A larger number of velocity estimates helps us to better understand the behavior of ionospheric gradients under geomagnetic storm conditions.
Fault diagnosis for electrical distribution systems using structural analysis
Authors: Knüppel Thyge , Blanke Mogens , Østergaard Jacob
Published: October 2013

Fault tolerance in electrical distribution relies on the ability to diagnose possible faults and determine which components or units cause a problem or are close to doing so. Faults include defects in instrumentation, power generation, transformation and transmission. The focus of this paper is the design of efficient diagnostic algorithms, which is a prerequisite for fault‐tolerant control of power distribution. Diagnosis in a grid depends on available analytic redundancies and hence on network topology. When topology changes because of earlier fault(s) or caused by maintenance, analytic redundancy relations (ARR) are likely to change. The algorithms used for the diagnosis may need to change accordingly, and finding efficient methods to ARR generation is essential to employ fault‐tolerant methods in the grid. Structural analysis is based on graph‐theoretical results that offer to find analytic redundancies in large sets of equations only from the structure (topology) of the equations. A salient feature is an automated generation of redundancy relations. The method is indeed feasible in electrical networks, where circuit theory and network topology together formulate the constraints that define a structure graph. This paper shows how the three‐phase networks are modelled and analysed using structural methods, and it extends earlier results by showing how physical faults can be identified such that adequate remedial actions can be taken. The paper illustrates a feasible modelling technique for structural analysis of power systems, it demonstrates detection and isolation of failures in a network and shows how typical faults are diagnosed. Nonlinear fault simulations illustrate the results. Copyright © 2013 John Wiley & Sons, Ltd.
Simulations of Mars Rover Traverses
Authors: Zhou Feng , Arvidson Raymond E. , Bennett Keith , Trease Brian , Lindemann Randel , Bellutta Paolo , Iagnemma Karl , Senatore Carmine
Published: October 2013

Artemis (Adams‐based Rover Terramechanics and Mobility Interaction Simulator) is a software tool developed to simulate rigid‐wheel planetary rover traverses across natural terrain surfaces. It is based on mechanically realistic rover models and the use of classical terramechanics expressions to model spatially variable wheel‐soil and wheel‐bedrock properties. Artemis's capabilities and limitations for the Mars Exploration Rovers (Spirit and Opportunity) were explored using single‐wheel laboratory‐based tests, rover field tests at the Jet Propulsion Laboratory Mars Yard, and tests on bedrock and dune sand surfaces in the Mojave Desert. Artemis was then used to provide physical insight into the high soil sinkage and slippage encountered by Opportunity while crossing an aeolian ripple on the Meridiani plains and high motor currents encountered while driving on a tilted bedrock surface at Cape York on the rim of Endeavour Crater. Artemis will continue to evolve and is intended to be used on a continuing basis as a tool to help evaluate mobility issues over candidate Opportunity and the Mars Science Laboratory Curiosity rover drive paths, in addition to retrieval of terrain properties by the iterative registration of model and actual drive results.
ABANDONED FLOODPLAIN PLANT COMMUNITIES ALONG A REGULATED DRYLAND RIVER
Authors: Reynolds L. V. , Shafroth P. B. , House P. K.
Published: October 2013

Rivers and their floodplains worldwide have changed dramatically over the last century because of regulation by dams, flow diversions and channel stabilization. Floodplains no longer inundated by river flows following dam‐induced flood reduction comprise large areas of bottomland habitat, but the effects of abandonment on plant communities are not well understood. Using a hydraulic flow model, geomorphic mapping and field surveys, we addressed the following questions along the Bill Williams River, Arizona: (i) What per cent of the bottomland do abandoned floodplains comprise? and (ii) Are abandoned floodplains quantitatively different from adjacent xeric and riparian surfaces in terms of vegetation composition and surface sediment? We found that nearly 70% of active channel and floodplain area was abandoned following dam installation. Abandoned floodplains along the Bill Williams River tend to be similar to each other yet distinct from neighbouring habitats: they have been altered physically from their historic state, leading to distinct combinations of surface sediments, hydrology and plant communities. Abandoned floodplains may transition to xeric communities over time but are likely to retain some riparian qualities as long as there is access to relatively shallow ground water. With expected increases in water demand and drying climatic conditions in many regions, these surfaces and associated vegetation will continue to be extensive in riparian landscapes worldwide. Copyright © 2013 John Wiley & Sons, Ltd.
AN OBJECTIVE AND PARSIMONIOUS APPROACH FOR CLASSIFYING NATURAL FLOW REGIMES AT A CONTINENTAL SCALE
Authors: Archfield S. A. , Kennen J. G. , Carlisle D. M. , Wolock D. M.
Published: October 2013

Hydro‐ecological stream classification—the process of grouping streams by similar hydrologic responses and, by extension, similar aquatic habitat—has been widely accepted and is considered by some to be one of the first steps towards developing ecological flow targets. A new classification of 1543 streamgauges in the contiguous USA is presented by use of a novel and parsimonious approach to understand similarity in ecological streamflow response. This novel classification approach uses seven fundamental daily streamflow statistics (FDSS) rather than winnowing down an uncorrelated subset from 200 or more ecologically relevant streamflow statistics (ERSS) commonly used in hydro‐ecological classification studies. The results of this investigation demonstrate that the distributions of 33 tested ERSS are consistently different among the classification groups derived from the seven FDSS. It is further shown that classification based solely on the 33 ERSS generally does a poorer job in grouping similar streamgauges than the classification based on the seven FDSS. This new classification approach has the additional advantages of overcoming some of the subjectivity associated with the selection of the classification variables and provides a set of robust continental‐scale classes of US streamgauges. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.
When the role fits: How firm status differentials affect corporate takeovers
Authors: Shen Rui , Tang Yi , Chen Guoli
Published: October 2013

This study explores the implications of interfirm status differentials for firm behaviors in corporate takeover transactions. We argue that the more the status differential between two firms is aligned with expectations of their roles embedded in the specific economic activity, the easier it is for them to agree on the appropriate means to reach consensus on the transaction. Using the empirical context of the U.S. corporate takeover market, we found that the greater the status differential between an acquirer and a target, the more positively the market reacts to both the acquirer and the target upon the announcement of the acquisition deal, the more likely it is for the deal to be completed, and the more likely the acquirer is to achieve better post‐acquisition performance. Copyright © 2013 John Wiley & Sons, Ltd.
Parylene Mobile Microplates Integrated with an Enzymatic Release for Handling of Single Adherent Cells
Authors: Teshima Tetsuhiko , Onoe Hiroaki , Kuribayashi‐Shigetomi Kaori , Aonuma Hiroka , Kamiya Koki , Ishihara Hirotaka , Kanuka Hirotaka , Takeuchi Shoji
Published: October 2013

An approach for manipulating single adherent cells is developed that is integrated with an enzymatic batch release. This strategy uses an array of releasable microfabricated mobile substrates, termed microplates, formed from a biocompatible polymer, parylene. A parylene microplate array of 10–70 μm in diameter can be formed on an alginate hydrogel sacrificial layer by using a standard photolithographic process. The parylene surfaces are modified with fibronectin to enhance cell attachment, growth, and stretching. To load single cells onto these microplates, cells are initially placed in suspension at an optimized seeding density and are allowed to settle, stretch, and grow on individual microplates. The sacrificial layer underneath the microplate array can be dissolved on a time‐scale of several seconds without cytotoxicity. This system allows the inspection of selected single adherent cells. The ability to assess single cells while maintaining their adhesive properties will broaden the examination of a variety of attributes, such as cell shape and cytoskeletal properties.
Design and implementation of task scheduling strategies for massive remote sensing data processing across multiple data centers
Authors: Zhang Wanfeng , Wang Lizhe , Ma Yan , Liu Dingsheng
Published: October 2013

Data intensive applications of remote sensing data processing are more and more widespread resulting from the evolutions in computer and network technologies. Especially, bags‐of‐tasks (BoTs) applications with a mass of sharing input files and directed acyclic graph (DAG) applications with data dependencies in a widely distributed computing environment bring new challenges. In this article, a strategy of partitioning group based on hypergraph (PGH) is introduced to formulate the model of sharing files. Within the PGH algorithm, BoTs applications would be partitioned into several groups to minimize the time of data transferring. We also adopted another scheduling policy, which is called optimized task tree (OTT) strategy to handle the DAG workflow of massive remote sensing data processing with data dependencies. A scheduling queue of DAG tasks would be updated according to the priorities changing. With the help of GridSim simulation environment, we designed the Gridlets within scheduler to test the performance of PGH and OTT. Copyright © 2013 John Wiley & Sons, Ltd.
Physiological Oxygen Prevents Frequent Silencing of the DLK1-DIO3 Cluster during Human Embryonic Stem Cells Culture
Authors: Xie Pingyuan , Sun Yi , Ouyang Qi , Hu Liang , Tan Yueqiu , Zhou Xiaoying , Xiong Bo , Zhang Qianjun , Yuan Ding , Pan Yi , Liu Tiancheng , Liang Ping , Lu Guangxiu , Lin Ge
Published: October 2013

Genetic and epigenetic alterations are observed in long-term culture (>30 passages) of human embryonic stem cells (hESCs); however, little information is available in early cultures. Through a large-scale gene expression analysis between initial-passage hESCs (ihESCs, <10 passages) and early-passage hESCs (ehESCs, 20–30 passages) of 12 hESC lines, we found that the DLK1-DIO3 gene cluster was normally expressed and showed normal methylation pattern in ihESC, but was frequently silenced after 20 passages. Both the DLK1-DIO3 active status in ihESCs and the inactive status in ehESCs were inheritable during differentiation. Silencing of the DLK1-DIO3 cluster did not seem to compromise the multilineage differentiation ability of hESCs, but was associated with reduced DNA damage-induced apoptosis in ehESCs and their differentiated hepatocyte-like cell derivatives, possibly through attenuation of the expression and phosphorylation of p53. Furthermore, we demonstrated that 5% oxygen, instead of the commonly used 20% oxygen, is required for preserving the expression of the DLK1-DIO3 cluster. Overall, the data suggest that active expression of the DLK1-DIO3 cluster represents a new biomarker for epigenetic stability of hESCs and indicates the importance of using a proper physiological oxygen level during the derivation and culture of hESCs. Stem Cells  2014;32:391–401
Exploring the missing link: an empirical study of software fixes
Authors: Hamill Maggie , Goseva‐Popstojanova Katerina
Published: October 2013

Many papers have been published on analysis and prediction of software faults and/or failures, but few addressed the software fixes made to correct the faults and prevent failures from reoccurring. This paper contributes towards filling this gap by focusing on empirical characterization of software fixes. The results are based on the data extracted from a safety–critical NASA mission. In particular, 21 large‐scale software components (which together constitute over 8000 files and millions of lines of code) were analysed. The unique characteristic of this work is the fact that links were established from software faults (i.e. the root causes) to (potential or observed) failures and consequently to fixes made to correct these faults. Specifically, for the fixes associated with individual failures, the spread across software components and types of software artifacts being fixed was studied. Our results showed that significant number of software failures required fixes in multiple software components and/or multiple software artifacts (i.e. 15% and 26%, respectively). The results also showed that the patterns of software components that were often fixed together were significantly affected by the software architecture. Furthermore, the types of fixed software artifacts were highly correlated with fault type and they had different distributions for prerelease and post‐release failures. Copyright © 2013 John Wiley & Sons, Ltd.
A selective sigma‐2 receptor ligand antagonizes cocaine‐induced hyperlocomotion in mice
Authors: Lever John R. , Miller Dennis K. , Green Caroline L. , Fergason‐cantrell Emily A. , Watkinson Lisa D. , Carmack Terry L. , Fan Kuo‐hsien , Lever Susan Z.
Published: October 2013

Cocaine functions, in part, through agonist actions at sigma‐1 (σ1) receptors, while roles played by sigma‐2 (σ2) receptors are less established. Attempts to discriminate σ2 receptor‐mediated effects of cocaine in locomotor hyperactivity assays have been hampered by the lack of potent and selective antagonists. Certain tetrahydroisoquinolinyl benzamides display high σ2 receptor affinity, and excellent selectivity for binding to σ2 over σ1 receptors. The behavioral properties of this structural class of σ ligands have not yet been investigated. The present study evaluated 5‐bromo‐N‐[4‐(6,7‐dimethoxy‐3,4‐dihydro‐1H‐isoquinolin‐2‐yl)‐butyl)]‐2,3‐dimethoxy‐benzamide, 1, a ligand shown by others to bind preferentially to σ2 over σ1 receptors, as well as dopamine D2 and D3 sites. First, we determined binding to monoamine transporters and opioid receptors, and noted 57‐fold selectivity for σ2 receptors over the serotonin transporter, and >800‐fold selectivity for σ2 receptors over the other sites tested. We then examined 1 in locomotor activity studies using male CD‐1® mice, and saw no alteration of basal activity at doses up to 31.6 µmol/kg. Cocaine produced a fivefold increase in locomotor activity, which was attenuated by 66% upon pretreatment of mice with 1 at 31.6 µmol/kg. In vivo radioligand binding studies also were performed, and showed no occupancy of σ1 receptors or the dopamine transporter by 1, or its possible metabolites, at the 31.6 µmol/kg dose. Thus, ligand 1 profiles behaviorally as a σ2 receptor‐selective antagonist that is able to counteract cocaine's motor stimulatory effects. Synapse 68:73–84, 2014. © 2013 Wiley Periodicals, Inc.
Multistage magma emplacement and progressive strain accumulation in the shallow‐level Krkonoše‐Jizera plutonic complex, Bohemian Massif
Authors: Žák Jiří , Verner Kryštof , Sláma Jiří , Kachlík Václav , Chlupáčová Marta
Published: October 2013

Field relationships combined with new U‐Pb zircon geochronology suggest that the shallow‐level Krkonoše‐Jizera plutonic complex, northern Bohemian Massif, was assembled successively from bottom to top, starting with emplacement of the separately evolved S‐type Tanvald granite (317.3 ± 2.1 Ma), followed by at least two voluminous batches of the I‐type porphyritic Liberec (319.5 ± 2.3 Ma) and Jizera (320.1 ± 3.0 Ma and 319.3 ± 3.7 Ma) granites. The intrusive sequence was completed by uppermost, minor intrusions of the equigranular Harrachov (315.0 ± 2.7 Ma) and Krkonoše granites. The I‐type granites exhibit an unusually complex pattern of superposed feldspar phenocryst and magnetic fabrics as revealed from the anisotropy of magnetic susceptibility (AMS). The outer Liberec granite preserves margin‐parallel foliations and lineations, interpreted to record emplacement‐related strain captured by cooling from the pluton floor and walls. In contrast, the inner Jizera, Harrachov, and Krkonoše granites were overprinted by synmagmatic strain resulting from dextral movements along regional strike‐slip faults cutting the opposite ends of the plutonic complex. Late‐stage felsic dikes in the Liberec and Jizera granites reorient from horizontal to vertical (lineation‐perpendicular) attitude in response to changing the least principal stress direction, whereas mafic schlieren do not do so, representing only randomly oriented small‐scale thermal‐mechanical instabilities in the phenocryst framework. In general, this case example challenges the common approach of inferring pluton‐wide magma flow from interpolated foliation, lineation, and schlieren patterns. More likely, magmatic fabrics in large plutons record complex temporal succession of superposed strains resulting from diverse processes at multiple scales.
Dielectric breakdown and mechanical properties of polylactic acid of different spherulite sizes
Authors: Matsugasaki Naru , Shinyama Katsuyoshi , Fujita Shigetaka
Published: October 2013

The degree of crystallinity of polylactic acid (PLA) was increased by heat treatment, and the dielectric breakdown strength and mechanical properties of the obtained PLA of different spherulite sizes were studied. PLA heat‐treated at a temperature of 120 °C or higher showed rapid increases in spherulite size. At both measurement temperatures of 25 and 80 °C, the dielectric breakdown strength (EB) showed rapid reduction. The tensile strength at break and breaking elongation showed rapid reduction when the heat treatment temperature was 120 °C or higher. © 2013 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Modularity and mental architecture
Authors: Robbins Philip
Published: October 2013

Debates about the modularity of cognitive architecture have been ongoing for at least the past three decades, since the publication of Fodor's landmark bookThe Modularity of Mind. According to Fodor, modularity is essentially tied to informational encapsulation, and as such is only found in the relatively low‐level cognitive systems responsible for perception and language. According to Fodor's critics in the evolutionary psychology camp, modularity simply reflects the fine‐grained functional specialization dictated by natural selection, and it characterizes virtually all aspects of cognitive architecture, including high‐level systems for judgment, decision making, and reasoning. Though both of these perspectives on modularity have garnered support, the current state of evidence and argument suggests that a broader skepticism about modularity may be warranted.WIREs Cogn Sci2013, 4:641–649. doi: 10.1002/wcs.1255

This article is categorized under:

Philosophy > Foundations of Cognitive Science
Paramagnetic inorganic nanoparticles as T1MRI contrast agents
Authors: Lee Soo Hong , Kim Byung Hyo , Na Hyon Bin , Hyeon Taeghwan
Published: October 2013

Magnetic resonance imaging (MRI) is one of the most powerful molecular imaging techniques and can noninvasively visualize and quantify biological processes within the living organisms. The introduction of exogenous contrast agents has allowed specific visualization of biological targets as well as enhanced the sensitivity of MRI. Recently, paramagnetic inorganic nanoparticles showing positive T1 contrast effect have been investigated as T1 MRI contrast agents. Since the first trials of spherical nanoparticles of manganese oxide and gadolinium oxide, inorganic nanoparticles of various compositions and shapes have been used for in vivo and in vitro MRI because of their distinct signal enhancement in MR images. However, for clinical applications, important and complex issues such as safety and efficiency should be investigated by active research encompassing multiple disciplines, including chemistry, biology, biomedical engineering, and medicine.

This article is categorized under:

Diagnostic Tools > Diagnostic Nanodevices

Diagnostic Tools > In Vivo Nanodiagnostics and Imaging
Synthesis, X‐ray Studies, and Catalytic Efficacy of a Novel Iron Complex Containing an N,O‐Type Bidentate Thiazoline Ligand
Authors: Amini Mojtaba , Bigdeli Mina , Delsouz‐Hafshejani Sepideh , Ellern Arkady , Woo L. Keith
Published: October 2013

The reactions of FeCl3·6H2O and 2‐(2′‐hydroxyphenyl)‐2‐thiazoline as a bidentate O‐N donor thiazoline ligand (thoz) afford a five‐coordinate FeIII complex [Fe(thoz)2Cl] with a distorted square pyramidal configuration. Complex [Fe(thoz)2Cl] was isolated as air‐stable crystalline solids and fully characterized, including by single‐crystal X‐ray structure analysis. Complex [Fe(thoz)2Cl] shows very efficient reactivity in the oxidation of sulfides to their corresponding sulfoxides using urea hydrogen peroxide (UHP) as the oxidant at room temperature in air.
Factors Influencing Surgeons’ Intraoperative Leadership: Video Analysis of Unanticipated Events in the Operating Room
Authors: Parker Sarah Henrickson , Flin Rhona , McKinley Aileen , Yule Steven
Published: October 2013

Background

The achievement of surgical goals and the successful functioning of operating room (OR) teams are dependent on leadership. The attending surgeon is a team leader during an operation, with responsibility for task accomplishment by the clinical team. This study examined surgeons’ leadership behaviors during surgical procedures, with particular reference to the effect of intraoperative events on leadership.

Methods

Videos of operations (n = 29) recorded at three UK teaching hospitals were analyzed to identify and classify surgeons’ intraoperative leadership behaviors using the Surgeons’ Leadership Inventory. The frequency and type of leadership behaviors were compared before and after the point of no return (PONR) (n = 24), and during an unexpected intraoperative event (n = 5).

Results

Most of the surgeons’ leadership behaviors were directed toward the resident during an operation. No significant differences were found for the overall number or type of leadership behaviors pre‐ and post‐PONR. The frequency of leadership behaviors classified as “Training” and “Supporting others” significantly decreased during an unanticipated intraoperative event.

Discussion

Overall, surgeons engaged in the same leadership behaviors throughout the course of an operation unless they were dealing with an unanticipated event. Surgeons appeared to adopt a “one size fits all” leadership style approach regardless of the team or situation. Additionally, surgeons seemed to limit their intraoperative leadership focus to other surgeons rather than to the wider OR team.
Discovery of Lamproites near Vattikod Area, NW Margin of the Cuddapah Basin, Eastern Dharwar Craton, Southern India
Authors: Kumar Alok , Ahmed Suhel , Priya R. , Sridhar M.
Published: October 2013

A cluster of lamproite dykes are located 1 km west of Vattikod village at the NW margin of the Cuddapah basin, Eastern Dharwar craton, southern India, during the pursuit for locating primary diamond source rocks by adapting multifarious applications. These exotic rocks are emplaced along WNW-ESE to NW-SE trending fractures in the granitic rocks belonging to the Peninsular Gneissic Complex. Ten out of twelve lamproites occur near Vattikod village and one each is located in the vicinity of Marepalli and Gundrapalli villages respectively. These lamproites, though highly altered, contain microphenocrysts of altered olivine, clinopyroxene, phlogopite, leucite and sanidine and translucent to opaque, amoeboid shaped patches of glass set in a groundmass rich in carbonate, phlogopite, serpentine, and chlorite. This new cluster of lamproites constitutes a part of the recently discovered Ramadugu lamproite field. The Vattikod and Ramadugu lamproites, together with those from Krishna lamproite field and the Cuddapah basin, constitute, a wide spectrum of ultrapotassic magmatism emplaced in and around the Palaeo-Mesoproterozoic Cuddapah basin in southern India.
Systematics, Biometry of the species Opsidiscus from the Middle Cambrian succession of the Spiti Basin, India
Authors: Pandey Shivani , Parcha Suraj Kumar
Published: October 2013

The Middle Cambrian succession of the Parahio Valley in general and Debsakhad section in particular is dominated by trilobites. Genus Opsidiscus, along with other trilobite forms dominates the lower Middle Cambrian succession. In the present study two new species of Opsidiscus, Opsidiscus wadiai and Opsidiscus srikantiai are reported from the lower Middle Cambrian succession of Debsakhad section. The species were differentiated on their morphological features and their multivariate analysis. The multivariate analysis applied here is used as a supplement method to qualitative analysis in order to differentiate between the cranidial characters of Opsidiscus. The qualitative study of each species studied individually shows more or less close affiliation as is observed by different quantitative methods. The presence of Opsidiscus has a great stratigraphic significance in this region, as they first appear from informal Stage 5 of Series 3 and goes up to the Drumian Stage of Series 3 of the Cambrian System in the Debsakhad section, which helps to correlate this section with other well known sections of the Middle Cambrian.
Occurrence of well-crystallized Nontronite in the Gas Vesicles of a Megaporphyritic Basalt Flow near Nighoj, Ahmednagar district, Maharashtra
Authors: Sarkar P. K. , Upasani D. V. , Soman A. C.
Published: October 2013

Occurrence of well crystallized nontronite in a megaporphyritic basalt flow from Nighoj area, Maharashtra, India is reported. Thin section studies of the vesicles from periphery to the centre reveal the presence of greenish palagonite, probably indicating the stages of devitrification of glass and the weathering of palagonite to the formation of nontronite. The centre of the vesicles is marked by the presence of dark greenish-brown, radiating and fibrous sheets of nontronite. X-ray diffraction (XRD) analysis reveals the dominant presence of smectite (nontronite) as the major phase with traces of pyroxene. Scanning Electron Microscopy (SEM) shows well developed sheets of nontronite within the gas vesicles of the megaporphyritic basalt flows. In the present investigation, the nontronite within the gas vesicles of the megaporphyritic basalts at Nighoj was formed in-situ due to the devitrification of glass containing palagonite. Palagonite is an intermediate step in the alteration that may be accomplished by the steam generated in quenching of the lava. Weathering of palagonite under conditions of poor drainage is essential to the genesis of nontronite as has been suggested by Victor and Vernon (1946).
Promoting Self-Determination for Better Health and Wellbeing for Adolescents who have an Intellectual Disability
Authors: Carrington Suzanne , Lennox Nicholas , O'Callaghan Michael , McPherson Lyn , Selva Gitta
Published: October 2013

The focus of this paper is on an Australian research project that evaluated the effectiveness of a resource called theAsk Health Diary, which is used in the school curriculum to promote self-determination for better health and wellbeing for adolescents who have an intellectual disability. Education and health researchers used questionnaires and interviews to gather data from adolescents attending special schools and special education units located in secondary schools in south-east Queensland, their teachers and their parents/carers. This paper reports on two research questions: First, ‘How did the teachers use theAsk Health Diaryto promote self-determination in health?’, and second, ‘How did teachers, parents/carers and students perceive the benefits and value of theAsk Health Diary?’ The findings indicate that theAsk Health Diaryprovides a sound curriculum framework for teachers, adolescents and parents/carers to work together to promote self-determination and better health outcomes for young people who have an intellectual disability.