bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal structure of the bacteriophage T4 late-transcription coactivator gp33 with the β-subunit flap domain of
Escherichia coli
RNA polymerase
Authors: Twist Kelly-Anne F. , Campbell Elizabeth A. , Deighan Padraig , Nechaev Sergei , Jain Vikas , Geiduschek E. Peter , Hochschild Ann , Darst Seth A. 
Published: December 2011

Activated transcription of the bacteriophage T4 late genes, which is coupled to concurrent DNA replication, is accomplished by an initiation complex containing the host RNA polymerase associated with two phage-encoded proteins, gp55 (the basal promoter specificity factor) and gp33 (the coactivator), as well as the DNA-mounted sliding-clamp processivity factor of the phage T4 replisome (gp45, the activator). We have determined the 3.0 Å-resolution X-ray crystal structure of gp33 complexed with its RNA polymerase binding determinant, the β-flap domain. Like domain 4 of the promoter specificity
σ
factor (
σ
4
), gp33 interacts with RNA polymerase primarily by clamping onto the helix at the tip of the β-flap domain. Nevertheless, gp33 and
σ
4
are not structurally related. The gp33/β-flap structure, combined with biochemical, biophysical, and structural information, allows us to generate a structural model of the T4 late promoter initiation complex. The model predicts protein/protein interactions within the complex that explain the presence of conserved patches of surface-exposed residues on gp33, and provides a structural framework for interpreting and designing future experiments to functionally characterize the complex.
Functional reconstitution of human eukaryotic translation initiation factor 3 (eIF3)
Authors: Sun Chaomin , Todorovic Aleksandar , Querol-Audí Jordi , Bai Yun , Villa Nancy , Snyder Monica , Ashchyan John , Lewis Christopher S. , Hartland Abbey , Gradia Scott , Fraser Christopher S. , Doudna Jennifer A. , Nogales Eva , Cate Jamie H. D. 
Published: December 2011

Protein fate in higher eukaryotes is controlled by three complexes that share conserved architectural elements: the proteasome, COP9 signalosome, and eukaryotic translation initiation factor 3 (eIF3). Here we reconstitute the 13-subunit human eIF3 in
Escherichia coli
, revealing its structural core to be the eight subunits with conserved orthologues in the proteasome lid complex and COP9 signalosome. This structural core in eIF3 binds to the small (40S) ribosomal subunit, to translation initiation factors involved in mRNA cap-dependent initiation, and to the hepatitis C viral (HCV) internal ribosome entry site (IRES) RNA. Addition of the remaining eIF3 subunits enables reconstituted eIF3 to assemble intact initiation complexes with the HCV IRES. Negative-stain EM reconstructions of reconstituted eIF3 further reveal how the approximately 400 kDa molecular mass structural core organizes the highly flexible 800 kDa molecular mass eIF3 complex, and mediates translation initiation.
Temperature perception and signal transduction - mechanisms across multiple organisms.
Authors: Penfield S. , Kendall S. , MacGregor D. 
Published: December 2011

Abstract

This chapter reviews the current state of knowledge of how temperature is measured by all manner of life forms. Some mechanisms turn out to be highly specialized in particular phyla, while some, presumably more ancient, are apparently widely conserved across species. It covers perception of temperature in animals through the gating of channels, by microorganism using diverse molecular mechanisms, and by plants through chromatin and transcription. Finally, the role of heat shock response in estimating the effect of climate change, specifically increased temperature, on those species most at risk, is discussed.
Temperature adaptation in changing climate: marine fish and invertebrates.
Authors: Abele D. 
Published: December 2011

Abstract

This chapter focuses on the adaptive physiological and ecological responses to warming in cold-temperate marine ectotherms. To understand centrally important traits of thermal tolerance, adaptive traits that restrict the capacities of cold stenotherms from Antarctic environments to acclimatize to the present warming trend in Western Antarctica are studied. The present knowledge of regulatory pathways that support metabolic adaptations to warmer temperatures is also discussed.
Perennial field crops.
Authors: Bertrand A. 
Published: December 2011

Abstract

In Canada, perennial forage crops and rangelands are grown on over 34 million ha, which represent more than 50% of all agricultural land. The productivity of perennial crops depends on climatic conditions. For perennial crops, however, both summer and winter climatic conditions are the determining factors. Yield is mainly dependent on the conditions prevailing during the growing period, while long-term persistence depends largely on the severity of winter conditions. This chapter focuses on current and future climatic conditions of eastern Canada, but conclusions could be applied to countries where the winter is characterized by freezing temperatures and snow cover.
Invasion by alien macrophytes in freshwater ecosystems of India.
Authors: Shah M. A. , Reshi Z. A. 
Published: December 2011

Abstract

This chapter describes the invasion of freshwater ecosystems in India by alien macrophytes, discusses the impact of plant invasion on freshwater ecosystems, and presents some strategies for the management of aquatic invasions. A preliminary checklist of aquatic alien plant species found in the Indian freshwater ecosystems is included.
Scintillator-oriented combinatorial search in Ce-doped (Y,Gd)3(Ga,Al)5O12 multicomponent garnet compounds
Authors: Kamada K , Yanagida T , Pejchal J , Nikl M , Endo T , Tsutumi K , Fujimoto Y , Fukabori A , Yoshikawa A 
Published: December 2011

Abstract
Ce-doped (Y
y
Gd1−y
)3(Ga
x
Al1−x
)5O12(x = 0, 1, 2, 3, 4 and y = 1, 2, 3) single crystals are grown by the micro-pulling down method. X-ray diffraction and electron probe microanalysis techniques are employed to check their structure and chemical composition, respectively. Optical and photoluminescence characteristics are measured and radioluminescence spectra, light yield and scintillation decay measurements are further made to evaluate the scintillation performance. We show that balanced Gd and Ga admixture in the Y3Al5O12 structure can considerably increase the scintillation efficiency, and the spectrally corrected light yield value exceeds 44 000 photon MeV−1. Scintillation decay times approach that of Ce3+ photoluminescence decay and an additional less intense slower component is also observed. Physical aspects of energy transfer process and 5d1 excited state depopulation are discussed. The micro-pulling down technique is shown as an ideal tool for a directed combinatorial search for targeted single crystal compositions to reveal those with the highest figure-of-merit for a given application field.
On the current density limiting effect in SF6-based mixtures
Authors: Belevtsev A A , Firsov K N , Kazantsev S Yu , Kononov I G , Podlesnykh S V 
Published: December 2011

Abstract
This paper reports on the investigation of the current density limiting effect in a self-sustained volume discharge in SF6-based mixtures due to a self-action of the discharge current on the media it passes through. The mechanism of this phenomenon in terms of electron-impact dissociation is examined. The argument is advanced that in the planar geometry the limiting effect treated may provoke triggering a spatially uniform volume discharge in the media stated even in the absence of pre-ionization. It is shown that the dissociation mathematics developed by the authors allows the quantitative estimation of the averaged expenditures of energy per formation of a dissociation fragment. Specifically, when applied to pure SF6 this finding enables the assessment of the energy spent for F-atom formation. For the first time the influence of current pulse duration on the discharge voltage has been experimentally revealed. Both thorough qualitative and quantitative considerations including relevant numerical simulation have been performed.
Defect-related energy structures of AlN nanotips probed by photoluminescence
Authors: Chen Haitao , Chen Guoshuai , Zhou Xuming , Zhu Wenming , Chen Xiaobing , Zeng Xianghua 
Published: December 2011

Abstract
Large-scale AlN nanotip arrays were fabricated via a facile catalysis-free approach using AlCl3 powder and NH3 as starting materials. These nanotips exhibit two intense broad emissions centred at about 375 and 480 nm. Both bands do not change significantly or freeze out at a low temperature, showing the features of photoionization of deep donor electrons. Photoluminescence and photoluminescence excitation spectral examination as well as the possible mechanism involved are systematically investigated. It reveals that the two bands are connected with the electronic states determined by the nitrogen vacancy and complex defects. The related energy structures are also provided. This work provides a possible mechanism for defect-related emissions in various AlN nanostructures.
Genetic Architecture of Maize Kernel Composition in the Nested Association Mapping and Inbred Association Panels
Authors: Cook Jason P. , McMullen Michael D. , Holland James B. , Tian Feng , Bradbury Peter , Ross-Ibarra Jeffrey , Buckler Edward S. , Flint-Garcia Sherry A. 
Published: December 2011

Abstract
The maize (Zea mays) kernel plays a critical role in feeding humans and livestock around the world and in a wide array of industrial applications. An understanding of the regulation of kernel starch, protein, and oil is needed in order to manipulate composition to meet future needs. We conducted joint-linkage quantitative trait locus mapping and genome-wide association studies (GWAS) for kernel starch, protein, and oil in the maize nested association mapping population, composed of 25 recombinant inbred line families derived from diverse inbred lines. Joint-linkage mapping revealed that the genetic architecture of kernel composition traits is controlled by 21–26 quantitative trait loci. Numerous GWAS associations were detected, including several oil and starch associations in acyl-CoA:diacylglycerol acyltransferase1-2, a gene that regulates oil composition and quantity. Results from nested association mapping were verified in a 282 inbred association panel using both GWAS and candidate gene association approaches. We identified many beneficial alleles that will be useful for improving kernel starch, protein, and oil content.
Hybrid Incompatibility in Arabidopsis Is Determined by a Multiple-Locus Genetic Network
Authors: Burkart-Waco Diana , Josefsson Caroline , Dilkes Brian , Kozloff Nora , Torjek Otto , Meyer Rhonda , Altmann Thomas , Comai Luca 
Published: December 2011

AbstractThe cross between Arabidopsis thaliana and the closely related species Arabidopsis arenosa results in postzygotic hybrid incompatibility, manifested as seed death. Ecotypes of A. thaliana were tested for their ability to produce live seed when crossed to A. arenosa. The identified genetic variation was used to map quantitative trait loci (QTLs) encoded by the A. thaliana genome that affect the frequency of postzygotic lethality and the phenotypes of surviving seeds. Seven QTLs affecting the A. thaliana component of this hybrid incompatibility were identified by crossing a Columbia × C24 recombinant inbred line population to diploid A. arenosa pollen donors. Additional epistatic loci were identified based on their pairwise interaction with one or several of these QTLs. Epistatic interactions were detected for all seven QTLs. The two largest additive QTLs were subjected to fine-mapping, indicating the action of at least two genes in each. The topology of this network reveals a large set of minor-effect loci from the maternal genome controlling hybrid growth and viability at different developmental stages. Our study establishes a framework that will enable the identification and characterization of genes and pathways in A. thaliana responsible for hybrid lethality in the A. thaliana × A. arenosa interspecific cross.
MaizeRough Endosperm3Encodes an RNA Splicing Factor Required for Endosperm Cell Differentiation and Has a Nonautonomous Effect on Embryo Development
Authors: Fouquet Romain , Martin Federico , Fajardo Diego S. , Gault Christine M. , Gómez Elisa , Tseung Chi-Wah , Policht Tyler , Hueros Gregorio , Settles A. Mark 
Published: December 2011

AbstractEndosperm and embryo development are coordinated via epigenetic regulation and signaling between these tissues. In maize (Zea mays), the endosperm–embryo signals are not known, but endosperm cellularization is a key event for embryos to form shoots and roots. We screened seed mutants for nonautonomous functions in endosperm and embryo development with genetically nonconcordant seeds and identified the recessive mutant rough endosperm3 (rgh3). The wild-type Rgh3 allele is required in the endosperm for embryos to develop and has an autonomous role in embryo and seedling development. Endosperm cell differentiation is defective in rgh3. Results from endosperm cell culture indicate that rgh3 mutants remain in a proliferative state through mid-seed development. Rgh3 encodes the maize U2AF35 Related Protein (URP), an RNA splicing factor involved in both U2 and U12 splicing. The Rgh3 allele produces at least 19 alternative splice variants with only one isoform encoding a full-length ortholog to URP. The full-length RGH3α isoform localizes to the nucleolus and displays a speckled pattern within the nucleoplasm, and RGH3α colocalizes with U2AF65. A survey of alternatively spliced transcripts found that, in the rgh3 mutant, a fraction of noncanonical splicing events are altered. Our findings suggest that differentiation of maize endosperm cell types is necessary for embryos to develop. The molecular cloning of Rgh3 suggests that alternative RNA splicing is needed for cell differentiation, development, and plant viability.
Evaluation of cheating detection methods in academic writings
Authors: Patel Ahmed , Bakhtiyari Kaveh , Taghavi Mona 
Published: December 2011

PurposeThis paper aims to focus on plagiarism and the consequences of anti‐plagiarism services such as Turnitin.com, iThenticate, and PlagiarismDetect.com in detecting the most recent cheatings in academic and other writings.Design/methodology/approachThe most important approach is plagiarism prevention and finding proper solutions for detecting more complex kinds of plagiarism through natural language processing and artificial intelligence self‐learning techniques.FindingsThe research shows that most of the anti‐plagiarism services can be cracked through different methods and artificial intelligence techniques can help to improve the performance of the detection procedure.Research limitations/implicationsAccessing entire data and plagiarism algorithms is not possible completely, so comparing is just based on the outputs from detection services. They may produce different results on the same inputs.Practical implicationsAcademic papers and web pages are increasing over time, and it is very difficult to capture and compare documents with all available data on the network in an up to date manner.Originality/valueAs many students and researchers use the plagiarism techniques (e.g. PDF locking, ghost‐writers, dot replacement, online translators, previous works, fake bibliography) to cheat in academic writing, this paper is intended to prevent plagiarism and find suitable solutions for detecting more complex kinds of plagiarism. This should also be of grave concern to teachers and librarians to provide up to date/standard anti‐plagiarism services. The paper proposes some new solutions to overcome these problems and to create more resilient and intelligent future systems.
Archiving in the networked world: preserving plagiarized works
Authors: Seadle Michael 
Published: December 2011

PurposePlagiarism has become a salient issue for universities and thus for university libraries in recent years. This paper aims to discuss three interrelated aspects of preserving plagiarized works: collection development issues, copyright problems, and technological requirements. Too often these three are handled separately even though in fact each has an influence on the other.Design/methodology/approachThe paper looks first at the ingest process (called the Submission Information Package or SIP), then at storage management in the archive (the AIP or Archival Information Package), and finally at the retrieval process (the DIP or Distribution Information Package).FindingsThe chief argument of this paper is that works of plagiarism and the evidence exposing them are complex objects, technically, legally and culturally. Merely treating them like any other work needing preservation runs the risk of encountering problems on one of those three fronts.Practical implicationsThis is a problem, since currently many public preservation strategies focus on ingesting large amounts of self‐contained content that resembles print on paper, rather than on online works that need special handling. Archival systems also often deliberately ignore the cultural issues that affect future usability.Originality/valueThe paper discusses special handling and special considerations for archiving works of plagiarism.
Laying the information literacy foundation: a multiple‐media solution
Authors: Gustavson Amy , Whitehurst Angela , Hisle David 
Published: December 2011

PurposeThis paper seeks to provide a solution for teaching comprehensive information literacy instruction when time is limited during one‐shot library instruction sessions. It aims to focus on one technique to solve this dilemma – the creation of a multi‐media tutorial: Library 101: Introduction to Research. The paper aims to educate librarians of the many technological tools, which could be employed to enrich library instruction.Design/methodology/approachUsing the Oakleaf Information Literacy Instruction Assessment Cycle (ILIAC), librarians gathered assessment data and determined student research skill deficits in Fall 2009. To address knowledge gaps, the authors systematically designed a multi‐media tutorial with ten tools.FindingsThe paper finds that the tutorial identified students' areas of weakness prior to library instruction. As a result, librarians could focus on identified topics during the session and increase student learning. Annual re‐evaluation of the tools and data are needed in order to update the program and ensure student learning occurs.Research limitations/implicationsThe limitations of the creation process include incomplete software evaluation early in the process, learning how to collaborate with different project management styles, developing a realistic timeline, and the need for a robust assessment management system to collect data. The effectiveness of this tutorial needs more empirical evaluation.Practical implicationsThe paper may help inform those planning to create a tutorial by suggesting useful, low‐cost tools for its creation and determining how to incorporate student learning outcomes and assessment into asynchronous instruction.Originality/valueThis paper fulfills an identified need to determine students' knowledge gaps through learning outcome assessment and respond to these gaps with asynchronous instruction methods.
Whether big deals are really big for engineering college libraries?
Authors: Nagaraja Aragudige , Gangadhar K.C. , Vasanthakumar M. 
Published: December 2011

PurposeLibrary consortia have played a vital role in sharing information resources among participating libraries. In India, engineering college libraries subscribe to many electronic resources through the Indian Digital Library of Engineering Science and Technology (INDEST) consortium. This paper aims to identify the collection development of electronic resources through INDEST to predict the most required and useful model for engineering colleges.Design/methodology/approachThe list of colleges that subscribe to electronic resources through INDEST was studied online and analyzed.FindingsIt is evident that most colleges only subscribed IEL online through INDEST. Some colleges have subscribed to different resources from more than one publisher. The bundles of resources subscribed through INDEST have not fully supported all the courses offered by the institutions. It is revealed that the bibliographical databases for searching the literature in technological sciences were not subscribed to by any colleges participating in INDEST.Originality/valueThe results of this study are useful for engineering college libraries to develop the collection of online journals in the digital era.
Opening the “black box”
Authors: Cavélius Florence 
Published: December 2011

PurposeInstitutional investors use the information disclosed by listed companies to analyze the performance of their investments. The purpose of this paper is to open the “black box” of the construction of financial disclosure by analyzing the internal reporting systems of firms with reference to the information disclosed.Design/methodology/approachUsing indexes, the quality of the financial disclosure and the internal reporting systems are measured, and analyzed with a view to finding some links between them. It is expected that the quality of disclosure is dependent on the quality of the internal reporting.FindingsComplex interactions between internal reporting and financial disclosure are revealed, which leads to the identification of a typology of practices. The dependence of the relationship may be troubled by the willingness of the firm to communicate, or by the internal methods of control. According to the various cases, different levels of usefulness of the information for the investor are expected.Originality/valueThis paper is a first attempt to analyse information disclosed by firms with regards to the internal information at their disposal.
The role of the balanced scorecard in the formulation and control of strategic processes
Authors: Naro Gérald , Travaillé Denis 
Published: December 2011

PurposeThe aim of this paper is to confront the Balanced Scorecard (BSC) with Simons’ levers of control model and to discuss its role in the various phases of the strategic process. The authors examine the role of the BSC as a tool of interactive and diagnostic control by making a distinction between its design phase and its phase of use.Design/methodology/approachAn action research approach, based on two cases, was used to investigate the role of the balanced scorecard in strategic processes.FindingsThe results show that the BSC generates a process of collective elucidation favouring the forming of emergent strategies and a process of control of the change favouring the collective representations on the strategy. The BSC thus seems to be a relevant tool for interactive control during its implementation stage. On the other hand, the authors’ observations also show the failure of the BSC as a system of diagnostic control and of interactive control during its using stage. Ultimately, it is shown that the model of Simons provides the BSC with a relevant theoretical framework to clarify the practice of strategic control.Research limitations/implicationsThe study highlights the interest of field studies, and more particularly, processuals and longitudinal approaches, in management accounting research.Practical implicationsThe study of two cases underlines the strategic contribution of the BSC by highlighting its role in building a strategy.Originality/valueThe field study allows us to observe how the design of a management control tool such as the BSC occurs during the strategy‐forming phase.