bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

BACKGROUNDThe 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.METHODSPatients 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.RESULTSFor 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.CONCLUSIONSQuantification 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

ABSTRACTWhen 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

ABSTRACTAnamorsin 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.
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

AbstractHigh‐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

AbstractWe 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

AbstractRock‐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)
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

RATIONALEThe 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.METHODSFor 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.RESULTSThe 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.CONCLUSIONSThe 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

AbstractExtreme 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

SUMMARYFault 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.
ABANDONED FLOODPLAIN PLANT COMMUNITIES ALONG A REGULATED DRYLAND RIVER
Authors: Reynolds L. V. , Shafroth P. B. , House P. K. 
Published: October 2013

ABSTRACTRivers 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

ABSTRACTHydro‐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.
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

SUMMARYData 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

Abstract
Genetic and epigenetic alterations are observed in long-term culture (&gt;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, &lt;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

SUMMARYMany 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.