bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness and Drug Survival of TNF Inhibitors in the Treatment of Ankylosing Spondylitis: A Prospective Cohort Study
Authors: Heinonen Arto V. , Aaltonen Kalle J. , Joensuu Jaana T. , Lähteenmäki Jukka P. , Pertovaara Marja I. , Romu Matti K. , Hirvonen Hanna E. , Similä Aki K. , Blom Marja L. , Nordström Dan C. 
Published: October 2015

Objective.The aim of this research was to describe the effectiveness and drug survival of tumor necrosis factor (TNF) inhibitors in the treatment of ankylosing spondylitis (AS) and to analyze the effect of concomitant treatment with conventional disease-modifying antirheumatic drugs.Methods.Patients with AS identified from the National Register for Biologic Treatment in Finland starting their first TNF inhibitor treatment between July 2004 and December 2011 were included. Treatment response was measured as an improvement of 50% (or 20 mm) after 6 months of treatment onset compared to the baseline Bath AS Disease Activity Index (BASDAI) score. Treatment response and 2-year drug survival were modeled with logistic regression and time-dependent Cox proportional hazard models, respectively.Results.The study comprised 543 patients, of whom 123 also commenced a second TNF inhibitor during the followup. Treatment was discontinued within 24 months by 25% and 28% of the users of the first and the second TNF inhibitors, respectively. BASDAI response at 6 months was achieved by 52% and 25% of the users of the first and the second TNF inhibitors, respectively. Etanercept (ETN; HR 0.42, 95% CI 0.29–0.62) and adalimumab (ADA; HR 0.48, 95% CI 0.30–0.77) were associated with better drug survival in comparison to infliximab (IFX). Also, concurrent use of sulfasalazine (SSZ; HR 0.70, 95% CI 0.49–0.99) decreased the hazard for treatment discontinuation.Conclusion.TNF inhibitors are equipotent in the treatment of AS; however, ETN and ADA were found superior to IFX in drug survival. The use of SSZ improves treatment continuation.
A Slope Constrained 4th Order Multi-Moment Finite Volume Method with WENO Limiter
Authors: Sun Ziyao , Teng Honghui , Xiao Feng 
Published: October 2015

AbstractThis paper presents a new and better suited formulation to implement the limiting projection to high-order schemes that make use of high-order local reconstructions for hyperbolic conservation laws. The scheme, so-called MCV-WENO4 (multi-moment Constrained finite Volume with WENO limiter of 4th order) method, is an extension of the MCV method of Ii & Xiao (2009) by adding the 1st order derivative (gradient or slope) at the cell center as an additional constraint for the cell-wise local reconstruction. The gradient is computed from a limiting projection using the WENO (weighted essentially non-oscillatory) reconstruction that is built from the nodal values at 5 solution points within 3 neighboring cells. Different from other existing methods where only the cell-average value is used in the WENO reconstruction, the present method takes account of the solution structure within each mesh cell, and thus minimizes the stencil for reconstruction. The resulting scheme has 4th-order accuracy and is of significant advantage in algorithmic simplicity and computational efficiency. Numerical results of one and two dimensional benchmark tests for scalar and Euler conservation laws are shown to verify the accuracy and oscillation-less property of the scheme.
Modeling and Simulation of the Interstitial Medium Deformation Induced by the Needle Manipulation During Acupuncture
Authors: Deleuze Yannick , Thiriet Marc , Sheu Tony Wen-Hann 
Published: October 2015

AbstractIn this paper, we study the effects of inserted needle on the subcutaneous interstitial flow. A goal is to describe the physical stress affecting cells during acupuncture treatment. The model consists of the convective Brinkman equations to describe the flow through a fibrous medium. Numerical studies in FreeFem++ are performed to illustrate the acute physical stress developed by the implantation of a needle that triggers the physiological reactions of acupuncture. We emphasize the importance of numerical experiments for advancing in modeling in acupuncture.
A Compact Third-Order Gas-Kinetic Scheme for Compressible Euler and Navier-Stokes Equations
Authors: Pan Liang , Xu Kun 
Published: October 2015

AbstractIn this paper, a compact third-order gas-kinetic scheme is proposed for the compressible Euler and Navier-Stokes equations. The main reason for the feasibility to develop such a high-order scheme with compact stencil, which involves only neighboring cells, is due to the use of a high-order gas evolution model. Besides the evaluation of the time-dependent flux function across a cell interface, the high-order gas evolution model also provides an accurate time-dependent solution of the flow variables at a cell interface. Therefore, the current scheme not only updates the cell averaged conservative flow variables inside each control volume, but also tracks the flow variables at the cell interface at the next time level. As a result, with both cell averaged and cell interface values, the high-order reconstruction in the current scheme can be done compactly. Different from using a weak formulation for high-order accuracy in the Discontinuous Galerkin method, the current scheme is based on the strong solution, where the flow evolution starting from a piecewise discontinuous high-order initial data is precisely followed. The cell interface time-dependent flow variables can be used for the initial data reconstruction at the beginning of next time step. Even with compact stencil, the current scheme has third-order accuracy in the smooth flow regions, and has favorable shock capturing property in the discontinuous regions. It can be faithfully used from the incompressible limit to the hypersonic flow computations, and many test cases are used to validate the current scheme. In comparison with many other high-order schemes, the current method avoids the use of Gaussian points for the flux evaluation along the cell interface and the multi-stage Runge-Kutta time stepping technique. Due to its multidimensional property of including both derivatives of flow variables in the normal and tangential directions of a cell interface, the viscous flow solution, especially those with vortex structure, can be accurately captured. With the same stencil of a second order scheme, numerical tests demonstrate that the current scheme is as robust as well-developed second-order shock capturing schemes, but provides more accurate numerical solutions than the second order counterparts.
Dynamics and Instability of a Vortex Ring Impinging on a Wall
Authors: Ren Heng , Lu Xi-Yun 
Published: October 2015

AbstractDynamics and instability of a vortex ring impinging on a wall were investigated by means of large eddy simulation for two vortex core thicknesses corresponding to thin and thick vortex rings. Various fundamental mechanisms dictating the flow behaviors, such as evolution of vortical structures, formation of vortices wrapping around vortex rings, instability and breakdown of vortex rings, and transition from laminar to turbulent state, have been studied systematically. The evolution of vortical structures is elucidated and the formation of the loop-like and hair-pin vortices wrapping around the vortex rings (called briefly wrapping vortices) is clarified. Analysis of the enstrophy of wrapping vortices and turbulent kinetic energy (TKE) in flow field indicates that the formation and evolution of wrapping vortices are closely associated with the flow transition to turbulent state. It is found that the temporal development of wrapping vortices and the growth rate of axial flow generated around the circumference of the core region for the thin ring are faster than those for the thick ring. The azimuthal instabilities of primary and secondary vortex rings are analyzed and the development of modal energies is investigated to reveal the flow transition to turbulent state. The modal energy decay follows a characteristic –5/3 power law, indicating that the vortical flow has become turbulence. Moreover, it is identified that the TKE with a major contribution of the azimuthal component is mainly distributed in the core region of vortex rings. The results obtained in this study provide physical insight of the mechanisms relevant to the vortical flow evolution from laminar to turbulent state.
Simulation of Two-Dimensional Scramjet Combustor Reacting Flow Field Using Reynolds Averaged Navier-Stokes WENO Solver
Authors: Huang Juan-Chen , Lai Yu-Hsuan , Guo Jeng-Shan , Yang Jaw-Yen 
Published: October 2015

AbstractThe non-equilibrium chemical reacting combustion flows of a proposed long slender scramjet system were numerically studied by solving the turbulent Reynolds averaged Navier-Stokes (RANS) equations. The Spalart-Allmaras one equation turbulence model is used which produces better results for near wall and boundary layer flow field problems. The lower-upper symmetric Gauss-Seidel implicit scheme, which enables results converge efficiently under steady state condition, is combined with the weighted essentially non-oscillatory (WENO) scheme to yield an accurate simulation tool for scramjet combustion flow field analysis. Using the WENO schemes high-order accuracy and its non-oscillatory solution at flow discontinuities, better resolution of the hypersonic flow problems involving complex shock-shock/shock-boundary layer interactions inside the flow path, can be achieved. Two types of scramjet combustor with cavity-based and strut-based fuel injector were considered as the testing models. The flow characteristics with and without combustion reactions of the two types combustor model were studied with a transient hydrogen/oxygen combustion model. The detailed results of aerodynamic data are obtained and discussed, moreover, the combustion properties of varying the equivalent ratio of hydrogen, including the concentration of reacting species, hydrogen and oxygen, and the reacting products, water, are demonstrated to study the combustion process and performance of the combustor. The comparisons of flow field structures, pressure on wall and velocity profiles between the experimental data and the solutions of the present algorithms, showed qualitatively as well as the quantitatively in good agreement, and validated the adequacy of the present simulation tool for hypersonic scramjet reacting flow analysis.
First records of winter sea ice concentration in the southwest Pacific sector of the Southern Ocean
Authors: Ferry Alexander J. , Crosta Xavier , Quilty Patrick G. , Fink David , Howard William , Armand Leanne K. 
Published: October 2015

AbstractWe use a Generalized Additive Model (GAM) to provide the first winter sea ice concentration record from two cores located within the southwest Pacific sector of the Southern Ocean. To compliment the application of GAM, a time series analysis on satellite records of sea ice concentration data was used to extend the standard 13.25 year time series used for paleoceanography. After comparing GAM sea ice estimates with previously published paleo sea ice data we then focus on a new paleo winter sea ice record for marine sediment core E27‐23 (59°37.1'S, 155°14.3'E), allowing us to provide a more comprehensive view of winter sea ice dynamics for the southwest Pacific Ocean. The paleo winter sea ice concentration estimates provide the first suggestion that winter sea ice within the southwestern Pacific might have expanded during the Antarctic Cold Reversal. Throughout the Holocene, core E27‐23 documents millennial scale variability in paleo winter sea ice coverage within the southwest Pacific. Holocene winter sea ice expansion may have resulted from the Laurentide Ice Sheet deglaciation, increased intensity of the westerly winds, as well as a northern migration of the Subtropical and/or Sub‐Antarctic Fronts. Brief consideration is given to the development of a paleo summer sea ice proxy. We conclude that there is no evidence that summer sea ice ever existed at core sites SO136‐111 and E27‐23 over the last 220 and 52,000 years, respectively.
Hypoxia‐driven variations in iron and manganese shuttling in the Baltic Sea over the past 8 kyr
Authors: Lenz Conny , Jilbert Tom , Conley Daniel J. , Slomp Caroline P. 
Published: October 2015

AbstractThe Baltic Sea has experienced three major intervals of bottom water hypoxia following the intrusion of seawater circa 8 kyr ago. These intervals occurred during the Holocene Thermal Maximum (HTM), Medieval Climate Anomaly (MCA), and during recent decades. Here we show that sequestration of both Fe and Mn in Baltic Sea sediments generally increases with water depth, and we attribute this to shelf‐to‐basin transfer (“shuttling”) of Fe and Mn. Burial of Mn in slope and basin sediments was enhanced following the lake‐brackish/marine transition at the beginning of the hypoxic interval during the HTM. During hypoxic intervals, shelf‐to‐basin transfer of Fe was generally enhanced but that of Mn was reduced. However, intensification of hypoxia within hypoxic intervals led to decreased burial of both Mn and Fe in deep basin sediments. This implies a nonlinearity in shelf Fe release upon expanding hypoxia with initial enhanced Fe release relative to oxic conditions followed by increased retention in shelf sediments, likely in the form of iron sulfide minerals. For Mn, extended hypoxia leads to more limited sequestration as Mn carbonate in deep basin sediments, presumably because of more rapid reduction of Mn oxides formed after inflows and subsequent escape of dissolved Mn to the overlying water. Our Fe records suggest that modern Baltic Sea hypoxia is more widespread than in the past. Furthermore, hypoxia‐driven variations in shelf‐to‐basin transfer of Fe may have impacted the dynamics of P and sulfide in the Baltic Sea thus providing potential feedbacks on the further development of hypoxia.
The nature and origin of Mafic Mound in the South Pole‐Aitken Basin
Authors: Moriarty Daniel P. , Pieters Carle M. 
Published: October 2015

Abstract“Mafic Mound” is a distinctive and enigmatic feature 75 km across and 1 km high near the center of the vast South Pole‐Aitken Basin (SPA). Using several modern data sets, we characterize the composition, morphology, and gravity signature of the structure in order to assess its origin. Mafic Mound is found to exhibit a perched circular depression and a homogeneous high‐Ca pyroxene‐bearing composition. Several formation hypotheses based on known lunar processes are evaluated, including the possibilities that Mafic Mound represents (1) uplifted mantle, (2) SPA‐derived impact melt, (3) a basalt‐filled impact crater, or (4) a volcanic construct. Individually, these common processes cannot fully reproduce the properties of Mafic Mound. Instead, we propose a hybrid origin in which Mafic Mound is an edifice formed by magmatic processes induced by the formation and evolution of SPA. This form of nonmare volcanism has not previously been documented on the Moon.
Threshold size for fluid inclusion decrepitation
Authors: Campione Marcello , Malaspina Nadia , Frezzotti Maria Luce 
Published: October 2015

AbstractFluid inclusions in igneous and metamorphic rocks are equilibrated at pressures reaching a few tens of kilobars at mantle depths. These microsystems experience decompression as a consequence of uplift processes, such as subaerial volcanic eruptions. On decompression, inclusion fluid overpressure is known to bring about the mechanical failure of the crystal matrix through either stretch or decrepitation, depending on ductile or brittle failure mechanism of the matrix, respectively. On the one hand, laboratory experiments performed on synthetic inclusions at one atmosphere show that the decrepitation temperature is strongly size dependent, with the smaller cavities observed to decrepitate at higher temperatures. On the other hand, natural fluid inclusions, which undergo migration through a pressure gradient, are often found intact below a critical size. Here by modeling fluid inclusions as spherical cavities in a continuous elastic medium and by adopting a nonlocal stress approach to fracturing, we demonstrate that the decrepitation phenomenon is predicted to be characterized by a threshold size of the cavity, below which decrepitation would not be allowed. In order to validate our model, two independent experimental data sets relating internal pressure to cavity size are utilized to calculate pertinent model parameters and to evaluate their consistency.
Export production fluctuations in the eastern equatorial Pacific during the Pliocene‐Pleistocene: Reconstruction using barite accumulation rates
Authors: Ma Zhongwu , Ravelo Ana Christina , Liu Zhonghui , Zhou Liping , Paytan Adina 
Published: October 2015

AbstractExport production is an important component of the carbon cycle, modulating the climate system by transferring CO2 from the atmosphere to the deep ocean via the biological pump. Here we use barite accumulation rates to reconstruct export production in the eastern equatorial Pacific over the past 4.3 Ma. We find that export production fluctuated considerably on multiple time scales. Export production was on average higher (51 g C m−2 yr−1) during the Pliocene than the Pleistocene (40 g C m−2 yr−1), decreasing between 3 and 1 Ma (from more than 60 to 20 g C m−2 yr−1) followed by an increase over the last million years. These trends likely reflect basin‐scale changes in nutrient inventory and ocean circulation. Our record reveals decoupling between export production and temperatures on these long (million years) time scale. On orbital time scales, export production was generally higher during cold periods (glacial maxima) between 4.3 and 1.1 Ma. This could be due to stronger wind stress and higher upwelling rates during glacial periods. A shift in the timing of maximum export production to deglaciations is seen in the last ~1.1 million years. Results from this study suggest that, in the eastern equatorial Pacific, mechanisms that affect nutrient supply and/or ecosystem structure and in turn carbon export on orbital time scales differ from those operating on longer time scales and that processes linking export production and climate‐modulated oceanic conditions changed about 1.1 million years ago. These observations should be accounted for in climate models to ensure better predictions of future climate change.
X‐Linked Intellectual Disability Genetics
Authors: Schwartz Charles E 
Published: October 2015

Abstract

Intellectual disability (ID) is a common disability affecting 2–3% of the general population. X‐linked intellectual disability (XLID) disorders, caused by the defects of genes on the X chromosome, affect 1.7 of 1000 males. Patients with XLID require long‐term family involvement, medical care and social services with enormous attendant burden and cost.
XLID is a medically important and biologically significant group of disorders for which the prospects for further progress on the understanding of their molecular basis have improved with advances in technological approaches. As such, worldwide efforts over the past 25 years have identified 124 XLID genes involved in 124 XLID syndromes and 53 nonsyndromal XLID conditions. About 70% these genes fall into three categories of biological process or function: structural molecule, catalytic activity or transcription regulatory activity. In‐depth analysis of the genes will assist with understanding not only XLID but also cognitive function and brain function in general.

Key Concepts

XLID conditions can be partitioned into two broad categories: syndromal and nonsyndromal

Molecular analysis allows for splitting XLID conditions thought to be similar

Molecular analysis allows for determining distinct XLID entities are allelic

XLID proteins fall into 3–4 major categories of function

Better understanding of XLID gene function may lead to treatment therapies
Evolutionary Aspects of Annelid Regeneration
Authors: Martinez‐Acosta Veronica G , Zoran Mark J 
Published: October 2015

AbstractAnnelids, like many other invertebrate animals, replace lost body parts in a process called regeneration. However, the ability to regenerate lost segments is present in some groups and not others; for example, leeches do not regenerate lost segments. Anterior and posterior regeneration involves the formation of a bud containing stem cells that differentiate into the new head or tail segments. Annelid regeneration also involves remodelling of surviving body fragments. The ability of annelids to regenerate tail segments appears to be nearly universal among species capable of regeneration. The ability to regenerate head segments, although common, is not universal and can depend on the number of segments lost. The absence and presence of regeneration across annelid groups, including closely related species, suggests that regeneration ability may be an ancient trait that has been lost in some species during annelid evolution.Key ConceptsAnnelids vary in their capability for regenerating body segments, including among closely related species.The ability of annelids to regenerate posterior segments appears to be nearly universal.The ability of annelids to regenerate anterior segments, although common, is not universal and is often limited depending on the number of segments lost.Annelid regeneration may involve both epimorphic and morphallactic mechanisms.Multiple losses and gains of regeneration ability have likely occurred during annelid evolution.Why regenerative ability among annelids varies extensively remains unclear.With development of new techniques for genetic analysis and microscopy, annelids are becoming important model systems for the study of regeneration.
Pathogenic Mechanisms and Clinical Consequences of Chromosomal Aberrations in Man
Authors: Poot Martin , Hochstenbach Ron 
Published: October 2015

AbstractStructural genome variations (SVs) found in patients with ‘cytogenetic disorders’ are classified as deletions, duplications, translocations, inversions, insertion translocations and complex chromosome rearrangements. Some SVs are phenotypically neutral, butde novoSVs in isolated patients or SVs inherited from a diseased parent are generally considered pathogenic. A phenotypic effect results either from gene dosage‐dependent mechanisms, for example, haploinsufficiency, or mechanisms based on disruption of the genomic architecture, such that genes, parts of genes or regulatory elements are truncated, fused or relocated and their interactions disturbed. This mechanism predominantly affects gene expression. Third, mixed mutational mechanisms in which an SV is combined with a different mutation on the other, homologous chromosome, have been documented. Inferred mechanisms of pathogenicity need corroboration by mRNA sequencing. In addition, future studies with model systems such as inducible pluripotent stem cells from patients and transgenic organisms should substantiate current inferences regarding phenotypic effects of SVs.Key ConceptsStructural genome variations (SVs) result either from one or two chromosome breaks; for example, terminal deletions, reciprocal translocations or from more than 2 breaks, that is, complex chromosome rearrangements.The rate of detection and the apparent complexity of the detected SVs increase with improving resolution of detection techniques.SVs may exert pathogenic effects by gene dosage alterations, disruption of genomic architecture and mixed mutational mechanisms.Genes which encode proteins that engage in physical interactions with other proteins may cause phenotypic effects after gene dosage alterations.Disruption of genomic architecture by SVs may provoke phenotypic effects by altering the transcription of genes in the vicinity of the chromosome break.If a deletion on one chromosome is combined with a deletion or a single nucleotide variant in the same deleted segment on the other, homologous chromosome, a mixed mutational mechanism, such as ‘unmasking’, may arise.In counselling families with at least one individual with an SV multiple, possibly pathogenic mechanisms have to be considered.