bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct microbial communities associated with buried soils in the Siberian tundra
Authors: Gittel Antje , Bárta Jiří , Kohoutová Iva , Mikutta Robert , Owens Sarah , Gilbert Jack , Schnecker Jörg , Wild Birgit , Hannisdal Bjarte , Maerz Joeran , Lashchinskiy Nikolay , Čapek Petr , Šantrůčková Hana , Gentsch Norman , Shibistova Olga , Guggenberger Georg , Richter Andreas , Torsvik Vigdis L , Schleper Christa , Urich Tim 
Published: December 2013

AbstractCryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze–thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes.
Intranuclear verrucomicrobial symbionts and evidence of lateral gene transfer to the host protist in the termite gut
Authors: Sato Tomoyuki , Kuwahara Hirokazu , Fujita Kazuma , Noda Satoko , Kihara Kumiko , Yamada Akinori , Ohkuma Moriya , Hongoh Yuichi 
Published: December 2013

Abstract
In 1944, Harold Kirby described microorganisms living within nuclei of the protists Trichonympha in guts of termites; however, their taxonomic assignment remains to be accomplished. Here, we identified intranuclear symbionts of Trichonympha agilis in the gut of the termite Reticulitermes speratus. We isolated single nuclei of T. agilis, performed whole-genome amplification, and obtained bacterial 16S rRNA genes by PCR. Unexpectedly, however, all of the analyzed clones were from pseudogenes of 16S rRNA with large deletions and numerous sequence variations even within a single-nucleus sample. Authentic 16S rRNA gene sequences were finally recovered by digesting the nuclear DNA; these pseudogenes were present on the host Trichonympha genome. The authentic sequences represented two distinct bacterial species belonging to the phylum Verrucomicrobia, and the pseudogenes have originated from each of the two species. Fluorescence in situ hybridization confirmed that both species are specifically localized, and occasionally co-localized, within nuclei of T. agilis. Transmission electron microscopy revealed that they are distorted cocci with characteristic electron-dense and lucent regions, which resemble the intranuclear symbionts illustrated by Kirby. For these symbionts, we propose a novel genus and species, ‘Candidatus Nucleococcus trichonymphae’ and ‘Candidatus Nucleococcus kirbyi’. These formed a termite-specific cluster with database sequences, other members of which were also detected within nuclei of various gut protists, including both parabasalids and oxymonads. We suggest that this group is widely distributed as intranuclear symbionts of diverse protists in termite guts and that they might have affected the evolution of the host genome through lateral gene transfer.
Optical investigation of the natural electron doping in thin MoS2 films deposited on dielectric substrates
Authors: Sercombe D. , Schwarz S. , Pozo-Zamudio O. Del , Liu F. , Robinson B. J. , Chekhovich E. A. , Tartakovskii I. I. , Kolosov O. , Tartakovskii A. I. 
Published: December 2013

AbstractTwo-dimensional (2D) compounds provide unique building blocks for novel layered devices and hybrid photonic structures. However, large surface-to-volume ratio in thin films enhances the significance of surface interactions and charging effects requiring new understanding. Here we use micro-photoluminescence (PL) and ultrasonic force microscopy to explore the influence of the dielectric environment on optical properties of a few monolayer MoS2 films. PL spectra for MoS2 films deposited on SiO2 substrates are found to vary widely. This film-to-film variation is suppressed by additional capping of MoS2 with SiO2 and SixNy, improving mechanical coupling of MoS2 with surrounding dielectrics. We show that the observed PL non-uniformities are related to strong variation in the local electron charging of MoS2 films. In completely encapsulated films, negative charging is enhanced leading to uniform optical properties. Observed great sensitivity of optical characteristics of 2D films to surface interactions has important implications for optoelectronics applications of layered materials.
Scholarly journals at the periphery: the case of Croatia
Authors: GRGIĆ Ivana HEBRANG 
Published: December 2013

ABSTRACTThis paper analyses 231 Croatian journals available on the national online platform, the Hrčak portal. To qualify for analysis journals had to be peer reviewed and to have published at least one issue in 2012. Some differences from the results of previous studies were noted. More journals are internationally oriented and the number of times they are accessed apparently depends on their scientific field. Publishers are still mostly not‐for‐profit but are more likely now to apply article processing/publication charges. This is new for Croatia and raises questions about the potential influence of this trend on the availability and visibility of scientific results. The results are relevant not only to Croatia but may also be representative of other countries at the ‘periphery‘.
Green and gold open access in India
Authors: MUKHERJEE Bhaskar 
Published: December 2013

ABSTRACTThis paper examines the characteristics of 462 open access (OA) journals being published in India under the green, gold and hybrid models. The sample of journals was selected from DOAJ, IndianJournal.com and Open J‐Gate. Journal characteristics were measured in terms of growth, subjects, publishers, and citations under each model. While characteristics such as growth, subject, and publisher have been identified by exploring the journal's website only, the citation count of these journals has been calculated by using Google Scholar and the Indian Citation Index. The gold road is now the most popular form of OA publishing in the subcontinent. There is a great variation in the size of OA journals and in their publishers. One publisher has more than 77 journals, but 264 publishers publish a single journal only. Overall, the OA journal landscape is greatly influenced by a few key publishers and journals. While 43% of journals charge publication fees and the fees vary from as low as US$10 to as high as US$400, the highest impact factor of the gold OA journals has been noted as 0.58. The data presented here suggest that publication fees are not a major barrier to authorship within the fields of computer science, pharmacy, and medicine.
Defining and responding to plagiarism
Authors: WAGER Elizabeth 
Published: December 2013

ABSTRACTA clear definition of plagiarism and the ability to classify it into more or less serious forms would help editors and publishers to devise policies to handle this problem. Text‐matching software is a useful tool for measuring the extent of text copying but it cannot detect plagiarized tables or figures, plagiarism of ideas, or plagiarism in translation. Furthermore, a working definition of plagiarism in relation to research reports needs to take into account factors such as the originality of the copied material, its position in the report, the adequacy of referencing, and the intention of the authors as well as the extent of the copying. This article considers all these factors and proposes possible definitions of major and minor plagiarism in relation to scholarly publications which might be used as the basis for anti‐plagiarism policies in conjunction with resources such as the COPE flowcharts.
Resequencing Data Indicate a Modest Effect of Domestication on Diversity in Barley: A Cultigen With Multiple Origins
Authors: Morrell Peter L. , Gonzales Ana M. , Meyer Kapua K.T. , Clegg Michael T. 
Published: December 2013

Abstract
The levels of diversity and extent of linkage disequilibrium in cultivated species are largely determined by diversity in their wild progenitors. We report a comparison of nucleotide sequence diversity in wild and cultivated barley (Hordeum vulgare ssp. spontaneum and ssp. vulgare) at 7 nuclear loci totaling 9296bp, using sequence from Hordeum bulbosum to infer the ancestral state of mutations. The sample includes 36 accessions of cultivated barley, including 23 landraces (cultivated forms not subject to modern breeding) and 13 cultivated lines and genetic stocks compared to either 25 or 45 accessions of wild barley for the same loci. Estimates of nucleotide sequence diversity indicate that landraces retain &gt;80% of the diversity in wild barley. The primary population structure in wild barley, which divides the species into eastern and western populations, is reflected in significant differentiation at all loci in wild accessions and at 3 of 7 loci in landraces. “Oriental” landraces have slightly higher diversity than “Occidental” landraces. Genetic assignment suggests more admixture from Occidental landraces into Oriental landraces than the converse, which may explain this difference. Based on θπ for silent sites, modern western cultivars have ~73% of the diversity found in landraces and ~71% of the diversity in wild barley.
Broad absorption features in wind-dominated ultraluminous X-ray sources?
Authors: Middleton Matthew J. , Walton Dominic J. , Roberts Timothy P. , Heil Lucy 
Published: December 2013

Abstract
The luminosities of ultraluminous X-ray sources (ULXs) require an exotic solution with either supercritical accretion modes on to stellar-mass black holes or subcritical accretion on to intermediate-mass black holes (IMBHs) being invoked. Discriminating between the two is non-trivial due to the present lack of a direct mass measurement. A key expectation of the supercritical mode of accretion is the presence of powerful radiatively driven winds. Here we analyse XMM–Newton data from NGC 5408 X-1 and NGC 6946 X-1 and find that strong soft residuals present in the X-ray spectra can be reconciled with broadened, blueshifted absorption by a partially ionized, optically thin phase of this wind. We derive initial values for the physical parameters of the wind; we also discuss other possible origins for the observed features.
Overexpression of FGF9 in colon cancer cells is mediated by hypoxia-induced translational activation
Authors: Chen Tsung-Ming , Shih Yu-Heng , Tseng Joseph T. , Lai Ming-Chih , Wu Chih-Hao , Li Yi-Han , Tsai Shaw-Jenq , Sun H. Sunny 
Published: December 2013

AbstractHuman fibroblast growth factor 9 (FGF9) is a potent mitogen involved in many physiological processes. Although FGF9 messenger RNA (mRNA) is ubiquitously expressed in embryos, FGF9 protein expression is generally low and restricted to a few adult organs. Aberrant expression of FGF9 usually results in human malignancies including cancers, but the mechanism remains largely unknown. Here, we report that FGF9 protein, but not mRNA, was increased in hypoxia. Two sequence elements, the upstream open reading frame (uORF) and the internal ribosome entry site (IRES), were identified in the 5' UTR of FGF9 mRNA. Functional assays indicated that FGF9 protein synthesis was normally controlled by uORF-mediated translational repression, which kept the protein at a low level, but was upregulated in response to hypoxia through a switch to IRES-dependent translational control. Our data demonstrate that FGF9 IRES functions as a cellular switch to turn FGF9 protein synthesis ‘on’ during hypoxia, a likely mechanism underlying FGF9 overexpression in cancer cells. Finally, we provide evidence to show that hypoxia-induced translational activation promotes FGF9 protein expression in colon cancer cells. Altogether, this dynamic working model may provide a new direction in anti-tumor therapies and cancer intervention.
Tranexamic Acid Impairs γ-Aminobutyric Acid Receptor Type A–mediated Synaptic Transmission in the Murine Amygdala
Authors: Kratzer Stephan , Irl Hedwig , Mattusch Corinna , Bürge Martina , Kurz Jörg , Kochs Eberhard , Eder Matthias , Rammes Gerhard , Haseneder Rainer 
Published: December 2013

Abstract

Background:
Tranexamic acid (TXA) is commonly used to reduce blood loss in cardiac surgery and in trauma patients. High-dose application of TXA is associated with an increased risk of postoperative seizures. The neuronal mechanisms underlying this proconvulsant action of TXA are not fully understood. In this study, the authors investigated the effects of TXA on neuronal excitability and synaptic transmission in the basolateral amygdala.

Methods:
Patch clamp recordings and voltage-sensitive dye imaging were performed in acute murine brain slices. Currents through N-methyl-d-aspartate, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid, and γ-aminobutyric acid receptor type A (GABAA) receptors were recorded. GABAA receptor–mediated currents were evoked upon electrical stimulation or upon photolysis of caged GABA. TXA was applied at different concentrations.

Results:
Voltage-sensitive dye imaging demonstrates that TXA (1 mM) reversibly enhances propagation of neuronal excitation (mean ± SEM, 129 ± 6% of control; n = 5). TXA at concentrations of 0.1, 0.3, 1, 5, or 10 mM led to a dose-dependent reduction of GABAA receptor–mediated currents in patch clamp recordings. There was no difference in the half-maximal inhibitory concentration for electrically (0.76 mM) and photolytically (0.84 mM) evoked currents (n = 5 to 9 for each concentration), and TXA did not affect the paired-pulse ratio of GABAA receptor–mediated currents. TXA did not impact glutamatergic synaptic transmission.

Conclusions:
This study clearly demonstrates that TXA enhances neuronal excitation by antagonizing inhibitory GABAergic neurotransmission. The results provide evidence that this effect is mediated via postsynaptic mechanisms. Because GABAA receptor antagonists are known to promote epileptiform activity, this effect might explain the proconvulsant action of TXA.
Evaluating the use of ABBA-BABA statistics to locate introgressed loci
Authors: Martin Simon H. , Davey John W. , Jiggins Chris D. 
Published: December 2013

ABSTRACTSeveral methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson’sDstatistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use ofDby applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole genome data fromHeliconiusbutterflies to investigate the behavior ofDin small genomic regions. We find thatDis unreliable in this situation as it gives inflated values when effective population size is low, causingDoutliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistica modified version of a statistic originally developed to estimate the genome-wide fraction of admixture.is not subject to the same biases asD, and is better at identifying introgressed loci. Finally, we show that bothDandoutliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.
Developing a framework for the identification of criminogenic needs in offenders with intellectual disability and personality disorder: the Treatment Need Matrix
Authors: Taylor Jon 
Published: December 2013

Purpose
– The criminogenic needs and psychological vulnerabilities of offenders with intellectual disability (ID) has only recently received attention within the academic literature. The purpose of this paper is to provide an overview of an approach to identifying such needs in order to inform treatment planning and service delivery.

Design/methodology/approach
– The paper describes the methods employed to identify relevant psychological variables for this population, provides an overview of the framework and describes the practices employed to establish the relevance of a range of criminogenic needs.

Findings
– A range of psychological variables derived from a systematic literature review are presented in the context of an assessment framework.

Research limitations/implications
– The Treatment Need Matrix (TNM) is currently an experimental framework for identifying the needs of offenders with ID (and personality disorder (PD)). Further research is needed to establish the reliability and validity of the tool.

Practical implications
– The TNM offers clinicians a practical methodology for determining the significance of a range of psychological variables cited in the literature as relevant treatment targets for offenders with IDs.

Originality/value
– The specific criminogenic needs of offenders with ID (and PD) has received little attention within the academic and research communities. This paper offers a novel approach to the identification of relevant treatment targets for individuals with such difficulties.
The differences between successful and unsuccessful new manufacturing products in international markets
Authors: Haluk Koksal Mehmet 
Published: December 2013

Purpose
– Developing new products for international markets offers great growth opportunities for companies by positively influencing company performance. Specifically, the research purpose is to determine the effects of new product success factors on the measures of company export performance, namely export sales, export growth and export profitability.

Design/methodology/approach
– The study examines the new product success factors, discriminating successful new products from unsuccessful ones in international markets. A pre-tested structured questionnaire is employed for collecting data from the companies. The population frame consists of exporting manufacturing companies and was determined from the records of the Export Promotion Centre of Turkey (IGEME). Of the 250 questionnaires sent out, 116 were completed and returned yielding a response rate of 46.4 percent. The study analysed data from 202 new product projects.

Findings
– The research determined that various new product success factors have different levels of effect on company performance in international markets, mainly measured in terms of sales, market share and profitability. Specifically, it identified that pre-development and development activities, a large and fast-growing foreign market with huge demand, order of entry and large and well-executed advertising activities differentiate successful new products from unsuccessful ones. Product characteristics are, on the other hand, not found to be a strong factor differentiating successful new products from unsuccessful ones in international markets.

Originality/value
– The main objective of the study is to integrate knowledge from two disciplines and expand new product success factors for international markets. The paper aims to bring together all the factors leading to the success of new products in international markets, and to test the effects of those factors on company performance. It is hoped that the findings will help managers and policy makers.
Shopping online without thinking: being emotional or rational?
Authors: Ozen Hilal , Engizek Nil 
Published: December 2013

Purpose
– This study aims to explore whether hedonic motivations of Turkish consumers have any potential impact on their impulse buying tendencies (IBT) in the online environment. Besides, it also covers which dimension of hedonic shopping motivation has the strongest effect on online IBT.

Design/methodology/approach
– An online survey was conducted to test the structural model. A total of 430 Turkish online consumers served as the sample. Data analysis was conducted using confirmatory factor analysis and structural equation modelling.

Findings
– Findings confirm that hedonic value drives online IBT. While three dimensions of hedonic shopping motivation (adventure, relaxation and value) affect online IBT in a positive way, social shopping was related negatively to online IBT. It was also found that idea shopping does not have a significant effect on online IBT.

Originality/value
– Given the occurrence of impulse buying in online shopping and the importance of hedonic motivations on consumer behavior, this study provides useful insights into impulse buying behavior in an online setting. In developing markets like Turkey what is the role of hedonic shopping motivations in online IBT? This study is unique in addressing this question for Turkish online consumers.
Institutional entrepreneurship in building the Brazilian market of functional yogurts
Authors: Almeida Felipe , de Paula Nilson , Pessali Huascar 
Published: December 2013

Purpose– The aim of this paper is to present an analytical narrative of the construction of the Brazilian market of functional yogurt, highlighting the role of Danone as an institutional entrepreneur.Design/methodology/approach– After putting together a theoretical basis from business studies and institutional economics, the paper explores factual evidence of strategic moves by dairy firms in Brazil.Findings– Danone, despite being a second mover, has been able to effectively make use of new values and collective concerns regarding food functionality to create a favourable institutional set in which to operate. Other firms have not been able to challenge its position in the market, simply abiding by the concepts and values created by Danone.Practical implications– On the one hand, case studies based on traditional economic theories usually approach markets with supply and demand adjustment tools or taking technology as exogenous and the sole determinant of the existence of a market. On the other hand, traditional business theories highlight an individual entrepreneur as the only relevant object of analysis. This study offers an alternative guideline to study markets with creative players that craft not only new physical products or directly delivered services, but also concepts and ideas. Studies of other markets or similar markets in different countries can benefit from its insights.Originality/value– The functional yogurt market in Brazil has not previously been object of academic research, and the combined framework of analysis in this study may offer guidance for other market studies.