bluuebunny/crossref_metadata_2025_split huggingface dataset:
LRH-1 mediates anti-inflammatory and antifungal phenotype of IL-13-activated macrophages through the PPARγ ligand synthesis
Authors: Lefèvre Lise , Authier Hélène , Stein Sokrates , Majorel Clarisse , Couderc Bettina , Dardenne Christophe , Eddine Mohamad Ala , Meunier Etienne , Bernad José , Valentin Alexis , Pipy Bernard , Schoonjans Kristina , Coste Agnès 
Published: April 2015

AbstractLiver receptor homologue-1 (LRH-1) is a nuclear receptor involved in the repression of inflammatory processes in the hepatointestinal tract. Here we report that LRH-1 is expressed in macrophages and induced by the Th2 cytokine IL-13 via a mechanism involving STAT6. We show that loss-of-function of LRH-1 in macrophages impedes IL-13-induced macrophage polarization due to impaired generation of 15-HETE PPARγ ligands. The incapacity to generate 15-HETE metabolites is at least partially caused by the compromised regulation of CYP1A1 and CYP1B1. Mice with LRH-1-deficient macrophages are, furthermore, highly susceptible to gastrointestinal and systemic Candida albicans infection. Altogether, these results identify LRH-1 as a critical component of the anti-inflammatory and fungicidal response of alternatively activated macrophages that acts upstream from the IL-13-induced 15-HETE/PPARγ axis.
Connecting the oxidation of soot to its redox cycling abilities
Authors: Antiñolo María , Willis Megan D. , Zhou Shouming , Abbatt Jonathan P.D. 
Published: April 2015

AbstractAlthough it is known that soot particles are emitted in large quantities to the atmosphere, our understanding of their environmental effects is limited by our knowledge of how their composition is subsequently altered through atmospheric processing. Here we present an on-line mass spectrometric study of the changing chemical composition of hydrocarbon soot particles as they are oxidized by gas-phase ozone, and we show that the surface-mediated loss rates of adsorbed polycyclic aromatic hydrocarbons in soot are directly connected to a significant increase in the particle redox cycling abilities. With redox cycling implicated as an oxidative stress mechanism that arises after inhalation of atmospheric particles, this work draws a quantitative connection between the detailed heterogeneous chemistry occurring on atmospheric particles and a potential toxic mechanism attributable to that aerosol.
Copy Number Variants and Genetic Polymorphisms in TBX21, GATA3, Rorc, Foxp3 and Susceptibility to Behcet's Disease and Vogt-Koyanagi-Harada Syndrome
Authors: Liao Dan , Hou Shengping , Zhang Jun , Fang Jing , Liu Yunjia , Bai Lin , Cao Qingfeng , Aize Kijlstra  , Yang Peizeng 
Published: April 2015

AbstractThis study aimed to investigate the role of genetic variants including single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) of TBX21, GATA3, Rorc and Foxp3 genes in Behcet's disease (BD) and Vogt-Koyanagi-Harada (VKH) syndrome in a Chinese Han population. Genotyping of 25 SNPs was performed by iPLEX system (Sequenom) or polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). TaqMan real time PCR was used to assess CNVs. The expression of Rorc and Foxp3 were examined by real-time PCR and cytokine production was measured by ELISA. High Rorc CNV was associated with the susceptibility to BD (P = 8.99 × 10−8, OR = 3.0) and low Foxp3 CNV predisposed to BD in female patients (P = 1.92 × 10−5, OR = 3.1). CNVs for the investigated genes were not altered in VKH syndrome. Further functional studies demonstrated that the relative mRNA expression levels of Rorc were increased in individuals with high Rorc copy number, but not for Foxp3. Increased production of IL-1β and IL-6 was found in individuals carrying a high CNV of Rorc. Our study showed that high CNVs of Rorc and low CNVs of Foxp3 confer risk for BD but not for VKH syndrome. The tested 25 SNPs in TBX21, GATA3, Rorc and Foxp3 did not associate with BD and VKH syndrome.
E. coli OxyS non-coding RNA does not trigger RNAi in C. elegans
Authors: Akay Alper , Sarkies Peter , Miska Eric A. 
Published: April 2015

AbstractThe discovery of RNA interference (RNAi) in C. elegans has had a major impact on scientific research, led to the rapid development of RNAi tools and has inspired RNA-based therapeutics. Astonishingly, nematodes, planaria and many insects take up double-stranded RNA (dsRNA) from their environment to elicit RNAi; the biological function of this mechanism is unclear. Recently, the E. coli OxyS non-coding RNA was shown to regulate gene expression in C. elegans when E. coli is offered as food. This was surprising given that C. elegans is unlikely to encounter E. coli in nature. To directly test the hypothesis that the E. coli OxyS non-coding RNA triggers the C. elegans RNAi pathway, we sequenced small RNAs from C. elegans after feeding with bacteria. We clearly demonstrate that the OxyS non-coding RNA does not trigger an RNAi response in C. elegans. We conclude that the biology of environmental RNAi remains to be discovered.
Independent Controls of Differently-Polarized Reflected Waves by Anisotropic Metasurfaces
Authors: Ma Hui Feng , Wang Gui Zhen , Kong Gu Sheng , Cui Tie Jun 
Published: April 2015

AbstractWe propose a kind of anisotropic planar metasurface, which has capacity to manipulate the orthogonally-polarized electromagnetic waves independently in the reflection mode. The metasurface is composed of orthogonally I-shaped structures and a metal-grounded plane spaced by a dielectric isolator, with the thickness of about 1/15 wavelength. The normally incident linear-polarized waves will be totally reflected by the metal plane, but the reflected phases of x- and y-polarized waves can be controlled independently by the orthogonally I-shaped structures. Based on this principle, we design four functional devices using the anisotropic metasurfaces to realize polarization beam splitting, beam deflection and linear-to-circular polarization conversion with a deflection angle, respectively. Good performances have been observed from both simulation and measurement results, which show good capacity of the anisotropic metasurfaces to manipulate the x- and y-polarized reflected waves independently.
Synthesis and antitumor mechanisms of a copper(ii) complex of anthracene-9-imidazoline hydrazone (9-AIH)
Authors: Qin Qi-Pin , Liu Yan-Cheng , Wang Hai-Lu , Qin Jiao-Lan , Cheng Feng-Jie , Tang Shang-Feng , Liang Hong 
Published: April 2015

Abstract
A new anthracycline derivative, anthracene-9-imidazoline hydrazone (9-AIH), was synthesized and selected as an antitumor ligand to afford a copper(ii) complex of 9-AIH, cis-[CuIICl2(9-AIH)] (1). Complex 1 was structurally characterized by IR, elemental analysis, ESI-MS and single crystal X-ray diffraction analysis. By MTT assay, it was revealed that 1 showed overall a higher in vitro cytotoxicity than 9-AIH towards a panel of human tumour cell lines, with IC50 values from 0.94–3.68 μM, in which the BEL-7404 cell line was the most sensitive to 1. By spectral analyses and gel electrophoresis, the DNA binding affinity of 9-AIH and 1 was determined. 9-AIH was suggested to bind with DNA in an intercalative mode, with a quenching constant of 1.04 × 104 M−1 on the EB–DNA complex. While for 1, both intercalative and covalent binding modes were suggested. By flow cytometry, 1 was found to block the cell cycle of BEL-7404 cells in a dose-dependent mode, in which it induced the G2/M phase arrest at 0.5 μM and induced the S phase arrest at higher concentrations of 1.0 or 2.0 μM. From the cellular morphological observations under different fluorescence probe staining, a dose-dependent manner of 1 to induce cell apoptosis in the late stage was suggested. Comparatively, equivalent apoptotic cells, respectively, in the early and late stages were found when incubated with 2.0 μM of 9-AIH. The mitochondrial membrane potential measured by JC-1 staining and the ROS generation in cells detected using a DCFH-DA probe suggested that the cell apoptosis induced by 1 might undergo the ROS-related mitochondrial pathway. Accordingly, the mutant p53 expression was found to be suppressed and the caspase cascade (caspase-9/3) was consequently activated by 1. This action mechanism for 1 in the BEL-7404 cells was unique and was not found in the presence of 9-AIH under the same conditions, indicating their different antitumor mechanism. Furthermore, the in vivo acute toxicity of 1 tested on mice indicated that 1 should be a high cytotoxic antitumor agent, with the LD50 value in the range of 32–45 mg kg−1, which is much higher than that of 9-AIH. From the above results, the central Cu(ii) of 1 in the coordinated mode with 9-AIH was believed to play a key role in exerting both the high cytotoxicity and the effective antitumor mechanism.
Capture and Brief Invasive Procedures Using Electronarcosis Does Not Appear to Affect Postrelease Habits in Male Atlantic Sturgeon During the Spawning Season
Authors: Balazik Matthew T. 
Published: April 2015

Abstract
With advances in technology and demand for life history information, researchers are increasingly conducting invasive procedures on fish that require an anesthetic. This study examined the effectiveness of electronarcosis as a field anesthetic on Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus during the spawning season in the James River, Virginia. Concerns about sampling Atlantic Sturgeon during spawning runs prompted our examining whether movements after capture, narcosis, and tagging were noticeably modified. An electronarcosis system, which consisted of a power supply, fiberglass tank, and hardware cloth, were set up both on land and on a sampling boat. During the spawning season Atlantic Sturgeon were caught and implanted with Vemco V16 telemetry tags using electronarcosis as an anesthetic. Anesthesia induction, surgery, and recovery averaged 5 min. Telemetry data from the tagging year was compared with returning fish tagged in previous years. This showed movements during the spawning season and spawning exit dates were similar between the two groups, suggesting that electronarcosis was effective and time-efficient for conducting invasive procedures. Capturing and implanting transmitters in Atlantic Sturgeon during spawning runs does not appear to modify spawning movements. Managers may benefit from targeting adult Atlantic Sturgeon and other iteroparous anadromous fishes in rivers during spawning periods, which is typically very efficient due to high densities of fish during that period.
Received February 21, 2014; accepted December 31, 2014
Reservoir Rehabilitations: Seeking the Fountain of Youth
Authors: Pegg Mark A. , Pope Kevin L. , Powell Larkin A. , Turek Kelly C. , Spurgeon Jonathan J. , Stewart Nathaniel T. , Hogberg Nick P. , Porath Mark T. 
Published: April 2015

Abstract
Aging of reservoirs alters the functions, and associated services, of these systems through time. The goal of habitat rehabilitation is often to alter the trajectory of the aging process such that the duration of the desired state is prolonged. There are two important characteristics in alteration of the trajectory—the amplitude relative to current state and the subsequent rate of change, or aging—that ultimately determine the duration of extension for the desired state. Rehabilitation processes largely fall into three main categories: fish community manipulation, water quality manipulation, and physical habitat manipulation. We can slow aging of reservoirs through carefully implemented management actions, perhaps even turning back the hands of time, but we cannot stop aging. We call for new, innovative perspectives that incorporate an understanding of aging processes in all steps of rehabilitation of reservoirs, especially in planning and assessing.
El envejecimiento de los reservorios altera las funciones y los servicios que están asociados a estos ecosistemas. El objetivo de la rehabilitación de hábitats suele ser alterar la trayectoria del proceso de envejecimiento de manera tal que prolonga la duración de un estado deseable del sistema. Existen dos características importantes cuando se altera dicha trayectoria -amplitud relativa del estado actual y la subsecuente tasa de cambio, o envejecimiento- que últimamente determinan la duración del estado deseado. La mayoría de los procesos de rehabilitación caen en tres grandes categorías: manipulación de comunidades ícticas, manipulación de la calidad del agua y manipulación del hábitat físico. Es posible retardar el envejecimiento de los reservorios implementando cuidadosamente medidas de manejo, e incluso tal vez regresando el tiempo, pero no es posible detener el envejecimiento. Aquí se hace referencia a perspectivas novedosas que incorporan la comprensión del proceso de envejecimiento en todos los pasos de la rehabilitación de reservorios, particularmente en lo que se refiere a planeación y evaluación.
A new aliphatic alcohol and cytotoxic chemical constituents from Acorus gramineus rhizomes
Authors: Kim Ki Hyun , Kang Hee Rae , Eom Hee Jeong , Kim Chung Sub , Choi Sang Un , Lee Kang Ro 
Published: April 2015

Abstract
A new aliphatic alcohol, (2R,6R)-oct-7-ene-2,6-diol (1), and seven other known compounds (2-8) were isolated from Acorus gramineus rhizomes. The structure of 1 was elucidated by a combination of extensive spectroscopic analyses, including 2D NMR, HR-MS, and the modified Mosher’s method. Compounds 3-8 displayed consistent antiproliferative activities against the cell lines tested with IC50 values ranging from 7 to 48 μm.
The Very precise Echelle SpectroPolarimeter on the Araki telescope (VESPolA)
Authors: Arasaki Takayuki , Ikeda Yuji , Shinnaka Yoshiharu , Itose Chisato , Nakamichi Akika , Kawakita Hideyo 
Published: April 2015

Abstract
We report on the construction of a high-resolution spectropolarimeter, the Very precise Echelle SpectroPolarimeter on the Araki telescope (VESPolA). The instrument operates in the visible spectral range, i.e., 400–850 nm, and is mounted on the 1.3 m Araki telescope at the Koyama Astronomical Observatory of Kyoto Sangyo University (Kyoto, Japan). It employs an echelle-type spectrograph and a non-ripple super-achromatic half-wave plate, resulting in high polarimetric accuracy of δP &lt; 0.1% for linear polarization with a spectral resolution of R = 8000 at the central wavelengths and a wide wavelength coverage of δλ = 150–250 nm in a single exposure. VESPolA is designed for 1–2 m telescopes that have a Cassegrain focus. This configuration provides a dozen polarization line profiles of various nuclear species from the target spectra simultaneously, and we can therefore obtain complementary information on both the geometry and the velocity field of the nebular emission lines from the circumstellar envelopes. We evaluated the performance of our system by observing a spectroscopic standard star and several polarization standard stars during 2012–2013. VESPolA achieved a spectral resolution 7750 &lt; R &lt; 8250, with a polarimetric accuracy of δP &lt; 0.1% for linear polarization and a limiting magnitude of mv = 7.8 mag with δP &lt; 0.1% and an integration time of 4 hr. We show preliminary results of variable stars P Cyg, β Lyr, and VY CMa. We observed polarization profiles across the Hα and He lines, as well as the TiO absorption bands, which indicate a complex spatial distribution and velocity field of the surrounding gaseous nebulae.
Ensembler: Enabling high-throughput molecular simulations at the superfamily scale
Authors: Parton Daniel L. , Grinaway Patrick B. , Hanson Sonya M. , Beauchamp Kyle A. , Chodera John D. 
Published: April 2015

The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on anomicsscale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept pace. It should now be possible to study protein dynamics across entire (super)families, exploiting both available structural biology data and conformational similarities across homologous proteins. Here, we present a new tool for enabling high-throughput simulation in the genomics era.Ensemblertakes any set of sequences—from a single sequence to an entire superfamily— and shepherds them through various stages of modeling and refinement to produce simulation-ready structures. This includes comparative modeling to all relevant PDB structures (which may span multiple conformational states of interest), reconstruction of missing loops, addition of missing atoms, culling of nearly identical structures, assignment of appropriate protonation states, solvation in explicit solvent, and refinement and filtering with molecular simulation to ensure stable simulation. The output of this pipeline is an ensemble of structures ready for subsequent molecular simulations using computer clusters, supercomputers, or distributed computing projects like Folding@home.Ensemblerthus automates much of the time consuming process of preparing protein models suitable for simulation, while allowing scalability up to entire superfamilies. A particular advantage of this approach can be found in the construction of kinetic models of conformational dynamics—such as Markov state models (MSMs)—which benefit from a diverse array of initial configurations that span the accessible conformational states to aid sampling. We demonstrate the power of this approach by constructing models for all catalytic domains in the human tyrosine kinase family, using all available kinase catalytic domain structures from any organism as structural templates.Ensembleris free and open source software licensed under the GNU General Public License (GPL) v2. It is compatible with Linux and OS X. The latest release can be installed via the conda package manager, and the latest source can be downloaded fromhttps://github.com/choderalab/ensembler.
Development of a computational efficient tool for robust structural optimization
Authors: Motta Renato de Siqueira , Afonso Silvana Maria Bastos , Lyra Paulo Roberto , Willmersdorf Ramiro Brito 
Published: April 2015

Purpose
– Optimization under a deterministic approach generally leads to a final design in which the performance may degrade significantly and/or constraints can be violated because of perturbations arising from uncertainties. The purpose of this paper is to obtain a better strategy that would obtain an optimum design which is less sensitive to changes in uncertain parameters. The process of finding these optima is referred to as robust design optimization (RDO), in which improvement of the performance and reduction of its variability are sought, while maintaining the feasibility of the solution. This overall process is very time consuming, requiring a robust tool to conduct this optimum search efficiently.

Design/methodology/approach
– In this paper, the authors propose an integrated tool to efficiently obtain RDO solutions. The tool encompasses suitable multiobjective optimization (MO) techniques (encompassing: Normal-Boundary Intersection, Normalized Normal-Constraint, weighted sum method and min-max methods), a surrogate model using reduced order method for cheap function evaluations and adequate procedure for uncertainties quantification (Probabilistic Collocation Method).

Findings
– To illustrate the application of the proposed tool, 2D structural problems are considered. The integrated tool prove to be very effective reducing the computational time by up to five orders of magnitude, when compared to the solutions obtained via classical standard approaches.

Originality/value
– The proposed combination of methodologies described in the paper, leads to a very powerful tool for structural optimum designs, considering uncertainty parameters, that can be extended to deal with other class of applications.
Acceleration of free-vibrations analysis with the Dual Reciprocity BEM based on ℋ-matrices and CUDA
Authors: Wei Yixiong , Wang Qifu , Huang Yunbao , Wang Yingjun , Xia Zhaohui 
Published: April 2015

Purpose
– The purpose of this paper is to present a novel strategy used for acceleration of free-vibration analysis, in which the hierarchical matrices structure and Compute Unified Device Architecture (CUDA) platform is applied to improve the performance of the traditional dual reciprocity boundary element method (DRBEM).

Design/methodology/approach
– The DRBEM is applied in forming integral equation to reduce complexity. In the procedure of optimization computation, ℋ-Matrices are introduced by applying adaptive cross-approximation method. At the same time, this paper proposes a high-efficiency parallel algorithm using CUDA and the counterpart of the serial effective algorithm in ℋ-Matrices for inverse arithmetic operation.

Findings
– The analysis for free-vibration could achieve impressive time and space efficiency by introducing hierarchical matrices technique. Although the serial algorithm based on ℋ-Matrices could obtain fair performance for complex inversion operation, the CUDA parallel algorithm would further double the efficiency. Without much loss in accuracy according to the examination of the numerical example, the relative error appeared in approximation process can be fixed by increasing degrees of freedoms or introducing certain amount of internal points.

Originality/value
– The paper proposes a novel effective strategy to improve computational efficiency and decrease memory consumption of free-vibration problems. ℋ-Matrices structure and parallel operation based on CUDA are introduced in traditional DRBEM.
An evolutionary approach for simultaneous optimization of material property distribution and topology of FG structures
Authors: Maleki Jebeli Saeed , Shariat Panahi Masoud 
Published: April 2015

Purpose
– The purpose of this paper is to introduce an evolutionary heuristic method for simultaneous optimization of topology and material property distribution of functionally graded (FG) structures under a prescribed loading condition.

Design/methodology/approach
– The proposed procedure is inspired by heuristic nature of bi-directional evolutionary structural optimization (BESO) and genetic algorithm (GA). The optimization algorithm is developed in the context of minimum compliance (maximum stiffness) design problem. The problem is modeled by means of finite element method (FEM). The element-wise material volume fractions and elements’ status (i.e. existence or nonexistence in FE model) are introduced as design variables. After FE analysis, sensitivities are obtain and filtered according to BESO. Having determined sensitivities, by means of a heuristic scheme combined by GA, topology and material property distribution for the next cycle of optimization are determined by updating design variables.

Findings
– The adopted method has been tested by means of several examples previously reported in literature. The comparison showed the superiority of the proposed method against its rival in terms of relative reduction in compliance, smoother material property distribution and computational cost.

Originality/value
– The value of the described method lies in its simple (yet efficient) nature. In contrast with its only rival in literature which more relied on mathematical approach, proposed method uses a series of logic-based heuristic ideas to drive reasonable solutions but with far less computational cost.