bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early crocodylomorph increases top tier predator diversity during rise of dinosaurs
Authors: Zanno Lindsay E. , Drymala Susan , Nesbitt Sterling J. , Schneider Vincent P. 
Published: March 2015

AbstractTriassic predatory guild evolution reflects a period of ecological flux spurred by the catastrophic end-Permian mass extinction and terminating with the global ecological dominance of dinosaurs in the early Jurassic. In responding to this dynamic ecospace, terrestrial predator diversity attained new levels, prompting unique trophic webs with a seeming overabundance of carnivorous taxa and the evolution of entirely new predatory clades. Key among these was Crocodylomorpha, the largest living reptiles and only one of two archosaurian lineages that survive to the present day. In contrast to their existing role as top, semi-aquatic predators, the earliest crocodylomorphs were generally small-bodied, terrestrial faunivores, occupying subsidiary (meso) predator roles. Here we describe Carnufexcarolinensis a new, unexpectedly large-bodied taxon with a slender and ornamented skull from the Carnian Pekin Formation (~231 Ma), representing one of the oldest and earliest diverging crocodylomorphs described to date. Carnufex bridges a problematic gap in the early evolution of pseudosuchians by spanning key transitions in bauplan evolution and body mass near the origin of Crocodylomorpha. With a skull length of >50 cm, the new taxon documents a rare instance of crocodylomorphs ascending to top-tier predator guilds in the equatorial regions of Pangea prior to the dominance of dinosaurs.
High-resolution far-field ghost imaging via sparsity constraint
Authors: Gong Wenlin , Han Shensheng 
Published: March 2015

AbstractGhost imaging (GI) is a method to nonlocally image an object with a single-pixel detector. However, the speckle's transverse size at the object plane limits the system's imaging resolution for conventional GI linear reconstruction algorithm. By combining the sparsity constraint of imaging object with ghost imaging method, we demonstrate experimentally that ghost imaging via sparsity constraint (GISC) can dramatically enhance the imaging resolution even using the random measurements far below the Nyquist limit. The image reconstruction algorithm of GISC is based on compressive sensing. Factors affecting the reconstruction quality of high-resolution GISC, such as the receiving system's numerical aperture and the object's sparse representation basis, are also investigated experimentally. This high-resolution imaging technique will have great applications in the microscopy and remote-sensing areas.
Self-generated Local Heating Induced Nanojoining for Room Temperature Pressureless Flexible Electronic Packaging
Authors: Peng Peng , Hu Anming , Gerlich Adrian P. , Liu Yangai , Zhou Y. Norman 
Published: March 2015

AbstractMetallic bonding at an interface is determined by the application of heat and/or pressure. The means by which these are applied are the most critical for joining nanoscale structures. The present study considers the feasibility of room-temperature pressureless joining of copper wires using water-based silver nanowire paste. A novel mechanism of self-generated local heating within the silver nanowire paste and copper substrate system promotes the joining of silver-to-silver and silver-to-copper without any external energy input. The localized heat energy was delivered in-situ to the interfaces to promote atomic diffusion and metallic bond formation with the bulk component temperature stays near room-temperature. This local heating effect has been detected experimentally and confirmed by calculation. The joints formed at room-temperature without pressure achieve a tensile strength of 5.7 MPa and exhibit ultra-low resistivity in the range of 101.3 nOhm·m. The good conductivity of the joint is attributed to the removal of organic compounds in the paste and metallic bonding of silver-to-copper and silver-to-silver. The water-based silver nanowire paste filler material is successfully applied to various flexible substrates for room temperature bonding. The use of chemically generated local heating may become a potential method for energy in-situ delivery at micro/nanoscale.
Role of liposome and peptide in the synergistic enhancement of transfection with a lipopolyplex vector
Authors: Munye Mustafa M. , Ravi Jascindra , Tagalakis Aristides D. , McCarthy David , Ryadnov Maxim G. , Hart Stephen L. 
Published: March 2015

AbstractLipopolyplexes are of widespread interest for gene therapy due to their multifunctionality and high transfection efficiencies. Here we compared the biological and biophysical properties of a lipopolyplex formulation with its lipoplex and polyplex equivalents to assess the role of the lipid and peptide components in the formation and function of the lipopolyplex formulation. We show that peptide efficiently packaged plasmid DNA forming spherical, highly cationic nanocomplexes that are taken up efficiently by cells. However, transgene expression was poor, most likely due to endosomal degradation since the polyplex lacks membrane trafficking properties. In addition the strong peptide-DNA interaction may prevent plasmid release from the complex and so limit plasmid DNA availability. Lipid/DNA lipoplexes, on the other hand, produced aggregated masses that showed poorer cellular uptake than the polyplex but contrastingly greater levels of transgene expression. This may be due to the greater ability of lipoplexes relative to polyplexes to promote endosomal escape. Lipopolyplex formulations formed spherical, cationic nanocomplexes with efficient cellular uptake and significantly enhanced transfection efficiency. The lipopolyplexes combined the optimal features of lipoplexes and polyplexes showing optimal cell uptake, endosomal escape and availability of plasmid for transcription, thus explaining the synergistic increase in transfection efficiency.
Probing Immobilization Mechanism of alpha-chymotrypsin onto Carbon Nanotube in Organic Media by Molecular Dynamics Simulation
Authors: Zhang Liyun , Xiao Xiuchan , Yuan Yuan , Guo Yanzhi , Li Menglong , Pu Xuemei 
Published: March 2015

AbstractThe enzyme immobilization has been adopted to enhance the activity and stability of enzymes in non-aqueous enzymatic catalysis. However, the activation and stabilization mechanism has been poorly understood on experiments. Thus, we used molecular dynamics simulation to study the adsorption of α-chymotrypsin (α-ChT) on carbon nanotube (CNT) in aqueous solution and heptane media. The results indicate that α-ChT has stronger affinity with CNT in aqueous solution than in heptane media, as confirmed by more adsorption atoms, larger contact area and higher binding free energies. Although the immobilization causes significant structure deviations from the crystal one, no significant changes in secondary structure of the enzyme upon adsorption are observed in the two media. Different from aqueous solution, the stabilization effects on some local regions far from the surface of CNT were observed in heptane media, in particular for S1 pocket, which should contribute to the preservation of specificity reported by experiments. Also, CNT displays to some extent stabilization role in retaining the catalytic H-bond network of the active site in heptane media, which should be associated with the enhanced activity of enzymes. The observations from the work can provide valuable information for improving the catalytic properties of enzymes in non-aqueous media.
Palladium-Mediated Dealkylation of N-Propargyl-Floxuridine as a Bioorthogonal Oxygen-Independent Prodrug Strategy
Authors: Weiss Jason T. , Carragher Neil O. , Unciti-Broceta Asier 
Published: March 2015

AbstractHerein we report the development and biological screening of a bioorthogonal palladium-labile prodrug of the nucleoside analogue floxuridine, a potent antineoplastic drug used in the clinic to treat advanced cancers. N-propargylation of the N3 position of its uracil ring resulted in a vast reduction of its biological activity (~6,250-fold). Cytotoxic properties were bioorthogonally rescued in cancer cell culture by heterogeneous palladium chemistry both in normoxia and hypoxia. Within the same environment, the reported chemo-reversible prodrug exhibited up to 1,450-fold difference of cytotoxicity whether it was in the absence or presence of the extracellular palladium source, underlining the precise modulation of bioactivity enabled by this bioorthogonally-activated prodrug strategy.
A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations
Authors: Miya Fuyuki , Kato Mitsuhiro , Shiohama Tadashi , Okamoto Nobuhiko , Saitoh Shinji , Yamasaki Mami , Shigemizu Daichi , Abe Tetsuo , Morizono Takashi , Boroevich Keith A. , Kosaki Kenjiro , Kanemura Yonehiro , Tsunoda Tatsuhiko 
Published: March 2015

AbstractWhole-exome sequencing (WES) is a useful method to identify disease-causing mutations, however, often no candidate mutations are identified using commonly available targeted probe sets. In a recent analysis, we also could not find candidate mutations for 20.9% (9/43) of our pedigrees with congenital neurological disorder using pre-designed capture probes (SureSelect V4 or V5). One possible cause for this lack of candidates is that standard WES cannot sequence all protein-coding sequences (CDS) due to capture probe design and regions of low coverage, which account for approximately 10% of all CDS regions. In this study, we combined a selective circularization-based target enrichment method (HaloPlex) with a hybrid capture method (SureSelect V5; WES) and achieved a more complete coverage of CDS regions (~97% of all CDS). We applied this approach to 7 (SureSelect V5) out of 9 pedigrees with no candidates through standard WES analysis and identified novel pathogenic mutations in one pedigree. The application of this effective combination of targeted enrichment methodologies can be expected to aid in the identification of novel pathogenic mutations previously missed by standard WES analysis.
A Unified Lorenz-Like System and Its Tracking Control*
Authors: Li Chun-Lai , Zhao Yi-Bo 
Published: March 2015

Abstract
This paper introduces the finding of a unified Lorenz-like system. By gradually tuning the only parameter d, the reported system belongs to Lorenz-type system in the sense defined by Člikovský. Meanwhile, this system belongs to Lorenz-type system, Lü-type system, Chen-type system with d less than, equivalent to and greater than 1.5, respectively, according to the classification defined by Yang. However, this system can only generate a succession of Lorenz-like attractors. Some basic dynamical properties of the system are investigated theoretically and numerically. Moreover, the tracking control of the system with exponential convergence rate is studied. Theoretical analysis and computer simulation show that the proposed scheme can allow us to drive the output variable x1 to arbitrary reference signals exponentially, and the guaranteed exponential convergence rate can be estimated accurately.
The Prediction of Wave Competitions in Inhomogeneous Brusselator Systems*
Authors: Cui Xiao-Hua , Dong Yun-Xia , Huang Xiao-Qing , Li Ning 
Published: March 2015

AbstractThe competition of waves has remained a hot topic in physics over the past few decades, especially the area of pattern control. Because of improved understanding of various dynamic behaviors, many practical applications have sprung up recently. The prediction of wave competitions is also very important and quite useful in these fields. This paper considers the behaviors of wave competitions in simple, inhomogeneous media which is modeled by Brusselator equations. We present a simple rule to judge the results of wave competitions utilizing the dispersion relation curves and the waves coming from different wave sources. Moreover, this rule can also be used to predict the results of wave propagation. It provides methods of obtaining the desired waves with given frequencies in inhomogeneous media. All our results are concluded and verified by computer simulations.
Reliability in Pragmatics
Authors: McCready E. 
Published: March 2015

AbstractThis book is an exploration of how knowledge about the reliability of information sources manifests itself in linguistic phenomena and use, focusing on cooperation in language use and how considerations of reliability influence what is done with the information acquired through language. Empirically, the book provides a detailed consideration of the phenomena of hedging and evidentiality and analyzes them using tools from game theory, dynamic semantics, and formal epistemology. Hedging is argued to be a mechanism used by speakers to protect their reputations for cooperativity from damage inflicted by infelicitous discourse moves. The pragmatics of evidential use is also stated in terms of the sorts of histories of interaction that influence reputation: on the analysis of the book, past experience with the evidence source indexed by the evidential determines how the process of adding information will proceed. The book makes many new connections between seemingly disparate aspects of linguistic meaning and practice.
Early Greek Relative Clauses
Authors: Probert Philomen 
Published: March 2015

AbstractThis book contributes to an old debate now enjoying a revival: should we expect languages spoken a few thousand years ago, such as Proto-Indo-European, to be less well-equipped than modern languages when it comes to subordinate clauses? Early Greek relative clauses provide a test case for this problem. Early Greek uses several kinds of relative clause, but all these are usually thought to come from one, or at most two, prehistoric types. In a new look at the evidence, this book finds that a rich variety of relative clause types has been in place for a considerable time. The reconstruction of prehistoric linguistic stages requires detailed work on the individual languages descending from them. A substantial part of the book is therefore devoted to a new look at the relative clause systems found in a wide variety of early Greek texts. It emerges that the same basic system is in use across all these texts. Different kinds of relative clause predominate in different kinds of text, however, because relative clause syntax and semantics interact with the needs of different kinds of text. The widespread currency of the same system across different dialects and genres speaks against the idea that significant aspects of this system were only just emerging. Moreover, in all the texts considered there is little genuine competition between the different constructions, such as we ought to find if some constructions were gaining ground from others. Each construction has its own syntactic and semantic conditions.
Introduction
Authors: Probert Philomen 
Published: March 2015

AbstractChapter 1 explains what the book is about, and how it is structured. The book has a middle and two outer layers. In the middle (chapters 4–13) is a serious new look at the synchronic systems of relative clauses found in several varieties of early Greek. This may be read on its own by those who simply want to know about early Greek relative clauses. The first outer layer (chapters 3 and 14) introduces a long-standing debate about relative clause syntax in the prehistory of the Indo-European language family, and considers how Greek evidence can contribute to this debate. The outermost layer (chapters 2 and 15) considers the implications for a broader debate about subordination in languages spoken a few thousand years ago. Chapter 1 also points out some of the things this book is not about (participial relative clauses, particles in relative clauses).
Matters of case
Authors: Probert Philomen 
Published: March 2015

AbstractChapter 7 introduces several problems concerning the case of the relative pronoun and of the ‘antecedent’, beginning with attractio inversa (in traditional terms, attraction of the antecedent into the case of the relative pronoun) and attractio relativi (traditionally, attraction of the relative pronoun into the case of the antecedent). Attractio relativi is a classical Greek phenomenon. This chapter argues that supposed earlier examples are unconvincing, as are supposed examples in Cretan inscriptions of the fifth century BC. However, in free relative clauses attractio relativi alleviates a problem that already exists in early Greek. Attractio relativi makes it easier to work out the syntactic role of a free relative clause in the sentence, under circumstances that make this difficult. Chapter 7 lays out the hypothesis that in the texts considered in this book, semi-free relative clauses and relative-correlative sentences are deployed to solve this problem.
Stellar Superfluids
Authors: Page D. , Lattimer J. M. , Prakash M. , Steiner A. W. 
Published: March 2015

AbstractThe roles of neutron superfluidity and proton superconductivity in neutron stars are discussed, focusing on both thermal evolution (i.e., cooling) as well as the dynamical evolution (i.e., spin-down). The existence of pairing in neutron stars is considered by examining the pairing phenomenon in laboratory nuclei. The properties of neutron stars are summarized, including their interior compositions and crusts. Pairing in dense matter, expectations of pairing in deconfined quark matter, and the various neutrino processes that occur in dense matter are discussed. Simplified analytical models of neutron star cooling are presented. The so-called minimal cooling paradigm supposes that enhanced neutrino emission processes are quickly quenched by superfluidity or superconductivity. The observation is considered of the first real-time cooling of any isolated neutron star—the young neutron star in the supernova remnant of Cassiopeia A. Other observations of neutron stars and their dynamical evolution may also indicate the presence of superfluidity.
4D-VAR: four-dimensional variational assimilation
Authors: Talagrand O. 
Published: March 2015

AbstractIn this chapter, four-dimensional variational assimilation (4D-VAR) is described in the context of statistical linear estimation, in which it defines the best linear unbiased estimate (BLUE) of the state of the observed system from the available data. It consists in minimizing a scalar objective function that measures the quadratic difference between the estimated state and the data, weighted by the inverse covariance matrix of the data errors. 4D-VAR can be extended heuristically to the case of nonlinear models or observation operators. It is made possible in practice through the use of the adjoint equations, which allow explicit computation of the gradient of the objective function at a non-prohibitive cost. 4D-VAR is used operationally in a number of major meteorological centres, where it has brought significant improvement in the quality of the forecasts. 4D-VAR, together with the ensemble Kalman filter, is one of the two most powerful assimilation methods currently available.
Introduction to the Kalman filter
Authors: Snyder C. 
Published: March 2015

Abstract
This chapter introduces The Kalman filter, which implements Bayesian data assimilation for linear, Gaussian systems. Its update equations can also be derived as the best linear unbiased estimator (BLUE) and its covariance. Some of the Kalman filter’s detailed properties are reviewed here: linear transformations of the state and observations, extending the state vector to include observed variables, and temporal correlation in the model or observation errors. The Kalman filter can be applied to nonlinear and non-Gaussian systems via either the extended Kalman filter or the BLUE, although both approaches are clearly sub-optimal. The ensemble Kalman filter (EnKF) employs sample covariances from an ensemble of forecasts at each update time and allows practical implementation of an approximate Kalman filter. The EnKF is consistent with a Monte- Carlo implementation of the BLUE. Many of the EnKF’s properties, including basic effects of sampling error, can be understood in the context of Kalman-filter theory.
Background error covariances
Authors: Berre L. 
Published: March 2015

Abstract
This chapter deals with the estimation and specification of realistic background error covariances, which is a key issue in data assimilation, since these covariances are used to filter and propagate observations. The underlying equations of error evolution are summarized, and associated simulation techniques are also presented, based on either ensemble techniques or the so-called NMC method. Another important source of information on background error covariances corresponds to innovation-based estimates, which may be combined with ensemble data assimilation to estimate model error covariances, for instance. Moreover, because the covariance matrix is huge, diagnostics of its main components and salient features have to be employed. The possibility of modelling this matrix using a sequence of sparse operators is then reviewed, in addition to filtering methods that account for the finite ensemble size and associated sampling noise effects.
Data assimilation in meteorology
Authors: Rabier F. , Fisher M. 
Published: March 2015

Abstract
This chapter discusses some of the implementation details that are necessary to apply data assimilation in the context of numerical weather prediction (NWP). It is divided into three parts. The first part addresses the processing of observations, which includes the transformation of raw data into a form that can be processed by a data assimilation system, quality control, and data thinning. The second part discusses two important aspects of data assimilation for NWP: (i) filtering of the analysis to remove spurious inertia–gravity waves and (ii) methods to handle nonlinearities and non-Gaussian error statistics. The third part discusses the development of parallel algorithms for four-dimensional variational data assimilation (4D-VAR), in order to better exploit the parallel nature of the computers on which it is run and to maintain its status as an important and viable NWP data assimilation algorithm into the foreseeable future.
Combining models and data in large-scale oceanography
Authors: Fukumori I. 
Published: March 2015

Abstract
This chapter describes examples of combining observations with numerical models in the context of studying ocean circulation. Model–data syntheses provide complete descriptions of the ocean, including elements not directly measured, and are conducive to understanding mechanisms of ocean circulation. The estimates, in conjunction with the models and their associated tools, such as the models’ adjoints, allow quantitative analyses of processes and causal mechanisms. Salient differences exist between model–data syntheses intended for studying processes and those meant for numerical forecasting. While the latter focus on obtaining optimal estimates at discrete instances (i.e. successive initial conditions), the former require explicit physical accounting of the system’s entire temporal evolution. This chapter also describes some of the practical techniques for implementing advanced estimation methods with large models, including Kalman filters, related smoothers, and adjoint methods, as well as ways to estimate and prescribe prior uncertainties, including their covariance.
The LHC machine: from beam commissioning to operation and future upgrades
Authors: Giovannozzi Massimo 
Published: March 2015

AbstractThis chapter describes the current status of the LHC. General machine parameters are reviewed and the beam commissioning process is presented, showing the evolution of the machine’s performance over recent years. The highlights of the powerful complex of injectors are described, in order to provide a global picture of the impressive performance of CERN’s flagship machine, which relies on both the astonishing quality of the LHC itself and the incredible flexibility of the injectors. The focus is on proton physics performance, with emphasis on the different possible scenarios leading to an upgrade of the LHC performance. Finally, the prospects for the development of the machine into the far future are briefly discussed.