bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidential futures: The case of Spanish
Authors: Escandell-Vidal Victoria 
Published: August 2014

AbstractIn Spanish there is no systematic correlation between future tense and future time reference. This is shown by, at least, three facts: the range of possible interpretations for the inflected future ; the late acquisition of the future tense as a means of expressing futurity; and the prevalence of the periphrastic future construction ‘ir a + inf.’ as the most usual way to express futurity in all dialects. A natural explanation requires the following hypothesis to be accepted: the inflected future in Spanish encodes neither temporal nor modal information, but an evidential meaning. The inflected future encodes a procedural instruction to interpret the propositional content as the result of a mental process by the speaker. This hypothesis explains not only the variety of discourse uses, but also the otherwise surprising data of first language acquisition and the distribution of forms in spoken Spanish.
Testing for Neglected Nonlinearity Using Twofold Unidentified Models under the Null and Hexic Expansions
Authors: Cho Jin Seo , Ishida Isao , White Halbert 
Published: August 2014

Abstract
We revisit the twofold identification problem discussed by Cho, Ishida, and White (2011), which arises when testing for neglected nonlinearity by artificial neural networks. We do not use the so-called “no-zero” condition and employ a sixth-order expansion to obtain the asymptotic null distribution of the quasi-likelihood ratio (QLR) test. In particular, we avoid restricting the number of explanatory variables in the activation function by using the distance and direction method discussed in Cho and White (2012). We find that the QLR test statistic can still be used to handle the twofold identification problem appropriately under the set of mild regularity conditions provided here, so that the asymptotic null distribution can be obtained in a manner similar to that in Cho, Ishida, and White ( 2011). This also implies that the weighted bootstrap in Hansen (1996) can be successfully exploited when testing the linearity hypothesis using the QLR test.
Common Nonlinearities in Multiple Series of Stock Market Volatility
Authors: Anderson Heather M. , Vahid Farshid 
Published: August 2014

AbstractDecreases in stock market returns often lead to higher increases in volatility than increases in returns of the same magnitude, and it is common to incorporate these so-called leverage effects in GARCH and stochastic volatility models. Recent research has also found it useful to account for leverage in models of realized volatility, as well as in models of the continuous and jump components of realized volatility. This chapter explores the use of smooth transition autoregressive (STAR) models for capturing leverage effects in multiple series of the continuous components of realized volatility. We find that the leverage effect is well captured by a common nonlinear factor driven by returns, even though the persistence in each country’s volatility is country specific. A three-country model that incorporates both country specific persistence and a common leverage effect offers slight forecast improvements for mid-range horizons, relative to other models that do not allow for the common nonlinearity.
Modeling Time-Varying Volatility in Financial Returns: Evidence from the Bond Markets
Authors: Amado Cristina , Laakkonen Helinä 
Published: August 2014

AbstractThe “unusually uncertain” phase in the global financial markets has inspired many researchers to study the effects of ambiguity (or “Knightian uncertainty”) on the decisions made by investors and their implications for the capital markets. We contribute to this literature by using a modified version of the time-varying GARCH model of Amado and Teräsvirta (2013) to analyze whether the increasing uncertainty has caused excess volatility in the US and European government bond markets. In our model, volatility is multiplicatively decomposed into two time-varying conditional components: the first being captured by a stable GARCH(1,1) process and the second driven by the level of uncertainty in the financial market.
Oracle Efficient Estimation and Forecasting With the Adaptive Lasso and the Adaptive Group Lasso in Vector Autoregressions
Authors: Callot Laurent A.F. , Kock Anders Bredahl 
Published: August 2014

Abstract
We show that the adaptive Lasso (aLasso) and the adaptive group Lasso (agLasso) are oracle efficient in stationary vector autoregressions where the number of parameters per equation is smaller than the number of observations. In particular, this means that the parameters are estimated consistently at a √T-rate, that the truly zero parameters are classified as such asymptotically, and that the non-zero parameters are estimated as efficiently as if only the relevant variables had been included in the model from the outset. The group adaptive Lasso differs from the adaptive Lasso by dividing the covariates into groups whose members are all relevant or all irrelevant. Both estimators have the property that they perform variable selection and estimation in one step. We evaluate the forecasting accuracy of these estimators for a large set of macroeconomic variables. The plain Lasso is found to be the most precise procedure overall. The adaptive and the adaptive group Lasso are less stable but mostly perform at par with common factor models.
Bias and Uncertainty in Analyst Earnings Expectations at Different Forecast Horizons
Authors: Aiolfi Marco , Rodriguez Marius , Timmermann Allan 
Published: August 2014

AbstractFinancial analysts’ earnings forecasts are upwards biased with a bias that gets bigger, the longer the forecast horizon. One explanation of this bias is that it reflects asymmetric loss of positive and negative forecast errors: a positive bias may benefit analysts but also compromises the accuracy of their forecasts, especially at short horizons. We use the linex loss function proposed by Varian (1975) and show that this model can generate a monotonically decreasing bias in forecast errors as a function of the length of the forecast horizon.
Fundamentals of Fluid Dynamics
Authors: Ruban Anatoly I. , Gajjar Jitesh S. B. 
Published: August 2014

Abstract
This chapter starts with a discussion of the continuum hypothesis and the conditions under which it can be used. The origin of the internal forces acting in moving fluids is then identified and the notion of the surface stress and the stress tensor are introduced, as is the rate-of-strain tensor. The constitutive equation, which relates the surface stress to the deformational motion of a fluid, is then derived. Newton’s Second Law and the law of conservation of energy are applied to deduce the equations governing fluid motion. These are known as the Navier–Stokes equations. They are derived for both incompressible fluid flows and compressible flows of a perfect gas. The chapter concludes with a demonstration of how the Navier–Stokes equations can be expressed in curvilinear coordinates.
FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution
Authors: Newman Aaron M. , Bratman Scott V. , Stehr Henning , Lee Luke J. , Liu Chih Long , Diehn Maximilian , Alizadeh Ash A. 
Published: August 2014

Abstract
Summary: For practical and robust de novo identification of genomic fusions and breakpoints from targeted paired-end DNA sequencing data, we developed Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm (FACTERA). Our method has minimal external dependencies, works directly on a preexisting Binary Alignment/Map file and produces easily interpretable output. We demonstrate FACTERA’s ability to rapidly identify breakpoint-resolution fusion events with high sensitivity and specificity in patients with non-small cell lung cancer, including novel rearrangements. We anticipate that FACTERA will be broadly applicable to the discovery and analysis of clinically relevant fusions from both targeted and genome-wide sequencing datasets.
Availability and implementation: http://factera.stanford.edu.
Contact: arasha@stanford.edu or diehn@stanford.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A novel feature-based approach to extract drug–drug interactions from biomedical text
Authors: Bui Quoc-Chinh , Sloot Peter M.A. , van Mulligen Erik M. , Kors Jan A. 
Published: August 2014

Abstract
Motivation: Knowledge of drug–drug interactions (DDIs) is crucial for health-care professionals to avoid adverse effects when co-administering drugs to patients. As most newly discovered DDIs are made available through scientific publications, automatic DDI extraction is highly relevant.
Results: We propose a novel feature-based approach to extract DDIs from text. Our approach consists of three steps. First, we apply text preprocessing to convert input sentences from a given dataset into structured representations. Second, we map each candidate DDI pair from that dataset into a suitable syntactic structure. Based on that, a novel set of features is used to generate feature vectors for these candidate DDI pairs. Third, the obtained feature vectors are used to train a support vector machine (SVM) classifier. When evaluated on two DDI extraction challenge test datasets from 2011 and 2013, our system achieves F-scores of 71.1% and 83.5%, respectively, outperforming any state-of-the-art DDI extraction system.
Availability and implementation: The source code is available for academic use at http://www.biosemantics.org/uploads/DDI.zip
Contact: q.bui@erasmusmc.nl
BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters
Authors: Chu Justin , Sadeghi Sara , Raymond Anthony , Jackman Shaun D. , Nip Ka Ming , Mar Richard , Mohamadi Hamid , Butterfield Yaron S. , Robertson A. Gordon , Birol Inanç 
Published: August 2014

Abstract
Large datasets can be screened for sequences from a specific organism, quickly and with low memory requirements, by a data structure that supports time- and memory-efficient set membership queries. Bloom filters offer such queries but require that false positives be controlled. We present BioBloom Tools, a Bloom filter-based sequence-screening tool that is faster than BWA, Bowtie 2 (popular alignment algorithms) and FACS (a membership query algorithm). It delivers accuracies comparable with these tools, controls false positives and has low memory requirements.
Availability and implementaion: www.bcgsc.ca/platform/bioinfo/software/biobloomtools
Contact: cjustin@bcgsc.ca or ibirol@bcgsc.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Evaluating the predictive performance of empirical estimators of natural mortality rate using information on over 200 fish species
Authors: Then Amy Y , Hoenig John M , Hall Norman G , Hewitt David A ,   Handling editor: Ernesto Jardim
Published: August 2014

AbstractMany methods have been developed in the last 70 years to predict the natural mortality rate, M, of a stock based on empirical evidence from comparative life history studies. These indirect or empirical methods are used in most stock assessments to (i) obtain estimates of M in the absence of direct information, (ii) check on the reasonableness of a direct estimate of M, (iii) examine the range of plausible M estimates for the stock under consideration, and (iv) define prior distributions for Bayesian analyses. The two most cited empirical methods have appeared in the literature over 2500 times to date. Despite the importance of these methods, there is no consensus in the literature on how well these methods work in terms of prediction error or how their performance may be ranked. We evaluate estimators based on various combinations of maximum age (tmax), growth parameters, and water temperature by seeing how well they reproduce &gt;200 independent, direct estimates of M. We use tenfold cross-validation to estimate the prediction error of the estimators and to rank their performance. With updated and carefully reviewed data, we conclude that a tmax-based estimator performs the best among all estimators evaluated. The tmax-based estimators in turn perform better than the Alverson–Carney method based on tmax and the von Bertalanffy K coefficient, Pauly’s method based on growth parameters and water temperature and methods based just on K. It is possible to combine two independent methods by computing a weighted mean but the improvement over the tmax-based methods is slight. Based on cross-validation prediction error, model residual patterns, model parsimony, and biological considerations, we recommend the use of a tmax-based estimator (M=4.899tmax−0.916, prediction error = 0.32) when possible and a growth-based method (M=4.118K0.73L∞−0.33 , prediction error = 0.6, length in cm) otherwise.
Therapeutic uses of anti-interleukin-6 receptor antibody
Authors: Kang Sujin , Tanaka Toshio , Kishimoto Tadamitsu 
Published: August 2014

Abstract
Cytokine-targeted therapy has generated a paradigm shift in the treatment of several immune-mediated diseases. Interleukin-6 (IL-6), which was initially identified as B-cell stimulatory factor 2, is a prototypical cytokine with wide-ranging biological effects on immune cells such as B and T cells, on hepatocytes, hematopoietic cells, vascular endothelial cells and on many others. IL-6 is thus crucially involved in the regulation of immune responses, hematopoiesis and inflammation. When infections and tissue injuries occur, IL-6 is promptly synthesized and performs a protective role in host defense against such stresses and traumas. However, excessive production of IL-6 during this emergent process induces potentially fatal complications, including systemic inflammatory response syndrome (SIRS), and dysregulated, persistently high expression of IL-6 causes the onset or development of various chronic immune-mediated disorders. For these reasons, IL-6 blockade was expected to become a novel therapeutic strategy for various diseases characterized by IL-6 overproduction. Indeed, worldwide clinical trials of tocilizumab, a humanized anti-IL-6 receptor monoclonal antibody, have successfully proved its outstanding efficacy against rheumatoid arthritis, juvenile idiopathic arthritis and Castleman disease, leading to the approval of tocilizumab for the treatment of these diseases. Moreover, various reports regarding off-label use of tocilizumab strongly suggest that it will be widely applicable for acute, severe complications such as SIRS and cytokine-release syndrome and other refractory chronic immune-mediated diseases.
Lack of Awareness of Human Immunodeficiency Virus (HIV) Infection: Problems and Solutions With Self-reported HIV Serostatus of Men Who Have Sex With Men
Authors: Sanchez Travis H. , Kelley Colleen F. , Rosenberg Eli , Luisi Nicole , O'Hara Brandon , Lambert Rodriques , Coleman Raphael , Frew Paula , Salazar Laura F. , Tao Sijia , Clarke William , del Rio Carlos , Sullivan Patrick S. 
Published: August 2014

Background.  Lack of human immunodeficiency virus (HIV) infection awareness may be a driver of racial disparities in HIV infection among men who have sex with men (MSM). Lack of awareness is typically measured by comparing HIV test result to self-reported HIV status. This measure may be subject to reporting bias and alternatives are needed.Methods.  The InvolveMENt study examined HIV disparities between black and white MSM from Atlanta. Among HIV-positive participants who did not report knowing they were positive, we examined other measures of awareness: HIV viral load (VL) &lt;1000 copies/mL (low VL), antiretroviral (ARV) drugs in blood, and previous HIV case surveillance report.Results.  Using self-report only, 32% (62 of 192) of black and 16% (7 of 45) of white MSM were not aware of their HIV infection (P = .03). Using self-report and low VL, 25% (48 of 192) black and 16% (7 of 45) white MSM lacked awareness (P = .18). Using self-report and ARVs, 26% (50 of 192) black and 16% (7 of 45) white MSM lacked awareness (P = .14). Using self-report and surveillance report, 15% (28 of 192) black and 13% (6 of 45) white MSM lacked awareness (P = .83).Conclusions.  Self-report only may overestimate true lack of awareness of HIV status for black MSM. If, as our data suggest, black MSM are not less likely to be aware of their HIV infection than are white MSM, then this factor is not a substantial driver of HIV disparity. Future HIV research that depends on accurate measurement of HIV status awareness should consider including additional laboratory and case surveillance data.
Safety and Efficacy Study of an Ozone Laser Combined Therapy Using Puncture Needle in the Treatment of Patients With Cervical Spondylosis
Authors: Gu Ke , Yan Yuqiu , Wei Wu , Li Yan , Liu Wenli , Guo Yang , Yu Long 
Published: August 2014

Study Design and Methods:
Fifty-eight patients with cervical spondylosis (CS) were treated with patented technology of ozone laser combined therapy using puncture needle between August 2008 and February 2010. Visual Analogue Scale (VAS) score changes before and 6 months after surgery and MacNab score criteria 6 months after surgery were analyzed.

Background and Objective:
CS normally occurs over the age of 50 and broadly presents as either myelopathy or radiculopathy. Complementary treatment strategies have long been envisaged as a possible alternative in alleviating neck pain associated with CS; however, it is still in moderate use due to lack of adequate and convincing evidence of its safety and efficacy. The current study was to define and understand the therapeutic effects and safety of a newly developed patented technology, ozone, and laser via puncture needle, in the treatment of CS.

Results:
The VAS score of preoperative neck and shoulder pain was (6.57±1.34) scores, which decreased to 1.80±0.65 at 1-week postsurgery, and was completely alleviated by the end of 1 month (VAS score 0–2 after 1, 3, and 6 mo after surgery) (Kruskal-Wallis rank-sum test, H=1.680, P=0.000). VAS scores did not exhibit any significant rebound within 6 months after surgery (29 patients were excellent; 23 good; and 6 were fair, overall excellent, and good rate of 89.6%).

Conclusion:
Ozone and laser combined therapy via puncture needle for the treatment of CS is safe and effective.
Genome-wide Comparative Analysis Reveals Possible Common Ancestors of NBS Domain Containing Genes in HybridCitrus sinensisGenome and OriginalCitrus clementinaGenome
Authors: Wang Yunsheng , Zhou Lijuan , Li Dazhi , Lawton-Rauh Amy , Srimani Pradip K. , Dai Liangying , Duan Yongping , Luo Feng 
Published: August 2014

AbstractBackgroundRecently available whole genome sequences of three citrus species: oneCitrus clementinaand twoCitrus sinensisgenomes have made it possible to understand the features of candidate disease resistance genes with nucleotide-binding sites (NBS) domain in Citrus and how NBS genes differ between hybrid and original Citrus species.ResultWe identified and re-annotated NBS genes from three citrus genomes and found similar numbers of NBS genes in those citrus genomes. Phylogenetic analysis of all citrus NBS genes across three genomes showed that there are three approximately evenly numbered groups: one group contains the Toll-Interleukin receptor (TIR) domain and two different groups that contain the Coiled Coil (CC) domain. Motif analysis confirmed that the two groups of CC-containing NBS genes are from different evolutionary origins. We partitioned NBS genes into clades using NBS domain sequence distances and found most clades include NBS genes from all three citrus genomes. This suggests that NBS genes in three citrus genomes may come from shared ancestral origins. We also mapped the re-sequenced reads of three pomelo and three Mandarin orange genomes onto theCitrus sinensisgenome. We found that most NBS genes of the hybridC. sinensisgenome have corresponding homologous genes in both pomelo and mandarin genome. The homologous NBS genes in pomelo and mandarin may explain why the NBS genes in their hybridCitrus sinensisare similar to those inCitrus clementinain this study. Furthermore, sequence variation amongst citrus NBS genes were shaped by multiple independent and shared accelerated mutation accumulation events among different groups of NBS genes and in different citrus genomes.ConclusionOur comparative analyses yield valuable insight into the understanding of the structure, evolution and organization of NBS genes inCitrusgenomes. There are significantly more NBS genes inCitrusgenomes compared to other plant species. NBS genes in hybridC. sinensisgenomes are very similar to those in progenitorC. clementinagenome and they may be derived from possible common ancestral gene copies. Furthermore, our comprehensive analysis showed that there are three groups of plant NBS genes while CC-containing NBS genes can be divided into two groups.
Coordinated Evolution of Influenza A Surface Proteins
Authors: Neverov Alexey D. , Kryazhimskiy Sergey , Plotkin Joshua B. , Bazykin Georgii A. 
Published: August 2014

AbstractSurface proteins hemagglutinin (HA) and neuraminidase (NA) of the human influenza A virus evolve under selection pressure to escape the human adaptive immune response and antiviral drug treatments. In addition to these external selection pressures, some mutations in HA are known to affect the adaptive landscape of NA, and vice versa, because these two proteins are physiologically interlinked. However, the extent to which evolution of one protein affects the evolution of the other is unknown. Here we develop a novel phylogenetic method for detecting the signatures of such genetic interactions between mutations in different genes – that is, intergene epistasis. Using this method, we show that influenza surface proteins evolve in a coordinated way, with substitutions in HA affecting substitutions in NA and vice versa, at many sites. Of particular interest is our finding that the oseltamivir-resistance mutations in NA in subtype H1N1 were likely facilitated by prior mutations in HA. Our results illustrate that the adaptive landscape of a viral protein is remarkably sensitive to its genomic context and, more generally, imply that the evolution of any single protein must be understood within the context of the entire evolving genome.