bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mixed Micellar Properties and Related Interaction Parameters of Butanediyl‐1,4‐bis(dodecyl dimethyl ammonium bromide) Gemini Surfactant with Nonionic Amphiphiles
Authors: Kabir‐ud‐Din  , Sharma Gaurav , Koya P. Ajmal 
Published: January 2014

AbstractMixed micellization of cationic gemini surfactant butanediyl‐1,4‐bis(dimethyldodecylammonium bromide) with nonionic surfactants (sorbitan esters, alcohols and phenol ethoxylates) and triblock copolymers has been studied tensiometrically. Various physicochemical parameters of the studied systems including ideal CMC values, experimental and ideal micellar compositions, interaction parameters, activity coefficients of the components, etc. have been evaluated by considering theoretical models of Clint, Rubingh, Rosen and Maeda. The experimental critical micelle concentration (CMC) values of the mixed micelles were lower than the CMC values of the individual components and showed a negative deviation from ideal CMC (CMC*) values. The analysis reveals that the mole fractions of gemini are lower compared to the nonionic surfactants/triblock polymers and the values of ΔGm°, ΔGad°, Gmin and ΔGexm show that the spontaneity of the studied mixed micelles relatively decreases as the content of the gemini in the bulk phase increases.
Gender and incidence of dementia in the Framingham Heart Study from mid‐adult life
Authors: Chêne Geneviève , Beiser Alexa , Au Rhoda , Preis Sarah R. , Wolf Philip A. , Dufouil Carole , Seshadri Sudha 
Published: January 2014

BackgroundGender‐specific risks for dementia and Alzheimer's disease (AD) starting in midlife remain largely unknown.MethodsProspectively ascertained dementia/AD and cause‐specific mortality in Framingham Heart Study (FHS) participants was used to generate 10‐ to 50‐year risk estimates of dementia/AD on the basis of the Kaplan–Meier method (cumulative incidence) or accounting for competing risk of death (lifetime risk [LTR]).ResultsOverall, 777 cases of incident dementia (601 AD) occurred in 7901 participants (4333 women) over 136,266 person‐years. Whereas cumulative incidences were similar in women and men, LTRs were higher in women older than 85 years of age. LTR of dementia/AD at age 45 was 1 in 5 in women and 1 in 10 in men. Cardiovascular mortality was higher in men with rate ratios decreasing from approximately 6 at 45 to 54 years of age to less than 2 after age 65.ConclusionSelective survival of men with a healthier cardiovascular risk profile and hence lower propensity to dementia might partly explain the higher LTR of dementia/AD in women.
BAYESIAN ASYMMETRIC LOGIT MODEL FOR DETECTING RISK FACTORS IN MOTOR RATEMAKING
Authors: Pérez-Sánchez J.M. , Negrín-Hernández M.A. , García-García C. , Gómez-Déniz E. 
Published: January 2014

AbstractModelling automobile insurance claims is a crucial component in the ratemaking procedure. This paper focuses on the probability that a policyholder reports a claim, where the classical logit link does not provide a right model. This is so because databases related with automobile claims are often unbalanced, containing more non-claims than the presence of claims. In this work an asymmetric logit model, which takes into account the large number of non-claims in the portfolio, is considered. Both, logit and asymmetric logit models from a Bayesian point of view, are used to a sample that was collected from a major automobile insurance company in Spain in 2009, resulting in a dataset of 2,000 passenger vehicle. We establish the validity of the asymmetric model in front of the conventional logit link. The use of a garage, the age of the vehicle and the duration of the client's relation with the company are all shown to be significant explanatory variables by the logit model. The asymmetric model includes, in addition, the length of time the policyholder has held a driving licence and the type of use made of the vehicle. The asymmetric model provides a better fit to the data examined.
Commutator methods for the spectral analysis of uniquely ergodic dynamical systems
Authors: TIEDRA DE ALDECOA R. 
Published: January 2014

AbstractWe present a method, based on commutator methods, for the spectral analysis of uniquely ergodic dynamical systems. When applicable, it leads to the absolute continuity of the spectrum of the corresponding unitary operators. As an illustration, we consider time changes of horocycle flows, skew products over translations and Furstenberg transformations. For time changes of horocycle flows we obtain absolute continuity under assumptions weaker than those to be found in the literature, and for skew products over translations and Furstenberg transformations we obtain countable Lebesgue spectrum under assumptions not previously covered in the literature.
Quantum vortex dynamics under the tangent representation of the local induction approximation
Authors: Van Gorder Robert A. 
Published: January 2014

AbstractWe derive the local induction approximation (LIA) for a quantum vortex filament in the arclength coordinate frame where the tangent vector is the unknown function. The equation for the tangent vector to the filament is then converted to a potential form, which ends up being a type of nonlinear Schrödinger equation that governs the tangential LIA model (T-LIA). Such a formulation was previously derived by Umeki for the standard fluid model (in the absence of superfluid friction terms). While it is challenging to generalize many of the exact solutions found for the standard LIA to the quantum LIA model, we demonstrate that the T-LIA model facilitates this generalization nicely. Indeed, under the T-LIA model, we are able to construct a variety of solutions. The Hasimoto solution related to elastica is one of the fundamental solutions present for the standard fluid model; however, using the T-LIA model, we are able to demonstrate the existence of such a solution, thereby extending the Hasimoto solution to the superfluid case. In the zero-temperature limit, purely self-similar solutions are shown to exist for the T-LIA model. As the superfluid warms (so that the influence of the normal flow is no longer negligible), the analogue to the self-similar solution is a new class of solutions, which depend on the similarity variable as well as a time-dependent additive scaling. In other words, the self-similar structures gradually deform as the magnitude of the normal-fluid velocity increases, which makes complete physical sense. When dealing with small deviations from the central axis of alignment, we can describe such solutions analytically. There exists a family of helical vortex filaments in the presence of a normal fluid impinging on the vortex, in complete agreement with the previously studied results for the LIA model. Finally, a number of soliton solutions are shown to exist in different regimes of the T-LIA model.
The Political Economy of European Wine Regulations
Authors: Meloni Giulia , Swinnen Johan 
Published: January 2014

AbstractThe wine market in the European Union is heavily regulated. Despite the many distortions in the wine market as a consequence, reforming the regulations has proven difficult. This paper analyzes the political economy mechanism that created existing wine regulations. We document the historical origins of the regulations and relate these to political pressures that resulted from international integration, technological innovations, and economic developments. (JEL Classifications: K23, L51, N44, N54, Q13)
A NEW UNIQUE CONTINUATION PROPERTY FOR THE KORTEWEG–DE VRIES EQUATION
Authors: CHEN MO , GAO PENG 
Published: January 2014

AbstractThe aim of this paper is to obtain a new unique continuation property (UCP) for the Korteweg–de Vries equation posed on a finite interval. Compared with the previous UCP, we need fewer conditions on the solution. For this purpose, we have to establish a global Carleman estimate for the Korteweg–de Vries equation.
Two new nematode species, Linhystera breviapophysis and L. longiapophysis (Xyalidae, Nematoda), from the East China Sea
Authors: Yu Tingting , Huang Yong , Xu Kuidong 
Published: January 2014

Two new species of free-living nematodes discovered from the sediments in the East China Sea are described: Linhystera breviapophysis sp. nov. and L. longiapophysis sp. nov. Both species possess a dorso-caudally directed gubernacular apophysis, which makes them distinctly different from the two already known species of Linhystera. Linhystera breviapophysis is characterized by a gubernacular apophysis about 3.3 μm long, the presence of a crown of cervical setae and a filiform tail. Linhystera longiapophysis is characterized by a prominent gubernacular apophysis about 10 μm long, sparse cervical setae and a long filiform tail. An emended diagnosis of Linhystera and a pictorial dichotomous key to the species are given.
Synergistic cytotoxicity of gemcitabine, clofarabine and edelfosine in lymphoma cell lines
Authors: Valdez B C , Zander A R , Song G , Murray D , Nieto Y , Li Y , Champlin R E , Andersson B S 
Published: January 2014

AbstractTreatments for lymphomas include gemcitabine (Gem) and clofarabine (Clo) which inhibit DNA synthesis. To improve their cytotoxicity, we studied their synergism with the alkyl phospholipid edelfosine (Ed). Exposure of the J45.01 and SUP-T1 (T-cell) and the OCI-LY10 (B-cell) lymphoma cell lines to IC10–IC20 levels of the drugs resulted in strong synergistic cytotoxicity for the 3-drug combination based on various assays of cell proliferation and apoptosis. Cell death correlated with increased phosphorylation of histone 2AX and KAP1, decreased mitochondrial transmembrane potential, increased production of reactive oxygen species and release of pro-apoptotic factors. Caspase 8-negative I9.2 cells were considerably more resistant to [Gem+Clo+Ed] than caspase 8-positive cells. In all three cell lines [Gem+Clo+Ed] decreased the level of phosphorylation of the pro-survival protein AKT and activated the stress-activated protein kinase/c-Jun N-terminal kinase (SAPK/JNK) stress signaling pathway, which in J45.01 cells resulted in the phosphorylation and heterodimerization of the transcription factors ATF2 and c-Jun. The observed rational mechanism-based efficacy of [Gem+Clo+Ed] based on the synergistic convergence of several pro-death and anti-apoptotic signaling pathways in three very different cell backgrounds provides a powerful foundation for undertaking clinical trials of this drug combination for the treatment of lymphomas.
Collective Autoionization in Multiply-Excited Systems: A novel ionization process observed in Helium Nanodroplets
Authors: LaForge A. C. , Drabbels M. , Brauer N. B. , Coreno M. , Devetta M. , Di Fraia M. , Finetti P. , Grazioli C. , Katzy R. , Lyamayev V. , Mazza T. , Mudrich M. , O'Keeffe P. , Ovcharenko Y. , Piseri P. , Plekan O. , Prince K. C. , Richter R. , Stranges S. , Callegari C. , Möller T. , Stienkemeier F. 
Published: January 2014

AbstractFree electron lasers (FELs) offer the unprecedented capability to study reaction dynamics and image the structure of complex systems. When multiple photons are absorbed in complex systems, a plasma-like state is formed where many atoms are ionized on a femtosecond timescale. If multiphoton absorption is resonantly-enhanced, the system becomes electronically-excited prior to plasma formation, with subsequent decay paths which have been scarcely investigated to date. Here, we show using helium nanodroplets as an example that these systems can decay by a new type of process, named collective autoionization. In addition, we show that this process is surprisingly efficient, leading to ion abundances much greater than that of direct single-photon ionization. This novel collective ionization process is expected to be important in many other complex systems, e.g. macromolecules and nanoparticles, exposed to high intensity radiation fields.
MAGIC: access portal to a cross-platform gene expression compendium for maize
Authors: Fu Qiang , Fierro Ana Carolina , Meysman Pieter , Sanchez-Rodriguez Aminael , Vandepoele Klaas , Marchal Kathleen , Engelen Kristof 
Published: January 2014

Abstract
Summary: To facilitate the exploration of publicly available Zea mays expression data, we constructed a maize expression compendium, making use of an integration methodology and a consistent probe to gene mapping based on the 5b.60 sequence release of Z. mays. The compendium is made available through a web portal MAGIC that hosts a variety of analysis tools to easily browse and analyze the data. Our compendium is different from previous initiatives in combining expression values across different experiments by providing a consistent gene annotation across different platforms.
Availability and implementation: http://bioinformatics.intec.ugent.be/magic/
Contact: kathleen.marchal@ugent.be
Supplementary information: Supplementary data are available at Bioinformatics online.
Characterizing cancer subtypes as attractors of Hopfield networks
Authors: Maetschke Stefan R. , Ragan Mark A. 
Published: January 2014

Abstract
Motivation: Cancer is a heterogeneous progressive disease caused by perturbations of the underlying gene regulatory network that can be described by dynamic models. These dynamics are commonly modeled as Boolean networks or as ordinary differential equations. Their inference from data is computationally challenging, and at least partial knowledge of the regulatory network and its kinetic parameters is usually required to construct predictive models.
Results: Here, we construct Hopfield networks from static gene-expression data and demonstrate that cancer subtypes can be characterized by different attractors of the Hopfield network. We evaluate the clustering performance of the network and find that it is comparable with traditional methods but offers additional advantages including a dynamic model of the energy landscape and a unification of clustering, feature selection and network inference. We visualize the Hopfield attractor landscape and propose a pruning method to generate sparse networks for feature selection and improved understanding of feature relationships.
Availability: Software and datasets are available at http://acb.qfab.org/acb/hclust/
Contact: m.ragan@uq.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
Evolutionary solution for the RNA design problem
Authors: Esmaili-Taheri Ali , Ganjtabesh Mohammad , Mohammad-Noori Morteza 
Published: January 2014

Abstract
Motivation: RNAs play fundamental roles in cellular processes. The function of an RNA is highly dependent on its 3D conformation, which is referred to as the RNA tertiary structure. Because the prediction or experimental determination of these structures is difficult, so many works focus on the problems associated with the RNA secondary structure. Here, we consider the RNA inverse folding problem, in which an RNA secondary structure is given as a target structure and the goal is to design an RNA sequence that folds into the target structure. In this article, we introduce a new evolutionary algorithm for the RNA inverse folding problem. Our algorithm, entitled Evolutionary RNA Design, generates a sequence whose minimum free energy structure is the same as the target structure.
Results: We compare our algorithm with INFO-RNA, MODENA, RNAiFold and NUPACK approaches for some biological test sets. The results presented in this article indicate that for longer structures, our algorithm performs better than the other mentioned algorithms in terms of the energy range, accuracy, speedup and nucleotide distribution. Particularly, the generated RNA sequences in our method are much more reliable and similar to the natural RNA sequences.
Availability and implementation: The web server and source code are available at http://mostafa.ut.ac.ir/corna/erd.
Contact: mgtabesh@ut.ac.ir
Correcting density-dependent effects in abundance estimates from bottom-trawl surveys
Authors: Kotwicki Stan , Ianelli James N. , Punt André E. 
Published: January 2014

Abstract
Indices of abundance are important for estimating population trends in stock assessment and ideally should be based on fishery-independent surveys to avoid problems associated with the hyperstability of the commercial catch per unit effort (cpue) data. However, recent studies indicate that the efficiency of the survey bottom trawl (BT) for some species can be density-dependent, which could affect the reliability of survey-derived indices of abundance. A function qe∼f(u), where qe is the BT efficiency and u the catch rate, was derived using experimentally derived acoustic dead-zone correction and BT efficiency parameters obtained from combining a subset of BT catch data with synchronously collected acoustic data from walleye pollock (Theragra chalcogramma) in the eastern Bering Sea (EBS). We found that qe decreased with increasing BT catches resulting in hyperstability of the index of abundance derived from BT survey. Density-dependent qe resulted in spatially and temporarily variable bias in survey cpue and biased population age structure derived from survey data. We used the relationship qe∼f(u) to correct the EBS trawl survey index of abundance for density-dependence. We also obtained a variance–covariance matrix for a new index that accounted for sampling variability and the uncertainty associated with the qe. We found that incorporating estimates of the new index of abundance changed outputs from the walleye pollock stock assessment model. Although changes were minor, we advocate incorporating estimates of density-dependent qe into the walleye pollock stock assessment as a precautionary measure that should be undertaken to avoid negative consequences of the density-dependent qe.
Hazard warning: model misuse ahead
Authors: Dickey-Collas Mark , Payne Mark R. , Trenkel Verena M. , Nash Richard D. M. 
Published: January 2014

AbstractThe use of modelling approaches in marine science, and in particular fisheries science, is explored. We highlight that the choice of model used for an analysis should account for the question being posed or the context of the management problem. We examine a model-classification scheme based on Richard Levins' 1966 work suggesting that models can only achieve two of three desirable model attributes: realism, precision, and generality. Model creation, therefore, requires trading-off of one of these attributes in favour of the other two: however, this is often in conflict with the desires of end-users (i.e. mangers or policy developers). The combination of attributes leads to models that are considered to have empirical, mechanistic, or analytical characteristics, but not a combination of them. In fisheries science, many examples can be found of models with these characteristics. However, we suggest that models or techniques are often employed without consideration of their limitations, such as projecting into unknown space without generalism, or fitting empirical models and inferring causality. We suggest that the idea of trade-offs and limitations in modelling be considered as an essential first step in assessing the utility of a model in the context of knowledge for decision-making in management.
A redshift-dependent colour–luminosity relation in Type 1a supernovae
Authors: Mohlabeng Gopolang M. , Ralston John P. 
Published: January 2014

Abstract
Type 1a supernova magnitudes are used to fit cosmological parameters under the assumption that the model will fit the observed redshift dependence. We test this assumption with the Union 2.1 compilation of 580 sources. Several independent tests find that the existing model fails to account for a significant correlation of supernova colour and redshift. The correlation of magnitude residuals relative to the Λ CDM model and colour × redshift has a significance equivalent to 13 standard deviations, as evaluated by randomly shuffling the data. Extending the existing B − V colour correction to a relation linear in redshift improves the goodness of fit χ2 by more than 50 units, an equivalent 7σ significance, while adding only one parameter. The colour−redshift correlation is quite robust, cannot be attributed to outliers and passes several tests of consistency. We review previous hints of redshift dependence in colour parameters found in bin-by-bin fits interpreted as parameter bias. We show that neither the bias nor the change Δχ2 of our study can be explained by those effects. The previously known relation that bluer supernovae have larger absolute luminosity tends to empirically flatten out with increasing redshift. The best-fitting cosmological dark energy density parameter is revised from ΩΛ = 0.71 ± 0.02 to ΩΛ = 0.74 ± 0.02 assuming a flat universe. One possible physical interpretation is that supernovae or their environments evolve significantly with increasing redshift.
Modeling the functional relationship network at the splice isoform level through heterogeneous data integration
Authors: Li Hong-Dong , Menon Rajasree , Eksi Ridvan , Guerler Aysam , Zhang Yang , Omenn Gilbert S. , Guan Yuanfang 
Published: January 2014

AbstractFunctional relationship networks, which reveal the collaborative roles between genes, have significantly accelerated our understanding of gene functions and phenotypic relevance. However, establishing such networks for alternatively spliced isoforms remains a difficult, unaddressed problem due to the lack of systematic functional annotations at the isoform level, which renders most supervised learning methods difficult to be applied to isoforms. Here we describe a novel multiple instance learning-based probabilistic approach that integrates large-scale, heterogeneous genomic datasets, including RNA-seq, exon array, protein docking and pseudo-amino acid composition, for modeling a global functional relationship network at the isoform level in the mouse. Using this approach, we formulate a gene pair as a set of isoform pairs of potentially different properties. Through simulation and cross-validation studies, we showed the superior accuracy of our algorithm in revealing the isoform-level functional relationships. The local networks reveal functional diversity of the isoforms of the same gene, as demonstrated by both large-scale analyses and experimental and literature evidence for the disparate functions revealed for the isoforms ofPtbp1andAnxa6by our network. Our work can assist the understanding of the diversity of functions achieved by alternative splicing of a limited set of genes in mammalian genomes, and may shift the current gene-centered network prediction paradigm to the isoform level.Author summaryProteins carry out their functions through interacting with each other. Such interactions can be achieved through direct physical interactions, genetic interactions, or co-regulation. To summarize these interactions, researches have established functional relationship networks, in which each gene is represented as a node and the connections between the nodes represent how likely two genes work in the same biological process. Currently, these networks are established at the gene level only, while each gene, in mammalian systems, can be alternatively spliced into multiple isoforms that may have drastically different interaction partners. This information can be mined through integrating data that provide isoform-level information, such as RNA-seq and protein docking scores predicted from amino acid sequences. In this study, we developed a novel algorithm to integrate such data for predicting isoform-level functional relationship networks, which allows us to investigate the collaborative roles between genes at a high resolution.