bluuebunny/crossref_metadata_2025_split huggingface dataset:
Making sense and making use of Altmetrics in research evaluation
Authors: Bucknell Terry 
Published: December 2014

>> See video of presentation (35 min.) Monitoring and measuring the success of published research has long been a problematic area for institutions, funders and publishers. Recent government reviews, such as the Research Excellence Framework in the UK, have placed increasing demands on authors to provide substantial evidence of the academic and wider impact of their work. Over reliance on indices such as the Impact Factor has led to questionable tactics – with researchers seemingly choosing to submit work produced in the format that is most likely to have accrued impact demonstrated in the form of citations (i.e. published articles). But what about other outputs, and the other attention the work has received, and its application in real-world practices?Altmetrics, or alternative metrics, have evolved in the last few years as an alternative to only using the Impact Factor, and offer a much richer picture of how a piece of research has been received. Instead of only looking at how the work is received within academia (most often via a citation count) altmetrics track the sharing and discussion of research in a much wider range of online sources – including global traditional and social media, post-publication peer-review forums, and public policy documents.A focus on the qualitative data rather than the quantitative enables a better understanding of where and why the work is being discussed and potentially put into practice. It also offers a chance to focus on an individual article instead of making an assumption based on the perceived quality of the journal it is published in – a key pain point for those involved in research evaluation.A relatively new field, there is still much work to be done into what, why, and how the attention surrounding a paper should (or should not) be measured. There is already a justified concern that they will simply become another number by which a researcher can be judged, and a danger that they will be used to indicate quality where in reality they can offer nothing of the sort.What they do provide, however, is a valuable insight into the wider reception of research, and in a much more immediate way than citation counts alone are able to give. New tools are being developed at a rapid pace to enable institutions and funders to more easily track where the research their authors publish is being picked up – to help identify success stories and to further validate their knowledge of their audiences.We will give a brief overview of the progress within the field of altmetrics to date, including tangible use cases amongst academics and institutional managers, and explore how by pulling together academic impact (the more traditional bibliometrics) and the wider societal impact (altmetrics) it is possible to benefit from delving deeper into the context and engagement surrounding research.
Data policies and data archives as prerequisites of reproducible published research in economics journals
Authors: Vlaeminck Sven 
Published: December 2014

>> See video of presentation (19 min.) In economics - as in many other branches of the social sciences- collaboratively working on data and sharing data is not very common, yet. This is also reflected in the professions’ journals, where policies on data management and data sharing currently exist for a small minority of journals only.I would like to introduce the presentation with some empirical results of a survey, in which economists working for the project EDaWaX (European Data Watch, a project funded by the German Research Foundation) analysed the data sharing behaviour of 488 US and European applied economists. Subsequently we give an overview on data policies of journals in economics and business studies. In the course of the EDaWaX project, the data policies in a sample of more than 300 economics journals have been analysed. The talk suggests guidelines for data policies aiming to foster replication of published research and presents some characteristics of journals equipped with those data policies as well as the status quo in disseminating underlying research data of empirically based articles.Against this analytical background the talk identifies some challenges associated with the current e-infrastructure for providing publication-related research data by journals. The presentation also shows a technical solution for some of these challenges. In particular, the talk presents a pilot application for a publication-related data archive for scholarly journals in the social sciences, which has been developed in the first funding phase of the EDaWaX-project. The aim of this open source tool is to empower editors of scholarly journals to easily manage research data for empirically based articles in their journals. The application mainly targets open research data but is also capable of interlinking data and publications even in the case of confidential or proprietary data.In conclusion the talk outlines the further development of our application and sketches other tasks of the project’s second funding phase.More information on the project is available on www.edawax.de
NMR Analysis of Base‐Pair Opening Kinetics in DNA
Authors: Szulik Marta W. , Voehler Markus , Stone Michael P. 
Published: December 2014

AbstractBase pairing in nucleic acids plays a crucial role in their structure and function. Differences in the base‐pair opening and closing kinetics of individual double‐stranded DNA sequences or between chemically modified base pairs provide insight into the recognition of these base pairs by DNA processing enzymes. This unit describes how to quantify the kinetics for localized base pairs by observing changes in the imino proton signals by nuclear magnetic resonance spectroscopy. The determination of all relevant parameters using state‐of‐the art techniques and NMR instrumentation, including cryoprobes, is discussed. © 2014 by John Wiley & Sons, Inc.
Detection of Hydrogen Bonds in Dynamic Regions of RNA by NMR Spectroscopy
Authors: Dallmann Andre , Sattler Michael 
Published: December 2014

AbstractNMR spectroscopy is a powerful tool to study the structure and dynamics of nucleic acids. In this unit, we give an overview of important experiments to determine and characterize hydrogen bonds in nucleic acids and provide detailed instructions for setting up recently developed sensitivity‐improved NMR pulse sequences, i.e., BEST selective long‐range HNN‐COSY, selective BEST‐TROSY‐HNNCOSY, and Py H(CC)NN‐COSY. The strengths and limitations of these experiments will also be discussed. Detailed step‐by‐step protocols are provided for each of the three pulse sequences, with special emphasis on adjusting and setting of delays and shaped pulses. The NMR pulse sequences with example datasets and optimized, nonstandard adiabatic pulse shapes used for selective 15N magnetization transfer are provided. These experiments enable NMR analysis of a broad variety of RNAs ranging from low to high molecular weight and complexity. © 2014 by John Wiley & Sons, Inc.
Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services
Authors: Lopez Rodrigo , Cowley Andrew , Li Weizhong , McWilliam Hamish 
Published: December 2014

AbstractThe European Bioinformatics Institute (EMBL‐EBI) provides access to a wide range of databases and analysis tools that are of key importance in bioinformatics. As well as providing Web interfaces to these resources, Web Services are available using SOAP and REST protocols that enable programmatic access to our resources and allow their integration into other applications and analytical workflows. This unit describes the various options available to a typical researcher or bioinformatician who wishes to use our resources via Web interface or programmatically via a range of programming languages. © 2014 by John Wiley & Sons, Inc.
Clustal Omega
Authors: Sievers Fabian , Higgins Desmond G. 
Published: December 2014

AbstractClustal Omega is a package for making multiple sequence alignments of amino acid or nucleotide sequences, quickly and accurately. It is a complete upgrade and rewrite of earlier Clustal programs. This unit describes how to run Clustal Omega interactively from a command line, although it can also be run online from several sites. The unit describes a basic protocol for taking a set of unaligned sequences and producing a full alignment. There are also protocols for using an external HMM or iteration to help improve an alignment. © 2014 by John Wiley & Sons, Inc.
Detection of small‐scale folds at a solar wind reconnection exhaust
Authors: Mistry R. , Eastwood J. P. , Hietala H. 
Published: December 2014

AbstractObservations of reconnection in the solar wind over the last few years appear to indicate that the majority of large‐scale reconnecting current sheets are roughly planar, and that reconnection itself is quasi‐steady. Most studies of solar wind exhausts have used spacecraft with large separations and relatively low time cadence ion measurements. Here we present multipoint Cluster observations of a reconnection exhaust and the associated current sheet at ACE and Wind, enabling it to be studied on multiple length scales and at high time resolution. While analysis shows that on large scales the current sheet is planar, detailed measurements using the four closely spaced Cluster spacecraft show that the trailing edge of the reconnection jet is nonplanar with folds orthogonal to the reconnection plane, with length scales of approximately 230 ion inertial lengths. Our findings thus suggest that while solar wind current sheets undergoing reconnection may be planar on large scales, they may also exhibit complex smaller‐scale structure. Such structure is difficult to observe and has rarely been detected because exhausts are rapidly convected past the spacecraft in a single cut; there is therefore a limited set of spacecraft trajectories through the exhaust which would allow the nonplanar features to be intercepted. We consider how such nonplanar reconnection current sheets can form and the processes which may have generated the 3‐D structure that was observed.
Diel cycle of lake‐air CO2 flux from a shallow lake and the impact of waterside convection on the transfer velocity
Authors: Podgrajsek E. , Sahlée E. , Rutgersson A. 
Published: December 2014

AbstractTwo years of eddy covariance measurements of lake carbon dioxide (CO2) fluxes reveal a diel cycle with higher fluxes during night. Measurements of partial pressure in the air (pCO2a) and in the water (pCO2w), during 4 months, show that the high nighttime fluxes are not explained by changes in the difference between pCO2a and pCO2w. Analyzing the transfer velocity (k600,meas), which is a measure of the efficiency of the gas transfer, with respect to wind speed, shows that variations in wind speed do not explain the diel cycle. During nighttime, when the fluxes are high, the wind is normally low. Thus, a solely wind‐based parameterization of the transfer velocity (ku,CC) results in large errors compared to k600,meas, especially for wind speeds lower than 6 m s−1. The mean absolute percentage error between ku,CC and k600,meas is 79%. By subtracting ku,CC from k600,meas, we investigate how waterside convection influence k600,meas. Our results show that the difference (k600,meas − ku,CC) increases with increasing waterside convection. Separating the transfer velocity parameterization in two parts, one depending on the wind speed and one depending on waterside convection, the mean absolute percentage error compared to the measurements reduces to 22%. The results in this paper show that the high nighttime CO2 fluxes can, to a large extent, be explained by waterside convection and that a transfer velocity parameterization based on both wind speed and waterside convection better fits the measurements compared to a parameterization based solely on wind speed.
Evidence of a change in water chemistry in Canada's subarctic associated with enhanced winter streamflow
Authors: Spence C. , Kokelj S. V. , Kokelj S. A. , McCluskie M. , Hedstrom N. 
Published: December 2014

AbstractEnhanced winter streamflow is a characteristic of a nival/pluvial regime that has emerged in parts of the subarctic Canadian Shield because of increasingly common late summer rains. This phenomenon is part of a widespread trend toward higher winter streamflow in watersheds across the circumpolar north. There may be implications for biogeochemical systems as streamflow regimes undergo these types of changes associated with climate warming. Streamflow and geochemical fluxes were observed over 2 years with different winter flow conditions in a subarctic Canadian Shield catchment. Results show that higher wintertime loads of carbon and solutes associated with enhanced winter streamflow were in association with an expansion of contributing areas to run off over what would have existed during typical winter recession. Furthermore, the wet fall conditions that lead to enhanced winter streamflow require water tables close to the topographic surface in highly conductive organic soil layers, which is a similar to the condition during the spring melt. Fall rainfall‐runoff leaves an ample volume of water in the lakes that are ubiquitous in this landscape. This water maintains winter streamflow during a time when it traditionally would have ceased. A slowing of biological activity under lake ice increases net mineralization and nitrification rates. This convergence of nitrogen cycling and winter streamflow produced a disproportionate flux of inorganic nitrogen from the study catchment. A conceptual model of how enhanced winter streamflow changes water chemistry in a lake‐dominated shield landscape is proposed and may be used as a benchmark to guide hypotheses of process interactions, change in other landscapes, or across scales.
Metal‐Organic Frameworks: Coordination Polymer Nanoparticles and Macrostructures
Authors: Reboul Julien , Kitagawa Susumu 
Published: December 2014

Abstract
Organization at the atomic scale of metal cations by connecting them with organic linkers leads to the construction of hybrid crystalline microporous frameworks, also known as porous coordination polymers (PCPs). Owing to their high loading capacity and their chemical composition versatility, PCPs are attractive for applications such as gas storage, catalysis, sensing, proton conduction, or adsorptive separation. Beside the conventional research that aims at designing PCP crystal characteristics at the molecular scale, recent research efforts focused on the modulation of the crystal size and shape and on the synthesis of polycrystalline macrostructures with well‐defined morphologies. Indeed, a major challenge today is to develop strategies that allow the integration of PCPs into readily applicable devices, which fully exploit the attributes of these promising materials. The highly reactive surfaces of PCPs (composed of partially coordinated organic ligands or uncoordinated metal centers), the possible modulation of the coordination equilibrium at the crystal surface, and the large number of PCP frameworks available (implying a large range of possible synthesis conditions) make their synthesis compatible with a wide range of physicochemical and mechanical microfabrication methods. Syntheses of uniform PCP nanocrystal suspensions, crystal assemblies in the form of membranes, pattern surfaces, hollow spheres, coatings, or multiporous architectures were therefore reported. This chapter aims to review the most promising strategies reported so far to synthesize PCP nanocrystals and PCP‐based macrostructures and composites.
Metal‐Organic Frameworks: Aluminium‐Based Frameworks
Authors: Stock Norbert 
Published: December 2014

Abstract
Metal–organic frameworks (MOFs) containing light and environmentally benign metals have attracted researchers from industry and academia since they are believed to be well suited for applications especially in the field of gas storage. Aluminum is one element of choice for the synthesis of such MOFs since it leads to stable and highly porous materials that can also be formed in water as a green solvent. The stability and the small number of Al‐based MOFs stems from the same factors: the high charge (+3) of the metal ion and the small ionic radius. Hence dissolution of these MOFs in water is often kinetically hindered and at the same time they are almost exclusively obtained as microcrystalline products. The latter fact has impeded the structure elucidation and the determination of structure property relationships and hence the intensive investigation of this class of compounds. Recent progress in the synthesis and characterization of Al‐MOFs has demonstrated that certain structural motifs are predominantly observed, depending on the substitution pattern of the polycarboxylate based linker molecules and the solvent employed. Here, the synthesis and structural trends in Al‐based MOFs are summarized.
Metal‐Organic Frameworks: Mechanochemical Synthesis Strategies
Authors: Friščić Tomislav 
Published: December 2014

Abstract
This contribution provides a systematic overview of the recent developments in the use of mechanochemical synthesis, i.e., chemical synthesis aided or induced by mechanical force, for making one‐, two‐, and three‐dimensional coordination polymers, including porous metal–organic frameworks (MOFs). The overview is organized into sections that address experimental mechanochemical techniques, types of chemical reactions utilized for the mechanosynthesis of coordination polymers, structural characterization of mechanochemical products, as well as synthetic strategies and reaction mechanisms underlying the mechanochemical assembly of porous MOF structures. The presented examples reveal mechanochemistry as a reliable and natural way for conducting the synthesis of porous MOFs in a rapid, clean, and efficient fashion, as well as a new tool to screen for new MOF topologies and probe the fundamental structure templating factors controlling their assembly.
Automatisierte Detektion von Proteinphosphorylierung durch Nanoliter‐Enzymreaktionen auf Mikroarrays
Authors: Küster Simon K. , Pabst Martin , Zenobi Renato , Dittrich Petra S. 
Published: December 2014

AbstractWir beschreiben eine neue, empfindliche Screening‐Methode zur Detektion von Proteinphosphorylierung in komplexen Proteinproben. Der proteolytische Verdau einer Probe wird zuerst mithilfe von nano‐Flüssigchromatographie (nano‐LC) aufgetrennt, das Eluat wird unmittelbar danach hochfrequent in Mikrotröpfchen kompartimentiert und schließlich auf eine Mikroarray‐MALDI‐Platte abgelegt. Nach Aufbringen eines Ölfilms werden pL‐Tröpfchen einer Phosphataselösung zu jeder zweiten Fraktion auf der Mikroarray‐Platte hinzugefügt. Dies induziert in den Fraktionen eine Verschiebung der Massen der phosphorylierten Peptide um n×−80 Da und führt somit zu einem Zickzackprofil des chromatographischen Peaks. Zur Identifizierung wird nun die MALDI‐MS‐Spur der gesamten Trennung von einem Matlab‐Skript auf diese induzierten chromatographischen Peakmuster hin untersucht, wodurch auch Phosphopeptide von sehr geringer Intensität erkannt werden. Die hier vorgestellte Screening‐Methode verwendet keine Peaklisten und es bedarf auch keiner umfangreichen MS/MS‐Experimente.
Total Synthesis of Albicidin: A Lead Structure from Xanthomonas albilineans for Potent Antibacterial Gyrase Inhibitors
Authors: Kretz Julian , Kerwat Dennis , Schubert Vivien , Grätz Stefan , Pesic Alexander , Semsary Siamak , Cociancich Stéphane , Royer Monique , Süssmuth Roderich D. 
Published: December 2014

AbstractThe peptide antibiotic albicidin, which is synthesized by the plant pathogenic bacterium Xanthomonas albilineans, displays remarkable antibacterial activity against various Gram‐positive and Gram‐negative microorganisms. The low amounts of albicidin obtainable from the producing organism or through heterologous expression are limiting factors in providing sufficient material for bioactivity profiling and structure–activity studies. Therefore, we developed a convergent total synthesis route toward albicidin. The unexpectedly difficult formation of amide bonds between the aromatic amino acids was achieved through a triphosgene‐mediated coupling strategy. The herein presented synthesis of albicidin confirms the previously determined chemical structure and underlines the extraordinary antibacterial activity of this compound. The synthetic protocol will provide multigram amounts of albicidin for further profiling of its drug properties.
The fabrication of full color P(St‐MAA) photonic crystal structure on polyester fabrics by vertical deposition self‐assembly
Authors: Liu Guojin , Zhou Lan , Wu Yujiang , Wang Cuicui , Fan Qinguo , Shao Jianzhong 
Published: December 2014

ABSTRACTThree‐dimensional (3D) photonic crystals with face‐centered cubic structure were successfully fabricated on soft polyester fabrics via vertical deposition self‐assembly, with monodisperse P(St‐MAA) microspheres prepared by soap‐free emulsion copolymerization. The resultant polyester fabrics exhibited bright structural colors through the well‐ordered photonic crystal microstructure without any chemical dyes and pigments. The tunable structural colors across the whole visible region confirmed by reflectance spectra could be adjusted by controlling the diameters of the microspheres and viewing angles, and this was consistent with the law of the Bragg diffraction. The resultant polyester fabrics also presented some favorable properties including double‐sided coloration effect, clear fabric texture, and soft fabric handle. The structural coloration by vertical deposition self‐assembly of P(St‐MAA) photonic crystals may provide a new strategy for textile coloration without using chemical colorants, and have a potential to reduce the pollution in the current textile dyeing and printing processes. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 41750.
Flammability and thermal behaviors of polypropylene composite containing modified kaolinite
Authors: Tang Wufei , Gu Xiaoyu , Jiang Yu , Zhao Jingran , Ma Wenjun , Jiang Peng , Zhang Sheng 
Published: December 2014

ABSTRACTExfoliatied kaolinite (E‐Kaol) was prepared by intercalating DMSO and KAc into kaolinite successively followed by irradiation under ultrasonic. The modified kaolinite was then introduced to polypropylene (PP) by melt blending in order to improve the fire performance of the composite. The flammability and thermal behaviors of PP composite were analyzed by limit oxygen index, vertical burning test, cone calorimeter test, and thermal‐gravimetric analysis, respectively. The microstructure of PP composites was characterized by Fourier‐transformed infrared spectroscopy, X‐ray diffraction, and scanning electron microscope (SEM). It was demonstrated the presence of only 1 phr E‐Kaol could improve the LOI values of PP/MCAPP/ATH composite from 26.4 to 28.0, and decrease the peak value of heat release rate and smoke production rate of the PP/MCAPP/ATH by 60.7% and 39.1%, respectively, compared with that of PP sample. Morphology analysis by SEM showed that E‐Kaol in PP composite was beneficial to forming rigid and compact char structure. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 41761.