bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photoluminescence of magnesium and silicon doped cubic GaN
Authors: Powell R. E. L. , Novikov S. V. , Foxon C. T. , Akimov A. V. , Kent A. J. 
Published: January 2014

AbstractWe have studied time‐integrated and time‐resolved photoluminescence (PL) spectra and the transport properties of cubic GaN layers doped with different amounts of either magnesium (p‐type) or silicon (n‐type). In Mg doped material a broad blue peak was observed whose origin in cubic material has not been well established. Our temperature dependent and time resolved PL results as well as the observation of strong self‐compensation in Mg‐doped cubic GaN have allowed us to present a model for the origin of this emission in cubic material. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Generic event‐based monitoring and adaptation methodology for heterogeneous distributed systems
Authors: Inzinger Christian , Hummer Waldemar , Satzger Benjamin , Leitner Philipp , Dustdar Schahram 
Published: January 2014

SUMMARYThe Cloud computing paradigm provides the basis for a class of platforms and applications that face novel challenges related to multi‐tenancy, adaptivity, and elasticity. To account for service delivery guarantees in the face of ever increasing levels of heterogeneity, scale, and dynamism, service provisioning in the Cloud has raised the demand for systematic and flexible approaches to monitoring and adaptation of applications. In this paper, we tackle this issue and present a framework for efficient runtime management of Cloud environments and distributed heterogeneous systems in general. A novel domain‐specific language termed MONINA is introduced that allows to define integrated monitoring and adaptation functionality for controlling such systems. We propose a mechanism for optimal deployment of the defined control operators onto available computing resources. Deployment is based on solving a quadratic programming problem, which aims at achieving minimized reaction times, low overhead, and scalable monitoring and adaptation. The monitoring infrastructure is based on a distributed messaging middleware, providing high level of decoupling and allowing new monitoring nodes to join the system dynamically. We provide a detailed formalization of the problem domain, discuss architectural details, highlight the implementation of the developed prototype, and put our work into perspective with existing work in the field. Copyright © 2014 John Wiley & Sons, Ltd.
Comparing three online testing modalities: Using static, active, and interactive online testing modalities to assess middle school students' understanding of fundamental ideas and use of inquiry skills related to ecosystems
Authors: DeBoer George E. , Quellmalz Edys S. , Davenport Jodi L. , Timms Michael J. , Herrmann‐Abell Cari F. , Buckley Barbara C. , Jordan Kevin A. , Huang Chun‐Wei , Flanagan Jean C. 
Published: January 2014

AbstractOnline testing holds much promise for assessing students' complex science knowledge and inquiry skills. In the current study, we examined the comparative effectiveness of assessment tasks and test items presented in online modules that used either a static, active, or interactive modality. A total of 1,836 students from the classrooms of 22 middle school science teachers in 12 states participated in the study as part of normal classroom activities. Students took assessments in the three different modalities on three consecutive days. The assessments tested key concepts about ecosystems and students' ability to use inquiry skills in an ecosystems context. Our in‐depth analyses focused on how the different modalities elicited specific content knowledge of ecosystems (e.g., producers, consumers, predator–prey relationships) and specific inquiry skills (e.g., designing and interpreting experiments). We also investigated student use of technology supports, such as replaying animations or inspecting graphs. The results showed that the interactive modality enabled the testing of more complex reasoning and that additional experience working in the online environment improved student performance for all the modalities, especially for the interactive modality. Each of the three modalities provided useful information about students' understanding of ecosystems and related inquiry skills as well as their misconceptions. The study begins to build a knowledge base of what types of science knowledge and skills may be effectively measured in three different modalities of online assessment. © 2014 Wiley Periodicals, Inc. J Res Sci Teach 51: 523–554, 2014
Better moods for better eating?: How mood influences food choice
Authors: Gardner Meryl P. , Wansink Brian , Kim Junyong , Park Se‐Bum 
Published: January 2014

AbstractHow do moods influence one's preference for foods? By introducing the role of enjoyment‐ versus health‐oriented benefits of foods in the mood and food consumption relationship, this research informs both temporal construal theory and mood management framework by positing that mood influences the choice between healthy versus indulgent foods through its impact on temporal construal, which alters the weights people put on long‐term health benefits versus short‐term mood management benefits when making choices. The results from four experiments show that a positive mood cues distal, abstract construal and increases the salience of long‐term goals such as health, leading to greater preference for healthy foods over indulgent foods. The results also show that a negative mood cues proximal construal and increases the salience of immediate, concrete goals such as mood management, leading to greater preference for indulgent foods over healthy foods.
Early Cretaceous granitoids of the Samarka terrane (Sikhote-Alin’): geochemistry and sources of melts
Authors: Kruk N.N. , Simanenko V.P. , Gvozdev V.I. , Golozubov V.V. , Kovach V.P. , Serov P.I. , Kholodnov V.V. , Moskalenko E.Yu. , Kuibida M.L. 
Published: January 2014

Abstract
We present new data on the geologic position, composition, and isotope characteristics of the Early Cretaceous granitoids of the Samarka terrane, Sikhote-Alin’, formed on a transform continental margin. Geological and geochronological data show that these granitoids were generated at two stages of magmatism: in the first half (Hauterivian–Barremian, 130–123 Ma) and second half (Albian–Cenomanian, 110–98 Ma) of the Early Cretaceous. Granitoids of the first stage form an autonomous (free of basic precursors) unimodal melanogranite–granite association and are characterized by normal alkalinity with domination of K over Na, low contents of Ca, and elevated contents of Al2O3. By composition, these are S-granites with a model Nd age of ∼1.3 Ga. Granitoids of the second stage are of more diverse petrogeochemical types. They show wider variations in K/Na and A/CNK, are richer in Ca and, sometimes, Sr, and are poorer in P than the granitoids of the first stage. Their compositions form a continuous trend from S- to I-granites, and their model Nd age is ≤1.2 Ga. Comparison of the petrochemical, trace-element, and isotope characteristics of the Early Cretaceous granitoids and upper-crustal rocks (sandstones and siltstones of the turbidite matrix of a Jurassic accretionary prism and basalts from the inclusions in it) of the Samarka terrane and the coeval garrboids has shown that the potassic S-granitoids formed at the early (Hauterivian–Barremian) stage of magmatism as a result of the anatexis of upper-crustal sedimentary rocks. At the late (Albian–Early Cenomanian) stage, the intrusion of mantle magmas led to a temperature increase in the lower crust, which favored more active anatexis, involvement of high-melting substrates (oceanic basalts) in the granite formation, and interaction of mantle and crustal magmas. This resulted in a great diversity of granitoids (from S- to I-type).
Pooling Capital and Spreading Risk: Maritime Investment in East Asia at the Beginning of the Seventeenth Century
Authors: Oka Mihoko , Gipouloux François 
Published: January 2014

Foreign/long-distance trade has been one of the most popular themes in socio-economic history. However, the perceptions that we have of the role played by international trade in economic development is highly dependent on the actors we are focussing on. The universal actors of trade include ship owners, captains, crews, cargo owners, investors, mediators, agents, dealers, and so on. These actors, however, tend to be treated much like “merchants.” In this study, we focus particularly on capital investors to clarify the practical institutions of foreign trade that came to be organised in pre-modern maritime East Asia.In Japan, the pooling of capital seems to have started in the early stages of foreign trade, although it can be clearly observed only in the fourteenth and fifteenth centuries with the advent of Sino–Japan trade on the ships authorised by the Ming dynasty. In this trade, merchants from Hakata and Sakai were particularly active in making investments, even though the nominal ship owners were the central government and/or powerful lords like the Ōuchi () and Hosokawa () family. This fact ensured that these two port cities emerged as the centres of capital pooling in Japan, and remained so till the beginning of the seventeenth century.The form of investment, which is mainly associated with a particular part of Japan and which we try to clarify in this paper, has been callednagegane() in previous studies. The termnageganeusually refers to a type of investment wherein the payments are exempt in the case of a shipwreck;nageganewas utilised in the trades through Nagasaki during the seventeenth century. This exemption is very similar tocambio maritimo(bottomry), which was used in the medieval and pre-modern Mediterranean trade and transformed intoprestamo à la gruesa(Spanish) oremprestimo ao risco(Portuguese), which was used in transoceanic Iberian trades.
The Factory and the People of Nagasaki: Otona, Tolk, Compradoor
Authors: Yoko Matsui 
Published: January 2014

The Dutch East India Company was forced to move its factory in Japan from Hirado to Nagasaki by the order of the bakufu in 1641. Following that move, the Dutch were no longer allowed to freely go out into the city or to trade with city people. In order to have any contact with the people outside Deshima, they needed proper mediation of the Japanese officials. The interpreters (tolken, Oranda-tsūji, ) are well known as the intermediaries between the Japanese authorities and the Dutch residents of Deshima, but they were not the only ones who worked between the two sides. In this paper, I would like to deal with the Deshima Otona as the official responsible for the Dutch compound, and the compradoors, suppliers of the daily necessities for the Dutch factory, and to consider these officials within the context of the Nagasaki city system in order to compare this situation with that prevailing in Canton.Otona literally means “head” or “chief” and indicates a prominent member who is in charge of a certain group. In the cities of Edo-period Japan, the townspeople were controlled through their organisation in groups, which were given a considerable amount of autonomy. These groups consisted, in their turn, of members who were officially recognised by both the group organisation itself and the lord of the domain in which the city was located, because they owned a house, ran a family business, and performed some kind of public service (kuyaku, ).
Stopping of a relativistic electron beam in a plasma irradiated by an intense laser field
Authors: Nersisyan H.B. , Deutsch C. 
Published: January 2014

AbstractThe effects of a radiation field (RF) on the interaction process of a relativistic electron beam (REB) with an electron plasma are investigated. The stopping power of the test electron averaged with a period of the RF has been calculated assuming an underdense plasma, ω0 > ωp, where ω0is the frequency of the RF and ωpis the plasma frequency. In order to highlight the effect of the radiation field we present a comparison of our analytical and numerical results obtained for nonzero RF with those for vanishing RF. In particular, it has been shown that the weak RF increases the mean energy loss for small angles between the velocity of the REB and the direction of polarization of the RF while decreasing it at large angles. Furthermore, the relative deviation of the energy loss from the field-free value is strongly reduced with increasing the beam energy. Special case of the parallel orientation of the polarization of the RF with respect to the beam velocity has been also considered. At high-intensities of the RF two extreme regimes have been distinguished when the excited harmonics cancel effectively each other reducing strongly the energy loss or increasing it due to the constructive interference. Moreover, it has been demonstrated that the energy loss of the ultrarelativistic electron beam increases systematically with the intensity of the RF exceeding essentially the field-free value.
Numerical study of positron production with short-pulse high-intensity lasers
Authors: Hanus Vaclav , Drska Ladislav , d'Humieres Emmanuel , Tikhonchuk Vladimir 
Published: January 2014

AbstractOne-dimensional particle-in-cell and Monte-Carlo (FLUKA) simulation methods were used together, in order to investigate the production of positrons in lead targets, illuminated by a short-pulse high-intensity laser. The study is focused on lead targets of 1 mm thickness and more and pulses of intensity in the range 1019–1022 W/cm2. The calculations provided an estimate of an absolute number of positrons and the ratio of electrons and positrons emerging from the target. The thickness of the target is scaled in order to find an optimal thickness that could provide a neutral electron-positron beam.
Simulations of femtosecond laser pulse interaction with spray target
Authors: Psikal J. , Klimo O. , Limpouch J. 
Published: January 2014

AbstractLaser interactions with spray targets (clouds of submicron droplets) are studied here via numerical simulations using two-dimensional particle-in-cell codes. Our simulations demonstrate an efficient absorption of laser pulse energy inside the spray. The energy absorption efficiency depends on the inter-droplet distance, size of the cloud of droplets, and laser pulse intensity, as well as on the pre-evaporation of droplets due to laser pulse pedestal. We investigate in detail proton acceleration from the spray. Energy spectra of protons in various acceleration directions vary significantly depending on the density profile of the plasma created from the droplets and on laser intensity. The spray target can be alternative of foil targets for high intensity high repetition ultrahigh contrast femtosecond lasers. However, at intensities >1021 W/cm2, the efficiency of laser absorption and ion acceleration from the droplets drops significantly in contrast to foils.
Public Access to Environmental Information: A Comparative Analysis of Nigerian Legislation with International Best Practice
Authors: Etemire Uzuazo 
Published: January 2014

AbstractPublic access to environmental information is a recurring theme in many international environmental law regimes. Nigeria has ratified and committed itself to many such regimes over the years. And yet, until recently, it had a culture of secrecy in (environmental) governance that was sustained by legislation, with the attendant harm to the environment and public well-being. This changed in 2011, with the enactment of the Nigerian Freedom of Information (FOI) Act. This article uniquely assesses the value of the Nigerian FOI Act in relation to what may largely be considered international best practice principles on public access to environmental information as generally reflected in the UNECE’s Aarhus Convention. Even though Nigeria is not a party to it, it is argued that the Convention is still legally and politically relevant to Nigeria. This comparative analysis will reveal areas where the Nigerian FOI Act aligns with, probably goes beyond, but also falls short of best practice, thus leading to some suggestions for improvement in the Act in order to ensure better public access to environmental information.
CD28 and CD3 have complementary roles in T-cell traction forces
Authors: Bashour Keenan T. , Gondarenko Alexander , Chen Haoqian , Shen Keyue , Liu Xin , Huse Morgan , Hone James C. , Kam Lance C. 
Published: January 2014

SignificanceCells have the remarkable ability to sense the mechanical properties of the extracellular environment. This has been developed primarily in the context of cell interaction with extracellular matrix through integrins, but recent studies showed that T cells exhibit mechanosensing through CD3 and CD28, nonintegrin receptors that provide activation and costimulatory signals. This report demonstrates that T cells generate significant forces through the T-cell receptor (TCR) and CD28, and delineates the contributions of each in force generation. Moreover, the distribution of force generation and local assembly of active signaling intermediates suggest similarities between TCR- and integrin-based connections between the cell and substrate.
Farnesoid X receptor (FXR) gene deficiency impairs urine concentration in mice
Authors: Zhang Xiaoyan , Huang Shizheng , Gao Min , Liu Jia , Jia Xiao , Han Qifei , Zheng Senfeng , Miao Yifei , Li Shuo , Weng Haoyu , Xia Xuan , Du Shengnan , Wu Wanfu , Gustafsson Jan-Åke , Guan Youfei 
Published: January 2014

Significance
Farnesoid X (FXR) receptor is a ligand-activated transcription factor that regulates bile acid, lipid and glucose metabolism. It can be activated by endogenous bile acids, including chenodeoxycholic acid. This study uncovers a unique role for FXR to regulate urine volume independently of antidiuretic hormone and identifies aquaporin 2 as a direct target gene of FXR in renal collecting ducts. These findings provide a unique mechanism involved in the regulation of urinary concentrating process. The present study may also help understand the pathogenesis of hepatorenal syndrome, a state with increased circulating bile acid levels and impaired renal function.
Modeling tissue contamination to improve molecular identification of the primary tumor site of metastases
Authors: Vincent Martin , Perell Katharina , Nielsen Finn Cilius , Daugaard Gedske , Hansen Niels Richard 
Published: January 2014

AbstractMotivation: Contamination of a cancer tissue by the surrounding benign (non-cancerous) tissue is a concern for molecular cancer diagnostics. This is because an observed molecular signature will be distorted by the surrounding benign tissue, possibly leading to an incorrect diagnosis. One example is molecular identification of the primary tumor site of metastases because biopsies of metastases typically contain a significant amount of benign tissue.Results: A model of tissue contamination is presented. This contamination model works independently of the training of a molecular predictor, and it can be combined with any predictor model. The usability of the model is illustrated on primary tumor site identification of liver biopsies, specifically, on a human dataset consisting of microRNA expression measurements of primary tumor samples, benign liver samples and liver metastases. For a predictor trained on primary tumor and benign liver samples, the contamination model decreased the test error on biopsies from liver metastases from 77 to 45%. A further reduction to 34% was obtained by including biopsies in the training data.Availability and implementation: http://www.math.ku.dk/∼richard/msgl/.Contact: vincent@math.ku.dkSupplementary information: Supplementary data are available at Bioinformatics online.
Differential RISC association of endogenous human microRNAs predicts their inhibitory potential
Authors: Flores Omar , Kennedy Edward M. , Skalsky Rebecca L. , Cullen Bryan R. 
Published: January 2014

Abstract
It has previously been assumed that the generally high stability of microRNAs (miRNAs) reflects their tight association with Argonaute (Ago) proteins, essential components of the RNA-induced silencing complex (RISC). However, recent data have suggested that the majority of mature miRNAs are not, in fact, Ago associated. Here, we demonstrate that endogenous human miRNAs vary widely, by &gt;100-fold, in their level of RISC association and show that the level of Ago binding is a better indicator of inhibitory potential than is the total level of miRNA expression. While miRNAs of closely similar sequence showed comparable levels of RISC association in the same cell line, these varied between different cell types. Moreover, the level of RISC association could be modulated by overexpression of complementary target mRNAs. Together, these data indicate that the level of RISC association of a given endogenous miRNA is regulated by the available RNA targetome and predicts miRNA function.
Persistently stalled replication forks inhibit nucleotide excision repair in trans by sequestering Replication protein A
Authors: Tsaalbi-Shtylik Anastasia , Moser Jill , Mullenders Leon H. F. , Jansen Jacob G. , de Wind Niels 
Published: January 2014

Abstract
Rev3, the catalytic subunit of DNA polymerase ζ, is essential for translesion synthesis of cytotoxic DNA photolesions, whereas the Rev1 protein plays a noncatalytic role in translesion synthesis. Here, we reveal that mammalian Rev3−/− and Rev1−/− cell lines additionally display a nucleotide excision repair (NER) defect, specifically during S phase. This defect is correlated with the normal recruitment but protracted persistence at DNA damage sites of factors involved in an early stage of NER, while repair synthesis is affected. Remarkably, the NER defect becomes apparent only at 2 h post-irradiation indicating that Rev3 affects repair synthesis only indirectly, rather than performing an enzymatic role in NER. We provide evidence that the NER defect is caused by scarceness of Replication protein A (Rpa) available to NER, resulting from its sequestration at stalled replication forks. Also the induction of replicative stress using hydroxyurea precludes the accumulation of Rpa at photolesion sites, both in Rev3−/− and in wild-type cells. These data support a model in which the limited Rpa pool coordinates replicative stress and NER, resulting in increased cytotoxicity of ultraviolet light when replicative stress exceeds a threshold.
Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system
Authors: Shin Sunguk , Park Joonhong 
Published: January 2014

Abstract
Pyrosequencing of the 16S ribosomal RNA gene (16S) has become one of the most popular methods to assess microbial diversity. Pyrosequencing reads containing ambiguous bases (Ns) are generally discarded based on the assumptions of their non-sequence-dependent formation and high error rates. However, taxonomic composition differed by removal of reads with Ns. We determined whether Ns from pyrosequencing occur in a sequence-dependent manner. Our reads and the corresponding flow value data revealed occurrence of sequence-specific N errors with a common sequential pattern (a homopolymer + a few nucleotides with bases other than the homopolymer + N) and revealed that the nucleotide base of the homopolymer is the true base for the following N. Using an algorithm reflecting this sequence-dependent pattern, we corrected the Ns in the 16S (86.54%), bphD (81.37%) and nifH (81.55%) amplicon reads from a mock community with high precisions of 95.4, 96.9 and 100%, respectively. The new N correction method was applicable for determining most of Ns in amplicon reads from a soil sample, resulting in reducing taxonomic biases associated with N errors and in shotgun sequencing reads from public metagenome data. The method improves the accuracy and precision of microbial community analysis and genome sequencing using 454 pyrosequencing.